cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/9e34836122d20a123ff2c38d95527e28
title: Barre Woods Soil Warming Experiment at Harvard Forest since 2001

description: Two of the major results of our original soil warming study were that: (1) warming stimulated the decay of a labile soil carbon pool; and (2) it also increased the availability of inorganic nitrogen to plants. Because of the small size of the original warming plots an important question we have not been able to answer conclusively is: Has the increase in available nitrogen led to an increase in carbon storage in the vegetation? And if yes, how much? In a systems context an additional question is: What is the balance between the carbon lost from the soil and the carbon stored in the vegetation in response to soil warming? We are now addressing these important questions with a new warming experiment in the Barre Woods area of the Harvard Forest. The Barre Woods site was chosen because it is of similarities to the Prospect Hill site - stand age, tree species composition, and soil type. There is no evidence of a plow horizon at the Barre Woods site, though surrounding stone walls indicate past use as pastureland. Historical records indicate the site was destroyed during the 1938 hurricane and then regrew naturally. During the summer and fall of 2001 we buried 3.4 miles of heating cable in a 30 x 30m plot. Cables were buried at a 10cm depth, spaced 20cm apart. A second 30 x 30m area was delineated to serve as the control plot. Results from the original soil warming experiment confirmed that the soil disturbance associated with the installation of heating cables has had no effect on soil temperatures and only minor and variable impacts on soil moisture. In April 2002, we began a one-year period of baseline measurements before turning on the heat in the new megaplot. These measurements included nitrogen mineralization, trace gas fluxes (CO2, CH4, N2O), tree growth (dendrometer bands), an under story species survey, canopy foliage analysis (C:N, NIR), and lysimetry. Thermistors were installed in both plots to begin tracking soil temperatures. The baseline measurements have confirmed that there are no significant differences between the two plots for key ecosystem processes prior to the initiation of the warming manipulation. We will turn on the power in April 2003 to begin the "manipulation phase" of this study. From this study, we expect to determine whether or not warming results in the movement of nitrogen from the soil to the trees and to learn how this movement affects the net carbon balance of the ecosystem.
DOI: 10.5281/zenodo.10018904
title: Table of nature-based solution examples in Ireland

description: A compendium of examples of nature-based solutions case studies, and actions that have been implemented through various schemes and projects, for the report "Identification and assessment of best practice in nature-based solutions for climate action and ecosystem restoration in Ireland".
DOI: 10.5281/zenodo.10018905
title: Table of nature-based solution examples in Ireland

description: A compendium of examples of nature-based solutions case studies, and actions that have been implemented through various schemes and projects, for the report "Identification and assessment of best practice in nature-based solutions for climate action and ecosystem restoration in Ireland".
DOI: 10.5281/zenodo.10246547
title: Table of nature-based solution examples in Ireland

description: A compendium of examples of nature-based solutions case studies, and actions that have been implemented through various schemes and projects, for the report "Identification and assessment of best practice in nature-based solutions for climate action and ecosystem restoration in Ireland".
DOI: 10.6084/m9.figshare.24710961
title: The global speciation continuum of the cyanobacterium <i>Microcoleus</i>

description: <b>Abstract:</b>Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium <i>Microcoleus</i>. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that <i>Microcoleus vaginatus</i> represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.Alignments provided here were used in the paper "The global speciation continuum of the cyanobacterium <i>Microcoleus</i>" by Stanojković, A., Skoupý, S., Johannesson, H. & Dvořák, P.
DOI: 10.6084/m9.figshare.24710961.v2
title: The global speciation continuum of the cyanobacterium <i>Microcoleus</i>

description: <b>Abstract:</b>Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium <i>Microcoleus</i>. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that <i>Microcoleus vaginatus</i> represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.Alignments provided here were used in the paper "The global speciation continuum of the cyanobacterium <i>Microcoleus</i>" by Stanojković, A., Skoupý, S., Johannesson, H. & Dvořák, P.
DOI: 10.6073/pasta/9b4c11098c2d6d2ce81b88b8a5ba5dd9
title: Demography and Morphology of Ericaceous Species on a Sand Plain in Montague MA 1994-1996

