cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4788868
title: Sea urchin density data

description: Data for the manuscript "Fear outweighs risk in adult sea urchins: prey size mediates consumptive and non-consumptive effects on top-down controlled marine ecosystems". Data from the sea urchin density surveys at high risk and low risk sites
DOI: 10.6084/m9.figshare.4788826
title: Predicting Membrane Protein Types Dataset4

description: Predicting Membrane Protein Types Dataset4
DOI: 10.6084/m9.figshare.4788865.v1
title: Halo lengths

description: <i>Data for the manuscript "Fear outweighs risk in adult sea urchins: prey size mediates consumptive and non-consumptive effects on top-down controlled marine ecosystems". Data from the experiment to determine predator influence on sea urchin grazing impact</i><br>
DOI: 10.6084/m9.figshare.4788826.v1
title: Predicting Membrane Protein Types Dataset4

description: Predicting Membrane Protein Types Dataset4
DOI: 10.6084/m9.figshare.4788814
title: Predicting Membrane Protein Types Dataset3

description: Predicting Membrane Protein Types Dataset3
DOI: 10.6084/m9.figshare.4788823
title: Behavioral data and task instructions

description: Behavioral data for gameplay and confidence report for N=57 subjects analyzed in the experiment.<br>Please open the README.pdf for instructions.Please download only the last version, as previous versions are susceptible to incompleteness or errors.
DOI: 10.6084/m9.figshare.4788853.v1
title: Data for large carnivores as socioecological keystone species

description: This file set contains the data analysed in Williams, K.S., Williams, S.T., Janse van Rensburg, N., Fitzgerald, L.E., Sheppard, E.C., Bell, S. and Hill, R.A. (in review) Large carnivores as socioecological keystone species.<br><br>There are three types of data included:1. data from a camera trap survey <br>2. data from interviews <br>3. data from scat analysis on leopard and brown hyaena scats <br><br>Please see the article for further details. <br><br><br>
DOI: 10.6084/m9.figshare.4788802
title: Predicting Membrane Protein Types Dataset2

description: Predicting Membrane Protein Types
DOI: 10.6084/m9.figshare.4788814.v1
title: Predicting Membrane Protein Types Dataset3

description: Predicting Membrane Protein Types Dataset3
DOI: 10.6084/m9.figshare.4788796
title: Predicting Membrane Protein Types Dataset1

description: Predicting Membrane Protein Types
DOI: 10.6084/m9.figshare.4788823.v1
title: Behavioral data

description: Behavioral data for gameplay and confidence report for all N=17 subjects.Please open the README.pdf for instructions.
DOI: 10.6084/m9.figshare.4788796.v1
title: Predicting Membrane Protein Types Dataset1

description: Predicting Membrane Protein Types
DOI: 10.6084/m9.figshare.4788823.v2
title: Behavioral data

description: Behavioral data for gameplay and confidence report for N=57 subjects analyzed in the experiment.Please open the README.pdf for instructions.
DOI: 10.6084/m9.figshare.4788823.v4
title: Behavioral data and task instructions

description: Behavioral data for gameplay and confidence report for N=57 subjects analyzed in the experiment.<br>Please open the README.pdf for instructions.Please download only the last version, as previous versions are susceptible to incompleteness or errors.
DOI: 10.6084/m9.figshare.4788823.v3
title: Behavioral data

description: Behavioral data for gameplay and confidence report for N=57 subjects analyzed in the experiment.Please open the README.pdf for instructions.
DOI: 10.6084/m9.figshare.4788736
title: Predicting Membrane Protein Types by Discrete Cosine Transform of Sequence

description: Predicting Membrane Protein Types by Discrete Cosine Transform of Sequence
DOI: 10.6084/m9.figshare.4788736.v1
title: Predicting Membrane Protein Types by Discrete Cosine Transform of Sequence

description: Predicting Membrane Protein Types by Discrete Cosine Transform of Sequence
DOI: 10.6084/m9.figshare.4788589
title: Final P. Pseudolobata Transcriptome

