cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.96949.v7
title: Supplementary material: When does cyclic dominance lead to stable spiral waves?

description: In these notes, we provide some supplementary material to the manuscript "When does cyclic dominance lead to stable spiral waves?". The notes include a schematic description of the model and movies allowing the visualization of the results. See file "index.html" for comments and captions to the movies.
DOI: 10.6084/m9.figshare.96909
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96916
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in UTF-8 (X)HTML5 with RDFa semantics. Images are embedded in the files as data URIs and equations are provided in MathML. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html The more recent (second) 2010.tar.gz archive contains both the Jekyll sources and HTML site for the notebook entries in 2010, corresponding to https://github.com/cboettig/2010/releases/tag/2010-archive, which can be viewed at http://carlboettiger.info/2010
DOI: 10.6084/m9.figshare.96936.v1
title: Gliding motility assay using 5.5mM D2O in solution.

description: This is a gliding motility assay using kinesin-1 and rhodamine labeled microtubules. Images were taken with an Andor Luca EMCCD camera on an Olympus IX-71 microscope using a 60x 1.42NA PlanApo objective. This is the first set in a series of images taken investigating speed variations of microtubules due to the inclusion of heavy water in the motility assay. Measured speeds in this fileset will be lower than reported in the publication due to the glass slide being brought up to the temperature of 32°C by the objective heater. This assay contained 5528mM of D2O.
DOI: 10.6084/m9.figshare.96919.v1
title: Lab Notebook, 2011

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2011 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96936.v3
title: Gliding motility assay using 5.5M D2O in solution. Assay 01—ROI 1/15.

description: This is a gliding motility assay using kinesin-1 and rhodamine labeled microtubules. Images were taken with an Andor Luca EMCCD camera on an Olympus IX-71 microscope using a 60x 1.42NA PlanApo objective. This is the first set in a series of images taken investigating speed variations of microtubules due to the inclusion of heavy water in the motility assay. Measured speeds in this fileset will be lower than reported in the publication due to the glass slide being brought up to the temperature of 32°C by the objective heater. This assay contained 5528mM of D2O.
DOI: 10.6084/m9.figshare.96909.v1
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96919.v2
title: Lab Notebook, 2011

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2011 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96936.v2
title: Gliding motility assay using 5.5mM D2O in solution. Assay 01—ROI 1/15.

description: This is a gliding motility assay using kinesin-1 and rhodamine labeled microtubules. Images were taken with an Andor Luca EMCCD camera on an Olympus IX-71 microscope using a 60x 1.42NA PlanApo objective. This is the first set in a series of images taken investigating speed variations of microtubules due to the inclusion of heavy water in the motility assay. Measured speeds in this fileset will be lower than reported in the publication due to the glass slide being brought up to the temperature of 32°C by the objective heater. This assay contained 5528mM of D2O.
DOI: 10.6084/m9.figshare.96916.v1
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96919.v4
title: Lab Notebook, 2011

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2011 (http://www.carlboettiger.info/archives.html). Entries are archived in UTF-8 (X)HTML5 with RDFa semantics. Images are embedded in the files as data URIs and equations are provided in MathML. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96907
title: Oil sensor v01 results

description: The first trial of our proof of principle oil spill sensor. This data shows the spectral reaction of the sensor when immersed in varying concentrations of toluene in water. Toluene is one of a range of aromatic hydrocarbonds often found in crude oil. The data attached is broken up into four files. The raw specral data for all the ppm concentartions of toluene, the summary of the vally seperation within the specral data (as calculated with vally detection software) and finally 2 graphs showing this data.
DOI: 10.6084/m9.figshare.96919.v3
title: Lab Notebook, 2011

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2011 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96889
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96916.v2
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96889.v1
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96885
title: Gaussian Job Archive for C51H80Mg2N4O10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96888
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96885.v1
title: Gaussian Job Archive for C51H80Mg2N4O10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96888.v1
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96916.v3
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in plain text UTF-8. Written in pandoc-flavored Markdown. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96916.v4
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in (X)HTML5. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96883
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96886.v1
title: Sexual Selection and Life-History Evolution with Age-Dependent Paternal Mutation

description: A preliminary talk to be delivered to a graduate student seminar. Here I examine how sexual selection affects the rate of germ-line mutations delevered to offspring. Preliminary static results based on varying parameters within the mate choice function, the trait growth function and the intrinsic rate of increase on the generation time, which I use as a basic index of the impact of sperm-originating mutations on offspring.
DOI: 10.6084/m9.figshare.96916.v6
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in UTF-8 (X)HTML5 with RDFa semantics. Images are embedded in the files as data URIs and equations are provided in MathML. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html The more recent (second) 2010.tar.gz archive contains both the Jekyll sources and HTML site for the notebook entries in 2010, corresponding to https://github.com/cboettig/2010/releases/tag/2010-archive, which can be viewed at http://carlboettiger.info/2010
DOI: 10.6084/m9.figshare.96882
title: Gaussian Job Archive for C44H70Mg2N4O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96883.v1
title: Gaussian Job Archive for C9H13F3O3S

