cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7961237.v1
title: Additional file 1: of Comparative genomics reveals a lack of evidence for pigeons as a main source of stx2f-carrying Escherichia coli causing disease in humans and the common existence of hybrid Shiga toxin-producing and enteropathogenic E. coli pathotypes

description: Table S1. Characteristics of all 223 stx2f-carrying strains analysed in this study; accession number, country, source, isolation year, in silico serotype, in silico ST, rpoB sequence analysis and assembly statistics. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7961228
title: Additional file 1: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S1. Sequencing statistics of culture-enriched microbiomes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7961228.v1
title: Additional file 1: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S1. Sequencing statistics of culture-enriched microbiomes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7961216
title: Additional file 11: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S5. Number of resistance genes observed per microbiome and selectome with 70 percent identity to reference resistance genes from MERGEM. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7961213
title: Additional file 10: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S7. Families of antibiotic resistance genes associated with potential species of origin. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.7961216.v1
title: Additional file 11: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S5. Number of resistance genes observed per microbiome and selectome with 70 percent identity to reference resistance genes from MERGEM. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7961213.v1
title: Additional file 10: of Culture-enriched human gut microbiomes reveal core and accessory resistance genes

description: Table S7. Families of antibiotic resistance genes associated with potential species of origin. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.7961156
title: Xylem vessel and Parenchyma cell

description: This is an early version of the xylem shown in the "Xylem dysfunction during bacterial disease" figure set. <br><br>It is meant to be cropped.
DOI: 10.6084/m9.figshare.7961135
title: Squamate reptile vomeronasal type 2 receptor phylogenies and alignments

description: Gene alignments of vomeronasal type 2 receptor genes in squamate reptiles (transmembrane domains only), and resulting gene trees.
DOI: 10.6084/m9.figshare.7961120
title: Reconstructed global monthly land air-temperature dataset (1880-2017)

description: <pre>[List.dat] This file stored all station with valid location information, consist of: id used in GHCN4 (column 1), code used only for pure numerical id (column 2), longitude (column 3), latitude (column 4), and elevation (column 5).</pre><pre>[Raw_GHCN4_Data.DAT] This file is all data we used for the reconstruction. It has 14 columns. The first column is station code that is consistent with List.dat, the second column is year, and columns 3-14 are data in 12 months. The data are presenting at 0.01C. Missing values are flagged as -9999.</pre><pre>[Reconstructed_GHCN4_Data.DAT] This file consists of all reconstructed data. It has exactly same data structure with Raw_GHCN4_Data.DAT.</pre><pre>Using this dataset you should cite the follow paper:</pre><pre>Wang, Kang and Clow, Gary D. (2019). Reconstructed global monthly land air-temperature dataset (1880–2017). Geoscience Data Journal. DOI: https://doi.org/10.1002/gdj3.84</pre>
DOI: 10.6084/m9.figshare.7961117
title: Tomato plant - stem and leaves

description: Lineart of tomato seedling
DOI: 10.6084/m9.figshare.7961102
title: Dataset for: Analysis of paediatric visual acuity using Bayesian copula model with sinh-arcsinh marginal densities

description: We analyse paediatric ophthalmic data from a large sample of children aged between 3 and 8 years. We modify the Bayesian additive conditional bivariate copula regression model of Klein and Kneib (2015) by using sinh-arcsinh marginal densities with location, scale and shape parameters that depend smoothly on a covariate. We perform Bayesian inference about the unknown quantities of our model using a specially tailored Markov chain Monte Carlo algorithm. We gain new insights about the processes which determine transformations in visual acuity with respect to age, including the nature of joint changes in both eyes as modelled with the age-related copula dependence parameter. We analyse posterior predictive distributions to identify children with unusual sight characteristics, distinguishing those who are bivariate, but not univariate outliers. In this way we provide an innovative tool that enables clinicians to identify children with unusual sight who may otherwise be missed. We compare our simultaneous Bayesian method with the two-step frequentist generalized additive modelling approach of Vatter and Chavez-Demoulin (2015).
DOI: 10.6084/m9.figshare.7961087
title: Vesicle release model for ribbon synapse

