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At least 325 records · Page 18

Omics-Lethal Human Viruses, West Nile Experiment WCN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus (WNV NY99 clone 382) and mutant (WNVE218A) virus infection. Sample data was obtained frommouse cortical neuron tissue for mRNA and miRNA expression analysis. Biological replicate experiments were conducted in the same conditions and with data processed independently (WCN002). Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Bioclimatic distribution of vegetation for general circulation model studies

Four global bioclimatic schemes which qualify climates on the basis of the distribution of vegetation, including the Holdridge (1947), Thornthwaite (1948), Koeppen (1936), and Troll and Paffen (1964) schemes, were applied to two global climate data sets to produce maps of global vegetation distribution: the Rand set described by Schutz and Gates (1971, 1973, and 1974) and the Shea (1986) data set. The results show that only 38 to 40 percent of the observed land surface, mapped as 31 vegetation types, could be replicated by applying the four schemes to these data sets. The simulations were significantly improved by further subdividing and regrouping the climates defined by the schemes and by regrouping the observed vegetation types. With these alterations, 77 percent of the predicted vegetative landscape coresponded with the observed distribution of vegetation.

Prentice, Katharine Culbertson↗

Correction to Unveiling the Role of Al 2 O 3 in Preventing Surface Reconstruction During High-Voltage Cycling of Lithium-Ion Batteries

A correction to this article was necessary to replace the original Figure 2 with the actual data in the revised Figure 2 shown here. An error was made while preparing the graphs from the neutron diffraction analysis software, and panel a was accidentally inserted into the panel b–d spots, such that all four panels were replicates. Since the original analysis of the data collected was made correctly, the conclusions and key points related to this section and the whole article remain unchanged. The revised goodness factors are slightly different because the refinements were repeated with small changes to the refinement conditions. The corresponding author has obtained approval from all coauthors in the article prior the submission of the Correction. The authors apologize for any inconveniences caused.

25 ENERGY STORAGE↗

Methane dissociative chemisorption and detailed balance on Pt(111): Dynamical constraints and the modest influence of tunneling

A dynamically biased (d-) precursor mediated microcanonical trapping (PMMT) model of the activated dissociative chemisorption of methane on Pt(111) is applied to a wide range of dissociative sticking experiments, and, by detailed balance, to the methane product state distributions from the thermal associative desorption of adsorbed hydrogen with coadsorbed methyl radicals. Tunneling pathways were incorporated into the d-PMMT model to better replicate the translational energy distribution of the desorbing methane product from the laser induced thermal reaction of coadsorbed hydrogen and methyl radicals occurring near T{sub s} = 395 K. Although tunneling is predicted to be inconsequential to the thermal dissociative chemisorption of CH{sub 4} on Pt(111) at the high temperatures of catalytic interest, once the temperature drops to 395 K the tunneling fraction of the reactive thermal flux reaches 15%, and as temperatures drop below 275 K the tunneling fraction exceeds 50%. The d-PMMT model parameters of (E{sub 0} = 58.9 kJ/mol, s = 2, η{sub v} = 0.40) describe the apparent threshold energy for CH{sub 4}/Pt(111) dissociative chemisorption, the number of surface oscillators involved in the precursor complex, and the efficacy of molecular vibrational energy to promote reaction, relative to translational energy directed along the surface normal. Molecular translations parallel to the surface and rotations are treated as spectator degrees of freedom. Transition state vibrational frequencies are derived from generalized gradient approximation-density functional theory electronic structure calculations. The d-PMMT model replicates the diverse range of experimental data available with good fidelity, including some new effusive molecular beam and ambient gas dissociative sticking measurements. Nevertheless, there are some indications that closer agreement between theory and experiments could be achieved if a surface efficacy less than one was introduced into the modeling as an additional dynamical constraint.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Increased leaf area index and efficiency drive enhanced production under elevated atmospheric [ CO 2 ] in a pine‐dominated stand showing no progressive nitrogen limitation

