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At least 883 records · Page 49

Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis , the causative agent of plague

Adaptive processes in bacterial species can occur rapidly in laboratory culture, leading to genetic divergence between naturally occurring and laboratory-adapted strains. Differentiating wild and closely-related laboratory strains is clearly important for biodefense and bioforensics; however, DNA sequence data alone has thus far not provided a clear signature, perhaps due to lack of understanding of how diverse genome changes lead to adapted phenotypes. Protein abundance profiles from mass spectrometry-based proteomics analyses are a molecular measure of phenotype. Proteomics data contains sufficient information that powerful statistical methods can uncover signatures that distinguish wild strains of Yersinia pestis from laboratory-adapted strains.

59 BASIC BIOLOGICAL SCIENCES↗

Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network

The National Oceanic and Atmospheric Administration (NOAA), in partnership with the U.S. National Park Service (NPS), established the Ocean Noise Reference Station Network (NRS) in 2014 as a foundational component of NOAA’s Ocean Noise Strategy. This long-term effort aims to characterize baseline ocean ambient sound conditions across diverse marine environments and to inform management of noise impacts on protected species and habitats within U.S. waters. The NRS is now composed of 13 autonomous passive acoustic monitoring stations strategically positioned across the U.S. Exclusive Economic Zone (EEZ), extending from Arctic regions to tropical waters in depths ranging from 33 to 4,790 m. These locations include several National Marine Sanctuaries and National Parks, such as the recently designated Chumash Heritage National Marine Sanctuary off the coast of California. Each station is equipped to continuously sample low-frequency underwater sound at five kHz, enabling the detection of anthropogenic, geophysical, and biological acoustic signals. To date the network has sampled over 72 years of calibrated acoustic data. The spatial breadth and consistent methodology of the NRS allow for comparative acoustic assessments across diverse marine ecosystems. In addition to applied research functions, the NRS has served as a platform for education and training, offering opportunities for students to develop skills for marine science and data analysis. Looking forward, the NRS project team is focused on network expansion, improved data delivery, and broader integration with collaborative scientific initiatives. NRS recordings are being archived in partnership with NOAA’s National Centers for Environmental Information to enhance accessibility and long-term utility. Efforts are underway to develop standardized metadata and summary products to accompany raw audio files, making the data more usable for a wide range of stakeholders in the ocean science community. The NRS is evolving into a fully integrated national framework for ocean sound monitoring that supports scientific inquiry, management decision-making, national security interests, and public engagement with ocean acoustic environments.

Long-term monitoring↗

Prediction of room-temperature multiferroicity in strained MoCr 2 S 6 monolayer

The contrasting d-orbital occupation required for ferroelectricity vs ferromagnetism makes it difficult for their coexistence in two-dimensional materials, especially at high temperature. To resolve this intrinsic contradiction, we propose a layered MoCr 2 S 6 multiferroics by alloying magnetic Cr element into the ferroelectric 1T phase of the MoS 2 matrix. First-principles calculations disclose that a spontaneous symmetry breaking, depending on the Mo atom displacement, leads to a robust ferroelectricity, which coexists with a ferromagnetic order originated from two neighboring Cr atoms. The effect can be further enhanced by tensile strain to bring about a room-temperature multiferroicity. Our results shed new light on the fundamental understanding of multiferroics and display promising applications in spintronics and multistate data storage.

2D materials↗

Mind the gap: Bridging the divide between AI aspirations and the reality of autonomous microscopy

What does materials science look like in the “Age of Artificial Intelligence?” Each material’s domain—synthesis, characterization, and modeling—has a different answer to this question, motivated by unique challenges and constraints. This work focuses on the tremendous potential of autonomous characterization within electron microscopy. We present our recent advancements in developing domain-aware, multimodal models for microscopy analysis capable of describing complex atomic systems. We then address the critical gap between the theoretical promise of autonomous microscopy and its current practical limitations, showcasing recent successes while highlighting the necessary developments to achieve robust, real-world autonomy.

2D materials↗

Modeling the Transfer Function for the Dark Energy Survey

We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg 2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.

79 ASTRONOMY AND ASTROPHYSICS↗

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Science & Technology - Other Topics↗

Saturday Science with Geoff Fairchild

In this first episode, we sit down (on a chairlift) with Computer Scientist Geoff Fairchild to talk about how his team is using Los Alamos National Laboratory’s supercomputing capabilities to data mine social media and reveal trends relating to health and safety.

