cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6987011.v2
title: A review of transfer theory and characterization of measured performance for differential mobility analyzers

description: Particle transfer theory for steady-state differential mobility analyzers (DMAs) with and without diffusion is reviewed in detail with a particular focus on the assumptions and approximations made in the analysis. Impacts of the approximations are discussed and, where available, methods to reduce the errors of these approximations are suggested. The nondiffusing theory uses just one approximation, affecting the centroid calculation, which can be readily addressed via numerical modeling of the electric field. The diffusing theory makes numerous approximations to achieve an analytical expression. One of the most serious of these, neglecting secondary flows in the vicinities of the aerosol entrance and exit slits, could be improved upon using a numerical model of the flow field. Losses in the aerosol entrance plumbing can perturb the inlet profile to the classification region. The maximum effects on the transfer function are estimated to be a 1% increase in the mean mobility and a 14% reduction of the nondiffusing contribution to the variance. Methods of fitting transfer theory to measurements are also reviewed. Tandem differential mobility analyzer measurements generally do not have the resolving power to distinguish different shapes of the transfer function but newer measurements using truly monomobile ions have the potential to more rigorously test the diffusive transfer model. In adjusting the width of the theoretical transfer function to fit measurements from a real DMA demonstrating nonideal performance, it is physically more meaningful and accurate to use an additive adjustment to the variance as opposed to a multiplicative adjustment to the width. Copyright (c) 2018 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.6987014.v1
title: Adaptive Component-wise Multiple-Try Metropolis Sampling

description: One of the most widely used samplers in practice is the component-wise Metropolis-Hastings (CMH) sampler that updates in turn the components of a vector valued Markov chain using accept-reject moves generated from a proposal distribution. When the target distribution of a Markov chain is irregularly shaped, a ‘good’ proposal distribution for one region of the state space might be a ‘poor’ one for another region. We consider a component-wise multiple-try Metropolis (CMTM) algorithm that chooses from a set of candidate moves sampled from different distributions. The computational efficiency is increased using an adaptation rule for the CMTM algorithm that dynamically builds a better set of proposal distributions as the Markov chain runs. The ergodicity of the adaptive chain is demonstrated theoretically. The performance is studied via simulations and real data examples.
DOI: 10.6084/m9.figshare.6987011.v1
title: A Review of Transfer Theory and Characterization of Measured Performance for Differential Mobility Analyzers

description: Particle transfer theory for steady-state differential mobility analyzers with and without diffusion is reviewed in detail with a particular focus on the assumptions and approximations made in the analysis. Impacts of the approximations are discussed and, where available, methods to reduce the errors of these approximations are suggested. The non-diffusing theory uses just one approximation, affecting the centroid calculation, which can be readily addressed via numerical modeling of the electric field. The diffusing theory makes numerous approximations to achieve an analytical expression. One of the most serious of these, neglecting secondary flows in the vicinities of the aerosol entrance and exit slits, could be improved upon using a numerical model of the flow field. Losses in the aerosol entrance plumbing can perturb the inlet profile to the classification region. The maximum effects on the transfer function are estimated to be a 1% increase in the mean mobility and a 14% reduction of the non-diffusing contribution to the variance. Methods of fitting transfer theory to measurements are also reviewed. TDMA measurements generally do not have the resolving power to distinguish different shapes of the transfer function but newer measurements using truly monomobile ions have the potential to more rigorously test the diffusive transfer model. In adjusting the width of the theoretical transfer function to fit measurements from a real DMA demonstrating non-ideal performance, it is physically more meaningful and accurate to use an additive adjustment to the variance as opposed to a multiplicative adjustment to the width.
DOI: 10.6084/m9.figshare.6987014.v2
title: Adaptive Component-Wise Multiple-Try Metropolis Sampling

description: One of the most widely used samplers in practice is the component-wise Metropolis–Hastings (CMH) sampler that updates in turn the components of a vector-valued Markov chain using accept–reject moves generated from a proposal distribution. When the target distribution of a Markov chain is irregularly shaped, a “good” proposal distribution for one region of the state–space might be a “poor” one for another region. We consider a component-wise multiple-try Metropolis (CMTM) algorithm that chooses from a set of candidate moves sampled from different distributions. The computational efficiency is increased using an adaptation rule for the CMTM algorithm that dynamically builds a better set of proposal distributions as the Markov chain runs. The ergodicity of the adaptive chain is demonstrated theoretically. The performance is studied via simulations and real data examples. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6987014.v4
title: Adaptive Component-Wise Multiple-Try Metropolis Sampling

