cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10519824
title: Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence

description: R and Mathematica scripts for "Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence"

This respository contains code accompanying the manuscript "Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence" by Pajares-Murgó et al.  The file *data.csv* contains the data obtained in the experiment of PSF. The dataset is divided by columns: Tray indicates each 15-cell plastic tray, ISO (individual soil sources) indicates the soil beneath 6 adult individuals of each species, ISE (individual seed sources) indicates the seeds collected from 5 adult individual of each species, CANOPY_soil and RECRUIT indicate the plant species, and success is the binomial variable that indicates the the proportion of experimental cells with soil of species j containing a seedling of species i at the end of the experiment.  The file *recruitment_density.csv* contains the data on the recruitment of plant species observed in the field. The dataset is divided by columns: CANOPY and RECRUIT indicate the plant species, Fij indicates the frequency of recruitment between pairs of species, Eij indicates the efficiency of recruitment between pairs of species (estimated as the number of saplings of species i recruiting under species j divided by the cover of the canopy and recruit species), cover_can indicates the cover of canopy species and cover_rec indicates the cover of recruit species.  The files *1. Testing for species-specific PSFs*, *2. Field crossvalidation*, *Pairwise-level feedback* and *Community-level feedback* contain an implementation of the models described in the Main Text, suitable for numerical integration, along with other useful functions for generating figures and analysis in the Main Text and figures and tables in the Supplementary Information.   Please email mpajares@ujaen.es or jmalcan@ujaen.es with any questions.
DOI: 10.5281/zenodo.10520057
title: The existence and the search method for global solutions of Navier-Stokes equation

description: We formulate and prove the variational extremum principle for viscous incompressible and compressible fluid, from which principle follows that the Naviet-Stokes equations represent the extremum conditions of a certain functional. We describe the method of seeking solution for these equations, which consists in moving along the gradient to this functional extremum. We formulate the conditions of reaching this extremum, which are at the same time necessary and sufficient conditions of this functional global extremum existence.

Then we consider the so-called closed systems. We prove that for them the necessary and sufficient conditions of global extremum for the named functional  always exist. Accordingly, the search for global extremum is always successful, and so the unique solution of Naviet-Stokes is found. 

We contend that the systems described by Naviet-Stokes equations with determined boundary solutions (pressure or speed) on all the boundaries, are closed systems. We show that such type of systems include systems bounded by impenetworkrable walls, by free space under a known pressure, by movable walls under known pressure, by the so-called generating surfaces, through which the fluid flow passes with a known speed.
DOI: 10.5281/zenodo.10520058
title: The existence and the search method for global solutions of Navier-Stokes equation

description: We formulate and prove the variational extremum principle for viscous incompressible and compressible fluid, from which principle follows that the Naviet-Stokes equations represent the extremum conditions of a certain functional. We describe the method of seeking solution for these equations, which consists in moving along the gradient to this functional extremum. We formulate the conditions of reaching this extremum, which are at the same time necessary and sufficient conditions of this functional global extremum existence.

Then we consider the so-called closed systems. We prove that for them the necessary and sufficient conditions of global extremum for the named functional  always exist. Accordingly, the search for global extremum is always successful, and so the unique solution of Naviet-Stokes is found. 

We contend that the systems described by Naviet-Stokes equations with determined boundary solutions (pressure or speed) on all the boundaries, are closed systems. We show that such type of systems include systems bounded by impenetworkrable walls, by free space under a known pressure, by movable walls under known pressure, by the so-called generating surfaces, through which the fluid flow passes with a known speed.
DOI: 10.34740/kaggle/dsv/7415916
title: Balochi Language to English Translation Dataset
DOI: 10.25345/c55d8nr5c
title: MassIVE MSV000093877 - Temporal multi-omic profiling reveals chemoradiotherapy-specific dualistic metabolic rewiring that supports glioblastoma tumor recurrence
title: Untargeted Metabolomics of patient-derived glioblastoma (GBM) cells treated with chemoradiotherapy (TMZRT) and the mitochondrial pyruvate carrier (MPC) inhibitor, UK-5099.
DOI: 10.5281/zenodo.10520090
title: Understanding Logical Expressions with Negations: Its Complicated
DOI: 10.5281/zenodo.10520091
title: Understanding Logical Expressions with Negations: Its Complicated
DOI: 10.5281/zenodo.10520094
title: Data and Code for "Limitations of XAI Methods for Process-Level Understanding in the Atmospheric Sciences" by Silva and Keller

