cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3426062.v19
title: Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

description: Firefly inputs and outputs for the paper "Refining the reaction mechanism of O<sub>2</sub> towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.<br><br>Three files are NOT inputs/outputs of quantum chemical computations:<br>- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.<br><br>-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol). <br>
DOI: 10.6084/m9.figshare.3426062.v20
title: Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

description: Firefly inputs and outputs for the paper "Refining the reaction mechanism of O<sub>2</sub> towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.<br><br>Three files are NOT inputs/outputs of quantum chemical computations:<br>- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.<br><br>-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol). <br>
DOI: 10.6084/m9.figshare.3426062.v22
title: Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

description: Firefly inputs and outputs for the paper "Refining the reaction mechanism of O<sub>2</sub> towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.<br>Four files are NOT inputs/outputs of quantum chemical computations:<br>- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.<br><br>-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol). <br><br>-BSSE.xls contains the energies for the evaluation of the effect of BSSE on the differences between the energies of radical-pairs at 80 angstrom distance and the values obtained by summing the energies of separate substrates. The gas-phase data clearly show that no BSSE error exists. The difference in solution energies is likewise independent of the SCF energy, and comes about simply due to the way the PCM model treats a system with two separated cavities: the final column ("total interaction") shows that in the radical pair the difference of solvation energy (vs. independent substrates) is almost exactly equal to the difference of total energy. I am still trying to understand why such difference is only apparent in the radical pair system, and not in the HODMe:O2 system. <br>
DOI: 10.6084/m9.figshare.3426062.v21
title: Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

description: Firefly inputs and outputs for the paper "Refining the reaction mechanism of O<sub>2</sub> towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.<br>Four files are NOT inputs/outputs of quantum chemical computations:<br>- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.<br><br>-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol). <br><br>-BSSE.xls contains the energies for the evaluation of the effect of BSSE on the differences between the energies of radical-pairs at 80 angstrom distance and the values obtained by summing the energies of separate substrates. The gas-phase data clearly show that no BSSE error exists. The difference in solution energies is likewise independent of the SCF energy, and comes about simply due to the way the PCM model treats a system with two separated cavities: the final column ("total interaction") shows that in the radical pair the difference of solvation energy (vs. independent substrates) is almost exactly equal to the difference of total energy. I am still trying to understand why such difference is only apparent in the radical pair system, and not in the HODMe:O2 system. <br>
DOI: 10.6084/m9.figshare.3425774
title: Re-examination of Mereschkowsky’s genus <i>Tetramphora</i> (Bacillariophyta) and its separation from <i>Amphora</i>

description: The raphid diatom genus <i>Amphora</i> has been subject to considerable revision over the previous 30 years, with many species transferred to newly created or existing genera. Despite these efforts, recent work has demonstrated that taxa presently assigned to the genus continue to be non-monophyletic and further revision is required. This investigation re-examines Mereschkowsky’s genus <i>Tetramphora</i>, which he described as including all <i>Amphora</i> species with four chloroplasts, arranged in pairs linked by large pyrenoids. Although largely ignored over the last 100 years, recent work has shown that taxa aligning with <i>Tetramphora</i> are monophyletic and distinct from <i>Amphora sensu stricto</i>. Nine species belonging to <i>Tetramphora</i> are illustrated and described, based on light and scanning electron microscope observations, as well as a preliminary molecular phylogeny for the group. From these observations, we designate Mereschkowsky’s <i>T</i>. <i>ostrearia</i> as the generitype of <i>Tetramphora</i>, recognize <i>T</i>. <i>lineolata</i>, and transfer the <i>Amphora</i> taxa, <i>A</i>. <i>decussata</i>, <i>A</i>. <i>sulcata</i>, <i>A</i>. <i>rhombica</i>, <i>A</i>. <i>intermedia</i> and <i>A</i>. <i>securicula</i>, and the <i>Halamphora</i> taxon <i>H</i>. <i>chilensis</i> to <i>Tetramphora</i>. In addition, three new species, <i>T</i>. <i>fontinalis</i>, <i>T</i>. <i>lineolatoides</i> and <i>T</i>. <i>robusta</i>, are described.
DOI: 10.6084/m9.figshare.3425774.v1
title: Re-examination of Mereschkowsky’s genus <i>Tetramphora</i> (Bacillariophyta) and its separation from <i>Amphora</i>

