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At least 199 records · Page 11

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

Optically accessible high-finesse millimeter-wave resonator for cavity quantum electrodynamics with atom arrays

Cavity quantum electrodynamics (QED) is a powerful tool in quantum science, enabling preparation of nonclassical states of light and scalable entanglement of many atoms coupled to a single field mode. While the most coherent atom-photon interactions have been achieved using superconducting millimeter-wave cavities coupled to Rydberg atoms, these platforms so far lack the optical access required for trapping and addressing individual atomic qubits. We present a millimeter-wave Fabry-Pérot cavity with finesse 5.8⁢(1) ×10 7 at a temperature of 1 K providing generous transverse optical access (numerical aperture 0.56). Conflicting goals of strong atom-photon coupling and optical access motivate a near-confocal geometry. Close to confocality, however, postparaxial corrections to the cavity spectrum introduce unexpected degeneracies between transverse modes, leading to excess cavity loss. Modeling these corrections allows for tuning the cavity geometry to evade this loss, producing a high finesse that will enable cavity QED experiments with trapped atoms deep in the strong coupling regime.

Zhang, Tony [Stanford Univ., CA (United States); S↗

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’s R and Spearman’s ρ coefficients as well as Kendall’s τ and Top–Down correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spear man’s ρ, Kendall’s τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

59 BASIC BIOLOGICAL SCIENCES↗

Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil

The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S . viridis . All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S . italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C 4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.

59 BASIC BIOLOGICAL SCIENCES↗

There's No Place Like Home: Residential Parking, Electrical Access, and Implications for the Future of Electric Vehicle Charging Infrastructure

In March 2021, the cumulative sale of plug-in electric vehicles (PEVs), including plug-in hybrid electric vehicles (PHEV) and battery electric vehicles (BEV), reached 1.8 million in the United States (Argonne National Laboratory 2021). However, PEV adoption is still in its infancy; its market share has just reached around 3% of new light-duty vehicle (LDV) sales by the end of 2020 (Alliance for Automotive Innovation 2021). Current trends suggest that PEV market share in the United States is increasing. The U.S. Energy Information Administration's (EIA's) 2020 Annual Energy Outlook forecasts PEV registrations to exceed 8 million vehicles by 2030 (AEO 2020). PEV adoption is expected to be led by states that are regulating the sale of zero emission vehicles (ZEVs) (California Air Resources Board). California continues to push for more aggressive ZEV regulations; the state recently issued an executive order aimed at 100% of LDV sales being ZEVs by 2035 (Office of Governor Newsom). At the federal level, the Biden administration has shown great ambition in encouraging broader electric vehicle (EV) adoption, including setting the goal of installing 500,000 new chargers nationwide (The White House 2021). Access to charging infrastructure is consistently cited as one of the primary barriers to the increased sale of PHEVs and BEVs (Carley et al. 2019). In the United States, PEV charging options are often described using a pyramid structure, with residential charging as the foundation, workplace charging in the middle, and public charging on top (Figure 1). The existing electricity system, which generates, transmits, and distributes electric fuel to residential households, has helped PEVs partially overcome the "chicken and egg" conundrum that has haunted other alternative fuels. Viable home access to electric charging is also an important equity issue, because non-residential PEV charging options (e.g., workplace or public charging stations) are generally more expensive. Households without residential charging access may experience higher total cost of PEV ownership if non-residential charging options are more costly.

33 ADVANCED PROPULSION SYSTEMS↗

AOI-2, A Novel Access Control Blockchain Paradigm for Cybersecure Sensor Infrastructure in Fossil Power Generation Systems

