cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25390/caryinstitute.22312177.v2
title: Data associated with: Han, B.A., Varshney, K.R., LaDeau, S., Subramaniam, A., Weathers, K.C., Zwart, J. A synergistic future for AI and ecology. PNAS 120 (38) (2023).

description: The file is associated with:Han, B.A., Varshney, K.R., LaDeau, S., Subramaniam, A., Weathers, K.C., Zwart, J. A synergistic future for AI and ecology. PNAS 120 (38) (2023).<b>Abstract:</b>Research in both ecology and artificial intelligence (AI) strives for predictive understanding of complex systems, where nonlinearities arise from multidimensional interactions and feedbacks across multiple scales. After a century of advances built on a staggered cycle of computational development and ecological adaptation, we foresee a critical need for intentional synergy to meet current societal challenges against the backdrop of global change.The unpredictability of systems-level phenomena and associated challenges in understanding resilience dynamics are critical challenges on a rapidly changing planet. Here, we spotlight both the promise and the urgency of a synergistic convergence research paradigm between ecology and AI. The systems studied in ecology are a challenge to fully and holistically model, even using the most prominent AI technique today: deep neural networks. Moreover, ecological systems have emergent and resilient behavior that should inspire new, robust AI architectures and methodologies. We share several examples of how challenges in ecological systems modeling will require advances in AI techniques that are themselves inspired by the systems they seek to model.Both fields have inspired each other, albeit indirectly, in an evolution toward this convergence. Here we emphasize the need for more purposeful synergy to accelerate understanding of ecological resilience whilst building the resilience currently lacking in modern AI. There are persistent epistemic barriers that require attention in both disciplines, yet the implications of a successful convergence go beyond advancing ecological disciplines or achieving an artificial general intelligence -- they are critical for both persisting and thriving in an uncertain future.<b>File list:</b>AIandML_results_SHARE.csv - contains literature search results from Clarivate Web of Science.
DOI: 10.25390/caryinstitute.22312177.v1
title: Data associated with: Beyond AI for X: A Synergistic Future for AI and Ecology

description: The file is associated with:
B.A. Han, K.R. Varshney, S. LaDeau, A. Subramanian, K.C. Weathers, J. Zwart. <em>Submitted.</em> Beyond ‘AI for X’: A Synergistic Future for AI and Ecology.
<strong>Abstract: </strong>
Research in both ecology and artificial intelligence (AI) strives for predictive understanding of complex systems, where nonlinearities arise from multidimensional interactions and feedbacks across multiple scales. After a century of advances built on a staggered cycle of computational development and ecological adaptation, we foresee a critical need for intentional synergy to meet current societal challenges against the backdrop of global change. 
The unpredictability of systems-level phenomena and associated challenges in understanding resilience dynamics are critical challenges on a rapidly changing planet. Here, we spotlight both the promise and the urgency of a synergistic convergence research paradigm between ecology and AI. The systems studied in ecology are a challenge to fully and holistically model, even using the most prominent AI technique today: deep neural networks. Moreover, ecological systems have emergent and resilient behavior that should inspire new, robust AI architectures and methodologies. We share several examples of how challenges in ecological systems modeling will require advances in AI techniques that are themselves inspired by the systems they seek to model. 
Both fields have inspired each other, albeit indirectly, in an evolution toward this convergence. Here we emphasize the need for more purposeful synergy to accelerate understanding of ecological resilience whilst building the resilience currently lacking in modern AI. There are persistent epistemic barriers that require attention in both disciplines, yet the implications of a successful convergence go beyond advancing ecological disciplines or achieving an artificial general intelligence -- they are critical for both persisting and thriving in an uncertain future. 
<strong>File list:</strong>
AIandML_results_SHARE.csv - contains literature search results from Clarivate Web of Science.
DOI: 10.25390/caryinstitute.22312177
title: Data associated with: Han, B.A., Varshney, K.R., LaDeau, S., Subramaniam, A., Weathers, K.C., Zwart, J. A synergistic future for AI and ecology. PNAS 120 (38) (2023).

