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This thesis explores the use of design concepts in lighting and space simulations to derive how spatially adjustable lighting (intensity, direction and color) can impact building energy savings and human factors (glare) considerations.
Earth system models (ESMs) and general circulation models (GCMs) are heavily used to provide inputs to sectoral impact and multisector dynamic models, which include representations of energy, water, land, economics, and their interactions. Therefore, representing the full range of model uncertainty, scenario uncertainty, and interannual variability that ensembles of these models capture is critical to the exploration of the future co-evolution of the integrated human–Earth system. The pre-eminent source of these ensembles has been the Coupled Model Intercomparison Project (CMIP). With more modeling centers participating in each new CMIP phase, the size of the model archive is rapidly increasing, which can be intractable for impact modelers to effectively utilize due to computational constraints and the challenges of analyzing large datasets. In this work, we present a method to select a subset of the latest phase, CMIP6, featuring models for use as inputs to a sectoral impact or multisector dynamics models, while prioritizing preservation of the range of model uncertainty, scenario uncertainty, and interannual variability in the full CMIP6 ensemble results. This method is intended to help impact modelers select climate information from the CMIP archive efficiently for use in downstream models that require global coverage of climate information. This is particularly critical for large-ensemble experiments of multisector dynamic models that may be varying additional features beyond climate inputs in a factorial design, thus putting constraints on the number of climate simulations that can be used. We focus on temperature and precipitation outputs of CMIP6 models, as these are two of the most used variables among impact models, and many other key input variables for impacts are at least correlated with one or both of temperature and precipitation (e.g., relative humidity). Besides preserving the multi-model ensemble variance characteristics, we prioritize selecting CMIP6 models in the subset that preserve the very likely distribution of equilibrium climate sensitivity values as assessed by the latest Intergovernmental Panel on Climate Change (IPCC) report. This approach could be applied to other output variables of climate models and, possibly when combined with emulators, offers a flexible framework for designing more efficient experiments on human-relevant climate impacts. It can also provide greater insight into the properties of existing CMIP6 models.
Over the past 50 years, humans have extracted the Earth’s groundwater stocks at a steep rate, largely to fuel global agro-economic development. Given society’s growing reliance on groundwater, we explore ‘peak water limits’ to investigate whether, when and where humanity might reach peak groundwater extraction. Using an integrated global model of the coupled human–Earth system, we simulate groundwater withdrawals across 235 water basins under 900 future scenarios of global change over the twenty-first century. Here we find that global non-renewable groundwater withdrawals exhibit a distinct peak-and-decline signature, comparable to historical observations of other depletable resources (for example, minerals), in nearly all (98%) scenarios, peaking on average at 625 km 3 yr -1 around mid-century, followed by a decline through 2100. The peak and decline occur in about one-third (82) of basins, including 21 that may have already peaked, exposing about half (44%) of the global population to groundwater stress. Most of these basins are in countries with the highest current extraction rates, including the United States, Mexico, Pakistan, India, China, Saudi Arabia and Iran. Furthermore, these groundwater-dependent basins will probably face increasing costs of groundwater and food production, suggesting important implications for global agricultural trade and a diminished role for groundwater in meeting global water demands during the twenty-first century.
We report the transformation of mercury (Hg) in the environment plays a vital role in the cycling of Hg and its risk to the ecosystem and human health. Of particular importance are Hg oxidation/reduction and methylation/demethylation processes driven or mediated by the dynamics of light, microorganisms, and organic carbon, among others. Advances in understanding those Hg transformation processes determine our capacity of projecting and mitigating Hg risk. Here, we provide a critical analysis of major knowledge gaps in our understanding of Hg transformation in nature, with perspectives on approaches moving forward. Our analysis focuses on Hg transformation processes in the environment, as well as emerging methodology in exploring these processes. Future avenues for improving the understanding of Hg transformation processes to protect ecosystem and human health are also explored.
