cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc27tj1n
title: CCDC 2080101: Experimental Crystal Structure Determination

description: Related Article: Vladimir A. Kulbachinskii, Yan V. Zubavichus, Roman D. Svetogorov, Nikolai S. Ezhikov, Roman A. Lunin, Boris M. Bulychev|2021|Carbon|182|51|doi:10.1016/j.carbon.2021.05.043
DOI: 10.24431/rw1k58u
title: Fish and Invertebrate Bottom Trawl Dataset, Arctic Integrated Ecosystem Research Program, August - September 2019.

description: These data are part of the Arctic IES component of the Arctic Integrated Ecosystem Research Program (IERP), sponsored by the North Pacific Research Board (NPRB), Collaborative Alaskan Arctic Studies Program (formerly the North Slope Borough/Shell Baseline Studies Program), Bureau of Ocean Energy Management (BOEM), and the Office of Naval Research Marine Mammals and Biology Program. To investigate the distribution, life history, and interactions of biological communities in the U.S. Continental Region of the NE Chukchi Sea a survey was conducted from August - September 2019. Demersal fishes and epibenthic fauna were targeted with a 3 m plumb-staff beam trawl. Specimen for additional processing were collected. Catches were processed (see methods). Files included in this dataset are as follows: Haul Data: OS201901BottomTrawlDeploymentDatav2.csv Catch: OS201901BottomTrawlCatchSummary.csv Specimen Collection: OS201901BottomTrawlSpecimenCollection.csv
DOI: 10.24431/rw1k58v
title: Fish and Invertebrate Bottom Trawl Dataset, Arctic Integrated Ecosystem Research Program, August - September 2017

description: These data are part of the Arctic IES component of the Arctic Integrated Ecosystem Research Program (IERP), sponsored by the North Pacific Research Board (NPRB), Collaborative Alaskan Arctic Studies Program (formerly the North Slope Borough/Shell Baseline Studies Program), Bureau of Ocean Energy Management (BOEM), and the Office of Naval Research Marine Mammals and Biology Program. To investigate the distribution, life history, and interactions of biological communities in the U.S. Continental Region of the NE Chukchi Sea a survey was conducted from August - September 2017. Demersal fishes and epibenthic fauna were targeted with a 3 m plumb-staff beam trawl. Specimen for additional processing were collected. Catches were processed (see methods). Files included in this dataset are as follows: Haul Data: OS201701BottomTrawlDeploymentDatav2.csv Catch: OS201701BottomTrawlCatchSummary.csv Specimen Collection: OS201701BottomTrawlSpecimenCollection.csv
DOI: 10.24431/rw1k58w
title: Fish and Invertebrate Bottom Trawl Dataset, Arctic Integrated Ecosystem Research Program, August - September 2017

description: These data are part of the Arctic IES component of the Arctic Integrated Ecosystem Research Program (IERP), sponsored by the North Pacific Research Board (NPRB), Collaborative Alaskan Arctic Studies Program (formerly the North Slope Borough/Shell Baseline Studies Program), Bureau of Ocean Energy Management (BOEM), and the Office of Naval Research Marine Mammals and Biology Program. To investigate the distribution, life history, and interactions of biological communities in the U.S. Continental Region of the NE Chukchi Sea a survey was conducted from August - September 2017. Demersal fishes and epibenthic fauna were targeted with a 3 m plumb-staff beam trawl. Specimen for additional processing were collected. Catches were processed (see methods). Files included in this dataset are as follows: Haul Data: OS201701BottomTrawlDeploymentDatav2.csv Catch: OS201701BottomTrawlCatchSummary.csv Specimen Collection: OS201701BottomTrawlSpecimenCollection.csv
DOI: 10.24431/rw1k58x
title: Fish and Invertebrate Bottom Trawl Dataset, Arctic Integrated Ecosystem Research Program, August - September 2019.

