cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14356607
title: CorcesNatureGenetics2016

description: scATAC-seq dataset processed for inclusion in scATAC.Explorer R package. scATAC.Explorer is an R package containing a curated collection of publicly available scATAC-seq datasets that can easily be searched and retrieved within R. Included datasets are processed into a consistent format for ease of analysis.<br>This dataset was not generated by our lab. Please also give credit to the source the dataset was retrieved from, included in reference field.
DOI: 10.6084/m9.figshare.14356595
title: BuenrostroCell2018

description: scATAC-seq dataset processed for inclusion in scATAC.Explorer R package. scATAC.Explorer is an R package containing a curated collection of publicly available scATAC-seq datasets that can easily be searched and retrieved within R. Included datasets are processed into a consistent format for ease of analysis.<br>This dataset was not generated by our lab. Please also give credit to the source the dataset was retrieved from, included in reference field.
DOI: 10.5281/zenodo.5140206
title: Data from: Microbe-dependent heterosis in maize

description: Data and statistical code associated with the manuscript "<strong>Microbe-dependent heterosis in maize" </strong>Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021) PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118 <strong>19 October 2020: </strong>new version posted to add <strong>fum_16S_ITS.zip</strong> Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage. <strong>27 July 2021: </strong>new version posted to add <strong>Expt4_data.xlsx</strong> and <strong>SynCom_colonization_data.xlsx</strong> . <strong>Expt4_data.xlsx </strong>= Raw data from Experiment 4 (Kansas field experiment, summer 2020) <strong>SynCom_colonization_data.xlsx</strong> = Raw measurements of colonization rates of SynCom bacterial strains in 4 maize genotypes
DOI: 10.25345/c51c2c
title: MassIVE MSV000087890 - Penicillium brasilianum cultivated on PDA and PDA control
title: extract from Penicillium brasilianum cultivated on PDA
DOI: 10.6084/m9.figshare.9977420
title: Code and data to reproduce the analyses in "Parasite species richness and host range are not spatially conserved"

description: Code and data to reproduce the article:<br>&gt; Dallas, T. and P. Jordano. 2021. Parasite species richness and host range are not spatially conserved.<br><br><br>
DOI: 10.6084/m9.figshare.9977420.v1
title: Code and data to reproduce the analyses in "Parasite species richness and host range are not spatially conserved"

description: Code and data to reproduce the article:<br>&gt; Dallas, T. and P. Jordano. 2021. Parasite species richness and host range are not spatially conserved.<br><br><br>
DOI: 10.5517/ccdc.csd.cc27qzyx
title: CCDC 2077680: Experimental Crystal Structure Determination

description: Related Article: Shengyang Guan, Thomas Pickl, Christian Jandl, Leon Schuchmann, Xiaoyu Zhou, Philipp J. Altmann, Alexander Pöthig|2021|Org.Chem.Front.|8|4061|doi:10.1039/D1QO00588J
DOI: 10.5517/ccdc.csd.cc27qzzy
title: CCDC 2077681: Experimental Crystal Structure Determination

description: Related Article: Shengyang Guan, Thomas Pickl, Christian Jandl, Leon Schuchmann, Xiaoyu Zhou, Philipp J. Altmann, Alexander Pöthig|2021|Org.Chem.Front.|8|4061|doi:10.1039/D1QO00588J
DOI: 10.5517/ccdc.csd.cc27xd2n
title: CCDC 2082861: Experimental Crystal Structure Determination

description: Related Article: Yanhua Hu, Zhenfeng Zhang, Yangang Liu, Wanbin Zhang|2021|Angew.Chem.,Int.Ed.|60|16989|doi:10.1002/anie.202106566
DOI: 10.6084/m9.figshare.15062358
title: Vibrio jascida genomes

description: This is a collection of seven novel V. jascida genomes isolated by the participants of the 2018 Microbial Diversity Course at the Marine Biological Laboratory (Peggy Lai, Danielle Campbell, Brittni Bertolet, Sarah Schwenck, and Monica E. McCallum).<br>The genomes are available as a courtesy of the course, but please get in touch with Rachel Whitaker (https://mcb.illinois.edu/faculty/profile/rwhitakr) if you wish to use them for anything.<br>An analysis of these genomes is available here:<br>https://merenlab.org/tutorials/vibrio-jasicida-pangenome/<br>
DOI: 10.6084/m9.figshare.15062358.v1
title: Vibrio jascida genomes

