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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Developing and tuning a community scale energy model for a disadvantaged community

This work describes the development of a community-scale energy model for a mixed-use low-income community located in Huntington Beach, CA. An accurate community-scale energy model is useful for evaluating the use of limited capital resources used to invest in clean energy technologies. This work lays out the process of developing such a model while relying primarily on publicly available data and highlighting critical partnerships necessary for model development success. The primary contribution of this work is the demonstration of the process used to develop an accurate energy model for a disadvantaged community when minimal building and energy use data is available. The heart of the model is the physics-based community scale energy modeling platform URBANopt. Using a bottom-up load modeling approach, energy simulated energy use falls within 3% or less of aggregate annual utility data, and within 10% or less aggregate monthly utility data. The demonstrated model development and tuning process can be used by others to characterize other atypical communities, which may differ significantly from prototypical models.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

The importance of cycle-by-cycle data in performing rapid battery technology development and validation

Lithium-ion battery (LiB) technology is playing a crucial role in transforming the predominantly fossil fuel-based transportation and stationary storage sectors to achieve a low-carbon economy. Rapid innovation in the LiB materials to electrode to cell design is happening to satisfy the performance, life, and safety metrics required by those myriads of applications. Lately, advanced analytics, such as machine-learning or artificial intelligence (ML/AI) techniques, are being used more frequently to aid in expedited LiB technology development, performance validation, and life prediction. The success of these techniques often relies on a large volume of well-defined and high-quality battery test data. On the other hand, most battery developers and research and development (R&D) communities are still following a classical approach to develop batteries, which is running calendar- and/or cycle-aging tests, performing reference performance tests (RPTs), and conducting post-mortem analyses periodically without paying attention to the wealth of data often not collected during the calendar or cycle life aging tests. This sparse data collection approach is time- and resource-intensive, requiring data capture and evaluation of months to years of RPT data to diagnose accurate battery state of performance, health, and safety. Even so, the underlying aging modes and mechanisms can be missed. If collected properly, battery test data during cycling or calendaring can be efficiently combined with ML/AI techniques to create powerful tools in the rapid diagnosis of battery state of performance, health, and safety along with insights into underlying aging modes and mechanisms. In this report, we discuss the importance of effective cycle-by-cycle (CBC) data collection with example case studies. Within a reasonable timeframe, RPT data are often inadequate in capturing many of the crucial battery aging dynamics, which often predominantly show up in CBC test data. Finally, we also show examples of ML/AI techniques that use CBC data in rapid diagnosis and projection of LiB state of health (SOH) to motivate the scientific community in collecting and using CBC data to facilitate expeditious technology development and validation.

25 ENERGY STORAGE↗

DOE OSTI2020

Herbicide, fertilization, and planting density effects on intensively managed loblolly pine early stand development

Production forestry in the southeast US has been partially transitioned to intensively managed short rotations (~10 years), in which multiple silvicultural interventions are performed during forest development. Understanding the responses to silvicultural practices and continued refinement of site-specific recommendations is critical to sustainably maximize forest production. We evaluated the effects of silvicultural practices (herbicide, fertilization, and planting density) on growth, stand homogeneity, and above- and belowground biomass accumulation and partitioning of loblolly pine (Pinus taeda) throughout early stand development (age 5 years) in the southeastern US. Five treatments with eight replications each were tested: no herbicide and no fertilization (C); herbicide only (H); herbicide and half-reduced fertilization rate (R); herbicide and full fertilization (F); and increased stand density (60+ %; 1346 vs. 2152 trees per hectare) with herbicide and full fertilization rate (D). Allometric equations generated from destructive harvests were applied to annual diameter measurements to estimate plot-level biomass and allocation. Herbicide was crucial to promote stand uniformity and increase yield (~600+ % stem biomass compared with C at age 5). Aboveground biomass was similar in R and F treatments, which was ~25% higher than in H at age 5. Increasing planting density along with multiple herbicide and fertilizer applications yielded higher biomass without compromising individual tree size (diameter and height). There was little effect of silviculture practices on allocation patterns. Our results parallel what was found for fertilization with herbicide from a number of loblolly stands under similar conditions and indicate a ~28% volume gain with fertilization during early stand development. Similarly, our results were consistent with other studies implementing similar differences in planting density and suggest a ~26% volume gain through early stand development with an initial 60% increase in planting density. Furthermore, our study helps to understand complex relationships between production and silvicultural practices during early stand development and demonstrates that silvicultural prescriptions can be optimized to increase sustainability of production forestry