description: The raphid diatom genus <i>Amphora</i> has been subject to considerable revision over the previous 30 years, with many species transferred to newly created or existing genera. Despite these efforts, recent work has demonstrated that taxa presently assigned to the genus continue to be non-monophyletic and further revision is required. This investigation re-examines Mereschkowsky’s genus <i>Tetramphora</i>, which he described as including all <i>Amphora</i> species with four chloroplasts, arranged in pairs linked by large pyrenoids. Although largely ignored over the last 100 years, recent work has shown that taxa aligning with <i>Tetramphora</i> are monophyletic and distinct from <i>Amphora sensu stricto</i>. Nine species belonging to <i>Tetramphora</i> are illustrated and described, based on light and scanning electron microscope observations, as well as a preliminary molecular phylogeny for the group. From these observations, we designate Mereschkowsky’s <i>T</i>. <i>ostrearia</i> as the generitype of <i>Tetramphora</i>, recognize <i>T</i>. <i>lineolata</i>, and transfer the <i>Amphora</i> taxa, <i>A</i>. <i>decussata</i>, <i>A</i>. <i>sulcata</i>, <i>A</i>. <i>rhombica</i>, <i>A</i>. <i>intermedia</i> and <i>A</i>. <i>securicula</i>, and the <i>Halamphora</i> taxon <i>H</i>. <i>chilensis</i> to <i>Tetramphora</i>. In addition, three new species, <i>T</i>. <i>fontinalis</i>, <i>T</i>. <i>lineolatoides</i> and <i>T</i>. <i>robusta</i>, are described.
DOI: 10.6084/m9.figshare.3425765
title: The legacy of the F344 rat as a cancer bioassay model (a retrospective summary of three common F344 rat neoplasms)

description: The Fischer 344 (F344) rat was used by the National Toxicology Program (NTP) for over 5 decades for toxicity and carcinogenicity studies. However, in 2006, the NTP decided to switch to a different rat stock due largely to high background control incidences of Leydig cell tumors (LCTs) and mononuclear cell leukemia (MNCL), also known as large granular lymphocytic (LGL) leukemia. In the current review, we aim (1) to provide a summary of NTP bioassays with treatment-associated effects involving MNCL and LCTs in addition to male F344-specific tunica vaginalis mesothelioma (TVM); (2) to describe important pathobiological differences between these F344 rat tumor responses and similar target tissue-tumor response in humans; and (3) to present the NTP reasons for switching away from the F344 rat. We show that due to the highly variable background incidence of F344 MNCL, more reliance on historical control data than is usual for most tumor responses is warranted to evaluate potential effect of any chemical treatment in this rat strain. The high spontaneous incidence of LCTs in the testes of male F344 rats has made this tumor endpoint of little practical use in identifying potential testicular carcinogenic responses. TVM responses in F344 rats have a biological plausible relationship to LCTs unlike TVM in humans. Given their high spontaneous background incidence and species-specific biology, we contend that MNCL and LCT, along with TVM responses, in F344 rat carcinogenicity studies are inappropriate tumor types for human health risk assessment and lack relevance in predicting human carcinogenicity.
DOI: 10.6084/m9.figshare.3425765.v1
title: The legacy of the F344 rat as a cancer bioassay model (a retrospective summary of three common F344 rat neoplasms)

description: The Fischer 344 (F344) rat was used by the National Toxicology Program (NTP) for over 5 decades for toxicity and carcinogenicity studies. However, in 2006, the NTP decided to switch to a different rat stock due largely to high background control incidences of Leydig cell tumors (LCTs) and mononuclear cell leukemia (MNCL), also known as large granular lymphocytic (LGL) leukemia. In the current review, we aim (1) to provide a summary of NTP bioassays with treatment-associated effects involving MNCL and LCTs in addition to male F344-specific tunica vaginalis mesothelioma (TVM); (2) to describe important pathobiological differences between these F344 rat tumor responses and similar target tissue-tumor response in humans; and (3) to present the NTP reasons for switching away from the F344 rat. We show that due to the highly variable background incidence of F344 MNCL, more reliance on historical control data than is usual for most tumor responses is warranted to evaluate potential effect of any chemical treatment in this rat strain. The high spontaneous incidence of LCTs in the testes of male F344 rats has made this tumor endpoint of little practical use in identifying potential testicular carcinogenic responses. TVM responses in F344 rats have a biological plausible relationship to LCTs unlike TVM in humans. Given their high spontaneous background incidence and species-specific biology, we contend that MNCL and LCT, along with TVM responses, in F344 rat carcinogenicity studies are inappropriate tumor types for human health risk assessment and lack relevance in predicting human carcinogenicity.
DOI: 10.6084/m9.figshare.3425759
title: images.tar

description: Neurovault's statmaps for benchmarking<br>
DOI: 10.6084/m9.figshare.3425759.v1
title: images.tar

description: Neurovault's statmaps for benchmarking<br>
DOI: 10.6084/m9.figshare.3425756
title: Normative data for phonemic and semantic verbal fluency test in the adult French–Quebec population and validation study in Alzheimer’s disease and depression