description: This is a collection of seven novel V. jascida genomes isolated by the participants of the 2018 Microbial Diversity Course at the Marine Biological Laboratory (Peggy Lai, Danielle Campbell, Brittni Bertolet, Sarah Schwenck, and Monica E. McCallum).<br>The genomes are available as a courtesy of the course, but please get in touch with Rachel Whitaker (https://mcb.illinois.edu/faculty/profile/rwhitakr) if you wish to use them for anything.<br>An analysis of these genomes is available here:<br>https://merenlab.org/tutorials/vibrio-jasicida-pangenome/<br>
DOI: 10.6084/m9.figshare.14558502
title: OTU Table O. Strigosa Characterization

description: OTU Table accompanying publication Characterization of the Gut Microbiome in Wild Rocky Mountainsnails (<i>Oreohelix strigosa</i>) by Chalifour & Li 2021. <b></b>
DOI: 10.6084/m9.figshare.14558496
title: Mapping File O. Strigosa Characterization

description: This mapping file accompanies the manuscript, Characterization of the Gut Microbiome in Wild Rocky Mountainsnails (<i>Oreohelix strigosa</i>), Chalifour & Li 2021. <b></b>
DOI: 10.6084/m9.figshare.14361032.v1
title: FreshAdultMouseBrainCellRanger1.1.0

description: scATAC-seq dataset processed for inclusion in scATAC.Explorer R package. scATAC.Explorer is an R package containing a curated collection of publicly available scATAC-seq datasets that can easily be searched and retrieved within R. Included datasets are processed into a consistent format for ease of analysis.<br>This dataset was not generated by our lab. Please also give credit to the source the dataset was retrieved from, included in reference field.
DOI: 10.6084/m9.figshare.15062367
title: Impact of a Nutrition Education Intervention on Salt/Sodium Related Knowledge, Attitude and Practice of University Students

description: This study aimed to assess salt related knowledge, attitude, and practices (KAP) among non-medical students at the University of Sharjah before and after administering an evidence-based nutrition education workshop and leaflet to students. Convenient sampling method was used to recruit 90 students to investigate KAP related to dietary salt/sodium intake. The KAP components were assessed before, immediately after and 4-weeks after administering an evidence-based educational workshop and leaflet.
DOI: 10.6084/m9.figshare.15062367.v1
title: Impact of a Nutrition Education Intervention on Salt/Sodium Related Knowledge, Attitude and Practice of University Students

description: This study aimed to assess salt related knowledge, attitude, and practices (KAP) among non-medical students at the University of Sharjah before and after administering an evidence-based nutrition education workshop and leaflet to students. Convenient sampling method was used to recruit 90 students to investigate KAP related to dietary salt/sodium intake. The KAP components were assessed before, immediately after and 4-weeks after administering an evidence-based educational workshop and leaflet.
DOI: 10.5281/zenodo.5140252
title: A High-resolution template and tractography framework for cardiac myofiber architecture description by diffusion MRI : an application to the ventriclar junctions

description: Data and materials regarding the submission of the paper. See Data Avaibility section and https://github.com/valeryozenne/Cardiac-Structure-Database
DOI: 10.5281/zenodo.5140199
title: Accompanying data set for the manuscript "REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention"

description: This data set contains all experimental and theoretical data included in the manuscript " REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention", namely: Figure 2: Raw data from theoretical model showing contributions of individual model components, Kaff = 0.3 Normalized data from theoretical model showing contributions of individual model components, Kaff = 0.3 Experimental NRTI Drug Screen 180 nt TTCA 500 nM dNTP Figure 3: Experiment-dNTP-Concentration-Screen Theory-dNTP-Concentration-Screen Experiment-Template-Length-Screen Theory-Template-Length-Screen Experiment-Sequence-Screen Theory-Sequence-Screen Figure 4: Experimental-NRTI-Drug-Screen-90nt-TCAA-only Theory-TCAA90-Kaff=0point2 Experimental-NRTI-Drug-Screen-GGCA-only Theory-GGCA180-Kaff=0point2 Figure 5: GGCA-vs-TTCA-Specificity-Analysis
DOI: 10.48366/r138542
title: A comprehensive Raman Spectroscopic analysis of Apollo returned rock samples

