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At least 1,657 records · Page 92

Making social networks more human: A topological approach

A key problem in social network analysis is to identify nonhuman interactions. State-of-the-art bot-detection systems like Botometer train machine-learning models on user-specific data. Unfortunately, these methods do not work on data sets in which only topological information is available. In this paper, we propose a new, purely topological approach. Our method removes edges that connect nodes exhibiting strong evidence of non-human activity from publicly available electronic-social-network datasets, including, for example, those in the Stanford Network Analysis Project repository (SNAP). Our methodology is inspired by classic work in evolutionary psychology by Dunbar that posits upper bounds on the total strength of the set of social connections in which a single human can be engaged. We model edge strength with Easley and Kleinberg's topological estimate; label nodes as “violators” if the sum of these edge strengths exceeds a Dunbar-inspired bound; and then remove the violator-to-violator edges. We run our algorithm on multiple social networks and show that our Dunbar-inspired bound appears to hold for social networks, but not for nonsocial networks. Our cleaning process classifies 0.04% of the nodes of the Twitter-2010 followers graph as violators, and we find that more than 80% of these violator nodes have Botometer scores of 0.5 or greater. Furthermore, after we remove the roughly 15 million violator-violator edges from the 1.2-billion-edge Twitter-2010 follower graph, 34% of the violator nodes experience a factor-of-two decrease in PageRank. PageRank is a key component of many graph algorithms such as node/edge ranking and graph sparsification. Thus, this artificial inflation would bias algorithmic output, and result in some incorrect decisions based on this output.

97 MATHEMATICS AND COMPUTING↗

Jay : A software framework for prototyping and evaluating offloading applications in hybrid edge clouds

Abstract We present Jay , a software framework for offloading applications in hybrid edge clouds. Jay provides an API, services, and tools that enable mobile application developers to implement, instrument, and evaluate offloading applications using configurable cloud topologies, offloading strategies, and job types. We start by presenting Jay 's job model and the concrete architecture of the framework. We then present the programming API with several examples of customization. Then, we turn to the description of the internal implementation of Jay instances and their components. Finally, we describe the Jay Workbench, a tool that allows the setup, execution, and reproduction of experiments with networks of hosts with different resource capabilities organized with specific topologies. The complete source code for the framework and workbench is provided in a GitHub repository.

Silva, Joaquim↗

Human readiness levels and Human Views as tools for user-centered design

The Human Readiness Level (HRL) scale is a simple nine-level scale that brings structure and consistency to the real-world application of user-centered design. It enables multidisciplinary consideration of human-focused elements during the system development process. Use of the standardized set of questions comprising the HRL scale results in a single human readiness number that communicates system readiness for human use. The Human Views (HVs) are part of an architecture framework that provides a repository for human-focused system information that can be used during system development to support the evaluation of HRL levels. Here, this paper illustrates how HRLs and HVs can be used in combination to support user-centered design processes. A real-world example for a U.S. Army software modernization program is described to demonstrate application of HRLs and HVs in the context of user-centered design.

42 ENGINEERING↗

Using Visual Systems Mapping to Improve Transparency and Comparability of Life Cycle Assessment Baseline Scenarios

Visual systems mapping is a systems engineering approach used to represent complex processes and interactions. This study evaluates its application for documenting assumptions in life cycle assessment (LCA) baseline scenarios. In LCA, the baseline or reference case represents the business as usual system against which changes in impacts (e.g., emissions) are assessed. These baseline assumptions are particularly influential in biomass LCAs, yet they often vary across studies due to regional context, system boundaries, and simplifying assumptions that are not consistently or transparently documented. As a result, key feedbacks, omitted processes, and boundary choices may remain unclear, limiting comparability across studies and weakening their usefulness for decision-making. This study examines whether visual systems mapping can improve the transparency and comparability of biomass LCA baseline scenarios. A case study of five published biomass-related LCAs were reviewed, and their baseline scenarios were translated into visual system maps to identify included processes, omitted components, and underlying assumptions. The analysis demonstrates that visual systems mapping can make baseline assumptions more explicit, highlight excluded dynamics, and improve documentation of system boundaries. Based on these findings, the study recommends the use of visual systems mapping alongside open data repositories and reproducible workflows to support greater transparency, reproducibility, and comparability in LCAs. These improvements can strengthen the role of LCAs in informing decisions related to sustainable biomass systems.

