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At least 1,315 records · Page 73

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative’s FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

97 MATHEMATICS AND COMPUTING↗

Materials Data Science Ontology(MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science

Ontologies have gained popularity in the scientific community as a way to standardize terminologies in organizations’ data. Although certain cohorts have created frameworks with rules and guidelines on creating ontologies, there exist significant variations in how Materials Science ontologies are currently developed. We seek to provide guidance in the form of a unified automated framework for developing interoperable and modular ontologies for Materials Data Science that simplifies the ontology terms matching by establishing a semantic bridge up to the Basic Formal Ontology(BFO). This framework provides key recommendations on how ontologies should be positioned within the semantic web, what knowledge representation language is recommended, and where ontologies should be published online to boost their findability and interoperability. Two fundamental components of the MDS-Onto framework are the bilingual package called FAIRmaterials for ontology creation and FAIRLinked, for FAIR data creation. To showcase the practical capabilities of FAIRmaterials, we present two exemplar domain ontologies of MDS-Onto: Synchrotron X-Ray Diffraction and Photovoltaics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Opening doors to physical sample tracking and attribution in Earth and environmental sciences

Physical samples and their associated data and metadata underpin scientific discoveries across disciplines and can enable new science when appropriately archived. However, there are significant gaps in current practices and infrastructure that prevent accurate provenance tracking, reproducibility, and attribution. For most samples, descriptive metadata are often sparse, inaccessible, or absent. Samples and associated data and metadata may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkage or provenance tracking as new information is generated over time. The Earth Science Information Partners (ESIP) Physical Samples Curation Cluster has therefore developed guidance for scientific authors on ‘Publishing Open Research Using Physical Samples.’ This involved synthesizing existing practices, gathering community feedback, and assessing real-world examples. We identified improvements needed to enable authors to efficiently cite and link Earth science samples and related data, and track their use. Our goal is to help improve discoverability, interoperability, and reuse of physical samples, and associated data and metadata. Though primarily focused on the needs of Earth and environmental sciences, these guidelines are broadly applicable.

58 GEOSCIENCES↗

Cancer genomics predicts disease relapse and therapeutic response to neoadjuvant chemotherapy of hormone sensitive breast cancers

Several studies provide insight into the landscape of breast cancer genomics with the genomic characterization of tumors offering exceptional opportunities in defining therapies tailored to the patient’s specific need. However, translating genomic data into personalized treatment regimens has been hampered partly due to uncertainties in deviating from guideline based clinical protocols. Here we report a genomic approach to predict favorable outcome to treatment responses thus enabling personalized medicine in the selection of specific treatment regimens. The genomic data were divided into a training set of N = 835 cases and a validation set consisting of 1315 hormone sensitive, 634 triple negative breast cancer (TNBC) and 1365 breast cancer patients with information on neoadjuvant chemotherapy responses. Patients were selected by the following criteria: estrogen receptor (ER) status, lymph node invasion, recurrence free survival. The k-means classification algorithm delineated clusters with low- and high- expression of genes related to recurrence of disease; a multivariate Cox’s proportional hazard model defined recurrence risk for disease. Classifier genes were validated by Immunohistochemistry (IHC) using tissue microarray sections containing both normal and cancerous tissues and by evaluating findings deposited in the human protein atlas repository. Based on the leave-on-out cross validation procedure of 4 independent data sets we identified 51-genes associated with disease relapse and selected 10, i.e. TOP2A, AURKA, CKS2, CCNB2, CDK1 SLC19A1, E2F8, E2F1, PRC1, KIF11 for in depth validation. Expression of the mechanistically linked disease regulated genes significantly correlated with recurrence free survival among ER-positive and triple negative breast cancer patients and was independent of age, tumor size, histological grade and node status. Importantly, the classifier genes predicted pathological complete responses to neoadjuvant chemotherapy (P < 0.001) with high expression of these genes being associated with an improved therapeutic response toward two different anthracycline-taxane regimens; thus, highlighting the prospective for precision medicine. Our study demonstrates the potential of classifier genes to predict risk for disease relapse and treatment response to chemotherapies. The classifier genes enable rational selection of patients who benefit best from a given chemotherapy thus providing the best possible care. The findings encourage independent clinical validation.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating efficacy of indoor non-pharmaceutical interventions against COVID-19 outbreaks with a coupled spatial-SIR agent-based simulation framework

