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At least 1,081 records · Page 60

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry

Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).

47 OTHER INSTRUMENTATION↗

OpenStudio® HPXML workflow [SWR-25-13]

OpenStudio-HPXML allows running residential EnergyPlus™ simulations using an HPXML file for the building description. It is intended to be used by user interfaces or other automated software workflows that automatically produce the HPXML file. OpenStudio-HPXML can accommodate a wide range of different building technologies and geometries. End-to-end simulations typically run in 3-10 seconds, depending on complexity, computer platform and speed, etc. For more information on running simulations, generating HPXML files with the appropriate inputs to run EnergyPlus, etc., please visit the documentation linked below. https://openstudio-hpxml.readthedocs.io/en/latest

Horowitz, Scott↗

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗

SIRIUS: Science-Driven Data Management for Multi-Tiered Storage

The data sets being generated by large applications on very large-scale systems are increasing in both size and complexity. At the same time, there are new ways available to store and access these data sets. The goal in this project is to develop software that applications can use to make use of new and existing storage technologies in more sophisticated ways. One challenge in scientific data management is handling ‘hot’ vs ‘cold’ data. Data that is hot is data that is needed (or will be needed soon) in order for the program to continue progressing, while cold data is either output (and so will not be need further during the life of the program) or will not be needed until significantly later in the program’s run. Hot data should be stored in a way that allows fast access. On most systems, economic factors lead to an inverse relationship between storage performance and storage capacity and so fast access storage is limited. This makes it important to correctly place hot and cold data and avoid cold data unnecessarily consuming precious resources. In this reporting period, we addressed this challenge in various ways and at various levels. Data management frameworks offer only limited control to applications in how data is stored. We have added software capabilities for seamlessly moving data between layers of the storage technology using promote and demote functions to existing software frameworks. This gives direct control to applications in deciding what priority data receives. Additionally, we integrated different storage layer management frameworks in order to allow data to be exchanged and moved between storage layers in a consistent way across the application. Further, applications are not always able to directly decide what storage level makes sense for a given piece of data without an understanding of the underlying storage technologies. Data storage frameworks are often positioned to make these sorts of decisions in service of the application. We have added machine-learning based capabilities to data staging frameworks in order to make intelligent decisions about where data should be stored given learning about patterns in previous usage of similar data.

97 MATHEMATICS AND COMPUTING↗

The Uniform Methods Project: Smart Thermostat Evaluation Protocol

A smart thermostat is an internet-connected device that controls home heating, ventilation, and air-conditioning (HVAC) equipment and can automatically adjust temperature set points to optimize performance and achieve energy savings. Smart thermostat features often include two way communication, occupancy detection (such as geofencing and occupancy sensors), schedule learning, and seasonal optimization algorithms. Smart thermostats can control most conventional HVAC systems, including central air conditioners, heat pumps, and forced air furnaces. Several types of residential utility programs offer smart thermostats as replacements measures. Working with smart thermostat vendors, utilities can offer separate optimization programs to produce energy savings beyond those achieved by installing a smart thermostat. From an evaluation perspective, smart thermostat programs have several noteworthy features. First, the energy savings from a smart thermostat may change over the life of the device. As a smart thermostat is connected to the internet, original equipment manufacturers can update the thermostat software to improve the thermostat's energy efficiency. Likewise, users can adjust the thermostat settings and schedules over time in response to changes in weather, thermal comfort, energy prices, or preferences for energy efficiency. Additionally, many thermostat manufacturers offer seasonal optimization programs that recommend changes or make minor, automated adjustments to the thermostat settings to improve energy efficiency. These opt-in programs are now standard offerings for many smart thermostat manufacturers and provided at no additional cost to users. The potential for software updates and continuous optimization and the evolving nature of user interactions mean future energy savings may differ from first-year savings and the energy savings of smart thermostats may need to be evaluated more than once. Second, smart thermostats often have small unit energy savings relative to a home's total energy consumption, especially in comparison to whole- home retrofit programs. This can make it difficult to detect the smart thermostat savings in billing or advanced metering infrastructure (AMI) meter consumption data. For example, as cooling loads in many regions average about 20% of annual electricity consumption, smart thermostat savings of 10% of cooling energy use would equate to a 2% reduction in home electricity consumption. Evaluators should use regression analysis of whole-home billing consumption or advanced metering infrastructure (AMI) meter consumption data to evaluate smart thermostat savings because, as explained at greater length below , these data are usually available to evaluators and regression can control for the impacts of weather and other potentially confounding factors on a home's energy consumption. Finally, as with other energy efficiency programs, participation in smart thermostat programs is self-selective. As discussed at greater length below , smart thermostat participants tend to be, among other things, younger, higher-income, and more likely to adopt electric vehicles (EVs) and internet connected devices than nonparticipants. These differences are often unobservable to the evaluator and correlated with a home's energy consumption, creating the potential for bias in estimating savings. Due to the small unit savings of thermostats, errors and biases from self-selection that may not be very consequential when evaluating a whole- home retrofits (e.g., ±2% of home electricity consumption) can have a major impact when evaluating the savings and cost-effectiveness of smart thermostat programs. A percentage point change in the estimated savings could affect the cost-effectiveness of a program. This means it is important for evaluators to assess and to minimize the potential for error from selection bias in estimating smart thermostat program savings. The Uniform Methods Project provides model protocols for determining energy savings and demand reductions that result from specific energy efficiency measures implemented through state and utility programs. In most cases, the measure protocols are based on a particular option identified by the International Performance Verification and Measurement Protocol ; however, this work provides a more detailed approach to implementing that option. Each chapter is written by technical experts in collaboration with their peers, reviewed by industry experts, and subject to public review and comment. The UMP protocols can be used by utilities, program administrators, public utility commissions, evaluators, and other stakeholders for both program planning and evaluation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Data processing for a cosmic ray experiment onboard the solar probes Helios 1 and 2: Experiment 6

