cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/ce09d0b2391721cf41d856cc892c4ef1
title: Little Rock Lake Experiment at North Temperate Lakes LTER: Physical Limnology 1983 - 2000

description: The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources. Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA. In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages. The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively. Starting in 1990 the lake was allowed to recover naturally with the curtain still in place. Data were collected through 2000. The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification. Funding for this project was provided by the USEPA and NSF. Parameters characterizing the physical limnology of the treatment (north basin, stations 1 and 3) and reference basin (south basin, station 2 and 4) are usually measured at one station in the deepest part of each basin (stations 1 and 2) at 0.5 to 1-m depth intervals depending on the parameter. Parameters measured at depth include water temperature, vertical penetration of photosynthetically active radiation (PAR), dissolved oxygen, chlorophyll and phaeopigments. Additional derived parameters include fraction of surface PAR at each depth and percent oxygen saturation. Auxiliary data include time of day, air temperature, cloud cover, and wind speed and direction and secchi depth. Sampling Frequency: varies - Number of sites: 4
DOI: 10.6073/pasta/a9a588125decfd592a180d674844a3a2
title: Little Rock Lake Experiment at North Temperate Lakes LTER: Snow and Ice Depth 1984 - 2000

description: The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources. Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA. In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages. The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively. Starting in 1990 the lake was allowed to recover naturally with the curtain still in place. Data were collected through 2000. The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification. Funding for this project was provided by the USEPA and NSF. Snow and ice depth are measured during the winter months on the reference and treatment basins of Little Rock Lake. Sampling Frequency: varies - Number of sites: 4
DOI: 10.17031/637b5e4a8d3ae
title: Monthly CPR data grouped in Northeast Pacific region (> 1000 m isobath)

description: CSV file containing CPR data. Taxa are summed within each grouping (given in headings), monthly means have been calculated for a Northeast Pacific region > 1000 m isobath. Plankton abundance counts are recorded according to standard CPR methodology, see Richardson et al. (2006, Prog in Oceanog 68. 27-74). Units are "Number of cells per sample” for the phytoplankton groupings, and “Number of organisms per sample” for the zooplankton groupings.
DOI: 10.6073/pasta/c20efc8d5547164599cf1d1acc751a60
title: Little Rock Lake Experiment at North Temperate Lakes LTER: Secchi Disk Depth; Other Auxiliary Sample Data 1983 - 2000

description: The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources. Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA. In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages. The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively. Starting in 1990 the lake was allowed to recover naturally with the curtain still in place. Data were collected through 2000. The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification. Funding for this project was provided by the USEPA and NSF. Secchi Disk data were collected from the treatment and reference basins of Little Rock Lake at one station in the deepest part of each basin. Auxiliary data associated with each sampling event include time of day, air temperature, wind direction and speed, wave height, and cloud cover at the time of sampling. Sampling Frequency: varies - Number of sites: 2
DOI: 10.6073/pasta/4d9677bb701b6484b1a1f112cb246d98
title: Little Rock Lake Experiment at North Temperate Lakes LTER: Zooplankton count 1983 - 2000

description: The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources. Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA. In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages. The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively. Starting in 1990 the lake was allowed to recover naturally with the curtain still in place. Data were collected through 2000. The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification. Funding for this project was provided by the USEPA and NSF. Zooplankton samples are collected from the treatment and reference basins of Little Rock Lake at at two to nine depths using a 30L Schindler Patalas trap (53um mesh). Zooplankton samples are preserved in buffered formalin and archived. Data are summed over sex and stage and integrated volumetrically over the water column to provide a lake-wide estimate of organisms per liter for each species. Sampling Frequency: varies - Number of sites: 2
DOI: 10.6073/pasta/d950f45b3cbd21d4eecbdab320dfd860
title: Little Rock Lake Experiment at North Temperate Lakes LTER: pH and Alkalinity 1983 - 2000

description: The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources. Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA. In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages. The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively. Starting in 1990 the lake was allowed to recover naturally with the curtain still in place. Data were collected through 2000. The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification. Funding for this project was provided by the USEPA and NSF. pH and alkalinity of the treatment and reference basins of Little Rock Lake are measured at one station in the deepest part of each basin at the top and bottom of the epilimnion, mid-thermocline, and top, middle, and bottom of the hypolimnion. During the course of the study, three different types of electrodes were used to measure pH. Sampling Frequency: varies - Number of sites: 2
DOI: 10.6084/m9.figshare.20752597.v1
title: JavaScript reader

description: A function to read the file using Node.js.
DOI: 10.6084/m9.figshare.20752603
title: Python reader