description: Final trinity and velvet pipeline assembly output of P. pseudolobata that was used for all subsequent analysis<br>
DOI: 10.6084/m9.figshare.4788586
title: Transcriptome Annotation File

description: Annotated transcripts in our P. pseudolobata transcriptome from the Annocript pipeline<br>
DOI: 10.6084/m9.figshare.4788589.v1
title: Final P. Pseudolobata Transcriptome

description: Final trinity and velvet pipeline assembly output of P. pseudolobata that was used for all subsequent analysis<br>
DOI: 10.6084/m9.figshare.4788583
title: matrix.counts.matrix

description: Raw counts matrix for transcripts for our P. pseudolobata differential expression analysis<br>
DOI: 10.6084/m9.figshare.4788586.v1
title: Transcriptome Annotation File

description: Annotated transcripts in our P. pseudolobata transcriptome from the Annocript pipeline<br>
DOI: 10.6084/m9.figshare.4788568
title: XFEM_Fracture2D (supplementary)

description: <b>Resolving the crack tip extension lengths</b><br><br>This is a supplementary (and separate) piece of code to the Matlab program XFEM_Fracture2D that attempts to justify the adequacy/inadequacy of the gradient-based energy minimization algorithm to solve for the critical crack tip extensions under the assumption (or the discretization constraint) of fixed-length crack tip extensions that is adopted by XFEM discretization in XFEM_Fracture2D<br><br>More specifically, the code included herein attempts to verify that the critical crack tip extension lengths can be determined provided: the cracks are <i>non-competing</i>, or the cracks are <i>competing </i>but the energy function is <i>convex</i>. Conversely, it is shown that the critical crack tip extension lengths can not be resolved robustly if the cracks are <i>competing</i> and the energy function is <i>non-convex</i> or <i>concave</i>. <br><br>Note that sufficiently small crack tip extensions are assumed in all cases.<br><br>Crack tip competition is defined as the fracture configuration where more than one crack tip has the same energy release rate. A convex energy function can be visualized as one where for any crack tip extension it's curvature is positive whereas a concave energy function is one where for any crack tip extension it's curvature is negative. There also exists the case of a non-convex or a partially-convex energy function which means that the curvature of the function is positive for certain crack tip extensions while negative for others; note that the non-convex case can not be resolved robustly either.<br><br>In order to resolve the cases of competing unstable crack growth while satisfying the XFEM discretization constraint of fixed-length crack tip extensions, it is necessary to:<br><br>1) perform a multi-trial energy minimization considering an explicit approximation of the total energy function via Tailor's series expansion so as to first determine the "ideal" crack tip extension lengths. This step (called the off-line solution step) serves to identify the critical crack tips exactly.<br>2) Given that the "ideal" crack tip extension lengths can not be represented in the XFEM discretization, the solution is to coarse the "ideal" solution by rounding it off to fit the XFEM discretization. <br><br>This two step procedure in combination with the gradient-based energy minimization algorithm proves to be effective in resolving the case of competing crack growth and a non-convex energy function, as demonstrated by the solutions to the fabricated cases that can be executed by running the attached Matlab code. <br><br>However, the proposed algorithm can not be implemented successfully in XFEM_Fracture2D because it is not possible to compute the curvature of the energy function with respect to the crack tip extension lengths sufficiently accurately. So, in the end, XFEM_Fracture2D can not be used to robustly resolve the case of competing crack growth and a non-convex energy function.<br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.4788583.v1
title: matrix.counts.matrix

description: Raw counts matrix for transcripts for our P. pseudolobata differential expression analysis<br>
DOI: 10.6084/m9.figshare.4788511
title: Portal Rodent Trapping Forecasts for March 2017