description: This is the raw data (as netcdf) and processed data (as .Rdata files), alongside the analysis script (proc_bst.R) for "Limitations of XAI Methods for Process-Level Understanding in the Atmospheric Sciences" by Silva and Keller.
DOI: 10.5281/zenodo.10520095
title: Data and Code for "Limitations of XAI Methods for Process-Level Understanding in the Atmospheric Sciences" by Silva and Keller

description: This is the raw data (as netcdf) and processed data (as .Rdata files), alongside the analysis script (proc_bst.R) for "Limitations of XAI Methods for Process-Level Understanding in the Atmospheric Sciences" by Silva and Keller.
DOI: 10.5281/zenodo.10499186
title: Spatial Transcriptomic analysis (GeoMx) of SNc ventral tier dopamine cells in control and PD subjects

description: The repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of SNc ventral tier TH+ cells from Controls (n=10) and Early Parkinson's Disease subjects (n=8). A total 73 Regions of Interest were analysed. The processed counts and metadata are provided as an R Seurat object (geomx_110124_seurat.v5.Rdata). In addition raw DCC files are provided (DCC_Rademacher_2024.zip). The data was generated as part of the study Rademacher et al.,"Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration", 2024.

This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020529) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.
DOI: 10.5281/zenodo.10511809
title: Spatial Transcriptomic analysis (GeoMx) of SNc ventral tier dopamine cells in control and PD subjects

description: The repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of SNc ventral tier TH+ cells from Controls (n=10) and Early Parkinson's Disease subjects (n=8). A total 73 Regions of Interest were analysed. The processed counts and metadata are provided as an R Seurat object (geomx_110124_seurat.v5.Rdata). In addition raw DCC files are provided (DCC_Rademacher_2024.zip). The data was generated as part of the study Rademacher et al.,"Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration", 2024.

This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020529) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.
DOI: 10.5281/zenodo.10393326
title: Lagrangian particle release experiments from Prend et al. (2024)

description: This repository contains netCDF files with results from the Lagrangian particle release experiments presented in Prend et al. (2024). Please reach out to the corresponding author, Channing Prend (cprend@uw.edu) with any questions about the file contents.
DOI: 10.5281/zenodo.10393325
title: Lagrangian particle release experiments from Prend et al. (2024)

description: This repository contains netCDF files with results from the Lagrangian particle release experiments presented in Prend et al. (2024). Please reach out to the corresponding author, Channing Prend (cprend@uw.edu) with any questions about the file contents.
DOI: 10.6084/m9.figshare.25006937
title: Raw LC-MS/MS data files for yeast Leu mistranslation

description: This research identifies and quantifies mistranslation of phenylalanine codons with leucine across the Saccharomyces cerevisiae proteome.
DOI: 10.6084/m9.figshare.25006937.v1
title: Raw LC-MS/MS data files for yeast Leu mistranslation

description: This research identifies and quantifies mistranslation of phenylalanine codons with leucine across the Saccharomyces cerevisiae proteome.
DOI: 10.6084/m9.figshare.25008491
title: Bico da pedra reservoir water balance

description: Water balance of the Bico da Pedra reservoir to determine the monthly flow flowing into the reservoir.
DOI: 10.6084/m9.figshare.25008491.v1
title: Bico da pedra reservoir water balance

description: Water balance of the Bico da Pedra reservoir to determine the monthly flow flowing into the reservoir.
DOI: 10.5281/zenodo.10519984
title: Nanoscale Operando Characterization of Electrolyte-Gated Organic Field-Effect Transistors Reveals Charge Transport Bottlenecks

