cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.157059
title: Experiment 3: perceived size of test and reference arrays at high and low spatial frequency

description: For the control conditions, the rows of data indicate the proportion of times participants perceived a unbound test array as being larger than a fixed unbound reference array. For the binding ring conditions, the rows of indicate the proportion of times participants perceived a binding ring array as being larger than a fixed unbound reference array. In the high spatial frequency (HSF condition), both arrays were high-pass filtered. In the low spatial frequency (LSF) condition, both arrays were low-passed filtered. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.157060
title: Experiment 4: perceived size of test and reference arrays with lines only present either within the interior of the elements or connecting the elements

description: In experiment 4a the first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows of indicate the proportion of times participants perceived an array with a line connecting the local elements as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.<br>In experiment 4b the first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows of indicate the proportion of times participants perceived an array with a line intersecting only the interiors of the elements as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.157087.v1
title: If your results are unpredictable, does it make them any less true? HTDE 2013.1

description: Lecture on hard-to-define events (follow-up on HTDE 2012) in biology and the development of scientific theory.
DOI: 10.6084/m9.figshare.157079.v1
title: Raw data for figure 1 and figure 2

description: Raw data tables showing the number of female wasps that landed on each plant with the different blends (A,B or C).
DOI: 10.6084/m9.figshare.157087.v2
title: If your results are unpredictable, does it make them any less true? HTDE 2013.1

description: Lecture on hard-to-define events (follow-up on HTDE 2012) in biology and the development of scientific theory.
DOI: 10.6084/m9.figshare.157058
title: Experiment 2: reversal choices

description: For subjects 1-10, values indicate the average difference in a radius at which participants made a reversal choice in the staircase for each of the five conditions tested labelled: BR Shift Xº. Each condition was tested 4 times and 5 reversals were recorded resulted in 20 total reversals. The 1st reversal of each trial was excluded from analysis. The mean for each subject(shown) was automatically computed by the stimulus presentation software: Adjustable_BR_Staircase.m on the basis of the remaining 4 reversals per trial. A copy of the program is available upon request.
DOI: 10.6084/m9.figshare.157059.v1
title: Experiment 3: percieved size of test and reference arrays at high and low spatial frequency

description: For the control conditions, the rows of data indicate the proportion of times participants perceived a unbound test array as being larger than a fixed unbound reference array. For the binding ring conditions, the rows of indicate the proportion of times participants perceived a binding ring array as being larger than a fixed unbound reference array. In the high spatial frequency (HSF condition), both arrays were high-pass filtered. In the low spatial frequency (LSF) condition, both arrays were low-passed filtered. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.156989
title: Crowd4Discovery ventral medial primary neuronal culture experiment 1

description: In this pilot experiment, Danny (@badomens) has treated fixed cultured ventral midbrain neurons with a pH-sensitive dye called pHrodo, which accumulates and "glows" red inside acidic compartments of the endocytic pathway. Danny is comparing untreated neurons ("steady-state") vs 24-hr amphetamine-treated neurons ("400µM"). He also treated these cells with an antibody that recognizes a protein called LC3, which marks intracellular structures called autophagosomes, which deliver cellular bits to the recycling centers of cells. This LC3-specific antibody was visualized with a second, fluorescent antibody that "glows" green. Yellow indicates co-localization of endocytic compartments with autophagosomes. <br> This experiment is now being done using a confocal microscope to thoroughly assess colocalization of the two labels.
DOI: 10.6084/m9.figshare.157060.v1
title: Experiment 4: percieved size of test and reference arrays with lines only present either within the interior of the elements or connecting the elements

description: In experiment 4a the first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows of indicate the proportion of times participants perceived an array with a line connecting the local elements as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.<br>In experiment 4b the first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows of indicate the proportion of times participants perceived an array with a line intersecting only the interiors of the elements as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.157057
title: Experiment 1: Proportion of participants perceiving test arrays as being larger than reference arrays

description: The first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows indicate the proportion of times participants perceived a binding ring array as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.156989.v1
title: Crowd4Discovery autophagy experiment 1

