cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22568647
title: Supplementary_Table_4_RNA-Seq_analysis.xlsx

description: Supplementary Table 4. A. Results from the DESeq2 differential analysis of gene expression in adenoma and colonic mucosa tissues before and after the dietary intervention. The number of DE miRNAs annotated with a validated interaction is also reported. B. List of biological processes, cell type- and disease-specific signatures enriched in the set of differentially expressed genes.
DOI: 10.6084/m9.figshare.19721629.v1
title: Experiences and knowing people/nature relations in watery spaces

description: Writing prompt and qualitative data descriptions in word file.
DOI: 10.5066/p92p8oud
title: Scanned field notebooks from a USGS Benchmark Glacier: South Cascade Glacier, Washington,1957 - 2022

description: This data release is a collection of data and field notes documenting snow and ice changes on South Cascade Glacier, Washington, USA. The field records relate to glaciological research and reflect evolving interpretations of glacier mass balance, climatology, hydrology, and other glacier-related research conducted at the site between 1957 to 2022 in association with the USGS Benchmark Glacier Project. Notebooks have been scanned in their entirety in PDF format. The USGS Benchmark Glacier Project has monitored targeted mountain glaciers across North America since research was initiated at South Cascade Glacier in 1957. Data from the five benchmark glaciers located in Alaska, Washington, and Montana, provide continental-scale insight into 20th century climate forcing and represent one of the longest continuous records of North American glacier mass balance. These intensively studied glaciers provide insight into the connection between climate and glaciers at multiple scales.
DOI: 10.5281/zenodo.7806224
title: Dataset for paper "X-ray spectra emitted by electronic brachytherapy unit Papillon 50 measured with CdTe spectrometer"

description: This dataset contains: 1) raw ".mca" files with pulse-height spectra of Papillon 50 unit obtained with X-123CdTe spectrometer.<br> 2) Unfolded photon fluence spectra. The dataset related to the paper "X-ray spectra emitted by electronic brachytherapy unit Papillon 50 measured with CdTe spectrometer."
DOI: 10.5281/zenodo.7806223
title: Dataset for paper "X-ray spectra emitted by electronic brachytherapy unit Papillon 50 measured with CdTe spectrometer"

description: This dataset contains: 1) raw ".mca" files with pulse-height spectra of Papillon 50 unit obtained with X-123CdTe spectrometer.<br> 2) Unfolded photon fluence spectra. The dataset related to the paper "X-ray spectra emitted by electronic brachytherapy unit Papillon 50 measured with CdTe spectrometer."
DOI: 10.6073/pasta/83a6e55c2c54b66b7088765882b6c1b9
title: The Jefferson Project 2019 water quality data from three vertical profiler stations in Lake George, NY, USA.

description: The Jefferson Project at Lake George -- a partnership between Rensselaer Polytechnic Institute, IBM Research, and Lake George Association -- combines Internet of Things technology and powerful analytics with science to create a new model for environmental monitoring and prediction. The project is building a computing platform that captures and analyzes data from a network of sensors tracking water quality and movement. These sensor data are combined with other monitoring and experimental data to create a thorough understanding of the factors that drive the lake's food web, hydrology, and water quality. More information about The Jefferson Project is available at https://jeffersonproject.rpi.edu/ In 2019, The Jefferson Project deployed three vertical profiler stations on the lake, collecting data on water quality and weather. Meteorological data have been included with the Jefferson Project Weather Station dataset for 2019. These vertical profiler stations are named VP_AnthonysNose, VP_CalvesPen, and VP_TeaIsland. The water quality data are collected by a YSI EXO2 Multi-parameter sonde sensors. The sensors collect data at 1 meter depth increments, starting at 1 meter and proceeding to 2 meters off bottom. The data are transferred in near real-time to an off-site database for monitoring and review. The data provided here have undergone data correction by Jefferson Project researchers.
DOI: 10.21227/k2xa-r534
title: Head and neck cancer analysis dataset

