cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7293044
title: Database for machine learning of hydrogen storage materials properties

description: Database for machine learning of hydrogen storage materials properties


Matthew Witmana, Mark Allendorfa, Vitalie Stavilaa


aSandia National Laboratories, Livermore, CA


 


Description


This ML-HydPARK dataset provides a csv file of metal hydride compositions, capacities, and thermodynamic values that can be used as target properties for building, training, and testing machine learning models. It has been parsed and cleaned from the DOE’s original publicly available HydPARK database according to the procedure in [1] to make it more suitable for immediate use with data-driven models. Generally, this removed duplicate entries, removed entries missing critical data, and attempted to fix various entries with obvious errors in the data. It is continuously updated under version control as new metal alloy hydrides are published in the open literature. Most entries contain data on the enthalpy and entropy of the hydriding reaction, as well the maximum hydrogen capacity, for which compositional machine learning models can be trained [1,2].


 


Acknowledgements


The authors gratefully acknowledge research support from the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Fuel Cell Technologies Office through the Hydrogen Storage Materials Advanced Research Consortium (HyMARC). This work was supported by the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy
or the United States Government.


 


References



	
Witman, M.; Ling, S.; Grant, D. M.; Walker, G. S.; Agarwal, S.; Stavila, V.; Allendorf, M. D. Extracting an Empirical Intermetallic Hydride Design Principle from Limited Data via Interpretable Machine Learning. J. Phys. Chem. Lett. 2020, 11, 40–47.
	
Witman, M.; Ek, G.; Ling, S.; Chames, J.; Agarwal, S.; Wong, J.; Allendorf, M. D.; Sahlberg, M.; Stavila, V. Data-Driven Discovery and Synthesis of High Entropy Alloy Hydrides with Targeted Thermodynamic Stability. Chem. Mater. 2021, 33, 4067–4076.



 


Contact


Please email mwitman@sandia.gov , mdallen@sandia.gov, or vnstavi@sandia.gov for questions or to request addition of recent data from the literature to this dataset.
DOI: 10.5281/zenodo.7548017
title: Bibliographic Data from the Digital Twin Anomaly Detection Decision-Making for Bridge Management Systematic Review

description: This database contains all the bibliographic information about the 8673 records found after applying the Search Strategy used for the Digital Twin Anomaly Detection Decision-Making for Bridge Management Systematic Review. Such strategy consisted on using seven initial keywords and similar terms of interest (namely: bridge and bridges, etc.): Bridge. Digital twin. Bridge information modelling. Finite elements. Bridge health monitoring. Anomaly detection algorithm. Cultural heritage. Six initial queries were done combining the first keyword with the rest of them: bridge* AND "digital twin*" bridge* AND (BrIM OR "bridge information model*") bridge* AND (FEM OR FEA OR "finite element method*" OR "finite element analy*") bridge* AND ("bridge health monitoring" OR "structural health monitoring") bridge* AND (ADA OR "anomaly detection algorithm*") bridge* AND ("cultural heritage" OR "monument* bridge*" OR "old bridge*" OR "ancient bridge*" OR "historic* bridge*") As a first screening step, the combination of these 6 initial searches was done to obtain relevant works containing at least three of the main keywords of interest: #1 AND #2 #1 AND #3 #1 AND #4 #1 AND #5 #1 AND #6 #2 AND #3 #2 AND #4 #2 AND #5 #2 AND #6 #3 AND #4 #3 AND #5 #3 AND #6 #4 AND #5 #4 AND #6 #5 AND #6 All records found in Scopus where downloaded both in .ris and .csv format and are included in this database. The search was conducted on 10/12/2022. Note: Searches 10, 14, 17 and 21 did not return any records.
description: This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101066739.
DOI: 10.5281/zenodo.10679873
title: Assessing a Nutrition Intervention in Nursing Homes
DOI: 10.5281/zenodo.10679874
title: Assessing a Nutrition Intervention in Nursing Homes
DOI: 10.5281/zenodo.10680082
title: Arsenic-poor fluids promote strong As partitioning into pyrite

description: The data presented here includes all tabulated data contained in the manuscript draft entitled "Extreme As partitioning into pyrite from low-As fluids" by Martin Kutzschbach, Frederik Dunkel, Christof Kusebauch, Ferry Schiperski, Frederik Börner, Henrik Drake, and Manuel Keith and the associated supplementary material (in .pdf "_Data_repository_Kutzschbach_etal_2024")