Fossil power generation systems are increasingly vulnerable to attack from both cybercriminals as well as internal threats. These vulnerabilities demand that emerging technologies such as blockchains be utilized to secure the data involved in the information flows within the Supervisory Control and Data Acquisition (SCADA) systems of the fossil power generation plants. The publicly accessible blockchain protocols, although secure, are visible to everyone. Even private blockchains currently are unable to support different levels of access to different participants, which is a critical requirement for the existing SCADA systems running the power plants. In light of the above, novel blockchain protocols that are specifically adapted to fossil power generation environments need to be developed in order to achieve the goal of cybersecure sensor networks. In this work, we address this question by creating a novel blockchain technology, namely smart private ledger, for cybersecure communication within the fossil power generation systems. A lab-scale sensor network consisting of strain and temperature sensors is constructed to develop the ledger. The technology has hierarchical access control which is compatible with the existing SCADA systems in fossil power plants. The sensor data is used with cryptographic digital signatures and secret sharing protocols within the nodes of the blockchain technology. The research results will lead to cybersecurity for machine-to-machine interactions, infrastructure for secure data logging for sensors, decentralized data storage, and second-layer technologies for high volume machine-to-machine interactions in the power plants. The work aims to largely address the concerns for the security of distributed sensor networks in such systems that can be compromised by insider threats and by cybercriminals. The research has led to the training of the next generation of engineers and scientists in the important areas of sensor engineering and blockchain technology.

01 COAL, LIGNITE, AND PEAT↗

LA100 Equity Strategies. Chapter 6: Universal Access to Safe and Comfortable Home Temperatures

The LA100 Equity Strategies project integrates community guidance with robust research, modeling, and analysis to identify strategy options that can increase equitable outcomes in Los Angeles' clean energy transition. This chapter focuses on housing weatherization and cooling technologies as means to increase access to safe and comfortable home temperatures. Lack of cooling access and use can have severe health impacts on building occupants during heat waves. Specifically, NREL developed and used a residential building stock model to simulate the energy use of 50,000 dwellings representing the diversity of housing types, appliances, climate zones, and household incomes across Los Angeles. We compared a baseline scenario with seven upgrade scenarios. Five scenarios cooled the entire household and featured cooling systems at varying efficiency levels with various improvements to the envelope, roof, and shading, and two scenarios cooled a single room in a household with no prior cooling using either a room air-conditioning or a heat pump system. For each scenario, we evaluated impacts on utility bills, payback periods, and changes in energy burdens, as well as ability to achieve safe and comfortable temperatures. We also examined the effects of building types (multifamily vs. single-family) on indoor air temperatures. Based on the results of modeling, analysis, and community guidance, we identified six short-term and two long-term strategies for improving access to building envelope upgrades and cooling strategies that could save lives and maintain safe home temperatures for Los Angeles' low-income households during heat waves. Research was guided by input from the community engagement process, and associated equity strategies are presented in alignment with that guidance.

air conditioning↗

Precursor Analysis Report: Remote Access Attack on Oldsmar Water Treatment Facility 2021

The Remote Access Attack on Oldsmar Water Treatment Facility 2021 Precursor Analysis Report leverages publicly available information about the Oldsmar cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. On 5 February 2021, an adversary gained unauthorized remote access to Bruce T. Haddock Water Treatment Plant in Oldsmar, Florida, which provides treated water to 15,000 customers. The adversary accessed the facility’s Supervisory Control and Data Acquisition (SCADA) workstation and human machine interface (HMI) to change the chemical concentration of sodium hydroxide, commonly referred to as lye and used to regulate acidity levels, from 100 parts per million (PPM) to 11,100 PPM. The chemical was raised to lethal levels that if ingested could lead to serious soft tissue damage, burns, or even death. The facility, however, had redundancies and alarms in place to alert personnel of dangerous chemical levels, and facility officials stated it would have taken 24 to 36 hours for the chemical changes to affect the water supply. Researchers and analysts identified six unique techniques utilized during the attack with a total of 23 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Four of the identified techniques used during the Oldsmar cyber attack were precursors to the triggering event. Analysis identified 21 observables associated with these precursor techniques, 20 of which were assessed to have an increased likelihood of being perceived in the minutes preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Evaluating the Curtailment Risk of Non-Firm Utility-Scale Solar Photovoltaic Plants under a Novel Last-In First-Out Principle of Access Interconnection Agreement

