cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5519/lp5a5t1d
title: Hans Sloane's Collection of Vegetables and Vegetable Substances

description: Hans Sloane’s Collection of Vegetables and Vegetable Substances originally consisted of 12,752 botanical specimens, most housed in small glass and wooden boxes. Sealed inside these boxes were parts of plants such as seeds, beans, leaves, bark and gum, that were collected between the 1680s and 1750s. All sorts of people from around the world were involved in the transportation and exchange of these specimens. In London, Sloane had these items put into boxes, where they were numbered and a corresponding description of the item was entered into his manuscript catalogue.

Today, the Vegetable Substances collection comprises more than 8000 surviving specimens/boxes and the original three-volume manuscript catalogue. This dataset includes a transcription of said manuscript and all 12,752 handwritten entries. At the core of these entries is information about what the object is, and from here, the level of detail is varied. This ranges from information about people and places, local uses of plants, margin annotations (which detail cabinet and drawer numbers where Sloane kept these things in his house) to bibliographic references, and modern determinations.

Users are recommended to consult the 'Data description and change log' before using the resources provided here.

A version of the transcription can also be found in the NHM library catalogue (Primo), together with images of the manuscript catalogue pages: https://nhm.primo.exlibrisgroup.com/permalink/44NHM_INST/16ehpmm/alma9936352402081.

Please note: This dataset preserves the data in Sloane’s catalogue in their original form to retain authenticity and facilitate research. As such, some entries contain language that may be offensive and that is not acceptable nor appropriate in an inclusive environment.

This work was supported by a grant from the Arts and Humanities Research Council Towards a National Collection Programme (Grant AH/W003457/1).
DOI: 10.6073/pasta/6df40a30859a7293db9a76fc4fff8cec
title: Critical slowing down: vegetation height, cover and composition assess resilience of tidal fresh, brackish and salt marshes following experimental disturbance at twelve sites across the estuarine landscape

description: We investigated the relative recovery rates of vegetation cover, vegetation height and community composition over a period of &gt;10 years after experimental disturbance in 12 tidal marshes (two oligohaline, three mesohaline and seven polyhaline sites) across the estuarine landscape on the coast of Georgia, USA. Vegetation was removed from three by three meter plots (four per site) with herbicide in 2006 followed by repeated clipping through 2009. Vegetation height, cover and composition was assessed in experimental and control plots (4 of each per site) from 2010 to 2020. The goal of the study was to assess how quickly the sites recovered from disturbance, how this varied in different types of marshes, and how results varied depending on whether recovery was assessed by vegetation height, cover or composition.
DOI: 10.6073/pasta/a9071a2ce1b78242c2ad1dda5854ec78
title: SBC LTER: Time series of quarterly NetCDF files of kelp biomass in the canopy from Landsat 5, 7 and 8, since 1984 (ongoing)

description: This data file represents a time series of canopy area of giant
 kelp, Macrocystis pyrifera, and bull kelp,
 Nereocystis luetkeana, and canopy biomass of
 giant kelp derived from Landsat 5 Thematic Mapper (TM), Landsat 7
 Enhanced Thematic Mapper Plus (ETM+), Landsat 8 Operational Land
 Imager (OLI), and Landsat 9 Operational Land Imager 2 satellite
 imagery, along with relevant metadata. The kelp canopy is composed
 of the portions of fronds and stipes floating on the surface of
 the water. Canopy area (m) data are given for individual 30 x 30
 meter pixels for all coastal areas of Baja California, Mexico,
 California, Oregon, and the outer coast of Washington (including
 offshore islands). Biomass data (wet weight, kg) are given for
 individual 30 x 30 meter pixels in the coastal areas extending
 from near Ano Nuevo, CA through the southern range limit in Baja
 California (including offshore islands), representing the range
 where giant kelp is the dominant canopy forming species.
 
 
 Data were derived from the three Landsat sensors listed above.
 Observations are made on a 16 day repeat cycle, for each
 instrument, but the temporal coverage is irregular because of
 cloud cover, instrument failure, and the mission length of each
 sensor (TM: 1984 – 2011, ETM+: 1999 – present, OLI: 2013 –
 present). Estimates of canopy area are derived from the fractional
 cover of kelp canopy determined from satellite surface
 reflectance. Estimates of kelp canopy biomass are derived from the
 relationship between giant kelp fractional cover determined from
 satellite surface reflectance and empirical measurements of giant
 kelp canopy biomass in long-term SBC LTER study plots obtained
 using SCUBA. The different Landsat sensors were calibrated to each
 other using simulated Landsat data derived from hyperspectral
 imagery. Missing data due to the ETM+ scan line corrector error
 were filled using a synchrony-based gap filling method.
 