Additionally, it includes:

-the location of all investigated transects (.png_files; name is the # of the)

-The elemental distribution across the transects (.xlxs file "transet locations")

-The input code for the PhreeqC calculation of As-speciation presented in Figure 5 (.pqi file)

-All literature data used to construct Figure 7  (in .pdf "_Data_repository_Kutzschbach_etal_2024")

-The detailed results of the modelling of As sequestration from fluids by formation of pyrite as a function   of fluid volume and DAs (py/fluid) values presented in Figure 8 (in .pdf "_Data_repository_Kutzschbach_etal_2024")

-This is the abstract of the manuscript draft:

Pyrite is a ubiquitous sulfide mineral found in diverse geological settings and holds great significance in the formation of Au deposits as well as the safe utilization of groundwater due to its remarkable ability to incorporate substantial amounts of As. However, despite its importance, there remains a dearth of fundamental data on the partitioning of As between pyrite and fluid, which is key for accurately modeling the As distribution in these environments.

Here, we present new insights into the partitioning behavior of As between pyrite and fluid at conditions that mimic natural fluid systems. Pyrite was synthesized by replacement of natural siderite in hydrothermal experiments at 200°C and pH 5 applying a wide range of fluid As concentrations, spanning from 0.001 to 100 µg/g. The As distribution and concentration in synthetic pyrite was analyzed by quantitative LA-ICP-MS mapping providing a high spatial resolution and sensitivity at 2-3 µm image pixel size at a detection limit of ~1 µg/g at the single pixel scale. Pyrite-fluid partition coefficients (DAs(py/fluid)) between synthetic pyrite and experimental fluid agree with previously published data for high fluid As concentrations of 1 µg/g to 100 µg/g (DAs < 2000). However, at low As concentrations in the experimental fluid (<1 µg/g), a steep increase in the DAs(py/fluid) values of up to ~30,000 was detected, demonstrating even stronger As partitioning into pyrite. This previously unknown relation holds significant implications for natural fluid systems which frequently exhibit similar As concentrations. Our findings contribute to a better understanding of As mobility and scavenging, which in turn is important for understanding the formation and fingerprinting of mineral deposits as well as for secure utilization of groundwater resources.
DOI: 10.5281/zenodo.8060809
title: Extreme As partitioning into pyrite from low-As fluids

description: The data presented here includes all tabulated data contained in the manuscript draft entitled "Extreme As partitioning into pyrite from low-As fluids" by Martin Kutzschbach, Frederik Dunkel, Christof Kusebauch, Ferry Schiperski, Frederik Börner, Henrik Drake, and Manuel Keith and the associated supplemantary material Additionally it includes the input code for the PhreeqC calculation of As-speciation presented in Figure 5, all literature data used to construct Figure 7 and the detailed results of the modelling of As sequestration from fluids by formation of pyrite as a function of fluid volume and DAs (py/fluid) values. presented in Figure 8. Abstract of the manuscript draft: Pyrite is a ubiquitous sulfide mineral found in diverse geological settings and holds great significance in the formation of Au deposits and the safe utilization of groundwater due to its remarkable ability to incorporate substantial amounts of As. However, despite its importance, there remains a dearth of fundamental data on the partitioning of As between pyrite and fluid, which is key for accurately modeling the As distribution in these environments <br> Here, we present new insights into the partitioning behavior of As between pyrite and fluid at conditions that mimic natural fluid systems. Pyrite was synthesized by replacement of natural siderite in hydrothermal experiments at 200°C and pH 5 applying a wide range of fluid As concentrations spanning from 0.001 to 100 µg/g. The As distribution and concentration in synthetic pyrite was analyzed by quantitative LA-ICP-MS mapping providing a high spatial resolution and sensitivity at 2-3 µm image pixel size at a detection limit of ~1 µg/g at the single pixel scale. Pyrite-fluid partition coefficients (DAs(py/fluid)) based on the As concentration of the synthetic pyrite and the experimental fluid agree with previously published data for high fluid As concentrations of 1 µg/g to 100 µg/g (DAs &lt; 2000). However, at low As concentrations in the experimental fluid (&lt;1 µg/g), a steep increase in the DAs(py/fluid) values of up to ~41,000 was detected, demonstrating a high degree of fractionation of As into pyrite. This yet unknown relation holds significant implications for natural fluid systems which frequently exhibit comparable low fluid As concentrations. Our findings contribute to a better understanding of As sinks and its possible mobilization, which is crucial for the formation and fingerprinting of mineral deposits and the secure utilization of groundwater resources.
DOI: 10.25919/nehs-qd25
title: Parkes observations for project P1226 semester 2023OCTS_23