Davis, Maggie [ORNL] (ORCID:0000000181319328)↗

Temperature response and brine availability to heated boreholes in bedded salt

Abstract There is a growing need for disposal of high‐level nuclear waste. To reduce uncertainty associated with brine availability to repository excavations in salt formations, a collaboration between Sandia, Los Alamos, and Lawrence Berkeley National Laboratories is performing a series of borehole‐scale coupled process tests. Here, we report on the first round of the Brine Availability Test in Salt (BATS) project, a “shakedown” experiment called Phase 1s. Experimental testing included placing a resistive heater, a 260‐W radiative heater, and a 750‐W radiative heater within previously drilled horizontal boreholes at the Waste Isolation Pilot Plant (WIPP) while monitoring temperature and water inflow. The experiments successfully achieved the targeted temperature of 120 °C when using the 750‐W radiative heater. Simulations using FEHM (Finite Element Heat and Mass transfer code) and TOUGH‐FLAC (Transport Of Unsaturated Groundwater and Heat–Fast Lagrangian Analysis of Continua) were able to accurately predict the coupled thermo–hydro–mechanical–chemical response of salt, matching the observed temperature and brine production. Due to the extremely low permeability of salt, these systems take many years to reach steady state when perturbed by mining activities. Long‐term numerical simulations are used to develop the initial pressure and saturation conditions. The inclusion of a damaged rock zone with higher permeability around the borehole also affects the saturation and pressure distributions and plays an important role in dissipating the potential for thermal pressurization. Knowledge gained from this round of experimentation and simulation will be used to conduct the next BATS project experiment in new boreholes at WIPP.

58 GEOSCIENCES↗

The MolSSI QCArchive project: An open-source platform to compute, organize, and share quantum chemistry data

The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface. Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at the website. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchiveInfrastructure is open-source (BSD-3C), code repositories can be found at github, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection

Early detection of solid tumors through a simple screening process, such as the proteomic analysis of biofluids, has the potential to significantly alter the management and outcomes of cancers. The application of advanced targeted proteomics measurements and data analysis strategies to uniformly collected serum or plasma samples would enable longitudinal studies of cancer risk, progression, and response to therapy that have the potential to significantly reduce cancer burden in general. In this article, we describe a generalizable workflow combining robust, multiplexed targeted proteomics measurements applied to longitudinal samples from the Department of Defense Serum Repository with a Random Forest machine learning method for developing and initially evaluating the performance of candidate biomarker panels for early detection of cancers. The effectiveness of this approach was demonstrated in a cohort of 175 head and neck squamous cell carcinoma patients. The outlined protocols include methods for sample preparation, instrument analysis, and data analysis and interpretation using this workflow.

Longitudinal analysis, machine learning, cancer, e↗

Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.

Environmental Molecular Sciences Laboratory↗

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)

Khurana, Mridul↗

Visual Systems Mapping to Define and Compare Woody Biomass LCAs for Sustainable Systems

The challenge addressed in this research centres on the need to choose between several biomass sources and energy production processes, while supporting rural economies and resilience of forest systems. A key barrier to effective decision-making for strategies using biomass is the lack of standardized and transparent life cycle assessment (LCA) baselines. These baselines are critical for assessing the impacts of biomass strategies but often vary due to regional factors and chosen simplifying assumptions of the LCAs. However, omitting key variables can mean the LCA omits key feedback and balancing loops relevant to fully assessing impacts of the change or test scenario. To address these complexities, this project employs a systems engineering approach: visual systems mapping. This technique is used to define the boundaries and dynamic behaviours of LCA baselines, enhancing transparency. By examining five literature sources and their documented baseline scenarios, the systems mapping case-studies demonstrates an approach to documenting and archiving these baselines. Recommendations are that visual systems mapping should be used to document key assumptions, such as baselines, of LCAs. Further, where possible open data repositories should hold key information about LCA baselines and reproducible workflows (e.g., using open-source tools) should be used to improve transparency and comparability in LCAs. Given the consensus within the broader scientific community on the importance of replicable data practices, this research reinforces the need for standardized frameworks and systems engineering tools in LCAs. This research demonstrates a pathway to more transparent, standardized, and comparable LCAs, that may bolster decisions for biomass systems.

Davis, Maggie [ORNL] (ORCID:0000000181319328)↗

The Role of National Research and Education Networks Providing Connectivity and Advanced Network Services to Virtual Communities in Collaborative R&E Projects. CUDI: The Mexican Case Part 1, , In: ISUM 2015: High Performance Computer Applications

This paper describes the role of National Research and Education Networks (NRENs) and their aim to provide a seamless, large scale, high-speed, low-latency network to accelerate scientific and education discovery for national, regional or global collaborative projects that are dependent on the use of modern high performance distributed computing systems (HPDCS) to process mathematical models, produce new knowledge and drive innovation when resolving complex problems. NRENs have become the mainstream of communication and collaboration to integrate the efforts of large geographically distributed teams of Virtual Communities (VC) that - train, teach and learn-, -create, use and share- knowledge, data, information and communications technology resources (e.g. computer and information systems, middleware, tools, instruments, data sets, repositories, applications and services) building e-infrastructures necessary to meet the collaborative projects’ goals. The paper focuses on the current status of the Mexican NREN: CUDI, its future organization and political support, necessary to provide seamless, large scale, high-speed, low latency and secure national backbone and international links providing connectivity, advanced network services and technical support to VCs and their e-infrastructures in collaborative R&E projects within the country, the LAC region and worldwide.