With the increasing share of distributed energy resources on the electric grid, utility companies are facing significant decisions about infrastructure upgrades. An alternative to extensive and capital-intensive upgrades is to offer non-firm interconnection opportunities to distributed generators, via a coordinated operation of utility scale resources. This paper introduces a novel flexible interconnection option based on the last-in, first-out principles of access aimed at minimizing the unnecessary non-firm generation energy curtailment by balancing access rights and contribution to thermal overloads. Although we focus on solar photovoltaic (PV) plants in this work, the introduced flexible interconnection option applies to any distributed generation technology. The curtailment risk of individual non-firm PV units is evaluated across a range of PV penetration levels in a yearlong quasi-static time-series simulation on a real-world feeder. The results show the importance of the size of the curtailment zone in the curtailment risk distribution among flexible generation units as well as that of the “access right” defined by the order in which PV units connect to the grid. Case study results reveal that, with a proper selection of curtailment radius, utilities can reduce the total curtailment of flexible PV resources by up to more than 45%. Findings show that non-firm PV generators can effectively avoid all thermal limit-related upgrade costs.

14 SOLAR ENERGY↗

Proposed preliminary criteria for space shuttle access equipment at the operational site

A comparison was made between the methods of access utilized, or proposed, by the military, commercial airlines, and the space shuttle Phase B contractors. The methodology was subjected to consideration for space shuttle use and similarity to current space shuttle access concepts. The Phase B contractor concepts were in turn examined for degree of use of the state-of-the-art and progressive extension of new cost-effective ideas. This comparison disclosed a need for better definition of the criteria/requirements for space shuttle access equipment. Preliminary criteria, needed prior to initiation of the detail design (Phase C/D effort) of ground hardware for the operational site, are presented.

Beck, P. E.↗

Magnetospheric access of solar particles and the configuration of the distant geomagnetic field, volume 1

The access of 1.2 to 40 MeV protons and 0.4 to 1.0 MeV electrons from interplanetary space to the polar cap regions was investigated with an experiment on board a low altitude, polar-orbiting satellite (0G0 4). A total of 333 quiet time observations of the electron polar cap boundary give a mapping of the boundary between open and closed geomagnetic field lines. Observations of events associated with co-rotating regions of enhanced proton flux in interplanetary space were used to establish the characteristics of the 1.2 to 40 MeV proton access windows. The results were compared to particle access predictions of the distant geomagnetic tail configurations. The role played by interplanetary anisotropies in the observation of persistent polar cap features is discussed. Special emphasis is given to the problem of nonadiabatic particle entry through regions where the magnetic field is changing direction.

Evans, L. C.↗

Acceptance test report (MI-74067-009-00). SVWS access arm (Serial number AA-09-03) (drawing 75M08129-13)

Acceptance tests were conducted at Kennedy Space Center of the Saturn Vehicle Workshop Spacecraft Access Arm and related equipment. The tests were conducted to prove complete system capability to operate satisfactorily under conditions required to support spacecraft operations and activities. The SVWS Access Arm, serial number AA-09-03, is a Command Module Service Arm, S/A 9, which was removed from the mobile launcher and modified to support the SVWS operations. The C/M environmental chamber was removed and a completely new chamber was installed. The retract system was redesigned to remove the automatic/remote control capability and replaced with a local manual control. The SVWS Access Arm System was successfully tested and supported spacecraft processing without major problems.

Hagood, J. T.↗

Random-access technique for modular bathymetry data storage in a continental shelf wave refraction program

A study was conducted of an alternate method for storage and use of bathymetry data in the Langley Research Center and Virginia Institute of Marine Science mid-Atlantic continental-shelf wave-refraction computer program. The regional bathymetry array was divided into 105 indexed modules which can be read individually into memory in a nonsequential manner from a peripheral file using special random-access subroutines. In running a sample refraction case, a 75-percent decrease in program field length was achieved by using the random-access storage method in comparison with the conventional method of total regional array storage. This field-length decrease was accompanied by a comparative 5-percent increase in central processing time and a 477-percent increase in the number of operating-system calls. A comparative Langley Research Center computer system cost savings of 68 percent was achieved by using the random-access storage method.