 
 Data are organized into a single NetCDF file and contain the
 quarterly area and biomass means for each Landsat pixel across the
 three sensors. Relevant metadata such as number of Landsat
 estimates from which the mean was derived, the number of estimates
 from each sensor, standard error for each quarterly estimate,
 spatial coordinates, and date are all included in the file. For
 assistance with the data, please contact sbclter@msi.ucsb.edu.
DOI: 10.6084/m9.figshare.28428992
title: Supplementary Material for: Anti-Vascular Endothelial Growth Factor Treatment Outcomes in Macular Telangiectasia: A Systematic Review

description: Purpose: To assess clinical outcomes of anti-vascular endothelial growth factor agents (anti-VEGF) for patients with Macular Telangiectasia (MacTel). 
Methods: A systematic literature search on Ovid MEDLINE, Embase, and Cochrane Library was performed from inception to June 2024 for comparative studies on anti-VEGF agents in MacTel. The primary outcomes were the change in best-corrected visual acuity (BCVA). Secondary outcomes were central macular thickness (CMT), central choroidal thickness (CCT), and fluorescein angiography (FA) leakage. 
Results: Ten studies on 377 eyes of 239 patients followed up over 23.4 ± 8.3 months were included. Mean (SD) BCVA changed from 0.42 (0.39) to 0.35 (0.18) over 23.4 (8.3) months of follow up in non-proliferative MacTel. Mean BCVA changed from 0.66 (0.43) to 0.52 (0.34) at final follow-up in eyes with choroidal neovascularization (CNV). Five studies reported improved visual acuity, one showed improved FA leakage without visual acuity benefit, and four found no functional benefit. In non-proliferative MacTel, four studies showed no functional improvement, two reported significant functional and morphological improvements, and one suggested potential benefits in improving BCVA. In proliferative MacTel, two studies demonstrated improvement in both anatomical and functional outcomes, while one indicated that anti-VEGF treatment might produce improved results. In non-proliferative MacTel, mean CMT changed from 201 (32) µm to 199 (29) µm. CMT in patients with CNV decreased from an initial of 328.23 (161.16) µm to 267.44 (118.56) µm at final follow up. CCT in proliferative MacTel eyes decreased from 272.37 (52.65) µm and 247.40 (48.80) µm on anti-VEGF therapy. Overall, FA leakage outcomes were improved on ranibizumab therapy. No study documented any significant adverse effects with treatment.
Conclusion: Anti-VEGF agents may be associated with favourable anatomical and functional outcomes, particularly in proliferative MacTel, however, future large-scale clinical trials are warranted.
DOI: 10.6084/m9.figshare.28429013
title: Supplementary Material for: Development and validation of a Japanese outcome tool for perceptual assessment of speech in patients with cleft palate

description: Introduction: The lack of a standardized evaluation method for cleft palate speech makes it difficult to exchange information at the domestic and global levels. We aimed to develop and validate a Japanese outcome tool for the perceptual assessment of speech in patients with cleft palate.
Methods: The tool we developed was based on the Cleft Audit Protocol for Speech-Augmented (CAPS-A) with modifications to some speech parameters. We developed Japanese speech samples and parameters for the Japanese Cleft Speech Outcome Tool (CAPS-A-Japan: CAPS-A-JP). This study was conducted in the Japancleft speech working group at the Japanese Cleft Palate Association. In Phase 1, we constructed and developed the speech sampling protocol. In Phase 2, After the revision of the definitions and criteria for several cleft speech characteristics and the speech sample, a total of 20 audio recordings were tested. In Phase 3, criterion validity was assessed by comparing the CAPS-A-JP resonance outcomes reported for 40 cases with the outcomes of the clinical investigations. In Phase 4, a listening experiment with six Japanese speech-language-hearing therapists was conducted twice to test the intra- and inter-rater reliabilities for 20 cases. Intra-class correlation coefficients (ICCs) were used to analyze reliability.
Results: The mean percentage agreement on criterion validity for resonance was 71% on high-pressure sentences but 54% on low-pressure sentences. The inter-rater reliability was rated moderate/good (ICC: 0.45–0.80), except for developmental immaturities/errors that were rated fair. The ICC was very low or incalculable for hyponasality and syllable error patterns because there were few cases of hyponasality and syllable errors. The intra-rater reliability was rated as good/very good. The ICC was very low or incalculable in hyponasality, nasal emission, and syllable error patterns.
Conclusions: The standardized outcome tool, CAPS-A-JP, was developed for the first time in Japan. Future research is required to optimize this tool based on the inclusion of a training protocol.
DOI: 10.6084/m9.figshare.781240
title: Gaussian Job Archive for C4H8O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6085/aa/pisco_kelpforest.1.7
title: PISCO Kelp Forest Community Surveys

