cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20357475.v2
title: Molecular evolution of vision-related genes may contribute to marsupial photic niche adaptations

description: Vision plays an essential role in the life of many animals. While most mammals are night-active (nocturnal), many have adapted to novel light environments. This includes diurnal (day-active) and crepuscular (twilight-active) species. Here, we used integrative approaches to investigate the molecular evolution of 112 vision-related genes across 19 marsupial genomes representing most marsupial orders. We found that four genes (<em>GUCA1B</em>, <em>GUCY2F</em>, <em>RGR</em>, and <em>SWS2</em>) involved in retinal phototransduction likely became functionally redundant in the ancestor of marsupials, a group of largely obligate nocturnal mammals. We also show evidence of rapid evolution and positive selection of bright-light vision genes in the common ancestor of <em>Macropus</em> (kangaroos, wallaroos, and wallabies). <em>Macropus</em>-specific amino acid substitutionsin opsin genes (<em>LWS</em> and <em>SWS1</em>), in particular, may be an adaptation for crepuscular vision in this genus via opsin spectral sensitivity tuning. Our study set the stage for functional genetics studies and provides a stepping-stone to future research efforts that fully capture the visual repertoire of marsupials.
DOI: 10.17632/c3trp7jt3n
title: Comparison of Yarrowia lipolytica growth and rProt synthesis when cultured in different vessels

description: 1. Introduction
The aim of this experiment was to quantitatively describe the costs of culturing Y. lipolytica strain synthesizing a fluorescent reporter protein (rProt) in different volumes / different vessels.

2. Methodology
The Yarrowia lipolytica strain used in this experiment was JMY2810 (genotype: MATa, ura3::pTEF-RedStar2-LEU2-Zeta-URA3ex-pTEF-empty, leu2-270, xpr2-322; phenotype: ΔAEP, ΔAXP, suc+, ura+, leu+, intracellular RedStarII, Zeta platform). The YPG medium was composed as follows [g L-1]: yeast extract, 10 (BTL, Lodz, Poland); peptone 20 (BTL); glycerol, 35 (POCH). Precultures were developed in standard YPG medium. All the media were autoclaved. Technical parameters of the culturing vessels used and shaking parameters are presented in Table 1 (pdf). 
The main cultures were continued for 48 h and samples were collected at the end of the cultivation time. Precultures were developed for 18h at 28 °C in the 300mL shake flasks. The main cultures were inoculated at 5% (v/v).
Samples were analyzed for growth and fluorescence from the reporter protein (RedStar2) following dilution in 0.75% NaCl (POCH) to match a linear range of the methods. Absorbance was measured at 600 nm in transparent 96-well plates (Costar; Merck). FL was determined under at ex/em 550/595 nm in black opaque plates (Thermo Fisher Scientific). Both measurements were done using a Tecan Spark automatic plate reader (Tecan Group Ltd., Mannedorf, Switzerland). pH level at the end of cultures was determined in the supernatant using indicatory strips (POCh, Poland).
The concentration of the carbon source and the main metabolites was analyzed through HPLC, under the following conditions: Agilent Technologies 1200 series (Agilent Technologies, Santa Clara, USA), equipped with a refractive-index detector (G1362A) and a Rezex ROA-Organic Acid H+ column (Phenomenex, Torrance, USA), and 0.005 N H2SO4 as eluent at a flow rate of 0.6 [mL/min], at 40 °C. The 96-well plate cultures were pooled to obtain sufficient amounts of the supernatant. The analysis was conducted in technical duplicate.
Statistical significance of the difference in a given measure was assessed by analysis of variance (ANOVA) test, with a significance level set at p-value &lt; 0.05 (RStudio and Visual Studio Code, Microsoft), and equality of variances was checked with the Levene test. The homogenous groups were calculated using Tukey HSD post-hoc analysis (RStudio with relevant packages). The results were calculated based on 5 – 48 biological repetitions.

