cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/6c29c57b9c618161dab7f573cda8c0d3
title: Land cover classification of central Arizona-Phoenix using Landsat Enhanced Thematic Mapper (ETM) data, year 2005

description: A fundamental dataset required for ecosystem analysis consists of the major types of land cover present in the study area and their areal percentages. Land cover refers to the physical nature of the surficial materials present in a given area such as water, grass, clay-rich soil, asphalt, or concrete. Land cover classification can be used as input into a variety of ecological models, and land cover maps can be constructed to aid in planning field sampling strategy. The land cover types can also be linked to different land use categories to investigate temporal and spatial changes in the urban ecosystem.
DOI: 10.6084/m9.figshare.20449866
title: tree.anno.txt

description: other information of phylogenetic tree.
DOI: 10.6084/m9.figshare.20449866.v1
title: tree.anno.txt

description: other information of phylogenetic tree.
DOI: 10.6073/pasta/fbfb83353709feeeb80d5330526e7087
title: SBC LTER: Ocean: Ocean Currents and Biogeochemistry: Nearshore water profiles (monthly CTD and chemistry), ongoing since 2000

description: This data package contains water chemistry measurements taken monthly at these reefs in the nearshore areas of the Santa Barbra Channel, CA, USA: Arroyo Quemado, Bullito, Naples, Arroyo Burro, Mohawk and Carpinteria. Measurements include standard CTD parameters, nutrients, pigments, particulate CN, total dissolved N and P, stable isotopes of C and N (not all parameters are measured at all stations). Sampling began in November 2000. Some stations are sampled only occasionally. During the first 2 years, CTD data were collected with a SBE19 Seacat Profiler and water samples with a pump. Starting in February 2003, a SBE19-Plus with a rosette sampler was used. There are 3 tables in this dataset. Water chemistry and profiles from "registered stations" (see geographic coverage) are in 2 tables with "registered" in their name. CTD profiles are often collected ad hoc, or as "stations of opportunity". These have been collected in a third table as "non-registered". The station codes for these may be reused, and are not recorded in metadata (but can be found in data).
DOI: 10.6073/pasta/efba21bf44cf73de177ea037274318f7
title: SBC LTER: Reef: Kelp Nitrogen uptake in Carpinteria and Mohawk kelp forests, 2016-2017

description: A large on-going time-series monthly water samples have been taken at 1m, 5 m and 10 m depth from the offshore edge of five kelp forests near Santa Barbara, CA, USA (Arroyo Burro, Arroyo Quemado, Carpinteria, Mohawk, Naples). See dataset: http://sbc.lternet.edu/cgi-bin/showDataset.cgi?docid=knb-lter-sbc.10. Two datasets are presented here. One is a field study conducted in two of the sites (Mohawk or Carpinteria) to test the N uptake of giant kelp (Macrocystis pyrifera) and phytoplankton from May 2016 to October 2017. In situ rates of urea, ammonium and nitrate uptake by giant kelp blades and phytoplankton, which were enclosed together within polyethylene blade bags, from the surface canopy of Mohawk or Carpinteria kelp forests. The second dataset has the results of laboratory experiments for testing the direct uptake of urea by whole blades and natural phytoplankton communities entrained in surface canopy waters.
DOI: 10.5281/zenodo.6968453
title: ICB_Riaz_RNAseq

description: Processed RNAseq data used for ICB_Riaz data object. Publication: https://pubmed.ncbi.nlm.nih.gov/29033130/. Raw data obtained from https://www.ebi.ac.uk/ena/browser/view/PRJNA356761?show=reads. Processed with https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto Dataset details: https://predictio.ca/dataset/12.
DOI: 10.5281/zenodo.6968452
title: ICB_Riaz_RNAseq

description: Processed RNAseq data used for ICB_Riaz data object. Publication: https://pubmed.ncbi.nlm.nih.gov/29033130/. Raw data obtained from https://www.ebi.ac.uk/ena/browser/view/PRJNA356761?show=reads. Processed with https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto Dataset details: https://predictio.ca/dataset/12.
DOI: 10.6084/m9.figshare.20383014.v14
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.6084/m9.figshare.20449878
title: Table ST2 - significant motifs shared between Sm1, Sm2 and Sm3 cells compared between control and APM using ATAC-seq and TFEA