description: The file is associated with:Han, B.A., Varshney, K.R., LaDeau, S., Subramaniam, A., Weathers, K.C., Zwart, J. A synergistic future for AI and ecology. PNAS 120 (38) (2023).<b>Abstract:</b>Research in both ecology and artificial intelligence (AI) strives for predictive understanding of complex systems, where nonlinearities arise from multidimensional interactions and feedbacks across multiple scales. After a century of advances built on a staggered cycle of computational development and ecological adaptation, we foresee a critical need for intentional synergy to meet current societal challenges against the backdrop of global change.The unpredictability of systems-level phenomena and associated challenges in understanding resilience dynamics are critical challenges on a rapidly changing planet. Here, we spotlight both the promise and the urgency of a synergistic convergence research paradigm between ecology and AI. The systems studied in ecology are a challenge to fully and holistically model, even using the most prominent AI technique today: deep neural networks. Moreover, ecological systems have emergent and resilient behavior that should inspire new, robust AI architectures and methodologies. We share several examples of how challenges in ecological systems modeling will require advances in AI techniques that are themselves inspired by the systems they seek to model.Both fields have inspired each other, albeit indirectly, in an evolution toward this convergence. Here we emphasize the need for more purposeful synergy to accelerate understanding of ecological resilience whilst building the resilience currently lacking in modern AI. There are persistent epistemic barriers that require attention in both disciplines, yet the implications of a successful convergence go beyond advancing ecological disciplines or achieving an artificial general intelligence -- they are critical for both persisting and thriving in an uncertain future.<b>File list:</b>AIandML_results_SHARE.csv - contains literature search results from Clarivate Web of Science.
DOI: 10.34740/kaggle/dsv/7155965
title: Learning Analytics Link Collection
DOI: 10.5281/zenodo.10304595
title: Gene prioritization scores and drug target information

description: This data folder accompanies the article Sadler MC, Auwerx C, Deelen P, Kutalik Z. Multi-layered genetic approaches to identify approved drug targets. Cell Genomics 3, no. 7 (July 2023): 100341(https://doi.org/10.1016/j.xgen.2023.100341).
It contains disease-drug-target links as well as gene prioritisation scores of all the assessed methods.
DOI: 10.5281/zenodo.10304596
title: Gene prioritization scores and drug target information

description: This data folder accompanies the article Sadler MC, Auwerx C, Deelen P, Kutalik Z. Multi-layered genetic approaches to identify approved drug targets. Cell Genomics 3, no. 7 (July 2023): 100341(https://doi.org/10.1016/j.xgen.2023.100341).
It contains disease-drug-target links as well as gene prioritisation scores of all the assessed methods.
DOI: 10.34770/8ad7-jj80
title: Data for "Double-Sided Electron Energy Analyzer for Measurement of Non-Maxwellian Electron Energy Distributions"

description: Data needed to reproduce figures in the publication
DOI: 10.6073/pasta/786b6952a85cd4f3f6c04cb107847024
title: Bird Communities in Forest Openings at Harvard Forest 2014-2015

description: Currently, many of the most severely declining neotropical migrants in the northeastern United States are disturbance dependent, early-successional species. Much of their decline is attributed to loss of suitable habitat. Large clearcuts (&gt;5.0 ha) are widely considered to be optimal habitat for most shrubland bird species. However, it is well documented that certain species are capable of breeding within significantly smaller patches of habitat (less than 2.0 ha), which are most commonly created through group selection harvest cuttings.
 The goal of this research is to determine habitat characteristics translatable to habitat value for shrubland birds for use in conservation programs to maximize biological value. This research will provide an assessment of the value of forest openings for shrubland birds, helping to define the suitability of forest canopy openings for specific bird species. This project will describe the conservation value of shrubland openings deemed too small to sustain full suites of specialist shrubland birds by providing threshold patch area values for individual species able to use these smaller patches.
DOI: 10.5281/zenodo.10304664
title: «ПРЕКРАСНЫЕ ЖЕНСКИЕ ОБРАЗЫ РУССКОЙ ЛИТЕРАТУРЫ»
DOI: 10.5281/zenodo.10304663
title: «ПРЕКРАСНЫЕ ЖЕНСКИЕ ОБРАЗЫ РУССКОЙ ЛИТЕРАТУРЫ»
DOI: 10.5281/zenodo.10129470
title: Environmental DNA captures signals of the internal structure of a pond metacommunity