description: Dataset of the paper "Nanoscale Operando Characterization of Electrolyte-Gated Organic Field-Effect Transistors Reveals Charge Transport Bottlenecks" published in Advanced Materials, DOI: 10.1002/adma.202309767
DOI: 10.5281/zenodo.10519985
title: Nanoscale Operando Characterization of Electrolyte-Gated Organic Field-Effect Transistors Reveals Charge Transport Bottlenecks

description: Dataset of the paper "Nanoscale Operando Characterization of Electrolyte-Gated Organic Field-Effect Transistors Reveals Charge Transport Bottlenecks" published in Advanced Materials, DOI: 10.1002/adma.202309767
DOI: 10.5281/zenodo.10425521
title: IODP Expedition 363 Ion chromatography

description: Cation and anion concentration in interstitial water samples was measured by ion chromatography using a conductivity detector. Cation analytes include calcium, magnesium, potassium, and sodium. Anion analytes include chloride, sulfate, and bromide.
DOI: 10.5281/zenodo.10425522
title: IODP Expedition 363 Ion chromatography

description: Cation and anion concentration in interstitial water samples was measured by ion chromatography using a conductivity detector. Cation analytes include calcium, magnesium, potassium, and sodium. Anion analytes include chloride, sulfate, and bromide.
DOI: 10.5281/zenodo.10519770
title: Complete H coding sequence from a 1912 measles virus (Berlin, Germany)

description: This is the complete coding sequence of the H gene of a measles virus from 1912. This virus caused a fatal measles-related bronchopneumonia in the young patient, whose lung is preserved by the Berlin Museum of Medical History of the Charité (Berlin, Germany).

A first consensus genome was already published based on short Illumina reads generated from 9 libraries (DOI: 10.1126/science.aba9411). However, the coding sequence of the H gene still contained ambiguous positions, including at certain coding positions.

Since the original publication, we have built and sequenced an additional 9 libraries (following slight variations of the method described in the article), more than doubling the number of high-quality reads. Using the same base call criteria (at least three unique reads, majority rule), this enlarged dataset now allows for the recovery of a completely unambiguous H sequence coding sequence. 

Importantly, more conservative base call criteria (at least 10 unique reads, 90% agreement) only result in 22 ambiguous positions, out of which only two would encode different amino acids. The majority bases at these two positions account for 87% and 88% of all observed bases.

Therefore, we consider that this consensus nucleotide sequence (and its translation) represents a very high quality estimate of the underlying viral sequence.
DOI: 10.5281/zenodo.10519771
title: Complete H coding sequence from a 1912 measles virus (Berlin, Germany)

description: This is the complete coding sequence of the H gene of a measles virus from 1912. This virus caused a fatal measles-related bronchopneumonia in the young patient, whose lung is preserved by the Berlin Museum of Medical History of the Charité (Berlin, Germany).

A first consensus genome was already published based on short Illumina reads generated from 9 libraries (DOI: 10.1126/science.aba9411). However, the coding sequence of the H gene still contained ambiguous positions, including at certain coding positions.

Since the original publication, we have built and sequenced an additional 9 libraries (following slight variations of the method described in the article), more than doubling the number of high-quality reads. Using the same base call criteria (at least three unique reads, majority rule), this enlarged dataset now allows for the recovery of a completely unambiguous H sequence coding sequence. 

Importantly, more conservative base call criteria (at least 10 unique reads, 90% agreement) only result in 22 ambiguous positions, out of which only two would encode different amino acids. The majority bases at these two positions account for 87% and 88% of all observed bases.