description: Significantly enriched and depleted TFEA motifs (padj &lt; 1e-5) from SAEC-ATAC-seq analysis following APM exposure for all three SAECs, categorized by shared motifs to reflect the Venn diagrams in Figure 2B.
DOI: 10.6073/pasta/3bd77a7668afe44321adf6e063643338
title: MCR LTER: Coral Reef: Benthic Photosynthetically Active Radiation (PAR), ongoing since 2009

description: These data contain a time-series from sequential deployments of an ALW-CMP PAR sensor recording quanta of photosynthetically active radiation underwater between wavelengths 400 nm to 700 nm every two seconds. The sensor window is wiped free of algae periodically to prevent fouling. Deployments are three to six months in length. The sensor was mounted at 17 m depth on the fore reef, and at 2 m depth on the Backreef. PAR irradiance is measured as quanta in micromoles of photons per square meter per second.
DOI: 10.6073/pasta/b66a2c5f28eb4b29540fce214c711a83
title: MCR LTER: Coral Reef: Benthic Water Temperature, ongoing since 2005

description: A continuous time series of water temperature is measured with bottom-mounted thermistors at six sites around the shores of Moorea, on the fringing reef, backreef, and forereef. The forereef temperature is recorded at 10, 20, 30 and 40 m, the backreef at 1 m and the fringing reef at 1 and 5 m. SBE 39s are deployed to the forereef and backreef. Onset HOBOs are deployed on the fringing reef. Temperature data are processed and resampled to a 20 minute time step.
DOI: 10.6084/m9.figshare.20449887
title: Table ST3 - significant motifs shared between Sm2 and Sm3 cells exposed to APM or WSP and evaluated by ATAC-seq and TFEA

description: Significantly enriched and depleted TFEA motifs (padj &lt; 1e-5) from SAEC-ATAC-seq analysis for Sm2 and Sm3 cells exposed to APM or WSP, categorized by shared motifs to reflect the Venn diagrams in Figure 3B.
DOI: 10.6084/m9.figshare.20449899
title: Table ST4 - significant motifs in Sm1, Sm2 and Sm3 cells between control and APM evaluated by ATAC-seq using PRO-seq features

description: Significantly enriched and depleted TFEA motifs (padj &lt; 1e-5) from SAEC-ATAC-seq analysis for all SAEC lines exposed to APM within regions defined by all PRO-seq TREs in Sm1 cells.
DOI: 10.6084/m9.figshare.20449899.v1
title: Table ST4 - significant motifs in Sm1, Sm2 and Sm3 cells between control and APM evaluated by ATAC-seq using PRO-seq features

description: Significantly enriched and depleted TFEA motifs (padj &lt; 1e-5) from SAEC-ATAC-seq analysis for all SAEC lines exposed to APM within regions defined by all PRO-seq TREs in Sm1 cells.
DOI: 10.6084/m9.figshare.20383014.v15
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, w<sub>e</sub> <sub>report</sub> the <sub>sequencing</sub> <sub>and</sub> <sub>assembly</sub> <sub>of</sub> <sub>the</sub> <sub><em>L</em></sub><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.6073/pasta/7b5dbedeacf0832c330510f864ccae62
title: Climate data for D1 chart recorder, 1982 - 1988.

description: Climatological data were collected from a Niwot Ridge climate station (D1 at 3743 m) throughout the year. Parameters measured were temperature, relative humidity, solar radiation, wind speed and run of wind. The station was instrumented with a thermohygrograph (regularly calibrated and checked with maximum and minimum thermometers and psychrometers), which was equipped with a Bourdon tube (to measure temperature) and a banjo-spread hair element (to measure relative humidity). The thermohygrograph was situated in a white, all wood, louvered Stevenson screen which was oriented with the door facing north. Solar radiation was recorded on a bimetalic strip mechanical actinometer. Ninety percent of solar radiation from 360 to 2000 nm was transmitted through the instrument's glass dome. Wind speed (peak gust) was measured with a 3-cup, AC-generating anemometer that continuously recorded onto an Esterline Angus strip chart recorder. Run of wind was measured with a Belford totalizing cup anenometer with a counter (at a height of approximately 3 meters above ground). Average wind speed was calculated from the peak gust trace. The thermohygrograph and actinometer both used wind-up or battery-driven clock drives that rotated the recording chart on a right cylindrical drum with a fixed period between 24 h and 861 h depending on the gears used. These clock mechanisms were virtually identical and therefore completely interchangeable among the instruments.
DOI: 10.6073/pasta/97ed9868c880396b977af42d2f2f321a
title: Climate data for D1 data loggers (CR23X and CR1000), 2000 - ongoing, daily.

