cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7795/710.20210915
title: Measurement and simulation data for "Identification of aliasing effects in measurements of unknown MTFs"

description: The provided data set and simulation software enables the immediate replication of the results presented in "Identification of aliasing effects in measurements of unknown MTFs." The research data is structured with respect to the figures presented in the contribution. Each subfolder contains all necessary measurement or simulation data to receive the figure from the contribution by running a MATLAB file. Therefore, it is possible to compare the results with full context to those presented in the contribution. The simulations demonstrate the influence of aliasing on MTF measurements employing the slanted slit algorithm. The measurement data saved as *.mat files contains the tilted slit images as recorded by the camera detectors. Each set of measurement data contains the following variables: -binning -&gt; The pixel binning factor applied in the camera -camera -&gt; The name of teh camera device -exptime -&gt; The employed exposure time -magnification -&gt; The applied microscope magnification -*image -&gt; The recorded LSF images The specimen under test is a calibration objective manufactured by Zeiss with infinite to finite imaging, a focus distance of f_s = 50mm and an f-number a_s = 4. The following abbreviations are employed in the labeling of the subfolders: MTF -&gt; Modulation Transfer Function Pco -&gt; Refers to the camera model Pco Panda camera employed in the experiment Bas -&gt; Refers to the camera model Basler Ace 2 camera employed in the experiment 20x,10x,6.3x -&gt; Refers to the magnification of the microscope objectives employed in the experiment The experimental data is evaluated employing the slanted slit algorithm and shows the influence of aliasing and uncorrected influences from detector and objective characteristics on the MTF measurement. The oversampling achievable by the slanted slit method is demonstrated to resolve the aliasing issues and provides a tool to identify and correct aliasing errors in unknown MTF measurements.
description: description of the individual files: Each subfolder refers to a figure in the contribution. Each folder contains a "HOWTO.txt" file with instructions how to generate the graphical output of the measurement or simulation data. The Figs.: 3-4 contain simualtion results 2,5-9 contain measurement results Recommended software to open the data: MATLAB R2016b, Python (https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.loadmat.html) - The simulation and data evaluation files are *.m files and require MATLAB to be executed. However, they may be opened in a text editor to view the code. - The measurement data are stored as structs in *.mat files. These may be opened with MATLAB, but may also be imported into Python and transfered into alternative data formats like *.h5. Acknowledgements: We want to acknowledge the support of this project by Trioptics GmbH (Strandbaddamm 6, 22880 Wedel,Germany).
DOI: 10.5519/qd.wm99wqzl
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6092 records)
DOI: 10.6084/m9.figshare.16867249.v1
title: Ties that bind data.rar

description: In this folder there is the data to replicate the paper "The ties that bind and transform: knowledge remittances, relatedness, and the direction of technical change". In the folder there is a .dta file that contains the data in Stata format, and an .xls file that provides a description of the variables.
DOI: 10.6084/m9.figshare.14573556
title: OSM_Ist_Izm.gdb.rar

description: The datasets were created from OpenStreetMap building polygons.
DOI: 10.6084/m9.figshare.14573556.v1
title: OSM_Ist_Izm.gdb.rar

description: The datasets were created from OpenStreetMap building polygons.
DOI: 10.6084/m9.figshare.16867150.v1
title: CD4 melanoma TILs TCR repertoires

description: TCR repertoires of sorted CD4 CD39 PD-1 double-positive (DP) and not double-positive (nDP) tumor-infiltrating lymphocytes derived from metastasized lymph nodes of melanoma patients (mp).
DOI: 10.6084/m9.figshare.16867144.v1
title: BrainScience_data_2021.xlsx

description: Measurements of enhancement in reading speed for different types of social relationship sentences and its relationship with personality traits (BIS/BAS)<br>
DOI: 10.6084/m9.figshare.16867108.v1
title: Data for: Constraining whole genome duplication events in geological time

description: This dataset contains files to estimate the timing of the whole genome duplication event in Cornus using the software MCMCtree and codeml.<br>This dataset accompanies the chapter "Constraining whole genome duplication events in geological time" in the Methods in Molecular Biology series on Polyploidy, edited by Yves Van de Peer, Zhen Li and Arthur Zwaenepoel.
DOI: 10.6084/m9.figshare.16867327
title: TCR repertoires of melanoma patient 41 (mp41) TILs

description: T cell receptor repertoires of bulk TILs of mp41 expanded in variable cultivation settings for 9 days.<br>
DOI: 10.6084/m9.figshare.16867327.v1
title: TCR repertoires of melanoma patient 41 (mp41) TILs