3. Results
The raw results from fluorescence and optical density measurements, as well as the HPLC data, are presented in the Table S1 (xlsx) excel file. 
A graphical presentation of the data processed using statistical analysis is given in the main manuscript as Figures 1 to 4.
DOI: 10.6084/m9.figshare.1472942.v1
title: Crop Rotation Effects on Beauregard Sweetpotato Yield

description: Data showing the effect of crop rotation on Beauregard sweetpotato yield potential.
DOI: 10.6084/m9.figshare.21989735.v1
title: Cryptocurrency News Datasets

description: A total of 12,750 news headlines are obtained in the period between October 2021 and November 2022 from CoinTelegraph, CryptoNews and CryptoPotato.
DOI: 10.6084/m9.figshare.8323832.v1
title: VOC and NO2 levels for each plot

description: VOC and NO<sub>2</sub> levels for each plot
DOI: 10.6084/m9.figshare.11559852.v2
title: Assessing_the_reliability_of_predicted_plant_trait_distributions_at_the_global_scale.txt

description: Global trait data (SLA, LNC, height, wood density) of vascular plants, georeferenced at community mean level. Data includes intra-specific trait variation. We also have global predictions of these traits at 0.5degree resolution.<br>
DOI: 10.6084/m9.figshare.17138672.v4
title: 3DS_WAVE_VELOCITYMODEL_EPS.dat

description: The first column in the provided text file for the S-wave velocity model represents the Latitude, second column is the Longitude, third column is the depth (after topography correction), the fourth column is the S-wave velocity.<br>We also provide the input text file for the parameters used in the inversion.
DOI: 10.6084/m9.figshare.22631242.v1
title: Lead exposure levels.xlsx

description: The attachment summarizes the lead exposure levels of environmental media and diets in LMICs and 31 provinces in China.
DOI: 10.6084/m9.figshare.23849724.v1
title: 0.dataset.xlsx

description: Raw data used in this study
DOI: 10.6084/m9.figshare.12505712.v1
title: Questionnaire

description: The questionnaire used for user testing of transect tool that is submitted to CaGIS
DOI: 10.6084/m9.figshare.21453828.v1
title: Overall (Daily)State.csv

description: This is a dataset containing daily confirmed cases of covid 19 in Nigeria.
DOI: 10.6084/m9.figshare.23504907.v1
title: Dataset used in the paper "<strong>Temperature dissimilarity drives flower-visitor interaction turnover across elevation in the Mexican Transition Zone" </strong>accepted for publication in Journal of Biogeography

description: We established 10 sampling sites separated by ~200–500 m in elevation on the eastern slope of Cofre de Perote, spanning an elevational gradient from 4 to 3,425 m.a.s.l. Cofre de Perote is an extant volcano in the eastern part of the MTZ (between 19° 25’ 5.7” and 19° 36’ 54” N, and 94 ̊ 44’ 43.5” and 97 ̊ 09’ 36.9” W), right at the confluence of the volcanic transversal belt and the Sierra Madre Oriental. Cofre de Perote has an elevation of 4,282 m and its geological origin dates back to the Miocene (~20 million years ago, Figure 1). Our sampling sites were located in the Jamapa River basin, which encompasses the eastern slope of Cofre de Perote. Each of the sampling sites displayed different types of vegetation and were classified as coastal dunes (4–30 m elevation; temperature when the sampling was carried out ranging from 32 to 36 °C), dry deciduous forest (30–1,000 m; 23–31 °C), cloudy mountain forest (1,500–2,500 m; 19–20 °C), pine-oak forest (3,000 m; 10–16 °C), or fir forest (3,500 m; 7–13 °C); the tree line is located at approximately 3,700 m of elevation. We are providing interaction networks involving interactions between plants and their floral visitors for each elevation studied (n= 10). In addition, we are providing a general metadata with the information of each site where collections were performed.
DOI: 10.6084/m9.figshare.24210960.v1
title: Spectral data.CSV

description: Spectral data of h=0.3
DOI: 10.6084/m9.figshare.25609902.v1
title: The global dryland lake storage (GDLS) dataset