description: R Code for the study of "Environmental DNA captures signals of the internal structure of a pond metacommunity"
description: There are 4 code files, the 'metacommunity_uk_ponds_20230328.Rmd' is to create the figures in the paper, the 'function_barplot.R' and 'function_forest.R' are the supported files to make the figures; the 'model_15species.R' and 'model_48species.R' are for generating the models.
The UK_ponds_metabarcoding_mct_rawdata.zip file contains all the raw sequencing data.
DOI: 10.5281/zenodo.10129469
title: Environmental DNA captures signals of the internal structure of a pond metacommunity

description: R Code for the study of "Environmental DNA captures signals of the internal structure of a pond metacommunity"
description: There are 4 code files, the 'metacommunity_uk_ponds_20230328.Rmd' is to create the figures in the paper, the 'function_barplot.R' and 'function_forest.R' are the supported files to make the figures; the 'model_15species.R' and 'model_48species.R' are for generating the models.
The UK_ponds_metabarcoding_mct_rawdata.zip file contains all the raw sequencing data.
DOI: 10.6073/pasta/a22489722af84ff13d06b01189f6aa11
title: Diurnal Patterns of Cavitation in Red Maple, Paper Birch and White Ash at Harvard Forest 2011-2012

description: Previous work at Harvard Forest has suggested that woody plants cavitate and re-dissolve embolisms in xylem on a daily basis. Here we investigated the common assumption that severing stems and petioles under water preserves the hydraulic continuity in the xylem conduits opened by the cut when the xylem is under tension. In red maple and white ash, higher PLC in the afternoon occurred when the measurement segment was excised under water at native xylem tensions, but not when xylem tensions were relaxed prior to sample excision. Bench drying vulnerability curves in which measurement samples were excised at native versus relaxed tensions showed a dramatic effect of cutting under tension in red maple, a moderate effect in sugar maple, and no effect in paper birch. These results suggest that sampling methods can generate PLC patterns indicative of repair under tension by inducing a degree of embolism that is itself a function of xylem tensions at the moment of sample excision.
DOI: 10.5066/p9yiauzq
title: Elevation, Flow Accumulation, Flow Direction, and Stream Definition Data in Support of the Illinois StreamStats Upgrade to the Basin Delineation Database

description: The U.S. Geological Survey (USGS), in cooperation with the Illinois Center for Transportation and the Illinois Department of Transportation, prepared hydro-conditioned geographic information systems (GIS) layers for use in the Illinois StreamStats application. These data were used to delineate drainage basins and compute basin characteristics for updated peak flow and flow duration regression equations for Illinois. This dataset consists of raster grid files for elevation (dem), flow accumulation (fac), flow direction (fdr), and stream definition (str900) for each 8-digit Hydrologic Unit Code (HUC) area in Illinois merged into a single dataset. There are 51 full or partial HUC 8s represented by this data set: 04040002, 05120108, 05120109, 05120111, 05120112, 05120113, 05120114, 05120115, 05140202, 05140203, 05140204, 05140206, 07060005, 07080101, 07080104, 07090001, 07090002, 07090003, 07090004, 07090005, 07090006, 07090007, 07110001, 07110004, 07110009, 07120001, 07120002, 07120004 (0712003 was combined into this HUC), 07120005, 07120006, 07120007, 07130001, 07130002, 07130003, 07130004, 07130005, 07130006, 07130007, 07130008, 07130009, 07130010, 07130011, 07130012, 07140101, 07140105, 07140106, 07140108, 07140201, 07140202, 07140203, and 07140204.
DOI: 10.6073/pasta/9b6575ac51cc67b380eab7e7ca6945b6
title: Xylem Embolism Formation, Refilling and Water Storage in Tree Trunks at Harvard Forest 2012