description: This comparison shows the Raman spectroscopic (scattering) analysis of minerals found in rock and soil samples returned from Apollo lunar missions, including Apollo 11, 12, 14, 15, 16, and 17. The contributions added in the comparison have analyzed Apollo returned lunar rock samples using more than one spectroscopic method, but only the intensity peaks from Raman spectral analysis are discussed here. This comparison will help the researchers and students in Earth and lunar sciences to build a general knowledge of the polymorphs of minerals on the lunar surface.
DOI: 10.6073/pasta/a2891bc60d2f09cb0064f235074d202a
title: Data for: Soil Nutrients Increase Long-term Soil Carbon Gains Threefold on Retired Farmland

description: These data report soil C for almost four decades following intensive agricultural soil disturbance along an experimentally imposed gradient in nitrogen (N) added annually in combination with other macro- and micro-nutrients. Data were collected at the Cedar Creek Ecosystem Science Reserve (CCESR), a U.S. Long Term Ecological Research (USLTER) site located in central Minnesota, USA. Soil % C accumulated over the course of the study in unfertilized control plots leading to a gain of 6.1 Mg C ha-1 in the top 20 cm of soil. Nutrient addition increased soil % C accumulation leading to a gain of 17.8 Mg C ha-1 in fertilized plots, nearly a threefold increase over the control plots. These results demonstrate that substantial increases in soil C in successional grasslands following agricultural abandonment occurs over decadal timescales, and that C gain is increased by high supply rates of soil nutrients. In addition, soil % C continued to increase for decades under elevated nutrient supply, suggesting that short-term nutrient-addition experiments underestimate the effects of soil nutrients on soil C accumulation.
DOI: 10.5281/zenodo.5140275
title: Phenomenological EOS Data Set

description: The MATLAB workspace file eos_data_set.mat contains the parameters and physical properties of 1,966,225 phenomenological neutron star (NS) equations of state (EOS).
DOI: 10.5063/kk996d
title: Diet composition and habitat use of piscivorous fishes (Arctic grayling, burbot, Dolly Varden, inconnu, and northern pike) in Chena, Unalakleet, and upper Yukon watersheds, 2013-2015

description: Predation on anadromous salmon can have important consequences for both predators and prey. Salmon provide large seasonal pulses of energy and nutrients via carcasses, eggs, and juveniles to many freshwater consumers, and conversely predation can represent a significant source of mortality for juvenile salmon. Recent declines of Chinook salmon (Oncorhynchus tshawytscha) populations in Alaska have raised concern that predation might inhibit their recovery. Using this dataset, we quantified patterns of predation by freshwater fishes on juvenile salmon across seasons, habitats, predator sizes, and streamflow levels in the Arctic-Yukon-Kuskokwim region of Alaska. We analyzed piscivore stomach contents and identified prey using DNA sequence ‘barcoding’. In coastal rivers, juvenile pink (O. gorbuscha) and chum (O. keta) salmon contributed heavily to Arctic grayling (Thymallus arcticus) and Dolly Varden char (Salvelinus malma) diets, coho salmon (O. kisutch) prey were rare, and Chinook salmon were not detected. In interior rivers, Arctic grayling, burbot (Lota lota), and northern pike (Esox lucius) consumed small numbers of Chinook salmon. Predation on Chinook salmon was documented disproportionately in sloughs during a summer of exceptionally high streamflow. Dietary and distributional patterns suggested northern pike and burbot may exclude salmon from sloughs in low-gradient river reaches that would otherwise provide suitable rearing habitat. The data also provided tentative support for the hypothesis that high streamflow induces juvenile Chinook salmon to move from mainstem habitats into sloughs, where they face an increased risk of mortality. Incorporating predation risk into climate adaptation, fisheries management, and habitat restoration decisions may help to facilitate Chinook salmon recovery. This analysis can be reproduced using the csv data files and 2 R scripts included. The analysis was conducted using R version 4.0.5. Run R scripts in this order: 1) Compile_discharge.R (compiles discharge data from USGS gauges) 2) Salmon_predation_data_analysis.R (reads in data from csv files, analyzes data, and produces output figures and tables)
DOI: 10.5281/zenodo.5139957
title: Phenomenological EOS Data Set

description: The MATLAB workspace file eos_data_set.mat contains the parameters and physical properties of 1,966,225 phenomenological neutron star (NS) equations of state (EOS).
DOI: 10.5281/zenodo.5138447
title: Phenomenological EOS Data Set

description: The MATLAB workspace file eos_data_set.mat contains the parameters and physical properties of 1,966,225 phenomenological neutron star (NS) equations of state (EOS).
DOI: 10.5281/zenodo.5140303
title: Accompanying data set for the manuscript "REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention"