description: Fast Radio Bursts(FRBs) are often proposed as useful cosmological probes, however much work is needed to better understand the foreground environment that it propgates through, such as the Galactic ISM and Milky Way Halo. We propose to observe three satellite dwarf spheroidal galaxies of the Milky Way to search for FRBs and pulsars. We plan to take advantage of the new CryoPAF's wide field of view to survey high stellar density dwarf satellite galaxies with substantial angular sizes: Fornax, Sculptor and Sagittarius II. Detections of FRBs and pulsars will allow us to measure the Circumgalactic Medium contribution to FRB dispersion and also the dark matter halos of these dwarf galaxies.
DOI: 10.5281/zenodo.10669991
title: SAM-Seq_Maize

description: Epigenetic regulations, including chromatin accessibility, nucleosome positioning, and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM- seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. In addition, we uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also facilitated the identification of DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains harbouring antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations of gene activity. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms in model as well non-model plant species with limited genomic and epigenomic information.
description: SAM-Seq was performed on seven day old leaves of maize accession B73.

Bigwig file of mCG, mCHG, mCHH methylation and accessibility over the AGPv4 reference genome.
DOI: 10.5281/zenodo.10669992
title: SAM-Seq_Maize

description: Epigenetic regulations, including chromatin accessibility, nucleosome positioning, and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM- seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. In addition, we uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also facilitated the identification of DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains harbouring antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations of gene activity. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms in model as well non-model plant species with limited genomic and epigenomic information.
description: SAM-Seq was performed on seven day old leaves of maize accession B73.

Bigwig file of mCG, mCHG, mCHH methylation and accessibility over the AGPv4 reference genome.
DOI: 10.6073/pasta/6ef003c2a3a1647eea371c7f707063c7
title: 2023 Forest Composition Data at the University of Michigan Biological Station, Pellston, MI

description: In many forests worldwide, insect disturbances are increasing, impacting plant community composition and forest structure. However, the extent to which these changes in community composition and structure influence the amount of C stored annually in plant biomass, or net primary production (NPP), remains poorly understood. We examined whether plant community composition, structural change, and NPP respond similarly to increasing disturbance severity and to the treatment types preferentially affecting large and small diameter trees. This knowledge is vital to management and modeling when trying to make inferences about the structural and functional response of forested ecosystems to various levels of disturbance caused by insects. The Forest Resilience Threshold Experiment (FoRTE) is a replicated study of disturbance type and severity using stem-girdling to achieve four levels of gross defoliation from 0% (control) to 85%. Utilizing five years of leaf litter, seedling, and portable canopy LiDAR data, we analyzed relationships between community composition, structure and NPP across disturbance severity. Our results 5-years after the initiation of the girdling disturbance shows that mid-successional Fagus and Acer species dominate seedling and sapling composition, irrespective of disturbance severities. In contrast, the canopy was predominantly occupied by Acer and Populus species, surpassing Quercus and Fagus. Despite the prediction that high canopy mortality would foster an environment favorable to early successional species, their expected dominance didn’t manifest in any of the plots. NPP exhibited high resistance to disturbance across the gradient of disturbance severity, regardless of compositional changes and level of tree mortality. This suggests a decoupling between composition and production following altered functional responses to disturbance. As we manage forests for greater stability in the face of increasing disturbance and intensifying climate change, our analysis suggests that C cycling stability may be possible despite substantial community compositional changes.
DOI: 10.5281/zenodo.10680211
title: DIAGNOSIS AND TREATMENT OF DIARRHEA SYNDROME IN PATIENTS WITH COVID -19
DOI: 10.5281/zenodo.10680212
title: DIAGNOSIS AND TREATMENT OF DIARRHEA SYNDROME IN PATIENTS WITH COVID -19
DOI: 10.5281/zenodo.10625519
title: SAM-Seq_wt_rep1