description: Monthly lake areas, surface elevation, and storage changes for 105,400 lakes and reservoirs in global drylands. This dataset contains five files:<b>1. 1_Dryland_lakeArea.parquet</b><br>Monthly lake areas (square kilometer) for 105400 lakes and reservoirs from Mar 1984 to Dec 2020.<br><b>2. 2_Dryland_lakeElevation.</b><b>parquet</b><br>Monthly lake elevation (m) for 105400 lakes and reservoirs from Mar 1984 to Dec 2020.<br><b>3. 3_Dryland_lakeStorage.</b><b>parquet</b><br>Monthly active lake storage (million cubic meter) for 105400 lakes and reservoirs from Mar 1984 to Dec 2020.<b>4. 4_Dryland_lakeLocation.</b><b>zip</b><br>Point shapefile for 105400 lakes and reservoirs. Derived from the HydroLAKES v1.0 dataset.<b>5. </b><b>5_Dryland_lakeUncertainty.csv</b><br>The uncertainty for DEM-based hypsometric relationship. Column "source" represents the DEM source. "occurrence_min" represents the minimum occurrence value for a lake. "occurrence_max" represents the maximum occurrence value for a lake. "elevation_min" represents the minimum value of the DEM (typically the water surface elevation of the DEM). "elevation_max" represents the maximum value of the DEM within the lake mask. "occurrence_lowestElev" represents the occurrence value that is corresponding to the DEM water surface. "number_of_occurrences" represents the number of occurrences that are less than 98%. "occurrence_pct" represents the percentage of exposed occurrences over entire occurrence range (occurrence_lowestElev/occurrence_max). "occurrence_sd" represents the standard deviation of occurrence values (smaller value means a more uniform distribution of occurrence).<b>6. </b><b>displayExample</b><b>.</b><b>ipynb</b><br>A Python example to show the location of a given lake and to plot monthly time series of area/elevation/storage for this lake.<br>Please cite: G. Zhao, H. Gao, Y. Li, Q. Tang, R. I. Woolway, J. Merder, L. Rosa, A. M. Michalak (2024), Decoupling of surface water storage from precipitation in global drylands due to anthropogenic activity, Nature Water<br>
DOI: 10.6084/m9.figshare.28233620.v1
title: Diversity and Horizontal Gene Transfer of Viruses in <i>Exserohilum turcicum</i> Population from Northern Corn Leaf Blight of Maize

description: <b>Raw chromatogram files (.ab1) and corresponding fasta sequences (.fasta) from Sanger sequencing validation of PCR amplification products.</b>
DOI: 10.6084/m9.figshare.28464461.v1
title: Mexico's High Resolution Climate Database (MexHiResClimDB): Monthly and yearly normals of Tmin, Tavg, Tmax and precipitation in Mexico for the 1971-2000 period

description: Monthly and yearly normals of Tmin, Tavg, Tmax and precipitation in Mexico for the 1971-2000 period. These normals were computed from the monthly values of the MexHiResClimDB which were in turn determined from the daily gridded values. <br>Filesmonthlynorm7100precip.zip Precipitation monthly normals, 1971-2000 periodmonthlynorm7100avgtmin.zip Minimum temperature monthly normals, 1971-2000 periodmonthlynorm7100avgtmax.zip Maximum temperature monthly normals, 1971-2000 periodmonthlynorm7100avgtavg.zip Average temperature monthly normals, 1971-2000 period<br>yearnorm7100precip.zip Precipitation yearly normal 1971-2000 periodyearnorm7100avgtmin.zip Minimum temperature yearly normal 1971-2000 periodyearnorm7100avgtmax.zip Maximum temperature yearly normal 1971-2000 periodyearnorm7100avgtavg.zip Average temperature yearly normal 1971-2000 period<br><br>
DOI: 10.6084/m9.figshare.7605653.v2
title: Annular Rupture Successfully Salvaged by Valve-in-Valve Implantation