Contagious respiratory diseases, such as COVID-19, depend on sufficiently prolonged exposures for the successful transmission of the underlying pathogen. It is important that organizations evaluate the efficacy of non-pharmaceutical interventions aimed at mitigating viral transmission among their personnel. We have developed a operational risk assessment simulation framework that couples a spatial agent-based model of movement with an agent-based SIR model to assess the relative risks of different intervention strategies. By applying our model on MIT’s Stata center, we assess the impacts of three possible dimensions of intervention: one-way vs unrestricted movement, population size allowed onsite, and frequency of leaving designated work location for breaks. We find that there is no significant impact made by one-way movement restrictions over unrestricted movement. Instead, we find that reducing the frequency at which individuals leave their workstations combined with lowering the number of individuals admitted below the current recommendations lowers the likelihood of highly connected individuals within the contact networks that emerge, which in turn lowers the overall risk of infection. We discover three classes of possible interventions based on their epidemiological effects. By assuming a direct relationship between data on secondary attack rates and transmissibility in the agent-based SIR model, we compare relative infection risk of four respiratory illnesses, MERS, SARS, COVID-19, and Measles, within the simulated area, and recommend appropriate intervention guidelines.

60 APPLIED LIFE SCIENCES↗

A theoretical investigation of the effect of Ga alloying on thermodynamic stability, electronic-structure, and oxidation resistance of Ti 2 AlC MAX phase

We present a systematic investigation of thermodynamic stability, phase-reaction, and chemical activity of Al containing disordered Ti 2 (Al-Ga)C MAX phases using machine-learning driven high-throughput framework to understand the oxidation resistance behavior with increasing temperature and exposure to static oxygen. The A-site (at Al) disordering of Ti 2 AlC with Ga shows significant change in the chemical activity of Al with increasing temperature and exposure to static oxygen, which is expected to enable surface segregation of Al, thereby, the formation of Al 2 O 3 and improved oxidation resistance. We performed in-depth convex hull analysis of ternary Ti-Al-C, Ti-Ga-C, and Ti-Al-Ga-C based MAX phase, and provide detailed contribution arising from electronic, chemical and vibrational entropies. The thermodynamic analysis shows change in the Gibbs formation enthalpy (ΔG form ) at higher temperatures, which implies an interplay of temperature-dependent enthalpy and entropic contributions in oxidation resistance Ga doped Ti 2 AlC MAX phases. A detailed electronic structure and chemical bonding analysis using crystal orbital Hamilton population method reveal the origin of change in phases stability and in oxidation resistance in disorder Ti2(Al 1-x Ga x )C MAX phases. Our electronic structure analysis correlate well with the change in oxidation resistance of Ga doped MAX phases. We believe our study provides a useful guideline to understand to role of alloying on electronic, thermodynamic, and oxidation related mechanisms of bulk MAX phases, which can work as a precursor to understand oxidation behavior of twodimensional MAX phases, i.e., MXenes (transition metal carbides, carbonitrides and nitrides).

36 MATERIALS SCIENCE↗

Entropy removal of medical diagnostics

Shannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and quantitatively applied Shannon entropy in a systematic way to quantify the entropy of clinical situations using diagnostic variables (true and false positives and negatives, respectively). Decision tree representations of medical decision-making tools can be generated using diagnostic variables found in literature and entropy removal can be calculated for these tools. This concept of clinical entropy removal has significant potential for further use to bring forth healthcare innovation, such as quantifying the impact of clinical guidelines and value of care and applications to Emergency Medicine scenarios where diagnostic accuracy in a limited time window is paramount. This analysis was done for 623 diagnostic tools and provided unique insights into their utility. For studies that provided detailed data on medical decision-making algorithms, bootstrapped datasets were generated from source data to perform comprehensive machine learning analysis on these algorithms and their constituent steps, which revealed a novel and thorough evaluation of medical diagnostic algorithms.

97 MATHEMATICS AND COMPUTING↗

Efficient and assured reinforcement learning-based building HVAC control with heterogeneous expert-guided training

Abstract Building heating, ventilation, and air conditioning (HVAC) systems account for nearly half of building energy consumption and $$20\%$$ of total energy consumption in the US. Their operation is also crucial for ensuring the physical and mental health of building occupants. Compared with traditional model-based HVAC control methods, the recent model-free deep reinforcement learning (DRL) based methods have shown good performance while do not require the development of detailed and costly physical models. However, these model-free DRL approaches often suffer from long training time to reach a good performance, which is a major obstacle for their practical deployment. In this work, we present a systematic approach to accelerate online reinforcement learning for HVAC control by taking full advantage of the knowledge from domain experts in various forms . Specifically, the algorithm stages include learning expert functions from existing abstract physical models and from historical data via offline reinforcement learning, integrating the expert functions with rule-based guidelines, conducting training guided by the integrated expert function and performing policy initialization from distilled expert function. Moreover, to ensure that the learned DRL-based HVAC controller can effectively keep room temperature within the comfortable range for occupants, we design a runtime shielding framework to reduce the temperature violation rate and incorporate the learned controller into it. Experimental results demonstrate up to 8.8 X speedup in DRL training from our approach over previous methods, with low temperature violation rate.