description: Climatological data were collected from a Niwot Ridge climate station (D1) throughout the year. From July 5 2000 through October 23 2013, data were recorded using a Campbell Instruments CR23X data logger. Subsequently, data were recorded using a Campbell Instruments CR1000 data logger. Maximum and minimum values are recorded instantaneously, with a sampling interval of 5 seconds. Daily averages and totals were calculated from 17,280 individual measurements. This instrument was programmed to generate both hourly and daily output. Beginning in June 25 2009, 10 minute output was also generated. Daily output generated by the logger ended in 2014.
DOI: 10.5281/zenodo.6959023
title: Fire behavior dataset of Campos Amazônicos Fire Experiment (Amazonas, Brazil)

description: This dataset presents fire behavior data related to the Campos Amazônicos Fire Experiment (CAFE) (Amazonas, Brazil) project. Located within a protected area within the largest enclave of tropical savanna in the Southern Amazon, CAFE comprises a careful and systematic experimental design that was conceived from the start to evaluate satellite observations and their potential and limitations in studying spatial and temporal fire dynamics in tropical savannas. More information about the experimental design can be found in the following publication: Alves, D. B.; Fidelis, A.; Pérez-Cabello, F.; Alvarado, S. T.; Conciani, D. E.; Cambraia, B. C.; Silveira, A. L. P.; Silva, T. S. F. Impact of Image Acquisition Lag-Time on Monitoring Short-Term Postfire Spectral Dynamics in Tropical Savannas: the Campos Amazônicos Fire Experiment. Journal of Applied Remote Sensing v. 16, n. 3 (2022) - https://doi.org/10.1117/1.JRS.16.034507 _________________________________________________________________________________________________________ August 08, 2022 - Version 1.0 includes data from 24 experimental fires carried out in 2019 (12 in Early-Dry Season - EDS; 12 in Middle-Dry Season - MDS), each corresponding to a plot of 1 hectare (100x100 meters). Controlled burning occurred during two separate field campaigns in 2019, the first between May 19th and 25th, and the second between August 22nd and 26th. The files available include: i) a table (Fire_behavior_dataset.csv) that contains the fire parameters calculated for each experimental fire performed; ii) a text file (List_of_variables.rtf), which details each variable available in the table. _________________________________________________________________________________________________________ We thank the management team of the Campos Amazônicos National Park, and in particular to its Fire Brigade (squad leaders José Furtado Neto, Genaldo Júnior, Ademilton Carvalho, Simei Limoeiro, José Alexandre Medeiros, Antonio Machado and Leandro Lacerda, and on behalf of them to all other members of the brigade), who ensure safe burning of all fire experiments (SISBIO license number 67210-5). This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grant numbers 2019/07357-8; 2015/06743-0); the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant numbers 154660/2018-3; 441968/2018-0; 303988/2018-5)
DOI: 10.5281/zenodo.6959022
title: Fire behavior dataset of Campos Amazônicos Fire Experiment (Amazonas, Brazil)