description: In the attachment, all related data to generate diagrams of ribbon synapse with ModelCa is available.<br>
DOI: 10.6084/m9.figshare.7961102.v1
title: Dataset for: Analysis of paediatric visual acuity using Bayesian copula model with sinh-arcsinh marginal densities

description: We analyse paediatric ophthalmic data from a large sample of children aged between 3 and 8 years. We modify the Bayesian additive conditional bivariate copula regression model of Klein and Kneib (2015) by using sinh-arcsinh marginal densities with location, scale and shape parameters that depend smoothly on a covariate. We perform Bayesian inference about the unknown quantities of our model using a specially tailored Markov chain Monte Carlo algorithm. We gain new insights about the processes which determine transformations in visual acuity with respect to age, including the nature of joint changes in both eyes as modelled with the age-related copula dependence parameter. We analyse posterior predictive distributions to identify children with unusual sight characteristics, distinguishing those who are bivariate, but not univariate outliers. In this way we provide an innovative tool that enables clinicians to identify children with unusual sight who may otherwise be missed. We compare our simultaneous Bayesian method with the two-step frequentist generalized additive modelling approach of Vatter and Chavez-Demoulin (2015).
DOI: 10.6084/m9.figshare.7961120.v1
title: Reconstructed global monthly land air-temperature dataset (1880-2017)

description: <pre>[List.dat] This file stored all station with valid location information, consist of: id used in GHCN4 (column 1), code used only for pure numerical id (column 2), longitude (column 3), latitude (column 4), and elevation (column 5).</pre><pre>[Raw_GHCN4_Data.DAT] This file is all data we used for the reconstruction. It has 14 columns. The first column is station code that is consistent with List.dat, the second column is year, and columns 3-14 are data in 12 months. The data are presenting at 0.01C. Missing values are flagged as -9999.</pre><pre>[Reconstructed_GHCN4_Data.DAT] This file consists of all reconstructed data. It has exactly same data structure with Raw_GHCN4_Data.DAT.</pre><pre>Using this dataset you should cite the follow paper: []</pre>
DOI: 10.6073/pasta/54a41c062a42c0538e2a0aa6dd347bdb
title: Anaktuvuk River, Alaska, USA tussock tundra flowering in response to fire severity, 2008-2015

description: Eriophorum vaginatum flower counts from annual photographs at the severe, moderate, and unburned Anaktuvuk River, Alaska, USA flux tower sites during peak flowering season (6/17-7/20).
DOI: 10.6084/m9.figshare.7961051
title: Hookworm egg toxicity HTS screen and HeLa toxicity Hitpick Results.xlsx

description: Results of repeat testing of 268 compounds discovered in a HTS screen for inhibition of hookworm eggs hatching. Compounds were tested in singlicate at 10 uM. 100% effect is 10 uM albendazole. The same compounds were also tested against HeLa cells to rule out compounds that have the potential to be toxic to humans. 100% effect is 2.5 ug/mL puromycin.<br>
DOI: 10.6084/m9.figshare.7961087.v1
title: Vesicle release model for ribbon synapse

description: In the attachment, all related data to generate diagrams of ribbon synapse with ModelCa is available.<br>
DOI: 10.6084/m9.figshare.7961051.v1
title: Hookworm egg toxicity HTS screen and HeLa toxicity Hitpick Results.xlsx

description: Results of repeat testing of 268 compounds discovered in a HTS screen for inhibition of hookworm eggs hatching. Compounds were tested in singlicate at 10 uM. 100% effect is 10 uM albendazole. The same compounds were also tested against HeLa cells to rule out compounds that have the potential to be toxic to humans. 100% effect is 2.5 ug/mL puromycin.<br>
DOI: 10.6084/m9.figshare.7961018
title: Integrated Proteomics and Metabolomics Analysis Reveals Differential Lipid Metabolism in HUVEC under high and low shear stress