description: In this pilot experiment, Danny (@badomens) has treated fixed cultured ventral midbrain neurons with a pH-sensitive dye called pHrodo, which accumulates and "glows" red inside acidic compartments of the endocytic pathway. Danny is comparing untreated neurons ("steady-state") vs 24-hr amphetamine-treated neurons ("400µM"). He also treated these cells with an antibody that recognizes a protein called LC3, which marks intracellular structures called autophagosomes, which deliver cellular bits to the recycling centers of cells. This LC3-specific antibody was visualized with a second, fluorescent antibody that "glows" green. Yellow indicates co-localization of endocytic compartments with autophagosomes. <br> This experiment is now being done using a confocal microscope to thoroughly assess colocalization of the two labels.
DOI: 10.6084/m9.figshare.157058.v1
title: Experiment 2: reversal choices

description: For subjects 1-10, values indicate the average difference in a radius at which participants made a reversal choice in the staircase for each of the five conditions tested labelled: BR Shift Xº. Each condition was tested 4 times and 5 reversals were recorded resulted in 20 total reversals. The 1st reversal of each trial was excluded from analysis. The mean for each subject(shown) was automatically computed by the stimulus presentation software: Adjustable_BR_Staircase.m on the basis of the remaining 4 reversals per trial. A copy of the program is available upon request.
DOI: 10.6084/m9.figshare.156989.v3
title: Crowd4Discovery ventral medial primary neuronal culture experiment 1

description: In this pilot experiment, Danny (@badomens) has treated fixed cultured ventral midbrain neurons with a pH-sensitive dye called pHrodo, which accumulates and "glows" red inside acidic compartments of the endocytic pathway. Danny is comparing untreated neurons ("steady-state") vs 24-hr amphetamine-treated neurons ("400µM"). He also treated these cells with an antibody that recognizes a protein called LC3, which marks intracellular structures called autophagosomes, which deliver cellular bits to the recycling centers of cells. This LC3-specific antibody was visualized with a second, fluorescent antibody that "glows" green. Yellow indicates co-localization of endocytic compartments with autophagosomes. <br> This experiment is now being done using a confocal microscope to thoroughly assess colocalization of the two labels.
DOI: 10.6084/m9.figshare.156989.v2
title: Crowd4Discovery ventral medial primary culture experiment 1

description: In this pilot experiment, Danny (@badomens) has treated fixed cultured ventral midbrain neurons with a pH-sensitive dye called pHrodo, which accumulates and "glows" red inside acidic compartments of the endocytic pathway. Danny is comparing untreated neurons ("steady-state") vs 24-hr amphetamine-treated neurons ("400µM"). He also treated these cells with an antibody that recognizes a protein called LC3, which marks intracellular structures called autophagosomes, which deliver cellular bits to the recycling centers of cells. This LC3-specific antibody was visualized with a second, fluorescent antibody that "glows" green. Yellow indicates co-localization of endocytic compartments with autophagosomes. <br> This experiment is now being done using a confocal microscope to thoroughly assess colocalization of the two labels.
DOI: 10.6084/m9.figshare.157057.v1
title: Experiment 1: Proportion of particpants percieving test arrays as being larger than reference arrays

description: The first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows indicate the proportion of times participants perceived a binding ring array as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.157057.v2
title: Experiment 1: Proportion of particpants perceiving test arrays as being larger than reference arrays

description: The first five rows of data indicate the proportion of times participants perceived an unbound test array as being larger than a fixed unbound reference array. The second five rows indicate the proportion of times participants perceived a binding ring array as being larger than a fixed unbound reference array. Each proportion was calculated from 20 trials.
DOI: 10.6084/m9.figshare.156862
title: Number of animal species described each year

description: Data and graph of number of animal species described each year based on data from Taxatoy and Index of Organism Names (ION)
DOI: 10.6084/m9.figshare.156862.v1
title: Number of animal species described each year

description: Data and graph of number of animal species described each year based on data from Taxatoy and Index of Organism Names (ION)
DOI: 10.6084/m9.figshare.156850
title: Appendix 1. Individual abstract-level data for abstracts presented at the BSG meeting in 1995 and 2005.

description: The dataset shows the extraction of data related to individual abstracts presented at the BSG meetings in 1995 and 2005. Classification of abstracts by type of study and topic area and details of subsequent peer-reviewed publications are shown.
DOI: 10.6084/m9.figshare.156850.v1
title: Appendix 1. Individual abstract-level data for abstracts presented at the BSG meeting in 1995 and 2005.

description: The dataset shows the extraction of data related to individual abstracts presented at the BSG meetings in 1995 and 2005. Classification of abstracts by type of study and topic area and details of subsequent peer-reviewed publications are shown.
DOI: 10.6084/m9.figshare.156849
title: Appendix 2. Unadjusted odds ratios (OR) for subsequent publication of abstracts presented to the British Society of Gastroenterology in 2005 compared to 1995.