description: Epigenetic regulations, including chromatin accessibility, nucleosome positioning, and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM- seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. In addition, we uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also facilitated the identification of DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains harbouring antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations of gene activity. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms in model as well non-model plant species with limited genomic and epigenomic information.
DOI: 10.6084/m9.figshare.19749200
title: Correlation of the transcription factors <i>IRF4</i> and <i>BACH2</i> with the abnormal <i>NFATC1</i> expression in T cells from chronic myeloid leukemia patients

description: T cell dysfunction is a common characteristic of patients with myeloid leukemia and is closely related to clinical efficacy and prognosis. In order to clarify the mechanisms leading to the T cell dysfunction, we characterized the gene expression profile of T cells from chronic myelogenous leukemia (CML) patients by microarray analysis and investigated the related regulating pathway. We employed gene expression profiling, bioinformatics and real-time quantitative reverse transcription PCR (RT-qPCR) to detect genes differentially expressed in CML patients versus healthy donors. There were 1704 genes differentially expressed between CD3<sup>+</sup> T cells from CML patients and healthy donors, including 868 up-regulated genes and 836 down-regulated genes, which mostly related to T cell functional pathways. In particular, lower expression of <i>NFATC1</i>, a member of the TCR signaling pathway, was detected in CD3<sup>+</sup> T cells from CML patients. We further found that the expression of <i>IRF4</i> and <i>BACH2</i>, transcription factors that potentially regulate <i>NFATC1</i>, in CD3<sup>+</sup> T cells from CML patients was significantly lower than that in healthy donors. We for the first time observed the altered gene expression profiles of CD3<sup>+</sup> T cells from CML patients, and the results suggested that <i>IRF4</i>, <i>BACH2</i> and <i>NFATC1</i> may be involved in regulating T cell dysfunction in CML patients in the form of a transcriptional regulatory network. These findings may provide potential targets for tyrosine kinase inhibitors in combination with other targeted immunotherapies .
DOI: 10.6084/m9.figshare.19749200.v1
title: Correlation of the transcription factors <i>IRF4</i> and <i>BACH2</i> with the abnormal <i>NFATC1</i> expression in T cells from chronic myeloid leukemia patients

description: T cell dysfunction is a common characteristic of patients with myeloid leukemia and is closely related to clinical efficacy and prognosis. In order to clarify the mechanisms leading to the T cell dysfunction, we characterized the gene expression profile of T cells from chronic myelogenous leukemia (CML) patients by microarray analysis and investigated the related regulating pathway. We employed gene expression profiling, bioinformatics and real-time quantitative reverse transcription PCR (RT-qPCR) to detect genes differentially expressed in CML patients versus healthy donors. There were 1704 genes differentially expressed between CD3<sup>+</sup> T cells from CML patients and healthy donors, including 868 up-regulated genes and 836 down-regulated genes, which mostly related to T cell functional pathways. In particular, lower expression of <i>NFATC1</i>, a member of the TCR signaling pathway, was detected in CD3<sup>+</sup> T cells from CML patients. We further found that the expression of <i>IRF4</i> and <i>BACH2</i>, transcription factors that potentially regulate <i>NFATC1</i>, in CD3<sup>+</sup> T cells from CML patients was significantly lower than that in healthy donors. We for the first time observed the altered gene expression profiles of CD3<sup>+</sup> T cells from CML patients, and the results suggested that <i>IRF4</i>, <i>BACH2</i> and <i>NFATC1</i> may be involved in regulating T cell dysfunction in CML patients in the form of a transcriptional regulatory network. These findings may provide potential targets for tyrosine kinase inhibitors in combination with other targeted immunotherapies .