Instruction finetuning is a popular paradigm to align large language models (LLM) with human intent. Despite its popularity, this idea is less explored in improving the LLMs to align existing foundation models with scientific disciplines, concepts and goals. In this work, we present SciTune as a tuning framework to improve the ability of LLMs to follow scientific multimodal instructions. To test our methodology, we use a human-generated scientific instruction tuning dataset and train a large multimodal model LLaMA-SciTune that connects a vision encoder and LLM for science-focused visual and language understanding. LLaMA-SciTune significantly outperforms the state-of-the-art models in the generated figure types and captions in multiple scientific multimodal benchmarks. In comparison to the models that are fine-tuned with machine generated data only, LLaMA-SciTune surpasses human performance on average and in many sub-categories on the ScienceQA benchmark.
Future socioeconomic and climate scenarios have been explored using integrated assessment models (IAMs) to understand interactions between human development and global environmental change in the long run. However, differences in trade modeling approaches are an important source of uncertainty in the assessments, particularly for regional projections. Here, we explore the critical role of trade modeling in assessing the potential future of global agroeconomics and terrestrial carbon emissions with a well-established IAM, the Global Change Assessment Model (GCAM). We update the crop trade modeling framework in GCAM from a Heckscher-Ohlin-Vanek (HOV) structure with integrated world markets (IWM) to a newly developed logit-based Armington approach with segmented regional markets (SRM). The updates make it possible to study the sensitivity of model projections of future agroeconomics and terrestrial carbon emissions to assumptions of the state and magnitude of global market integration. Our results demonstrate that assuming full global market integration, represented by homogeneous product modeling, neglecting economic geography, and excluding margins and tariffs, could lead to lower cropland use (i.e., by 115 million hectares globally) and terrestrial carbon fluxes (i.e., by 25%) by the end of the century. However, the results are highly heterogeneous across regions with more pronounced regional trade responses driven by global market integration. Our study highlights the critical role of trade modeling around product differentiation, economic geography, and regional trade parameterization in global economic or integrated assessment modeling. The results also imply that further reconciliations in trade model approaches could improve the convergence of regional results among models in model intercomparison studies.
The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose, is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. In this work we have explored the potential of B. coagulans MA-13 as a source of metabolites and enzymes to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra- cellular glycosyl hydrolase (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as β-galactosidase (GH42) and α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism, since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Probiotics which are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this work we have proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in treatment of gastrointestinal diseases.
This work introduces a knowledge-informed framework that integrates human expertise and prior interest into active learning-driven autonomous experimentation, which enhances the exploration efficiency through more targeted experimentation.
Early fire detection in industrial environments is critical to preventing equipment damage, personal injury, and operational disruptions. Traditional smoke detectors, while effective, often experience delays due to the time required for smoke to reach sensors, allowing fires to spread. Manual fire watch operations and human surveillance of camera feeds are resource-intensive and prone to human error. To address these challenges, this paper explores the application of convolutional neural networks for automated fire detection, specifically in industrial settings. By leveraging 11 different pre-trained machine vision models from TensorFlow and enhancing them with transfer learning on a custom-built industrial fire dataset, we optimized fire detection performance. Here, we analyzed each machine vision model architecture in terms of its depth, width, and input image resolution, considering both resource requirements and detection accuracy. We further explored the option of combining multiple models into an ensemble classifier to evaluate whether the performance improvements could justify the much greater computational complexity and other practical impacts. A cost-benefit analysis is presented to evaluate the trade-offs between performance and computational expense. Our findings identify that EfficientNetV2L, specifically tailored for industrial applications, provides the optimal balance between costs involved in training and using the model versus the overall fire detection performance. Additionally, we present a qualitative analysis of model performance using the technique of gradient-based class activation mapping to provide explainability by visualizing model decisions.
