cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/459596691a72d77049f23ff090fcd4fc
title: Adult Population Survey of Hemlock Woolly Adelgid in Massachusetts 2003-2005

description: To effectively document insect presence and abundance a statistically based sampling plan is necessary. No such plan for the hemlock woolly adelgid is currently available in the published literature. Two interrelated sampling strategies allow a researcher to enter a site and determine with a given level of probability whether or not an HWA infestation is present and the level of infestation. A ground based sampling plan is also critical to the ‘ground truthing’ of aerial survey systems. A fully developed sampling plan requires relatively extensive datasets obtained over time, and may include the use of computer-generated data obtained through re-sampling techniques. The results obtained through the Harvard Forest Summer Research Program should provide a firm foundation for further development of an HWA sampling program. Data collection is on-going.
DOI: 10.6073/pasta/5677d6ad35a7ce15083ed75dcb9c2a77
title: Seed Bank in Hemlock Removal Experiment at Harvard Forest 2004-2015

description: The impending loss of hemlock trees due to hemlock woolly adelgid (Adelges tsugae) infestation prompted the need to identify species of plants able to colonize areas where hemlock has been removed. We investigated species present in the seed bank (in 2004 and 2010), the seedling bank (in 2004 and 2010), and seed rain (from 2005-2015) in the Harvard Forest Hemlock Removal Experiment. In 2004, Kelley Sullivan and Aaron Ellison determined the distribution of seeds buried in the soil in the six hemlock and two hardwood stands, before canopy treatments were applied (data files hf105-01, hf105-02). In 2010, Elizabeth Farnsworth and Aaron Ellison examined the distribution of plant species present five years after the simulated hemlock removal experiment was performed and six years after the baseline, pre-treatment study of the seedbank (data files hf105-03, hf105-04, hf105-05). In the 2010 study, we hypothesized that the composition of the seed and seedling banks and seed rain would diverge among the two treatments and the controls, based on the differential impacts of harvesting versus adelgid attack on the standing vegetation. We further hypothesized that the older (deeper) strata of the seedbanks of the treatment plots would have been exhausted over time, thus yielding poor germination relative to the top strata that continually receive seed rain. Identical methods of characterizing the composition of the seedbank and the aboveground vegetation at seedbank core locations were applied in both 2004 and 2010. Additional comparisons were made with long-term data collected on overall plant species composition in the Simes plots (datasets HF 106, HF126), and with data on seed rain (data file hf105-05). This study provides a unique temporal documentation of changes in the seedbank, seed rain, and vegetation under conditions of a changing overstory.
DOI: 10.6073/pasta/496e7e2b9fcc73d69d7eda233b392c34
title: Understory Vegetation in Hemlock Removal Experiment at Harvard Forest since 2003

description: Hemlock decline in New England is caused by direct and indirect effects of invasion of the hemlock woolly adelgid. Direct damage from the insect is causing gradual mortality of hemlock, and widespread harvesting of hemlock in advance of mortality, in contrast, causes immediate mortality and removal of biomass from the site. Although both processes affect thousands of acres of forest annually we have only a limited understanding of their effects on forest ecosystem function and productivity and the nature of the subsequent forest community. We anticipate that harvesting will yield different consequences than gradual mortality from the insect. Therefore we designed an experiment to simulate these contrasting impacts, by logging or girdling hemlock stands. Results from the experimental treatments are compared to the changes observed in forests that are being infested by the adelgid, and can also be included in integrated analyses of a suite of large experiments that form a core component of the Harvard Forest LTER program.
DOI: 10.6073/pasta/5ecbf08f2309fca9b20c593424d10988
title: Light Environment in Hemlock Removal Experiment at Harvard Forest since 2003

description: The impending loss of hemlock trees due to hemlock woolly adelgid (Adelges tsugae) infestation is expected to lead to changes in the light environment of the forest understory. These changes will both drive succession and will themselves be altered by successional processes. The light reaching the forest floor is measured using hemispherical canopy photographs. Photographs were taken in summer of 2003 and in December 2004 and May 2005 (both deciduous-tree leaf-off condition), prior to the application of the logging and girdling treatments, and then in September 2005 (deciduous tree leaf-on condition) after logging and girdling. Subsequent photographic series will be taken annually in spring (leaf-off) and summer/fall (leaf-on).
DOI: 10.6084/m9.figshare.24747036.v1
title: Druceiella_hillmani_augustus_gene_model.aa

description: <pre>This repository has 14 items including this README file. These files were generated from the analyses of <i>*Druceiella hillmani*</i> genome project and could be useful for repeating the analyses. Here we listed the file names with their brief description.<br></pre>
DOI: 10.5281/zenodo.10260210
title: PERCEIVE Design Cultural Probe Kit Tools