description: Trunks of large trees play an important role in whole-plant water balance but technical difficulties have limited most hydraulic research to small stems, leaves and roots. To investigate the dynamics of water-related processes in tree trunks, such as winter embolism refilling, xylem hydraulic vulnerability, and water storage, volumetric water content (VWC) in the main stem was monitored continuously using frequency domain moisture sensors in adult Betula papyrifera trees from early spring through the beginning of winter. An air injection technique was developed to estimate hydraulic vulnerability of the trunk xylem. Trunk VWC increased in early spring and again in autumn concurrent with root pressure during both seasons. Diurnal fluctuations and a gradual decrease in trunk VWC through the growing season were observed, which, in combination with VWC increase after significant rainfall events and depletion during periods of high water demand, indicate the importance of stem water storage in both short-and long-term water balance. Comparisons between the trunk air injection results and conventional branch hydraulic vulnerability curves showed no evidence of “vulnerability segmentation” between the main stem and small branches in B. papyrifera. Measurements of VWC following air injection, together with evidences from air injection and xylem dye perfusion, indicate that embolized vessels can be refilled by active root pressure but not in the absence of root pressure. The precise, continuous and non-destructive measurement of wood water content using frequency domain sensors provides an ideal way to probe many hydraulic processes in large tree trunks that are otherwise difficult to investigate.
DOI: 10.17903/fk2/eawwd9
title: Χρήση Διαδικτύου και Κοινωνικές Σχέσεις

description: Στο συγκεκριμένο έργο δεδομένων βρείτε όλα τα αρχεία και το συνοδευτικό υλικό που χρησιμοποιούνται στο βιβλίο "Μέθοδοι συλλογής δεδομένων με τη χρήση ηλεκτρονικού ερωτηματολογίου και μεθοδολογία έρευνας" και για την έρευνα "Χρήση Διαδικτύου και Κοινωνικές Σχέσεις" που διέπει το σύνολο του βιβλίου. Όπως επισημαίνεται στο τρίτο κεφάλαιο του συγγράμματος το κεντρικό ερευνητικό πρόβλημα τίθεται ως εξής: “Ποιες σχέσεις αναπτύσσουν οι Έλληνες εντός και εκτός διαδικτύου;” ενώ τα ερευνητικά ερωτήματα που τέθηκαν είναι τα ακόλουθα: ΕΕ1:Τι είδους σχέσεις επιδιώκουν να αναπτύξουν τα άτομα στο διαδίκτυο και σε ποιο βαθμό; ΕΕ2:Εντοπίζονται διαφοροποιήσεις στο διαδικτυακό κοινωνικό κεφάλαιο που αναπτύσσουν τα άτομα, αναλόγως με το κοινωνικο-δημογραφικό τους προφίλ; ΕΕ3:Ποια η συσχέτιση της διαπροσωπικής εμπιστοσύνης με τις διαστάσεις του διαδικτυακού κοινωνικού κεφαλαίου; ΕΕ4:Ποια από τις διαστάσεις του διαδικτυακού κοινωνικού κεφαλαίου ερμηνεύει περισσότερο τη διαπροσωπική εμπιστοσύνη; ΕΕ5:Τι είδους σχέσεις επιδιώκουν να αναπτύξουν τα άτομα στην καθημερινή τους ζωή -εκτός διαδικτύου - και σε ποιο βαθμό; ΕΕ6:Εντοπίζονται διαφοροποιήσεις στο κοινωνικό κεφάλαιο που αναπτύσσουν τα άτομα στην καθημερινή τους ζωή - εκτός διαδικτύου-, αναλόγως με το κοινωνικο-δημογραφικό τους προφίλ; ΕΕ7:Ποιά η συσχέτιση της διαπροσωπικής εμπιστοσύνης με τις διαστάσεις του κοινωνικού κεφαλαίου που αναπτύσσουν τα άτομα στην καθημερινή τους ζωή - εκτός διαδικτύου; ΕΕ8:Ποιά από τις διαστάσεις του κοινωνικού κεφαλαίου - εκτός διαδικτύου - ερμηνεύει περισσότερο τη διαπροσωπική εμπιστοσύνη; ΕΕ9:Ποια είναι τα επίπεδα διαπροσωπικής εμπιστοσύνης εκείνων των ατόμων που έχει παραβιαστεί η ιδωτικότητά τους στο διαδίκτυο ή που θεωρούν ότι οι αξιόπιστες πληροφορίες στο διαδίκτυο είναι λίγες; Tα ως άνω ερευνητικά ερωτήματα απαντώνται στα κεφάλαια 7-9 του βιβλίου. Το ηλεκτρονικό ερωτηματολόγιο της έρευνας είναι διαθέσιμο εδώ.
DOI: 10.5281/zenodo.10304481
title: Dynamics of bacterial recombination in the human gut microbiome — figure data

