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At least 1,171 records · Page 65

Ten questions concerning Large Language Models (LLMs) for building applications

Large Language Models (LLMs) are emerging as powerful AI tools capable of transforming how building information is collected, processed, analyzed, and applied across diverse research areas. Their capabilities can help building operators, facility managers and other stakeholders such as designers, architects and engineers by providing actionable insights for decision-making across planning, construction, operations, and maintenance of buildings and facilities. This paper explores ten key questions concerning the role of LLMs in shaping sustainable, intelligent, and human-centric buildings. From fundamental definitions to advanced applications, we examine how LLMs facilitate decision-making across the life cycle of buildings and energy systems. LLMs can enhance life cycle assessments (LCA), building energy simulations, and real-time data integration, empowering more efficient and adaptive human-AI environments. They can also contribute to streamlining regulatory compliance, improving post-occupancy evaluations, and fostering more inclusive and participatory design processes. Additionally, this paper addresses the ethical challenges posed by LLMs, such as bias, data privacy, and environmental impacts, and explores their potentials in advancing intelligent digital twins (DT) for ongoing building operations and maintenance. Built upon our applied research using LLMs and the review of tools, datasets, and research gaps, we provide a forward-looking perspective on how LLMs can drive innovation, collaboration, and productivity in the built environment while supporting ethical and effective implementation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A historical perspective on the regulation of cellulose biosynthesis

Cellulose is a β-1,4 linked glucose polymer that is synthesized by higher plants, algae and even by some bacteria and animals, making it the most abundant polymer on earth. As the major load bearing structure of the plant cell wall, it is hugely important in terms of plant growth and development, and in recent years it has gained interest for its biotechnological applications. Naturally, there has been a large concerted research effort to uncover the regulatory mechanisms underpinning cellulose synthesis. During the last century, several major breakthroughs in our understanding of cellulose synthesis in algae, bacteria, and plants have been pivotal in advancing the field of cellulose research, improving the likelihood that cellulose synthesis could be feasibly adapted for sustainable purposes. In this work, we will summarize the major hypotheses and advancements made during the last century on the regulation of cellulose biosynthesis, focusing on Arabidopsis thaliana.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cement and concrete as carbon sinks: Transforming a climate challenge into a carbon storage opportunity

Cement and concrete, while traditionally recognized as the main contributors to anthropogenic CO 2 emissions, also have untapped capacity to serve as substantial and scalable carbon sinks. This perspective examines how engineered mineral carbonation can transform cement-based materials into functional carbon storage systems, generating both environmental and economic value. We review the fundamental mechanisms of CO 2 uptake in cementitious systems, highlighting current limitations in reaction kinetics, phase control, and durability under varying environmental conditions. Emphasis is placed on the utilization of alkaline industrial residues and emerging magnesium-based cements, which offer synergistic pathways for carbon sequestration and circular resource use. We further assess the performance trade-offs associated with CO 2 uptake and the feasibility of deploying these technologies on industrial scales. A strategic roadmap is proposed that integrates scientific innovation, regulatory alignment, and carbon accounting in the life cycle to accelerate the adoption of carbon-storing concrete. This perspective provides a comprehensive framework to advance cement and concrete as engineered carbon sinks and supports the transition to a climate-positive construction industry.

Carbon storage↗

Techno-economic evaluation of emission control configurations for AMP/PZ-based post-combustion CO 2 capture

Minimizing the environmental impacts of amine-based post-combustion carbon capture technologies is essential for regulatory compliance and public acceptance. Experimental campaigns at RWE's CO 2 capture pilot plant in Niederaussem using CESAR1 demonstrated that combining existing emission abatement technologies can substantially reduce the concentration of amines and degradation products in the CO 2 -depleted flue gas to below the detection limit of an infrared spectrometer. The campaign confirmed that a proprietary dry bed technology (OEASE aerozone™) or a second water wash can reduce AMP and PZ emissions to below 1 mg/Nm 3 . However, an acid or chemically active wash downstream of the water wash is necessary to reduce NH 3 emissions to very low levels (<2 mg/Nm 3 ). Combining a dry bed with an acid wash significantly reduces both the required acid solution and the resulting acid waste. The techno-economic analysis indicates that implementing emission mitigation technologies provides substantial environmental benefits for the CESAR1 process, with only a marginal increase (<1 €/tCO 2 ) in both the carbon capture cost (CCC) and CO 2 avoidance cost (CAC). The additional capital cost associated with extra column packing is offset by operational cost savings from reduced solvent losses. For stringent emission permits targeting NH 3 , a configuration combining a dry bed upstream of the water wash followed by an acid wash achieves the best balance between emission control and cost efficiency. This configuration results in a Levelized Cost of Electricity (LCOE) of 143 €/MWh, a CCC of 45.4 €/tCO 2 , and a CAC of 88.4 €/tCO 2 .