Computer Science↗

Chemical durability of glasses

The chemical durability of silicate glasses has long been studied for many applications, in particular when glasses are subjected to environmental weathering and aqueous corrosion. Typical applications include optical instruments, glass vessels, radioactive waste confinement, and bone reparation. Glass corrosion involves ion exchange, water diffusion, network dissolution-recondensation, and secondary phase precipitation. These reactions may impact, among other things, the release of contaminants from waste glasses, and the glass mechanical, optical and catalytic properties. The glass corrosion mechanisms and alteration product formation have been well studied as a function of many environmental parameters (temperature, pH, water composition, etc.). The present chapter describes the general phenomena behind glass corrosion and details glass dissolution in aqueous conditions on one hand and glass vapor hydration on the other hand. The latter phenomenon has not received the same level of attention in the literature relative to the corrosion in aqueous solutions. Research and Development needs, in particular in complex systems such as radioactive waste geological repositories, are discussed in the conclusion of the chapter.

Abdelouas, Abdesselam↗

Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors

Aims/hypothesis Progression to type 1 diabetes is associated with genetic factors, the presence of autoantibodies and a decline in beta cell insulin secretion in response to glucose. Very little is known regarding the molecular changes that occur in human insulin-secreting beta cells prior to the onset of type 1 diabetes. Herein, we applied an unbiased proteomics approach to identify changes in proteins and potential mechanisms of islet dysfunction in islet-autoantibody-positive organ donors with pre-symptomatic stage 1 type 1 diabetes (HbA1c ≤42 mmol/mol [6.0%]). We aimed to identify pathways in islets that are indicative of beta cell dysfunction. Methods Multiple islet sections were collected through laser microdissection of frozen pancreatic tissues from organ donors positive for single or multiple islet autoantibodies (AAb + , n=5), and age (±2 years)- and sex-matched non-diabetic (ND) control donors (n=5) obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD). Islet sections were subjected to MS-based proteomics and analysed with label-free quantification followed by pathway and functional annotations. Results Analyses resulted in ~4500 proteins identified with low false discovery rate (<1%), with 2165 proteins reliably quantified in every islet sample. We observed large inter-donor variations that presented a challenge for statistical analysis of proteome changes between donor groups. We therefore focused on only the donors with stage 1 type 1 diabetes who were positive for multiple autoantibodies (mAAb + , n=3) and genetic risk compared with their matched ND controls (n=3) for the final statistical analysis. Approximately 10% of the proteins (n=202) were significantly different (unadjusted p<0.025, q<0.15) for mAAb + vs ND donor islets. The significant alterations clustered around major functions for upregulation in the immune response and glycolysis, and downregulation in endoplasmic reticulum (ER) stress response as well as protein translation and synthesis. The observed proteome changes were further supported by several independent published datasets, including a proteomics dataset from in vitro proinflammatory cytokine-treated human islets and single-cell RNA-seq datasets from AAb + individuals. Conclusions/interpretation In situ human islet proteome alterations in stage 1 type 1 diabetes centred around several major functional categories, including an expected increase in immune response genes (elevated antigen presentation/HLA), with decreases in protein synthesis and ER stress response, as well as compensatory metabolic response. The dataset serves as a proteomics resource for future studies on beta cell changes during type 1 diabetes progression and pathogenesis. Data availability The LC-MS raw datasets that support the findings of this study have been deposited in the online repository: MassIVE (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with accession no. MSV000090212.

Autoantibody-positive↗

Mass Spectrometry Imaging of Biological Tissue: An Approach for Multicenter Studies

