cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5tb0z59k
title: MassIVE MSV000093633 - Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate
title: Native top-down mass spectrometry is a powerful structural biology tool that can localize post-translational modifications, explore ligand-binding interactions, and elucidate the three-dimensional structure of proteins and protein complexes in the gas-phase. Fourier-transform ion cyclotron resonance-MS offers distinct capabilities for nTDMS, owing to its ultra-high resolving power, mass accuracy, and robust fragmentation techniques. Previous nTDMS studies using FTICR have mainly applied to over-expressed recombinant proteins and protein complexes. Here, we report the first nTDMS study that directly analyzes human heart tissue lysate by direct infusion FTICR-MS without prior chromatographic separation strategies. We have achieved comprehensive nTDMS characterization of cardiac contractile proteins that play critical roles in heart contraction and relaxation. Specifically, our results reveal structural insights into ventricular myosin light chain 2, ventricular myosin light chain 1, and alpha-tropomyosin in the sarcomere, the basic contractile unit of cardiac muscle. Furthermore, we localize the calcium binding domain in MLC-2v. In summary, our nTDMS platform extends the application of FTICR-MS to directly characterize the structure, PTMs, and metal-binding of endogenous proteins from heart tissue lysate without prior separation methods.
DOI: 10.6073/pasta/af2da50d4f72d3f1f76fae102785700a
title: Ants in an Induced Drought Experiment at the Caxiuana National Forest in Brazil 2011-2012

description: Environmental change scenarios caused by low precipitation forecast species loss in tropical regions. We used one year of data from a rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress, and covarying changes in humidity, soil respiration, and tree species richness, size, and total biomass and its diversity affected species richness and composition (relative abundance) of ground-dwelling ants. Induced drought reduced ant richness, whereas increased humidity and variability in biomass increased it. Species composition differed between control and rainfall-excluded plots. Occurrence of many ant species was strongly reduced, but some generalist groups of ants were favored by induced drought. The expected loss of ant species and changes in ant species composition in tropical forests likely will lead to cascading effects on ecosystem processes and services they mediate.
DOI: 10.6073/pasta/092d12d3379d682fc9264f7f8182febf
title: Ant Resource Detection Distance at the Caxiuana National Forest in Brazil 2017-2018

description: Environmental change scenarios of low precipitation forecast species loss in tropical regions. These losses can affect generalist species that provide important ecosystem services, such as controlling the rate at which nutrients become available for uptake by other organisms in tropical forests. Here, we use a long-term rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress affects the detection distance of food resources (baits) in a generalist ant guild (number of colonies, richness, and composition) that remove resources on the ground. We found that (i) overall the distance of resource removal by generalist ants did not change with drought; (ii) however, comparing ant species that occurred in drought-induced and control environments, workers walked shorter distances in the drought habitat; (iii) the number of resources detected by ant colonies in the drought-induced habitat decreased by 50%. Although generalist ants are considered resilient to habitat disturbance, the effect of reduced rainfall can negatively affect the services mediated by them. The rate of removal and consumption of resources in tropical forests may be related to abundance of generalist ants; losses in both nest density and walking distances may cause cascading effects on ecosystem processes and the services they mediate.
DOI: 10.3886/e195543v1
title: Time-Restricted Eating Experiences & Perspectives (TREEP) Study