The data processing system for the Helios experiment 6, measuring energetic charged particles of solar, planetary and galactic origin in the inner solar system, is described. The aim of this experiment is to extend knowledge on origin and propagation of cosmic rays. The different programs for data reduction, analysis, presentation, and scientific evaluation are described as well as hardware and software of the data processing equipment. A chronological presentation of the data processing operation is given. Procedures and methods for data analysis which were developed can be used with minor modifications for analysis of other space research experiments.

Mueller-Mellin, R.↗

Orbits: Computer simulation

In rotating machinery dynamics an orbit (Lissajous curve) represents the dynamic path of the shaft centerline motion during shaft rotation and resulting precession. The orbit can be observed with an oscilloscope connected to XY promixity probes. The orbits can also be simulated by a computer. The software for HP computer simulates orbits for two cases: (1) Symmetric orbit with four frequency components with different radial amplitudes and relative phase angles; and (2) Nonsymmetric orbit with two frequency components with two different vertical/horizontal amplitudes and two different relative phase angles. Each orbit carries a Keyphasor mark (one-per-turn reference). The frequencies, amplitudes, and phase angles, as well as number of time steps for orbit computation, have to be chosen and introduced to the computer by the user. The orbit graphs can be observed on the computer screen.

Muszynska, A.↗

Spectroscopic aspects of differential method for sounding gas composition of the atmosphere

The problems concerning the dynamics of populations of the sounded atmospheric gas molecule levels taking into account the nonmonochromatic character of radiation, durations of exciting and sounding pulses, rates of relaxation of excited vibration-rotation states population along different channels in a natural multicomponent mixture of gases and air were investigated. The problems of spectroscopic software, completeness and accuracy of the initial spectroscopic information, information on channels and rates of relaxation from the viewpoint of developing specific schemes of sounding are discussed. The values of deviations of vibration-rotation level populations of some atmospheric molecules from their equilibrium value at simultaneous action of double frequency radiation on the sounding path and the corresponding dynamic variation of lidar return amplitude were estimated. The importance of nonlinear spectrosopic effects in the lidar return value variation at sounding radiation frequency equaling the resonance frequency of vibration-rotation transition in the problem on sounding the humidity profiles and concentrations of gaseous pollutants was also estimated.

Zuev, V. V.↗

The predictive information obtained by testing multiple software versions

Multiversion programming is a redundancy approach to developing highly reliable software. In applications of this method, two or more versions of a program are developed independently by different programmers and the versions are combined to form a redundant system. One variation of this approach consists of developing a set of n program versions and testing the versions to predict the failure probability of a particular program or a system formed from a subset of the programs. The precision that might be obtained, and also the effect of programmer variability if predictions are made over repetitions of the process of generating different program versions, are examined.

Lee, Larry D.↗

A strategy for reducing turnaround time in design optimization using a distributed computer system

There is a need to explore methods for reducing lengthly computer turnaround or clock time associated with engineering design problems. Different strategies can be employed to reduce this turnaround time. One strategy is to run validated analysis software on a network of existing smaller computers so that portions of the computation can be done in parallel. This paper focuses on the implementation of this method using two types of problems. The first type is a traditional structural design optimization problem, which is characterized by a simple data flow and a complicated analysis. The second type of problem uses an existing computer program designed to study multilevel optimization techniques. This problem is characterized by complicated data flow and a simple analysis. The paper shows that distributed computing can be a viable means for reducing computational turnaround time for engineering design problems that lend themselves to decomposition. Parallel computing can be accomplished with a minimal cost in terms of hardware and software.

Young, Katherine C.↗

Simulated final approach path captures using the microwave landing system

Computer simulation results are presented for intercepting final approach paths using various Microwave Landing System (MLS) path capture concepts. This study, conducted under the Advanced Transport Operating System (ATOPS) program, simulated these captures using the MD-80 aircraft as the study model. Several different capture concepts were investigated. Systems that could be retrofitted into existing aircraft with minimum hardware and software changes were considered. An enhanced ILS look-alike capture provided improved tracking performance over conventional ILS without using a full-up path computer. The other concepts used waypoint databases and path computers to provide smart captures. These captures included lateral path intercepts as well as vertical path control. Winds, turbulence, and MLS noise were included in the simulation. In all cases, acceptable tracking errors were obtained during transition to the final approach path.

