cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10089715
title: Supplementary material for High-Performance Earthquake Simulations with Advanced Material Models

description: This repository contains the setup files to run the simulations, analyse the results and create the plots, used in my PhD thesis "High-Performance Earthquake Simulations with Advanced Material Models". Martin and David have contributed by providing reference solutions for the poroelasticity studies.
DOI: 10.5281/zenodo.10089716
title: Supplementary material for High-Performance Earthquake Simulations with Advanced Material Models

description: This repository contains the setup files to run the simulations, analyse the results and create the plots, used in my PhD thesis "High-Performance Earthquake Simulations with Advanced Material Models". Martin and David have contributed by providing reference solutions for the poroelasticity studies.
DOI: 10.6073/pasta/1cf982525a44fac34d50bccc6c4983ad
title: Atmospheric Gaseous Elemental Mercury Fluxes at Harvard Forest EMS Tower 2019-2020

description: In terrestrial ecosystems, dry deposition of atmospheric gaseous elemental mercury (GEM) is considered the dominant source of mercury accounting for 54% to 94% of mercury loads observed in soils, yet direct quantification of GEM deposition across forests is largely missing. The goal of this project is to quantify atmosphere-surface exchange of GEM at Harvard Forest for one full year, providing the first such record in a non-polluted forest. GEM exchange is measured using micrometeorological techniques using a large measurement tower, the only available method for direct, non-intrusive and time-extended measurements of net GEM exchange at the ecosystem level encompassing all underlying sinks and sources. A second objective was to partition GEM fluxes into canopy and soil contributions via deployment of two corresponding flux systems: one system was deployed above the forest canopy to measure ecosystem-level GEM exchange; a second system was deployed below the canopy to quantify soil contributions.
 This dataset contains an 18-month record of gaseous elemental mercury concentrations and fluxes measured at the EMS tower at Harvard Forest from May 2019 to August 2020.
DOI: 10.6084/m9.figshare.18392138
title: Soil phosphorus maps in China in the 1980s and 2010s

description: We evaluated the changes in topsoil available P (AP) and total P (TP) in China’s forestland, grassland, paddy fields and upland areas during the 1980s-2010s. Soil AP density and TP density maps in the 1980s and 2010s were produced by random forest models.
DOI: 10.6084/m9.figshare.18392138.v8
title: Soil phosphorus maps in China in the 1980s and 2010s

description: We evaluated the changes in topsoil available P (AP) and total P (TP) in China’s forestland, grassland, paddy fields and upland areas during the 1980s-2010s. Soil AP density and TP density maps in the 1980s and 2010s were produced by random forest models.
DOI: 10.25377/sussex.22960772.v1
title: Datasets 'Bt cotton, social networks and risk in rural India' & 'Education and marriage in rural India'

description: <strong>Datasets collected by A. Maertens. Zip files containing pdf / doc / dta files.</strong>
<br>
Stata (https://www.stata.com/) is required to view the .dta files - please refer to the read me.pdf before using the data collected. 
<br>
<strong>Introduction</strong>
<br>
These data were collected in the framework of Dr. Annemie Maertens’ PhD dissertation during the period August 2007 – July 2009. The dissertation was undertaken from Cornell University, but executed in India in collaboration with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). The project was sponsored through an NSF Doctoral Dissertation Improvement Grant (Grant No. 0649330).
<br>
The main goal of this project was to collect and analyze household survey data in the Indian states of Andhra Pradesh and Maharashtra in order to gain a better understanding of the role of social networks and identity in economic decision-making. The first panel of this research studied the role of social learning and social pressures in Bacillus thurigiensis (Bt) cotton adoption using data from three villages (Aurepalle, Kanzara and Kinkhed).
<br>
The data collection consisted of five phases: (1) qualitative round (to determine the topic of the two panels); (2) trial round (to field test the questionnaires); (3) training round (to train the enumerators); (4) quantitative collection round (to collect the household level, village level data); (4’) data entry of (4) ; (5) data validation round (to collect additional data to correct the missing variables and inconsistencies uncovered in (4’)).
<br>
<strong>Published papers resulting from these data</strong>
<br>
Maertens, A., AV Chari and D.R. Just. 2014. ‘Why Farmers Sometimes Love Risks: Evidence from India.’ Economic Development and Cultural Change, 62(2): 239-274 DOI: 10.1086/674028    
<br>
Maertens, A., AV Chari and D.R. Just. 2014. ‘Why Farmers Sometimes Love Risks: Evidence from India.’ Economic Development and Cultural Change, 62(2): 239-274. DOI: 10.2139/ssrn.2024678   
<br>
Maertens, A. and C.B. Barrett. 2013. ‘Empirical Methods for Identifying Social Network Effects on Technology Adoption.’ American Journal of Agricultural Economics Papers and Proceedings, 95(2):353-359. DOI:10.1093/ajae/aaw098
DOI: 10.5525/gla.researchdata.1556
title: Dataset for A 19 day Earth Tide Measurement with a MEMS Gravimeter

