cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.154685.v1
title: Figure 7 raw data: Effect of variable exposure to PTHrP (1-36) on bone nodules and AP activity in high plating density cultures.

description: RC cell cultures were maintained in control medium for 21 days (C/C), maintained in control medium and changed to medium containing PTHrP (1-36) on day 11 (C/P), treated with 100 nM PTHrP (1-36) for 21 days (P/P), or exposed to 100 nM PTHrP (1-36) for 10 days and then transferred to control medium on day 11 (P/C). The number of bone nodules (A) and AP activity (B) were determined on day 21.
DOI: 10.6084/m9.figshare.154682
title: Figure 4 raw data: Effect of continuous exposure to PTHrP (1-36) on bone nodules and ap-positive osteogenic cell colonies in low plating density cultures.

description: The number of bone nodules (A) and AP positive colonies (B) in RC cells plated in low density and continuously exposed to 0 to 100 nM PTHrP (1-36) for 18 days.
DOI: 10.6084/m9.figshare.154683
title: Figure 5 raw data: Effect of continuous and intermittent exposure to PTHrP (1-36) on bone nodules and AP-positive cell colonies in low plating density cultures.

description: The number of bone nodules (A) and AP-positive cell colonies (B) in RC cell cultures exposed to 100 nM PTHrP (1-36) for 1, 6, or 48 hr during each 48 hr treatment period.
DOI: 10.6084/m9.figshare.154681
title: Figure 3 raw data: Effect of PTH1R and PKA agonists on high plating density cultures.

description: Fig3A. The amount of cAMP was measured by EIA in 98 wells plated with RC cells and exposed to 0 to 100 nM PTHrP (1-36) for 10 min.<br>Fig3B. The number of bone nodules in 8 wells following treatment of RC cell cultures with 0 to 1 mM DBcAMP and 0 to 10 µM forskolin (Fsk).<br>Fig3C. The number of bone nodules in RC cell cultures. RC cells were grown in the absence (control) or presence of 50 nM PTHrP (7-34).
DOI: 10.6084/m9.figshare.154682.v1
title: Figure 4 raw data: Effect of continuous exposure to PTHrP (1-36) on bone nodules and ap-positive osteogenic cell colonies in low plating density cultures.

description: The number of bone nodules (A) and AP positive colonies (B) in RC cells plated in low density and continuously exposed to 0 to 100 nM PTHrP (1-36) for 18 days.
DOI: 10.6084/m9.figshare.154683.v1
title: Figure 5 raw data: Effect of continuous and intermittent exposure to PTHrP (1-36) on bone nodules and AP-positive cell colonies in low plating density cultures.

description: The number of bone nodules (A) and AP-positive cell colonies (B) in RC cell cultures exposed to 100 nM PTHrP (1-36) for 1, 6, or 48 hr during each 48 hr treatment period.
DOI: 10.6084/m9.figshare.154680
title: Figure 2 raw data: Effect of continuous exposure to PTHrP (1-36) and its removal after 10 days on bone nodules in high plating density cultures.

description: The effect of exposure of RC cells to 0 to 100 nM PTHrP (1-36) for 18 days on the number of bone nodules.
DOI: 10.6084/m9.figshare.154680.v1
title: Figure 2 raw data: Effect of continuous exposure to PTHrP (1-36) and its removal after 10 days on bone nodules in high plating density cultures.

description: The effect of exposure of RC cells to 0 to 100 nM PTHrP (1-36) for 18 days on the number of bone nodules.
DOI: 10.6084/m9.figshare.154681.v1
title: Figure 3 raw data: Effect of PTH1R and PKA agonists on high plating density cultures.

description: Fig3A. The amount of cAMP was measured by EIA in 98 wells plated with RC cells and exposed to 0 to 100 nM PTHrP (1-36) for 10 min.<br>Fig3B. The number of bone nodules in 8 wells following treatment of RC cell cultures with 0 to 1 mM DBcAMP and 0 to 10 µM forskolin (Fsk).<br>Fig3C. The number of bone nodules in RC cell cultures. RC cells were grown in the absence (control) or presence of 50 nM PTHrP (7-34).
DOI: 10.6084/m9.figshare.154613
title: Oxygen stable isotope analysis of water vole (Arvicola) incisor tooth enamel: a proxy record of terrestrial climate from MIS 9 Britain

