cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/4f20191011292158169313b543288565
title: Water Quality Data (Grab Samples) from the Taylor Slough, Everglades National Park (FCE), from May 2001 to Present

description: Water quality samples are being collected using ISCO autosamplers at all wetland sites (that is, all sites except TS/Ph-9, 10, and 11). The autosamplers contain 24 1L bottles. Water is sampled by programming the autosamplers to take composite samples once every 3 days. These samples are a composite of four 250mL subsamples drawn every 18 hours (a sampling scheme that captures a dawn, noon, dusk, and midnight sample in every three day composite). The samples are collected every 3-4 weeks and analyzed for total phosphorus (TP), total nitrogen (TN), and salinity. When sites are visited to collect these samples, we also collect a grab sample that is immediately put on ice. A portion of these grab samples is filtered through a Whatman GF/F filter immediately upon return to the lab, and the filtered samples are analyzed for inorganic nutrients such as NO2-, NO3-, NH4+, SRP, and DOC. The unfiltered fraction of these grab samples is analyzed for TP, TN, and TOC. We use these montly grab samples to generate relationships between TP and SRP, and between TN and NO2- + NO3- + NH4+. Dissolved nutrients are measured using standard rapid flow analyzer (RFA) techniques. TP is analyzed with a modified Solorzano and Sharp (1980) technique. TN is measured with an Antec TN analyzer, TOC and DOC are quantified on a Shimadzu TOC Analyzer, and salinity is measured with a YSI conductivity meter. In addition to the regular water quality monitoring, we use the rain level actuators at all freshwater sites to trigger water sampling after rain events exceed a given threshold of duration and/or intensity. As currently programmed, when the threshold of = 2.5 cm of rain per hour is passed, the autosampler at that site collects a 500mL sample 30 minutes after the threshold has been reached. Rain event samples are collected, treated, and analyzed as all other water quality samples.
DOI: 10.5281/zenodo.5768638
title: Supplementary_Petrova_Mokshina

description: In-depth analysis of flax lectin gene expression using FIBexDB. Supplementary Dataset. List genes in clusters and coexpression networks.
DOI: 10.5281/zenodo.5768637
title: Supplementary_Petrova_Mokshina

description: In-depth analysis of flax lectin gene expression using FIBexDB. Supplementary Dataset. List genes in clusters and coexpression networks.
DOI: 10.26180/16926868
title: National COVID-19 Clinical Evidence Taskforce Process Evaluation_Data

description: The Australian living guidelines for the clinical care of people with COVID-19: What worked, what didn't and why, a mixed methods process evaluation<br>
DOI: 10.6073/pasta/74d5336cf9f1297b475db8ec6ed08819
title: SBC LTER: Reef: Historical Kelp Database for giant kelp (Macrocystis pyrifera) biomass in California and Mexico

description: ISP Alginates (formerly Kelco Co.) has collected information on the abundance of giant kelp (Macrocystis pyrifera) in California and Mexico from routine aerial surveys since 1957. The standard protocol consists of an observer visually estimating the amount of harvestable giant kelp biomass within designated kelp beds from a small fixed-wing aircraft. Observations were recorded on paper data sheets in the field and archived in notebooks housed at ISP Alginates. With cooperation from ISP Alginates, the SBCLTER converted ISP Alginates long-term records of giant kelp biomass into a digital format. The database consists of a data table containing kelp biomass, a catalog of maps. The format ISP Alginates used to report kelp abundance data changed periodically over the course of the collecting period. These details, pus descriptions of designated kelp beds are described in the protocol document.
DOI: 10.6073/pasta/c17f1974ce68accc75e5372b8d10fc86
title: Canopy-Atmosphere Exchange of Carbon, Water and Energy at Harvard Forest EMS Tower since 1991