AMP↗

Proteogenomic Characterization of Endometrial Carcinoma

We undertook a comprehensive proteogenomic characterization of 95 endometrial carcinomas, of which 83 were endometrioid tumors and 12 were serous tumors. This analysis revealed new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new insights into proteomic markers of clinical and genomic tumor subgroups, some of which are in known druggable pathways. We performed a broad genome-wide acetylation survey, one of the first of its kind, yielding insights into regulatory mechanisms of histone acetylation. We also characterized the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, further our understanding of the molecular mechanisms underlying endometrial carcinoma, and identify new avenues for investigating potential therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗

Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome

Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, in this work, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites—tyrocitabines—from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of “Amadori synthases” and “abortive” tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.

59 BASIC BIOLOGICAL SCIENCES↗

Harnessing citizen science to contextualize adaptation mechanism discovery

Species occupying broad geographic regions have evolved multiple mechanisms to regulate phenological characteristics, enabling adaptations to diverse native habitats. By developing computer vision AI to process citizen science observations across native habitats over North America, we uncovered a consistent latitudinal trend of earlier flowering at higher latitudes in warm-season perennial grasses. To explore the underlying mechanisms of adaptation, we conducted common garden experiments with one species (switchgrass) and discovered the opposite latitudinal flowering-time trend. Integration of differential plasticity of GI-Hd1-FTL1 haplotypes of flowering time regulatory genes, haplotype range, and local environmental profiles found that observations from native habitats capture only part of the genotype-environment-phenotype spectrum established in common garden experiments, therefore reconciling the discrepancy. Two mechanisms emerged as key forces shaping current haplotype ranges and influencing future shifts. Our study highlights the power of combining citizen science observations with designed experiments to uncover mechanisms of adaptation across spatiotemporal scales.

FTL1↗

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

59 BASIC BIOLOGICAL SCIENCES↗

The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

Cell Biology↗

Cerium oxide impact on fresh and hardened properties of cementitious materials

Cements used in global nuclear waste treatment, storage, and disposal require thorough testing of fresh and cured properties to demonstrate regulatory compliance. Using actual radioactive wastes is often cost-prohibitive during early scoping tests necessitating the use of non-radiological surrogates. Cerium (Ce) is often used as a surrogate for actinides uranium (U) and plutonium (Pu) in spent nuclear fuel, yet few studies have explored how Ce impacts the properties used to qualify a cement for use. Here, this work compares the fresh and cured properties of three classes of cements – ordinary portland cements, ultra-high performance cement composites, and magnesium phosphate cements – each with and without ceria (CeO 2 ). Due to CeO 2 sorption of water (54 vol%) that effectively decreases the water available to hydrate and form binding cement phases, variations in key cement properties were detected that suggest surrogate CeO 2 –cementitious matrices may not be representative of matrix behaviors when using U and Pu sources.

36 MATERIALS SCIENCE↗

Large language model-driven database for thermoelectric materials

Thermoelectric materials have the ability to convert waste heat into electricity, offering a valuable solution for energy harvesting. However, their widespread use is hindered by low conversion efficiency, the reliance on expensive rare earth elements, and the environmental and regulatory concerns associated with lead-based materials. A fast and cost-effective way to identify highly efficient thermoelectric materials is through data-driven methods. These approaches rely on robust and comprehensive datasets to train models. Although there are several databases on thermoelectric materials, there is still a need to collect and integrate experimental data from peer-reviewed research articles to capture diverse compositions and properties of materials. Here, in this work, we developed a comprehensive database of 7,123 thermoelectric compounds, containing key information such as chemical composition, structural detail, seebeck coefficient, electrical and thermal conductivity, power factor, and figure of merit (ZT). We used the GPTArticleExtractor workflow, powered by large language models (LLM), to extract and curate data automatically from the scientific literature published in Elsevier journals. This process enabled the creation of a structured database that addresses the challenges of manual data collection. The open access database could stimulate data-driven research and advance thermoelectric material analysis and discovery.

Database↗

Evaluating the potential of plastic waste upcycling using thermochemical technologies: A case study in Spain

A plastic waste upcycling value chain model has been applied to assess the potential of processing packaging waste in Spain using thermo-chemical technologies to produce low-density polyethylene (LDPE) and polypropylene (PP), which are highly valuable materials. The model projects an annual profit of 120.6 M$\$$/yr, with a capital investment of 789.3 M$\$$, generating 3285 jobs and contributing 65.5 M$\$$/yr to Spain’s economy. The achieved circularity rate of the waste processing infrastructure exceeds 40 %, incorporating recycled HDPE and PET. Despite these advantages, regulatory gaps and market hesitancy toward recycled materials due to quality concerns hinder adoption. Additionally, economies of scale remain underutilized in Spain due to lower plastic waste collection levels compared to countries such as the United States. This network, while less profitable, is environmentally superior, yielding upcycled products with a Global Warming Potential 20–35 % lower than their virgin, fossil-fuel counterparts, confirming this as a viable and sustainable alternative.