description: In 1998, the Partnership for Interdisciplinary Studies of Coastal
 Oceans (PISCO) designed and initiated a large scale, long-term
 monitoring study of kelp forest ecosystems along portions of the
 southern, central and northern coast of California and southern
 Oregon, USA. The program is administered out of the University of
 California campuses in Santa Cruz and Santa Barbara and funded
 primarily by the David and Lucile Packard Foundation. The purpose of
 the study has been to characterize the regional and temporal patterns
 of kelp forest ecosystem structure and evaluate the relative
 contributions of biological and environmental variables in explaining
 observed spatial and temporal patterns. For this purpose, the
 ecological community and physical structure of kelp forest ecosystems
 have been surveyed using trained SCUBA divers. The biological
 structure includes the more conspicuous fishes, invertebrates, and
 macroalgae. The physical structure includes geomorphological
 attributes (substratum type and vertical relief). Among other
 applications, these surveys have informed the design and evaluation of
 the state-wide network of marine protected areas (MPAs) established by
 California’s Marine Life Protection Act. Over time, the role of the
 monitoring program for evaluating the ecological responses to the
 establishment of the MPAs greatly influenced both the spatial and
 temporal design of the monitoring program.
DOI: 10.24381/cds.0e89c522
title: Fire danger indices historical data from the Copernicus Emergency Management Service
DOI: 10.5067/atlas/atl13.003
title: ATLAS/ICESat-2 L3A Inland Water Surface Height, Version 3
DOI: 10.5281/zenodo.12750027
title: Observation of the first stepping process of three winter lightning discharges

description: Lightning  location results data. This dataset includes complete data, which means it has not undergone quality control.
DOI: 10.6084/m9.figshare.28428998
title: Supplementary Material for: Surgical Preferences and Fears: Misconceptions About Robotic-Assisted Surgery

description: Introduction and objective
Robotic-assisted surgery (RAS) is widely adopted across surgical fields, notably urology, but patient knowledge remains limited, often shaped by misconceptions. Previous research indicates factors like age, profession, and technology use influence RAS perceptions. This study investigates public knowledge, preferences, and misconceptions about RAS within a German cohort.
Methods
A cross-sectional survey at a university hospital’s open house gathered responses from 339 participants prior to an RAS exhibition. The questionnaire assessed demographics, surgical preferences, and RAS knowledge. Statistical analyses, including t-tests, chi-squared tests, ANOVA, and multivariate logistic regression, identified key associations.
Results
Results showed 71% (234) of participants favored RAS over conventional surgery, yet misconceptions persisted in 38% (122), particularly among pensioners (48% (46) , p &lt; 0.01). Misconceptions were linked to a preference for conventional surgery (43% (52) vs. 19% (36), p &lt; 0.01). Surgical preference emerged as a significant predictor of misconception. Concerns included surgeon skill (41%, 141) and machine malfunction (39%, 132), with younger participants fearing human error and older individuals fearing technical failure (p &lt; 0.01).
Conclusion
This local study reveals strong public support for RAS but underscores prevalent misconceptions, especially among older adults, suggesting that addressing misconceptions could foster acceptance and informed decision-making.
DOI: 10.13099/vip21000-04-0
title: Tissue Properties Database V4.0

description: Tissue Database
DOI: 10.17632/pyzxxvjphk.4
title: NMD Paper Full Westerns

description: Full blot westerns for all figures.
DOI: 10.21227/zxtz-k625
title: Comprehensive Hindi Hostile Post Detection Dataset (CM-HTHPD)

description: The Comprehensive Hindi Hostile Post Detection Dataset (CM-HTHPD) is collection of Twitter posts written in the Hindi language, focusing on various forms of hostile content. The dataset was gathered using the Twitter Developer API and subsequently annotated manually with sentiment labels using the Label Studio platform. The dataset is primarily aimed at facilitating research and analysis in the domain of hostile content detection and sentiment analysis in Hindi-language social media discourse. The size of the dataset is approx 8300.
DOI: 10.5067/497nqvj0cbex
title: SnowEx Meteorological Station Measurements from Grand Mesa, CO, Version 1
DOI: 10.5067/h9c1uvwn1uk3
title: SnowEx17 Laser Snow Microstructure Specific Surface Area Data, Version 1
DOI: 10.5067/q0310g1xulzs
title: SnowEx17 Community Snow Pit Measurements, Version 1
DOI: 10.5281/zenodo.10433810
title: Data Sets: Unsteady Land-Sea Breeze Circulations in the Presence of a Synoptic Pressure Forcing