Therefore, we consider that this consensus nucleotide sequence (and its translation) represents a very high quality estimate of the underlying viral sequence.
DOI: 10.5281/zenodo.10425519
title: IODP Expedition 363 ICP-AES elemental analysis (interstitial water)

description: Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.
DOI: 10.5281/zenodo.10425520
title: IODP Expedition 363 ICP-AES elemental analysis (interstitial water)

description: Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.
DOI: 10.6084/m9.figshare.25008629
title: Volume reservoir seasonal forecasts

description: Seasonal volume forecasts of the Bico da Pedra reservoir, based on forecasts from atmospheric models and simulation with the SMAP hydrological model.
DOI: 10.6084/m9.figshare.25008629.v1
title: Volume reservoir seasonal forecasts

description: Seasonal volume forecasts of the Bico da Pedra reservoir, based on forecasts from atmospheric models and simulation with the SMAP hydrological model.
DOI: 10.5281/zenodo.10425517
title: IODP Expedition 363 Hole summary

description: Report lists hole data: location, water depth, drilling, coring system, and core recovery.
DOI: 10.5281/zenodo.10425518
title: IODP Expedition 363 Hole summary

description: Report lists hole data: location, water depth, drilling, coring system, and core recovery.
DOI: 10.5066/p9mnklpj
title: EPA Impaired Waters presence and causes for HUC12 watersheds across the Conterminous U.S.
DOI: 10.5281/zenodo.10425515
title: IODP Expedition 363 Hole drilling summary

description: Report includes detailed drilling data: BHA length, bit parameters, and primary depth measurements.
DOI: 10.5281/zenodo.10425516
title: IODP Expedition 363 Hole drilling summary

description: Report includes detailed drilling data: BHA length, bit parameters, and primary depth measurements.
DOI: 10.6073/pasta/e43651bde3564e402cd0595e3ef26994
title: Forest tree, woody debris, and soil inventory data from long-term research plots for LTREB at the University of Michigan Biological Station

description: Disturbances to forests, such as logging or wildfires, typically lead to large losses of carbon and nutrients from both the plants and soils of the ecosystem. Virtually all forests are in some state of recovery from such disturbances, whether caused naturally or by humans. Knowledge of the time required for a forest to recover its original amounts of carbon and nutrients after a disturbance is not complete, nor is an understanding of how regrowing plants, recovering soils and the year to year variation in climate interact to control recovery as a forest ages. This project takes advantage of long existing research plots in forests at the University of Michigan Biological Station to figure out how changes in forest structure, carbon and nitrogen contents of the forests, and variations in climate act together through time to influence how fast trees grow, nitrogen is retained, and carbon is captured and stored in forests. Scientists and students will make regular measurements of the types of trees, their stem sizes and mass, their patterns of leaf arrangement, the amounts of carbon and nitrogen in soils, and other factors in five forest that were cut and burned in 1936, 1948, 1954, 1980, and 1998 and so today range from 20 years to 120 years old. Several nearby much older forests will also be sampled. This will let the project link disturbances, climate and ecology for forests that are broadly representative of those across the northern United States, Canada, Europe and Asia.
DOI: 10.5281/zenodo.10425509
title: IODP Expedition 363 Core drilling summary

description: Report includes detailed drilling data for each core: pump(s) used, mud pumped, strokes, shear pins/pressure, bit size/rotation, weight on bit, top drive torque, rate of penetration, core jams, winch and wirelines, core catcher/shoe and barrel, and whether core orientation, drillover, formation temperature, tracers, liners were used.
DOI: 10.5281/zenodo.10425510
title: IODP Expedition 363 Core drilling summary

description: Report includes detailed drilling data for each core: pump(s) used, mud pumped, strokes, shear pins/pressure, bit size/rotation, weight on bit, top drive torque, rate of penetration, core jams, winch and wirelines, core catcher/shoe and barrel, and whether core orientation, drillover, formation temperature, tracers, liners were used.
DOI: 10.6084/m9.figshare.24446608
title: data files

description: input files and mesh and tracer data files for first and final timestep
DOI: 10.57830/2302034
title: Navajo Sedge Inventory at Natural Bridges National Monument - Open Format Dataset (sensitive version)