description: Processed gravity dataset with timestamps.
DOI: 10.6073/pasta/20628b42085afd5481da6518d5760f30
title: Harmonic Baseline Experiments for Landsat-Based Forest Condition Monitoring in Southern New England 2017

description: This dataset was developed as part of a study of harmonic baseline model parameterization for forest condition monitoring using Landsat time series. We implemented a previously published harmonic modeling approach for forest condition monitoring in Google Earth Engine and systematically assessed the relative ability of condition change products generated using various model parameterizations for predicting pest abundances and defoliation during the 2016-2018 Lymantria dispar outbreak in southern New England. We ran a series of 32 experiments that considered a variety of parameter choices for establishing multi-year “baseline” models representing relatively stable forest conditions for each Landsat pixel in our study area. We tested a full set of factors including (a) spectral vegetation index used for model fitting, (b) baseline-modeling period, (c) frequencies of harmonic regression terms, and (d) differences in Landsat time series input imagery. We generated average condition score estimates for each of these 32 baseline parameterizations for a May 1 to September 30, 2017 monitoring period, then used Generalized Linear Mixed Models to test the relationships between ground-based observations of defoliation and defoliator abundance (larva and egg masses). This archived dataset includes the full set of experimental raster results, as well as a “reanalysis” product from a previous implementation of our condition monitoring workflow. More information on model parameterization rankings can be found in the associated publication (Pasquarella et al. 2021).
DOI: 10.5281/zenodo.8373070
title: Data set for the article: Modifying twist algorithms for determining the key length of a Vigenere cipher

description: Data supporting the work in the article: Modifying twist algorithms for determining the key length of a Vigen\`{e}re cipher.
DOI: 10.5281/zenodo.8373071
title: Data set for the article: Modifying twist algorithms for determining the key length of a Vigenere cipher

description: Data supporting the work in the article: Modifying twist algorithms for determining the key length of a Vigen\`{e}re cipher.
DOI: 10.6084/m9.figshare.24566038
title: Supplementary Material for: Association between F2-isoprostane metabolites and weight change in older women: a longitudinal analysis

description: Introduction: Theoretically, some metabolic traits may predispose older individuals to weight loss during aging, leading to increased all-cause mortality and many serious health issues. Biomarkers to robustly predict progressive weight loss during aging are, however, lacking. We prospectively assessed if urinary levels of F2-isoprostanes and their peroxisomal -oxidation metabolite, 2,3-dinor-5,6-dihydro-15-F2t-isoprostane (F2-IsoP-M), were associated with subsequent weight loss in middle-aged and older women.
Methods: Included in the analysis were 2066 women aged 40-70 years, a subset of a prospective cohort study. F2-isoprostanes (F2-IsoPs) and its β-oxidation metabolite F2-IsoP-M were measured in urine using gas chromatography-mass spectrometry. Measurements of anthropometry and exposures to major determinants of body weight were performed at baseline and repeated thrice over 15-year follow-up. The longitudinal associations of F2-IsoP-M and the F2-IsoP-M to its parent compound F2-IsoP ratio (MPR) with repeatedly measured weight changes were examined using linear mixed-effect models.
Results: After adjusting for time-varying covariates energy intake, physical activity, and comorbidity index, among others, levels of F2-IsoP-M and the MPR were both inversely associated with percentage of weight change. Weight in the highest quartile of these two biomarkers was 1.33% (95% CI = -2.41, -0.24) and 1.09% (95% CI = -2.16, -0.02) lower than those in the lowest quartile group, with P for trend of 0.01 and 0.03, respectively. The inverse association was consistently seen across follow-up periods, although appearing stronger with prolonged follow-up. There was no association between the parent compound F2-IsoPs and weight change.
Conclusion: This study demonstrates the first piece of evidence to associate F2-IsoP metabolism, peroxisomal β-oxidation, with weight loss in older women. Further investigations into the role of lipid peroxidation and peroxisomal β-oxidation in weight change among older individuals are warranted.
DOI: 10.6084/m9.figshare.24566038.v1
title: Supplementary Material for: Association between F2-isoprostane metabolites and weight change in older women: a longitudinal analysis