description: These data are part of the Arctic IES component of the Arctic Integrated Ecosystem Research Program (IERP), sponsored by the North Pacific Research Board (NPRB), Collaborative Alaskan Arctic Studies Program (formerly the North Slope Borough/Shell Baseline Studies Program), Bureau of Ocean Energy Management (BOEM), and the Office of Naval Research Marine Mammals and Biology Program. To investigate the distribution, life history, and interactions of biological communities in the U.S. Continental Region of the NE Chukchi Sea a survey was conducted from August - September 2019. Demersal fishes and epibenthic fauna were targeted with a 3 m plumb-staff beam trawl. Specimen for additional processing were collected. Catches were processed (see methods). Files included in this dataset are as follows: Haul Data: OS201901BottomTrawlDeploymentDatav2.csv Catch: OS201901BottomTrawlCatchSummary.csv Specimen Collection: OS201901BottomTrawlSpecimenCollection.csv
DOI: 10.5066/p9uiniq1
title: Ecological modeling output for the Everglades Agricultural Area Reservoir 2020

description: Ecological models facilitate evaluation and assessment of alternative approaches to restore the Greater Everglades ecosystem. The models of particular interest to the South Florida Water Management District for planning for the Everglades Agricultural Area (EAA) Reservoir were: (1) Cape Sable Seaside Sparrow Marl Prairie Indicator, (2) Florida apple snail (native) population model (EverSnail), (3) Wader Distribution Evaluation Modeling (WADEM), (4) Small-sized freshwater fish density, and (5) American alligator production probability (i.e., habitat suitability index (HSI)). We ran these models using hydrologic conditions (provided by the South Florida Water Management District, see Process Steps section below) for baseline and future conditions for the EAR.
DOI: 10.6084/m9.figshare.14787696
title: Supplementary Material for: Real-Life Clinical Data of Cabozantinib for Unresectable Hepatocellular Carcinoma

description: <b><i>Introduction:</i></b> Cabozantinib has been approved by the European Medicine Agency (EMA) for hepatocellular carcinoma (HCC) previously treated with sorafenib. Cabozantinib is also being tested in combination with immune checkpoint inhibitors in the frontline setting. Real-life clinical data of cabozantinib for HCC are still lacking. Moreover, the prognostic factors for HCC treated with cabozantinib have not been investigated. <b><i>Methods:</i></b> We evaluated clinical data and outcome of HCC patients who received cabozantinib in the legal context of named patient use in Italy. <b><i>Results:</i></b> Ninety-six patients from 15 centres received cabozantinib. All patients had preserved liver function (Child-Pugh A), mostly with an advanced HCC (77.1%) in a third-line setting (75.0%). The prevalence of performance status (PS) &gt; 0, macrovascular invasion (MVI), extrahepatic spread, and alpha-fetoprotein (AFP) &gt;400 ng/mL was 50.0, 30.2, 67.7, and 44.8%, respectively. Median overall survival (OS) and progression-free survival were 12.1 (95% confidence interval 9.4–14.8) and 5.1 (3.3–6.9) months, respectively. Most common treatment-related adverse events (AEs) were fatigue (67.7%), diarrhoea (54.2%), anorexia (45.8%), HFSR (43.8%), weight loss (24.0%), and hypertension (24.0%). Most common treatment-related Grade 3–4 AEs were fatigue (6.3%), HFSR (6.3%), and increased aminotransferases (6.3%). MVI, ECOG-PS &gt; 0, and AFP &gt;400 ng/mL predicted a worse OS. Discontinuation for intolerance and no new extrahepatic lesions at the progression were associated with better outcomes. <b><i>Conclusions:</i></b> In a real-life Western scenario (mostly in a third-line setting), cabozantinib efficacy and safety data were comparable with those reported in its registration trial. Data regarding the prognostic factors might help in patient selection and design of clinical trials.
DOI: 10.6084/m9.figshare.14787696.v1
title: Supplementary Material for: Real-Life Clinical Data of Cabozantinib for Unresectable Hepatocellular Carcinoma