description: A module to read the data into a Python dictionary.
DOI: 10.6084/m9.figshare.20752603.v1
title: Python reader

description: A module to read the data into a Python dictionary.
DOI: 10.6084/m9.figshare.20752597
title: JavaScript reader

description: A function to read the file using Node.js.
DOI: 10.6084/m9.figshare.20752609.v1
title: Matlab reader

description: A function to read the JSON file into Matlab.
DOI: 10.6084/m9.figshare.20752612
title: Full dataset (JSON)

description: A full set of particle filtration efficiency testing data, including five data points per test per lot and pressure resistance data in JSON format.
DOI: 10.6084/m9.figshare.20752612.v1
title: Full dataset (JSON)

description: A full set of particle filtration efficiency testing data, including five data points per test per lot and pressure resistance data in JSON format.
DOI: 10.6084/m9.figshare.20752753
title: Lot-averaged PFE data subset (CSV)

description: A CSV data file containing a subset of the JSON dataset, having one column for the lot-averaged PFE by the NaCl method and one column for lot-averaged PFE by the PSL method.
DOI: 10.6084/m9.figshare.20752609
title: Matlab reader

description: A function to read the JSON file into Matlab.
DOI: 10.6084/m9.figshare.20752753.v1
title: Lot-averaged PFE data subset (CSV)

description: A CSV data file containing a subset of the JSON dataset, having one column for the lot-averaged PFE by the NaCl method and one column for lot-averaged PFE by the PSL method.
DOI: 10.6084/m9.figshare.20752756
title: README

description: A README describing the repository, with a link to the equivalent GitHub repository.
DOI: 10.6084/m9.figshare.20752756.v1
title: README

description: A README describing the repository, with a link to the equivalent GitHub repository.
DOI: 10.6073/pasta/d9a211534f1849f3112c6205e63d3933
title: North Temperate Lakes LTER: Northern Highlands Stream Chemistry Survey 2006

description: We compared regional patterns in lake and stream biogeochemistry in the Northern Highlands Lake District (NHLD), Wisconsin, USA to ask how regional biogeochemistry differs as a function of the type of ecosystem considered (i.e., lakes versus streams); if lake-stream comparisons reveal regional patterns and processes that are not apparent from studies of a single ecosystem type; and if characteristics of streams and lakes scale similarly.Â Fifty-two streams were sampled using a stratified random design to determine regional distribution of 21 water chemistry variables during summer baseflow conditions. Sampling Frequency: once per site Number of sites: 52
DOI: 10.18430/m38f8u
title: X-ray diffraction data for the bifunctional ligase/repressor BirA from Klebsiella pneumoniae (Domain Swapped Dimer) (8F8U)
DOI: 10.5281/zenodo.7335545
title: Target References dataset (TargetCall)

description: Detailed description: Reference genomes used for the TargetCall as the target reference. All taken from NCBI RefSeq.
DOI: 10.5281/zenodo.7335544
title: Target References dataset (TargetCall)

description: Detailed description: Reference genomes used for the TargetCall as the target reference. All taken from NCBI RefSeq.
DOI: 10.6084/m9.figshare.20152955
title: NEGATIVE - XNAT - 1

description: First part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152955.v1
title: NEGATIVE - XNAT - 1

description: First part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152961
title: NEGATIVE - NPY Processed

description: Preprocessed negative images stored in numpy array format (npy)
DOI: 10.6084/m9.figshare.20152967
title: NEGATIVE - Tables

description: Tables describing the distributions of each of the negative images. They contain information such as subject, session, file path, partition (train, dev, test), and image projection (frontal, lateral).
DOI: 10.6084/m9.figshare.20152967.v1
title: NEGATIVE - Tables

description: Tables describing the distributions of each of the negative images. They contain information such as subject, session, file path, partition (train, dev, test), and image projection (frontal, lateral).
DOI: 10.6084/m9.figshare.20152973
title: POSITIVE - MIDS

description: Positive images in MIDS format.
DOI: 10.6084/m9.figshare.20152961.v1
title: NEGATIVE - NPY Processed

description: Preprocessed negative images stored in numpy array format (npy)
DOI: 10.6084/m9.figshare.20152973.v1
title: POSITIVE - MIDS

description: Positive images in MIDS format.
DOI: 10.6084/m9.figshare.20152979.v1
title: POSITIVE - Tables

description: Tables describing the distributions of each of the positive images. They contain information such as subject, session, file path, partition (train, dev, test), and image projection (frontal, lateral).
DOI: 10.6084/m9.figshare.20152985
title: POSITIVE - XNAT - 1