description: T cell receptor repertoires of bulk TILs of mp41 expanded in variable cultivation settings for 9 days.<br>
DOI: 10.6084/m9.figshare.16867102.v2
title: CD8 melanoma TILs TCR repertoires

description: TCR repertoires of sorted CD8 CD39 PD-1 double-positive (DP) and not double-positive (nDP) tumor-infiltrating lymphocytes derived from metastasized lymph nodes of melanoma patients (mp).<br>
DOI: 10.6084/m9.figshare.16867102.v1
title: Untitled Item

description: TCR repertoires of sorted CD8 CD39 PD-1 double-positive (DP) and not double-positive (nDP) tumor-infiltrating lymphocytes derived from metastasized lymph nodes of melanoma patients (mp).<br>
DOI: 10.6073/pasta/69475111c7c6e0faa8223eed968e8312
title: Criollo and Crossbred Steer Comparison: Weight Gain, Grazing, Carcass Quality, 2015-2017

description: Rarámuri Criollo cows have behavioral traits that are desirable for rangelands in arid environments, but calves from this biotype are difficult to market through conventional methods. One strategy to improve marketability is to crossbreed these cows with traditional beef breed bulls. However, it is unclear whether crossbred calves will achieve marketable weights and carcass qualities on rangeland and whether they will retain the desirable grazing behaviors of their mothers. We evaluated these traits for two cohorts of Rarámuri Criollo (JRC), Mexican Criollo (MC), and Criollo × beef-breed crossbred (XC) steers. Final live and carcass weights of XC were greater than JRC and MC, but all three groups were market ready at 30-mo after finishing on grass. Carcass quality and average daily gain did not differ among biotypes. Both JRC and XC steers exhibited grazing patterns similar to those previously observed in JRC cows. These results suggest JRC, MC, and XC steers can achieve desirable slaughter weights in 30 months using a rangeland-based grass-fed protocol, and JRC and XC steers retain desirable grazing behaviors of JRC cows.
DOI: 10.6084/m9.figshare.16867150
title: CD4 melanoma TILs TCR repertoires

description: TCR repertoires of sorted CD4 CD39 PD-1 double-positive (DP) and not double-positive (nDP) tumor-infiltrating lymphocytes derived from metastasized lymph nodes of melanoma patients (mp).
DOI: 10.6084/m9.figshare.16867144
title: BrainScience_data_2021.xlsx

description: Measurements of enhancement in reading speed for different types of social relationship sentences and its relationship with personality traits (BIS/BAS)<br>
DOI: 10.6084/m9.figshare.16867108
title: Data for: Constraining whole genome duplication events in geological time

description: This dataset contains files to estimate the timing of the whole genome duplication event in Cornus using the software MCMCtree and codeml.<br>This dataset accompanies the chapter "Constraining whole genome duplication events in geological time" in the Methods in Molecular Biology series on Polyploidy, edited by Yves Van de Peer, Zhen Li and Arthur Zwaenepoel.
DOI: 10.6084/m9.figshare.16867102
title: CD8 melanoma TILs TCR repertoires

description: TCR repertoires of sorted CD8 CD39 PD-1 double-positive (DP) and not double-positive (nDP) tumor-infiltrating lymphocytes derived from metastasized lymph nodes of melanoma patients (mp).<br>
DOI: 10.15129/8597108f-6daa-43e1-8d2d-796b97c36f3a
title: Data for: "Mefenamic acid solid dispersions: Impact of formulation composition on processing parameters, product properties and performance"

description: Dataset to support publication:"Mefenamic acid solid dispersions: Impact of formulation composition on processing parameters, product properties and performance" Data is provided in Microsoft excel format. Original data files are available upon request. Rheology: Temperature sweep and Frequency sweep data - Haake Mars III rotational rheometer Hot-melt-extrusion process data - Process 11, Thermo Fisher Filament diameter data XRPD data Thermal analysis - Netzsch Polyma DSC214 Mechanical testing: Texture Analyser TA-XT (Stable Micro Systems) equipped with a mini 3-point bend rig HPLC data and method validation - Agilent 1100 LC system equipped with G1315A Diode Array Detector Dissolution test data: ADT8i Dissolution bath (USP I, basket) apparatus with a closed loop setting and a T70+ UV/Visible Spectrophotometer (Automated Lab Systems) and Sirius Inform
DOI: 10.5517/ccdc.csd.cc24q0tq
title: CCDC 1987373: Experimental Crystal Structure Determination