description: Annular Rupture Successfully Salvaged by Valve-in-Valve Implantation
DOI: 10.17632/kpcgv763kc
title: Data related to article "Facemasks impair the recognition of facial expressions that stimulate empathy (sadness, fear and disgust): an ERP study"

description: In this study, ERPs were recorded in a group of 26 healthy male and female students engaged in recognizing 6 facial expressions of people wearing or not wearing surgical masks. Faces were preceded by the visual presentation of emotion prime words that were congruent or incongruent with the facial expression. The data of this collection are grand-average waveforms of Event-Related potentials (ERPs) recorded in healthy right-handed humans from 128 electrode sites at 512 Hz of sampling rate. The time epoch is 800 ms. ERP data were processed in two different ways: i) considering all EEG trials, or ii) only that not associated with an incorrect response. However, due to the largely uneven error rate across conditions (e.g., for masked faces or subtle emotions) ranging from 3.22 to 55.66%, the second method was considered unsound from the methodological point of view, and the more conservative and rigorous approach was preferred.  Differences across conditions (masked vs. unmasked) were in fact larger when considering only correct responses. It should be noted that ERPs computed on the correct recognitions mostly contained signals reflecting the processing of easier to recognize stimuli (e.g. happy unmasked faces).
DOI: 10.17632/x4s2jz55dx
title: Tomato fruits dataset for binary and multiclass classification

description: The dataset contains two batches each with 2400 images of tomatoes for binary and multiclass classification.
DOI: 10.6084/m9.figshare.19850938.v1
title: Crosshole Ground-Penetrating Radar study of glacial diamict succession outside Holbaek, Zealand, Denmark

description: Hi and welcome! Glad you're interested in our research!<br> Here are the data and code used for the paper <em>Crosshole Ground-Penetrating Radar in Clay-Rich Quaternary Deposits: Toward Characterization of High-Loss Media</em>, which is accepted in the Journal of Geophysical Research: Solid Earth and awaiting publication. The data repo is therefore under embargo until the paper is published. <br> The repo contains 4 main folders, each with their own detailed README:<br> <strong>Geological_site_description:</strong> The data describing the geology at the Holbæk (HOL) site. Also contains a long term storage .csv file of the sediment sample results. <br> <strong>GPR:</strong> The raw and semiprocessed GPR datafiles and metadata. Also contains a long term storage .csv file of the final GPR database. <br> <strong>GPS_and_survey_geometry:</strong> Contain everything related to the measurement of survey geometry as well as the GPS coordinates of the site. <br> <strong>python_processing _scripts: </strong>Contains the necessary python scripts to process the GPR data and recreate the figures containing results (fig 3-7). The bulk of the research is done in this folder. <br> The full-size of the unzipped folder is approx. 91 MB <br> We hope our data and scripts are useful!
DOI: 10.6084/m9.figshare.23773365.v2
title: <b>Reducing the fatal attraction of nocturnal insects using tailored and shielded road lights </b>

description: These Datasets contain insect catches from 2019-2022 from an Experimental field in Westhavelland (Project AuBe) and municipal sites in Baden-Württemberg (Project NaturLicht).
DOI: 10.6084/m9.figshare.28903109.v1
title: <b><i>Supplemental Files</i></b><b><i>:</i></b><b><i> </i></b><b>Early renal response to long term salt loading: Mitochondrial dysfunction, ER stress and uromodulin accumulation in the kidney medulla</b>.<b><i> </i></b>

description: This file consists of supplemental data from the manuscript titled.<b>Title: Early renal response to long term salt loading: Mitochondrial dysfunction, ER stress and uromodulin accumulation in the kidney medulla</b><b>Authors:</b>Humaira Parveen<sup>1*</sup>, Philipp Boder<sup>1*</sup>, William Mullen<sup>1</sup>, Delyth Graham<sup>1</sup>, Tom Van Agtmael<sup>1</sup>, Luca Rampoldi<sup>2</sup>, Christian Delles<sup>1#</sup>, Sheon Mary<sup>1#</sup><b>Affiliations</b><sup>1 </sup>School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, United Kingdom<sup>2</sup> Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
DOI: 10.6084/m9.figshare.861046.v2
title: Mouse PyX kinematic data - SPSS analysis