97 MATHEMATICS AND COMPUTING↗

A Big Data Approach to Analyzing Market Volatility

Understanding the microstructure of the financial market requires the processing of a vast amount of data related to individual trades, and sometimes even multiple levels of quotes. Analyzing such a large volume of data requires tremendous computing power that is not easily available to financial academics and regulators. Fortunately, public funded High Performance Computing (HPC) power is widely available at the National Laboratories in the US. In this paper we demonstrate that the HPC resource and the techniques for data-intensive sciences can be used to greatly accelerate the computation of an early warning indicator called Volume-synchronized Probability of Informed trading (VPIN). The test data used in this study contains five and a half year's worth of trading data for about 100 most liquid futures contracts, includes about 3 billion trades, and takes 140GB as text files. By using (1) a more efficient file format for storing the trading records, (2) more effective data structures and algorithms, and (3) parallelizing the computations, we are able to explore 16,000 different ways of computing VPIN in less than 20 hours on a 32-core IBM DataPlex machine. Our test demonstrates that a modest computer is sufficient to monitor a vast number of trading activities in real-time – an ability that could be valuable to regulators. Our test results also confirm that VPIN is a strong predictor of liquidity-induced volatility. With appropriate parameter choices, the false positive rates are about 7% averaged over all the futures contracts in the test data set. More specifically, when VPIN values rise above a threshold (CDF > 0.99), the volatility in the subsequent time windows is higher than the average in 93% of the cases.

97 MATHEMATICS AND COMPUTING↗

Big Data over a 100G network at Fermilab

As the need for Big Data in science becomes ever more relevant, networks around the world are upgrading their infrastructure to support high-speed interconnections. To support its mission, the high-energy physics community as a pioneer in Big Data has always been relying on the Fermi National Accelerator Laboratory to be at the forefront of storage and data movement. This need was reiterated in recent years with the data-taking rate of the major LHC experiments reaching tens of petabytes per year. At Fermilab, this resulted regularly in peaks of data movement on the Wide area network (WAN) in and out of the laboratory of about 30 Gbit/s and on the Local are network (LAN) between storage and computational farms of 160 Gbit/s. To address these ever increasing needs, as of this year Fermilab is connected to the Energy Sciences Network (ESnet) through a 100 Gb/s link. To understand the optimal system-and application-level configuration to interface computational systems with the new highspeed interconnect, Fermilab has deployed a Network Research & Development facility connected to the ESnet 100G Testbed. For the past two years, the High Throughput Data Program (HTDP) has been using the Testbed to identify gaps in data movement middleware [5] when transferring data at these high-speeds. The program has published evaluations of technologies typically used in High Energy Physics, such as GridFTP [4], XrootD [9], and Squid [8]. Furthermore, this work presents the new R&D facility and the continuation of the evaluation program.

97 MATHEMATICS AND COMPUTING↗

THE BRIGHT END OF THE ULTRAVIOLET LUMINOSITY FUNCTION AT z {approx} 8: NEW CONSTRAINTS FROM CANDELS DATA IN GOODS-SOUTH

We present new z {approx} 8 galaxy candidates from a search over {approx}95 arcmin{sup 2} of WFC3/IR data, tripling the previous search area for bright z {approx} 8 galaxies. Our analysis uses newly acquired WFC3/IR imaging data from the CANDELS Multi-Cycle Treasury program over the GOODS-South field. These new data are combined with existing deep optical Advanced Camera for Surveys (ACS) imaging to search for relatively bright (M {sub UV} < -19.5 mag) z {approx} 8 galaxy candidates using the Lyman break technique. These new candidates are used to determine the bright end of the UV luminosity function (LF) of star-forming galaxies at z {approx} 7.2-8.7, i.e., a cosmic age of 600 {+-} 80 Myr. To minimize contamination from lower redshift galaxies, we make full use of all optical ACS data and impose strict non-detection criteria based on an optical {chi}{sup 2} {sub opt} flux measurement. In the whole search area, we identify 16 candidate z {approx} 8 galaxies, spanning a magnitude range H {sub 160,AB} = 25.7-27.9 mag. The new data show that the UV LF is a factor {approx}1.7 lower at M {sub UV} < -19.5 mag than determined from the HUDF09 and Early Release Science (ERS) data alone. Combining this new sample with the previous candidates from the HUDF09 and ERS data allows us to perform the most accurate measurement of the z {approx} 8 UV LF yet. Schechter function fits to the combined data result in a best-fit characteristic magnitude of M {sub *}(z = 8) = -20.04 {+-} 0.46 mag. The faint-end slope is very steep, though quite uncertain, with {alpha} = -2.06 {+-} 0.32. A combination of wide-area data with additional ultra-deep imaging will be required to significantly reduce the uncertainties on these parameters in the future.

79 ASTRONOMY AND ASTROPHYSICS↗

A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities

Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.