description: Given
that thirteen cancers are associated with obesity, and 70% of US adults have
overweight/obesity currently, weight loss interventions are
a priority area for cancer prevention and control efforts. A
growing literature describes the public
interest and potential benefits of time-restricted
eating (TRE), a novel dietary approach which restricts the
time of eating, but not the amount or type of calories consumed. Recent
evidence suggests that TRE positively impacts metabolic health and weight
loss. The relative flexibility and simplicity of
TRE may enable individuals to adhere to the diet for longer periods
of time, which is critical for weight loss maintenance. However, TRE may also pose
challenges for individuals with less control over their schedules, leading to
reduced adherence over time. Knowledge of TRE facilitators and
barriers is needed to illuminate the viability of this dietary strategy as a
sustainable mechanism for both prevention and management of obesity and
resultant cancers. The TREEP mixed methods study is the first to explore
perceptions of TRE and the multi-level factors that act as facilitators
and barriers to long-term adherence. <br><br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov<br>
description: Eligibility criteria: US adult ages 18+ who
currently or formerly (past three months) followed TRE (i.e., consumed all
daily calories within a window of ≤ 12 hours) for a minimum of one week.
description: web-based survey; Collected via Prolific.<br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov
DOI: 10.3886/e195543v2
title: Time-Restricted Eating Experiences & Perspectives (TREEP) Study

description: Given
that thirteen cancers are associated with obesity, and 70% of US adults have
overweight/obesity currently, weight loss interventions are
a priority area for cancer prevention and control efforts. A
growing literature describes the public
interest and potential benefits of time-restricted
eating (TRE), a novel dietary approach which restricts the
time of eating, but not the amount or type of calories consumed. Recent
evidence suggests that TRE positively impacts metabolic health and weight
loss. The relative flexibility and simplicity of
TRE may enable individuals to adhere to the diet for longer periods
of time, which is critical for weight loss maintenance. However, TRE may also pose
challenges for individuals with less control over their schedules, leading to
reduced adherence over time. Knowledge of TRE facilitators and
barriers is needed to illuminate the viability of this dietary strategy as a
sustainable mechanism for both prevention and management of obesity and
resultant cancers. The TREEP mixed methods study is the first to explore
perceptions of TRE and the multi-level factors that act as facilitators
and barriers to long-term adherence. <br><br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov<br>
description: Eligibility criteria: US adult ages 18+ who
currently or formerly (past three months) followed TRE (i.e., consumed all
daily calories within a window of ≤ 12 hours) for a minimum of one week.
description: web-based survey; Collected via Prolific.<br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov
DOI: 10.3886/e195543v3
title: Time-Restricted Eating Experiences & Perspectives (TREEP) Study

description: Given
that thirteen cancers are associated with obesity, and 70% of US adults have
overweight/obesity currently, weight loss interventions are
a priority area for cancer prevention and control efforts. A
growing literature describes the public
interest and potential benefits of time-restricted
eating (TRE), a novel dietary approach which restricts the
time of eating, but not the amount or type of calories consumed. Recent
evidence suggests that TRE positively impacts metabolic health and weight
loss. The relative flexibility and simplicity of
TRE may enable individuals to adhere to the diet for longer periods
of time, which is critical for weight loss maintenance. However, TRE may also pose
challenges for individuals with less control over their schedules, leading to
reduced adherence over time. Knowledge of TRE facilitators and
barriers is needed to illuminate the viability of this dietary strategy as a
sustainable mechanism for both prevention and management of obesity and
resultant cancers. The TREEP mixed methods study is the first to explore
perceptions of TRE and the multi-level factors that act as facilitators
and barriers to long-term adherence. <br><br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov<br>
description: Eligibility criteria: US adult ages 18+ who
currently or formerly (past three months) followed TRE (i.e., consumed all
daily calories within a window of ≤ 12 hours) for a minimum of one week.
description: web-based survey; Collected via Prolific.<br>To request access to the data, please email the NCI Risk Factor Assessment Branch: rfab@mail.nih.gov
DOI: 10.6084/m9.figshare.24774222
title: BigWig files for developing human retina by cell major class

description: BigWig files for developing human retina by cell major class
DOI: 10.6084/m9.figshare.24774222.v4
title: BigWig files for developing human retina by cell major class

description: BigWig files for developing human retina by cell major class
DOI: 10.6084/m9.figshare.24774222.v3
title: TileSize-100-normMethod-None-ArchR.bw