description: Data associated with Figures 1-6, S1-41 in the manuscript "Dynamics of bacterial recombination in the human gut microbiome" (DOI: 10.1101/2022.08.24.505183)
DOI: 10.5281/zenodo.10304482
title: Dynamics of bacterial recombination in the human gut microbiome — figure data

description: Data associated with Figures 1-6, S1-41 in the manuscript "Dynamics of bacterial recombination in the human gut microbiome" (DOI: 10.1101/2022.08.24.505183)
DOI: 10.5066/p9que6dv
title: Adult mosquito and butterfly exposure to permethrin and relative risk following ULV sprays

description: This dataset contains data of permethrin residues on adult mosquitoes and adult butterflies following their exposure to ultra-low volume (ULV) sprays containing permethrin. The dataset also contains toxicity information for permethrin; first for adult mosquitoes and adult butterflies following their exposure to the ULV sprays, and for adult mosquitoes exposed during toxicity tests to determine median lethal dose levels (LD50).
DOI: 10.6084/m9.figshare.24135174
title: <b>Low-cost SNP array for genotype imputation optimized for breeding programs in the fish pacu </b><b><i>Piaractus mesopotamicus</i></b>

description: Pacu (<i>Piaractus mesopotamicus</i>) is one of the main native fish species for aquaculture in South America. Cost-effective genotyping strategies, involving low-density SNP arrays followed by genotype imputation, can facilitate the broader adoption of genomic selection for this species. In this study, we developed a 1K SNP array to be applied with genotype imputation strategies in breeding program of pacu. First, we assessed imputation accuracy across various SNP densities (9K, 7K, 5K, 2K, 1K, and 0.5K) from the commercial <i>Axiom 30 K SerraSNP</i> array to select the best subset for further analysis. Then, 15,166 (91.1%) imputed SNPs with high accuracy were obtained when we selected 1,068 SNPs to comprise the 1K SNP array (average accuracies of 0.90 ± 0.12 at the SNP level and 0.92 ± 0.06 for 290 genotyped individuals). The 1K SNP array was developed using the <i>Agriseq tGBS</i> platform. In the evaluation of array performance using 95 individuals, no discordant genotyping was observed between the <i>Agriseq tGBS</i> platform and the <i>Axiom 30 K SerraSNP</i> array. Ninety-one individuals had a call rate of 90% and above, and 92% of the SNPs were identified in at least 90% of the samples. Additionally, an average minor allele frequency (MAF) of 0.356 (± 0.108) and individual heterozygosity values ranging from 0.321 to 0.470 were found. The results showed that the constructed low-density SNP array exhibited high imputation accuracies and can explore genetic variations within pacu populations, making it a cost-effective tool for enhancing pacu production through genomic selection.
DOI: 10.57830/2301723
title: Southern Colorado Plateau Network Aquatic Macroinvertebrate Data Package for 2007-2019