description: The aim of this study was to assess the predictive values of  first-order textural [18F]FDG PET/CT features on overall survival of head and neck squamous cell carcinoma (HNSCC) patients. An analysis was performed in 83 patients with HNSCC. Out of primary [18F]FDG PET and CT studies metabolic and volumetric parameters were analyzed, namely standardized uptake values (VOIs), CT values of the volumes of interest (VOIs), metabolic tumor volume (MTV), total lesion glycolysis (TLG) as well as asphericity (ASP). Inter- and intratumoral heterogeneity was assessed by first-order textural parameters related to histogram features, namely coefficient of variation (COV), skewness (SKE), kurtosis (K), and entropy (E). Correlation between mentioned parameters and overall survival (OS) and patients’ age was investigated. Univariate, multivariate Cox regression and Kaplan-Meier analysis with respect to OS was performed.
DOI: 10.6073/pasta/f8c771d3bd43bd2dfe88da3c24da2e5d
title: Tree Growth and Coarse Woody Debris in Regenerating Forests at Harvard Forest since 2008

description: This project is a field-based study to measure sequestration of atmospheric carbon dioxide in a regenerating New England forest. This study established long-term biometric plots suitable for measuring changes in carbon storage through time in three forest stands: an early-20th-century conifer plantation, a naturally regenerating former conifer plantation harvested in the 1990s, and a conifer plantation scheduled for harvest next winter. The first three years of this project determined the initial carbon budget of these forest stands, measured carbon fluxes into and out of these stands, and laid the groundwork for future investigations. Subsequent years will investigate larger-scale questions, such as how successional patterns affect carbon sequestration, and how these patterns change with stand age. The work also addresses how forestry practices influence carbon sequestration, and provide guidance for how forest management could enhance terrestrial carbon uptake in the future.
DOI: 10.5066/p9mqlnl2
title: Coastal Salinity Index for Monitoring Drought

description: The Coastal Salinity Index was applied to salinity data obtained from sites in North Carolina, South Carolina, Georgia, Florida, Alabama, Mississippi, Louisiana, Texas, and Puerto Rico. This data release will provide all the salinity data and Coastal Salinity Index results for many coastal salinity gages.
DOI: 10.6084/m9.figshare.22203018
title: A comprehensive proteomics analysis of the response of <i>Pseudomonas aeruginosa</i> to nanoceria cytotoxicity

description: The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although <i>Pseudomonas aeruginosa</i> may be ubiquitous in nature, it is largely found in locations closely linked with human activity. <i>P. aeruginosa</i> san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of <i>P. aeruginosa</i> san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in <i>P. aeruginosa</i> san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in <i>P. aeruginosa</i> san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.
DOI: 10.6084/m9.figshare.22203018.v1
title: A comprehensive proteomics analysis of the response of <i>Pseudomonas aeruginosa</i> to nanoceria cytotoxicity

description: The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although <i>Pseudomonas aeruginosa</i> may be ubiquitous in nature, it is largely found in locations closely linked with human activity. <i>P. aeruginosa</i> san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of <i>P. aeruginosa</i> san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in <i>P. aeruginosa</i> san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in <i>P. aeruginosa</i> san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.
DOI: 10.6084/m9.figshare.22285501
title: A harmonized protocol for an international multicenter prospective study of nanotechnology workers: the NanoExplore cohort

description: Nanotechnology applications are fast-growing in many industrial fields. Consequently, health effects of engineered nanomaterials (ENMs) should be investigated. Within the EU-Life project NanoExplore, we developed a harmonized protocol of an international multicenter prospective cohort study of workers in ENM-producing companies. This article describes the development of the protocol, sample size calculation, data collection and management procedures and discusses its relevance with respect to research needs. Within this protocol, workers’ ENM exposure will be assessed over four consecutive working days during the initial recruitment campaign and the subsequent follow-up campaigns. Biomonitoring using noninvasive sampling of exhaled breath condensate (EBC), exhaled air, and urine will be collected before and after 4-day exposure monitoring. Both exposure and effect biomarkers, will be quantified along with pulmonary function tests and diagnosed diseases reported using a standardized epidemiological questionnaire available in four languages. Until now, this protocol was implemented at seven companies in Switzerland, Spain and Italy. The protocol is well standardized, though sufficiently flexible to include company-specific conditions and occupational hygiene measures. The recruitment, to date, of 140 participants and collection of all data and samples, enabled us launching the first international cohort of nanotechnology workers. All companies dealing with ENMs could join the NanoExplore Consortium, apply this harmonized protocol and enter in the cohort, concieved as an open cohort. Its protocol meets all requirements of a hypotheses-driven prospective study, which will assess and reassess effects of ENM exposure on workers’ health by updating the follow-up of the cohort. New hypothesis could be also considered.
DOI: 10.6084/m9.figshare.22285501.v1
title: A harmonized protocol for an international multicenter prospective study of nanotechnology workers: the NanoExplore cohort