description: First part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152979
title: POSITIVE - Tables

description: Tables describing the distributions of each of the positive images. They contain information such as subject, session, file path, partition (train, dev, test), and image projection (frontal, lateral).
DOI: 10.6084/m9.figshare.20152982
title: POSITIVE - XNAT - 2

description: Second part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152982.v1
title: POSITIVE - XNAT - 2

description: Second part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152985.v1
title: POSITIVE - XNAT - 1

description: First part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152988.v1
title: POSITIVE - XNAT - 3

description: Third part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20154035.v1
title: NEGATIVE - XNAT - 2

description: Second part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20152988
title: POSITIVE - XNAT - 3

description: Third part of Positive XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20154032.v1
title: NEGATIVE - XNAT - 3

description: Third part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20154032
title: NEGATIVE - XNAT - 3

description: Third part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20154035
title: NEGATIVE - XNAT - 2

description: Second part of Negative XNAT Images, in DICOM format.
DOI: 10.6084/m9.figshare.20154038
title: POSITIVE - NPY Processed

description: Preprocessed positive images stored in numpy array format (npy).
DOI: 10.6084/m9.figshare.20154038.v1
title: POSITIVE - NPY Processed

description: Preprocessed positive images stored in numpy array format (npy).
DOI: 10.6084/m9.figshare.20154041
title: NEGATIVE - MIDS

description: Negative images in MIDS format.
DOI: 10.6084/m9.figshare.20154041.v1
title: NEGATIVE - MIDS

description: Negative images in MIDS format.
DOI: 10.6084/m9.figshare.21675176
title: Quality Tools

description: Survey data
DOI: 10.6084/m9.figshare.21675176.v1
title: Quality Tools

description: Survey data
DOI: 10.6084/m9.figshare.21675092
title: Environmental Justice Implications of Accelerated Electric Vehicle Penetration

description: Modeled NO2 and PM2.5 concentrations at Census block centroids in a portion of Southern California. The reference case assumed that the number of electric vehicles were at a default level. The sensitivity cases assumed that certain policies were in place to accelerate the pepentration of electric vehicles into the fleet. Each census block group is labeled with the race ethnicity group predominantly makes up the respected group.
DOI: 10.5281/zenodo.7242347
title: A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity

description: In our manuscript, we utilized scRNA-seq libraries we generated from: -8 human psoriatic skin samples and 7 healthy control skin samples (ZIST.rds) -3 human psoriatic skin samples before and after tildrakizumab treatment (three_tildra_Trm1.rds) These *rds files are the Seurat objects for these data sets post-filtering and integration. For raw sequencing data corresponding to these samples, access can be found under accession number EGA: S00001005271. All methods underlying the generation and analysis of these datasets can be found in the original manuscript: Cook CP, Taylor M, Liu Y, et al. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. <em>Cell Rep Med</em>. 2022;3(8):100715. doi:10.1016/j.xcrm.2022.100715 Any additional questions or information requests can be addressed to Jeffrey.cheng@ucsf.edu or cook.675@berkeley.edu
DOI: 10.6084/m9.figshare.21675137
title: Stochastic processes structure both abundant and rare microbial communities involved in riverine nitrification and denitrification

description: Using high-throughput sequencing of archaeal <em>amoA</em>, bacterial <em>amoA</em>, <em>nirK</em>, and <em>nirS</em> genes, we investigated the biogeographic patterns and assembly mechanisms of nitrifying and denitrifying communities in the channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 rivers along the latitudinal gradient in China
DOI: 10.6084/m9.figshare.21675227
title: Gene-vegetarianism interactions detected in genome-wide analyses across 30 serum biomarkers: a population-based cohort study in UK Biobank (Supplementary Tables)