Xu, Shichao↗

Linking international technical specifications for acoustic characterization of marine energy converter sounds with environmental compliance criteria

As new ocean energy technologies emerge and are deployed for testing and operations, sound emissions are a potential concern for environmental effects to marine life. Consistent acoustic measurement and data analysis methods can help promote comparisons of technologies and transferability between project sites. In 2022, acoustic emissions from a prototype scale wave energy converter (WEC) were characterized for a range of environmental conditions and power generation states in the coastal waters off southern California using a set of international technical specifications. Results from the international technical specification analyses were applied to United States regulatory threshold criteria for acoustic impacts to marine mammals and examined in the context of European underwater noise monitoring guidelines. Weighted 24 hour cumulative sound exposure levels SEL24h calculated from the highest power generation state WEC sound pressure levels were often more than 20 dB below threshold criteria for temporary threshold shifts in five relevant marine mammal hearing groups. Following European Union recommendations for analyses and reporting, WEC sound characterization in third octave bands centered at 63 Hz and 125 Hz show clear spatial decay of WEC-generated noise, with more pronounced attenuation at 63 Hz, and a less marked but still detectable gradient at 125 Hz, collectively suggesting a relatively confined acoustic footprint under the observed conditions. The value of the international technical specification approach is highlighted by the isolation of WEC sounds from the surrounding soundscape. This allows for a robust characterization of acoustic emissions through a range of device power generation and sea states. Furthermore, in threshold-based regulatory contexts like the U.S., this facilitates direct evaluation of source contributions, while in broader monitoring frameworks used in the E.U. it provides a reproducible foundation for assessing the contribution of emerging ocean energy technologies to the underwater acoustic environment.

Haxel, Joseph H. (ORCID:0000000273864761)↗

Medication abortion via digital health in the United States: a systematic scoping review

Digital health, including telemedicine, has increased access to abortion care. The convenience, flexibility of appointment times, and ensured privacy to abortion users may make abortion services via telemedicine preferable. This scoping review systematically mapped studies conducted on abortion services via telemedicine, including their effectiveness and acceptability for abortion users and providers. All published papers included abortion services via telemedicine in the United States were considered. Articles were searched in PubMed, CINAHL, and Google Scholar databases in September 2022. The findings were synthesized narratively, and the PRISMA-ScR guidelines were used to report this study. Out of 757 retrieved articles, 33 articles were selected based on the inclusion criteria. These studies were published between 2011 and 2022, with 24 published in the last 3 years. The study found that telemedicine increased access to abortion care in the United States, especially for people in remote areas or those worried about stigma from in-person visits. The effectiveness of abortion services via telemedicine was comparable to in-clinic visits, with 6% or fewer abortions requiring surgical intervention. Both care providers and abortion seekers expressed positive perceptions of telemedicine-based abortion services. However, abortion users reported mixed emotions, with some preferring in-person visits. The most common reasons for choosing telemedicine included the distance to the abortion clinic, convenience, privacy, cost, flexibility of appointment times, and state laws imposing waiting periods or restrictive policies. Telemedicine offered a preferable option for abortion seekers and providers. The feasibility of accessing abortion services via telemedicine in low-resource settings needs further investigation.

60 APPLIED LIFE SCIENCES↗

Denary oxide nanoparticles as highly stable catalysts for methane combustion

Oxide nanoparticles with elemental and structural diversity are widely studied for catalysis and energy applications. While compositional control holds great promise for materials discovery, current oxide nanoparticles are typically limited to a few cations due to the intrinsic complexity in nanoscale multi-element mixing. Here we report the rational design and synthesis of single-phase multi-element oxide nanoparticles with tunable composition, size and structure. We have identified temperature-, oxidation- and entropy-driven synthesis strategies to mix a range of elements with largely dissimilar oxidation potentials (including palladium), thus greatly expanding the compositional space. Through rapid synthesis and screening, we obtained a denary multi-element oxide catalyst showing high performance and superior stability for catalytic methane combustion over 100 hours due to the high-entropy design and stabilization. Finally, our work therefore provides a viable synthesis route with clear guidelines for multi-element oxide nanoparticles and enables materials design in the multi-element space towards highly stable catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Best practices for experiments and reporting in photocatalytic CO 2 reduction