description: This data set contains all experimental and theoretical data included in the manuscript " REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention", namely: RESTRICT_model: MATLAB script for completing calculations in the RESTRICT theoretical model. Figure 2: Raw data from theoretical model showing contributions of individual model components, Kaff = 0.3 Normalized data from theoretical model showing contributions of individual model components, Kaff = 0.3 Experimental NRTI Drug Screen 180 nt TTCA 500 nM dNTP Figure 3: Experiment-dNTP-Concentration-Screen Theory-dNTP-Concentration-Screen Experiment-Template-Length-Screen Theory-Template-Length-Screen Experiment-Sequence-Screen Theory-Sequence-Screen Figure 4: Experimental-NRTI-Drug-Screen-90nt-TCAA-only Theory-TCAA90-Kaff=0point2 Experimental-NRTI-Drug-Screen-GGCA-only Theory-GGCA180-Kaff=0point2 Figure 5: GGCA-vs-TTCA-Specificity-Analysis
DOI: 10.5281/zenodo.5140198
title: Accompanying data set for the manuscript "REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention"

description: This data set contains all experimental and theoretical data included in the manuscript " REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention", namely: RESTRICT_model: MATLAB script for completing calculations in the RESTRICT theoretical model. Figure 2: Raw data from theoretical model showing contributions of individual model components, Kaff = 0.3 Normalized data from theoretical model showing contributions of individual model components, Kaff = 0.3 Experimental NRTI Drug Screen 180 nt TTCA 500 nM dNTP Figure 3: Experiment-dNTP-Concentration-Screen Theory-dNTP-Concentration-Screen Experiment-Template-Length-Screen Theory-Template-Length-Screen Experiment-Sequence-Screen Theory-Sequence-Screen Figure 4: Experimental-NRTI-Drug-Screen-90nt-TCAA-only Theory-TCAA90-Kaff=0point2 Experimental-NRTI-Drug-Screen-GGCA-only Theory-GGCA180-Kaff=0point2 Figure 5: GGCA-vs-TTCA-Specificity-Analysis
DOI: 10.6073/pasta/91ab5dd187eeeca97b34a8af4a66ee42
title: PIE LTER nutrient samples collected by Sigma Autosampler between 2001 and 2017 in three headwater sites of contrasting land use, and at the Parker and Ipswich River Dams as they enter into the Plum Island Sound estuary, Massachusetts.

description: Total organic nitrogen, total organic phosphorus, and nitrate concentrations collected frequently by Sigma autosampler (or volunteers in winter) from 5 sites. Sites include three headwater sites of contrasting land use (CC= Forest, SB = suburban, CS = wetland) and at the mouth of the Ipswich and Parker Rivers where they flow into the estuary.
DOI: 10.5281/zenodo.5140328
title: Concatenated matrix from: Pristimantis trachyblepharis species group, a clade of miniaturized frogs: description of four new species and insights into the evolution of body size within the genus

description: Matrix in nexus format that include sequences of <em>RAG1 </em>(1 - 600 bp), <em>16S</em> (601 - 1912 bp), and <em>12S</em> (1913 - 2819 bp) genes for 347 specimens belonging to the genus Pristimantis, in addition to several specimens of neotropical frog genera as outgroups.
DOI: 10.5281/zenodo.4009094
title: Concatenated matrix from: Pristimantis trachyblepharis species group, a clade of miniaturized frogs: description of four new species and insights into the evolution of body size within the genus

description: Matrix in nexus format that include sequences of <em>RAG1 </em>(1 - 600 bp), <em>16S</em> (601 - 1912 bp), and <em>12S</em> (1913 - 2819 bp) genes for 347 specimens belonging to the genus Pristimantis, in addition to several specimens of neotropical frog genera as outgroups.
DOI: 10.6084/m9.figshare.15062532
title: Untitled Item

description: (1) Lipinski<br>From Sam<br><pre>def lip_filter(m):<br> score = 0<br> if getHBD(m) &lt;= 5: score += 1<br> if getHBA(m) &lt;= 10: score += 1<br> if getMW(m) &lt; 500: score += 1<br> if getLogP(m)&lt;= 5: score += 1 return score &gt;= 3 </pre>(2) Molecules can only have 'C H O N S P N F Cl Br I' atoms.<br>(3) No radicals or formal charges
DOI: 10.6084/m9.figshare.15062532.v1
title: Untitled Item