description: The tower-based CO2 measurements and key meteorological drivers are intended to examine how regional and ecosystem level processes in a mid-latitude forest contribute to global carbon cycling. Specifically, we endeavor to understand quantitatively how and why forested ecosystems take up or release carbon, on time scales from hours to decades, and to elucidate responses to climate changes and management interventions. The tower was installed 1989 and the resulting eddy-flux measurements constitute the longest running record of the net-ecosystem carbon exchange in a North American Forest. The resulting long-term record of Net Ecosystem Exchange (NEE) has shown the effects of climate anomalies on carbon fluxes for seasonal and annual time scales. For example, reduced soil frost allows greater respiration in the winter leading to lower C sequestration. Cumulative gross photosynthesis depends on when the canopy emerges in the spring. Warmer springtime temperatures lead to greater uptake of C. As the NEE record is extended and augmented by supporting ecological measurements, we can further identify longer-term effects of climate perturbations on carbon fluxes and further define the relationship between stand history and carbon sequestration. Climatic anomalies in one season or year may have a longer-term effect on the sequestration of carbon in subsequent seasons or years. The flux and ecological measurements are coordinated with studies at other sites through the AmeriFlux network. By examining the relationships between carbon fluxes and the driving physical and biological variables across a range of sites we are enhancing understanding of the processes that control NEE.
DOI: 10.5281/zenodo.5755656
title: MACIE scores for human genome assembly GRCh37 Part 1 (Chr1 - Chr3)

description: MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional. For each non-synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not damaging protein functional and evolutionarily conserved” (MACIE01); “damaging protein functional and not evolutionarily conserved” (MACIE10); “not damaging protein functional and not evolutionarily conserved” (MACIE00); “both damaging protein functional and evolutionarily conserved” (MACIE11). MACIE_protein is the estimated posterior probability of “damaging protein functional”, which is the sum of MACIE10 and MACIE11; MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “damaging protein functional” or “evolutionarily conserved”, which is the sum of MACIE01, MACIE10, and MACIE11. For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.
DOI: 10.5281/zenodo.5755655
title: MACIE scores for human genome assembly GRCh37 Part 1 (Chr1 - Chr3)

description: MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional. For each non-synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not damaging protein functional and evolutionarily conserved” (MACIE01); “damaging protein functional and not evolutionarily conserved” (MACIE10); “not damaging protein functional and not evolutionarily conserved” (MACIE00); “both damaging protein functional and evolutionarily conserved” (MACIE11). MACIE_protein is the estimated posterior probability of “damaging protein functional”, which is the sum of MACIE10 and MACIE11; MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “damaging protein functional” or “evolutionarily conserved”, which is the sum of MACIE01, MACIE10, and MACIE11. For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.
DOI: 10.6073/pasta/0745bc0e052daa76fe5383616855a74b
title: MCR LTER: Coral Reef: Fish Counts versus Coral Diversity for Holbrook, et al. PLoS One 2015

description: To test the impact of the regional species pool on the coral-fish diversity relationship, the same experiment was conducted in lagoons of Schumann Island in Kimbe Bay, Papua New Guinea (5°31’S, 150°5’E), Lizard Island on the Great Barrier Reef, Australia (14º 41’S, 145º 27’E), and Moorea in French Polynesia (17° 30’S, 149° 50’W). Divers counted individuals of all species observed on or interacting with 45 patch reefs were constructed using six abundant, co-occurring coral species that were major habitat providers for fish. Fish were allowed to naturally colonize over 8-12 months and the patch reefs were surveyed by scuba divers four times during the period. The species of corals used in the experiment were selected to include species that exhibit a broad range of structural morphologies and potential sensitivities to climate change and other environmental stressors. These data support the manuscript: Holbrook, Sally J., Russel J. Schmitt, Vanessa Messmer, Andrew J. Brooks, Maya Srinivasan, Philip L. Munday and Geoffrey P. Jones, Reef Fishes in Biodiversity Hotspots are at Greatest Risk from Loss of Coral Species, accepted 2015, PLoS One.
DOI: 10.6084/m9.figshare.7618580
title: extended keyboard layouts for Apple

description: Three keyboard layouts that work with MacOS 10.13 and later. Just place them into the folder Library&gt;Keyboard LayoutsThe Syriac keyboard is arranged in a similar way to the Arabic keyboard for Mac, so that those typing Syriac occasionally, but Arabic often can easily use it.The Hebrew keyboard has extra letters with diacritics, so that it is easy to type Judaeo-Arabic.The Latin keyboard is extended to give all the diacritics required to transliterate Arabic, Hebrew and Syriac.
DOI: 10.6084/m9.figshare.13371231
title: The influence of topography and land use on hydrological and nutrient dynamics in two Andean streams from Northern Patagonia