Abstract Enhancement of net primary production (NPP) in forests as atmospheric [CO 2 ] increases is likely limited by the availability of other growth resources. The Duke Free Air CO 2 Enrichment (FACE) experiment was located on a moderate‐fertility site in the southeastern US, in a loblolly pine ( Pinus taeda L.) plantation with broadleaved species growing mostly in mid‐canopy and understory. Duke FACE ran from 1994 to 2010 and combined elevated [CO 2 ] (eCO 2 ) with nitrogen (N) additions. We assessed the spatial and temporal variation of NPP response using a dataset that includes previously unpublished data from 6 years of the replicated CO 2 × N experiment and extends to 2 years beyond the termination of enrichment. Averaged over time (1997–2010), NPP of pine and broadleaved species were 38% and 52% higher under eCO 2 compared to ambient conditions. Furthermore, there was no evidence of a decline in enhancement over time in any plot regardless of its native site quality. The relation between spatial variation in the response and native site quality was suggested but inconclusive. Nitrogen amendments under eCO 2 , in turn, resulted in an additional 11% increase in pine NPP. For pine, the eCO 2 ‐induced increase in NPP was similar above‐ and belowground and was driven by both increased leaf area index ( L ) and production efficiency (PE = NPP/ L ). For broadleaved species, coarse‐root biomass production was more than 200% higher under eCO 2 and accounted for the entire production response, driven by increased PE. Notably, the fraction of annual NPP retained in total living biomass was higher under eCO 2 , reflecting a slight shift in allocation fraction to woody mass and a lower mortality rate. Our findings also imply that tree growth may not have been only N‐limited, but perhaps constrained by the availability of other nutrients. The observed sustained NPP enhancement, even without N‐additions, demonstrates no progressive N limitation.

59 BASIC BIOLOGICAL SCIENCES↗

rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating

Existing methods for generating synthetic genotype data are ill-suited for replicating the effects of assortative mating (AM). We propose rb_dplr, a novel and computationally efficient algorithm for generating high-dimensional binary random variates that effectively recapitulates AM-induced genetic architectures using the Bahadur order-2 approximation of the multivariate Bernoulli distribution. The rBahadur R library is available through the Comprehensive R Archive Network at https://CRAN.R-project.org/package=rBahadur.

59 BASIC BIOLOGICAL SCIENCES↗

An Analysis of Published DAS Studies for Application to SPE Phase III

Distributed Acoustic Sensing (DAS) is an emerging technology capable of recording the acoustic wavefield at unprecedented spatial resolution. However, this new tool requires significant refinements before it becomes operational for explosion monitoring objectives. Recent studies have shown significant development of array processing with DAS data. In this report we explore three such array processing methods including DAS strain-rate data versus geophone measured ground motion, beamforming for event parameters, and machine learning based denoising. Prior to applying these algorithms to the Source Physics Experiment Phase II and Phase III data, we validate these methods through replication analysis.

47 OTHER INSTRUMENTATION↗

Data for: Miscanthus × giganteus changes soil structure and increases maximum water holding capacity

The data provided include results from a comparative study evaluating the impact of Miscanthus × giganteus (miscanthus) versus maize on soil structural properties and maximum water holding capacity (MWHC) across two Iowa sites. The dataset includes MWHC values determined using the Funnel Filter Paper Drainage (FFPD) method, as well as additional measurements of MWHC following structural disruption of the soil to isolate the effect of aggregation. It also contains three-dimensional micro-computed tomography (microCT) data used to quantify total porosity and pore size distribution (PSD) of soil aggregates at a 5 µm resolution. All data are provided as raw replicate-level measurements, organized by site, crop, and depth, along with processed summary files in table form in CSV (.csv) format to support reproducibility and downstream analysis.

Misanthus x giganteus↗

Long decoding runs for Galileo's convolutional codes

Decoding results are described for long decoding runs of Galileo's convolutional codes. A 1 k-bit/sec hardware Viterbi decoder is used for the (15, 1/4) convolutional code, and a software Viterbi decoder is used for the (7, 1/2) convolutional code. The output data of these long runs are stored in data files using a data compression format which can reduce file size by a factor of 100 to 1 typically. These data files can be used to replicate the long, time-consuming runs exactly and are useful to anyone who wants to analyze the burst statistics of the Viterbi decoders. The 1 k-bit/sec hardware Viterbi decoder was developed in order to demonstrate the correctness of certain algorithmic concepts for decoding Galileo's experimental (15, 1/4) code, and for the long-constraint-length codes in general. The hardware decoder can be used both to search for good codes and to measure accurately the performance of known codes.

Lahmeyer, C. R.↗

Human-Computer Interaction with Medical Decisions Support Systems

Decision Support Systems (DSSs) have been available to medical diagnosticians for some time, yet their acceptance and use have not increased with advances in technology and availability of DSS tools. Medical DSSs will be necessary on future long duration space missions, because access to medical resources and personnel will be limited. Human-Computer Interaction (HCI) experts at NASA's Human Factors and Ergonomics Laboratory (HFEL) have been working toward understanding how humans use DSSs, with the goal of being able to identify and solve the problems associated with these systems. Work to date consists of identification of HCI research areas, development of a decision making model, and completion of two experiments dealing with 'anchoring'. Anchoring is a phenomenon in which the decision maker latches on to a starting point and does not make sufficient adjustments when new data are presented. HFEL personnel have replicated a well-known anchoring experiment and have investigated the effects of user level of knowledge. Future work includes further experimentation on level of knowledge, confidence in the source of information and sequential decision making.