description: Predictions and 90% prediction intervals on the Portal rodent trapping results for 3/27 - 3/29/2017. Predictions are made for the next 12 months, by species and for total of all rodents, on all plots and on only the long-term controls. Details of the models used can be found at https://github.com/weecology/portalPredictions .
DOI: 10.6084/m9.figshare.4788511.v1
title: Portal Rodent Trapping Forecasts for March 2017

description: Predictions and 90% prediction intervals on the Portal rodent trapping results for 3/27 - 3/29/2017. Predictions are made for the next 12 months, by species and for total of all rodents, on all plots and on only the long-term controls. Details of the models used can be found at https://github.com/weecology/portalPredictions .
DOI: 10.6084/m9.figshare.4788025
title: Data driven CO2 fluxes in Asia

description: Output from Ichii et al. (2017) JGR-Biogeoscience:<br><br>Ichii K., M. Ueyama, M. Kondo, N. Saigusa, J. Kim, Ma. C. Alberto, J. Ardö, E.S. Euskirchen, M. Kang, T. Hirano, J. Joiner, H. Kobayashi, L. B. Marchesini, L. Merbold, A. Miyata, T.M. Saitoh, K. Takagi, A. Varlagin, M. S. Bret-Harte, K. Kitamura, Y. Kosugi, A. Kotani, K. Kumar, S.-G. Li, T. Machimura, Y. Matsuura, Y. Mizoguchi, T. Ohta, S. Mukherjee, Y. Yanagi, Y. Yasuda, Y. Zhang, F. Zhao (2017) New data-driven estimation of terrestrial CO2 fluxes in Asia using a standardized database of eddy covariance measurements, remote sensing data, and support vector regression. Journal of Geophysical Research Biogeosciences. 122, 767–795, doi: 10.1002/2016JG003640<br>
DOI: 10.6084/m9.figshare.4788025.v1
title: Ichii_et_al_JGR_2017.tar.gz

description: Ichii K., M. Ueyama, M. Kondo, N. Saigusa, J. Kim, Ma. C. Alberto, J. Ardö, E.S. Euskirchen, M. Kang, T. Hirano, J. Joiner, H. Kobayashi, L. B. Marchesini, L. Merbold, A. Miyata, T.M. Saitoh, K. Takagi, A. Varlagin, M. S. Bret-Harte, K. Kitamura, Y. Kosugi, A. Kotani, K. Kumar, S.-G. Li, T. Machimura, Y. Matsuura, Y. Mizoguchi, T. Ohta, S. Mukherjee, Y. Yanagi, Y. Yasuda, Y. Zhang, F. Zhao (2017) New data-driven estimation of terrestrial CO2 fluxes in Asia using a standardized database of eddy covariance measurements, remote sensing data, and support vector regression. Journal of Geophysical Research Biogeosciences. doi: 10.1002/2016JG003640<br>
DOI: 10.6084/m9.figshare.4787887
title: S8 Table

description: Summary of the %Area of Bcl-2.
DOI: 10.6084/m9.figshare.4787890
title: S9 Table

description: Summary of the %Area of Bax
DOI: 10.6084/m9.figshare.4787884
title: S7 Table

description: Summary of the %Area of p53
DOI: 10.6084/m9.figshare.4788025.v2
title: Data driven CO2 fluxes in Asia

description: Output from Ichii et al. (2017) JGR-Biogeoscience:<br><br>Ichii K., M. Ueyama, M. Kondo, N. Saigusa, J. Kim, Ma. C. Alberto, J. Ardö, E.S. Euskirchen, M. Kang, T. Hirano, J. Joiner, H. Kobayashi, L. B. Marchesini, L. Merbold, A. Miyata, T.M. Saitoh, K. Takagi, A. Varlagin, M. S. Bret-Harte, K. Kitamura, Y. Kosugi, A. Kotani, K. Kumar, S.-G. Li, T. Machimura, Y. Matsuura, Y. Mizoguchi, T. Ohta, S. Mukherjee, Y. Yanagi, Y. Yasuda, Y. Zhang, F. Zhao (2017) New data-driven estimation of terrestrial CO2 fluxes in Asia using a standardized database of eddy covariance measurements, remote sensing data, and support vector regression. Journal of Geophysical Research Biogeosciences. doi: 10.1002/2016JG003640<br>
DOI: 10.6084/m9.figshare.4787881
title: S6 Table