description: The oxygen stable isotopic composition of rainfall (δ18Ometeoric) is primarily related to air temperature. Phosphates in mammalian tooth enamel archive the oxygen isotope composition of local waters and rainfall (δ18Ophosphate) and acts as a proxy record of climatic change. In the water vole Arvicola (Rodentia), tooth growth, population dynamics, and taphonomy make upper incisors from fossil assemblages a high- resolution (approximately month long), summer-season record of climate. Using published δ18Ophosphate and meteorological data, strong and significant summer-specific models relating δ18Ophosphate with δ18Ometeoric and temperature were observed. These relationships, and a complimentary carbonate-based proxy, allowed the creation of two palaeothermometers. These were used to reconstruct climate from a warm-temperate, mid-Pleistocene interglacial sequence at Cudmore Grove, Essex, England. Summer surface water compositions were more enriched than present (-5.4‰vsmow). Mean summer palaeotemperatures were found to be warmer than present (meteorological thermometer, +22°C; carbonate thermometer, +21°C) but also warmer than other proxies indicate. Tooth phosphate based reconstructions broadly agree with other palaeoproxies but they are likely to over-estimate mean summer temperatures for a number of reasons, including: late-summer bias in climate sampling by voles; the local hydrological cycle of maritime western Europe; evaporative enrichment of surface waters; and ecological disparity between modern and fossil Arvicola. [Submitted as an integral part of the Masters of Science Degree in Quaternary Science, Royal Holloway, University of London, in 2005]
DOI: 10.6084/m9.figshare.154613.v1
title: Oxygen stable isotope analysis of water vole (Arvicola) incisor tooth enamel: a proxy record of terrestrial climate from MIS 9 Britain

description: The oxygen stable isotopic composition of rainfall (δ18Ometeoric) is primarily related to air temperature. Phosphates in mammalian tooth enamel archive the oxygen isotope composition of local waters and rainfall (δ18Ophosphate) and acts as a proxy record of climatic change. In the water vole Arvicola (Rodentia), tooth growth, population dynamics, and taphonomy make upper incisors from fossil assemblages a high- resolution (approximately month long), summer-season record of climate. Using published δ18Ophosphate and meteorological data, strong and significant summer-specific models relating δ18Ophosphate with δ18Ometeoric and temperature were observed. These relationships, and a complimentary carbonate-based proxy, allowed the creation of two palaeothermometers. These were used to reconstruct climate from a warm-temperate, mid-Pleistocene interglacial sequence at Cudmore Grove, Essex, England. Summer surface water compositions were more enriched than present (-5.4‰vsmow). Mean summer palaeotemperatures were found to be warmer than present (meteorological thermometer, +22°C; carbonate thermometer, +21°C) but also warmer than other proxies indicate. Tooth phosphate based reconstructions broadly agree with other palaeoproxies but they are likely to over-estimate mean summer temperatures for a number of reasons, including: late-summer bias in climate sampling by voles; the local hydrological cycle of maritime western Europe; evaporative enrichment of surface waters; and ecological disparity between modern and fossil Arvicola. [Submitted as an integral part of the Masters of Science Degree in Quaternary Science, Royal Holloway, University of London, in 2005]
DOI: 10.6084/m9.figshare.154584
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154583
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154584.v1
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154582
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154583.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154580
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154582.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154427
title: Data from "Effect of filament aspect ratio on the dielectric response of multiwalled carbon nanotube composites" (DOI:10.1063/1.3569596)

description: Subpercolated composites consisting of highly polar fillers in an insulating matrix have long been<br>predicted to exhibit a large dielectric constant. In this study, we examine the feasibility of experimentally reproducing such an effect based on a multiwalled carbon nanotubes (MWNTs)-polydimethylsiloxane (PDMS) composite system. MWNTs of different diameters were subjected to high-power ultrasound. The sonication-induced scission of nanotubes shows saturation at a final length dependent on the tube diameter, in agreement with a theoretical model. Sonication allows us to produce MWNTs with a prescribed mean aspect ratio between 10 and 55. Composites were formed from these MWNTs with PDMS elastomer at a fixed 1 wt% doping level, using a common solution-processing method. Results from AC impedance spectroscopy indicate that the tube length minimally affects the dielectric response of these composites when the doping level is below the percolation threshold.
DOI: 10.6084/m9.figshare.154580.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154385
title: Questionnaire

description: Raw data showing characteristics of patients, respondents and their responses to the questionnaire.
DOI: 10.6084/m9.figshare.154362
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154362.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154361
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Case counts are now updated infrequently. Newest data from 10/23/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (10/23/13). This file does not include historical data. There is a column with exposures by state; those data are from [1]. Some basic analyses are available on my blog (see link below) [1] Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154385.v1
title: Questionnaire