description: <b><i>Introduction:</i></b> Cabozantinib has been approved by the European Medicine Agency (EMA) for hepatocellular carcinoma (HCC) previously treated with sorafenib. Cabozantinib is also being tested in combination with immune checkpoint inhibitors in the frontline setting. Real-life clinical data of cabozantinib for HCC are still lacking. Moreover, the prognostic factors for HCC treated with cabozantinib have not been investigated. <b><i>Methods:</i></b> We evaluated clinical data and outcome of HCC patients who received cabozantinib in the legal context of named patient use in Italy. <b><i>Results:</i></b> Ninety-six patients from 15 centres received cabozantinib. All patients had preserved liver function (Child-Pugh A), mostly with an advanced HCC (77.1%) in a third-line setting (75.0%). The prevalence of performance status (PS) &gt; 0, macrovascular invasion (MVI), extrahepatic spread, and alpha-fetoprotein (AFP) &gt;400 ng/mL was 50.0, 30.2, 67.7, and 44.8%, respectively. Median overall survival (OS) and progression-free survival were 12.1 (95% confidence interval 9.4–14.8) and 5.1 (3.3–6.9) months, respectively. Most common treatment-related adverse events (AEs) were fatigue (67.7%), diarrhoea (54.2%), anorexia (45.8%), HFSR (43.8%), weight loss (24.0%), and hypertension (24.0%). Most common treatment-related Grade 3–4 AEs were fatigue (6.3%), HFSR (6.3%), and increased aminotransferases (6.3%). MVI, ECOG-PS &gt; 0, and AFP &gt;400 ng/mL predicted a worse OS. Discontinuation for intolerance and no new extrahepatic lesions at the progression were associated with better outcomes. <b><i>Conclusions:</i></b> In a real-life Western scenario (mostly in a third-line setting), cabozantinib efficacy and safety data were comparable with those reported in its registration trial. Data regarding the prognostic factors might help in patient selection and design of clinical trials.
DOI: 10.5281/zenodo.4959897
title: Cenote-Taker2 HMM Databases

description: HMMER-formatted database of viral genes for Cenote-Taker2
DOI: 10.6073/pasta/7e3e9a0de9a0a128e8db327fb92a43cb
title: PBG04 Reproductive effort of Big Bluestem, Indiangrass and Little Bluestem in the Patch-Burn Grazing Experiment at Konza Prairie

description: 'PBG' datasets are associated with a long-term, large-scale study that is addressing the effects of fire-grazing interactions in the context of a Patch-Burn Grazing management system designed to promote grassland heterogeneity. Effects of patch-burn grazing management on plant and animal diversity and the nature and variety of wildlife habitat are being assessed in two replicate management units, each consisting of three pastures (watersheds) designated C03A/C03B/C03C and C3SA/C3SB/C3SC. In each patch-burn grazing unit, one watershed is burned and two that are left unburned in a given year. The burning treatments are rotated annually so that each pasture is burned every third year. Each patch-burn grazing unit is paired with an annually-burned pasture for comparison with traditional grazing systems (C01A and C1SB). All grazing units are stocked with cow/calf pairs from approximately 1 May until 1 Oct at a stocking density equal to 3.2 ha per cow/calf. To examine the impact of patch burning and grazing in all 8 units, we monitor changes in plant species composition, residual biomass, grassland bird populations, insect populations, small mammal populations, soil nutrients, and stream water quality1 (1C3SA/C3SB/C3SC unit only). The KSU Department of Animal Science monitors cattle performance, including weight gain and body condition to assess the economic feasibility of using patch-burn management on a widespread basis. PBG041 includes data on flowering stem height (m) of three dominant prairie grasses: Andropogon gerardii (ANGE), Sorghastrum nutans (SONU), and Schizachyrium scoparium (ANSC). PBG042 includes flowering stem density (no. per sq. m) and mass (grams per sq. m) for the same grass species.
DOI: 10.6084/m9.figshare.14766102.v16
title: antspyt1w helper data

description: downloadable cloud data for testing and processing
DOI: 10.5281/zenodo.4959168
title: Deep attention networks for automated collective behavior discovery in epithelia

description: This dataset contains the raw timelapse movie data and parsed cell trajectory data, in the form of XML files, for the experimental data as described in our paper, "Deep attention networks for automated collective behavior discovery in epithelia". Timelapse movies (both transmitted light images and fluorescence images highlighting cell nuclei) are provided for human umbilical vein endothelial cells (HUVEC), Madin-Darby Canine Kidney (MDCK) cells, and MDA-MB-231 cells (a breast cancer line). XML files containing cell trajectory data (2D points in time) are provided for these same cell types. Trajectories are taken from the bulk region of the tissue (see paper) and XMLs are generated using the TrackMate plugin in ImageJ/FIJI. For MDCKs, additional XMLs are provided for cell trajectories taken from the edge region (see paper).
DOI: 10.6073/pasta/1c3bf3b6356ca85d81bc91b54d848a0d
title: Long-term growth, mortality and regeneration of trees in permanent vegetation plots in the Pacific Northwest, 1910 to present