97 MATHEMATICS AND COMPUTING↗

A modified eco-efficiency framework and methodology for advancing the state of practice of sustainability analysis as applied to green infrastructure: Sustainability Analysis of Rainwater Harvesting

We propose a modified eco-efficiency (EE) framework and novel sustainability analysis methodology for green infrastructure (GI) practices used in water resource management. Green infrastructure practices such as rainwater harvesting (RWH), rain gardens, porous pavements, and green roofs are emerging as viable strategies for climate change adaptation. The modified framework includes 4 economic, 11 environmental, and 3 social indicators. Using 6 indicators from the framework, at least 1 from each dimension of sustainability, we demonstrate the methodology to analyze RWH designs. We use life cycle assessment and life cycle cost assessment to calculate the sustainability indicators of 20 design configurations as Decision Management Objectives (DMOs). Five DMOs emerged as relatively more sustainable along the EE analysis Tradeoff Line, and we used Data Envelopment Analysis (DEA), a widely applied statistical approach, to quantify the modified EE measures as DMO sustainability scores. We also addressed the subjectivity and sensitivity analysis requirements of sustainability analysis, and we evaluated the performance of 10 weighting schemes that included classical DEA, equal weights, National Institute of Standards and Technology’s stakeholder panel, Eco-Indicator 99, Sustainable Society Foundation’s Sustainable Society Index, and 5 derived schemes. We improved upon classical DEA by applying the weighting schemes to identify sustainability scores that ranged from 0.18 to 1.0, avoiding the nonuniqueness problem and revealing the least to most sustainable DMOs. Our methodology provides a more comprehensive view of water resource management and is generally applicable to GI and industrial, environmental, and engineered systems to explore the sustainability space of alternative design configurations.

Sustainability Rainwater harvesting↗

Assessing Internet energy intensity: A review of methods and results

Assessing the average energy intensity of Internet transmissions is a complex task that has been a controversial subject of discussion. Estimates published over the last decade diverge by up to four orders of magnitude — from 0.0064 kilowatt-hours per gigabyte (kWh/GB) to 136 kWh/GB. This article presents a review of the methodological approaches used so far in such assessments: i) top–down analyses based on estimates of the overall Internet energy consumption and the overall Internet traffic, whereby average energy intensity is calculated by dividing energy by traffic for a given period of time, ii) model-based approaches that model all components needed to sustain an amount of Internet traffic, and iii) bottom–up approaches based on case studies and generalization of the results. Our analysis of the existing studies shows that the large spread of results is mainly caused by two factors: a) the year of reference of the analysis, which has significant influence due to efficiency gains in electronic equipment, and b) whether end devices such as personal computers or servers are included within the system boundary or not. For an overall assessment of the energy needed to perform a specific task involving the Internet, it is necessary to account for the types of end devices needed for the task, while the energy needed for data transmission can be added based on a generic estimate of Internet energy intensity for a given year. Separating the Internet as a data transmission system from the end devices leads to more accurate models and to results that are more informative for decision makers, because end devices and the networking equipment of the Internet usually belong to different spheres of control. -- Highlights: • Assessments of the energy intensity of the Internet differ by a factor of 20,000. • We review top–down, model-based, and bottom–up estimates from literature. • Main divergence factors are the year studied and the inclusion of end devices. • We argue against extending the Internet system boundary beyond data transmission. • Decision-makers need data that differentiates between end devices and transmission.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Estimating Carbon Flux and Storage: Constraint of the Community Land Model Using Observations at Different Temporal Scales

Terrestrial ecosystems deliver significant global services through their role in the global carbon cycle, energy balance and feedbacks to the climate system. Model projections generally agree under current ‘equilibrium’ conditions, but, despite extensive empirical research, current ESMs disagree on the long-term effects of climatic change and disturbance on the carbon cycle in part because of knowledge gaps and in part because empirical information is not readily incorporated into models. One way to reduce uncertainty in ESMs is to force them to agree with our best estimates of how ecosystems function. Major activities: We 1) developed and tested phenology and biomass data products, 2) tested which datasets were most suitable for data assimilation, 3) developed the data assimilation approaches at a single site and then expanded this to the globe.

54 ENVIRONMENTAL SCIENCES↗

MWRRETV2 Value-Added Product Report: The Retrieval of Liquid Water Path and Precipitable Water Vapor from Microwave Radiometer – 3-Channel (MWR3C) Data Sets

This report provides a short description of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility Microwave Radiometer – 3-Channel (MWR3C) Retrieval (MWRRETV2) Value-Added Product (VAP) algorithm. MWRRETV2 is an updated version of MWRRET, which extends the physical-iterative retrieval of liquid water path (LWP) and precipitable water vapor PWV) to 3-channel microwave radiometers beyond ARM's original standard 2-channel (23-and 31-GHz) systems. The 89-GHz channel in the 3-channel microwave radiometers has approximately three times the sensitivity to liquid water as the 31-GHz channel, thus improving LWP retrieval accuracy when LWP is less than 100 g/m2. We present a general overview of the technique, input parameters, and output products, and describe data quality checks.

47 OTHER INSTRUMENTATION↗