Visible-light-driven conversion of CO 2 to fuels and valuable compounds has experienced tremendous activity in recent years, aiming at storing solar energy into chemical bonds using CO 2 as a renewable feedstock, ultimately at massive scale. Despite these efforts, processes and catalytic systems are still at an early stage of development, with fundamental mechanistic challenges as pre-requisites for device design. In this context, collective efforts currently necessitate the exploration of a variety of approaches. On the other hand, an alignment of practices is required to ensure robustness, precision and accuracy of the results, as well as shared metrics and tools for advancing our understanding of the necessary processes. Here, this Perspective aims to provide guidelines and a framework towards these objectives.

photocatalysis↗

Corrugation-driven symmetry breaking in magic-angle twisted bilayer graphene

Abstract The discovery of unconventional superconductivity in magic-angle twisted bilayer graphene (tBLG) supported the twist-angle-induced flat band structure predictions made a decade earlier. Numerous physical properties have since been linked to the interlayer twist angle using the flat band prediction as a guideline. However, some key observations like the nematic phase and striped charge order behind the superconductivity are missing in this initial model. Here we show that a thermodynamically stable large out-of-plane displacement, or corrugation of the bilayer, induced by the interlayer twist, demonstrates partially filled states of the flat band structure, accompanied by a broken symmetry, in the magic-angle regime and the presence of symmetry breaking associated with the superconductivity in tBLG. The distinction between low and high corrugation can also explain the observed evolution of the vibrational spectra of tBLG as a function of twist angle. Our observation that large out-of-plane deformation modes enable partial filling of states near the Fermi energy may lead to a strategy for offsetting the effects of disorder in the local twist angle, which suppresses unconventional superconductivity and correlated insulator behavior in magic-angle tBLG.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Chapter 8. Hybrid Biological–Inorganic Systems for CO 2 Conversion to Fuels

The biological reduction of CO 2 into organic carbon is integral to the formation and maintenance of all life on earth. An urgent need to mitigate the effects of CO 2 on our atmosphere has provided an imperative to exploit biological CO 2 fixation for the conversion of CO2 into valuable and energy rich fuels. Photosynthesis uses only sunlight, water, and CO2 as starting materials to form all biomass.

CO2 Conversion to Fuels↗

Review on the growth, properties and applications of self-assembled oxide–metal vertically aligned nanocomposite thin films—current and future perspectives

Self-assembled oxide–metal nanocomposite thin films have aroused great research interest owing to their wide range of functionalities, including metamaterials with plasmonic and hyperbolic optical properties, and ferromagnetic, ferroelectric and multiferroic behaviors. Oxide–metal nanocomposites typically self-assemble as metal particles in an oxide matrix or as a vertically aligned nanocomposite (VAN) with metal nanopillars embedded in an oxide matrix. Among them, the VAN architecture is particularly interesting due to the vertical strain control and highly anisotropic structure, enabling the epitaxial growth of materials with large lattice mismatch. In this review, the driving forces behind the formation of self-assembled oxide–metal VAN structures are discussed. Specifically, an updated in-plane strain compensation model based on the areal strain compensation concept has been proposed in this review, inspired by the prior linear strain compensation model. It provides a guideline for material selection for designing VAN systems, especially those involving complex orientation matching relationships. Based on the model, several case studies are discussed, comparing the microstructure and morphology of different oxide–metal nanocomposites by varying the oxide phase. Specific examples highlighting the coupling between the electrical, magnetic and optical properties are also discussed in the context of oxide–metal nanocomposites. Finally, future research directions and needs are also discussed.

36 MATERIALS SCIENCE↗

Predicting the chemical reactivity of organic materials using a machine-learning approach

Stability and compatibility between chemical components are essential parameters that need to be considered in the selection of functional materials in configuring a system. In configuring devices such as batteries or solar cells, not only the functionality of individual constituting materials such as electrodes or electrolyte but also an appropriate combination of materials which do not undergo unwanted side reactions is critical in ensuring their reliable performance in long-term operation. While the universal theory that can predict the general chemical reactivity between materials is long awaited and has been the subject of studies with a rich history, traditional ways proposed to date have been mostly based on simple electronic properties of materials such as electronegativity, ionization energy, electron affinity and hardness/softness, and could be applied to only a small group of materials. Moreover, prediction has often been far from accurate and has failed to offer general implications; thus it was practically inadequate as a selection criterion from a large material database, i.e. data-driven material discovery. Herein, we propose a new model for predicting the general reactivity and chemical compatibility among a large number of organic materials, realized by a machine-learning approach. As a showcase, we demonstrate that our new implemented model successfully reproduces previous experimental results reported on side-reactions occurring in lithium–oxygen electrochemical cells. Furthermore, the mapping of chemical stability among more than 90 available electrolyte solvents and the representative redox mediators is realized by this approach, presenting an important guideline in the development of stable electrolyte/redox mediator couples for lithium–oxygen batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