description: One of the most widely used samplers in practice is the component-wise Metropolis–Hastings (CMH) sampler that updates in turn the components of a vector-valued Markov chain using accept–reject moves generated from a proposal distribution. When the target distribution of a Markov chain is irregularly shaped, a “good” proposal distribution for one region of the state–space might be a “poor” one for another region. We consider a component-wise multiple-try Metropolis (CMTM) algorithm that chooses from a set of candidate moves sampled from different distributions. The computational efficiency is increased using an adaptation rule for the CMTM algorithm that dynamically builds a better set of proposal distributions as the Markov chain runs. The ergodicity of the adaptive chain is demonstrated theoretically. The performance is studied via simulations and real data examples. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6987014.v3
title: Adaptive Component-Wise Multiple-Try Metropolis Sampling

description: One of the most widely used samplers in practice is the component-wise Metropolis–Hastings (CMH) sampler that updates in turn the components of a vector-valued Markov chain using accept–reject moves generated from a proposal distribution. When the target distribution of a Markov chain is irregularly shaped, a “good” proposal distribution for one region of the state–space might be a “poor” one for another region. We consider a component-wise multiple-try Metropolis (CMTM) algorithm that chooses from a set of candidate moves sampled from different distributions. The computational efficiency is increased using an adaptation rule for the CMTM algorithm that dynamically builds a better set of proposal distributions as the Markov chain runs. The ergodicity of the adaptive chain is demonstrated theoretically. The performance is studied via simulations and real data examples. Supplementary material for this article is available online.
DOI: 10.7284/108966
title: Multiplexed data collected during research cruise KN193-07 using a Hawaii UHDAS instrument system onboard the platform RV Knorr
DOI: 10.6084/m9.figshare.6985223
title: Nie et al Cancer clinical info and Rab11 image quantification 12-25-2018

description: Excel file for Rab11 staining quantification of colon cancer samples and clinical information
DOI: 10.6084/m9.figshare.6985223.v1
title: Nie et al Cancer clinical info and Rab11 image quantification 12-25-2018

description: Excel file for Rab11 staining quantification of colon cancer samples and clinical information
DOI: 10.7284/108981
title: Gravimeter data collected during research cruise KN194-04 using a Bell BGM-3 instrument system onboard the platform RV Knorr
DOI: 10.6084/m9.figshare.6985085
title: Full data for each experiment from Camouflage strategies interfere differently with observer search images

description: Numerous animals rely on camouflage for defence. Substantial past work has identified the presence of multiple strategies for concealment, and tested the mechanisms underpinning how they work. These include background matching, disruptive coloration to destroy target edges and distractive markings that may divert attention from key target features. Despite considerable progress, work has focused on how camouflage types prevent initial detection by naive observers. However, predators will often encounter multiple targets over time, providing the opportunity to learn or focus attention through search images. At present, we know almost nothing about how camouflage types facilitate or hinder predator performance over repeated encounters. Here, we use experiments with human subjects searching for targets on touch screens with different camouflage strategies, and control the experience that subjects have with target types. We show that different camouflage strategies affect how subjects improve in detecting targets with repeated encounters, and how performance in detection of one camouflage type depends on experience of other strategies. In particular, disruptive coloration is effective at preventing improvements in camouflage breaking during search image formation, and experience with one camouflage type (distraction) can decrease the ability of subjects to switch to and from search images for new camouflage types (disruption). Our study is the first to show how the success of camouflage strategies depends on how they prevent initial and successive detection, and on predator experience of other strategies. This has implications for the evolution of prey phenotypes, how we assess the efficacy of defences and predator–prey dynamics.
DOI: 10.6084/m9.figshare.6985085.v1
title: Full data for each experiment from Camouflage strategies interfere differently with observer search images

description: Numerous animals rely on camouflage for defence. Substantial past work has identified the presence of multiple strategies for concealment, and tested the mechanisms underpinning how they work. These include background matching, disruptive coloration to destroy target edges and distractive markings that may divert attention from key target features. Despite considerable progress, work has focused on how camouflage types prevent initial detection by naive observers. However, predators will often encounter multiple targets over time, providing the opportunity to learn or focus attention through search images. At present, we know almost nothing about how camouflage types facilitate or hinder predator performance over repeated encounters. Here, we use experiments with human subjects searching for targets on touch screens with different camouflage strategies, and control the experience that subjects have with target types. We show that different camouflage strategies affect how subjects improve in detecting targets with repeated encounters, and how performance in detection of one camouflage type depends on experience of other strategies. In particular, disruptive coloration is effective at preventing improvements in camouflage breaking during search image formation, and experience with one camouflage type (distraction) can decrease the ability of subjects to switch to and from search images for new camouflage types (disruption). Our study is the first to show how the success of camouflage strategies depends on how they prevent initial and successive detection, and on predator experience of other strategies. This has implications for the evolution of prey phenotypes, how we assess the efficacy of defences and predator–prey dynamics.
DOI: 10.6084/m9.figshare.6985013
title: Data from: The biogeography of invasion in tropical and temperate seagrass beds: testing interactive effects of predation and propagule pressure