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII

A key unmet need in the management of hemophilia A (HA) is the lack of clinically validated markers that are associated with the development of neutralizing antibodies to Factor VIII (FVIII) (commonly referred to as inhibitors). This study aimed to identify relevant biomarkers for FVIII inhibition using Machine Learning (ML) and Explainable AI (XAI) using the My Life Our Future (MLOF) research repository. The dataset includes biologically relevant variables such as age, race, sex, ethnicity, and the variants in the F8 gene. In addition, we previously carried out Human Leukocyte Antigen Class II (HLA-II) typing on samples obtained from the MLOF repository. Using this information, we derived other patient-specific biologically and genetically important variables. These included identifying the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity calculated using NetMHCIIpan. The data were processed and trained with multiple ML classification models to identify the top performing models. The top performing model was then chosen to apply XAI via SHAP, (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patient. Using XAI we provide a robust and ranked identification of variables that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. These variables could be validated as biomarkers and used in making clinical decisions and during drug development. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, & 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles), (iv) the minimum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

The development of natural gas and hydrogen pipeline capital cost estimating equations

Natural gas pipeline cost data collected by the Oil and Gas Journal (O&GJ) for interstate pipelines constructed from 1980 through 2017 were used to develop capital cost estimating equations that are a function of pipeline diameter, length, and U.S. region. Equations were developed for material, labor, miscellaneous, and right-of-way costs, the four cost components in the O&GJ data, for six different regions of the United States (U.S.). Each equation is a function of pipeline diameter and length. Adjustment mechanisms were then developed for converting the natural gas pipeline equations into equations for estimating the costs of hydrogen pipelines. These adjustments were based in part on an analysis completed by the National Institute for Standards and Technology (NIST). Here the results of this work were used to update cost models in the Hydrogen Delivery Scenario Analysis Model (HDSAM), developed by Argonne National Laboratory for the U.S. Department of Energy’s Hydrogen Program. Our analysis shows a wide range of pipeline cost across different U.S. regions, especially with respect to labor and right-of-way costs. The developed cost formulas for hydrogen pipelines are both important and timely as hydrogen is being considered as a zero-carbon energy carrier with the potential to decarbonize all energy sectors, and the cost of hydrogen transportation is essential for techno-economic analysis of its potential use in these sectors.

03 NATURAL GAS↗

DOE OSTI2018

The dynamics of integration, viral suppression and cell-cell transmission in the development of occult Hepatitis B virus infection

Out of several phases of HBV infection, the least understood phase is occult hepatitis B virus infection. The paucity of data due to non-availability of biological tissues and the prerequisite of ultra-sensitive assays for the detection of occult hepatitis B virus infection prompted us to utilize mathematical modeling in determining mechanisms that lead to occult hepatitis B virus infection and characteristics of HBV infection during occult hepatitis B virus infection. In this paper, we proposed two mathematical models (M1 and M2), considering two different phenomenon for episomal maintenance and accumulation of covalently closed circular DNA (cccDNA) in infected hepatocytes: (i) M1 – recirculation of the relaxed circular DNA/double-stranded linear DNA from cytoplasm to the nucleus, and (ii) M2 – reinfection of infected hepatocytes with virions. We further incorporated the dynamics of integrated Hepatitis B virus DNA (iHBV) to investigate its role in the development of occult hepatitis B virus infection. The analysis showed that the main mechanism for the spread of infection during occult hepatitis B virus infection is cell-to-cell transmission and not cell-free virus transmission. A significant viral suppression (of at least 99% from its peak production values) was essential but not sufficient in the development of occult hepatitis B virus infection under M1; however under M2, the viral suppression was neither sufficient nor essential as the inhibition of the production of HBsAg without viral suppression can also explain the development of occult hepatitis B virus infection. Our analysis also revealed that occult hepatitis B virus infection seropositive cases are more likely to progress into liver cirrhosis compared to occult hepatitis B virus infection seronegative cases. The iHBV was found to be mostly silent (by either being absent or non-productive for HBsAg) during occult hepatitis B virus infection. The viral suppression is neither essential nor sufficient to explain the development of occult hepatitis B virus infection on its own. Not only the viral suppression but the inhibition -of the production and the export of HBsAg from cccDNA and iHBV also plays an important role in the development of occult hepatitis B virus infection. Finally, this is the first study, which incorporates the dynamics of iHBV and shows that HBV primarily spreads via cell-cell transmission during occult hepatitis B virus infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Polycentric urban development and urban thermal environment: A case of Hangzhou, China