description: SPSS output for analysis of gait-related variables obtained via high-speed kinematic analysis in mice with unilateral corticospinal tract injury (or sham-injured mice). Please contact me with any questions or for further details. Associated with publication: Harel NY, Yigitkanli K, Fu Y, Cafferty WB, Strittmatter SM. Multimodal exercises simultaneously stimulating cortical and brainstem pathways after unilateral corticospinal lesion. Brain Res. 2013 Nov 13;1538:17-25. doi: 10.1016/j.brainres.2013.07.012.
DOI: 10.17632/yjz85cb3m7
title: Covid-19 Student Marks

description: Student Marks in English and non-English subjects, before and after Covid-19
DOI: 10.6084/m9.figshare.27274026.v1
title: <b>Biliary atresia and other pediatric cholestatic diseases</b>

description: The dataset comprises 2,576 ultrasound images from 1,019 infants with cholestatic diseases, including 664 fasting and 328 post-prandial images from 377 BA patients, and 1,004 fasting and 580 post-prandial images from 642 non-BA patients. Laboratory indicators such as total bilirubin (TBIL), direct bilirubin (DBIL), and gamma-glutamyl transpeptidase (GGT) are also included.
DOI: 10.6084/m9.figshare.29095478.v1
title: Spare parts

description: PredictionDataset collected in 5 years.
DOI: 10.17632/ftbdx4zcx7
title: Data for: Semi-Supervised Lexicon Generation Using Semantic Relations for Dream Content Analysis

description: Presented is an implementation of the SALAD algorithm for dream content analysis through word searching. Helper functions for constructing initial seed word dictionaries are provided in "hyponym_dictionary.py" which will also be used to construct the dictionaries from the seed words. "read_csv.py" reads and pre-processes the dream reports into a dictionary that captures the linguistic features of the words and sentences from the dreams. It also contains an implementation of the Improved Lesk Algorithm. The folder Series/ can be populated with data from any dream journal (you can take data from www.dreambank.net). The required data format is a csv file containing one dream in each row. The code "search_lemmas.py" performs the actual word search. The exact steps of SALAD and the parameters that need to be played around with to obtain the best results are described in the paper. The codes are written in Python 3.6 and can run on Python 3.6 and above.
DOI: 10.17632/z335r3hkf6
title: Electricity Prices In Australia 1953-2020

description: Data associated with submitted paper to Economic Analysis and Policy 'Australian Electricity Prices 1953-2020'
DOI: 10.6084/m9.figshare.28975343.v1
title: Data for our study.xlsx

description: This is the data supporting our submission.
DOI: 10.6084/m9.figshare.3513026.v1
title: Appendix F. Results of one-way ANOVAs testing for differences in (a) short sapling density, (b) tall sapling density, (c) volume of dead wood state 3, (d) volume of dead wood state 5, (e) canopy cover, and (f) canopy height among unlogged forest, older logged forest, and recently logged forest.

description: Results of one-way ANOVAs testing for differences in (a) short sapling density, (b) tall sapling density, (c) volume of dead wood state 3, (d) volume of dead wood state 5, (e) canopy cover, and (f) canopy height among unlogged forest, older logged forest, and recently logged forest.
DOI: 10.6084/m9.figshare.5106358.v1
title: Contributions Data

description: Data on contributions to Members of Congress by organizations that lobbied the 2014 Farm Bill. The data is derived from Federal Election Commission reports. <br>The Excel file "farmbill_contributions" contains the raw data (N=37,624) used to calculate the degree centrality of each organization.<br>The Excel file "contributions_centrality" is as summary file that contains the total contributions, the total number of recipients, and the degree centrality score for each organization (N=368).<br>The Excel file "agcomm_adjacency" contains an adjacency matrix of contribution ties between organizations that contributed to members of the House and Senate Agriculture Committees used to draw the sociogram in figure 1.
DOI: 10.6084/m9.figshare.4668823.v1
title: 6. MaxEnt output restructure R