description: Nanotechnology applications are fast-growing in many industrial fields. Consequently, health effects of engineered nanomaterials (ENMs) should be investigated. Within the EU-Life project NanoExplore, we developed a harmonized protocol of an international multicenter prospective cohort study of workers in ENM-producing companies. This article describes the development of the protocol, sample size calculation, data collection and management procedures and discusses its relevance with respect to research needs. Within this protocol, workers’ ENM exposure will be assessed over four consecutive working days during the initial recruitment campaign and the subsequent follow-up campaigns. Biomonitoring using noninvasive sampling of exhaled breath condensate (EBC), exhaled air, and urine will be collected before and after 4-day exposure monitoring. Both exposure and effect biomarkers, will be quantified along with pulmonary function tests and diagnosed diseases reported using a standardized epidemiological questionnaire available in four languages. Until now, this protocol was implemented at seven companies in Switzerland, Spain and Italy. The protocol is well standardized, though sufficiently flexible to include company-specific conditions and occupational hygiene measures. The recruitment, to date, of 140 participants and collection of all data and samples, enabled us launching the first international cohort of nanotechnology workers. All companies dealing with ENMs could join the NanoExplore Consortium, apply this harmonized protocol and enter in the cohort, concieved as an open cohort. Its protocol meets all requirements of a hypotheses-driven prospective study, which will assess and reassess effects of ENM exposure on workers’ health by updating the follow-up of the cohort. New hypothesis could be also considered.
DOI: 10.25345/c5k35mq2j
title: MassIVE MSV000091655 - GNPS - carbamazapene standard vs reclaimed water vs reclaimed water snow
title: Carbamazapene standard was compared to carbamazapene in reclaimed water and snow made from reclaimed water
DOI: 10.6073/pasta/502e4d48e1ee3e1c63ce56eb8425f614
title: The Jefferson Project 2019 weather data from ten surface weather stations on Lake George, NY, USA.

description: The Jefferson Project at Lake George – a partnership between Rensselaer Polytechnic Institute, IBM Research, and Lake George Association – combines Internet of Things technology and powerful analytics with science to create a new model for environmental monitoring and prediction. The project is building a computing platform that captures and analyzes data from a network of sensors tracking water quality and movement. These sensor data are combined with other monitoring and experimental data to create a thorough understanding of the factors that drive the lake's food web, hydrology, and water quality. More information about The Jefferson Project is available at https://jeffersonproject.rpi.edu/ In 2019, The Jefferson Project had seven weather monitoring stations around the lake collecting data on precipitation, temperature, wind speed, wind direction, barometric pressure, and relative humidiity. These stations are WX_CedarLane, WX_DFWI, WX_GullRock, WX_MossyPoint, WX_WhaleRock, WX_PilotKnob, and WX_Glenburnie. Weather data from three vertical profiler sites (VP_AnthonysNose, VP_CalvesPen, and VP_TeaIsland) are also included in this dataset. The stations have a sensor payload that include some combination of the following sensors: Rotronic HC2-S3 sensor, Campbell Scientific CS616 soil moisture sensor, Li-Cor LI-200R pyranometers, RM Young 85006 anemometer, Vaisala Weather Transmitter WXT series (520 & 530 models), HyQuest TB3 tipping bucket rain gauge, N-Con wet deposition sampler. The sensors collect data at high-frequency (~1 sample per minute) and the data is transferred in near real-time to off-site databases for monitoring and review by Jefferson Project researchers. Data provided is level 4 data which has undergone data correction and downsampling to an hourly frequency.
DOI: 10.7289/v5q23xk7
title: NOAA Climate Data Record (CDR) of SSM/I and SSMIS Microwave Brightness Temperatures, RSS Version 8
DOI: 10.5281/zenodo.6467876
title: Feature selection on microbial profiles of CRC samples with chopin2