description: (1) Lipinski<br>From Sam<br><pre>def lip_filter(m):<br> score = 0<br> if getHBD(m) &lt;= 5: score += 1<br> if getHBA(m) &lt;= 10: score += 1<br> if getMW(m) &lt; 500: score += 1<br> if getLogP(m)&lt;= 5: score += 1 return score &gt;= 3 </pre>(2) Molecules can only have 'C H O N S P N F Cl Br I' atoms.<br>(3) No radicals or formal charges
DOI: 10.6084/m9.figshare.15062553
title: Figure sources

description: Data source for figures<br>
DOI: 10.6084/m9.figshare.15062553.v1
title: Figure sources

description: Data source for figures<br>
DOI: 10.15468/y9pkzc
title: An elusive new species of gymnophthalmid lizard (Cercosaurinae, Selvasaura) from the Andes of northern Peru

description: This dataset contains the digitized treatments in Plazi based on the original journal article Echevarria, Lourdes Y., Venegas, Pablo J., Garcia-Ayachi, Luis A., Nunes, Pedro M. Sales (2021): An elusive new species of gymnophthalmid lizard (Cercosaurinae, Selvasaura) from the Andes of northern Peru. Evolutionary Systematics 5 (2): 177-187, DOI: http://dx.doi.org/10.3897/evolsyst.5.68520, URL: http://dx.doi.org/10.3897/evolsyst.5.68520
DOI: 10.15468/j97ddz
title: Cyanescent Gyroporus (Gyroporaceae, Boletales) from China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Huang, Cong, Zhang, Ming, Wu, Xing-Liang, Wu, Gang, Xu, Jian-Ping, Yang, Zhu L., Li, Yan-Chun (2021): Cyanescent Gyroporus (Gyroporaceae, Boletales) from China. MycoKeys 81: 165-183, DOI: http://dx.doi.org/10.3897/mycokeys.81.65660, URL: http://dx.doi.org/10.3897/mycokeys.81.65660
DOI: 10.7298/z4x4-0160
title: Data from: Sex- and context-dependent effects of acute isolation on vocal and non-vocal social behaviors in mice
DOI: 10.34943/dc24ca56-3084-4e6a-b3cb-826b8773ea03
title: Endeavour South Current Meter Deployed 2012-06-14

description: The Nortek Aquadopp Current Meter A3L4889 AQD2572 was deployed on 2012-06-14 at Endeavour South. This south section of the Endeavour Hydrothermal Vents includes two moorings to monitor the regional circulation. This device is a Current Meter. Acoustic Current Meters (ACM) measure current speed and direction, using the Doppler Effect. Aquadopp current metres have a sensor head that contains 3 acoustic transducers, a tilt sensor, a temperature sensor and a pressure sensor. The instrument transmits a short pulse of sound, and then listens to its echo to measure the change in pitch or frequency. The change in pitch can determine the velocity of the current. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 2.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.15468/f73eep
title: Review of the Australian and New Zealand orb-weaving spider genus Novakiella (Araneae, Araneidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Framenau, Volker W., Vink, Cor J., Scharff, Nikolaj, Baptista, Renner L. C., Castanheira, Pedro de S. (2021): Review of the Australian and New Zealand orb-weaving spider genus Novakiella (Araneae, Araneidae). Zoosystematics and Evolution 97 (2): 393-405, DOI: http://dx.doi.org/10.3897/zse.97.67788, URL: http://dx.doi.org/10.3897/zse.97.67788
DOI: 10.6073/pasta/0ff448f12a7a5b17299a57e0aaf05736
title: A search index for the ecocomDP R package

description: This data package contains summary information of datasets in the ecocomDP format published by EDI and NEON. This summary information is formatted in a search index used by the search function of the ecocomDP R package.
DOI: 10.25345/c5wj9h
title: MassIVE MSV000087891 - Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry
title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation plays key roles in altering viral binding/function and infectivity. However, the molecular structures and glycan heterogeneity of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report the complete structural elucidation of intact O-glycan proteoforms through a hybrid native and denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR)-MS. Native top-down TIMS-MS/MS separates the protein conformers of the S-RBD to reveal their gas-phase structural heterogeneity, and top-down FTICR-MS/MS provides in-depth glycoform analysis for unambiguous identification of the glycan structures and their glycosites. A total of eight O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that this hybrid top-down MS approach can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.