description: MaxEnt response curves (output) xlsx files and matlab script describing data post-processing (from maxent2xlsx).R script to produce response curves graphs in R format. CSV files describe the response curve (average and std) - input for R script
DOI: 10.6084/m9.figshare.12038634.v1
title: sgRNA dataset used in machine learning

description: Two high-quality sgRNA activity datasets (Cas9 and eSpCas9,) used in the machine learning experiments (see Thesis chapter 4).
DOI: 10.6084/m9.figshare.28054232.v1
title: C. maritimum maritimum pollinators at the Carpinteria Salt Marsh

description: C. maritimum maritimum (CHMAMA) pollinator observations at the Carpinteria Salt Marsh conducted by the SB Botanic Garden.Data and code for "Rare Plant’s Need for Native Pollinators Threatened by Invasive Plant-Pollinator Relationship”"Content:CHMAMAPaperAnalyses.Rmd: Code with the data analyses and visualization used in the paper.data folder:CHMAMA_Carp_ALLDATA.csv: csv version of the data that is used in the R markdown codeEtter_etal_CHMAMA_data.xlsx: excel version of the data, that has an additional metadata tab that explains how the data in that column was collectedcarpnetwork_plantEDITED.csv and carpnetwork_visitor_EDITED.csv: csvs used to make the plant and pollinator group specieslevel network statistics figures (had to make a column in excel that I was unable to do in R)<br><br>
DOI: 10.6084/m9.figshare.5947444.v1
title: Collection data for Australian Museum, Sydney, family Nannastacidae specimens (Crustacea, Cumacea)

description: The Australian Museum, Sydney (AM) holds a large number of specimens of Cumacea (Crustacea). Within the family Nannastacidae 10 genera and 108 species have been identified. Cumacea specimens in the museum have been collected around Australia during the last four decades, mostly by museum staff. Among these samples, 48 were described as new species in a recent publication by the author (Petrescu, 2018, <i>Rec. Aust. Mus. </i>70(1):1–111, see link below). Collection data for all AM specimens examined in the above work are prefixed “P”, are cross-referenced to the Australian Museum database, and are published here as a dataset. Specimens held in the “Grigore Antipa” National Museum of Natural History, Bucharest, Romania, are marked MGAB CUM.
DOI: 10.6084/m9.figshare.16565982.v1
title: Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals

description: One-to-one single copy protein-coding orthologs in 30 representative mammals (including <em>Homo sapiens, Gorilla gorilla, Papio anubis, Aotus nancymaae, Microcebus murinus, Mus musculus, Rattus norvegicus, Castor canadensis, Cavia porcellus, Chinchilla lanigera, Marmota marmota, Oryctolagus cuniculus, Orcinus orca, Delphinapterus leucas, Capra hircus, Sus scrofa, Equus caballus, Ceratotherium simum, Canis lupus familiaris, Enhydra lutris, Odobenus rosmarus, Neomonachus schauinslandi, Rousettus aegyptiacus, Desmodus rotundus, Condylura cristata, Loxodonta africana, Trichechus manatus, Choloepus didactylus, Phascolarctos cinereus, Ornithorhynchus anatinus</em>) were generated by OrthoFinder, an all-against-all BLASTP algorithm. In total, 5334 protein-coding sequences were generated. Further, codon-based alignments were generated using MACSE with default parameters. Poorly aligned regions and gaps were trimmed using Gblocks. Finally, 5333 alignments were generated (TTN was too long to align successfully).
DOI: 10.6084/m9.figshare.24551971.v2
title: NEST - SolAce Energy Demand and User Practice Data

description: Measurement data for the SolAce building at NEST. The dataset consists of 18 measurement points with a temporal resolution of 1 minute. The data has been recorded over the duration of one year (July 2019 to July 2023). Metadata for each measurement point is stored in a separate file on this repository.