description: Experimental data from Cheng et al. 2019 Diversity and Distributions 25:285-297.<br>https://doi.org/10.1111/ddi.12850<br>
DOI: 10.6084/m9.figshare.6985013.v1
title: Data from: The biogeography of invasion in tropical and temperate seagrass beds: testing interactive effects of predation andpropagule pressure

description: Experimental data from article published by Cheng et al. in Diversity and Distributions (in press).
DOI: 10.6084/m9.figshare.6984971
title: Data generated through the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast

description: This dataset relates to a study which identified potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58; as well as the development of a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions.<br>The dataset consists of two zipped file folders and a single spreadsheet in .xls format. The zipped folder <b>Dudnakova et al. Supp dataset 1.zip </b>contains two .eps files, and the zipped folder <b>Dudnakova et al. Supp dataset 3.zip</b> contains the subdirectory <b>qPCR data for paper</b> which consists of ten additional spreadsheets in .xls format.<br><b>Folder Supp dataset 1.zip</b> contains two image files in .eps format. The file <b>Supplementary Data 1A.eps</b> contains raw images of northern blots, showing northern analysis of pre-rRNA processing in the strains expressing mutant U3 and marked as A, B, C and D:<br>A. Hybridized with probe 04 (5’GGTTTTAATTGTCCTA) binding to the site is located in the ITS1 region 5’ to site A2.B. Hybridized with probe 03 (5’TGTTACCTCTGGGCCC) binding the site located in the ITS1 region of the pre-rRNA, 3’ to cleavage site A2.C. EtBr staining of the membrane showing 25S and 18S rRNAs.D. Northern analysis of pre-rRNA processing following transfer of the U3mutant strain to glucose medium for 36h.<br>The file <b>Supplementary Data 1B.eps</b> contains raw images of northern Blots from RNA IP experiment in U3 mut expressing cells, marked as A, B, C and D:<br>A. Northern blot showing expression of the wild type (U3 wt) and the truncated U3 (U3 mut). B. RNA IP northern blot from the strains expressing either TAP-Nop1 or TAP-Rrp9 and mutant U3.C. Northern blot showing expression of the wild type (U3 wt) and the truncated U3 (U3 mut). Lanes 1-3 and 4-6 for show biological triplicates.D. RNA IP northern blot from the strains expressing either TAP-Nop1 or TAP-Rrp9 and mutant U3.<br>The spreadsheet <b>Dudnakova et al. Supp dataset 2.xlsx</b> contains values for growth of the strains in the growth media indicated. <br>The zipped folder <b>Supplementary Dataset 3.zip </b>contains ten spreadsheets in .xls format, which show the Ct values obtained for the mRNA species indicated.<br>The .xls spreadsheets can be opened using Microsoft Excel software, and the .eps image files can be opened using graphic software such as Adobe Illustrator or alternatively Adobe Acrobat.<br><br>
DOI: 10.6084/m9.figshare.6985013.v2
title: Data from: The biogeography of invasion in tropical and temperate seagrass beds: testing interactive effects of predation andpropagule pressure

description: Experimental data from article published by Cheng et al. in Diversity and Distributions (in press).
DOI: 10.6084/m9.figshare.6985013.v4
title: Data from: The biogeography of invasion in tropical and temperate seagrass beds: testing interactive effects of predation and propagule pressure

description: Experimental data from Cheng et al. 2019 Diversity and Distributions 25:285-297.<br>https://doi.org/10.1111/ddi.12850<br>
DOI: 10.6084/m9.figshare.6984971.v1
title: Data generated through the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast

