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Herb Survey: Effect of Burning Patterns on Vegetation in the Fish Lake Burn Compartments
This study examines the effects of long-term prescribed burning treatments on vegetation structure and composition, productivity, and nutrient cycling in upland oak savanna and woodland vegetation. The basis for the study is an ongoing, experimental prescribed burning program begun in 1964 at Cedar Creek, and a similar program operating since 1962 on the adjacent Helen Allison Savanna property (owned by The Nature Conservancy). These prescribed burning programs are designed to subject upland oak communities (and some old fields) to different burn frequencies and patterns of burning, with the ultimate objectives of 1) restoring and maintaining the historically important savanna and open woodland vegetation, and 2) providing information about the effects of different burning patterns on vegetation structure and composition. This study addresses the latter of these two purposes and expands on it by also investigating possible influences of fire on resource availability (nutrients, water, and light) and net primary productivity. This study represents a continuation and expansion of experiments 015 and 094.
Data and Code in support of Caterpillar abundance in a northern hardwood forest: exogenous effects, endogenous feedbacks, and multidecadal trends.
In this study, we analyzed caterpillar abundance and biomass measured over 50 years (1970 - 2021) in the Hubbard Brook Experimental Forest, New Hampshire, USA. We tested mechanisms for determination of caterpillar abundance that included weather, host plant quality, and predator abundance. This dataset includes data, R code, and spatial files supporting this study. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Short-Term Effects on Vegetation in Soil Warming Plus Nitrogen Addition Experiment at Harvard Forest 2006
The purpose of this experiment is to examine the interactive affects of warming and N additions on plant diversity. The experiment consists of four treatments (control, heated +N, heated -N, +N only) with six replicates per treatment in a completely randomized design. Average soil temperature in the heated plots will be elevated 5 deg C above ambient by the use of buried heating cables placed at 10 cm depth in the soil and spaced 20 cm apart. The heating cables will be controlled by a data logger that monitors thermistors (5 per plot) every 10 min. Plots will automatically turn on and off to maintain a 5 deg C temperature difference between the heated and control plots. The N addition plots (heated +N, +N only) will be fertilized following the protocol of the Chronic Nitrogen Addition Study. An aqueous solution of NH4NO3 will be applied at a rate equivalent to the low N plots at the chronic N study (5 g m-2 yr-1). Fertilizer will be applied in equal monthly doses during the growing season (Apr-Oct). The control plots and unfertilized, heated plots (heated -N) will receive water only.
Effects of Warming on Soil Microbial Oxidative Activity at Harvard Forest 2013
As Earth’s climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community’s capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
Effects of Long-Term Soil Warming on Ecosystem Function at Harvard Forest 2019
Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.
Effects of Long-Term Soil Warming on Microbial Yield, Acquisition, and Stress Traits at Harvard Forest 2014
Soil microbial traits drive ecosystem functions. This relationship can explain why microbial functional diversity is typically positively correlated with ecosystem function. However, microbial adaptation to climate change related warming stress can shift microbial traits with direct implications for carbon cycling in the soil. Here, we investigated how long-term warming affects the relationship between microbial trait diversity and ecosystem function. Soils were sampled after 24 years of +5\degree C warming alongside unheated control soils from the Harvard Forest Long-Term Ecological Research site. Ecosystem function was estimated from six different enzyme activities and microbial biomass. This data was coupled with metatranscriptomics sequencing, where reads were assigned to yield, acquisition, or stress trait categories. We found that in organic horizon soils, warming decreased the richness of acquisition-related traits. In the mineral soils, we observed that heated soils exhibited a negative relationship with the richness of acquisition related traits. These results suggest that the microbial communities exposed to long-term warming is shifting away from a resource acquisition life history strategy.