description: Introduction: Theoretically, some metabolic traits may predispose older individuals to weight loss during aging, leading to increased all-cause mortality and many serious health issues. Biomarkers to robustly predict progressive weight loss during aging are, however, lacking. We prospectively assessed if urinary levels of F2-isoprostanes and their peroxisomal -oxidation metabolite, 2,3-dinor-5,6-dihydro-15-F2t-isoprostane (F2-IsoP-M), were associated with subsequent weight loss in middle-aged and older women.
Methods: Included in the analysis were 2066 women aged 40-70 years, a subset of a prospective cohort study. F2-isoprostanes (F2-IsoPs) and its β-oxidation metabolite F2-IsoP-M were measured in urine using gas chromatography-mass spectrometry. Measurements of anthropometry and exposures to major determinants of body weight were performed at baseline and repeated thrice over 15-year follow-up. The longitudinal associations of F2-IsoP-M and the F2-IsoP-M to its parent compound F2-IsoP ratio (MPR) with repeatedly measured weight changes were examined using linear mixed-effect models.
Results: After adjusting for time-varying covariates energy intake, physical activity, and comorbidity index, among others, levels of F2-IsoP-M and the MPR were both inversely associated with percentage of weight change. Weight in the highest quartile of these two biomarkers was 1.33% (95% CI = -2.41, -0.24) and 1.09% (95% CI = -2.16, -0.02) lower than those in the lowest quartile group, with P for trend of 0.01 and 0.03, respectively. The inverse association was consistently seen across follow-up periods, although appearing stronger with prolonged follow-up. There was no association between the parent compound F2-IsoPs and weight change.
Conclusion: This study demonstrates the first piece of evidence to associate F2-IsoP metabolism, peroxisomal β-oxidation, with weight loss in older women. Further investigations into the role of lipid peroxidation and peroxisomal β-oxidation in weight change among older individuals are warranted.
DOI: 10.5281/zenodo.10363051
title: Data set for the article: An artificial neural network approach to finding the key length of the Vigenere cipher

description: Data supporting the work in the article: An artificial neural network approach to finding the key length of the Vigen\`{e}re cipher.
DOI: 10.5281/zenodo.10363050
title: Data set for the article: An artificial neural network approach to finding the key length of the Vigenere cipher

description: Data supporting the work in the article: An artificial neural network approach to finding the key length of the Vigen\`{e}re cipher.
DOI: 10.6084/m9.figshare.24494926
title: Supplementary Material for: Bone Marrow Mesenchymal Stem Cells Release miR-378a-5p-Carried Extracellular Vesicles to Alleviate Rheumatoid Arthritis

description: This study investigates whether bone marrow mesenchymal stem cells (BMSCs)-derived extracellular vesicles (EVs) can affect rheumatoid arthritis (RA) by delivering microRNA (miR)-378a-5p to regulate the IRF1/STAT1 axis. We identified RA-associated miRNAs using GEO microarray dataset GSE121894. We found the most important miRNAs in RA synovial tissues using RT-qPCR. BMSCs-derived EVs were ultracentrifuged and co-cultured with HSMECs in vitro. Dual-luciferase and RIP studies examined miR-378a-5p's specific binding to IRF1. We also measured angiogenesis, migration, and proliferation using CCK-8, Transwell, and tube formation assays. CIA (collagen-induced arthritis) mice models were created by inducing arthritis and scoring it. RA synovial tissues had low miR-378a-5p expression, whereas BMSC-derived EVs had high levels. The transfer of miR-378a-5p by BMSC-derived EVs to HSMECs boosted proliferation, migration, and angiogenesis. miR-378a-5p inhibited IRF1. MiR-378a-5p-containing BMSC-derived EVs decreased STAT1 phosphorylation and HSMEC IRF1 expression. EVs with miR-378a-5p mimic promoted HSMEC proliferation, migration, and angiogenesis, whereas dexmedetomidine inhibited STAT1 phosphorylation. In CIA mice, BMSC-derived EVs containing miR-378a-5p enhanced synovial vascular remodeling and histopathology. Thus, miR-378a-5p from BMSC-derived EVs promotes HSMEC proliferation, migration, and angiogenesis, inactivating the IRF1/STAT1 axis and preventing rheumatoid arthritis.
DOI: 10.6084/m9.figshare.24756537
title: Supplementary Material for: Advanced Glycation End Products-induced Activation of Keratinocytes: a Mechanism Underlying Cutaneous Immune Response in Psoriasis