description: <b>Objective:</b> Verbal fluency tasks are principally used to assess lexical access and have shown usefulness for differential diagnosis. The purpose of Study 1 was to provide normative data in the adult French–Quebec population (Canada) for semantic verbal fluency (animals), for two sets of phonemic verbal fluency (TNP and PFL), and for letter P alone (60 seconds per category/letter). The objectives of Study 2 were to establish the diagnostic and predictive validity of the present tasks and normative data in Alzheimer’s disease (AD) and major depressive episode (MDE). <b>Method:</b> The normative sample consisted of 932 participants aged 19–91 years. Based on multiple linear regressions, equations to calculate <i>Z</i>-scores were provided. To assess validity, performance of 62 healthy participants was compared to 62 participants with AD and 41 with MDE aged over 50. <b>Results:</b> Age and education, but not gender, predicted performance on each verbal fluency task. Healthy adults aged 50 and younger had a better performance on semantic than phonemic verbal fluency. In comparison to MDE, AD participants had lower performance on animals and TNP, but not on letter P. Ninety percent of people with a <i>Z</i>-score ≤ −1.50 on semantic verbal fluency had AD and the global accuracy was 76.6%. Test–retest reliability over one year was high for both animals (<i>r</i> = .711) and TNP (<i>r</i> = .790) in healthy older participants, but dropped for animals in people with AD (<i>r</i> = .493). <b>Conclusions:</b> These data will strengthen accurate detection of verbal fluency deficits in French–Quebec adults.
DOI: 10.6084/m9.figshare.3425756.v1
title: Normative data for phonemic and semantic verbal fluency test in the adult French–Quebec population and validation study in Alzheimer’s disease and depression

description: <b>Objective:</b> Verbal fluency tasks are principally used to assess lexical access and have shown usefulness for differential diagnosis. The purpose of Study 1 was to provide normative data in the adult French–Quebec population (Canada) for semantic verbal fluency (animals), for two sets of phonemic verbal fluency (TNP and PFL), and for letter P alone (60 seconds per category/letter). The objectives of Study 2 were to establish the diagnostic and predictive validity of the present tasks and normative data in Alzheimer’s disease (AD) and major depressive episode (MDE). <b>Method:</b> The normative sample consisted of 932 participants aged 19–91 years. Based on multiple linear regressions, equations to calculate <i>Z</i>-scores were provided. To assess validity, performance of 62 healthy participants was compared to 62 participants with AD and 41 with MDE aged over 50. <b>Results:</b> Age and education, but not gender, predicted performance on each verbal fluency task. Healthy adults aged 50 and younger had a better performance on semantic than phonemic verbal fluency. In comparison to MDE, AD participants had lower performance on animals and TNP, but not on letter P. Ninety percent of people with a <i>Z</i>-score ≤ −1.50 on semantic verbal fluency had AD and the global accuracy was 76.6%. Test–retest reliability over one year was high for both animals (<i>r</i> = .711) and TNP (<i>r</i> = .790) in healthy older participants, but dropped for animals in people with AD (<i>r</i> = .493). <b>Conclusions:</b> These data will strengthen accurate detection of verbal fluency deficits in French–Quebec adults.
DOI: 10.6084/m9.figshare.3425753
title: The relevance of dawsonite precipitation in CO2 sequestration in the Mihalyi-Repcelak area, NW Hungary

description: Raman spectra of dawsonite, table
DOI: 10.6084/m9.figshare.3425738
title: Key Challenges of Research Communication - De Gruyter Open Author’s Survey 2016

description: The main goal of the research was to examine the attitudes of academic authors around the world towards open access publishing, including their experiences with open access, their publishing practices and their opinions about different publishing modelsEmails containing links to the survey were sent to 107,296 scholars listed on De Gruyter’s Open mailing lists in a period from December 2015 to January 2016. You can have a look at the survey questionnaire here: <br>http://survey2015.degruyteropen.com/<br>We received 1012 responses to the survey, so the response rate was 0,94%.More information about the survey might be found here:http://openscience.com/tag/key-challenges/<br>
DOI: 10.6084/m9.figshare.3425738.v1
title: Key Challenges of Research Communication - De Gruyter Open Author’s Survey 2016

description: The main goal of the research was to examine the attitudes of academic authors around the world towards open access publishing, including their experiences with open access, their publishing practices and their opinions about different publishing modelsEmails containing links to the survey were sent to 107,296 scholars listed on De Gruyter’s Open mailing lists in a period from December 2015 to January 2016. You can have a look at the survey questionnaire here: <br>http://survey2015.degruyteropen.com/<br>We received 1012 responses to the survey, so the response rate was 0,94%.More information about the survey might be found here:http://openscience.com/tag/key-challenges/<br>
DOI: 10.6084/m9.figshare.3425729
title: Investigation into the number of desktop items on University staff computers, broken down by department and operating system.

