cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4213047.v1
title: Supplementary Material for: A Codon Deletion at the Beginning of Green Fluorescent Protein Genes Enhances Protein Expression

description: Recombinant protein expression is one of the key issues in protein engineering and biotechnology. Among the different models for assessing protein production and structure-function studies, green fluorescent protein (GFP) is one of the preferred models because of its importance as a reporter in cellular and molecular studies. In this research we analyze the effect of codon deletions near the amino terminus of different GFP proteins on fluorescence. Our study includes Gly4 deletions in the enhanced GFP (EGFP), the red-shifted GFP and the red-shifted EGFP. The Gly4 deletion mutants and their corresponding wild-type counterparts were transcribed under the control of the T7 or Trc promoters and their expression patterns were analyzed. Different fluorescent outcomes were observed depending on the type of fluorescent gene versions. In silico analysis of the RNA secondary structures near the ribosome binding site revealed a direct relationship between their minimum free energy and GFP production. Integrative analysis of these results, including SDS-PAGE analysis, led us to conclude that the fluorescence improvement of cells expressing different versions of GFPs with Gly4 deleted is due to an enhancement of the accessibility of the ribosome binding site by reducing the stability of the RNA secondary structures at their mRNA leader regions.
DOI: 10.17632/4mr627f43d
title: Optimizing Resource Reallocation of Municipal Solid Waste Incineration During Operations Shutdown: A Centralized DEA Downsizing Model Incorporating Zero Sum Gains Variable

description: This dataset provides essential resources to ensure the reproducibility of our study, which focuses on optimizing resource reallocation strategies for municipal solid waste incineration during operational shutdowns.
DOI: 10.17632/7f323t8wsk
title: Origin, evolution and domestication of cultivated peanuts

description: Six representative gap-free genomes of peanuts were assembled. Complex transposable element activity, chromosomal rearrangement, and centromere expansion of subgenomes were characterized, contributing to the asymmetrical evolution since the origin of the tetraploid genome. Using these gap-free genomes, 521 peanut accessions collected worldwide were further resequenced and analyzed. This advancement aids in comprehensively understanding peanut origin and domestication, as well as exploring and enhancing breeding improvement.
DOI: 10.21943/auas.5143609.v1
title: Festivaldata on music- and filmfestivals in the Netherlands

description: Dataset of aggregated data on music festivals (2015 - 2019) and film festivals (2016 - 2019) in the Netherlands. Data is part of the 'Cultuurmonitor' and is presented and analysed in the book 'Festivals & Beleving' (Festivals & Experience'), out in summer 2022.
DOI: 10.6084/m9.figshare.28573559.v1
title: 亚热带蝙蝠越冬策略个体变异数据

description: 的日常活动数据<i>Ia io</i>冬期间黄昏
DOI: 10.6084/m9.figshare.5129197.v1
title: Supplementary Material for: Increased Plasma PCSK9 Levels Are Associated with Reduced Endotoxin Clearance and the Development of Acute Organ Failures during Sepsis

description: <b><i>Purpose:</i></b> We have recently shown that PCSK9 reduces the clearance of endotoxin and is therefore a critical regulator of the innate immune response during infection. However, plasma PCSK9 levels during human sepsis and their relationship to outcomes are not known. Our objective was to determine the relationship between plasma PCSK9 levels and the rate of endotoxin clearance, and then correlate PCSK9 levels with the development of acute organ failures in a cohort of patients with sepsis. <b><i>Methods:</i></b> Using human hepatocyte cells, we determined the threshold at which PCSK9 is able to reduce <i>Escherichia coli</i> endotoxin uptake by cultured human hepatocytes. In a single-centre observational cohort at St. Paul's Hospital in Vancouver, Canada, we recruited 200 patients who activated our Emergency Department's sepsis protocol and measured plasma PCSK9 and lipid levels at triage and throughout the admission. Outcomes were the development of sepsis-induced cardiovascular or respiratory failure. <b><i>Results:</i></b> We reviewed the literature and determined that the normal human range of PCSK9 found in plasma is 170-220 ng/ml, while levels of 250 ng/ml and above reduced <i>E. coli</i> endotoxin clearance in cultured human hepatocytes. In septic patients, the median levels associated with new-onset respiratory and cardiovascular failure were 370 (250-500) and 380 (270-530) ng/ml, respectively, versus 270 (220-380) ng/ml in patients who did not go on to develop any organ failure (p = 0.003 and 0.005, respectively). <b><i>Conclusions:</i></b> Plasma PCSK9 levels are greatly increased in sepsis. At normal levels, PCSK9 has no influence upon hepatocyte bacterial endotoxin clearance, but as levels rise, there is a progressive inhibition of clearance. During sepsis, PCSK9 levels are highly correlated with the development of subsequent multiple organ failure. Inhibition of PCSK9 activity is an attractive target for treating the spectrum of sepsis and septic shock.
DOI: 10.6084/m9.figshare.21614250.v1
title: A new ornithopod dinosaur, <i>Transylvanosaurus platycephalus</i> gen. et sp. nov. (Dinosauria: Ornithischia), from the Upper Cretaceous of the Haţeg Basin, Romania