description: A table containing a list of proteins identified in HUVEC under low and high in vitro Shear stress.
DOI: 10.6084/m9.figshare.7961015
title: CCDB_3699.jpg

description: A maximum intensity projection image of a caulobacter crescentus specimen taken on an IVEM.
DOI: 10.6084/m9.figshare.7961015.v1
title: CCDB_3699.jpg

description: A maximum intensity projection image of a caulobacter crescentus specimen taken on an IVEM.
DOI: 10.5258/soton/d1439
title: Dataset for: Monitoring PSA levels as chemical state-variables in metal-oxide memristors

description: Dataset supports: Tzouvadaki, I., Stathopoulos, S., Abbey, T., Michalas, L., & Prodromakis, T. (2020). Monitoring PSA levels as chemical state-variables in metal-oxide memristors. Scientific Reports. Medical interventions increasingly rely on biosensors that can provide reliable quantitative information. A longstanding bottleneck in realizing this, is various non-idealities that generate offsets and variable responses across sensors. Current mitigation strategies involve the calibration of sensors, performed in software or via auxiliary compensation circuitry thus constraining real-time operation and integration efforts. Here, we show that bio-functionalized metal-oxide memristors can be utilized for directly transducing biomarker concentration levels to discrete memory states. The introduced chemical state-variable is found to be dependent on the devices’ initial resistance, with its response to chemical stimuli being more pronounced for higher resistive states. We leverage this attribute along with memristors’ inherent state programmability for calibrating a biosensing array to render a homogeneous response across all cells. Finally, we demonstrate the application of this technology in detecting Prostate Specific Antigen in clinically relevant levels (ng/ml), paving the way towards applications in large multi-panel assays.
DOI: 10.1184/r1/7961012.v1
title: Assessment of historical annual temperature and precipitation indices change in the U.S. cities

description: This dataset provide:a) annual average temperature, total precipitation, and temperature and precipitation extremes calculations for 210 U.S. cities.<br>b) historical rates of annual temperature, precipitation, and extremes change in the 210 U.S. cities.c) estimated thresholds (reference levels) for the calculations of annual extreme indices including warm and cold days, warm and cold nights, and precipitation amount from very wet days in the 210 cities.<br>Annual average of daily mean temperature, T<sub>max</sub>, and T<sub>min</sub> are included for annual average temperature calculations. Calculations were based on the compiled daily temperature and precipitation records at individual cities.<br>Temperature and precipitation extreme indices include: warmest daily T<sub>max</sub> and T<sub>min</sub>, coldest daily T<sub>max</sub> and T<sub>min</sub>, warm days and nights, cold days and nights, maximum 1-day precipitation, maximum consecutive 5-day precipitation, precipitation amounts from very wet days.<br>Number of missing daily T<sub>max</sub>, T<sub>min</sub>, and precipitation values are included for each city.<br>Rates of change were calculated using linear regression, with some climate indices applied with Box-Cox transformation prior to linear regression.<br>See included README file for more information.
DOI: 10.6084/m9.figshare.7960967
title: State Laws, Economic, Demographic, and Political Variables (20 states) 2000-2008

description: Laws in 20 states from 2000 to 2008 that restrict access, rights, or community integration related activities based on immigration status. Legislation was then classified to determine if the law affected education, regulation, or social welfare. Also includes economic and demographic variables or those state/years.
DOI: 10.1184/r1/7961012.v2
title: Historical changes of annual temperature and precipitation indices in the U.S. cities