Polycentric urban structure has become popular worldwide, including in China. Previous studies revealed that polycentricity can remediate certain environmental problems; however, few studies have focused on how polycentricity affects the urban thermal environment. Using remote sensing data for the nighttime light and surface temperature, this study first explored the dynamics of polycentric urban development and thermal environment in Hangzhou during 2000-2010. Then their relationship was investigated in both morphological and functional dimensions. It was observed that from 2000 to 2006, Hangzhou experienced rapid polycentric development, especially in the functional dimension; however, this trend slowed down during 2006-2010. With the expansion of hot and medium-hot landscapes, the area with higher surface temperature enlarged notably, and warming trends were more significant in the suburbs than in the urban core. Polycentric urban development in both morphological and functional dimensions was positively correlated with the deterioration of the thermal environment. The regional differences in the urban thermal environment can be attributed to the distinctive functional orientations and development patterns of (sub)centers. Further, industrial sub-urbanization could be the underlying reason for the positive correlation because of its consistent distributions with the newly-expanded hot landscape and more contiguous hot landscape caused by the single land use pattern in industrial areas. Two policy implications about polycentric planning and landscape composition and configuration in industrial areas were proposed to mitigate the effect of urban heat island. The findings in this study are conductive to cities whose polycentric urban development is also industrial-based.

Yue, Wenze↗

DOE OSTI2018

Development of microstructure and texture during single and multiple pass friction stir processing of a strain hardenable aluminium alloy

Highlights: • Development of microstructure and texture during single and multiple pass FSP of a strain hardenable aluminium alloy • Strain induced boundary migration (SIBM) is the dominant nucleation mechanism for recrystallization • Weak crystallographic texture development influenced by SIBM with the relative dominance of shear texture components • Stable microstructure and texture development after multiple pass FSP • FSP is a promising method for the secondary processing of strain hardenable aluminium alloys - Abstract: In the present study, microstructure and texture development during single and multiple pass friction stir processing (FSP) of a strain hardenable wrought AlMg alloy (AA5086) was investigated. Subtle differences were observed while comparing with heat treatable alloys in the nucleation mechanism of the recrystallized microstructure observed in the nugget zone. Strain induced boundary migration was the dominant mechanism of microstructure evolution in the alloy, which influenced the crystallographic texture development by weakening it. Micro-texture measurements reveal variations in the crystallographic texture along the thickness of the sample. Recrystallization texture components were observed in the nugget zone indicative of a pronounced static recrystallization in the alloy as compared to the heat treatable alloys. Bulk texture measurements within the nugget zone of the optimally processed sample reveal a relatively dominant C component of shear texture. Average grain size in the nugget zone remained the same and the bulk crystallographic texture components were retained during multiple-pass FSP. The lower strain energies involved and the enhanced recovery processes due to the high temperature materials processing of the alloy during FSP resulted in a stable microstructure and texture. In summary, FSP could be promoted as a competent and suitable secondary processing technique for the bulk production of ultra-fine-grained materials in strain hardenable aluminium alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2025