description: Psoriasis is a common inflammatory skin disease, in which epidermal keratinocytes play a vital role in its pathogenesis via acting both as the responder and as the accelerator to the cutaneous psoriatic immune response. Advanced glycation end products (AGEs) are a class of proinflammatory metabolites that are commonly accumulating in cardiometabolic disorders. Recent studies have also observed increased level of AGEs in the serum and skin of psoriasis patients, but the role of AGEs in psoriatic inflammation has not been well investigated. In the present study, we initially detected abnormal accumulation of AGEs in epidermal keratinocytes of psoriatic lesion collected from psoriasis patients. Furthermore, AGEs promoted the proliferation of keratinocytes via up-regulated Keratin 17 (K17)-mediated p27KIP1 inhibition followed by accelerated cell cycle progression. More importantly, AGEs facilitated the production of interleukin-36 alpha (IL-36α) in keratinocytes, which could enhance T helper 17 (Th17) immune response. In addition, the induction of both K17 and IL-36α by AGEs in keratinocytes was dependent on the activation of signal transducer and activator of transcription 1/3 (STAT1/3) signaling pathways. At last, the effects of AGEs on keratinocytes were mediated by receptor for AGEs (RAGE). Taken together, these findings support that AGEs potentiate the innate immune function of keratinocytes, which contributes to the formation of psoriatic inflammation. Our study implicates AGEs as a potential pathogenic link between psoriasis and cardiometabolic comorbidities.
DOI: 10.6073/pasta/836870e77aeffcf7e4959db5490bc138
title: Long-Term Field Research Sites at Harvard Forest since 1937

description: The Harvard Forest is an iconic field station, hosting hundreds of field-based studies since it was founded in 1907. Site-based, long-term research increased sharply starting in 1988, when Harvard Forest became a Long-Term Ecological Research Site. This dataset documents the locations of most long-term research studies initiated since 1988; a few studies that began earlier and are still active are also included. Short-term studies, or studies that focus on sampling individual organisms, are not included.
DOI: 10.6073/pasta/34850e37fda3b971214788c327ea21f2
title: Multiple Element Limitation in Northeast Hardwood Ecosystems (MELNHE) - stomatal density and length 2021-2022

description: Stomatal density and length were measured on leaves of sugar maple (Acer sacharrum Marsh.) and yellow birch (Betula alleghaniensis Britton.) trees in New Hampshire at the Bartlett Experimental Forest, Hubbard Brook Experimental Forest, and Jeffers Brook as part of the Multiple Elementation Limitation in Northern Hardwood Ecosystems (MELNHE) study. Leaves were collected in late July and early August in 2021 and 2022 from the tops of dominant and codominant trees using a shotgun. These measurements were made on 3 leaves from each tree.
 These data correspond with other foliar trait data collected from the same trees in 2021 and 2022. That EDI package is as follows:
 Hong, S.D., K.E. Gonzales, C.R. See, and R.D. Yanai. 2021. MELNHE: Foliar Chemistry 2008-2016 in Bartlett, Hubbard Brook, and Jeffers Brook (12 stands) ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/b23deb8e1ccf1c1413382bf911c6be19
 This data package contains the stomatal density and length derived from the raw images in a separate EDI data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=321
 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6084/m9.figshare.24659325
title: Supplementary Material for: Entrectinib response to ROS1-fusion-positive non-small-cell lung cancer that progressed on crizotinib with leptomeningeal metastasis: A case report