Adolf, Jurine A.↗

CME Velocity and Acceleration Error Estimates Using the Bootstrap Method

The bootstrap method is used to determine errors of basic attributes of coronal mass ejections (CMEs) visually identified in images obtained by the Solar and Heliospheric Observatory (SOHO) mission's Large Angle and Spectrometric Coronagraph (LASCO) instruments. The basic parameters of CMEs are stored, among others, in a database known as the SOHO/LASCO CME catalog and are widely employed for many research studies. The basic attributes of CMEs (e.g. velocity and acceleration) are obtained from manually generated height-time plots. The subjective nature of manual measurements introduces random errors that are difficult to quantify. In many studies the impact of such measurement errors is overlooked. In this study we present a new possibility to estimate measurements errors in the basic attributes of CMEs. This approach is a computer-intensive method because it requires repeating the original data analysis procedure several times using replicate datasets. This is also commonly called the bootstrap method in the literature. We show that the bootstrap approach can be used to estimate the errors of the basic attributes of CMEs having moderately large numbers of height-time measurements. The velocity errors are in the vast majority small and depend mostly on the number of height-time points measured for a particular event. In the case of acceleration, the errors are significant, and for more than half of all CMEs, they are larger than the acceleration itself.

Michalek, Grzegorz↗

Application of Machine Learning Techniques to Delay Tolerant Network Routing

This dissertation discusses several machine learning techniques to improve routing in delay tolerant networks (DTNs). These are networks in which there may be long one-way trip times, asymmetric links, high error rates, and deterministic as well as non-deterministic loss of contact between network nodes, such as interplanetary satellite networks, mobile ad hoc networks and wireless sensor networks. This work uses historical network statistics to train a multi-label classifier to predict reliable paths through the network. In addition, a clustering technique is used to predict future mobile node locations. Both of these techniques are used to reduce the consumption of resources such as network bandwidth, memory and data storage that is required by replication routing methods often used in opportunistic DTN environments. Thesis contributions include: an emulation tool chain developed to create a DTN test bed for machine learning, the network and software architecture for a machine learning based routing method, the development and implementation of classification and clustering techniques and performance evaluation in terms of machine learning and routing metrics.

Dudukovich, Rachel M.↗

An Analysis of Database Replication Technologies with Regard to Deep Space Network Application Requirements

The Deep Space Network (DSN) has three communication facilities which handle telemetry, commands, and other data relating to spacecraft missions. The network requires these three sites to share data with each other and with the Jet Propulsion Laboratory for processing and distribution. Many database management systems have replication capabilities built in, which means that data updates made at one location will be automatically propagated to other locations. This project examines multiple replication solutions, looking for stability, automation, flexibility, performance, and cost. After comparing these features, Oracle Streams is chosen for closer analysis. Two Streams environments are configured - one with a Master/Slave architecture, in which a single server is the source for all data updates, and the second with a Multi-Master architecture, in which updates originating from any of the servers will be propagated to all of the others. These environments are tested for data type support, conflict resolution, performance, changes to the data structure, and behavior during and after network or server outages. Through this experimentation, it is determined which requirements of the DSN can be met by Oracle Streams and which cannot.

Oracle Database File System↗

Towards catchment classification in data-scarce regions

Assessing spatial variation in hydrologic processes can help to inform freshwater management and advance ecological understanding, yet many areas lack sufficient flow records on which to base classifications. Seeking to address this challenge, we apply concepts developed in data-rich settings to public, global data in order to demonstrate a broadly replicable approach to characterizing hydrologic variation. The proposed approach groups the basins associated with reaches in a river network according to key environmental drivers of hydrologic conditions. This initial study examines Colorado (USA), where long-term streamflow records permit comparison to previously distinguished flow regime types, and the Republic of Ecuador, where data limitations preclude such analysis. The flow regime types assigned to gages in Colorado corresponded reasonably well to the classes distinguished from environmental features. The divisions in Ecuador reflected major known biophysical gradients while also providing a higher resolution supplement to an existing depiction of freshwater ecoregions. Although freshwater policy and management decisions occur amidst uncertainty and imperfect knowledge, this classification framework offers a rigorous and transferrable means to distinguish catchments in data-scarce regions. The maps and attributes of the resulting ecohydrologic classes offer a departure point for additional study and data collection programs such as the placement of stations in under-monitored classes, and the divisions may serve as a preliminary template with which to structure conservation efforts such as environmental flow assessments.