Mass spectrometry imaging has become a popular tool for probing the chemical complexity of biological surfaces. This led to the development of a wide range of instrumentation and preparation protocols. It is thus desirable to evaluate and compare the data output from different methodologies and mass spectrometers. Here, we present an approach for the comparison of mass spectrometry imaging data from different laboratories (often referred to as multicenter studies). This is exemplified by the analysis of mouse brain sections in five laboratories in Europe and the USA. The instrumentation includes matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF), MALDI-QTOF, MALDIFourier transform ion cyclotron resonance (FTICR), atmospheric-pressure (AP)-MALDI-Orbitrap, and cluster TOF-secondary ion mass spectrometry (SIMS). Experimental parameters such as measurement speed, imaging bin width, and mass spectrometric parameters are discussed. All datasets were converted to the standard data format imzML and displayed in a common open-source software with identical parameters for visualization, which facilitates direct comparison of MS images. The imzML conversion also allowed exchange of fully functional MS imaging datasets between the different laboratories. The experiments ranged from overview measurements of the full mouse brain to detailed analysis of smaller features (depending on spatial resolution settings), but common histological features such as the corpus callosum were visible in all measurements. High spatial resolution measurements of AP-MALDI-Orbitrap and TOF-SIMS showed comparable structures in the low-micrometer range. We discuss general considerations for planning and performing multicenter studies in mass spectrometry imaging. This includes details on the selection, distribution, and preparation of tissue samples as well as on data handling. Such multicenter studies in combination with ongoing activities for reporting guidelines, a common data format (imzML) and a public data repository can contribute to more reliability and transparency of MS imaging studies.

Environmental Molecular Sciences Laboratory↗

Experimental determination of lead carbonate solubility at high ionic strengths: A Pitzer model description

In this article, solubility measurements of lead carbonate, PbCO 3 (cr), cerussite, as a function of total ionic strengths are conducted in the mixtures of NaCl and NaHCO 3 up to I = 1.2 mol•kg –1 and in the mixtures of NaHCO 3 and Na 2 CO 3 up to I = 5.2 mol•kg –1 , at room temperature (22.5 ± 0.5 °C). The solubility constant (log K sp ) for cerussite, PbCO 3 (cr) = Pb 2+ + CO 3 2- was determined as –13.76 ± 0.15 (2σ) with a set of Pitzer parameters describing the specific interactions of PbCO 3 (aq), Pb(CO 3 ) 2 2- , and Pb(CO 3 )Cl – with the bulk-supporting electrolytes, based on the Pitzer model. The model developed in this work can reproduce the experimental results including model-independent solubility values from the literature over a wide range of ionic strengths with satisfactory accuracy. The model is expected to find applications in numerous fields, including the accurate description of chemical behavior of lead in geological repositories, the modeling of formation of oxidized Pb–Zn ore deposits, and the environmental remediation of lead contamination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of a fluvial aquifer at a range of depths and scales: the Triassic St Bees Sandstone Formation, Cumbria, UK

Fluvial sedimentary successions represent porous media that host groundwater and geothermal resources. Additionally, they overlie crystalline rocks hosting nuclear waste repositories in rift settings. The permeability characteristics of an arenaceous fluvial succession, the Triassic St Bees Sandstone Formation in England (UK), are described, from core-plug to well-test scale up to ~1 km depth. Within such lithified successions, dissolution associated with the circulation of meteoric water results in increased permeability (K~10{sup −1}–10{sup 0} m/day) to depths of at least 150 m below ground level (BGL) in aquifer systems that are subject to rapid groundwater circulation. Thus, contaminant transport is likely to occur at relatively high rates. In a deeper investigation (> 150 m depth), where the aquifer has not been subjected to rapid groundwater circulation, well-test-scale hydraulic conductivity is lower, decreasing from K~10{sup −2} m/day at 150–400 m BGL to 10{sup −3} m/day down-dip at ~1 km BGL, where the pore fluid is hypersaline. Here, pore-scale permeability becomes progressively dominant with increasing lithostatic load. Notably, this work investigates a sandstone aquifer of fluvial origin at investigation depths consistent with highly enthalpy geothermal reservoirs (~0.7–1.1 km). At such depths, intergranular flow dominates in unfaulted areas with only minor contribution by bedding plane fractures. However, extensional faults represent preferential flow pathways, due to presence of high connective open fractures. Therefore, such faults may (1) drive nuclear waste contaminants towards the highly permeable shallow (< 150 m BGL) zone of the aquifer, and (2) influence fluid recovery in geothermal fields.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Leaching of Degraded Preservative Matrices, Based on Sodium Aluminophosphate Glasses, for High-Level Wastes

The chemical stability of vitrified high-level nuclear industry wastes in contact with water was studied experimentally in application to underground disposal of the wastes. The experiments were performed on samples of sodium aluminophosphate glass used in industrial solidification of wastes. Stable isotopes of strontium, cesium, uranium, and rare-earth elements as geochemical analogs of actinides were introduced into the glass to simulate radionuclides. It was observed that water vapor affects the degradation of the glass when vitrified wastes are placed in temporary repositories. It is shown that as a result of the degradation the rate of leaching of the glass in water increases significantly. In addition, a substantial portion of radionuclide simulators in colloidal form goes into the water medium.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