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
Oscillations in global modes of variability (MoVs) form global teleconnections that affect regional climate variability and modify the potential for severe and damaging weather conditions. Understanding the link between certain MoVs and regional climate can improve the ability to more accurately predict environmental conditions that impact human life and health. In this study, we explore the connection between different MoVs, including the Arctic oscillation (AO), Eurasian teleconnection, Indian Ocean dipole (IOD), North Atlantic oscillation (NAO), and El Niño southern oscillation (Nino34), with winter and summer climates in the High Mountain Asia (HMA) region, including geopotential height at 250 hPa (z250), 2 m air temperature (T2M), total precipitation (PRECTOT), and fractional snow cover area (fSCA). Relationships are explored for the same monthly period between the MoVs and the climate variables, and a lagged correlation analysis is used to investigate whether any relationship exists at different time lags. We find that T2M has a negative correlation with the Eurasian teleconnection in the Inner Tibetan Plateau and central China in both winter and summer and a positive correlation in western China in summer. PRECTOT has a positive correlation with all MoVs in most regions in winter, especially with the IOD, and a negative correlation in summer, especially with the Eurasian teleconnection. Snow cover in winter is positively correlated with most indices throughout many regions in HMA, likely due to wintertime precipitation also being positively correlated with most indices. Generally, the AO and NAO show similar correlation patterns with all climate variables, especially in the winter, possibly due to their oscillations being so similar. Furthermore, the AO and NAO are shown to be less significant in explaining the variation in HMA climate compared to other MoVs such as the Eurasian teleconnection. Overall, our results identify different time windows and specific regions within HMA that exhibit high correlations between climate and MoVs, which might offer additional predictability of the MoVs as well as of climate and weather patterns in HMA and throughout the globe.
The Software Defined Architectures (SODA) Synthesizer is an open-source compiler-based tool able to automatically generate domain-specialized systems targeting Application- Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) starting from high-level programming. SODA is composed of a high-level frontend, SODA-OPT, which leverages the multilevel intermediate representation (MLIR) framework to interface with productive programming tools (e.g., machine learning frameworks), identify kernels suitable for acceleration, and perform high-level optimizations, and of a state-of-the-art high-level synthesis backend, Bambu from the PandA framework, to generate custom accelerators. One specific application of the SODA Synthesizer is the generation of accelerators to enable ultra-low latency inference and control on autonomous systems for scientific discovery (e.g., electron microscopes, sensors in particle accelerators, etc.). This talk will discuss ongoing work on the SODA synthesizer to enable no-human-in-the-loop generation and design space exploration of the chiplets for highly specialized artificial intelligence accelerators. Connecting these highly specialized chiplets to general-purpose cores or programmable accelerators will allow to quickly deploy autonomous systems for scientific discovery.
Geological repositories for nuclear waste, including spent nuclear fuel, present a significant challenge for traditional International Atomic Energy Agency (IAEA) safeguards tools due to their inaccessibility and demanding operational conditions. The IAEA has been working closely with Member State organizations currently involved in repository construction and planning, including Euratom, the Finnish and Swedish regulatory authorities, and relevant facility operators. However, the verification challenge remains unsolved, and there persists an out- standing need for tools and approaches that will help the IAEA verify that no nuclear material is diverted from a repository environment. The challenge is also not static. Activities must encompass verification of the design, prior to and during the construction/operation phase, and post backfill. Throughout these various phases, it is imperative that the IAEA maintains a continuity of knowledge (CoK) of all material including information on material inventory and flow. This paper highlights these challenges and outlines how they might be addressed by using remote or autonomous vehicles. Specifically, we discuss the current state of the art in robotic autonomy for known or partially known environment mapping and patrolling, as well as shared autonomy, where humans collaborate with closed loop autonomation to complete tasks. We explore the feasibility of using rovers for these verification tasks, along with the challenges associated with system implementation. Hardware and software suggestions are provided based on the adoption of similar technologies in other comparable areas and ability to close technical gaps. Lastly, human-robotic interactions are considered based on the challenges of the environment of the repository and effective deployment and continued operation of the robot system.
Jeffrey Joe has been invited to give a presentation entitled, “Human Factors Challenges in Modernizing Nuclear Power Plant Control Rooms,” at the 2024 Human Systems Symposium. Experts conducting human factors and human systems research will gather and share research at this conference. This conference is a good opportunity to develop new business for INL via research collaborations, as attendees exchange knowledge and explore the latest trends, advancements, and challenges in the field of human systems research across the DOE national laboratories.