description: A network of more than 130 permanent vegetation plots provides long-term information on patterns and rates of forest succession in most of the major forest zones of the Pacific Northwest. The plot network extends from the coast to the Cascades in western Oregon and Washington and east to ponderosa pine forests in the Oregon Cascades. Most of the permanent plots were established during two intervals: from 1910 to 1948, and from 1970 to 1989. The earlier plots were established by U.S. Forest Service researchers to quantify timber growth in young stands of important commercial species and to help answer other applied forestry questions. The more recent period of plot establishment began under the Coniferous Forest Biome program of the International Biological Program during the 1970s, and continued under the Long-term Ecological Research program. A broader set of objectives motivated plot establishment since 1970, especially quantification of composition, structure, and population and ecosystem dynamics of natural forests. Plots have one of three spatial arrangements: (1) contiguous rectangles subjectively placed within an area of homogeneous forest; (2) circular plots subjectively placed within an area of homogeneous forest; and (3) circular plots systematically located on long transects to sample an entire watershed, ridge, or reserve. Rectangular study areas are mostly 1.0 ha or 0.4 ha (1.0 ac) in size (slope-corrected). Circular plots are 0.1 ha (0.247 ac), not corrected for slope. The tree stratum is the focus of work in closed-forest study areas. All trees larger than a minimum diameter (5 cm for most areas) are permanently tagged. Plots are censused every 5 or 6 years. Attributes measured or assessed at each census include tree diameter, tree vigor, and the condition of the crown and stem. The same attributes are recorded for trees (ingrowth) that have exceeded the minimum diameter since the previous census. In many plots tree locations are surveyed to provide a plot-specific x-y location. A mortality assessment is done for trees that have died since the previous census. The assessment characterizes rooting, stem, and crown condition, obvious signs of distress or disturbance, and the apparent predisposing and proximate causes of tree death.
DOI: 10.5066/p9xqxo9m
title: Overburden above the Ferris 23, 25, 31, 50 and 65 coal zones, Hanna Basin, Wyoming (fer*ovbg)

description: These ArcView shapefiles contain representations of the thickness of overburden above the Ferris coal zones in the Ferris coalfield, Hanna Basin, Wyoming. These datasets was created specifically for the National Coal Resource Assessment in the Northern Rocky Mountains and Great Plains Region.
DOI: 10.5066/p9ezardq
title: Diet Data from the Western Basin of Lake Erie Examining White and Yellow Perch, 2012-2016

description: A fish's diet is the integrated response of multiple ecological interactions including habitat use, foraging behavior, prey community characteristics, and inter-specific interactions. Fish diet samples have quantified how the invasion of white perch into Lake Erie in the early 1950s has influenced interactions with native yellow perch, which are similar in morphology and habitat use. Early research largely concluded that given the high foraging efficiency of white perch there is both high potential for inter-specific competition and that the invasion of white perch has negatively affected yellow perch. As part of a biannual (spring and autumn) Lake Erie Western Basin Forage Fish Assessment, the USGS Lake Erie Biological Station collected and analyzed diets of age-2-and-older yellow perch and white perch from 2012-2016 to assess possible inter-specific ecological interactions. Information collected from the diets (presence/absence of prey and dry weight of prey (g)) and effort data (coordinates of fish capture) have been uploaded. Information on how fish were captured and how diets were processed can be found in the meta data document provided.
DOI: 10.5066/p9awvmub
title: Drill hole and/or outcrop locations, Ferris Coal Zones in Hanna Basin, Wyoming, 23, 25, 31, 50 and 65 coal zones (fer*ptg)

description: These ArcView shapefiles contain representations of the public drill holes in the Ferris coal zones in the Ferris coalfield, Hanna Basin, Wyoming. These datasets were created specifically for the National Coal Resources Assessment in the Northern Rocky Mountains and Great Plains Region.
DOI: 10.5066/p97jhrx1
title: Southeast Regional Stream Quality Assessment Ecological Data