description: Rhabdodontid dinosaurs were a group of medium-sized iguanodontian ornithopods from the Late Cretaceous of Europe. The uppermost Cretaceous continental deposits from the Haţeg Basin of western Romania yielded a very rich assemblage of vertebrates including abundant rhabdodontid remains, which have been exclusively referred to the genus <i>Zalmoxes</i> thus far. Here we describe a new rhabdodontid dinosaur, <i>Transylvanosaurus platycephalus</i> gen. et sp. nov., from the uppermost Cretaceous of the Haţeg Basin. The holotype of the new taxon was discovered in early–late Maastrichtian strata near Pui in the eastern part of the basin and comprises the articulated basicranium and both frontals. <i>Transylvanosaurus</i> differs from all previously reported rhabdodontids in having particularly wide and crested frontals, elongated and straight paroccipital processes that make only a gentle lateral curve and project mostly posterolaterally, prominent and massive prootic processes that extend mainly anterolaterally and ventrally, wide and crest-like basal tubera that meet the long axis of the braincase at a very flat angle, widely splayed basipterygoid processes that extend mainly ventrolaterally and slightly anteriorly, as well as a well-developed notch on the lateral side of the basicranium that is continuous, straight, and inclined anteroventrally. Phylogenetic analyses employing two different datasets consistently recovered the new taxon within the Rhabdodontidae, at the base of the iguanodontian radiation. Based on the morphological comparisons presented herein, we propose a particularly close relationship between <i>Transylvanosaurus</i> and <i>Rhabdodon</i> from southern France, which in turn provides evidence for a more complex biogeographic history of the Rhabdodontidae than previously thought.
DOI: 10.6084/m9.figshare.24039210.v1
title: Remanufacturing System Scheduling of Batch Products with the Consideration of Dynamic Changes in Machine Efficiency Using an Improved Artificial Bee Colony Algorithm

description: This is the experimental data of the manuscript entitled "Remanufacturing System Scheduling of Batch Products with the Consideration of Dynamic Changes in Machine Efficiency Using an Improved Artificial Bee Colony Algorithm".
DOI: 10.6084/m9.figshare.28896281.v1
title: BAZA DANYCH

description: Udostępnione dane stanowiły dane wyjściowe dla badania poziomu rozwoju społeczno-gospodarczego gmin powiatu krośnieńskiego w roku 2018 i 2023.
DOI: 10.17632/vncnwr9hhg
title: Data for: Significance of flexion range of motion as a risk factor for kyphotic change after cervical laminoplasty

description: This data, including 99 patients with degenerative cervical myelopathy, is for the elucidation of risk factor for kyphotic change after cervical laminoplasty. The study population was divided into two cohorts: the cases with and without marked loss of cervical lordosis after laminoplasty [cervical lordosis loss (CLL) group and no cervical lordosis loss (NCLL) group, respectively].
DOI: 10.6084/m9.figshare.19383749.v1
title: Species-specific repeat libraries generated by RepeatModeler2 - Part 2

description: We identified repetitive elements (REs) in genome assemblies using RepeatModeler2.0 (Flynn et al. 2019) with search engine “ncbi”, which generated these libraries of repeat consensus sequences.<br><br><br><i>Authors: John S. Sproul, Scott Hotaling, Jacqueline Heckenhauer, Ashlyn Powell, Amanda M. Larracuente, Joanna L. Kelley, Steffen U. Pauls, and Paul B. Frandsen</i>
DOI: 10.6084/m9.figshare.23657361.v1
title: sTable1. Codes for oral antihyperglycemic, insulin, diabetic ketoacidosis, and diabetes-related microvascular complications

description: sTable1. Codes for oral antihyperglycemic, insulin, diabetic ketoacidosis, and diabetes-related microvascular complications
DOI: 10.6084/m9.figshare.3490211.v3
title: Dataset for practice session 1 in bioinformatics

description: Dataset for the practice in the data preprocessing and unsupervised learning in the introduction to bioinformatics course
DOI: 10.6084/m9.figshare.27190578.v1
title: Raw Data for "A low-cost morphing vehicle design for enhanced aerodynamic performance"