description: Table showing odds ratios for the subsequent publication in peer-reviewed journals of abstracts presented at the BSG meeting in 2005 compared to those presented at the 1995 meetings. Results are shown by classification of abstract by study type, main area of study and discipline for fundamental (life) sciences.
DOI: 10.6084/m9.figshare.156851.v1
title: Why should one use the polarizable embedding model for computational studies of photoactive proteins?

description: <strong>Slides from my PhD defense lecture held at the University of Southern Denmark on October 29th 2012.</strong> <strong><br></strong> The title for the defense lecture was was provided by the evaluation committee: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark
DOI: 10.6084/m9.figshare.156852.v1
title: Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins

description: The PhD thesis entitled "<em>Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins</em>" by Jógvan Magnus Haugaard Olsen was handed in on October 1st and defended on October 29th at the University of Southern Denmark. The evaluation committee consisted of: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark Abstract: In this thesis we present new developments in the pursuit of computationally efficient methods that can be used rationalize the processes that occur in photoactive proteins. We formulate an advanced polarizable embedding model rooted in so-called multilevel methods that takes advantage of the fact that the photonic processes that occur in photoactive proteins can often be localized in well-defined regions of the protein. In this model we employ the expensive but accurate quantum chemical methods only on the parts of the system that partake directly in the electronic process. The effects of the environment are incorporated by adding them to the quantum mechanical equations in an effective manner. We outline the theoretical basis of the model as well as the equations that need to be incorporated in the quantum chemical methods. The work presented here is an advancement of conventional multilevel methods in that we introduce an additional layer around the important part of the system where the interactions are described at a higher level of theory thereby allowing more accurate calculations to be performed. Furthermore, we describe some of essential elements of the implementation of the model which is an important part of the development of computationally efficient methods. Finally, we also demonstrate the model by performing numerical calculations on large molecular systems such as solute-solvent systems and photoactive proteins.
DOI: 10.6084/m9.figshare.156853.v1
title: The noise Pleistocene

description: Invited contribution to IDP2 lecture by Dr Luke Skinner and Prof David Hodell "The Earth System and Climate Change", Department of Earth Sciences, University of Cambridge, 14th February 2014.
DOI: 10.6084/m9.figshare.156849.v1
title: Appendix 2. Unadjusted odds ratios (OR) for subsequent publication of abstracts presented to the British Society of Gastroenterology in 2005 compared to 1995.

description: Table showing odds ratios for the subsequent publication in peer-reviewed journals of abstracts presented at the BSG meeting in 2005 compared to those presented at the 1995 meetings. Results are shown by classification of abstract by study type, main area of study and discipline for fundamental (life) sciences.
DOI: 10.6084/m9.figshare.156851.v2
title: Why should one use the polarizable embedding model for computational studies of photoactive proteins?

description: <strong>Slides from my PhD defense lecture held at the University of Southern Denmark on October 29th 2012.</strong> <strong><br></strong> The title for the defense lecture was was provided by the evaluation committee: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark
DOI: 10.6084/m9.figshare.156848
title: Appendix 2: Use of Probiotics in IBD - individual subject level data.

description: Table showing subject-level data for demographics, use and reason for use of probiotics and individual answers to the S-IBDQ questions.
DOI: 10.6084/m9.figshare.156848.v1
title: Appendix 2

description: Table showing subject-level data for demographics, use and reason for use of probiotics and individual answers to the S-IBDQ questions.
DOI: 10.6084/m9.figshare.156852.v2
title: Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins

description: The PhD thesis entitled "<em>Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins</em>" by Jógvan Magnus Haugaard Olsen was handed in on October 1st and defended on October 29th at the University of Southern Denmark. The evaluation committee consisted of: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark Abstract: In this thesis we present new developments in the pursuit of computationally efficient methods that can be used rationalize the processes that occur in photoactive proteins. We formulate an advanced polarizable embedding model rooted in so-called multilevel methods that takes advantage of the fact that the photonic processes that occur in photoactive proteins can often be localized in well-defined regions of the protein. In this model we employ the expensive but accurate quantum chemical methods only on the parts of the system that partake directly in the electronic process. The effects of the environment are incorporated by adding them to the quantum mechanical equations in an effective manner. We outline the theoretical basis of the model as well as the equations that need to be incorporated in the quantum chemical methods. The work presented here is an advancement of conventional multilevel methods in that we introduce an additional layer around the important part of the system where the interactions are described at a higher level of theory thereby allowing more accurate calculations to be performed. Furthermore, we describe some of essential elements of the implementation of the model which is an important part of the development of computationally efficient methods. Finally, we also demonstrate the model by performing numerical calculations on large molecular systems such as solute-solvent systems and photoactive proteins.
DOI: 10.6084/m9.figshare.156852.v3
title: Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins

description: The PhD thesis entitled "<em>Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins</em>" by Jógvan Magnus Haugaard Olsen was handed in on October 1st 2012 and defended on October 29th 2012 at the University of Southern Denmark. The PhD degree was obtained on November 8th 2012. The evaluation committee consisted of: Assoc. Prof. Hans Jørgen Aagard Jensen, Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Denmark Prof. Benedetta Mennucci, Dept. of Chemistry, Univeristy of Pisa, Italy Assoc. Prof. Stephan P. A. Sauer, Dept. of Chemistry, University of Copenhagen, Denmark Abstract: In this thesis we present new developments in the pursuit of computationally efficient methods that can be used rationalize the processes that occur in photoactive proteins. We formulate an advanced polarizable embedding model rooted in so-called multilevel methods that takes advantage of the fact that the photonic processes that occur in photoactive proteins can often be localized in well-defined regions of the protein. In this model we employ the expensive but accurate quantum chemical methods only on the parts of the system that partake directly in the electronic process. The effects of the environment are incorporated by adding them to the quantum mechanical equations in an effective manner. We outline the theoretical basis of the model as well as the equations that need to be incorporated in the quantum chemical methods. The work presented here is an advancement of conventional multilevel methods in that we introduce an additional layer around the important part of the system where the interactions are described at a higher level of theory thereby allowing more accurate calculations to be performed. Furthermore, we describe some of essential elements of the implementation of the model which is an important part of the development of computationally efficient methods. Finally, we also demonstrate the model by performing numerical calculations on large molecular systems such as solute-solvent systems and photoactive proteins.
DOI: 10.6084/m9.figshare.156844
title: Cocaine infusions earned before and during the dose-response challenge

description: This data set represents the number of cocaine infusions each subject earned for the last two days preceding (2a), and for the two consecutive sessions during (2b), the dose-response challenge for mice of each genotype. TRPC5 +/+ = wild-type; TRPC5 -/- = knock-down; "-2" = second to last day leading up to dose-response challenge; "-1" = last day leading up to dose-response challenge; S(0.05) = session with dose 0.05 mg/kg/infusion; S(0.1) = session with dose 0.1 mg/kg/infusion; S(0.75) = session with dose 0.75 mg/kg/infusion; S(2.0) = session with does 2.0 mg/kg/infusion; S1 = first daily session with respective dose; S2 = second daily session with respective dose
DOI: 10.6084/m9.figshare.156844.v1
title: Cocaine infusions earned before and during the dose-response challenge

description: This data set represents the number of cocaine infusions each subject earned for the last two days preceding (2a), and for the two consecutive sessions during (2b), the dose-response challenge for mice of each genotype. TRPC5 +/+ = wild-type; TRPC5 -/- = knock-down; "-2" = second to last day leading up to dose-response challenge; "-1" = last day leading up to dose-response challenge; S(0.05) = session with dose 0.05 mg/kg/infusion; S(0.1) = session with dose 0.1 mg/kg/infusion; S(0.75) = session with dose 0.75 mg/kg/infusion; S(2.0) = session with does 2.0 mg/kg/infusion; S1 = first daily session with respective dose; S2 = second daily session with respective dose
DOI: 10.6084/m9.figshare.156843
title: Number of infusions and active/inactive nose-pokes for saline or first 6 days of cocaine

description: This data set represents the number of infusions (1a) and the frequency of nose-pokes in the active/inactive portals (1b) for each subject for the saline pretest and for the first 6 days of cocaine responding for mice of each genotype. TRPC5+/+ = wild-type; TRPC5-/- = knock-down; C = Cocaine; Act = Active nose-poke portal; Inact = Inactive nose-poke portal
DOI: 10.6084/m9.figshare.156835
title: Reference Data

description: Flybase <em>D. melanogaster</em> Release 5.34 mRNA and polyadenylated ncRNA reference as GTF file for use with the bowtie suite of tools.