description: The study was a demographic analysis of Gaultheria procumbens conducted on the Montague Sand Plain. It compared the demographic parameters of above-ground stems between plowed and unplowed areas within scrub oak and hardwood sites. Past land use can have long-term effects on plant species distributional patterns if alterations in resources and environmental conditions have persistent effects on population demography ("environmental change") and/or if plants are intrinsically limited in their colonisation ability ("historical factors"). We evaluated the role of environmental alteration versus historical factors in controlling distributional patterns in Gaultheria procumbens (L.), a woody, clonal, understorey species with a pronounced restriction to areas that have never been ploughed and near absence from adjoining areas that were ploughed in the 19th century. The demographic study was conducted in scrub oak and hardwood plant communities on an extensive sand plain where it was possible to control for the effect of variation in environment prior to land use.
DOI: 10.5281/zenodo.10246540
title: Raw data with and without suppressor modification
DOI: 10.5281/zenodo.10246541
title: Raw data with and without suppressor modification
DOI: 10.5255/ukda-sn-856821
title: Virtual Tours of an Urban Park Produced Stress Recovery and Emotional Well-Being, 2022

description: The interest in urban green space as a provider/supporter of mental well-being is still growing. The question has largely moved on from “Will a walk in the park help with mental well-being?” to “Will a walk in any park do?” Over 1700 participants from the UK and China reported their affective states before and after virtually exploring the same urban park but with lower (5 species) or higher (18 species) biodiversity. In addition, half of the participants received a minor stress induction before exploring the park. Finally, all participants rated their perceived biodiversity (i.e. how many kinds of plants and animals they guessed to be present) The results showed that both parks with low and high biodiversity produced improved mood, especially in those participants who received the stress induction. The dataset includes three PANAS-X dimensions of the Affective States (Joviality, Serenity and Negative Affect) reported by the same participant at three points in time. Further, it includes Demographic information (gender, age and ethnicity), Nature connectedness, and subjective perceptions of biodiversity (i.e. how biodiverse the participant thought the video to be).
DOI: 10.6073/pasta/3c6f0e4b0fe8ed46d4c023b667e5ba7d
title: Stand and Community Response to Hemlock Woolly Adelgid in Southern New England since 1995

description: Hemlock woolly adelgid (HWA), Adelges tsugae, an introduced aphid-like insect from Asia, is expanding its range across the northeastern United States through the range of Tsuga canadensis (eastern hemlock) and can severely reduce or eliminate this important late-successional species. As part of a study investigating stand- and landscape-level forest dynamics resulting from HWA infestation, we examined initial community response of eight T. canadensis stands in south-central Connecticut and then continued to monitor these stands every other year. Our major objectives were to assess mortality patterns in T. canadensis, evaluate subsequent changes in stand microenvironment, and relate these and stand composition to initial patterns of regeneration, understory response, and community reorganization. Tsuga canadensis damage varied broadly across the study area ranging from near zero to greater than 95 % mortality. All size and age classes sampled were attacked by HWA, although smaller trees exhibited higher mortality rates than larger trees. All remaining T. canadensis sampled in seven of the eight stands were infested with HWA and over 90 % suffered at least 50 % foliar loss. Since 1995, overstory and understory mortality has risen 5 to 15 % per year to overall values of 50 to 99%. There has been no sign of tree recovery and the health and vigor of remaining trees deteriorated in all infested stands. Results suggest that trees on some sites can remain alive for over 10 years following initial infestation and remain standing for 6 to 8 years following mortality. Substantial accumulations of downed woody debris have developed in stands with severe HWA damage. Canopy gaps created by HWA damage significantly increased the amount of light reaching the forest floor and resulted in rapid understory vegetation responses. Prolific Betula lenta (black birch) establishment occurred in stands with moderate to severe T. canadensis mortality. In addition, opportunistic herbaceous species (Erechtites hieracifolia, Phytolacca americana) and non-native species (Ailanthus altissima, Microstegium vimineum) have recently invaded these stands. Due to mortality from HWA, T. canadensis seedlings were scarce in sampled stands, suggesting that advance regeneration and seedbanks will not be important mechanisms for T. canadensis reestablishment. Tsuga canadensis cannot sprout following defoliation and has no apparent resistance to HWA. Tree-ring analysis of hardwood and declining hemlock trees, coupled with age-structure analysis of newly established birch saplings was effective in determining the timing of initial HWA impact in stands of unknown infestation date. Over the last 10 years, radial growth of hemlock declined precipitously in most stands, while oak and maple growth exhibited concomitant, large annual increases. Therefore, dramatic reductions in T. canadensis across broad geographical areas appear imminent if HWA dispersal continues unimpeded and no effective natural enemies of HWA are found.
DOI: 10.6084/m9.figshare.24309217
title: Data for "Building a trap model of glassy dynamics from a local structural predictor of rearrangements"