description: Cultural Probe Kit design tools, developed to analyse and study visitors behaviours in the field of Cultural Heritage, in relation to Curiosity, Sense of Care, Social Cohesion and Authenticity
DOI: 10.5281/zenodo.10260211
title: PERCEIVE Design Cultural Probe Kit Tools

description: Cultural Probe Kit design tools, developed to analyse and study visitors behaviours in the field of Cultural Heritage, in relation to Curiosity, Sense of Care, Social Cohesion and Authenticity
DOI: 10.5281/zenodo.8016938
title: CO2 Electroreduction To Syngas With Tunable Composition In An Artificial Leaf

description: Experimental dataset corresponding to figures in the main manuscript and supporting information
DOI: 10.5281/zenodo.8016939
title: CO2 Electroreduction To Syngas With Tunable Composition In An Artificial Leaf

description: Experimental dataset corresponding to figures in the main manuscript and supporting information
DOI: 10.5517/ccdc.csd.cc2dp0rw
title: CCDC 2224738: Experimental Crystal Structure Determination

description: Related Article: Yu-Meng Zhao, Jia-Ping Wang, Xiang-Yi Chen, Meng Yu, Alyona A. Starikova, Jun Tao|2023|Inorg.Chem.Front.|10|7251|doi:10.1039/D3QI01706K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dp0vz
title: CCDC 2224741: Experimental Crystal Structure Determination

description: Related Article: Yu-Meng Zhao, Jia-Ping Wang, Xiang-Yi Chen, Meng Yu, Alyona A. Starikova, Jun Tao|2023|Inorg.Chem.Front.|10|7251|doi:10.1039/D3QI01706K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10259805
title: Example Dataset for Self2Comp
DOI: 10.5281/zenodo.10259806
title: Example Dataset for Self2Comp
DOI: 10.25573/serc.24747231
title: SERC ForestGEO inventory census data

description: ForestGEO inventory data consisting of three censuses
DOI: 10.25573/serc.24747231.v2
title: SERC ForestGEO inventory census data

description: ForestGEO inventory data consisting of three censuses
DOI: 10.25573/serc.24747231.v1
title: SERC ForestGEO inventory census data

description: ForestGEO inventory data consisting of three censuses
DOI: 10.5281/zenodo.10262738
title: Data from: Supervised classification of plant communities with artificial neural networks

description: This dataset was used to test the performance of artificial neural networks for supervised classification of plant communities, published in:
Černá L. & Chytrý M. (2005) Supervised classification of plant communities with artificial neural networks. Journal of Vegetation Science 16, 407-414. https://doi.org/10.1111/j.1654-1103.2005.tb02380.x
The meaning of the individual columns (separated by semicolons) in the file is as follows (for details see the above-mentioned article):

Plot no - unique number of the vegetation plot
Group expert - plot membership in classes 1-11 of the expert  classification
Subset expert random B - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for the expert classification
Subset expert dg species B - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by  diagnostic species, for the expert classification
Assignment expert random - a class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification
Assignment expert dg-sp - a class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification
Group cluster - plot membership in classes 1-11 of the numerical classification
Subset cluster random - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for numerical classification
Subset cluster dg species - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by diagnostic species, for expert classification, for numerical classification
Assignment cluster random - class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification, for numerical classification
Assignment cluster dg-sp - class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification, for numerical classification 
598 species, with cover/abundance estimates on an ordinal scale of 1-9
DOI: 10.5281/zenodo.10262737
title: Data from: Supervised classification of plant communities with artificial neural networks

description: This dataset was used to test the performance of artificial neural networks for supervised classification of plant communities, published in:
Černá L. & Chytrý M. (2005) Supervised classification of plant communities with artificial neural networks. Journal of Vegetation Science 16, 407-414. https://doi.org/10.1111/j.1654-1103.2005.tb02380.x
The meaning of the individual columns (separated by semicolons) in the file is as follows (for details see the above-mentioned article):

Plot no - unique number of the vegetation plot
Group expert - plot membership in classes 1-11 of the expert  classification
Subset expert random B - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for the expert classification
Subset expert dg species B - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by  diagnostic species, for the expert classification
Assignment expert random - a class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification
Assignment expert dg-sp - a class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification
Group cluster - plot membership in classes 1-11 of the numerical classification
Subset cluster random - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for numerical classification
Subset cluster dg species - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by diagnostic species, for expert classification, for numerical classification
Assignment cluster random - class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification, for numerical classification
Assignment cluster dg-sp - class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification, for numerical classification 
598 species, with cover/abundance estimates on an ordinal scale of 1-9
DOI: 10.6073/pasta/2ebc3678bd2d9b8b329bc833452b78e7
title: Air and Soil Temperature in Hemlock Removal Experiment at Harvard Forest since 2004