Poole, L. R.↗

Components of the airport access system

The organizations and agencies which make up or influence the airport access system are examined. These include the airport, the airline industry, the public and private transit agencies which provide ground access to the airport, and the regulatory agencies which affect all of these organizations and their actions. Each component, with the exception of the regulatory agencies is described in terms of its legal status, its sources of funds, and the nature of its relationship with the other components. Conclusions regarding the system components' effects on airport access and recommendations for changes which appear practical are presented.

Source record↗

Role of helicopters in airport access

The paper briefly reviews the role of helicopter systems in the provision of airport access services and evaluates the potential for the future development of such services in major metropolitan areas in the United States. The evaluation is based on a computer simulation of potential helicopter system proposed for 20 metropolitan areas. The simulation provides two indicators that are used to gage the extent of the feasibility of developing successful systems in these areas: (1) the cost per seat mile, and (2) the break-even number of passengers, expressed as a percentage of total air travelers. It is found that a few metropolitan areas presently have the potential of marginally supporting intra-urban helicopter airport access service. The access systems offer a viable alternative for air passengers placing a high value on their time, and provides the opportunity for better integrating the air transportation service of multiple airports in a given urban region.

Dajani, J. S.↗

Next generation communications satellites: Multiple access and network studies

Following an overview of issues involved in the choice of promising system architectures for efficient communication with multiple small inexpensive Earth stations serving hetergeneous user populations, performance evaluation via analysis and simulation for six SS/TDMA (satellite-switched/time-division multiple access) system architectures is discussed. These configurations are chosen to exemplify the essential alternatives available in system design. Although the performance evaluation analyses are of fairly general applicability, whenever possible they are considered in the context of NASA's 30/20 GHz studies. Packet switched systems are considered, with the assumption that only a part of transponder capacit is devoted to packets, the integration of circuit and packet switched traffic being reserved for further study. Three types of station access are distinguished: fixed (FA), demand (DA), and random access (RA). Similarly, switching in the satellite can be assigned on a fixed (FS) or demand (DS) basis, or replaced by a buffered store-and-forward system (SF) onboard the satellite. Since not all access/switching combinations are practical, six systems are analyzed in detail: three FS SYSTEMS, FA/FS, DA/ES, RA/FS; one DS system, DA/DS; and two SF systems, FA/SF, DA/SF. Results are presented primarily in terms of delay-throughput characteristics.

Stern, T. E.↗

A system for model access in tunnels with an unbreathable test medium

In many specialty wind tunnels, test gases other than ambient air are used to meet special testing requirements. A typical example is the use of freon as the test gas to achieve a realistic density ratio between gas and model for exploring flutter stability boundaries. Another example is the use of pressurized air to elevate the stream density and enhance Reynolds number or dynamic pressure simulation. Such specialty tunnels require a system of access o the model which will allow services and changes to the model without exposing personnel to the unnatural and perhaps hostile environment or requiring the venting and purging of the entire tunnel circuit. This paper will describe the plenum and model access systems for the forthcoming U.S. National Transonic facility where gaseous nitrogen (N2) at temperatures between 338 and 78 K and at pressures to 9 bars is used as the test medium. The operation at cold temperatures imposes some additional requirements which make the access systems more difficult to design and time consuming to operate than for conventional wind tunnels.

Howell, R. R.↗

Distributed reservation control protocols for random access broadcasting channels

Attention is given to a communication network consisting of an arbitrary number of nodes which can communicate with each other via a time-division multiple access (TDMA) broadcast channel. The reported investigation is concerned with the development of efficient distributed multiple access protocols for traffic consisting primarily of single packet messages in a datagram mode of operation. The motivation for the design of the protocols came from the consideration of efficient multiple access utilization of moderate to high bandwidth (4-40 Mbit/s capacity) communication satellite channels used for the transmission of short (1000-10,000 bits) fixed length packets. Under these circumstances, the ratio of roundtrip propagation time to packet transmission time is between 100 to 10,000. It is shown how a TDMA channel can be adaptively shared by datagram traffic and constant bandwidth users such as in digital voice applications. The distributed reservation control protocols described are a hybrid between contention and reservation protocols.

Greene, E. P.↗