cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1184/r1/5440162.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160307111751_Experiment 1

description: subject 160307111751 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440132
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160224104136_Experiment 1

description: subject 160224104136 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440135
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160224122535_Experiment 1

description: subject 160224122535 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440141
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160301110546_Experiment 1

description: subject 160301110546 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.Abstract: Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440141.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160301110546_Experiment 1

description: subject 160301110546 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.Abstract: Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440132.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160224104136_Experiment 1

description: subject 160224104136 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.1184/r1/5440135.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160224122535_Experiment 1

description: subject 160224122535 nii files. Part of a dataset from the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. See - https://doi.org/10.1184/R1/c.3889873.v1. For each participant 8 functional runs and one anatomical run are included.<br>Abstract:Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing.
DOI: 10.6084/m9.figshare.5440063
title: Ocean acidification in New Zealand waters: trends and impacts

description: The threat posed by ocean acidification (OA) to the diversity and productivity of New Zealand marine ecosystems is assessed in a synthesis of published trends and impacts. A 20-year time series in Subantarctic water, and a national coastal monitoring programme, provide insight into pH variability, and context for experimental design, modelling and projections. A review of the potential impact of changes in the carbonate system on the major phyla in New Zealand waters confirms international observations that calcifying organisms, and particularly their early life-history stages, are vulnerable. The synthesis considers ecosystem and socio-economic impacts, and identifies current knowledge gaps and future research directions, including mechanistic studies of OA sensitivity. Advanced ecosystem models of OA, that incorporate the indirect effects of OA and interactions with other climate stressors, are required for robust projection of the future status of New Zealand marine ecosystems.
DOI: 10.6084/m9.figshare.5439991
title: CVD Risk Prediction Synthetic Dataset

description: This is a synthetic dataset to teach students about using clinical and genetic covariates to predict cardiovascular risk in a realistic (but synthetic) dataset.<br>For the workshop materials, please go here: https://github.com/laderast/cvdNight1Contents:1) dataDictionary.pdf - pdf file describing all covariates in the synthetic dataset.2) fullPatientData.csv - csv file with multiple covariates3) genoData.csv - subset of patients in fullPatientData.csv with additional SNP calls.<br>
DOI: 10.6084/m9.figshare.5439994
title: Does heating stimulate germination in <i>Leptospermum scoparium</i> (mānuka; Myrtaceae)?

description: Fire regimes are powerful selective filters. In New Zealand, fire activity was rare before human settlement, and New Zealand’s indigenous woody flora shows little adaptation to frequent fire. One of the few woody indigenous species to show adaptation to frequent fire is <i>Leptospermum scoparium</i> (Myrtaceae), a Plio-Pleistocene immigrant from Australia. <i>Leptospermum scoparium</i> is a widespread early-successional shrub to small tree that frequently dominates post-fire successions, and shows geographically-variable pyriscent serotiny, a fire-adaptation in which seeds are retained in the canopy and open post-fire. Another widespread reproductive adaptation to fire is heat-stimulated germination. Some Australian <i>Leptospermum</i> respond positively to heat treatment, and observations in New Zealand suggest that the seeds of <i>L. scoparium</i> within thick-walled capsules open immediately after fire and successfully germinate, indicating at least no deleterious effect of heating. In some fire-prone systems such as Mediterranean shrublands, traits such as serotiny and heat-stimulated germination have been positively associated with traits associated with flammability (e.g. retention of dead fuel). Here we evaluate the effect of heat stimulation (short exposure to high temperatures) of capsules on germination in <i>L. scoparium</i> from New Zealand, and evaluate links between germination, serotiny and shoot-level flammability. Germination trials using seed collected from 12 populations indicated no consistent positive or negative effect of heat treatment on germination success (germinability). These trials suggest that the capsules of <i>L. scoparium</i> at least provide adequate insulation to heating. Germinability was not consistently related to either serotiny or flammability; nor was it related to latitude or elevation. While taxa from other fire-prone ecosystems may show coordinated trait responses to fire, the lack of association between physical measures of flammability and germination rates indicate that this is not the case in <i>L. scoparium</i>, New Zealand’s most fire-adapted indigenous woody species.
DOI: 10.6084/m9.figshare.5439994.v1
title: Does heating stimulate germination in <i>Leptospermum scoparium</i> (mānuka; Myrtaceae)?