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96916.v5
title: Lab Notebook, 2010

description: Permanent archive of Carl Boettiger's open lab notebook entries for the year 2010 (http://www.carlboettiger.info/archives.html). Entries are archived in UTF-8 (X)HTML5 with RDFa semantics. Images are embedded in the files as data URIs and equations are provided in MathML. Meets the goals of the Data Management Plan: http://www.carlboettiger.info/2012/10/09/data-management-plan.html
DOI: 10.6084/m9.figshare.96881
title: Gaussian Job Archive for C51H80Mg2N4O10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96881.v1
title: Gaussian Job Archive for C51H80Mg2N4O10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96882.v1
title: Gaussian Job Archive for C44H70Mg2N4O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.96874
title: Open access options for publishing neuroscience research

description: The field of neuroscience is locking away more research in subscription journals everyday, where many people around the world can’t access it, learn from it, or build on it. Instead, researchers can publish their work as open access, allowing people to access it, download it, and reuse it for free. This fileset includes a list (in .ods, .xls, and .pdf formats) of journals publishing open access research in neuroscience. Journals are divided up into three categories: (1) open access journals devoted to neuroscience, (2) open access journals which are not devoted exclusively to neuroscience, but publish research articles in the area as part of a broader portfolio, and (3) hybrid journals devoted to neuroscience which are subscription-based but offer an open access option. Each entry includes the title of the journal, publisher, license, article processing charge (APC), existence of fee waivers, and the journal's website. The author welcomes suggestions of journals that should be added to the list, and will update the fileset as needed. This work was originally posted on the author's blog (link below).
DOI: 10.6084/m9.figshare.96873
title: Fingerprint diagram of coarsening phenomena

description: We have proposed a procedure to identify and characterise key topological transformations of coarsening phenomena. The method is based on the linear expansion of the Navier–Stokes equations. As an example, we characterised a polymer foaming process which involves the formation of gas bubbles in a fluid (nucleation) and evolution of both liquid and gas until stabilization occurs. The file named XR_foaming shows micro-radiographs of the process (resolution 15 um). Similar micro-radiographs at 3 um resolution were recorded and normalised. We then calculated the difference between each image and its successor in order to highlight the structural changes (File Diff, 250 frames of 1000). We subsequently computed the optical flow from one difference image to the next one in the sequence obtaining an unique fingerprint of the fluid dynamics of a foam where the y axis is time (File: Fingerprint). This diagram provides a straightforward identification of events, their duration, and the time between them, as well as both general and local flow patterns and velocities. We'll provide freely the algorithm (Fortran) upon request and further details can be found in Verdejo et al. 2009, Phys.Chem. Chem.Phys., 11, 10860-10866. DOI: 10.1039/b913262g.
DOI: 10.6084/m9.figshare.96873.v1
title: Fingerprint diagram of coarsening phenomena

description: We have proposed a procedure to identify and characterise key topological transformations of coarsening phenomena. The method is based on the linear expansion of the Navier–Stokes equations. As an example, we characterised a polymer foaming process which involves the formation of gas bubbles in a fluid (nucleation) and evolution of both liquid and gas until stabilization occurs. The file named XR_foaming shows micro-radiographs of the process (resolution 15 um). Similar micro-radiographs at 3 um resolution were recorded and normalised. We then calculated the difference between each image and its successor in order to highlight the structural changes (File Diff, 250 frames of 1000). We subsequently computed the optical flow from one difference image to the next one in the sequence obtaining an unique fingerprint of the fluid dynamics of a foam where the y axis is time (File: Fingerprint). This diagram provides a straightforward identification of events, their duration, and the time between them, as well as both general and local flow patterns and velocities. We'll provide freely the algorithm (Fortran) upon request and further details can be found in Verdejo et al. 2009, Phys.Chem. Chem.Phys., 11, 10860-10866. DOI: 10.1039/b913262g.
DOI: 10.6084/m9.figshare.96874.v1
title: Open access options for publishing neuroscience research

description: The field of neuroscience locks away more research in subscription journals everyday, where many people around the world can’t access it, learn from it, or build on it. Instead, researchers can publish their work as open access, allowing others to read, distribute, and reuse it for free. This file set includes a list of journals (in .ods, .xls, and .pdf formats) which publish open access research in neuroscience. Journals are divided up into three categories: (1) open access journals focusing on neuroscience research, (2) open access journals which are not devoted exclusively to neuroscience, but publish articles in neuroscience as part of a broader portfolio, and (3) hybrid journals devoted to neuroscience which are subscription-based but offer an open access option. For all entries, the journal title, publisher, license, article processing charge (APC), existence of fee waivers, and the journal's website are listed. The majority of listed journals use a license that is fully compliant with the Budapest Open Access Initiative's definition of open access (CC-BY), while a smaller number of journals use the CC-BY-NC license, which is less open and puts restrictions on non-commercial use. The majority of journals listed also offer waivers for authors that are unable to pay publication charges. The author of this list welcomes feedback from anyone who is aware of journals that should be added, and will update the files here as needed. This work was originally posted on the author's blog (link below).
DOI: 10.6084/m9.figshare.96874.v2
title: Open access options for publishing neuroscience research