description: Fluvial dynamics are driven by multiple environmental factors and scales. Studies coupling hydrological and nutrient dynamics of mountain streams are almost non-existent in the Northern Patagonian region; which is characterised by a temperate-cold climate. We studied two adjacent streams with contrasting drainage basins: Casa de Piedra (41°07′30.11″S 71°27′13.16″W), which originates in a small mountain lake and runs through pristine landscapes, and Gutiérrez (41°09′36.18″S 71°24′37.19″W) that originates in a large piedmont lake and runs through an anthropized landscape. The streams displayed contrasting hydrological and nutrient dynamics. Casa de Piedra had higher discharge flashiness with shorter response delays to precipitation. Whereas the hydrology of Gutiérrez was buffered by the upstream lake, its nutrient exports were not. Differences observed in quality and timing in the export of coarse particulate organic matter and levels of phosphorus and nitrogen are explained by human activities affecting Gutiérrez but not Casa de Piedra. Moreover, the ratio of nitrogen:phosphorus suggests that phosphorus may be the limiting nutrient in the future, at the more densely populated basin. To summarise, Northern Patagonian streams flowing under marked geological and climate similarities, display stark differences in dynamics of their adjacent basins due to differences in topography and land use.
DOI: 10.6084/m9.figshare.13371231.v1
title: The influence of topography and land use on hydrological and nutrient dynamics in two Andean streams from Northern Patagonia

description: Fluvial dynamics are driven by multiple environmental factors and scales. Studies coupling hydrological and nutrient dynamics of mountain streams are almost non-existent in the Northern Patagonian region; which is characterised by a temperate-cold climate. We studied two adjacent streams with contrasting drainage basins: Casa de Piedra (41°07′30.11″S 71°27′13.16″W), which originates in a small mountain lake and runs through pristine landscapes, and Gutiérrez (41°09′36.18″S 71°24′37.19″W) that originates in a large piedmont lake and runs through an anthropized landscape. The streams displayed contrasting hydrological and nutrient dynamics. Casa de Piedra had higher discharge flashiness with shorter response delays to precipitation. Whereas the hydrology of Gutiérrez was buffered by the upstream lake, its nutrient exports were not. Differences observed in quality and timing in the export of coarse particulate organic matter and levels of phosphorus and nitrogen are explained by human activities affecting Gutiérrez but not Casa de Piedra. Moreover, the ratio of nitrogen:phosphorus suggests that phosphorus may be the limiting nutrient in the future, at the more densely populated basin. To summarise, Northern Patagonian streams flowing under marked geological and climate similarities, display stark differences in dynamics of their adjacent basins due to differences in topography and land use.
DOI: 10.6084/m9.figshare.13571221
title: Cetacean sighting records in the New Caledonia Basin, Tasman Sea, New Zealand

description: The distribution of marine mammal species in many areas remains poorly understood, especially as observations for some taxa are rare and large-scale surveys are time consuming and extremely costly. Here, we present 36 records of 7 cetacean species (<i>Balaenoptera brydei</i>, <i>B. musculus</i> subspp., <i>Delphinus delphis</i>, <i>Globicephala</i> sp., <i>Grampus griseus</i>, <i>Physeter macrocephalus</i>, <i>Pseudorca crassidens</i>) in the New Caledonia Basin, Tasman Sea, along with their associated biological and environmental data. Data were derived from a platform of opportunity during a seismic survey that ran between December 2015 and March 2016, inclusively. The two most frequently encountered species were sperm whales (<i>Physeter macrocephalus</i>, 13 sightings, 5 acoustic detections) and blue whales (<i>Balaenoptera musculus</i> subspp., 8 visual detections). All encountered species are known to occur in New Zealand waters at least occasionally, based on historical sightings and stranding records. However, data presented here are the first cetacean records for this specific area and demonstrate that seismic vessels can act as a platform of opportunity for studying cetacean distribution in poorly accessible areas. Such data will aid future research efforts including species distribution models on cetaceans in the South Pacific.
DOI: 10.6084/m9.figshare.13571221.v1
title: Cetacean sighting records in the New Caledonia Basin, Tasman Sea, New Zealand