description: Hanging gardens are an important part of the landscape at Natural Bridges National Monument (NABR) and are the most common type of spring within the park. These hanging gardens support a diversity of plant species including the federally listed threatened Navajo Sedge (Carex specuicola; CASP). CASP is confined to seep and spring emergences in sandstone outcroppings in the Four Corners area. Populations of CASP are known throughout northern Arizona and in southern Utah just south of NABR. Much of the potential habitat in southern Utah has not been surveyed for the species. Occurrences of CASP within NABR are at the northernmost extent of CASP’s range in the region and are also unique because they are in a canyon that is tributary to the Colorado River rather than the San Juan River. Since the extent of CASP populations were largely unknown, the objective of this project was to conduct a follow up inventory for CASP at hanging gardens in NABR to document occurrences of this species at NABR, its presence and absence in suitable habitat, and suggest sites to be incorporated into the regional monitoring program. Sites with positive occurrence of CASP could be targeted for increased protection by the park. Knowledge of these sites may also be used to advocate for management decisions such as the protection of water resources that recharge the springs of CASP habitat. This project resurveyed 64 previously known hanging gardens for CASP and documented and surveyed 26 new seeps found near the existing sites.
DOI: 10.5066/p9oicug4
title: Crop Specific Landsat Derived Reference Evapotranspiration, Evaporative Fraction, and Actual Evapotranspiration for 2016 in the California Central Valley

description: This dataset contains Landsat-derived images of Evaporative Fraction (ETf), Reference Evapotranspiration (ETo), and Actual Evapotranspiration (ETa) over a portion of California’s Central Valley for 15 dates in 2016. Each of the 15 images used in this study had three corresponding Tif files representing ETf, ETo, and ETa. Data used in this project was sourced from Landsat 8 Surface Reflectance Tier 1 images processed in Google Earth Engine (GEE). These images contain five visible and near-infrared (VNIR) bands and two short-wave infrared (SWIR) bands processed to orthorectified surface reflectance, and two thermal infrared (TIR) bands processed to orthorectified brightness temperature. To determine thermal properties of images to aid in ET calculation, the TIR Band 10 (B10) containing brightness temperature was chosen to determine Land Surface Temperature (LST).
DOI: 10.5281/zenodo.10425511
title: IODP Expedition 363 Gas safety report

description: This composite report returns data from two different gas chromatograph configurations (GC3 and NGA). Each row combines data from several measurements made on the same sample at the same time for a particular headspace or vacutainer sample. If data do not exist for a particular expedition, the column does not appear. Gas samples were measured by gas chromatography and either flame ionization detection (GC-FID) or thermal conductivity detection (GC-TCD). Reported analytes may include methane, ethane, ethene, propane, propene, n-butane, i-butane, n-pentane, i-pentane, n-hexane, i-hexane, n-heptane, i-heptane, nitrogen, oxygen, carbon monoxide, carbon dioxide, and hydrogen sulfide. When data are available, methane to (ethane + ethene) ratio (C1/C2�ratio) is reported. To identify individual samples and tests, see each separate analysis (GC3, NGAFID, and/or NGATCD).
DOI: 10.5281/zenodo.10425512
title: IODP Expedition 363 Gas safety report

description: This composite report returns data from two different gas chromatograph configurations (GC3 and NGA). Each row combines data from several measurements made on the same sample at the same time for a particular headspace or vacutainer sample. If data do not exist for a particular expedition, the column does not appear. Gas samples were measured by gas chromatography and either flame ionization detection (GC-FID) or thermal conductivity detection (GC-TCD). Reported analytes may include methane, ethane, ethene, propane, propene, n-butane, i-butane, n-pentane, i-pentane, n-hexane, i-hexane, n-heptane, i-heptane, nitrogen, oxygen, carbon monoxide, carbon dioxide, and hydrogen sulfide. When data are available, methane to (ethane + ethene) ratio (C1/C2�ratio) is reported. To identify individual samples and tests, see each separate analysis (GC3, NGAFID, and/or NGATCD).