Chemical upcycling↗

Performance assessment of 3D printed multi-material energy absorber for automotive bumper: pedestrian lower extremity protection

Designing an energy absorber for automotive bumpers involves balancing low-speed and high-speed impacts to ensure safety, reduce repair costs, and meet regulatory standards. Here, this study explores a novel design using multi-material 3D printing and structural optimization to fabricate a lightweight and cost-efficient energy absorber. The design effectively dissipates energy in low-speed collisions and minimizes force transmission in high-speed pedestrain impacts, helping to meet both safety and performance requirements. The energy absorber design combines 20% carbon fiber-reinforced acrylonitrile butadiene styrene (CF-ABS) and thermoplastic polyurethane (TPU) for optimal stiffness and flexibility. It uses 3D-printed lattice structures optimized through finite element simulations to help meet both low-speed and high-speed impact requirements. Full-scale energy absorbers were 3D-printed using optimized CF-ABS/TPU blends and tested under high-speed impact using the Flexible Pedestrian Legform Impactor (Flex-PLI). For fair comparison, a baseline bumper with a traditional triangular lattice structure, also 3D-printed from the same CF-ABS/TPU materials, was similarly tested. Interestingly, both the optimized and baseline 3D-printed energy absorbers showed nearly identical performance, successfully meeting injury limits. Their performances were also benchmarked against an injection-molded energy absorber. While both 3D-printed and injection-molded designs met injury limits, the 3D-printed absorber exhibited a higher tibia bending moment, indicating an opportunity for further optimization. A Techno-Economic Analysis compared the costs of producing energy absorbers using traditional manufacturing and 3D printing. The analysis highlighted that 3D printing offers cost benefits for low to medium production volumes, with the total cost per energy absorber at ∼ $\$$74, compared to traditional methods that become economical beyond 2000 units.

Additive manufacturing↗

Building kinetic models for metabolic engineering

Kinetic formalisms of metabolism link metabolic fluxes to enzyme levels, metabolite concentrations and their allosteric regulatory interactions. Though they require the identification of physiologically relevant values for numerous parameters, kinetic formalisms uniquely establish a mechanistic link across heterogeneous omics datasets and provide an overarching vantage point to effectively inform metabolic engineering strategies. Advances in computational power, gene annotation coverage, and formalism standardization have led to significant progress over the past few years. However, careful interpretation of model predictions, limited metabolic flux datasets, and assessment of parameter sensitivity remain as challenges. In this study we highlight fundamental considerations which influence model quality and prediction, advances in methodologies, and success stories of deploying kinetic models to guide metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Perspectives for artificial intelligence in bioprocess automation

Recent advances in artificial intelligence (AI) have rapidly changed the lab automation landscape, promoting self-driving laboratories (SDLs) that enable autonomous scientific discovery. These trends are increasingly applied in bioprocess development, yet bioprocessing faces unique challenges - biological complexity, regulatory and safety requirements, and multiscale experimentation - that distinguish it from other automation domains. Rather than pursuing full autonomy, we foresee that hybrid SDLs, combining AI-driven decision-making with sustained human oversight, represent the most practical near-term trajectory. This review examines three interconnected perspectives: (i) hybrid human-machine decision-making for bioprocessing; (ii) laboratory design considerations in the era of AI; and (iii) scale-up challenges when transitioning from screening to manufacturing. We highlight critical gaps in data standardization and the required community efforts necessary to realize autonomous bioprocess innovation.

Helleckes, Laura Marie↗

Genetically pliable green algae for bioproduction of modified fatty acids, nutritional therapeutic oils, and biopharmaceuticals

Homologous recombination (HR) is an essential tool for complex metabolic engineering in yeast, but transgene integration into plant and green algal nuclear genomes predominantly occurs by non-homologous end-joining. Species of the closely related, oleaginous trebouxiophytes Auxenochlorella and Prototheca, are unusual among the green algae in that HR is the favored mechanism for DNA integration into the nuclear genome. This property enables locus-specific targeting of gene cassettes encoding multiple enzymes for manipulating existing biochemical pathways or introducing new functions. Genetic malleability, and regulatory approval for human consumption, coupled with robust fermentation performance at industrial scale, establishes Auxenochlorella and Prototheca as prime candidates for algal production of biochemicals and biomaterials. The examples presented here highlight strain improvement and engineering for synthesis of hydroxylated fatty acids for biomaterials, structured triglycerides resembling human milk fat for infant nutrition, very-long-chain mono- and polyunsaturated fatty acids with nutraceutical or therapeutic potential, and cannabinoids for pharmacological applications.

Moseley, Jeffrey L. [University of California, Ber↗

Microbial spies and bloggers: programming cells to convert environmental information into discernible signals

Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. Here, in this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.

analyte↗

Quantitative multiplexed analysis of gene and protein expression patterns in Yarrowia lipolytica

In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model Yarrowia lipolytica. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δxbp1 cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence in situ hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.

Yarrowia lipolytica↗