description: This dataset contains the raw and processed data presented in the paper titled "A low-cost morphing vehicle design for enhanced aerodynamic performance".
DOI: 10.6084/m9.figshare.7570922.v5
title: SLR - Results PS

description: The csv table with the data of each paper (66 primary studies)
DOI: 10.6084/m9.figshare.1226520.v1
title: estres

description: estres
DOI: 10.6084/m9.figshare.23739984.v1
title: Putting theory to the test: an integrated computational/experimental chemostat model of the Tragedy of the Commons - raw data

description: Raw data for manuscript titled: <i>Putting theory to the test: An integrated computational/experimental chemostat model of the Tragedy of the Commons. </i><br><br>Empirical data is in the excel file tocpa_masterraw.xlsx. Each tab of the excel file contains the data for one figure/analysis and are named to correspond to the figure titles in the text.Random_allSims.txt and Random_Stable.txt are products of random simulation values used to determine the best parameter fit for the model.
DOI: 10.6084/m9.figshare.14280170.v1
title: [Natural canine distemper virus infection epizootiology characteristics in Belo Horizonte]

description: ABSTRACT The epizootiology profile of canine distemper in Belo Horizonte is outdated and does not harbor some important characteristics. A recent analysis of the virus distribution in relation to host and environmental characteristics associated with the main clinical signs and laboratory findings are important for adopting strategic measures to control the disease. The aim of this study was to determine the epizootiology characteristics of canine distemper virus infection associated with a variety of clinical and neurologic signs and laboratory findings in Belo Horizonte, helping to detect early infection and reduce morbidity and mortality rates. The evaluation of the epizootiology profile of 90 dogs revealed that the disease is more frequent in adult animals (1-6 years of age) and did not receive vaccines as recommended by the protocols. Extra neural and neural clinical signs were varied, with predominance for gastrointestinal and respiratory manifestations and myoclonus and motor deficit, respectively. Examination of the cerebrospinal fluid of 16 dogs showed a predominance of increase protein associated with lymphocytic pleocytosis. The immunochromatography test for antigen screening with samples of cerebrospinal fluid in 76 animals with neurological signs was effective in identifying the disease, unlike conjunctival swab samples, which should not be used.
DOI: 10.6084/m9.figshare.21308739.v1
title: Digital Surface Model Huon Coral Reef Terraces

description: <strong>Revised submission to Communications Earth and Environment (11/10/22):</strong> High interstadial sea levels over the past 420ka from the Huon Peninsula (Papua New Guinea) <br> <strong>Supplementary Data 5. Huon Digital Surface Model derived from Pleiades satellite imagery. </strong> We used tri-stereo 0.5 m-resolution Pleiades satellite images to calculate the topography of the Huon Peninsula terrace sequence. The open-source software Ames Stereopipeline (Beyer et al., 2018; reference 74 in the paper) allowed us to produce ortho-rectified images, point clouds and a 2 m-resolution DSM, to which we applied a -58.9 m vertical correction to account for the geoid height. We ground-checked absolute elevations of 10 control points along the coastline, that were all between 0 and 1 m elevation. We used a 30 m-resolution ALOS DSM to fill in the gaps that resulted from cloud coverage within the Pleiades DSM. The DSM is a Geotiff file, with UTM projection.
DOI: 10.6084/m9.figshare.8001218.v1
title: Detection of anti-correlation of hot and cold baryons in galaxy clusters

description: The largest clusters of galaxies in the Universe contain vast amounts of dark matter, plus baryonic matter in two principal phases, a majority hot gas component and a minority cold stellar phase comprising stars, compact objects, and low-temperature gas. Hydrodynamic simulations indicate that the highest-mass systems retain the cosmic fraction of baryons, a natural consequence of which is anti-correlation between the masses of hot gas and stars within dark matter halos of fixed total mass. We report observational detection of this anti-correlation based on 4 elements of a 9x9 element covariance matrix for nine cluster properties, measured from X-ray, optical, infrared and millimetre wavelength observations of 41 clusters from the Local Cluster Substructure Survey (LoCuSS). These clusters were selected using explicit and quantitative selection rules that were then encoded in our hierarchical bayesian model. Our detection of anti-correlation is consistent with predictions from contemporary hydrodynamic cosmological simulations that were not tuned to reproduce this signal. This result is reported in Farahi et al. (2019). Here we provide the posterior chains of our model.<br><br>See the readme file for more details.
DOI: 10.6084/m9.figshare.14955189.v1
title: Frontoparietal network resilience is associated with protection against cognitive decline in Parkinson’s disease