description: Aquatic ecological surveys are valuable to understanding the interaction between the biotic and abiotic components in rivers and streams. However, large-scale assessments of the water chemistry, geomorphology, and ecological community are usually not feasible due to limited resources. Beginning in 2013, the Regional Stream Quality Assessment Project of the US Geological Survey's National Water Quality Program, began sampling 89-120 streams in each of 5 regions across the conterminous United States - the Midwest (2013), Southeast (2014), Pacific Northwest (2015), Northeast (2016), and California (2017). Sampling included water and streambed sediment chemistry, stage and temperature (Journey and others, 2015). The abiotic data is available from the National Water Information System (nwis.waterdata.usgs.gov). Geospatial data for the Southeastern U.S. study sites are available from Qi and others (2017). Ecological data collected included benthic algae, macroinvertebrates, and fish communities, in addition to in-stream habitat and geomorphology measurements for each reach. Ecological and habitat data for the Southeastern United States are summarized in this data release.
DOI: 10.5066/f7rn36sx
title: Colorado Landcarbon: Accounting for Wildfire

description: Disturbance disrupts the balance between gross primary productivity and respiration, resulting in a net C loss for some time after a stand-replacing fire. However, our understanding of this process is based on a limited number of studies. Ecosystem C recovery post-fire must be explicitly and carefully examined in order to generate accurate predictions of C cycle impacts of future wildfires and change in fire regimes. Montane ponderosa and lodgepole pine forests, either single-species stands or mixed, dominate surface area in the Southern Rockies. These species have drastically different relationships with wildfire; the current narrative portrays ponderosa pine as accustomed to low-severity surface fires with low regeneration rates following high-severity wildfire, whereas lodgepole pine forests readily regenerate after a high-severity stand-replacing wildfire. Forests at the transition between lower montane and upper montane may be more sensitive to future climate change than their lower counterparts; e.g., a stand-replacing disturbance could cause montane ponderosa pine forests to yield to lodgepole pine. It is important to understand how wildfire impacts ecosystem C fluxes in these ecosystems and how landscape dynamics, including topographical changes in climate and distance from forest seed source, can be used to predict C cycle responses to future wildfire patterns. To date, no single study has collected data at an adequate temporal resolution to fully characterize the short-term, intermediate-term, and long-term response and recovery of forest soil respiration to pre-burn conditions. The aim of this work is to predict soil respiration and net primary productivity in pine forests of the southern Rocky Mountains based on time since fire, fire severity, forest type, and forest and soil properties, such as tree basal area, leaf area index and soil carbon pools. We sampled 5 wildfires and 1 high-severity prescribed fire as well as nearby unburned reference forests. The following time-since-fire intervals were sampled along a 30-yr chronosequence: 1-5 years (n=1), 5-10 years (n=1), 10-20 years (n=3), and 20-25 years (n=1).
DOI: 10.6073/pasta/26ac69ab2e0ac748d78ba0961851a705
title: WAT01 Konza Prairie long-term irrigation transect study

description: In 1991, an irrigation transect experiment was established near the Konza Prairie HQ to assess the effects of supplemental water on ecological processes in tallgrass prairie. The site is burned annually in the spring. The transect spans upland, hillside and lowland topographic positions with irrigation and sampling points (12) located at 10 m intervals. Adjacent control transects are marked on both sides of the irrigation transect. Irrigation is scheduled according to estimates of actual evapotranspiration and measures of plant water status. In 1992, an additional 4 irrigation sprinklers were added to the transect (2 at each end). In 1993, a second line of sprinklers and control plots was added (#16-31). At the time of peak aboveground biomass (late August to October), six 0.1 m2 quadrats are harvested at each of the 30 sites (no #9 due to rock outcrop) for the irrigated and control/non-irrigated lines. Biomass is separated into live grass, forb and woody. As of 2006, c.dead is no longer separated from live grass. Vegetative species composition was initially measured in 1991 at each site, and continues to be measured at midseason by using a modified Daubenmire canopy coverage technique in a 10 m2 circular plot. At approximately 10 day intervals, predawn and midday plant water potentials are measured in Andropogon gerardii at each site in both irrigated and control transects. Since 1992, reproductive effort of the dominant grasses Andropogon gerardii (ANGE), Sorghastrum nutans (SONU), Schizachyrium scoparius (ANSC) has been assessed in irrigated and control transects by measuring heights (n=9) and densities (n=4) of flowering stalks. In 1993, soil moisture measurements at 15 and 30 cm depths were begun with a Time Domain Reflectometry system. Data set also includes measured natural precipitation and supplemental water added to the site.