description: Related Article:  Tamara A. Bazhenova, Ilya A. Yakushev, Konstantin A. Lyssenko, Olga V. Maximova, Vladimir S. Mironov, Yuriy V. Manakin, Alexey B. Kornev, Alexander N. Vasiliev, Eduard B. Yagubskii|2020|Magnetochem.|6|60|doi:10.3390/magnetochemistry6040060
DOI: 10.5517/ccdc.csd.cc24q0sp
title: CCDC 1987372: Experimental Crystal Structure Determination

description: Related Article:  Tamara A. Bazhenova, Ilya A. Yakushev, Konstantin A. Lyssenko, Olga V. Maximova, Vladimir S. Mironov, Yuriy V. Manakin, Alexey B. Kornev, Alexander N. Vasiliev, Eduard B. Yagubskii|2020|Magnetochem.|6|60|doi:10.3390/magnetochemistry6040060
DOI: 10.5517/ccdc.csd.cc281fxp
title: CCDC 2086762: Experimental Crystal Structure Determination

description: Related Article: Kira I. Pashanova, Vladlena O. Bitkina, Ilya A. Yakushev, Maxim V. Arsenyev, Alexandr V. Piskunov |2021|Molecules|26|4622|doi:10.3390/molecules26154622
DOI: 10.5517/ccdc.csd.cc286y4l
title: CCDC 2092039: Experimental Crystal Structure Determination

description: Related Article: Anastasia Balakina, Tatyana Prikhodchenko, Vera Amozova, Tatyana Stupina, Victoria Mumyatova, Margarita Neganova, Ilya Yakushev, Alexey Kornev, Svyatoslav Gadomsky, Boris Fedorov, Denis Mishchenko|2021|Antioxidants|10|1451|doi:10.3390/antiox10091451
DOI: 10.15784/601474
title: Pennell Trough, Ross Sea bathymetry and glacial landforms

description: Bathymetry from multibeam echo sounding data in Pennell Trough, Ross Sea, Antarctica was collected onboard the RVIB Nathaniel B. Palmer (NBP) 15-02 cruise using a Kongsberg EM122 operating in dual swath mode at 12 kHz frequency with a 1°×1° beam width, swath angular coverage set to 62°×62°, and 30-60% overlap between survey lines. All raw, ping-edited geophysical data collected on NBP15-02 can be accessed using the Marine Geoscience Data System (Cruise DOI: 10.7284/901477). The bathymetry dataset here is gridded at 20-m resolution with a water depth-dependent vertical resolution on the order of decimeters. Two shapefiles are provided for ice-marginal landforms and meltwater landforms observable in the bathymetry data. The purpose of collecting the bathymetry data on cruise NBP15-02 was to better understand the glacial history of the Ross Sea, and the dataset, inclusive of bathymetry data and shapefiles of glacial landforms, from Pennell Trough are used to understand impacts on subglacial channel morphology and organization during the deglaciation of the region following the Last Glacial Maximum. The published dataset was used and analyzed in the article "Topographic controls on channelized meltwater in the subglacial environment" by Simkins, L.M., Greenwood, S.L., Munevar Garcia, S., Eareckson, E.A., Anderson, J.B., and Prothro, L.O, which was published in Geophysical Research Letters in 2021 (DOI: 10.1029/2021GL094678).
DOI: 10.6084/m9.figshare.16867379.v1
title: Supplementary Data from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: Phylogenetic data of 39 ABR gene homologs. For each of the genes, homologs protein sequences, protein information, sequence alignment and phylogenetic tree is supplied.
DOI: 10.6084/m9.figshare.16867382
title: Supplementary Table S2. A list of 416 genomes used in the inference of protein families in Escherichia. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867379
title: Supplementary Data from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: Phylogenetic data of 39 ABR gene homologs. For each of the genes, homologs protein sequences, protein information, sequence alignment and phylogenetic tree is supplied.
DOI: 10.6084/m9.figshare.16867382.v1
title: Supplementary Table S2. A list of 416 genomes used in the inference of protein families in Escherichia. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867391
title: Supplementary Table S4. A list of ABR gene & isolates where the gene is present on both plasmid and chromosome. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867391.v1
title: Supplementary Table S4. A list of ABR gene & isolates where the gene is present on both plasmid and chromosome. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867394.v1
title: Supplementary Table S3. A classification of ABR genes into chromosomal and plasmid genes according to their relative frequency on both replicon types. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867397
title: Supplementary Table S1. A list of genomes used in this study. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.