description: This study investigates the desktop clutter of University staff broken down by department and operating system, initial data collection began in November 2015 through the use of a Google Form (a copy is attached as DesktopItems_SurveyJune2016). The first data deposit was made in June 2016, future deposits will be made available as more data is collected.Note that coordinates for Universities were found by a maps.google.com in June 2016 and should be considered informative rather than precise.<br># The Survey<br>If you would like to contribute to this dataset and work in a University please do fill in the survey here: http://goo.gl/forms/IehEi6dyCEBIlbXW2<br><br>
DOI: 10.6084/m9.figshare.3425729.v1
title: Investigation into the number of desktop items on University staff computers, broken down by department and operating system.

description: This study investigates the desktop clutter of University staff broken down by department and operating system, initial data collection began in November 2015 through the use of a Google Form (a copy is attached as DesktopItems_SurveyJune2016). The first data deposit was made in June 2016, future deposits will be made available as more data is collected.Note that coordinates for Universities were found by a maps.google.com in June 2016 and should be considered informative rather than precise.
DOI: 10.6084/m9.figshare.3425729.v3
title: Investigation into the number of desktop items on University staff computers, broken down by department and operating system.

description: This study investigates the desktop clutter of University staff broken down by department and operating system, initial data collection began in November 2015 through the use of a Google Form (a copy is attached as DesktopItems_SurveyJune2016). The first data deposit was made in June 2016, future deposits will be made available as more data is collected.Note that coordinates for Universities were found by a maps.google.com in June 2016 and should be considered informative rather than precise.<br>If you would like to contribute to this dataset and work in a University please do fill in the survey here: http://goo.gl/forms/IehEi6dyCEBIlbXW2<br>
DOI: 10.6084/m9.figshare.3425729.v5
title: Investigation into the number of desktop items on University staff computers, broken down by department and operating system.

description: This study investigates the desktop clutter of University staff broken down by department and operating system, initial data collection began in November 2015 through the use of a Google Form (a copy is attached as DesktopItems_SurveyJune2016). The first data deposit was made in June 2016, future deposits will be made available as more data is collected.Note that coordinates for Universities were found by a maps.google.com in June 2016 and should be considered informative rather than precise.<br># The Survey<br>If you would like to contribute to this dataset and work in a University please do fill in the survey here: http://goo.gl/forms/IehEi6dyCEBIlbXW2<br><br>
DOI: 10.6084/m9.figshare.3425729.v4
title: Investigation into the number of desktop items on University staff computers, broken down by department and operating system.

description: This study investigates the desktop clutter of University staff broken down by department and operating system, initial data collection began in November 2015 through the use of a Google Form (a copy is attached as DesktopItems_SurveyJune2016). The first data deposit was made in June 2016, future deposits will be made available as more data is collected.Note that coordinates for Universities were found by a maps.google.com in June 2016 and should be considered informative rather than precise.<br># The Survey<br>If you would like to contribute to this dataset and work in a University please do fill in the survey here: http://goo.gl/forms/IehEi6dyCEBIlbXW2<br><br>
DOI: 10.6084/m9.figshare.3425684
title: 20160610 - ANDS - Monthly Tech Talk - Minting DOIs for Data.pptx

description: A description of how the John de Laeter Centre manage the minting of DOIs for both data and samples.<br>
DOI: 10.6084/m9.figshare.3425684.v1
title: 20160610 - ANDS - Monthly Tech Talk - Minting DOIs for Data.pptx

description: A description of how the John de Laeter Centre manage the minting of DOIs for both data and samples.<br>
DOI: 10.6084/m9.figshare.3425666
title: Quality measures for anticoagulation care

description: <b>Objective:</b> To systematically identify and assess current quality measures for anticoagulation in atrial fibrillation (AF), venous thromboembolism (VTE) treatment and surgical VTE prophylaxis. <b>Research design and methods:</b> Fifteen quality measure websites were searched as were bibliographic databases (January 2000–February 2016). Quality measures were included if developed in the United States and incorporating an aspect of anticoagulation for the aforementioned indications or if applicable but not indication specific (non-disease specific measure). Two reviewers independently extracted data regarding the characteristics of each quality measure. <b>Results:</b> Thirty-five measures were identified, mostly in VTE treatment (48.6%), followed by non-disease specific measures (25.7%), AF (17.6%) and surgical VTE prophylaxis (8.8%). Process measures predominated (82.9%). A majority of quality measures (65.7%) were focused on parenteral anticoagulants or warfarin and not applicable to novel oral anticoagulants (NOACs). Ten (28.6%) measures are used by the Centers for Medicare and Medicaid Services or as a core measure of The Joint Commission. Limitations include the inability to statistically pool data and possible publication bias given the nature of databases for quality measures. <b>Conclusions:</b> Quality measures are recognized in anticoagulation care. Areas for improvement include expanding beyond process measures and capturing adverse events and the advantages offered by NOACs.