description: Development Retina
DOI: 10.5281/zenodo.10354805
title: Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes - Gutnik et al - Tracing Datasets

description: Tracing datasets (MATLAB Structure Format) from C.elegans N2 and HI embryos, as well as N2:HI and HI:N2 hybrid embryos presented in Gutnik et al.2024 (Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes)
DOI: 10.5281/zenodo.10354806
title: Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes - Gutnik et al - Tracing Datasets

description: Tracing datasets (MATLAB Structure Format) from C.elegans N2 and HI embryos, as well as N2:HI and HI:N2 hybrid embryos presented in Gutnik et al.2024 (Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes)
DOI: 10.6073/pasta/d985e9688414db60119edbf16a3f99fb
title: Lymantria dispar Defoliation Survey at the Quabbin Watershed in Central Massachusetts 2017

description: For most of the 20th century, the invasive Lymantria dispar was the most serious insect threat to forests and shade trees in the northeastern United States, but outbreaks have been sporadic and light since 1989, after the successful establishment of a fungal pathogen, Entomophaga maimaiga. However, in 2016 a surprising new outbreak of Lymantria dispar began in southern New England, resulting in dramatic oak (Quercus spp.) mortality across thousands of forested hectares by 2018. In 2017, during the height of the outbreak, a rapid assessment of defoliation across 486 plots in six clusters (aka ‘hotspots’) across the Quabbin Watershed Forest in central Massachusetts was conducted. These sample points can be related to satellite-based defoliation estimates, and the tree and site data analyzed for predictors of defoliation severity.
DOI: 10.5519/qd.vzn0irbj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3716 records)
DOI: 10.6073/pasta/f9f5fc54a7429ef53367b66f9d8c6598
title: Tree Ring Data from the Lyford Mapped Tree Plot at Harvard Forest 1861-2014

description: Is it possible to reconstruct aboveground carbon/biomass from tree rings? If so, how far back in time can researchers go when using tree-ring data in the reconstruction of past biomass? Answers to these questions will have a significant impact on our understanding of dynamics in the terrestrial carbon sink. Long tree-ring records of biomass can reveal intra-annual to annual to multidecadal variations that cannot be resolved by forest census data that is not conducted annually. Additionally, while these dynamics might be resolved using remote sensing, most remotely-sensed products are only two decades or less in length. By having long records of carbon biomass, we can then identify not only the dominant drivers of biomass, but how the importance of these drivers might change during different eras as environmental factors change (e.g., climate, air pollution, disturbance). To test these and other questions, we collected tree-ring records from three 20m radius plots set within the Lyford Plot at the Harvard Forest. The Lyford Plot has been remeasured, on average, decadally since 1969. We can convert these data to biomass using allometric equations and compare tree-ring inferred aboveground biomass to the census data going back in time. Dye et al. (2016) have shown that these data fall within the range of uncertainty of census data sampled in similar plots going back to 1969. 
 Dye, A., Barker Plotkin, A., Bishop, D., Pederson, N., Poulter, B. and Hessl, A., 2016. Comparing tree‐ring and permanent plot estimates of aboveground net primary production in three eastern US forests. Ecosphere, 7(9).
DOI: 10.6073/pasta/66f633f17af5eda2f964aa018ced480b
title: Land Zones in New England 1940-2070 from 2017 Wildlands and Woodlands Report

description: This dataset contains two GIS datalayers, one CSV file and an associated R script used to produce figures for the 2017 Wildlands and Woodlands report. The “wedge diagram” data (HF360-01-landcover-data.csv) shows actual percent landcover estimates across New England from 1940 to 2010 and straight-line trends needed between 2010 to 2070 to reach the Wildlands and Woodland vision by 2060. The published diagram can be seen in figure 1 of the 2017 Wildlands and Woodland report.
 In hf360-03-community-forests.zip, the GIS layer shows towns that contain community forests as determined by the authors of the report.
 In hf360-04-wildland-woodland-zones.zip, the GIS layer shows Wildland and Woodland Zones as illustrated in the report. It was created by starting with the Wildland and Woodland zones from the 2010 report and adding in areas with high agricultural land use. These types are meant to be conceptual and not prescriptive.
 