description: Raw data showing characteristics of patients, respondents and their responses to the questionnaire.
DOI: 10.6084/m9.figshare.154427.v1
title: Data and plot scripts for DOI:10.1063/1.3569596

description: Subpercolated composites consisting of highly polar fillers in an insulating matrix have long been<br>predicted to exhibit a large dielectric constant. In this study, we examine the feasibility of experimentally reproducing such an effect based on a multiwalled carbon nanotubes (MWNTs)-polydimethylsiloxane (PDMS) composite system. MWNTs of different diameters were subjected to high-power ultrasound. The sonication-induced scission of nanotubes shows saturation at a final length dependent on the tube diameter, in agreement with a theoretical model. Sonication allows us to produce MWNTs with a prescribed mean aspect ratio between 10 and 55. Composites were formed from these MWNTs with PDMS elastomer at a fixed 1 wt% doping level, using a common solution-processing method. Results from AC impedance spectroscopy indicate that the tube length minimally affects the dielectric response of these composites when the doping level is below the percolation threshold.
DOI: 10.6084/m9.figshare.154350
title: Prospective Prediction of M. tuberculosis Inhibition Using Bayesian Models With Open Source Data - 3 years on

description: A description of using CDD to compare dataset. Analysis of predictions performed for M. tuberculosis activity 3 years ago. Comparison to data from GSK.
DOI: 10.6084/m9.figshare.154350.v1
title: Prospective Prediction of M. tuberculosis Inhibition Using Bayesian Models With Open Source Data - 3 years on

description: A description of using CDD to compare dataset. Analysis of predictions performed for M. tuberculosis activity 3 years ago. Comparison to data from GSK.
DOI: 10.6084/m9.figshare.154346
title: Scholarly impact of open access journals

description: Graphics and data accompany blog post about the impact of open science journals relative to non-OA.
DOI: 10.6084/m9.figshare.154427.v2
title: Effect of filament aspect ratio on the dielectric response of multiwalled carbon nanotube composites (DOI:10.1063/1.3569596) - data and plot scripts

description: Subpercolated composites consisting of highly polar fillers in an insulating matrix have long been<br>predicted to exhibit a large dielectric constant. In this study, we examine the feasibility of experimentally reproducing such an effect based on a multiwalled carbon nanotubes (MWNTs)-polydimethylsiloxane (PDMS) composite system. MWNTs of different diameters were subjected to high-power ultrasound. The sonication-induced scission of nanotubes shows saturation at a final length dependent on the tube diameter, in agreement with a theoretical model. Sonication allows us to produce MWNTs with a prescribed mean aspect ratio between 10 and 55. Composites were formed from these MWNTs with PDMS elastomer at a fixed 1 wt% doping level, using a common solution-processing method. Results from AC impedance spectroscopy indicate that the tube length minimally affects the dielectric response of these composites when the doping level is below the percolation threshold.
DOI: 10.6084/m9.figshare.154339
title: Vanderbilt Human Genetics Quals Phase I Study Guide

description: This is a study guide I put together years ago for studying for my qualifying exam in the Human Genetics Ph.D. program at Vanderbilt University. Several Ph.D. students have asked for it over the years, although its relevance is steadily decreasing over the years.
DOI: 10.6084/m9.figshare.154361.v1
title: Epidemiological analysis of fungal meningitis outbreak

description: Data from a blog post of basic epidemiological analysis of the outbreak, using the most up-to-date, publicly-available data, which is from Feb 4.
DOI: 10.6084/m9.figshare.154427.v4
title: Data from "Effect of filament aspect ratio on the dielectric response of multiwalled carbon nanotube composites" (DOI:10.1063/1.3569596)

description: Subpercolated composites consisting of highly polar fillers in an insulating matrix have long been<br>predicted to exhibit a large dielectric constant. In this study, we examine the feasibility of experimentally reproducing such an effect based on a multiwalled carbon nanotubes (MWNTs)-polydimethylsiloxane (PDMS) composite system. MWNTs of different diameters were subjected to high-power ultrasound. The sonication-induced scission of nanotubes shows saturation at a final length dependent on the tube diameter, in agreement with a theoretical model. Sonication allows us to produce MWNTs with a prescribed mean aspect ratio between 10 and 55. Composites were formed from these MWNTs with PDMS elastomer at a fixed 1 wt% doping level, using a common solution-processing method. Results from AC impedance spectroscopy indicate that the tube length minimally affects the dielectric response of these composites when the doping level is below the percolation threshold.
DOI: 10.6084/m9.figshare.154339.v1
title: Vanderbilt Human Genetics Quals Phase I Study Guide