High efficiency RF sources developments

Calabazas Creek Research, Inc. (CCR) and its collaborators are developing high efficiency RF sources operating from a few hundred MHz to C-Band and power levels from tens to hundreds of kilowatts with the goal of providing MW-relevant sources. The efficiencies approach or exceed 80% with projected costs as low as $0.50/ Watt. Sources under development include magnetrons with phase and amplitude control, single and multi-beam klystrons, multi-beam power grid tubes, and multiple beam IOTs. A magnetron system achieved more than 80% efficiency with fast amplitude control using modulation of the phase locking signal. This would be a low cost, high efficiency RF source for superconducting accelerators. An L-Band, single beam klystron was built with simulated efficiency of 80%. The klystron has yet to be tested to confirm the simulation results. CCR is currently developing a multi-beam klystron to produce more than 200 kW CW at 80% efficiency. Also in development is a multiple beam triode to produce 200 kW CW from 300 MHz to approximately 1 GHz. Not only does the simulated efficiency exceed 75%, but it would be the lowest cost RF source in this frequency range. Finally, CCR recently concluded research for a multiple beam IOT at 700 MHz using third harmonic drive to boost efficiency toward 85%. Successful development and transition to production of these sources will significantly alter the cost/performance landscape for RF power generation.

43 PARTICLE ACCELERATORS↗

DOE OSTI2019

Three-dimensional flow model development for thermal mixing and stratification modeling in reactor system transients analyses

Mixing, thermal-stratification, and mass transport phenomena in large pools or enclosures play major roles for the safety of reactor systems. Depending on the fidelity requirement and computational resources, various modeling methods, from the 0-D perfect mixing model to 3-D Computational Fluid Dynamics (CFD) models, are available. Each is associated with its own advantages and shortcomings. It is very desirable to develop an advanced and efficient thermal mixing and stratification modeling capability embedded in a modern system analysis code to improve the accuracy of reactor safety analyses and to reduce modeling uncertainties. An advanced system analysis tool, SAM, is being developed at Argonne National Laboratory for advanced non-LWR reactor safety analysis. While SAM is being developed as a system-level modeling and simulation tool, a reduced-order three-dimensional module is under development to model the mull-dimensional flow and thermal mixing and stratification in large enclosures of reactor systems. This paper provides an overview of the three-dimensional finite element flow model in SAM, including the governing equations, stabilization scheme, and solution methods. Additionally, several verification and validation tests are presented, including lid-driven cavity flow, natural convection inside a cavity, laminar flow in a channel of parallel plates. Here, based on the comparisons with the analytical solutions and experimental results, it is demonstrated that the developed 3-D fluid model can perform very well for a wide range of flow problems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2016

Goniothalamin prevents the development of chemically induced and spontaneous colitis in rodents and induces apoptosis in the HT-29 human colon tumor cell line

Colon cancer is the third most incident type of cancer worldwide. One of the most important risk factors for colon cancer development are inflammatory bowel diseases (IBD), thus therapies focusing on IBD treatment have great potential to be used in cancer prevention. Nature has been a source of new therapeutic and preventive agents and the racemic form of the styryl-lactone goniothalamin (GTN) has been shown to be a promising antiproliferative agent, with gastroprotective, antinociceptive and anti-inflammatory effects. As inflammation is a well-known tumor promoter, the major goal of this study was to evaluate the therapeutic and preventive potentials of GTN on chemically induced and spontaneous colitis, as well as the cytotoxic effects of GTN on a human colon tumor cell line (HT-29). GTN treatments inhibited TNBS-induced acute and chronic colitis development in Wistar rats, reducing myeloperoxidase levels and inflammatory cells infiltration in the mucosa. In spontaneous-colitis using IL-10 deficient mice (C57BL/6 background), GTN prevented colitis development through downregulation of TNF-α, upregulation of SIRT-1 and inhibition of proliferation (PCNA index), without signs of toxicity after three months of treatment. In HT-29 cells, treatment with 10 μM of GTN induced apoptosis by increasing BAX/BCL2, p-JNK1/JNK1, p-P38/P38 ratios as well as through ROS generation. Caspase 8, 9 and 3 activation also occurred, suggesting caspase-dependent apoptotic pathway, culminating in PARP-1 cleavage. Together with previous data, these results show the importance of GTN as a pro-apoptotic, preventive and therapeutic agent for IBD and highlight its potential as a chemopreventive agent for colon cancer. - Highlights: • Goniothalamin (GTN) inhibits the development of TNBS-induced colitis in rats. • Moreover, GTN prevents the development of spontaneous colitis in IL-10 deficient mice. • This activity relies on downregulation of TNF-α and upregulation of SIRT-1 expression. • GTN induces intrinsic apoptosis in HT-29 cells, involving ROS, MAPK and caspases. • These results highlight GTN as a potential chemopreventive agent for colon cancer.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