description: This dataset relates to a study which identified potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58; as well as the development of a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions.<br>The dataset consists of two zipped file folders and a single spreadsheet in .xls format. The zipped folder <b>Dudnakova et al. Supp dataset 1.zip </b>contains two .eps files, and the zipped folder <b>Dudnakova et al. Supp dataset 3.zip</b> contains the subdirectory <b>qPCR data for paper</b> which consists of ten additional spreadsheets in .xls format.<br><b>Folder Supp dataset 1.zip</b> contains two image files in .eps format. The file <b>Supplementary Data 1A.eps</b> contains raw images of northern blots, showing northern analysis of pre-rRNA processing in the strains expressing mutant U3 and marked as A, B, C and D:<br>A. Hybridized with probe 04 (5’GGTTTTAATTGTCCTA) binding to the site is located in the ITS1 region 5’ to site A2.B. Hybridized with probe 03 (5’TGTTACCTCTGGGCCC) binding the site located in the ITS1 region of the pre-rRNA, 3’ to cleavage site A2.C. EtBr staining of the membrane showing 25S and 18S rRNAs.D. Northern analysis of pre-rRNA processing following transfer of the U3mutant strain to glucose medium for 36h.<br>The file <b>Supplementary Data 1B.eps</b> contains raw images of northern Blots from RNA IP experiment in U3 mut expressing cells, marked as A, B, C and D:<br>A. Northern blot showing expression of the wild type (U3 wt) and the truncated U3 (U3 mut). B. RNA IP northern blot from the strains expressing either TAP-Nop1 or TAP-Rrp9 and mutant U3.C. Northern blot showing expression of the wild type (U3 wt) and the truncated U3 (U3 mut). Lanes 1-3 and 4-6 for show biological triplicates.D. RNA IP northern blot from the strains expressing either TAP-Nop1 or TAP-Rrp9 and mutant U3.<br>The spreadsheet <b>Dudnakova et al. Supp dataset 2.xlsx</b> contains values for growth of the strains in the growth media indicated. <br>The zipped folder <b>Supplementary Dataset 3.zip </b>contains ten spreadsheets in .xls format, which show the Ct values obtained for the mRNA species indicated.<br>The .xls spreadsheets can be opened using Microsoft Excel software, and the .eps image files can be opened using graphic software such as Adobe Illustrator or alternatively Adobe Acrobat.<br><br>
DOI: 10.6084/m9.figshare.6984968
title: NMR data for PAPY

description: A portion of 84 NMR spectra of urine from the Airwave Study.
DOI: 10.6084/m9.figshare.6985013.v3
title: Data from: The biogeography of invasion in tropical and temperate seagrass beds: testing interactive effects of predation andpropagule pressure

description: Experimental data from article published by Cheng et al. in Diversity and Distributions (in press).
DOI: 10.6084/m9.figshare.6984965
title: RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment

description: A table listing all the differentially expressed genes detected.
DOI: 10.6084/m9.figshare.6984968.v1
title: NMR data for PAPY

description: A portion of 84 NMR spectra of urine from the Airwave Study.
DOI: 10.6084/m9.figshare.6984797
title: Data from: The effects of agroforestry systems on bird diversity: A global synthesis.

description: Original data from: Bohada-Murillo, M., G.J. Castaño Villa and F.E. Fontúrbel (2019) The effects of agroforestry systems on bird diversity: A global synthesis. Land Degradation & Development. doi: 10.1002/ldr.3478<br><br>This entry contains three files:<br><br>(1) richness_data.csv - a CSV file containing the original data from species richness case studies included in the meta-analysis.<br>(2) abundance_data.csv - a CSV file containing the original data from bird abundance case studies included in the meta-analysis.<br>(3) references.txt - a numbered list (corresponding to the ref number in the richness and abundance data files) of the original data sources used.
DOI: 10.7284/108984
title: Gravimeter data collected during research cruise KN194-05 using a Bell BGM-3 instrument system onboard the platform RV Knorr
DOI: 10.6084/m9.figshare.6984578
title: The association between the etiology of a spinal cord injury and time to mortality in the United States: A 44-year investigation

description: <b>Objective:</b> To determine the association between spinal cord injury (SCI) etiology categories and mortality, and examine the association between etiology sub-categories and mortality. <b>Design:</b> Prospective cohort study. <b>Setting</b>: Model Systems and Shriners Hospital SCI units. <b>Participants</b>: Data were analyzed from 42,627 cases in the SCI Model System Collaborative Survival Study Database from 1973 to 2017. Those with SCI etiologies categorized as vehicular, violent, sports, falls, pedestrian, and medical were included. <b>Interventions</b>: Not applicable. <b>Outcome Measure</b>: Time to mortality after SCI. <b>Results:</b> Relative to the sports related etiology category, those with medical, pedestrian, violence, falls, and vehicular related SCIs had a 2.00 (95% confidence intervals (CIs): 1.79–2.24), 1.57 (CIs: 1.34–1.83), 1.54 (CIs: 1.41–1.68), 1.35 (CIs: 1.25–1.45), and 1.26 (CIs: 1.17–1.35) higher hazard for mortality, respectfully. Persons with SCIs from automobile crashes had a 1.38 (CIs: 1.23–1.56) higher hazard for mortality, whereas those with SCIs from motorcycle crashes had a 1.21 (CIs: 1.04–1.39) higher hazard for mortality, relative to other etiologies within the vehicular category. Those with SCIs from diving had a 1.37 (CIs: 1.18–1.59) higher hazard for mortality relative to other etiologies within the sports category. <b>Conclusions:</b> Injury etiology categories and certain sub-categories were associated with a higher risk for early mortality. Understanding how additional factors such as socioeconomic status, co-occurring injuries, medical co-morbidities, and environmental aspects interact with SCI etiologies may provide insights for how etiology of injury impacts survival. These findings may serve as a development for extending long-term life expectancy by informing SCI prevention programs and care post-injury.