description: The distribution of marine mammal species in many areas remains poorly understood, especially as observations for some taxa are rare and large-scale surveys are time consuming and extremely costly. Here, we present 36 records of 7 cetacean species (<i>Balaenoptera brydei</i>, <i>B. musculus</i> subspp., <i>Delphinus delphis</i>, <i>Globicephala</i> sp., <i>Grampus griseus</i>, <i>Physeter macrocephalus</i>, <i>Pseudorca crassidens</i>) in the New Caledonia Basin, Tasman Sea, along with their associated biological and environmental data. Data were derived from a platform of opportunity during a seismic survey that ran between December 2015 and March 2016, inclusively. The two most frequently encountered species were sperm whales (<i>Physeter macrocephalus</i>, 13 sightings, 5 acoustic detections) and blue whales (<i>Balaenoptera musculus</i> subspp., 8 visual detections). All encountered species are known to occur in New Zealand waters at least occasionally, based on historical sightings and stranding records. However, data presented here are the first cetacean records for this specific area and demonstrate that seismic vessels can act as a platform of opportunity for studying cetacean distribution in poorly accessible areas. Such data will aid future research efforts including species distribution models on cetaceans in the South Pacific.
DOI: 10.5281/zenodo.5756449
title: MACIE scores for human genome assembly GRCh37 Part 2 (Chr4 - Chr7)

description: MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional. For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.
DOI: 10.5281/zenodo.5756448
title: MACIE scores for human genome assembly GRCh37 Part 2 (Chr4 - Chr7)

description: MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional. For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.
DOI: 10.6084/m9.figshare.17147966
title: Can I afford to publish? A dilemma for African scholars

description: Data related to Ecology journals with 2019 Impact Factor, Open Access fees and their corresponding business model.<b> </b> <b> </b> <br>
DOI: 10.6084/m9.figshare.17147966.v1
title: Can I afford to publish? A dilemma for African scholars

description: Data related to Ecology journals with 2019 Impact Factor, Open Access fees and their corresponding business model.<b> </b> <b> </b> <br>
DOI: 10.6073/pasta/be0b964a5caedb3f9c89006eba29cbf7
title: Ants Under Climate Change at Harvard Forest and Duke Forest since 2009

description: Experimental field studies are needed to understand the consequences of global climatic changefor local community structure and associated ecosystem processes. We are using 5-m diameter open-top environmental chambers and 1m pvc minichambers to simultaneously manipulate air and soil temperatures at the Harvard Forest and at the Duke Forest in North Carolina. These field manipulations are designed to reveal the effects of temperature increases on the populations, communities, and associated ecosystem services of assemblages of ground-foraging ants. Ants are a model taxon for studying effects of global climatic change because they comprise the dominant fraction of animal biomass in many terrestrial communities and because they provide essential ecosystem services, including soil turnover, decomposition, and seed dispersal. The experiment is designed to test three predictions: 1. Projected atmospheric warming will lead to declines in ant species’ abundances at the warmer, southern extent of their ranges in the US. Conversely, projected atmospheric warming will lead to increases in abundance or range extensions of ant species at the cooler, northern extent of their ranges in the US. 2. Warming will change the relative abundance and composition of ant communities, and will lead to the loss of ant biodiversity. 3. Warming will potentially diminish ecosystem processes and services provided by ants, particularly with respect to the dispersal of seeds. To explore these, we are conducting two experiments. In one experiment, twelve open-top chambers at each site which will each be exposed air temperatures ranging from 1.5 to 7 deg C above ambient; soil temperatures will be increased simultaneously from 0 to ~ 2 deg C. After an initial year of pre-intervention measurements, the experiment will run for 3 consecutive years of continuous warming. In the second experiment, shade cloth and plastic greenhouse sheeting will be used to increase or decrease temperature by 0.5 deg C in sixty minichambers. The minichamber experiment was conducted in 2009 and will continue into 2010. The response variables measured in both experiments include ant activity, population densities and colony sizes of focal species, ant community diversity and species composition, and rates of seed dispersal and predation as mediated by ants.