GPH01 Grazing management effects on pollinator communities and habitat at Konza Prairie, 2024-2025
For all data files, data were collected in Konza Prairie LTER sites: N1A, N1B, C1A, K1B, and 1D during May, July, and August in both 2024 and 2025. The goal was to investigate variation in pollinator foraging and nesting habitat and in foraging and nesting pollinator communities across grazing regimes. Details for each file follow: 1. Plant-pollinator interactions (file = pollinatorNetworks); 2. Bees collected from ground nests (file = nestingBees); 3. Floral resources observed along transects (file = floralResources); 4. Bare ground cover and vegetation height measured along transects (file = otherHabitat); 5. Soil characteristics (file = soils)
MCR LTER: Coral Reef: Modeling the effects of selectively fishing key functional groups of herbivores on coral resilience; data for Cook et al., 2023 Ecosphere
These data and code were generated in support of the manuscript: Cook DT, Schmitt RJ, Holbrook SJ, and HV Moeller, Ecosphere. To investigate the impacts of selectively harvesting functional groups of herbivorous fishes on coral resilience, we used a dynamic model that is grounded by the coral reef system in Moorea, French Polynesia. Our model simulates the fraction of a reef occupied through time by classes of key benthic spaceholders (coral, two stages of macroalgae, and turf). Benthic and fishing dynamics are linked through the harvesting of two functional groups of herbivorous fishes. We utilize data collected on the abundance of fishes on the reef and in the catch in Moorea, French Polynesia to inform our model and to empirically explore patterns of fishing selectivity. These data and code were published in Ecosphere and were a part of the thesis of D. Cook (2023). This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
Urban Residential Surface and Subsurface Hydrology: Synergistic Effects of Low-Impact Features at the Parcel Scale
Accurately predicting the hydrologic effects of urbanization requires an understanding of how hydrologic processes are affected by low‐impact development practices. In this study, we explored how growing season surface runoff, deep drainage, and evapotranspiration on a residential parcel are affected by several low‐impact interventions, including three "impervious‐centric" interventions (disconnecting downspouts, disconnecting sidewalks, and adding a transverse slope to the driveway and front walk), two "pervious‐centric" interventions (decompacting soil and adding microtopography), and all possible "holistic" combinations. Results were compared to both a highly and moderately compacted baseline parcel under an average and a dry weather scenario for a temperate climate. We find that under reasonable assumptions for highly compacted soil, pervious areas are a major source of runoff and disconnecting impervious surfaces may be relatively less effective without improving soil conditions. Under both highly and moderately compacted soil conditions, combining efforts to decompact soil with impervious disconnection has a synergistic effect on reducing surface runoff and increasing deep drainage and evapotranspiration. All combinations of interventions enhance infiltration, but the partitioning of additional root zone water between deep drainage and evapotranspiration depends on the weather scenario. Importantly, when all low‐impact interventions are applied together, growing season deep drainage is higher than that from a vacant lot with no impervious surfaces. We infer that ecohydrologic interfaces between impervious and pervious areas are strong controls on urban hydrologic fluxes and that high‐resolution, process‐based models can be used to account for these interfaces and thereby improve predictions of the hydrologic effects of low‐impact interventions.
Cascade Project at North Temperate Lakes LTER: Aquatic heatwave effects on chlorophyll 2008-2019
Temperature and chlorophyll data were collated from multiple datasets to identify the effects of aquatic heatwaves on phytoplankton in three north temperate lakes, Peter Lake, Paul Lake, and Tuesday Lake between 2008 and 2019. Heatwaves were identified using a water temperature model constructed from temperature data from Sparkling Lake and Woodruff Airport between 1989 and 2022. Heatwave characteristics, water color, nutrients, grazing, and lake stability data are included to relate chlorophyll response to heatwaves to other conditions associated with a set of whole-lake experiments. The food web of Peter Lake was manipulated with largemouth bass additions between 2008 and 2011. Nutrient additions were made to Peter Lake and Tuesday Lake between 2013 and 2015, and again in Peter Lake in 2019. Paul Lake was always maintained as an unmanipulated reference lake. Full descriptions of the experiments can be found in Szydlowski et al., "Aquatic heatwaves increase surface chlorophyll concentrations in experimental and reference lakes."