DEET potentiates the development and persistence of anticholinesterase dependent chronic pain signs in a rat model of Gulf War Illness pain

Exposure to DEET (N,N-diethyl-meta-toluamide) may have influenced the pattern of symptoms observed in soldiers with GWI (Gulf War Illness; Haley and Kurt, 1997). We examined how the addition of DEET (400 mg/kg; 50% topical) to an exposure protocol of permethrin (2.6 mg/kg; topical), chlorpyrifos (CP; 120 mg/kg), and pyridostigmine bromide (PB;13 mg/kg) altered the emergence and pattern of pain signs in an animal model of GWI pain (). Rats underwent behavioral testing before, during and after a 4 week exposure: 1) hindlimb pressure withdrawal threshold; 2) ambulation (movement distance and rate); and 3) resting duration. Additional studies were conducted to assess the influence of acute DEET (10–100 μM) on muscle and vascular nociceptor K{sub v}7, K{sub DR}, Na{sub v}1.8 and Na{sub v}1.9. We report that a 50% concentration of DEET enhanced the development and persistence of pain-signs. Rats exposed to all 4 compounds exhibited ambulation deficits that appeared 5–12 weeks post-exposure and persisted through weeks 21–24. Rats exposed to only three agents (CP or PB excluded), did not fully develop ambulation deficits. When PB was excluded, rats also developed rest duration pain signs, in addition to ambulation deficits. There was no evidence that physiological doses of DEET acutely modified nociceptor K{sub v}7, K{sub DR}, Na{sub v}1.8 or Na{sub v}1.9 activities. Nevertheless, DEET augmented protocols decreased the conductance of K{sub v}7 expressed in vascular nociceptors harvested from chronically exposed rats. We concluded that DEET enhanced the development and persistence of pain behaviors, but the anticholinesterases CP and PB played a determinant role. - Highlights: • DEET accelerated and prolonged pain-like behaviors in a rat model of Gulf War Illness. • The development of pain behaviors were dependent upon chlorpyrifos and pyridostigmine. • Conductance of vascular nociceptor Kv7 was diminished 12 weeks following exposures. • DEET did not have any acute influence on nociceptor Kv7, Nav1.8, Nav1.9 or KDR.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Developing a small participant framework: An investigation of mode choice influential factors

An in-depth comprehension of the changing impact of mode choice influencing factors is essential in planning for behavior-adaptive mode shift policies. This study developed a framework to investigate a method of evaluation of the changes in mode choice using a small participation pool. A field application in Pima County, Arizona was developed to test the developed framework to evaluate the impact of a real transit experience. Twenty-two participants were recruited and repeated measurements were taken before and after their transit trip. The results revealed that people are less susceptible to their mental biases after a transit trip and consider more objective elements such as walking time. The developed framework resulted in successful evaluation methods that are reproducible for other application study designs. Thus, the results further present that low participant recruitment in application-based field studies can be accomplished using this developed methodology, for other regions and studies.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2017

The Drosophila DOCK family protein Sponge is required for development of the air sac primordium

