cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.91540.v1
title: Optogenetic control of genetically-targeted pyramidal neuron activity in prefrontal cortex

description: <strong>Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the drug in the blood based on an individual’s motivational state together with the pharmacokinetic properties of the drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the same mice. For collaborators interested in premade catheters for research please make a request at </strong><strong>www.neuro-cloud.net/nature-precedings/pomerenze</strong><strong>.</strong>
DOI: 10.6084/m9.figshare.91540.v2
title: Optogenetic control of genetically-targeted pyramidal neuron activity in prefrontal cortex

description: <strong>Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the drug in the blood based on an individual’s motivational state together with the pharmacokinetic properties of the drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the same mice. For collaborators interested in premade catheters for research please make a request at </strong><strong>www.neuro-cloud.net/nature-precedings/pomerenze</strong><strong>.</strong>
DOI: 10.6084/m9.figshare.91480
title: Neural Networks and Musical Style Recognition

description: 3rd year dissertation project for a BSc in Physics and Music, University of Wales, Cardiff, 1998. Abstract: This project attempts to discover if a neural net is capable of performing stylistic discrimination between two pieces of music by two different composers, JS Bach and Igor Stravinsky. It was found that, although the trained network was able to discriminate between two different pieces, that a large number of samples from different pieces only served to confuse the network, resulting in it categorising all the test patterns as Bachian in nature. However, when a smaller amount of training data was used, the results were better and easier to understand in terms of the internal logic of the network. Training was done with pattern files created from melodic line only, melodic and rhythmic lines, intervals between adjacent melodic notes and frequency of occurrence of notes in a discrete sample.
DOI: 10.6084/m9.figshare.91480.v1
title: Neural Networks and Musical Style Recognition

description: 3rd year dissertation project for a BSc in Physics and Music, University of Wales, Cardiff, 1998. Abstract: This project attempts to discover if a neural net is capable of performing stylistic discrimination between two pieces of music by two different composers, JS Bach and Igor Stravinsky. It was found that, although the trained network was able to discriminate between two different pieces, that a large number of samples from different pieces only served to confuse the network, resulting in it categorising all the test patterns as Bachian in nature. However, when a smaller amount of training data was used, the results were better and easier to understand in terms of the internal logic of the network. Training was done with pattern files created from melodic line only, melodic and rhythmic lines, intervals between adjacent melodic notes and frequency of occurrence of notes in a discrete sample.
DOI: 10.6084/m9.figshare.91476
title: Project summary for "Neural Networks and Musical Style Recognition"

description: 2 page project summary for my 3rd year BSc (Physics and Music) dissertation: "Neural Networks and Musical Style Recognition", completed in 1998.
DOI: 10.6084/m9.figshare.91517.v1
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91473
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes - effect of selection on the extrinsic incubation period of viruses.

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91517.v2
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91511.v1
title: Poster: 3D gravity gradient inversion by planting anomalous densities

description: Poster "<strong>3D gravity gradient inversion by planting anomalous densities</strong>" presented at the 73th EAGE Conference & Exhibition incorporating SPE EUROPEC, 2011, Vienna, Austria.
DOI: 10.6084/m9.figshare.91517.v3
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91473.v2
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes - effect of selection on the extrinsic incubation period of viruses.

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91473.v1
title: Genotypes

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91511.v2
title: Poster: 3D gravity gradient inversion by planting anomalous densities

description: Poster "<strong>3D gravity gradient inversion by planting anomalous densities</strong>" presented at the 73th EAGE Conference & Exhibition incorporating SPE EUROPEC, 2011, Vienna, Austria.
DOI: 10.6084/m9.figshare.91462
title: Static programming cycle

description: Development feedback cycle in a compiled programming language
DOI: 10.6084/m9.figshare.91517.v4
title: Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes

description: Figure included in the study "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes" in PLoS NTD, 2010. Abstract: "Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral ecology and evolution."
DOI: 10.6084/m9.figshare.91461
title: Dynamic programming cycle

description: Development feedback cycle in an interpreted programming language
DOI: 10.6084/m9.figshare.91462.v1
title: Static programming cycle

description: Development feedback cycle in a compiled programming language
DOI: 10.6084/m9.figshare.91461.v1
title: Dynamic programming cycle

description: Development feedback cycle in an interpreted programming language
DOI: 10.6084/m9.figshare.91467.v1
title: HH24 2702BSA02.jpg

description: Hamburger-Hamilton stage 24 chicken embryo, approximately 4 days of incubation, in the egg. Head at top, eye pigmented, trunk at bottom and extending to right. A BioRad AffyBlue agarose bead, on the order of 100 microns diameter, soaked in the neutral bovine serum albumin, has been implanted in the migration pathway of melanoblasts toward the developing forelimb. This technique can be used to test the impact of secreted growth factors, with which such beads can be impregnated, at localized regions of the epidermis.
DOI: 10.6084/m9.figshare.91511.v3
title: Poster: 3D gravity gradient inversion by planting anomalous densities

description: Poster "<strong>3D gravity gradient inversion by planting anomalous densities</strong>" presented at the 73th EAGE Conference & Exhibition incorporating SPE EUROPEC, 2011, Vienna, Austria.
DOI: 10.6084/m9.figshare.91458.v1
title: OA Dissemination Paths

description: In progress: A simplified flowchart of open access dissemination paths. Costs and barriers are intentially omitted because of the broad range of OA publishing agreements available. Please feel free to provide feedback on terminology or structure.<br><br>CC-BY
DOI: 10.6084/m9.figshare.91511.v4
title: Poster: 3D gravity gradient inversion by planting density anomalies

description: An animation of growth iterations during a 3D gravity gradient inversion by planting anomalous densities (Uieda and Barbosa, 2012). The inversion was performed on synthetic noise-corrupted data of the gzz component of the gravity gradient tensor. The synthetic data were produced by two prismatic sources with different depths and densities. We used two seeds (red and green prisms) in the inversion. The top most surface is the synthetic data. The one bellow that is the predicted (modeled) data at each iteration of the growth process. The neighboring prisms of the current solution are shown in black outlines. The prism chosen for the accretion at each iteration is shown in blue. <strong>References</strong> Uieda, L., and V. C. F. Barbosa (2012), Robust 3D gravity gradient inversion by planting anomalous densities, Geophysics, 77(4), G55-G66, doi:10.1190/geo2011-0388.1.
DOI: 10.6084/m9.figshare.91458.v2
title: OA Dissemination Paths

description: In progress: A simplified flowchart of open access dissemination paths. Costs and barriers are intentially omitted because of the broad range of OA publishing agreements available. I appreciate feedback on terminology or structure. I recognize that I'm not an expert - so please don't hesitate to point out any glaring misinterpretations of the general process.<br><br>CC-BY