13 HYDRO ENERGY↗

Special Issue “Mathematical Modeling of Viral Infections”

How an infection will progress in the body is dependent on myriad factors: the rate of spread of the agent, the immune response, what treatment may be applied, .... Clinically following the progression of the disease is limited to snapshots at discrete time points (longitudinally in an individual or in an in vitro/animal model if that is available, but most often from cross-sectional data over cohorts of individuals), and in many cases the data obtained are from a body compartment that is not the site of replication of the disease. We then infer disease progression by putting these discrete data together based on our biological knowledge of the systems involved. However, based on these snapshots, it is not straightforward to work out important disease properties, such as the rate of progression, pathogenicity, and treatment and immune response effects. Mathematical modelling provides a scientifically sound, reproducible method to describe the underlying dynamics that produce these data, as well as a means to investigate new scenarios, such as the effect of a new drug. Its impact has been demonstrated on a number of diseases, for example, contributing to a better understanding of the speed with which human immunodeficiency virus (HIV) replicates [1,2], the dynamics of different drug classes for HIV [3], the main mode of action of interferon in hepatitis C virus (HCV) [4], the effects of direct-acting antivirals in HCV [5], potential effects of the immune response [6], and many others [7–11].

Murray, John↗

A Support Database System for Integrated System Health Management (ISHM)

The development, deployment, operation and maintenance of Integrated Systems Health Management (ISHM) applications require the storage and processing of tremendous amounts of low-level data. This data must be shared in a secure and cost-effective manner between developers, and processed within several heterogeneous architectures. Modern database technology allows this data to be organized efficiently, while ensuring the integrity and security of the data. The extensibility and interoperability of the current database technologies also allows for the creation of an associated support database system. A support database system provides additional capabilities by building applications on top of the database structure. These applications can then be used to support the various technologies in an ISHM architecture. This presentation and paper propose a detailed structure and application description for a support database system, called the Health Assessment Database System (HADS). The HADS provides a shared context for organizing and distributing data as well as a definition of the applications that provide the required data-driven support to ISHM. This approach provides another powerful tool for ISHM developers, while also enabling novel functionality. This functionality includes: automated firmware updating and deployment, algorithm development assistance and electronic datasheet generation. The architecture for the HADS has been developed as part of the ISHM toolset at Stennis Space Center for rocket engine testing. A detailed implementation has begun for the Methane Thruster Testbed Project (MTTP) in order to assist in developing health assessment and anomaly detection algorithms for ISHM. The structure of this implementation is shown in Figure 1. The database structure consists of three primary components: the system hierarchy model, the historical data archive and the firmware codebase. The system hierarchy model replicates the physical relationships between system elements to provide the logical context for the database. The historical data archive provides a common repository for sensor data that can be shared between developers and applications. The firmware codebase is used by the developer to organize the intelligent element firmware into atomic units which can be assembled into complete firmware for specific elements.

FROM↗

An Autonomous MCP Bridge to Rucio: Enhancing Data Management Accessibility for High Energy Physics

The Rucio Data Management System [1] is an important tool used by High Energy Physics experiments, including those at Fermi National Accelerator Laboratory, to store and manage exabyte-scale scientific datasets. Despite its central role in coordinating data across globally distributed storage sites, Rucio's command line interface (CLI) presents a steep learning curve, and makes it difficult for scientists to navigate through. To solve this issue, a containerized Model Context Protocol (MCP) [2] server was built that connects Large Language Models directly to Rucio, allowing AI agents to handle data tasks by using simple, natural language rather than memorized terminal commands. The core engineering focus of this project was moving the server away from slow terminal commands that require text parsing and replacing them with a native Python Client API toolset and a planned REST API framework. Moving to the Python API handles data operations directly in memory, which helps clear up formatting errors, provides the AI with clean, structured JSON data and speeds up tool execution. To prove that the system actually works, a benchmarking pipeline was also built with various questions to test the AI across four different model configurations. The questions included finding data scopes, tracking down specific datasets, and checking replication rules. Through benchmarking, early runs showed that with raw terminal text, the model would get confused and stuck, whereas switching to the Python API to feed the AI clean, structured data yielded massive improvement. By creating an intelligent and autonomous bridge to a storage network, this project shows how AI can be implemented in scientific data management, which ultimately helps scientists at Fermilab spend less time sorting through data and more time focusing on their experiments and analysis.

Akella, Kashyap [William Rainey Harper Coll.]↗

The Raid distributed database system

Raid, a robust and adaptable distributed database system for transaction processing (TP), is described. Raid is a message-passing system, with server processes on each site to manage concurrent processing, consistent replicated copies during site failures, and atomic distributed commitment. A high-level layered communications package provides a clean location-independent interface between servers. The latest design of the package delivers messages via shared memory in a configuration with several servers linked into a single process. Raid provides the infrastructure to investigate various methods for supporting reliable distributed TP. Measurements on TP and server CPU time are presented, along with data from experiments on communications software, consistent replicated copy control during site failures, and concurrent distributed checkpointing. A software tool for evaluating the implementation of TP algorithms in an operating-system kernel is proposed.

Bhargava, Bharat↗