description: Summary of the Ct of p53,Bax,Bcl-2 and GAPDH
DOI: 10.6084/m9.figshare.4787878
title: S5 Table

description: Summary of the content of G0/G1,S and G2/M cells data
DOI: 10.6084/m9.figshare.4787875
title: S4 Table

description: Summary of the content of bone marrow apoptosis rate data
DOI: 10.6084/m9.figshare.4787677
title: rs_ab_ac_bc_variables

description: simulation of B-C correlations given A-B and A-C correaltion. The code (corr_a_b_c.m) and figures are hosted in github: https://github.com/Conxz/vis<br>simulated A-B and A-C correlation from 0.01 to 0.90 with a step of 0.01. the simulation was repeated 1000 times. <br>so the dimention of the data (matlab mat file) is 90x90x1000.<br><br>
DOI: 10.6084/m9.figshare.4787665
title: SVHN dataset batches

description: This is a copy of the SVHN dataset (http://ufldl.stanford.edu/housenumbers/), that has been formatted to work with both `cuda-convnet2` (https://github.com/akrizhevsky/cuda-convnet2) and `nengo_extras` (https://github.com/nengo/nengo_extras). I take no credit for this dataset.
DOI: 10.6084/m9.figshare.4787677.v2
title: rs_ab_ac_bc_variables

description: simulation of B-C correlations given A-B and A-C correaltion. The code (corr_a_b_c.m) and figures are hosted in github: https://github.com/Conxz/vis<br>simulated A-B and A-C correlation from 0.01 to 0.90 with a step of 0.01. the simulation was repeated 1000 times. <br>so the dimention of the data (matlab mat file) is 90x90x1000.<br><br>
DOI: 10.6084/m9.figshare.4787533
title: Descriptive characteristics of colon and rectal cancer recurrence in a Danish population-based study

description: <b>Background:</b> Recurrence is a common outcome among patients that have undergone an intended curative resection for colorectal cancer. However, data on factors that influence colorectal cancer recurrence are sparse. We report descriptive characteristics of both colon and rectal cancer recurrence in an unselected population. <b>Material and methods:</b> We identified 21,152 patients with colorectal cancer diagnosed between May 2001 and December 2011 and registered with the Danish Colorectal Cancer Group. Recurrences were identified in 3198 colon and 1838 rectal cancer patients during follow-up. We calculated the frequency, proportion, and incidence rates of colon and rectal cancer recurrence within descriptive categories, and the cumulative five- and ten-year incidences of recurrence, treating death as a competing risk. We used a Cox proportional hazard model to calculate hazard ratios (HR) and 95% confidence intervals (CI). <b>Results:</b> Recurrence risk was highest in the first three years of follow-up. Patients &lt;55 years old at initial diagnosis (incidence rate for colon: 7.2 per 100 person-years; 95% CI: 6.5–7.9; rectum: 8.1 per 100 person-years; 95% CI: 7.2–9.0) and patients diagnosed with stage III cancer (colon HR: 5.70; 95% CI: 4.61–7.06; rectal HR: 7.02; 95% CI: 5.58–8.82) had increased risk of recurrence. Patients diagnosed with stage III cancer from 2009 to 2011 had a lower incidence of recurrence than those diagnosed with stage III cancer in the years before. Cumulative incidences of colon and rectal cancer recurrence were similar for both cancer types among each descriptive category. <b>Conclusions:</b> In this population, increases in colorectal cancer recurrence risk were associated with younger age and increasing stage at diagnosis. Cumulative incidence of recurrence did not differ by cancer type. Descriptive characteristics of colon and rectal cancer recurrence may help to inform patient–physician decision-making, and could be used to determine adjuvant therapies or tailor surveillance strategies so that recurrence may be identified early, particularly within the first 3 years of follow-up.
DOI: 10.6084/m9.figshare.4787575
title: Proxy data