description: <strong>Objectives</strong>: To determine the associations of vegetarianism with 30 serum biomarkers, and to identify genetic variants that modify these associations. <strong>Design</strong>: A population-based cohort study. <strong>Setting</strong>: United Kingdom. <strong>Participants</strong>: A total of 155,375 UK Biobank participants with biomarker measurements, genetic data, dietary information, and relevant covariates were included. A rigorous sample of vegetarians was defined based on consistent responses to four questions in two dietary surveys. <strong>Main outcome measures</strong>: Effects of vegetarianism and gene-vegetarianism interactions on 30 serum biomarkers for diabetes, cancer, cardiovascular, skeletal, renal, and liver diseases. <strong>Results</strong>: Compared to a matched sample of non-vegetarians, vegetarians had significantly lower levels of all cholesterol measures and vitamin D, and a higher level of triglycerides, while no significant differences were observed for sex hormones. We found a genetic variant, rs72952628 (C/T), that modified the association between vegetarianism and serum calcium (<em>P</em> for interaction = 4.47e-08). Vegetarianism was associated with a 0.13 units decrease (95% confidence interval -0.09 to -0.18) in calcium in CC individuals, but with 0.30 units increase (0.14 to 0.46) in CT individuals. This variant is located in the gene <em>MMAA</em>, which is part of the vitamin B12 metabolism pathway; B12 has a high nutrient deficiency potential in vegetarians. Gene-based interaction analysis revealed two additional significant genic regions, <em>RNF168</em> in testosterone (<em>P</em> = 1.45e-06) and <em>ZNF277</em> in eGFR (<em>P</em> = 6.76e-07), which have previously been associated with testicular and renal traits, respectively. <strong>Conclusions</strong>: Vegetarianism was associated with 15 of the 30 serum biomarkers examined, and evidence of genetic modifications was found for three biomarkers: calcium, testosterone, and eGFR.
DOI: 10.5281/zenodo.7401544
title: CheckM v1 reference data

description: <strong>Precalculated data files for CheckM v1.<br> <br> Manuscript:</strong><br> CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.<br> https://genome.cshlp.org/content/early/2015/05/14/gr.186072.114 <strong>Installation instructions:</strong><br> https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm.
DOI: 10.21227/kggn-f214
title: CRAWDAD snu/wow_via_wimax

description: These tcpdump traces were captured by Xiaofei Wang at Seoul National University during the study of online gaming via Korean WiBro (Mobile WiMAX) network.date/time of measurement start: 2008-12-19 date/time of measurement end: 2009-04-13 collection environment: The measurement device is an Apple Macbook Pro with Intel Core 2 Duo CPU T8300, 2G RAM, and Nvidia 8800GT graphic card. The Macbook is equipped with a USB dongle based WiMAX network interface card (NIC). Also the XRO7000 Diagnostic Monitor from the XRONet is used in order to capture low layer behaviors of WiMAX. For higherlayer measurement, tcpdump-based Wireshark and TCPTrace are used. sanitization: The payload was cutoff by resampling (tcpreplay and tcpdump), and the header was anonymized by tcprewrite. Tracessnu/wow_via_wimax/tcpdump/wow_via_wimaxlast modified :Â 2010-08-01 short description :Â Tcpdump traces from Korean Mobile WiMAX gaming network. description :Â Tcpdump traces captured by Xiaofei Wang at Seoul National University during the study of online gaming via Korean WiBro (Mobile WiMAX) network. reason for most recent change :Â the initial version release date :Â 2010-08-01 date/time of measurement start :Â 2008-12-19 date/time of measurement end :Â 2008-12-19
DOI: 10.6084/m9.figshare.21675272
title: Table S7

description: <strong>Table S7. Differentially expressed (DE) genes identified by RNAseq in sample comparisons highlighting the effect of Niclosamide (NIC).</strong> <br> <strong>Entrez GeneID</strong> NCBI unique gene identifier <br> <strong>Gene Symbol</strong> Common abbreviated gene symbol <br> <strong>Aliases</strong> Alternate commonly used abbreviated gene symbols <br> <strong>description</strong> Gene name/Gene description <br> <strong>other_designations</strong> Alternate gene name/gene description <br> <strong>Base mean</strong> Mean of normalized counts <br> <strong>log2(FC)</strong> Log(base 2) fold change <br> <strong>StdErr</strong> Standard error <br> <strong>Wald-Stats</strong> Wald statistic <br> <strong>P-value</strong> P-value <br> <strong>P-adj</strong> Adjusted p-value (bonferroni correction) <br> <strong>Scaffold</strong> Scaffold where gene is located <br> <strong>Chromosome</strong> Chromosome where gene is located <br> <strong>Start</strong> Start of gene (bp position) <br> <strong>End</strong> End of gene (bp position) <br> <strong>Strand</strong> Strand gene is on <br> <strong>DE?(y/n)</strong> If gene is significantly differentially expressed (adjusted p-value ≤0.05, |log2(FC)|≥1) or not (y = yes, n=no) <br> <strong>Sample</strong> <strong>Description</strong> xx16 Vehicle treated no virus samples at 16 hours Nx16 Niclosamide treated no virus samples at 16 hours xx48 Vehicle treated no virus samples at 48 hours Nx48 Niclosamide treated no virus samples at 48 hours xV16 Vehicle treated virus samples at 16 hours NV16 Niclosamide treated virus samples at 16 hours xV48 Vehicle treated virus samples at 48 hours NV48 Niclosamide treated virus samples at 48 hours