description: The impending loss of hemlock trees due to hemlock woolly adelgid (Adelges tsugae) infestation is expected to lead to changes in the temperature regime of the forest understory. These changes will both drive succession and will themselves be altered by successional processes. Air temperature (1 m above forest floor) and soil temperature (at 10 cm depth) is measured at 1-minute intervals (hourly averages, minimum, and maximum are stored) using thermistors connected to Campbell 21-X dataloggers. Temperature measurements began 60-120 days prior to applications of the logging and girdling treatments, and will continue for the duration of the study.
DOI: 10.25387/g3.24282283
title: Supplemental Material for Maclary et al., 2023

description: Supplementary Material<br>
DOI: 10.25387/g3.24282283.v1
title: Supplemental Material for Maclary et al., 2023

description: Supplementary Material<br>
DOI: 10.15151/esrf-es-1335716535
title: Southern Germany cryo-EM BAG: Structural analysis of protein machineries using single particle cryo-EM

description: In the past, many macromolecular complexes could not be structurally characterized at atomic resolution as they were unsuitable for crystallization and X-ray crystallography and as electron microscopy could not provide high resolution data. This changed rapidly in the last decade, as tremendous progress was achieved in the single particle cryo electron microscopy (cryo-EM) field. Meanwhile, cryo-EM became the method of choice to determine the structure of such complexes, opening a new era of structural biology. In this BAG we will, using cryo-EM, determine the structures of complicated protein machineries including large multi-subunit complexes, protein-nucleic acid complexes and membrane protein complexes. Our projects will contribute to improve the understanding of the molecular basis of energy conversion and cellular respiration, nitrate and ammonium metabolism, ribosome and ribosome-associated functions, DNA damage repair and maintenance.
DOI: 10.6073/pasta/4b52a066841ed1ea20346b4643f5e6b5
title: Effects of Prey Availability on Sarracenia Physiology at Harvard Forest 2005

description: Allometric relationships exist between maximal mass-based net photosynthetic rates, leaf mass per unit area, and foliar Nitrogen (N) and Phosphorus (P) content, which hold across a diverse spectrum of over 2500 plant species worldwide. Carnivorous plants depart from this spectrum because they dedicate substantial leaf area to capturing prey, from which they derive N and P under very nutrient-limiting situations. We conducted a manipulative feeding experiment to test whether morphological and physiological allometric relationships of carnivorous plants when nutrients are not limiting are more similar to allometric relationships of non-carnivorous plants. We examined the effects of prey availability on photosynthetic rate (Amass), chlorophyll fluorescence, growth, architecture, and foliar nutrient and chlorophyll content of ten pitcher plant (Sarracenia) species. We tested the hypothesis that increased prey availability would stimulate Amass of one or more leaves, increase photosynthetic N- and P-use efficiencies (PNUEN, PNUEP), increase relative biomass allocation to photosynthetically efficient, non-predatory phyllodes rather than pitchers, increase overall plant biomass, and reduce stress-related chlorophyll fluorescence. This is the first multi-species, controlled feeding experiment using realistic prey treatments, measuring these physiological parameters directly, and elucidating mechanisms of nutrient stoichiometry and allometry in carnivorous plants. Increased prey availability increased chlorophyll content, Amass and photosystem efficiency (the Fv/Fm ratio) across the 10 Sarracenia species. These increases were most evident in younger leaves, as older leaves rapidly translocated nutrients to newer, growing tissues. Better-fed plants produced a significantly higher proportion of phyllodes than controls. Higher prey availability was associated with lower N:P ratios, and a shift from P- to N-limitation. PNUEP was significantly enhanced by supplementary feeding, whilst PNUEN was not. Overall biomass and root:shoot ratios were unaffected by feedings. Feeding shifted allometric relationships of P relative to Amass, N, and LMA from outside the third bivariate quartile to within the 50th bivariate percentile of the relationships found for non-carnivorous plants; other allometric relationships were unaffected. Carnivorous plants can plastically shift phosphorus allometry when nutrients are plentiful, but are less flexible in terms of nitrogen and other ecophysiological parameters.
DOI: 10.15151/esrf-es-1417798914
title: Cryo-EM structural studies of an assembly factor important for mitochondrial respiration

description: Investigating the structure of the MCIA complex to uncover the interaction between the core proteins and understand its function in relation to the OXPHOS system.
DOI: 10.17909/0b0p-fc98
title: K2-2/HIP116454

description: Light curves used in the K2 & TESS Synergy III paper. K2 light curve is from the engineering stage of the K2 mission, and TESS light curve is 120 second cadence from Sector 42.
DOI: 10.6073/pasta/e13188621994fec6ae706fd31d948b6c
title: Historical GIS Data for Harvard Forest Properties from 1908 to Present