description: Please see manuscript for details.
DOI: 10.6084/m9.figshare.20231685.v1
title: TKCGANrelated

description: for academic
DOI: 10.6084/m9.figshare.28120928.v1
title: Data.xlsx

description: This data is presented in the Figshare database as the original data of the article named Paleolake Evolution in the Lower Yellow River Plain Since the Last Deglaciation: Chronological Insights on Formation, Expansion, and Contraction, including the photoluminescence dating data, the carbon-14 dating data, the particle size and magnetic susceptibility data. It is hoped that these can provide reliable data on lake evolution in the lower Yellow River plain.
DOI: 10.21253/dmu.8323049.v1
title: Ground penetrating radar dataset

description: Each .zip archive contains a collection of .dat files obtained via a Ground Penetrating Radar (GPR).The numerical values in each file are obtained by defining sampling points with a grid of equally spaced lines (50 mm distance between each other) on each coordinate axis.<br>Archive names follow the convention "GPR_ <i>DATE</i>.zip" where <i>DATE </i>can be either 30-08-2017 or 31-08-2017 while .mat file names follow the convention "GPR_<i>X#</i>_<i>Y#</i>.dat" where<i> X#</i> spans from X0 to X13 and<i> Y#</i> from Y0 to Y22.<br> <br>
DOI: 10.6084/m9.figshare.27139818.v1
title: Router data in northern Taiwan

description: The data consist of router relationship data from northern Taiwan, covering Taipei City, New Taipei City, Keelung City, Taoyuan City, Hsinchu County, Hsinchu City, the Matsu area, and Yilan County.
DOI: 10.6084/m9.figshare.5230396.v1
title: Supplementary Material for: TPOAb and Thyroid Function Are Not Associated with Breast Cancer Outcome: Evidence from a Large-Scale Study Using Data from the Taxotere as Adjuvant Chemotherapy Trial (TACT, CRUK01/001)

description: <b><i>Background:</i></b> Small-scale studies correlated the presence of thyroid autoimmunity with both improved or worsened breast cancer outcome. <b><i>Objectives:</i></b> We aimed to clarify this association in a large cohort using the phase III, randomized, controlled Taxotere as Adjuvant Chemotherapy Trial (TACT, CRUK01/001). <b><i>Methods:</i></b> TACT women &gt;18 years old with node-positive or high-risk node-negative early breast cancer (pT1–3a, pN0–1, M0), with stored plasma (<i>n</i> = 1,974), taken 15.5 (median; IQR 7.0–24.0) months after breast surgery were studied. Patients had also received chemotherapy (100%), radiotherapy (1,745/1,974; 88.4%), hormonal therapy (1,378/ 1,974; 69.8%), or trastuzumab (48/1,974; 2.4%). History of thyroid diseases and/or related treatments was not available. The prognostic significance of autoantibodies to thyroid peroxidase (TPOAb; positive ≥6 kIU/L), free-thyroxine and thyrotropin (combined: euthyroid, hypothyroid, hyperthyroid) was evaluated for disease-free survival (DFS), overall-survival (OS), and time-to-recurrence (TTR), with Cox regression models in univariate and multivariable analyses. The extended median follow-up was 97.5 months. <b><i>Results:</i></b> No difference in DFS was found by TPOAb status (unadjusted hazard ratio [HR]: 0.97, 95%CI: 0.78–1.19; <i>p</i> = 0.75) and/or thyroid function (unadjusted HR [hypothyroid vs. euthyroid]: 1.15, 95% CI: 0.79–1.68; <i>p</i> = 0.46; unadjusted HR [hyperthyroid vs. euthyroid]: 1.14, 95% CI: 0.82–1.61; <i>p</i> = 0.44). Similar results were obtained for OS, TTR, multivariable analyses, when TPOAb titre by tertiles was considered, and in a subgroup of 123 patients with plasma collected before adjuvant treatments. <b><i>Conclusions:</i></b> No evidence for a prognostic role of TPOAb and/or thyroid function in moderate-to-high-risk early breast cancer was found in the largest and longest observational study to date.
DOI: 10.17632/33ghjt876c
title: PML report

description: This data involves a case of PML after HSCT and blinatumomab.
DOI: 10.17870/bathspa.13917593.v1
title: Reportage Illustration - 300 word statement

description: <i>Reportage Illustration as Visual Journalism in Two World Cups</i> brings together two projects that explore the potential of drawing to visually capture and communicate a unique testimony of global sporting events to open up new ways of audience engagement.<br>This item contains the 300 word statement.
DOI: 10.6084/m9.figshare.28836179.v1
title: Academic

description: AMO theory on academic staff OCBE towards environmental performance HEIs
DOI: 10.60893/figshare.apl.26771059.v1
title: Supplement Number 2

description: Pictures of particles flying into optical traps
DOI: 10.6084/m9.figshare.21444900.v1
title: Active layer thickness distributions from 2011 to 2100 on the Qinghai permafrost regions.