Feather, J. B.↗

Parallel machine architecture and compiler design facilities

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role.

Kuck, David J.↗

Guidelines and rules for automated assembly by robots in space

The development of an expert system for a 'Mechanical Design System' is discussed. Two different implementation approaches are described. One is coded in C, and the other is realized by a software package - 'Exsys.' The first method has the advantage of greater flexibility and quicker responses, while the latter one is easier to develop. This report discusses the feasible ways to establish a real mechanical intelligent design system applying artificial intelligence techniques so that the products designed by this system could best meet the requirements for space assembly.

Srivastava, Sadanand↗

DNET: A communications facility for distributed heterogeneous computing

This document describes DNET, a heterogeneous data communications networking facility. DNET allows programs operating on hosts on dissimilar networks to communicate with one another without concern for computer hardware, network protocol, or operating system differences. The overall DNET network is defined as the collection of host machines/networks on which the DNET software is operating. Each underlying network is considered a DNET 'domain'. Data communications service is provided between any two processes on any two hosts on any of the networks (domains) that may be reached via DNET. DNET provides protocol transparent, reliable, streaming data transmission between hosts (restricted, initially to DECnet and TCP/IP networks). DNET also provides variable length datagram service with optional return receipts.

Tole, John↗

An expert system for integrated structural analysis and design optimization for aerospace structures

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and design optimization tasks in the integrated aerospace structural design process. These expert systems were developed to work in conjunction with procedural finite element structural analysis and design optimization modules (developed in-house at SAT, Inc.). The complete software, AutoDesign, so developed, can be used for integrated 'intelligent' structural analysis and design optimization. The software was beta-tested at a variety of companies, used by a range of engineers with different levels of background and expertise. Based on the feedback obtained by such users, conclusions were developed and are provided.

Source record↗

Predictive Modeling of Cardiac Ischemia

The goal of the Contextual Alarms Management System (CALMS) project is to develop sophisticated models to predict the onset of clinical cardiac ischemia before it occurs. The system will continuously monitor cardiac patients and set off an alarm when they appear about to suffer an ischemic episode. The models take as inputs information from patient history and combine it with continuously updated information extracted from blood pressure, oxygen saturation and ECG lines. Expert system, statistical, neural network and rough set methodologies are then used to forecast the onset of clinical ischemia before it transpires, thus allowing early intervention aimed at preventing morbid complications from occurring. The models will differ from previous attempts by including combinations of continuous and discrete inputs. A commercial medical instrumentation and software company has invested funds in the project with a goal of commercialization of the technology. The end product will be a system that analyzes physiologic parameters and produces an alarm when myocardial ischemia is present. If proven feasible, a CALMS-based system will be added to existing heart monitoring hardware.

Anderson, Gary T.↗

Reuse of a Formal Model for Requirements Validation

This paper reports experience from how a project engaged in the process of requirements analysis for evolutionary builds can reuse the formally specified design model produced for a similar, earlier project in the same domain. Two levels of reuse are described here. First, a formally specified generic design model was generated on one project to systematically capture the design commonality in a set of software monitors on board a spacecraft. These monitors periodically check for faults and invoke recovery software when needed. The paper summarizes the use of the design model to validate the software design of the various monitors on that first project. Secondly, the paper describes how the formal design model created for the first project was reused on a second, subsequent project. The model was reused to validate the evolutionary requirements for the second project's software monitors, which were being developed in a series of builds. Some mismatches due to the very different architectures on the two projects suggested changes to make the model more generic. In addition, several advantages to the reuse of the first project's formal model on the second project are reported.

Lutz, Robyn R.↗

Onyx-Advanced Aeropropulsion Simulation Framework Created

The Numerical Propulsion System Simulation (NPSS) project at the NASA Glenn Research Center is developing a new software environment for analyzing and designing aircraft engines and, eventually, space transportation systems. Its purpose is to dramatically reduce the time, effort, and expense necessary to design and test jet engines by creating sophisticated computer simulations of an aerospace object or system (refs. 1 and 2). Through a university grant as part of that effort, researchers at the University of Toledo have developed Onyx, an extensible Java-based (Sun Micro-systems, Inc.), objectoriented simulation framework, to investigate how advanced software design techniques can be successfully applied to aeropropulsion system simulation (refs. 3 and 4). The design of Onyx's architecture enables users to customize and extend the framework to add new functionality or adapt simulation behavior as required. It exploits object-oriented technologies, such as design patterns, domain frameworks, and software components, to develop a modular system in which users can dynamically replace components with others having different functionality.

Reed, John A.↗