description: Zip file containing .csv files of all proxy records listed in Tables A1 and A2 of the paper "Was the Little Ice Age more or less El Niño-like than the Medieval Climate Anomaly? Evidence from hydrological and temperature proxy data".Tree ring records taken from the Mann et al. (2008) dataset are in a separate folder called "Mann2008". These are named as abbreviated location followed by a core number.All other file names follow the format [author][yyyy][optional suffix].Each file contains a "YearBP" column (age in years before present) and a column with proxy data points.All proxy records in this collection were originally downloaded from the NOAA Paleoclimatology/Pangaea Databases (https://www.ncdc.noaa.gov/data-access/paleoclimatology-data/datasets), including the Mann et al. (2008) tree ring dataset and the Tierney et al. (2015) coral dataset.<br><br>
DOI: 10.6084/m9.figshare.4787677.v1
title: rs_ab_ac_bc_variables

description: simulation of B-C correlations given A-B and A-C correaltion. The code (corr_a_b_c.m) and figures are hosted in github: https://github.com/Conxz/vis<br>simulated A-B and A-C correlation from 0.01 to 0.90 with a step of 0.01. the simulation was repeated 1000 times. <br>so the dimention of the data (matlab mat file) is 90x90x1000.<br><br>
DOI: 10.6084/m9.figshare.4787533.v1
title: Descriptive characteristics of colon and rectal cancer recurrence in a Danish population-based study

description: <b>Background:</b> Recurrence is a common outcome among patients that have undergone an intended curative resection for colorectal cancer. However, data on factors that influence colorectal cancer recurrence are sparse. We report descriptive characteristics of both colon and rectal cancer recurrence in an unselected population. <b>Material and methods:</b> We identified 21,152 patients with colorectal cancer diagnosed between May 2001 and December 2011 and registered with the Danish Colorectal Cancer Group. Recurrences were identified in 3198 colon and 1838 rectal cancer patients during follow-up. We calculated the frequency, proportion, and incidence rates of colon and rectal cancer recurrence within descriptive categories, and the cumulative five- and ten-year incidences of recurrence, treating death as a competing risk. We used a Cox proportional hazard model to calculate hazard ratios (HR) and 95% confidence intervals (CI). <b>Results:</b> Recurrence risk was highest in the first three years of follow-up. Patients &lt;55 years old at initial diagnosis (incidence rate for colon: 7.2 per 100 person-years; 95% CI: 6.5–7.9; rectum: 8.1 per 100 person-years; 95% CI: 7.2–9.0) and patients diagnosed with stage III cancer (colon HR: 5.70; 95% CI: 4.61–7.06; rectal HR: 7.02; 95% CI: 5.58–8.82) had increased risk of recurrence. Patients diagnosed with stage III cancer from 2009 to 2011 had a lower incidence of recurrence than those diagnosed with stage III cancer in the years before. Cumulative incidences of colon and rectal cancer recurrence were similar for both cancer types among each descriptive category. <b>Conclusions:</b> In this population, increases in colorectal cancer recurrence risk were associated with younger age and increasing stage at diagnosis. Cumulative incidence of recurrence did not differ by cancer type. Descriptive characteristics of colon and rectal cancer recurrence may help to inform patient–physician decision-making, and could be used to determine adjuvant therapies or tailor surveillance strategies so that recurrence may be identified early, particularly within the first 3 years of follow-up.
DOI: 10.6084/m9.figshare.4787506
title: Cultivation of Human Oral Mucosal Explants on Contact Lenses