description: Each file is a pickle file, which can be read using pythons pickle module.The files prs_KALJ.pkl, prs_SS.pkl, stats_KALJ.pkl, and stats_KALJ.pkl contain all data for the softness analysis, in pandas dataframes.The files Q_SS.pkl and Q_KALJ.pkl contain the computed inherent state Q(t) in dictionaries (keyed on (density, T) or just T) of numpy arrays.The files aging_S_KALJ.pkl and aging_S_SS.pkl contain the vs. waiting time curves, in dictionaries (keyed on T) of numpy arrays.<br>
DOI: 10.6084/m9.figshare.24309217.v1
title: Data for "Building a trap model of glassy dynamics from a local structural predictor of rearrangements"

description: Each file is a pickle file, which can be read using pythons pickle module.The files prs_KALJ.pkl, prs_SS.pkl, stats_KALJ.pkl, and stats_KALJ.pkl contain all data for the softness analysis, in pandas dataframes.The files Q_SS.pkl and Q_KALJ.pkl contain the computed inherent state Q(t) in dictionaries (keyed on (density, T) or just T) of numpy arrays.The files aging_S_KALJ.pkl and aging_S_SS.pkl contain the vs. waiting time curves, in dictionaries (keyed on T) of numpy arrays.<br>
DOI: 10.21227/jq12-5885
title: APCrack600

description: The dataset, named APCrack600, consisted of 600 images with a size of 3840×2160 pixels.  Pixel-wise annotations were performed on each crack image. The image samples were grouped into two categories: pavement cracks and others. The dataset, named APCrack600, consisted of 600 images with a size of 3840×2160 pixels.  Pixel-wise annotations were performed on each crack image. The image samples were grouped into two categories: pavement cracks and others. The dataset, named APCrack600, consisted of 600 images with a size of 3840×2160 pixels.  Pixel-wise annotations were performed on each crack image. The image samples were grouped into two categories: pavement cracks and others.
DOI: 10.5255/ukda-sn-856820
title: Improving the Uptake and Sustainability of Effective Interventions To Promote Prudent Antibiotic Use in Primary Care: Discrete Choice Experiments, 2017-2022