 
 Wildlands and Woodlands Report:
 Foster, D. R., Lambert, K. F., Kittredge, D. B., Donahue, B. M, Hart, C. M., Labich, W. G., Meyer, S., Thompson, J. , Buchanan, M., Levitt, J. N., Pershel, R., Ross, K., Elkins, G., Daigle, C., Hall, B., Faison, E. K., D'Amato, A. W., Forman, R. T. T., Del Tredici, P., Irland, L. C., Colburn, B. A., Orwig, D. A., Aber, J. D., Berger, A., Driscoll, C. T., Keeton, W. S., Lilieholm, R. J., Pederson, N., Ellison, A. M., Hunter, M. L., Fahey, T. J. 2017. Wildlands and Woodlands, Farmlands and Communities: Broadening the Vision for New England.
DOI: 10.25345/c5pk07c4b
title: MassIVE MSV000093634 - Ancestral allele of DNA polymerase gamma modifies mammalian antiviral tolerance
title: We report that the mitochondrial DNA (mtDNA) replicase POLG has a role in antiviral defence mechanisms to double-stranded DNA and positive-strand RNA virus infections (HSV-1, TBEV, SARS-CoV-2) and its p.W748S variant dampens innate immune responses. Our knock-in mouse data show that p.W748S compromises mtDNA replisome stability, causing mtDNA depletion, aggravated by virus infection. Low mtDNA and mtRNA release to cytoplasm and slow interferon response in MIRAS allow an early replicative advantage for viruses, leading to augmented proinflammatory response, progressive loss of GABAergic neurons, liver inflammation and necrosis. Our evidence suggests that POLG1 defects compromise antiviral tolerance, triggering epilepsy and liver disease.
DOI: 10.34740/kaggle/dsv/7098986
title: Reddit r/Jokes Dataset
DOI: 10.6084/m9.figshare.24786660.v3
title: Triatomine bug pictures from “Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms

description: Triatomine bug pictures from "Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms" (under review, Ecological Informatics, Elsevier; print ISSN: 1574-9541; online ISSN: 1878-0512). The access link will be available on the article web page upon publication.
DOI: 10.6073/pasta/556da43b5e8ed5ac8d3eabb09d046eea
title: Tree Ring Data from the Harvard Forest EMS Tower 1896-2014

description: Is it possible to reconstruct aboveground carbon/biomass from tree rings? If so, how far back in time can researchers go when using tree-ring data in the reconstruction of past biomass? Answers to these questions will have a significant impact on our understanding of dynamics in the terrestrial carbon sink. Long tree-ring records of biomass can reveal intra-annual to annual to multidecadal variations that cannot be resolved by forest census data that is not conducted annually. Additionally, while these dynamics might be resolved using remote sensing, most remotely-sensed products are only two decades or less in length. By having long records of carbon biomass, we can then identify not only the dominant drivers of biomass, but how the importance of these drivers might change during different eras as environmental factors change (e.g., climate, air pollution, disturbance). To test these and other questions, we collected tree-ring records from two 20m radius plots set within the footprint of the EMS tower plot at the Harvard Forest installed and continuously operated since 1989. We can convert these data to biomass using allometric equations and compare tree-ring inferred aboveground biomass to the census data going back in time. Dye et al. (2016) have shown that these data fall within the range of uncertainty of census data sampled in the Harvard Forest Lyford plot going back to 1969.
 Dye, A., Barker Plotkin, A., Bishop, D., Pederson, N., Poulter, B., Hessl, A. 2016. Comparing tree-ring and permanent plot estimates of aboveground net primary production in three eastern U.S. forests. Ecosphere 7: e01454.
DOI: 10.6084/m9.figshare.24786660
title: Triatomine bug pictures from “Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms"