The physiological effects of non-invasive brain stimulation fundamentally differ across the human cortex
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Dataset / Code: Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy
<p><strong>Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy</strong></p> <p><strong> </strong></p> <p>Harim I. Won<sup>1,#</sup>, Samuel Zinga<sup>1,#</sup>, Olga Kandror<sup>1</sup>, Tatos Akopian<sup>1</sup>, Ian D. Wolf<sup>1</sup>, Jessica T.P. Schweber<sup>1</sup>, Ernst W. Schmid<sup>2</sup>, Michael C. Chao<sup>1</sup>, Maya Waldor<sup>1</sup>, Eric J. Rubin<sup>1,*</sup>, Junhao Zhu<sup>1,3,*</sup></p> <p><strong> </strong></p> <p><sup>1</sup>Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.</p> <p><sup>2</sup>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts 02115, USA.</p> <p><sup>3</sup>CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.</p> <p><sup>#</sup>These authors contributed equally to this work.</p> <p>*Corresponding authors: <a href="mailto:zhujh@im.ac.cn">zhujh@im.ac.cn</a> (J.Z.), <a href="mailto:erubin@hsph.harvard.edu">erubin@hsph.harvard.edu</a> (E. J. R.)</p> <p><strong> </strong></p> <p><strong>Abstract</strong></p> <p>Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in <em>Mycobacterium smegmatis </em>(<em>Msm</em>)<em>, </em>a model for the human pathogen <em>M. tuberculosis </em>(<em>Mtb</em>). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential <em>Msm </em>proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future <em>Mtb</em> PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.</p> <p> </p>
Cirrus formation regimes - Data driven identification and quantification of mineral dust effect
<p>This repository contains the data for the paper: </p> <p>Authors: Kai Jeggle , David Neubauer , Hanin Binder and Ulrike Lohmann<br>Titel: Cirrus formation regimes - Data driven identification and quantification of mineral dust effect<br>Date: 2024</p> <p>Note that the scripts can be found in the accompanying code repository (https://github.com/tabularaza27/cloud_clustering)<br><br>Contents:<br><br>├── cirrus_cloud_trajectories.ftr<br>├── cluster_input_data.ftr<br>├── cluster_models<br>│ └── temperature_clustering_k4_12<br>│ ├── cloud_ids.npy<br>│ ├── model_params.json<br>│ └── trained_model.hdf5</p> <p>│ └── temperature_clustering_k4_24<br>│ ├── cloud_ids.npy<br>│ ├── model_params.json<br>│ └── trained_model.hdf5</p> <p>├── cluster_predictions.ftr<br>└── readme.txt<br><br>For more info, please have a look at the <em>readme.txt</em><br><br>This is an updated version of the data, containing updated models and predictions based on the Journal revisions</p>
Accounting for local temperature effect substantially alters afforestation patterns - data
<p>Output data produced in "Accounting for local temperature effect substantially alters afforestation patterns"</p> <p>Contact: michael.gregory.windisch@alumni.ethz.ch</p> <p>Content: Output of the partial equilibrium model MAgPIE (https://github.com/magpiemodel/magpie) version v4.3.1-BGP (https://github.com/magpiemodel/magpie/tree/v4.3.1-BGP) documentation (<a href="https://rse.pik-potsdam.de/doc/magpie/4.3.1/">https://rse.pik-potsdam.de/doc/magpie/4.3.1/</a>). Archived are all runs performed to obtain data and figures for the main assessment (main_output.zip) and the two sensitivity experiments (sensitivity_output_globalTCRE.zip; sensitivity_output_plantation.zip).</p> <p> </p> <p>Naming key:</p> <p>main_output control runs: BPHfillexp_ann_nobgp_{SSP}_noBECCS</p> <p>main_output experiment runs: BPHfillexp_ann_bph_{SSP}_local_{TCRE uncertainty}_noBECCS</p> <p>sensitivity analysis for global TCRE control runs: BPHfillexp_ann_nobgp_{SSP}_noBECCS</p> <p>sensitivity analysis for global TCRE experiment runs: BPHfillexp_ann_bph_{SSP}_global_{TCRE uncertainty}_noBECCS</p> <p>sensitivity analysis for plantation A/R control runs: BPH_plant_nobgp_{SSP}_noBECCS</p> <p>sensitivity analysis for plantation A/R experiment runs: BPH_plant_ann_bph_{SSP}_local_{TCRE uncertainty}_noBECCS</p>
National Survey on the Effects of COVID-19 on the Wellbeing of Mexican Households (ENCOVID-19- DECEMBER 2020)
<p>Amid the COVID-19 outbreak, the ENCOVID-19 provides information on the well-being of Mexican households in four main domains: labor, income, mental health, and food insecurity. It offers timely information to understand the social consequences of the pandemic and the lockdown measures. It is a project consisting of a series of cross-sectional telephone surveys collected in key moments of the COVID-19 pandemic. In addition to the four main domains and a set of COVID19-related questions, the survey includes new key indicators every month to capture the impact of the pandemic on issues like education, social programs, and crime. This is the sixth dataset of the project, corresponding to December 2020, collected nine months after the lockdown began in Mexico. Data collection was performed from November 27 to December 11, 2020.</p>
National Survey on the Effects of COVID-19 on the Wellbeing of Mexican Households (ENCOVID-19 - APRIL 2022)