description: {Mg (m/s): 0, 0.4, 1.2, 2 and α: 0°, and 180°}

Consult the details in Allouche et al. (2023): https://doi.org/10.1002/qj.4552. The latter corresponds to the steady state simulations of these transient ones here.All of these simulations have a domain extent (L_x, L_y, L_z=z_i) of (80 km, 5 km, 1.6 km). The numerical mesh (Nx, Ny, Nz) is (384, 24, 64). For plotting, the vertical levels vary for each variable. A variable at 'c_s nodes' is plotted at dz/2, dz, 2*dz, 3*dz, and so forth up to z_i. A variable on 'w nodes' is plotted at 0, dz, 2*dz, 3*dz, and so forth up to z_i. This information is given in the variable table below.

These simulations are given in a netcdf format (.nc). One is able to download and reshape these matrices.
DOI: 10.5281/zenodo.10622228
title: Dataset of the research: Co-inoculation with Bacillus thuringiensis RZ2MS9 and Bradyrhizobium japonicum improves stimulate soybean (Glycine max (L.) Merril) development and can stimulate phosphorus microbial disponibilization through soil's natural community

description: Plant growth-promoting rhizobacteria (PGPR) form beneficial interactions with plants, delivering biological services such as nitrogen fixation, phosphorus mobilization, and the synthesis of plant hormones and siderophores. The utilization of PGPR in agriculture offers a dual benefit: it minimizes the need for excessive fertilizer application while fostering more sustainable agricultural practices. However, it is necessary to understand the consequences of introducing foreign microbes into intricate ecosystems, such as the soil microbiome. This study comprehensively examined the effects of co-inoculating soybean with Bacillus thuringiensis (Bt) RZ2MS9 and Masterfix® Soja, a commercial rhizobia bioinoculant containing Bradyrhizobium japonicum (SEMIA 5079) and Bradyrhizobium elkanii (SEMIA 5019), under field conditions. The investigation focused on soybean growth and development, along with the implications for soil microbiome diversity and key traits. Our field results indicate that soybean development was significantly influenced by inoculation. Plants inoculated with only Bt or co-inoculated with rhizobia exhibited a higher shoot length compared to those in the control group. However, neither inoculation nor co-inoculation had a significant effect on shoot dry mass, stem diameter, grain quality, productivity, and plant lodging. Soil prokaryotic diversity and community structure remained unaltered by Bt inoculation or co-inoculation with rhizobia. The abundance of the genera Agromyces, Capillimicrobium, Luteitalea, and Anaeromyxobacter increased after co-inoculation of Bt and rhizobia, and potentially can be used as bioindicators of inoculants presence. The genes enriched after co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase, indicating gluconic acid release and phosphorus solubilization as a potentially relevant path to promote plant nutrition and growth. The nifA genes were increased only when Bradyrhizobium was inoculated alone, suggesting that this pathway could potentially be affected by Bt inoculation in free-living soil prokaryotes. This study has shown the synergistic activity of rhizobia and Bt on soybean development. This collaboration enhances plant growth while preserving the overall diversity of native bacteria in the soil, without causing significant interference over an extended period. Exploring various rhizobacteria consortia for their potential positive synergistic effects as bioinoculants is a promising approach for sustainable crop management.
DOI: 10.5281/zenodo.11093961
title: ImmuneLENS output for PCAWG (TCGA subset)

description: Output from ImmuneLENS (https://github.com/McGranahanLab/ImmuneLENS) applied to the TCGA subset of the PCAWG WGS dataset + all matched low depth TCGA samples
DOI: 10.5281/zenodo.13134350
title: RAIRS spectrum of a H2O:CS2 (400:60 ML) ice mixture at 6 K

description: The title is self-explanatory. First column contains wavenumbers in cm-1. Second column contains absorbance.  

The spectrum was collected in the SPACE TIGER setup at the Center for Astrophysics | Harvard & Smithsonian. We assume that the spectrum is the same as in transmittance mode except for the absorbance, that is a factor 2.32 higher (note that this factor is setup-dependent and was measured for the SPACE TIGER setup in Martín-Doménech et al. 2020).
DOI: 10.5281/zenodo.13858535
title: USPTO dataset used by enviFormer

description: This contains the exact version of the USPTO dataset used in the paper "Predictive Modeling of Biodegradation Pathways Using Transformer Architectures" by Brydon et al.