description: This is a study guide I put together years ago for studying for my qualifying exam in the Human Genetics Ph.D. program at Vanderbilt University. Several Ph.D. students have asked for it over the years, although its relevance is steadily decreasing over the years.
DOI: 10.6084/m9.figshare.154427.v3
title: Effect of filament aspect ratio on the dielectric response of multiwalled carbon nanotube composites (DOI:10.1063/1.3569596) - data and plot scripts

description: Subpercolated composites consisting of highly polar fillers in an insulating matrix have long been<br>predicted to exhibit a large dielectric constant. In this study, we examine the feasibility of experimentally reproducing such an effect based on a multiwalled carbon nanotubes (MWNTs)-polydimethylsiloxane (PDMS) composite system. MWNTs of different diameters were subjected to high-power ultrasound. The sonication-induced scission of nanotubes shows saturation at a final length dependent on the tube diameter, in agreement with a theoretical model. Sonication allows us to produce MWNTs with a prescribed mean aspect ratio between 10 and 55. Composites were formed from these MWNTs with PDMS elastomer at a fixed 1 wt% doping level, using a common solution-processing method. Results from AC impedance spectroscopy indicate that the tube length minimally affects the dielectric response of these composites when the doping level is below the percolation threshold.
DOI: 10.6084/m9.figshare.154346.v1
title: Open access journal impacts

description: Graphics accompany blog post about the impact of open science journals relative to non-OA. Post is available here:<strong> http://caitlinrivers.com/2013/01/open-access-journal-impact-statistics/</strong> and ipython notebook is available here http://nbviewer.ipython.org/4627579/
DOI: 10.6084/m9.figshare.154361.v3
title: Epidemiological analysis of fungal meningitis outbreak

description: Data from a blog post of basic epidemiological analysis of the outbreak, using the most up-to-date, publicly-available data, which is from Feb 11.
DOI: 10.6084/m9.figshare.154346.v2
title: Open access journal impacts & statistics

description: Graphics accompany blog post about the impact of open science journals relative to non-OA.
DOI: 10.6084/m9.figshare.154361.v4
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Updated weekly(ish). Newest data from 2/25/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (2/25/13). This file does not include historical data. There is a column with exposures by state; those data are from: Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154330
title: Quantitative Biology Practical

description: Some notes to accompany the Quantitative Biology Practical handout, and the handout itself.
DOI: 10.6084/m9.figshare.154331.v1
title: Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

description: The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python environment for the user, while being efficient and fast. The core computational kernels are implemented in Cuda and interface with the user-visible code with PyCuda, for maximum ease-of-use combined with high performance on \GPU hardware. This document provides background on the model and formulation of the numerical method, evidence of a validation exercise with well-known benchmarks---a spherical shell with a centered charge and one with an off-center charge--- and a demonstration with a realistic biological geometry (lysozyme molecule)
DOI: 10.6084/m9.figshare.154346.v3
title: Open access journal impacts & statistics

description: Graphics accompany blog post about the impact of open science journals relative to non-OA.
DOI: 10.6084/m9.figshare.154361.v5
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Updated weekly(ish). Newest data from 3/14/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (3/4/13). This file does not include historical data. There is a column with exposures by state; those data are from: Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154331.v2
title: Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

description: The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python environment for the user, while being efficient and fast. The core computational kernels are implemented in Cuda and interface with the user-visible code with PyCuda, for maximum ease-of-use combined with high performance on \GPU hardware. This document provides background on the model and formulation of the numerical method, evidence of a validation exercise with well-known benchmarks---a spherical shell with a centered charge and one with an off-center charge--- and a demonstration with a realistic biological geometry (lysozyme molecule)
DOI: 10.6084/m9.figshare.154346.v5
title: Scholarly impact of open access journals

description: Graphics and data accompany blog post about the impact of open science journals relative to non-OA.
DOI: 10.6084/m9.figshare.154361.v6
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Updated weekly(ish). Newest data from 3/11/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (3/11/13). This file does not include historical data. There is a column with exposures by state; those data are from: Updated analysis available via iPython notebook (see first link), more comprehensive but older analysis on my blog (see third link). Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978