description: This Zenodo entry contains the result of the feature selection algorithm implemented in chopin2 applied on MetaPhlAn3 microbial profiles of a public dataset of metagenomic stool samples collected from patients affected by the colorectal cancer (CRC) as well as from healthy individuals (Thomas AM 2019). The feature selection algorithm is implemented as a backward variable elimination method, and it makes use of the hyperdimensional computing paradigm as described in Cumbo F 2020.
description: {"references": ["Cumbo, Fabio at al. (2020). \"A brain-inspired hyperdimensional computing approach for classifying massive DNA methylation data of cancer\". MDPI Algorithms 2020"]}
DOI: 10.5281/zenodo.7545662
title: Feature selection on microbial profiles of CRC samples with chopin2

description: This Zenodo entry contains the result of the feature selection algorithm implemented through a backward variable elimination strategy and in chopin2 applied on MetaPhlAn3 microbial profiles of a public dataset of metagenomic stool samples collected from patients affected by the colorectal cancer (CRC) as well as from healthy individuals. Microbial profiles have been extracted through the curatedMetagenomicData package for R under the IDs <em>ThomasAM_2018a</em>, <em>ThomasAM_2018b</em>, and <em>ThomasAM_2019_a</em>. The feature selection algorithm is implemented as a backward variable elimination method, and it makes use of the vector-symbolic architecture described in Cumbo F 2020. Deposited data is described below: <em>datasets.tar.gz</em>: it contains the datasets used as input of <em>chopin2</em> as the result of merging the three datasets with relative abundances mentioned above, also stratified by age and sex (with prefix RA). The same datasets have been also binarized (with prefix BIN); <em>hd-models.tar.gz</em>: it contains the output of the feature selection performed with <em>chopin2</em> on the datasets with both relative abundance and binary profiles (RA and BIN); <em>ml-models.tar.gz</em>: it contains the result of the feature selection produced with classical wrapper-based techniques (i.e., Random Forest, Decision Tree, Support Vector Machine, Logistic Regression, and Extreme Gradient Boosting) in addition to a Python 3.8 script to reproduce the results.
description: {"references": ["Cumbo, Fabio at al. (2020). \"A brain-inspired hyperdimensional computing approach for classifying massive DNA methylation data of cancer\". MDPI Algorithms 2020"]}
DOI: 10.48567/f13f-z455
title: Marble Point Automatic Weather Station, 1993 quality-controlled observational data.
DOI: 10.48567/nb15-1h93
title: Butler Island Automatic Weather Station, 2004 quality-controlled observational data.
DOI: 10.5517/ccdc.csd.cc2dn3fm
title: CCDC 2223860: Experimental Crystal Structure Determination

description: Related Article: Igor Litvinov|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxldb
title: CCDC 2232012: Experimental Crystal Structure Determination

description: Related Article: Igor Litvinov|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxvhp
title: CCDC 2232263: Experimental Crystal Structure Determination

description: Related Article: Tyler G. Saint-Denis, Bowen Zhang, Rex C. Handford, Nicholas Settineri, Michael B. Hall, T. Don Tilley|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxvjq
title: CCDC 2232264: Experimental Crystal Structure Determination

description: Related Article: Tyler G. Saint-Denis, Bowen Zhang, Rex C. Handford, Nicholas Settineri, Michael B. Hall, T. Don Tilley|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxvkr
title: CCDC 2232265: Experimental Crystal Structure Determination

description: Related Article: Tyler G. Saint-Denis, Bowen Zhang, Rex C. Handford, Nicholas Settineri, Michael B. Hall, T. Don Tilley|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5519/qd.lbp0av27
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (44 records)
DOI: 10.22002/aeffy-dcr62
title: The Materials Provenance Store

description: A PostgreSQL dump of the Materials Provenance Store (MPS), a database containing metadata and experimental provenance from synthesis to measurement of primarily metal oxide solid state materials resulting from high throughput experimentation.
description: This material is based on work performed by the Liquid Sunlight Alliance, which is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Fuels from Sunlight Hub under Award DE-SC0021266. Development of the database schema was supported by Toyota Research Institute. Much of the underlying data was generated by research in the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy (Award No. DE-SC0004993). Storage for MEAD is provided by the Open Storage Network via XSEDE allocation INI210004. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-76SF00515.
DOI: 10.48567/ykzw-6960
title: Byrd Automatic Weather Station, 2004 quality-controlled observational data.