Also included is the pretrained enviFormer model that was created by pretraining on the USPTO dataset.
DOI: 10.5281/zenodo.14552025
title: Archaic data based on GRCh38 and T2T-CHM13

description: This dataset contains archaic human data based on the T2T-CHM13 and GRCh38 reference genomes. It includes autosome VCF files for the Altai-Neanderthal and Altai-Denisovan, as well as Altai-Neanderthal introgression callsets (BED file format) for 26 populations from the 1000 Genomes Project (1KG).
DOI: 10.5281/zenodo.14692262
title: PROV-to-BFO: v2025-01-19

description: What's Changed



Release v2025-01-19 by @tmprd in https://github.com/BFO-Mappings/PROV-to-BFO/pull/39


Full Changelog: https://github.com/BFO-Mappings/PROV-to-BFO/compare/v2024-11-23...v2025-01-19
DOI: 10.5281/zenodo.14746877
title: Molecular shuttle, wB97XD/Def2-svp, G =  -8172.276752

description: Gaussian 16 (C01) calculation
DOI: 10.5281/zenodo.14746910
title: Molecular shuttle, wB97XD/def2-svp TS half way point, E = -8175.3727   G = -8172.267664 DG = 5.7

description: Gaussian 16 (C01) calculation
DOI: 10.5281/zenodo.14746936
title: Molecular shuttle, wB97XD/def2-svp TS half way point, (calcfc) optimisation G =-8172.270606 DG = 3.8

description: Gaussian 16 (C01) calculation
DOI: 10.5281/zenodo.14748031
title: Molecular shuttle, B3LYP+GD3+BJ/Def2-svp, G = -8175.526700

description: Gaussian 16 (C01) calculation
DOI: 10.5281/zenodo.14748035
title: Molecular shuttle, B3LYP+GD3+BJ/def2-svp TS half way point, -8175.516132 DG = 6.6

description: Gaussian 16 (C01) calculation
DOI: 10.5281/zenodo.4589755
title: Predictions of the GRACE-derived terrestrial water storage anomalies generated by a Bayesian convolutional neural network

description: This dataset provides predictions of the GRACE-derived terrestrial water storage anomalies (TWSAs) to fill the approximately one-year gap (July 2017-May 2018) between GRACE and its successor GRACE Follow-On. The predictions were obtained by a Bayesian convolutional neural network driven by the ERA5-land data (monthly precipitation, temperature, TWSAs, and cumulative water storage changes). The training period is April 2002-March 2014, the test periods are April 2014-June 2017 and June 2018-August 2020.
DOI: 10.5281/zenodo.7794867
title: T cell ExTRECT scores for TCGA

description: T cell ExTRECT scores run for the pan cancer TCGA WES data
DOI: 10.6084/m9.figshare.24355237
title: <b>chromosome-level genome assembly </b><b>of the mud carp (</b><b><i>Cirrhinus molitorella</i></b><b>)</b>

description: We constructed high-quality chromosome-level genome assembly of <i>C. molitorella</i> using PacBio sequencing and Hi-C data. The evolutionary history of <i>C. molitorella</i> was studied by inferring dynamic changes of ancestral population sizes. The genetic basis of adaptation in <i>C. molitorella</i> was dissected by performing gene family expansion and contraction analyses and identifying positively selected genes (PSGs). This provides the basis for the ecological adaptability of <i>C. molitorella</i>.
DOI: 10.6084/m9.figshare.28037942
title: Antenna Data

description: Antenna's simulation and measurement data
DOI: 10.6103/share.w5.900
title: Survey of Health, Ageing and Retirement in Europe (SHARE) Wave 5
DOI: 10.6103/share.w6.900
title: Survey of Health, Ageing and Retirement in Europe (SHARE) Wave 6
DOI: 10.6103/share.w8.900
title: Survey of Health, Ageing and Retirement in Europe (SHARE) Wave 8
DOI: 10.7288/v4/magic/20218
title: Paleomagnetic imprints of sulfate reduction pathways in continental shelf sediments: organoclastic versus anaerobic oxidation of methane (Dataset)

description: Paleomagnetic, rock magnetic, or geomagnetic data found in the MagIC data repository from a paper titled: Paleomagnetic imprints of sulfate reduction pathways in continental shelf sediments: organoclastic versus anaerobic oxidation of methane