Dedicator of cytokinesis (DOCK) family genes are known as DOCK1-DOCK11 in mammals. DOCK family proteins mainly regulate actin filament polymerization and/or depolymerization and are GEF proteins, which contribute to cellular signaling events by activating small G proteins. Sponge (Spg) is a Drosophila counterpart to mammalian DOCK3/DOCK4, and plays a role in embryonic central nervous system development, R7 photoreceptor cell differentiation, and adult thorax development. In order to conduct further functional analyses on Spg in vivo, we examined its localization in third instar larval wing imaginal discs. Immunostaining with purified anti-Spg IgG revealed that Spg mainly localized in the air sac primordium (ASP) in wing imaginal discs. Spg is therefore predicted to play an important role in the ASP. The specific knockdown of Spg by the breathless-GAL4 driver in tracheal cells induced lethality accompanied with a defect in ASP development and the induction of apoptosis. The monitoring of ERK signaling activity in wing imaginal discs by immunostaining with anti-diphospho-ERK IgG revealed reductions in the ERK signal cascade in Spg knockdown clones. Furthermore, the overexpression of D-raf suppressed defects in survival and the proliferation of cells in the ASP induced by the knockdown of Spg. Collectively, these results indicate that Spg plays a critical role in ASP development and tracheal cell viability that is mediated by the ERK signaling pathway. - Highlights: • Spg mainly localizes in the air sac primordium in wing imaginal discs. • Spg plays a critical role in air sac primordium development. • Spg positively regulates the ERK signal cascade.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

The role of Rho-GEF Trio in regulating tooth root development through the p38 MAPK pathway

Highlights: • We have determined the role of Trio, a GTP exchange factor, in tooth development. • The Wnt1-cre;Trio{sup fl/fl} mice were created for in vivo study. • P38 MAPK pathway was found to be involved in Trio related root deformity. Trio, the Rho guanine nucleotide exchange factor (Rho-GEF), plays diverse roles in cell migration, cell axon guidance and cytoskeleton reorganization. Conserved during evolution, Trio encodes two guanine nucleotide exchange factor domains (GEFs) and activates small GTPases. The Rho-family small GTPases RhoA and Rac1, which are target molecules of Trio, have been described to engage in craniofacial development and tooth formation. However, the exact role of Trio in tooth development remains elusive. In this study, we generated Wnt1-cre;Trio{sup fl/fl} mice to address the potential function of Trio in tooth development. Wnt1-cre;Trio{sup fl/fl} mice showed short root deformity as well as decreased expression of odontogenic makers such as RUNX2, OSX, OCN, and OPN. In vitro, Trio was silenced in human stem cells of dental papilla (SCAPs). Compared with the control group, the proliferation and migration ability in the experimental group was disrupted. After knocking down Trio in SCAPs, the cells showed phenotypes of poor odontogenic differentiation and weak mineralized nodules. To study the underlying mechanism, we investigated the p38 MAPK pathway and found that loss of Trio blocked the cascade transduction of p38 MAPK signaling. In conclusion, we identified Trio as a novel coordinator in regulating root development and clarified its relevant molecular events.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Roles of miR-204 in retinal development and maintenance

Highlights: • miR-204 plays an important role in the development, maintenance, and diseases of the retina. • Various layers of the retina including RPE express miR-204. • Retinoblastoma, age-related macular degeneration, glaucoma and optic nerve injury are among the most common retinopathies caused by miR-204 dysfunction. • miR-204 target genes are involved in diverse signaling pathways crucial for retinal physiology. The retina is the innermost part of the eye of most vertebrates and it is essential for vision. The development, maintenance, and function of this laminated structure is tightly regulated by numerous genes. Deficiencies in the expression of these genes as well as deregulation of various molecular mechanisms can cause retinopathies and blindness. MicroRNAs (miRNAs) are one of the most important and effective molecular regulatory mechanisms that underlie the biology of the retina. miRNAs have specific functional roles in the development and maintenance of different retinal layers and retinal cell types. While previous studies have reported a large number of miRNAs linked to development, maintenance and diseases of the retina, no comprehensive study has properly discussed and integrated data from these studies. Given the particular importance of miR-204 in retinal biology, we intend to critically discuss the expression and functional significance of this miRNA in the development, maintenance, and pathologies of the retina. Moreover, we explore biological processes through which miR-204 influences retinal pathophysiology. This review highlights the crucial functions of miR-204 in the retina and suggests the putative mechanism of miR-204 action in retinal biology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats

Abstract Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community‐driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Dynamic enhancer landscapes in human craniofacial development

The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.

60 APPLIED LIFE SCIENCES↗