description: This study investigates the factors influencing preferences for delayed (or “backup”) antibiotic prescription: a strategy that can be used in primary care as part of antibiotic stewardship. The data are generated from discrete choice experiments performed in the UK, among both general practitioners (GPs), and members of the public (two samples: adults, and parents of child(ren) under 18). Respondents were presented with prescribing scenarios described by 6 attributes, and made a choice of their preferred type of antibiotic prescription. Respondents were recruited by commercial providers from existing on-line panels, and were sampled to be representative of the UK population in terms of sex, age, ethnicity, and country of residence within the UK. The survey was completed on-line. The dataset consists of anonymised survey responses, including the choice questions, and respondent characteristics such as age and gender.
DOI: 10.5281/zenodo.10089124
title: Reworking of Eoarchean to Mesoarchean continental crust in the Anshan-Benxi area, North China Craton: Evidence from Lianshanguan ca. 2.5 Ga syenogranites
DOI: 10.5281/zenodo.10089125
title: Reworking of Eoarchean to Mesoarchean continental crust in the Anshan-Benxi area, North China Craton: Evidence from Lianshanguan ca. 2.5 Ga syenogranites
DOI: 10.5281/zenodo.10246584
title: Reworking of Eoarchean to Mesoarchean continental crust in the Anshan-Benxi area, North China Craton: Evidence from Lianshanguan ca. 2.5 Ga syenogranites
DOI: 10.25345/c58s4k07v
title: MassIVE MSV000093551 - Tara_TREC_Campain_PositiveMode
title: Data dependent analysis in positive mode of SPE samples from the TARA campaign TREC.
DOI: 10.6084/m9.figshare.24712800
title: Evaluating the capacity for eDNA to function as a fish enumeration tool

description: raw eDNA data files and fish count data files
DOI: 10.6084/m9.figshare.24712800.v1
title: Evaluating the capacity for eDNA to function as a fish enumeration tool

description: raw eDNA data files and fish count data files
DOI: 10.25345/c5513v64h
title: MassIVE MSV000093552 - Tara_TREC_Campain_NegativeMode
title: Data dependent analysis in negative mode of samples from TARA TREC campaign
DOI: 10.5281/zenodo.10142416
title: NOMAD mini-app suite checkpoints

description: Checkpoint inputs for the execution of the NOMAD mini-apps suite. Calculation of ZrO2 crystal with the G0W0 implementations of exciting and Abinit, and FHI-aims, and hcp-Si test case for FHI-aims code.
DOI: 10.6084/m9.figshare.24092513
title: Study of silicone hydrogel contact lenses’ surface reflection characteristics using confocal microscopy

description: The physical and chemical properties of contact lenses (CLs) differ significantly from one another. This is already covered by the FDA classification, which divides soft lenses into groups and subgroups for additional characteristics. The differences relate to both the interior and surface of the lens. Several differences in the surface characteristics of individual contact lenses have been studied and demonstrated to date. However, one of their fundamental physical properties, that is light reflection or, quantitatively, reflectance has not been compared. This paper describes the surface differences of a range of silicone-hydrogel (SiHy) lenses using reflectance confocal microscopy. It shows the relationship between the amount of light reflected from the lens surface and the material parameters. Common SiHy lens materials were used in the study, including two lenses with surface modifications. Light incident at the interface between two media (phosphate-buffered saline and lens) with different refractive indices is partially reflected. The normalized results show significant differences between the reflection signals (1 vs 0.07), and that they are not correlated with the refractive index (R<sup>2</sup> = 0.5536). For the water content (%H<sub>2</sub>O), a general trend was observed that the higher the %H<sub>2</sub>O, the lower the reflection signal is (R<sup>2</sup> = 0.8105). The reflection signal and surface modulus show the best correlation. (R<sup>2</sup> = 0.9883). The proposed CLs analysis method, using reflectance confocal microscopy, provides data to differentiate between lenses with and without surface modifications.
DOI: 10.6084/m9.figshare.24092513.v1
title: Study of silicone hydrogel contact lenses’ surface reflection characteristics using confocal microscopy