description: This dataset presents fire behavior data related to the Campos Amazônicos Fire Experiment (CAFE) (Amazonas, Brazil) project. Located within a protected area within the largest enclave of tropical savanna in the Southern Amazon, CAFE comprises a careful and systematic experimental design that was conceived from the start to evaluate satellite observations and their potential and limitations in studying spatial and temporal fire dynamics in tropical savannas. More information about the experimental design can be found in the following publication: Alves, D. B.; Fidelis, A.; Pérez-Cabello, F.; Alvarado, S. T.; Conciani, D. E.; Cambraia, B. C.; Silveira, A. L. P.; Silva, T. S. F. Impact of Image Acquisition Lag-Time on Monitoring Short-Term Postfire Spectral Dynamics in Tropical Savannas: the Campos Amazônicos Fire Experiment. Journal of Applied Remote Sensing v. 16, n. 3 (2022) - https://doi.org/10.1117/1.JRS.16.034507 _________________________________________________________________________________________________________ August 08, 2022 - Version 1.0 includes data from 24 experimental fires carried out in 2019 (12 in Early-Dry Season - EDS; 12 in Middle-Dry Season - MDS), each corresponding to a plot of 1 hectare (100x100 meters). Controlled burning occurred during two separate field campaigns in 2019, the first between May 19th and 25th, and the second between August 22nd and 26th. The files available include: i) a table (Fire_behavior_dataset.csv) that contains the fire parameters calculated for each experimental fire performed; ii) a text file (List_of_variables.rtf), which details each variable available in the table. _________________________________________________________________________________________________________ We thank the management team of the Campos Amazônicos National Park, and in particular to its Fire Brigade (squad leaders José Furtado Neto, Genaldo Júnior, Ademilton Carvalho, Simei Limoeiro, José Alexandre Medeiros, Antonio Machado and Leandro Lacerda, and on behalf of them to all other members of the brigade), who ensure safe burning of all fire experiments (SISBIO license number 67210-5). This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grant numbers 2019/07357-8; 2015/06743-0); the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant numbers 154660/2018-3; 441968/2018-0; 303988/2018-5)
DOI: 10.5281/zenodo.6959334
title: Fuel loads monitoring dataset of Campos Amazônicos Fire Experiment (Amazonas, Brazil)

description: This dataset presents fuel loads monitoring data related to the Campos Amazônicos Fire Experiment (CAFE) (Amazonas, Brazil) project. Located within a protected area within the largest enclave of tropical savanna in the Southern Amazon, CAFE comprises a careful and systematic experimental design that was conceived from the start to evaluate satellite observations and their potential and limitations in studying spatial and temporal fire dynamics in tropical savannas. More information about the experimental design can be found in the following publication: Alves, D. B.; Fidelis, A.; Pérez-Cabello, F.; Alvarado, S. T.; Conciani, D. E.; Cambraia, B. C.; Silveira, A. L. P.; Silva, T. S. F. Impact of Image Acquisition Lag-Time on Monitoring Short-Term Postfire Spectral Dynamics in Tropical Savannas: the Campos Amazônicos Fire Experiment. Journal of Applied Remote Sensing v. 16, n. 3 (2022) - https://doi.org/10.1117/1.JRS.16.034507 _____________________________________________________________________________ August 08, 2022 - Version 1.0 includes data from 30 monitored experimental plots of 1 hectare each (100×100 m). Three experimental treatments were then established: 12 plots were burned in May (Early-Dry Season – EDS), further 12 plots were burned in August (Mid-Dry Season – MDS), and 6 plots were kept as control by ensuring fire exclusion throughout the duration of the experiment. Controlled burning occurred during two separate field campaigns in 2019, the first between May 19th and 25th, and the second between August 22nd and 26th. Measurements of fuel load were obtained from eight subplots of 0.5 × 0.5 m randomly distributed within each plot. Samples included graminoids, leaves and branches near the ground. Biomass was dried at 70°C for 48 hours, and weighed to determine total fuel load (kg. m<sup>-2</sup>) for each sample. Samples were taken before fire for all control, EDS and MDS burn plots during both field campaigns, and repeated sampling was carried out after fire for the burned plots. In 2020, all 30 monitored plots were sampled again in May and August. The files available include: i) a table (Fuel_load_measures.csv) that contains the measures of fuel loads for each plot; ii) a text file (List_of_variables.rtf), which details each variable available in the table. _____________________________________________________________________________ We thank the management team of the Campos Amazônicos National Park, and in particular to its Fire Brigade (squad leaders José Furtado Neto, Genaldo Júnior, Ademilton Carvalho, Simei Limoeiro, José Alexandre Medeiros, Antonio Machado and Leandro Lacerda, and on behalf of them to all other members of the brigade), who ensure safe burning of all fire experiments (SISBIO license number 67210-5). This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grant numbers 2019/07357-8; 2015/06743-0); the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant numbers 154660/2018-3; 441968/2018-0; 303988/2018-5).