description: Active layer thickness (ALT) at the baseline period (2001-2016) and ALT from 2011 to 2100 projected by the ensemble mean of 29 CMIP5 models under RCP4.5 scenarios over the permafrost region of the Qinghai Plateau.
DOI: 10.17632/zwvv3xx3rc
title: Species Distribution Modelling of Corals and Sponges from Research Vessel Survey Data in the Newfoundland and Labrador Region for Use in the Identification of Significant Benthic Areas

description: We used a species distribution modelling approach called random forest (RF) to predict the probability of occurrence and biomass of sponges, sea pens, and large and small gorgonian corals across the entire spatial extent of Fisheries and Oceans, Canada's (DFO) Newfoundland and Labrador Region. A suite of 66 environmental variables from different data sources were used. Models utilized catch records from the DFO multispecies trawl survey, DFO/industry northern shrimp surveys, and Spanish trawl surveys. Most models had excellent predictive capacity with cross-validated Area Under the Receiver Operating Characteristic Curve (AUC) values ranging from 0.786 to 0.926. Areas of suitable habitat were identified for each taxon and were contrasted against their known distribution. Generalized additive models (GAMs) were developed to predict the biomass distribution of each taxonomic group and serve as a comparison to the RF models. The RF and GAM models provided similar results, although GAMs provided superior predictions of biomass along the slopes of Newfoundland and Labrador for some taxonomic groups. Aside from providing continuous prediction maps of significant benthic taxa for the entire Newfoundland and Labrador Region that will be useful in ecosystem management decision-making processes, these results could be used to refine the outer boundaries of significant concentrations of these organisms identified by kernel density analyses and identify new suitable habitat not sampled by the trawl surveys.
DOI: 10.6084/m9.figshare.25671042.v1
title: Elsafty_RBCs_for_Segmentation_and_Detection_Slide_1

description: Each one of (Elsafty_RBCs_for_Segmentation_and_Detection_Slide_1-25) consists of three primary folders: "Cropped images,” "Masks,” and "Segmented images” corresponding to each slide/patient. The naming scheme for the cropped image, mask, and segmented image of every cell adheres to a consistent format, starting with the slide/patient number, followed by the unique patch/field number, and concluding with the (XYWH) coordination on the patch. All these images are conveniently stored in the lossless ".PNG" format.
DOI: 10.6084/m9.figshare.22359883.v3
title: <strong>EHPGS: A Statistical Package for Evaluation of Hybrid Performance in Plant Breeding via Genomic Selection </strong>

description: The dataset was used in the article "<strong>EHPGS: A Statistical Package for Evaluation of Hybrid Performance in Plant Breeding via Genomic Selection</strong>". In the dataset, the file name containing train.geno is the training population's genotype file, the file name containing train.pheno is the training population's phenotype file and the file name containing parent.geno is the parental lines' genotype file. The pumpkin dataset is originally from Wu et al. (2019) [1] ,and maize dataset and wheat dataset are originally from Guo et al. (2019) [2]. <br> 1. Wu, PY, Tung, CW, Lee, CY, and Liao, CT (2019) Genomic prediction of pumpkin hybrid performance. Plant Genome 12: 180082. 2. Guo, T, Yu, X, Li, X, Zhang, H, Zhu, C, Flint-Garcia, S. Michael, D, McMullen, JB, Holland, SJ, Szalma, RJ, and Yu, WJ (2019) Optimal Designs for Genomic Selection in Hybrid Crops. Mol Plant 12: 390-401.
DOI: 10.6084/m9.figshare.24147222.v1
title: Data.zip

description: The data are prepared to investigate changes in the intestinal microbiome in children with rotavirus enteritis.
DOI: 10.6084/m9.figshare.5400628.v2
title: Widefield GCaMP6 Imaging in Awake and Anesthetized Mice

description: Representative evoked and spontaneous GCaMP6 and HbO2 imaging data in awake and anesthetized mice associated with the manuscript "Functional Connectivity of Calcium Dynamics in Anesthetized and Awake Mice" by Wright et al., 2017 (PLOS ONE). Please see PLOS_DataSharing_Key for descriptions of individual items within this fileset.