description: The physical and chemical properties of contact lenses (CLs) differ significantly from one another. This is already covered by the FDA classification, which divides soft lenses into groups and subgroups for additional characteristics. The differences relate to both the interior and surface of the lens. Several differences in the surface characteristics of individual contact lenses have been studied and demonstrated to date. However, one of their fundamental physical properties, that is light reflection or, quantitatively, reflectance has not been compared. This paper describes the surface differences of a range of silicone-hydrogel (SiHy) lenses using reflectance confocal microscopy. It shows the relationship between the amount of light reflected from the lens surface and the material parameters. Common SiHy lens materials were used in the study, including two lenses with surface modifications. Light incident at the interface between two media (phosphate-buffered saline and lens) with different refractive indices is partially reflected. The normalized results show significant differences between the reflection signals (1 vs 0.07), and that they are not correlated with the refractive index (R<sup>2</sup> = 0.5536). For the water content (%H<sub>2</sub>O), a general trend was observed that the higher the %H<sub>2</sub>O, the lower the reflection signal is (R<sup>2</sup> = 0.8105). The reflection signal and surface modulus show the best correlation. (R<sup>2</sup> = 0.9883). The proposed CLs analysis method, using reflectance confocal microscopy, provides data to differentiate between lenses with and without surface modifications.
DOI: 10.6084/m9.figshare.21505203
title: Year effects drive beta diversity

description: Dataset of PRYER experiment established by Truman Young to measure priority effects across years. Communities consist of mixes of 4 native grasses, 4 exotic grasses, or both, either planted concurrently or with a two-week priority window. Also contains code used for beta diversity analyses and figures.Code updated 12/1/2023 to fix two typos in variable names.
DOI: 10.6084/m9.figshare.21505203.v3
title: Year effects drive beta diversity

description: Dataset of PRYER experiment established by Truman Young to measure priority effects across years. Communities consist of mixes of 4 native grasses, 4 exotic grasses, or both, either planted concurrently or with a two-week priority window. Also contains code used for beta diversity analyses and figures.Code updated 12/1/2023 to fix two typos in variable names.
DOI: 10.5066/p97c5x8w
title: Organochlorine residues and elemental contaminants in U.S. freshwater fish, 1976-1986: National Contaminant Biomonitoring Program

description: The National Contaminant Biomonitoring Program (NCBP), which was developed and maintained by the U.S. Fish and Wildlife Service (FWS), monitored concentrations of environmental contaminants in freshwater fish over a period of about 20 years. Beginning in the 1960s as a component of the multi-agency National Pesticide Monitoring Program (NPMP) and continuing through the mid-1980s, freshwater fish were periodically collected from a national network of stations for analysis of pesticides, PCBs, and other contaminants. The NPMP/NCBP database of contaminant concentrations is the most extensive of its kind, unique in its breadth and depth with respect to environmental contaminant concentrations in fish. The data and information from the NCBP are sought often by a national and international clientele; especially frequent users are biologists in FWS field offices and USGS Water Science Centers. The fish network was suspended by FWS in 1986 pending development of the Biomonitoring of Environmental Status and Trends (BEST) program. The BEST program and the NPMP/NCBP database were transferred to the National Biological Survey/Service (NBS) in 1993. At that time ongoing studies by NBS Inventory and Monitoring (I and M) and the USGS National Water Quality Assessment Program (NAWQA) generated new data at NCBP sites. The database was subsequently (1996) transferred to USGS. The database derived from the NCBP is unique in its ability to characterize the exposure of free-ranging organisms, including threatened and endangered species, to toxic contaminants.
DOI: 10.5281/zenodo.10246254
title: Data for the publication "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics"

description: Repository containing all the necessary data to replicate the study "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics", published in Biomechanics and Modeling in Mechanobiology (https://doi.org/10.1007/s10237-023-01792-5).
DOI: 10.5281/zenodo.10246255
title: Data for the publication "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics"

description: Repository containing all the necessary data to replicate the study "Mechanical communication within the microtubule through network-based analysis of tubulin dynamics", published in Biomechanics and Modeling in Mechanobiology (https://doi.org/10.1007/s10237-023-01792-5).