This article explores the best practices for conducting psychophysical experiments that investigate how colour rendition influences the perception of architectural environments. Here, we offer guidance that covers all stages of research from preliminary development to publication, focusing especially on experiments that investigate qualities such as perceived naturalness, vividness, preference or acceptability in response to changes in the spectral power distribution of light sources. This article is intended to be a consolidated guide for researchers and reviewers of this type of research. Key recommendations include: (1) New work should be motivated by clearly expressed research questions and, when possible, explicit hypotheses that build on the existing body of knowledge, (2) visual stimuli comprising spectral power distributions and visual targets should be deliberately engineered to probe the research questions, (3) experiments should be designed to lessen potential biases, (4) reporting of experimental conditions and statistical analyses should be thorough and (5) Results should be contextual, resisting overgeneralization that cannot be supported by the data. Our motivation is to encourage high-quality research that is credible and discourage poor quality research that slows scientific progress and misuses resources.
The fibroblast growth factor (FGF) family includes 22 proteins in humans. Based on their mode of action, there are three families of FGFs: paracrine FGFs (FGF 1–10, 16, 17, 18, 20, and 22), intracrine FGFs (FGF 11–14), and endocrine FGFs (FGF 19, 21, and 23). FGF signaling plays critical roles in embryonic development, tissue repair, regeneration, angiogenesis, and metabolic regulation. They exert their cellular functions by binding, dimerization, and activation of transmembrane FGF receptors (FGFRs). Aberrant FGF signaling is associated with various human diseases. Thus, understanding the unique properties of FGF signaling will help to explore new therapeutic interventions against FGF-mediated pathological conditions. This review will discuss the differential expression and regulation of each FGF under normal human physiological and pathological conditions. Moreover, we will outline current therapeutics and treatment strategies that have been developed against FGF-related pathology.
Geological repositories for nuclear waste, including spent nuclear fuel, present a significant challenge for traditional International Atomic Energy Agency (IAEA) safeguards tools due to their inaccessibility and demanding operational conditions. The IAEA has been working closely with Member State organizations currently involved in repository construction and planning, including Euratom, the Finnish and Swedish regulatory authorities, and relevant facility operators. However, the verification challenge remains unsolved, and there persists an out- standing need for tools and approaches that will help the IAEA verify that no nuclear material is diverted from a repository environment. The challenge is also not static. Activities must encompass verification of the design, prior to and during the construction/operation phase, and post backfill. Throughout these various phases, it is imperative that the IAEA maintains a continuity of knowledge (CoK) of all material including information on material inventory and flow. This paper highlights these challenges and outlines how they might be addressed by using remote or autonomous vehicles. Specifically, we discuss the current state of the art in robotic autonomy for known or partially known environment mapping and patrolling, as well as shared autonomy, where humans collaborate with closed-loop autonomation to complete tasks. We explore the feasibility of using rovers for these verification tasks, along with the challenges associated with system implementation. Hardware and software suggestions are provided based on the adoption of similar technologies in other comparable areas and ability to close technical gaps. Lastly, human-robotic interactions are considered based on the challenges of the environment of the repository and effective deployment and continued operation of the robot system.
Experimental science is enabled by the combination of synthesis, imaging, and functional characterization organized into evolving discovery loop. Synthesis of new material is typically followed by a set of characterization steps aiming to provide feedback for optimization or discover fundamental mechanisms. However, the sequence of synthesis and characterization methods and their interpretation, or research workflow, has traditionally been driven by human intuition and is highly domain specific. Here, we explore concepts of scientific workflows that emerge at the interface between theory, characterization, and imaging. In this study, we discuss the criteria by which these workflows can be constructed for special cases of multiresolution structural imaging and functional characterization, as a part of more general material synthesis workflows. Some considerations for theory–experiment workflows are provided. We further pose that the emergence of user facilities and cloud labs disrupts the classical progression from ideation, orchestration, and execution stages of workflow development. To accelerate this transition, we propose the framework for workflow design, including universal hyperlanguages describing laboratory operation, ontological domain matching, reward functions and their integration between domains, and policy development for workflow optimization. These tools will enable knowledge-based workflow optimization; enable lateral instrumental networks, sequential and parallel orchestration of characterization between dissimilar facilities; and empower distributed research.