description: This dataset provide:a) annual average temperature, total precipitation, and temperature and precipitation extremes calculations for 210 U.S. cities.<br>b) historical rates of annual temperature, precipitation, and extremes change in the 210 U.S. cities.c) estimated thresholds (reference levels) for the calculations of annual extreme indices including warm and cold days, warm and cold nights, and precipitation amount from very wet days in the 210 cities.<br>Annual average of daily mean temperature, T<sub>max</sub>, and T<sub>min</sub> are included for annual average temperature calculations. Calculations were based on the compiled daily temperature and precipitation records at individual cities.<br>Temperature and precipitation extreme indices include: warmest daily T<sub>max</sub> and T<sub>min</sub>, coldest daily T<sub>max</sub> and T<sub>min</sub>, warm days and nights, cold days and nights, maximum 1-day precipitation, maximum consecutive 5-day precipitation, precipitation amounts from very wet days.<br>Number of missing daily T<sub>max</sub>, T<sub>min</sub>, and precipitation values are included for each city.<br>Rates of change were calculated using linear regression, with some climate indices applied with Box-Cox transformation prior to linear regression.<br>See included README file for more information.<br>- 2019 June updated -<br>1. Baltimore was updated with the 2018 data (previously version shows NA for 2018) and new ID to reflect the GCHN ID of Baltimore-Washington International AP. city_info file was updated accordingly.<br>2. READ_ME file was updated to reflect the use of "wet days" index in this study. The 95% thresholds for calculation of wet days utilized all daily precipitation data from the reference period and can be different from the same index from some other studies, where only days with at least 1 mm of precipitation were utilized to calculate the thresholds. Thus the thresholds in this study can be lower than the ones that would've be calculated from the 95% percentiles from wet days (i.e., with at least 1 mm of precipitation).
DOI: 10.6084/m9.figshare.7960925
title: Acute changes in the colonic microbiota are associated with large intestinal forms of surgical colic.

description: The data and codes are from a study aimed at investigating changes in gut microbiota associated with large colon disease in horses. The study collected and compared faecal samples from surgical colic horses and horses admitted to the hospital for treatment of orthopaedic disease over a 3 months period.
DOI: 10.6084/m9.figshare.7960967.v1
title: Immigrant Related State Laws (20 states) 2000-2008

description: A list of laws in 20 states from 2000 to 2008 that restrict access, rights, or community integration related activities based on immigration status. Legislation was then classified to determine if the law affected education, regulation, or social welfare.
DOI: 10.6084/m9.figshare.7960967.v2
title: Immigrant Related State Laws (20 states) 2000-2008

description: A list of laws in 20 states from 2000 to 2008 that restrict access, rights, or community integration related activities based on immigration status. Legislation was then classified to determine if the law affected education, regulation, or social welfare.
DOI: 10.6084/m9.figshare.7960781
title: Data for PLOS ONE - PONE-D-19-03511R1

description: Effect of valsartan on the ICAM-4 activation on human red blood cells.
DOI: 10.6084/m9.figshare.7960967.v4
title: State Laws, Economic, Demographic, and Political Variables (20 states) 2000-2008

description: Laws in 20 states from 2000 to 2008 that restrict access, rights, or community integration related activities based on immigration status. Legislation was then classified to determine if the law affected education, regulation, or social welfare. Also includes economic and demographic variables or those state/years.
DOI: 10.6084/m9.figshare.7960967.v3
title: State Laws, Economic Variables, and Demographic Variables (20 states) 2000-2008

description: Laws in 20 states from 2000 to 2008 that restrict access, rights, or community integration related activities based on immigration status. Legislation was then classified to determine if the law affected education, regulation, or social welfare. Also includes economic and demographic variables or those state/years.
DOI: 10.6084/m9.figshare.7960781.v2
title: Data for PLOS ONE - PONE-D-19-03511R1

description: Effect of valsartan on the ICAM-4 activation on human red blood cells.
DOI: 10.6084/m9.figshare.7959473
title: Supplementary material for the paper “Quantification of predictive uncertainty in hydrological modelling by harnessing the wisdom of the crowd: A large-sample experiment at monthly timescale”