description: Triatomine bug pictures from "Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms" (under review, Ecological Informatics, Elsevier; print ISSN: 1574-9541; online ISSN: 1878-0512). The access link will be available on the article web page upon publication.
DOI: 10.6084/m9.figshare.24786660.v5
title: Triatomine bug pictures from “Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms"

description: Triatomine bug pictures from "Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms" (under review, Ecological Informatics, Elsevier; print ISSN: 1574-9541; online ISSN: 1878-0512). The access link will be available on the article web page upon publication.
DOI: 10.6084/m9.figshare.24786660.v4
title: “Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms"

description: Triatomine bug pictures from "Cellphone picture-based, genus-level automated identification of Chagas disease vectors: effects of picture orientation on the performance of five machine-learning algorithms" (under review, Ecological Informatics, Elsevier; print ISSN: 1574-9541; online ISSN: 1878-0512). The access link will be available on the article web page upon publication.
DOI: 10.6073/pasta/fb788fc1526a3875556d9bea872a12b9
title: Interagency Ecological Program and US Fish and Wildlife Service: Juvenile/Larval Fish and Zooplankton collections at Liberty Island, California 2002-2005 & 2013-2019

description: The U.S. Fish and Wildlife Service (USFWS) Lodi Fish and Wildlife Office (LFWO) Delta Juvenile Fish Monitoring Program (DJFMP) has intermittently sampled Liberty Island with various equipment since 2002. Liberty Island was a reclaimed agricultural island until it flooded in 1997-1998 and we subsequently left to passively restore as a tidally influenced wetland. Larval trawls and beach were the only sampling methods used during both early (2002-2005) and late (2009-2019) sampling periods. The main purpose of the sampling was to gather information about fish presence and abundance in Liberty Island during the passive restoration, with an emphasis on reproductive and early life-stages of native species. Larval trawls, or tow nets, were used to catch larval fish in 2004-2005 and again from 2013-2019. Zooplankton nets were used 2013-2019. Water quality measurements were collected alongside each tow.
DOI: 10.6073/pasta/26f4084a3fe8caa653ac070f10f41ef4
title: Tree Ring Data from Goose Egg State Forest NY 1681-2014

description: Is it possible to reconstruct aboveground carbon/biomass from tree rings? If so, how far back in time can researchers go when using tree-ring data in the reconstruction of past biomass? Answers to these questions will have a significant impact on our understanding of dynamics in the terrestrial carbon sink. Long tree-ring records of biomass can reveal intra-annual to annual to multidecadal variations that cannot be resolved by forest census data that is not conducted at annual time steps. Additionally, while these dynamics might be resolved using remote sensing, most remotely-sensed products are only two decades or less in length. By having long records of carbon biomass, we can then identify not only the dominant drivers of biomass, but how the importance of these drivers might change during different eras as environmental factors change (e.g., climate, air pollution, disturbance).
 To test these and other questions, we collected tree-ring records from three 30m radius plots set in Goose Egg State Forest in New York State. We chose this location because it has old oak dominated forests that can be compared to the long-term forests being studied for carbon dynamics at the Harvard Forest. We can convert these data to biomass using allometric equations and compare tree-ring inferred aboveground biomass to the census data going back in time to understand forest recovery and carbon dynamics in a heavily disturbance forest. Recruitment dates for some of the trees from these plots have been published in Pederson et al. (2017).
 Pederson, N., Young, A. B., Stan, A. B., Ariya, U., Martin-Benito, D. 2017. Low-Hanging DendroDynamic Fruits Regarding Disturbance in Temperate, Mesic Forests. In: Amoroso, M. M., Daniels, L. D., Baker, P. J., Camarero, J. J., Dendroecology: Tree-Ring Analyses Applied to Ecological Studies, Springer, Cham., Switzerland.
DOI: 10.5519/qd.9zo9a8dd
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (12 records)