description: <i>Purpose/Aim</i>: Autologous cultivated oral mucosal (OM) epithelial transplantation has been successfully used as corneal epithelial replacement in bilateral limbal stem cell deficiency. Recently, lotrafilcon A contact lens (CL) surface was described as a suitable carrier for cultured stem cells in corneal epithelial transplantation. Our aim was to establish explant cultures from human OM on CL carriers that are free of animal-derived materials and feeder cells. <i>Materials and methods</i>: Human cadaveric 2 mm OM explants were sutured onto CL surfaces and cultivated with fetal calf serum (FCS) or human serum (HS) supplemented culture medium without feeder cells. Confluent cultures were harvested and evaluated morphologically with hematoxylin and eosin stain and with immunofluorescence microscopy for the presence of p63, vimentin and cytokeratins (CK) 3, 4, 13 and 14. <i>Results</i>: Confluent cell sheets covering the whole CL surface were produced from OM explants after 2 weeks of culture with HS and after 3 weeks with FCS. A basal layer consisted of small, vimentin, p63 and CK14 positive putative stem/progenitor cells, which were present in the whole cell sheet. Large, CK3, CK4 and CK13 positive, differentiated cells appeared to spread above this confluent layer. <i>Conclusions</i>: We have established an animal-free culture system from human OM explants on CL surface. The cultured OM sheets contain large numbers of putative stem cells including limbal-like CK3 and CK14 positive cells. This method can be adapted to good manufacturing practice (GMP) conditions and has, therefore, great potential for clinical use.
DOI: 10.6084/m9.figshare.4787527
title: List vs Tree:Plant Diversity Data.xlsx

description: Data from the comparison of organismal diversity learning when using evolutionary trees as a tool to organize the biological information.
DOI: 10.6084/m9.figshare.4787092
title: Asymmetric division of the cortex-endodermis initial in Arabidopsis

description: Asymmetric division of the cortex-endodermis initial in Arabidopsis (overview and closeup)
DOI: 10.6084/m9.figshare.4787506.v1
title: Cultivation of Human Oral Mucosal Explants on Contact Lenses

description: <i>Purpose/Aim</i>: Autologous cultivated oral mucosal (OM) epithelial transplantation has been successfully used as corneal epithelial replacement in bilateral limbal stem cell deficiency. Recently, lotrafilcon A contact lens (CL) surface was described as a suitable carrier for cultured stem cells in corneal epithelial transplantation. Our aim was to establish explant cultures from human OM on CL carriers that are free of animal-derived materials and feeder cells. <i>Materials and methods</i>: Human cadaveric 2 mm OM explants were sutured onto CL surfaces and cultivated with fetal calf serum (FCS) or human serum (HS) supplemented culture medium without feeder cells. Confluent cultures were harvested and evaluated morphologically with hematoxylin and eosin stain and with immunofluorescence microscopy for the presence of p63, vimentin and cytokeratins (CK) 3, 4, 13 and 14. <i>Results</i>: Confluent cell sheets covering the whole CL surface were produced from OM explants after 2 weeks of culture with HS and after 3 weeks with FCS. A basal layer consisted of small, vimentin, p63 and CK14 positive putative stem/progenitor cells, which were present in the whole cell sheet. Large, CK3, CK4 and CK13 positive, differentiated cells appeared to spread above this confluent layer. <i>Conclusions</i>: We have established an animal-free culture system from human OM explants on CL surface. The cultured OM sheets contain large numbers of putative stem cells including limbal-like CK3 and CK14 positive cells. This method can be adapted to good manufacturing practice (GMP) conditions and has, therefore, great potential for clinical use.
DOI: 10.6084/m9.figshare.4787092.v1
title: Asymmetric division of the cortex-endodermis initial in Arabidopsis

description: Asymmetric division of the cortex-endodermis initial in Arabidopsis (overview and closeup)
DOI: 10.6084/m9.figshare.4787527.v1
title: List vs Tree:Plant Diversity Data.xlsx

description: Data from the comparison of organismal diversity learning when using evolutionary trees as a tool to organize the biological information.