description: Data in this package were collected from 2007-2019 as part of the Southern Colorado Plateau Network's long-term aquatic macroinvertebrate monitoring program. Data and subsequent analyses can be found in Cross References.
DOI: 10.6073/pasta/e286e622135a2d4171adb37de2e7c0a0
title: Monitoring Amphibians in the Declined Hemlocks at Harvard Forest 2013-2014

description: Disturbances such as outbreaks of nonnative insects and pathogens can devastate unique habitats and directly reduce biodiversity. The foundation tree species Tsuga canadensis (eastern hemlock) is declining due to infestation by the nonnative insect Adelges tsugae (hemlock woolly adelgid). The decline and expected elimination of hemlock from northeastern US forests is changing forest structure, function, and assemblages of associated species. We assessed changes in occupancy, detection probability, and relative abundance of two species of terrestrial salamanders, Plethodon cinereus (eastern red-back salamander) and Notopthalmus viridescens viridescens (eastern red-spotted newt), in the experimental removal of T. canadensis at Harvard Forest. Four treatments (logging, girdling, hemlock control and hardwood control) have been applied and replicated in eight 0.81-ha plots. Salamanders were sampled under cover boards and using visual encounter surveys in June-July of 2013 and 2014.
 Removal of the hemlock canopy increased occupancy of P. cinereus but significantly reduced its estimated detection probability and abundance. Estimated abundance of N. v. viridescens also declined dramatically after canopy manipulations. Our results suggest that ten years after hemlock loss due to either the adelgid or pre-emptive salvage logging, and 50-70 years later when these forests have become mid-successional mixed deciduous stands, that the abundance of these salamanders likely will be less than 50% of their abundance in current, intact hemlock stands.
DOI: 10.5519/qd.fcpzwsbn
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3278056 records)
DOI: 10.6073/pasta/6fd68596ded940145e9a1080e1e1b1c5
title: Prospect Hill Forest Plots at Harvard Forest 2013

description: Northern temperate forests function as an important carbon sink in the global carbon budget. Eddy covariance and plot-based measurements indicate that the Harvard Forest carbon sink is substantial and that the rate of carbon sequestration has increased over the past 20 years. A synthesis effort is underway to better understand how forest development, response to disturbance, and dominant tree species drive the patterns and mechanisms of forest carbon dynamics at the Harvard Forest. The goal of this project is to sample and analyze forest carbon stocks and dynamics across a suite of permanent plots established in 1937 and re-measured in 1992 in order to understand how and why forest carbon stocks have changed between 1937 and 2013. Data from this suite of plots will give spatial and temporal context to a synthesis of detailed, site-specific permanent forest plot studies. Other goals, such as vegetation biodiversity, and a more detailed study of root patterns in soils and belowground carbon distribution, are of strong interest but not addressed in detail in this sampling effort.
DOI: 10.5519/qd.ikmadcjp
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6073/pasta/d00665061c754109ac8ab66d6ab8ae12
title: Baseline Plant Abundances on Garlic Mustard Experiment Plots at Harvard Forest 2013

description: This is a five year project that investigates the reassembly of soil fungi and native plants in forests affected by biological invasion. The experiment brings together regional land managers to create comparative eradications of garlic mustard at nine distinct sites along a natural climate and nitrogen deposition gradient in New England. This dataset represents baseline plant abundances from 2013 at nine study plots in Harvard Forest. Species richness, Shannon diversity, and Pielou’s evenness were not different between invaded and non-invaded plots at Harvard Forest.