description: Since 1908, the Harvard Forest has conducted forest surveys approximately every 10-20 years on its three largest tracts (total 1033 ha). These maps have been digitized along with maps of environmental factors (topography, soils), disturbance (1938 hurricane, historical land-use), and silvicultural treatments. These datalayers will allow researchers to understand the influence of environment factors, disturbances, and silviculture on the structure and composition of modern forest stands as well as assisting in locating and describing research sites. The dataset also includes an elevation grid (NED 30 meter cells), and a shapefile of linear features (trails, stonewalls, etc). Original maps were transcribed to standardized basemaps by various researchers. These basemaps were then scanned and digitized as shapefiles in ArcView GIS 3.2. The shapefiles were then transformed to Massachusetts State Plane Meters NAD83 projection in ArcGIS and rubbersheeted to align better with aerial photographs downloaded from MassGIS. Locations of control points will be permanently archived at the Harvard Forest to facilitate transformation of future datalayers.
DOI: 10.15151/esrf-es-1415962840
title: Structural Biology at EMBL Grenoble, IBS-CIBB and IAB

description: This proposal clusters crystallography and bioSAXS projects at the EMBL Grenoble, IBS-CIBB and IAB. It combines groups working on different topics with a major focus on cell signaling proteins, drug discovery, long non-coding RNAs, nucleic acid-protein complexes, and host-pathogen interactions. The proposers have long-standing experience in the use, as well as the development of beam lines for macromolecular crystallography and biological small angle X-ray scattering and have participated in successive BAG applications over the years, mostly at the ESRF but also at other synchrotrons (i.e. Soleil, Petra III, and Diamond). As Stephen Cusack (former head of EMBL Grenoble) will be retiring at the end of 2023 we propose to change the BAG responsible to Andrew McCarthy for this application round.
DOI: 10.6073/pasta/38b5bf8887b039b3c0b81b4a317f8cbc
title: Prey Capture by Carnivorous Plants Worldwide 1923-2007

description: Available phylogenetic data illustrate that in all carnivorous lineages, the ancestral trap type is a sticky, flypaper-type trap (Ellison and Gotelli, 2001). In the Caryophyllales, pitfall traps (Nepenthes) and snap traps (Dionaea and Aldrovanda) are derived relative to the sticky pads of Drosera. Similarly, in the Lamiales, the sticky-leaved Pinguicula is ancestral to Genlisea with its eel (or lobster-pot) traps and Utricularia with its vacuum traps. In the Ericales, the Sarraceniaceae with its pitfall traps are derived relative to Roridula, another species with flypaper traps. Muller et al. (2004) hypothesed that carnivorous genera with rapidly evolving genomes (Genlisea and Utricularia) have more predictable and frequent captures of prey than do genera with more slowly evolving genomes; by extension it could be hypothesized that in general, carnivorous plants with more complex traps should have more predictable and frequent captures of prey than do those with relatively simple traps. Increases in predictability and frequency of prey capture could be achieved by evolving more elaborate mechanisms for attracting prey, by specializing on particular types of prey, or, as Darwin suggested, by specializing on particular (large) sizes of prey. In all cases, one would expect that prey actually captured would not be a random sample of the available prey. Furthermore, when multiple species of carnivorous plants co-occur, one would predict, again following Darwin that interspecific competition would lead to specialization on particular kinds of prey. Because the traps of carnivorous plants accumulate identifiable remains of prey, analysis of trap contents can provide an aggregate record of the prey that have been successfully "sampled" by the plant. Such samples could be used to begin to test the hypothesis that carnivorous plant genera differ in prey composition and to look for evidence of specialization in prey capture. Over the past 80 years, numerous ecologists have gathered data on prey contents of carnivorous plants of a number of species and genera from around the world, but these data have never been summarized or synthesized; this summary and synthesis is accomplished in Ellison et al. (2008). The accompanying data are in this file.
DOI: 10.5281/zenodo.10258051
title: Scripts Extracao Github
DOI: 10.5281/zenodo.10258052
title: Scripts Extracao Github
DOI: 10.6084/m9.figshare.24747228
title: Data used for demo of the code accompanying the <i>Assessing the limits of zero-shot foundation models in single-cell biology</i> paper.

description: This data consists of:the pancreas dataset described in the scIB manuscript,weights for scGPT human version of the model (version created on 23 Jun 2023, downloaded from authors GDrive), andweights for Geneformer (6 Layers version) accessed from <code>4302f48</code> commit of the ctheodoris/Geneformer repository.Data is organised in directories as required for the demo of the microsoft/zero-shot-scfoundation repository.