description: Introduction
C-ros oncogene 1 (ROS1) translocation is an oncogenic driver-mutation identified in 1% to 2% of non-small-cell lung cancer (NSCLC) cases. Although crizotinib, a tyrosine kinase inhibitor (TKI) against ALK/ROS1, is known to be effective against ROS1-fusion-positive NSCLC, such cases sometimes progress with brain metastases. The most frequently reported crizotinib-resistance mutation is ROS1 G2032R, and some studies have found that even newly developed ROS1 TKIs, such as entrectinib and lorlatinib, show a decreased efficacy against it. The optimal therapies for ROS1-fusion-positive NSCLC and how such cases can be sequenced have not yet been established. 
Case Presentation
We herein report a patient with ROS1-fusion-positive NSCLC diagnosed at 34 years old. Crizotinib was started at the diagnosis and switched after 25 months to cisplatin/pemetrexed/bevacizumab once the disease progressed with multiple brain metastases that were resistant to stereotactic radiation therapy. The cytotoxic chemotherapy stabilized the patient’s condition for 17 months until he developed leptomeningeal metastasis (LM). He underwent lumboperitoneal shunting and whole-brain radiotherapy, followed by crizotinib re-administration. Despite crizotinib treatment, his neurologic symptoms, such as double vision, headache, weakness in the legs, and walking difficulties, progressed. Eventually, subsequent entrectinib treatment was initiated, which resolved all of the symptoms mentioned above. Regrettably, liquid next-generation sequencing (NGS) had failed to detect the resistance mechanism due to minimal ctDNA in this case. 
Conclusion
These findings imply that sequential entrectinib administration may be effective in patients with disease progression limited to central nervous system metastases during crizotinib administration.
DOI: 10.6084/m9.figshare.24659325.v1
title: Supplementary Material for: Entrectinib response to ROS1-fusion-positive non-small-cell lung cancer that progressed on crizotinib with leptomeningeal metastasis: A case report

description: Introduction
C-ros oncogene 1 (ROS1) translocation is an oncogenic driver-mutation identified in 1% to 2% of non-small-cell lung cancer (NSCLC) cases. Although crizotinib, a tyrosine kinase inhibitor (TKI) against ALK/ROS1, is known to be effective against ROS1-fusion-positive NSCLC, such cases sometimes progress with brain metastases. The most frequently reported crizotinib-resistance mutation is ROS1 G2032R, and some studies have found that even newly developed ROS1 TKIs, such as entrectinib and lorlatinib, show a decreased efficacy against it. The optimal therapies for ROS1-fusion-positive NSCLC and how such cases can be sequenced have not yet been established. 
Case Presentation
We herein report a patient with ROS1-fusion-positive NSCLC diagnosed at 34 years old. Crizotinib was started at the diagnosis and switched after 25 months to cisplatin/pemetrexed/bevacizumab once the disease progressed with multiple brain metastases that were resistant to stereotactic radiation therapy. The cytotoxic chemotherapy stabilized the patient’s condition for 17 months until he developed leptomeningeal metastasis (LM). He underwent lumboperitoneal shunting and whole-brain radiotherapy, followed by crizotinib re-administration. Despite crizotinib treatment, his neurologic symptoms, such as double vision, headache, weakness in the legs, and walking difficulties, progressed. Eventually, subsequent entrectinib treatment was initiated, which resolved all of the symptoms mentioned above. Regrettably, liquid next-generation sequencing (NGS) had failed to detect the resistance mechanism due to minimal ctDNA in this case. 
Conclusion
These findings imply that sequential entrectinib administration may be effective in patients with disease progression limited to central nervous system metastases during crizotinib administration.
DOI: 10.6073/pasta/968fe01e9b507cbc9a4db9ee4ed671f1
title: Multiple Element Limitation in Northeast Hardwood Ecosystems (MELNHE) - Raw images for the analysis of stomatal density and length 2021-2022

description: Stomatal density and length were measured on leaves of sugar maple (Acer sacharrum Marsh.) and yellow birch (Betula alleghaniensis Britton.) trees in New Hampshire at the Bartlett Experimental Forest, Hubbard Brook Experimental Forest, and Jeffers Brook as part of the Multiple Elementation Limitation in Northern Hardwood Ecosystems (MELNHE) study. Leaves were collected in late July and early August in 2021 and 2022 from the tops of dominant and codominant trees using a shotgun. These measurements were made on 3 leaves from each tree.
 These data correspond with other foliar trait data collected from the same trees in 2021 and 2022. That EDI package is as follows:
 Hong, S.D., K.E. Gonzales, C.R. See, and R.D. Yanai. 2021. MELNHE: Foliar Chemistry 2008-2016 in Bartlett, Hubbard Brook, and Jeffers Brook (12 stands) ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/b23deb8e1ccf1c1413382bf911c6be19
 This data package contains the raw images underlying the data reported in a separate data package on stomatal density and length: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=372
 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.