description: The field of neuroscience is locking away more research in subscription journals everyday, where many people around the world can’t access it, learn from it, or build on it. Instead, researchers can publish their work as open access, allowing people to access it, download it, and reuse it for free. This fileset includes a list (in .ods, .xls, and .pdf formats) of journals publishing open access research in neuroscience. Journals are divided up into three categories: (1) open access journals devoted to neuroscience, (2) open access journals which are not devoted exclusively to neuroscience, but publish research articles in the area as part of a broader portfolio, and (3) hybrid journals devoted to neuroscience which are subscription-based but offer an open access option. Each entry includes the title of the journal, publisher, license, article processing charge (APC), existence of fee waivers, and the journal's website. The author welcomes suggestions of journals that should be added to the list, and will update the fileset as needed. This work was originally posted on the author's blog (link below).
DOI: 10.6084/m9.figshare.96814
title: Dyslexia in Healthcare Professionals

description: A description of dyslexia in radiography students and the coping straties
DOI: 10.6084/m9.figshare.96831.v1
title: Report on the International Workshop on Contributorship and Scholarly Attribution, May 16, 2012

description: On May 16, 2012, individuals from a wide range of sectors with interests in scholarly publishing gathered together at an invitation-only workshop at Harvard University to discuss authorship, contributorship and attribution, and to explore alternative models. The report summarises the problems identified with current attribution and citation practices, details the discussions and recommendations from the breakout groups on how they could be improved, and lists the projects being taken forward. IWCSA Report (2012). Report on the International Workshop on Contributorship and Scholarly Attribution, May 16, 2012. Harvard University and the Wellcome Trust.
DOI: 10.6084/m9.figshare.96799.v1
title: Impostor Syndrome Lecture

description: My lecture from the MA Thesis Development Seminar on the impostor syndrome
DOI: 10.6084/m9.figshare.96788
title: Mitigating effects of vaccination given constraints in supply and daily administration capacity

description: <strong>Overview</strong> Influenza viruses are a major cause of morbidity and mortality worldwide. Vaccination is a powerful tool for preventing or mitigating influenza outbreaks. Yet, vaccine supplies and daily administration capacities are limited, even in developed countries. Understanding how such constraints can alter the mitigating effects of vaccination is a crucial part of influenza preparedness plans. We present a mathematical model that explicitly takes into account vaccine supply and the number of vaccines administered per day and places data-informed limits on these parameters. We use the model to test several vaccination scenarios. The model can be used by government and medical officials to create customized pandemic preparedness plans based on the supply and administration constraints of specific communities. This work was published in full in Cruz-Aponte, M., McKiernan, E. C. and Herrera-Valdez, M. A. (2011). Mitigating effects of vaccination on influenza outbreaks given constraints in stockpile size and daily administration capacity. BMC Infectious Diseases 11(1), 207 (DOI below). <strong>Fileset</strong> This fileset includes: (1) a poster presented at the 32nd Annual Research and Education Forum held at the University of Puerto Rico, Medical Sciences campus (pdf), (2) the tex file used to generate the pdf, which can serve as a LaTeX poster template, (3) the bibtex file with references from the published article, and (4) all figures presented in the poster.
DOI: 10.6084/m9.figshare.96802.v1
title: Waiting for p&lt;0.05

description: In this submission, PatientsLikeMe considers the risks, benefits, and opportunity for collecting and analyzing data for ALS patients who are taking part in clinical trials. Our intent is to encourage discussion and debate about the best way to address the complex medical, ethical, and scientfic issues surrounding the collection of such data.
DOI: 10.6084/m9.figshare.96788.v1
title: Mitigating effects of vaccination given constraints in supply and daily administration capacity

description: <strong>Overview</strong> Influenza viruses are a major cause of morbidity and mortality worldwide. Vaccination is a powerful tool for preventing or mitigating influenza outbreaks. Yet, vaccine supplies and daily administration capacities are limited, even in developed countries. Understanding how such constraints can alter the mitigating effects of vaccination is a crucial part of influenza preparedness plans. We present a mathematical model that explicitly takes into account vaccine supply and the number of vaccines administered per day and places data-informed limits on these parameters. We use the model to test several vaccination scenarios. The model can be used by government and medical officials to create customized pandemic preparedness plans based on the supply and administration constraints of specific communities. This work was published in full in Cruz-Aponte, M., McKiernan, E. C. and Herrera-Valdez, M. A. (2011). Mitigating effects of vaccination on influenza outbreaks given constraints in stockpile size and daily administration capacity. BMC Infectious Diseases 11(1), 207 (DOI below). <strong>Fileset</strong> This fileset includes: (1) a poster presented at the 32nd Annual Research and Education Forum held at the University of Puerto Rico, Medical Sciences campus (pdf), (2) the tex file used to generate the pdf, which can serve as a LaTeX poster template, (3) the bibtex file with references from the published article, and (4) all figures presented in the poster.