<p>Amid the COVID-19 outbreak, the ENCOVID-19 provides information on the well-being of Mexican households in four main domains: labor, income, mental health, and food insecurity. It offers timely information to understand the social consequences of the pandemic and the lockdown measures. It is a project consisting of a series of cross-sectional telephone surveys collected in key moments of the COVID-19 pandemic. In addition to the four main domains and a set of COVID19-related questions, the survey includes new key indicators every month to capture the impact of the pandemic on issues like education, social programs, and crime. This is the eleventh dataset of the project, corresponding to April 2022, collected 24 months after the lockdown began in Mexico. Data collection was performed from March 17 to May 2, 2022.</p>
National Survey on the Effects of COVID-19 on the Wellbeing of Mexican Households (ENCOVID-19- MAY 2021)
<p>Amid the COVID-19 outbreak, the ENCOVID-19 provides information on the well-being of Mexican households in four main domains: labor, income, mental health, and food insecurity. It offers timely information to understand the social consequences of the pandemic and the lockdown measures. It is a project consisting of a series of cross-sectional telephone surveys collected in key moments of the COVID-19 pandemic. In addition to the four main domains and a set of COVID19-related questions, the survey includes new key indicators every month to capture the impact of the pandemic on issues like education, social programs, and crime. This is the ninth dataset of the project, corresponding to May 2021, collected thirteen months after the lockdown began in Mexico. Data collection was performed from May 21 to Jun 17, 2021.</p>
National Survey on the Effects of COVID-19 on the Wellbeing of Mexican Households (ENCOVID-19- OCTOBER 2021)
<p>Amid the COVID-19 outbreak, the ENCOVID-19 provides information on the well-being of Mexican households in four main domains: labor, income, mental health, and food insecurity. It offers timely information to understand the social consequences of the pandemic and the lockdown measures. It is a project consisting of a series of cross-sectional telephone surveys collected in key moments of the COVID-19 pandemic. In addition to the four main domains and a set of COVID19-related questions, the survey includes new key indicators every month to capture the impact of the pandemic on issues like education, social programs, and crime. This is the tenth dataset of the project, corresponding to October 2021, collected 19 months after the lockdown began in Mexico. Data collection was performed from October 20 to November 13, 2021.</p>
National Survey on the Effects of COVID-19 on the Wellbeing of Mexican Households (ENCOVID-19 - MARCH 2021)
<p>Amid the COVID-19 outbreak, the ENCOVID-19 provides information on the well-being of Mexican households in four main domains: labor, income, mental health, and food insecurity. It offers timely information to understand the social consequences of the pandemic and the lockdown measures. It is a project consisting of a series of cross-sectional telephone surveys collected in key moments of the COVID-19 pandemic. In addition to the four main domains and a set of COVID19-related questions, the survey includes new key indicators every month to capture the impact of the pandemic on issues like education, social programs, and crime. This is the sixth dataset of the project, corresponding to March 2021, collected one year after the lockdown began in Mexico. Data collection was performed from February 26 to March 27, 2021.</p>
Cross cultural tears: A systematic investigation of the interpersonal effects of emotional crying across different cultural backgrounds
<p>The present project wants to examine the importance of emotional crying as an attachment behaviour and its fundamental role across a number of diverse cultures.</p> <p>Emotional tears are uniquely human and have fascinated scholars across several decades (Vingerhoets, 2013). Some researchers argue that tearful crying played a significant role in the evolution of humankind with regard to social development and solidarity (Walter, 2006). Recent years have seen an increased interest in exploring the interpersonal effects of human tears (see Gračanin, Bylsma, & Vingerhoets, 2018 for a review), with findings that emotional tears foster approach or support behavior (Gračanin, Krahmer, Rinck, & Vingerhoets, 2018) and crying individuals being evaluated as more communal (e.g., Zickfeld, van de Ven, Schubert, & Vingerhoets, 2018). These findings generally fit the hypothesis that emotional tears constitute a social act, promote social bonding and fulfill an attachment function (Nelson, 2005; Bowlby, 1982; Gračanin, Bylsma, et al., 2018; Murube, Murube, & Murube, 1999; Radcliffe-Brown, 1922; Vingerhoets, 2013). The present projects aims to answer the question whether emotional tears present a fundamental form of solidarity and bonding and whether the findings on increased attributions of warmth and higher approach intentions for tearful individuals replicate across a number of diverse contexts.</p> <p><a href="https://osf.io/fj9bd">Published in OSF: https://osf.io/fj9bd</a>.</p> <p>The OPen SCience FRamework also includes:</p> <ul> <li>Data from the pilot study: https://osf.io/txcw3/</li> <li>General information about the translation process (including the Portuguese version https://osf.io/t4cas/),</li> <li>Data management and research protocol (https://osf.io/5bh7m/),</li> <li>Approvals from ethical committees (https://osf.io/v8rqh/),</li> <li>Data and descriptive document of supplementary analyses (https://osf.io/s8ack/),</li> <li>Data and syntax (https://osf.io/x2pks/),</li> <li>Information about stimuli (https://osf.io/x2pks/) </li> </ul>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.