description: Supplementary material for the paper “Quantification of predictive uncertainty in hydrological modelling by harnessing the wisdom of the crowd: A large-sample experiment at monthly timescale”
DOI: 10.6084/m9.figshare.7959425
title: UC_SMS

description: Complementary material for the paper:<br>The impact of Use Cases in real-world software development projects: A systematic mapping study
DOI: 10.6084/m9.figshare.7959473.v1
title: Supplementary material for the paper “Quantification of predictive uncertainty in hydrological modelling by harnessing the wisdom of the crowd: A large-sample experiment at monthly timescale”

description: Supplementary material for the paper “Quantification of predictive uncertainty in hydrological modelling by harnessing the wisdom of the crowd: A large-sample experiment at monthly timescale”
DOI: 10.6084/m9.figshare.7959425.v2
title: UC_SMS

description: Complementary material for the paper:<br>The impact of Use Cases in real-world software development projects: A systematic mapping study
DOI: 10.6084/m9.figshare.7959377
title: Supplementary Figure 33 DLS and SDS PAGE confirm AtzBSH2 incorporation into the 3-component assembly

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Preprint: doi: 10.1101/274183 Fig S33. <b>DLS and SDS PAGE confirm AtzBSH2 incorporation into the 3-component 4 assembly.</b> AtzAM1, AtzBSH2, and AtzCM1 were added and allowed to incubate at various concentrations, then analyzed with DLS which showed that the addition of AtzBSH2 continues to have an assembly at ~1 µm. The SDS PAGE gel samples were pelleted and samples of the three component assembly supernatant and pellet were analyzed. If AtzBSH2 is incorporated into the assembly, it should partition preferentially into the pellet. The gels show that a band at the expected MW weight of AtzBSH2 ~69kda is seen predominantly in the pellet with increasing AtzBSH2 concentrations (Also see Fig S34). Standards for SDS-PAGE used are the BioRAD Precision Plus Protein Unstained Protein Standards. GelDoc EZ System Strain-free Imaging (BioRAD) was used to image and analyze the SDS-PAGE gel. Full gel with annotated ladder is provided for verification. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation 14 protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final 15 reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 16 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM 17 EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size 25 determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>
DOI: 10.6084/m9.figshare.7959377.v1
title: Supplementary Figure 33 DLS and SDS PAGE confirm AtzBSH2 incorporation into the 3-component assembly

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Preprint: doi: 10.1101/274183 Fig S33. <b>DLS and SDS PAGE confirm AtzBSH2 incorporation into the 3-component 4 assembly.</b> AtzAM1, AtzBSH2, and AtzCM1 were added and allowed to incubate at various concentrations, then analyzed with DLS which showed that the addition of AtzBSH2 continues to have an assembly at ~1 µm. The SDS PAGE gel samples were pelleted and samples of the three component assembly supernatant and pellet were analyzed. If AtzBSH2 is incorporated into the assembly, it should partition preferentially into the pellet. The gels show that a band at the expected MW weight of AtzBSH2 ~69kda is seen predominantly in the pellet with increasing AtzBSH2 concentrations (Also see Fig S34). Standards for SDS-PAGE used are the BioRAD Precision Plus Protein Unstained Protein Standards. GelDoc EZ System Strain-free Imaging (BioRAD) was used to image and analyze the SDS-PAGE gel. Full gel with annotated ladder is provided for verification. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation 14 protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final 15 reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 16 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM 17 EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size 25 determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>
DOI: 10.6084/m9.figshare.12877975
title: Additional file 2 of Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information

description: Additional file 2:AddFile2_results_of_T-test_vs_RanksSum_test.xls Excel files. Results of t-test and rank-sum test. Here contains heat-maps of log10 transformed P-values computed by both student T-test and Rank-sum test based on the same datasets (e.g. 11 histone acetylation levels from Kurdistani SK et al. for probes binding and coupling verse probes binding but not coupling). (XLSX 66 KB)