description: Fire regimes are powerful selective filters. In New Zealand, fire activity was rare before human settlement, and New Zealand’s indigenous woody flora shows little adaptation to frequent fire. One of the few woody indigenous species to show adaptation to frequent fire is <i>Leptospermum scoparium</i> (Myrtaceae), a Plio-Pleistocene immigrant from Australia. <i>Leptospermum scoparium</i> is a widespread early-successional shrub to small tree that frequently dominates post-fire successions, and shows geographically-variable pyriscent serotiny, a fire-adaptation in which seeds are retained in the canopy and open post-fire. Another widespread reproductive adaptation to fire is heat-stimulated germination. Some Australian <i>Leptospermum</i> respond positively to heat treatment, and observations in New Zealand suggest that the seeds of <i>L. scoparium</i> within thick-walled capsules open immediately after fire and successfully germinate, indicating at least no deleterious effect of heating. In some fire-prone systems such as Mediterranean shrublands, traits such as serotiny and heat-stimulated germination have been positively associated with traits associated with flammability (e.g. retention of dead fuel). Here we evaluate the effect of heat stimulation (short exposure to high temperatures) of capsules on germination in <i>L. scoparium</i> from New Zealand, and evaluate links between germination, serotiny and shoot-level flammability. Germination trials using seed collected from 12 populations indicated no consistent positive or negative effect of heat treatment on germination success (germinability). These trials suggest that the capsules of <i>L. scoparium</i> at least provide adequate insulation to heating. Germinability was not consistently related to either serotiny or flammability; nor was it related to latitude or elevation. While taxa from other fire-prone ecosystems may show coordinated trait responses to fire, the lack of association between physical measures of flammability and germination rates indicate that this is not the case in <i>L. scoparium</i>, New Zealand’s most fire-adapted indigenous woody species.
DOI: 10.6084/m9.figshare.5439982
title: RESUME.xlsx

description: <pre>Full access to the obtained results.</pre>
DOI: 10.6084/m9.figshare.5439922
title: EffTE - Experiment Material

description: Different dependency graphs for test cases
DOI: 10.6084/m9.figshare.5439796
title: Algorithms for imputing partially observed recurrent events with applications to multiple imputation in pattern mixture models

description: Five algorithms are described for imputing partially observed recurrent events modeled by a negative binomial process, or more generally by a mixed Poisson process when the mean function for the recurrent events is continuous over time. We also discuss how to perform the imputation when the mean function of the event process has jump discontinuities. The validity of these algorithms is assessed by simulations. These imputation algorithms are potentially very useful in the implementation of pattern mixture models, which have been popularly used as sensitivity analysis under the non-ignorability assumption in clinical trials. A chronic granulomatous disease trial is analyzed for illustrative purposes.
DOI: 10.6084/m9.figshare.5439796.v1
title: Algorithms for imputing partially observed recurrent events with applications to multiple imputation in pattern mixture models

description: Five algorithms are described for imputing partially observed recurrent events modeled by a negative binomial process, or more generally by a mixed Poisson process when the mean function for the recurrent events is continuous over time. We also discuss how to perform the imputation when the mean function of the event process has jump discontinuities. The validity of these algorithms is assessed by simulations. These imputation algorithms are potentially very useful in the implementation of pattern mixture models, which have been popularly used as sensitivity analysis under the non-ignorability assumption in clinical trials. A chronic granulomatous disease trial is analyzed for illustrative purposes.
DOI: 10.6084/m9.figshare.5439922.v2
title: EffTE - Experiment Material

description: Different dependency graphs for test cases
DOI: 10.6084/m9.figshare.5439922.v1
title: Untitled Item

description: Different dependency graphs for test cases
DOI: 10.6084/m9.figshare.5439787
title: The Time of Origin and Genetic Diversity of Three Isolated Kokanee Populations in Southwest Alaska

description: We examined the time of origin and genetic diversity of native kokanee, the nonanadromous ecotype of Sockeye Salmon <i>Oncorhynchus nerka</i>, from three isolated lakes in the Katmai National Park and Preserve in southwest Alaska. These kokanee evolved independently from Sockeye Salmon when migration barriers arose, blocking ocean access. We used information about the relative age of each barrier to hypothesize the relative time of origin for kokanee in each lake. In addition, we used data from 13 microsatellite loci to test our time of origin hypotheses and assess genetic diversity of kokanee from these three lakes and proximate Sockeye Salmon populations. Coalescent-based estimates of the time of origin for kokanee in Jo-Jo Lake (170 years before present [ybp]) and Devil’s Cove Lake (6,583 ybp) were consistent with the relative age of barriers isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested that the barrier was older than hypothesized. Indices of intrapopulation diversity were lower for kokanee than for Sockeye Salmon. Estimates for kokanee population divergence (<i>R</i><sub>ST</sub>; the <i>F</i><sub>ST</sub> analog for microsatellites) among the three lakes were consistent with time of origin estimates. Furthermore, the most recently isolated kokanee (Jo-Jo Lake population) were most closely related to neighboring Sockeye Salmon. Only the kokanee from Jo-Jo Lake exhibited a relatively low historical effective population size (<i>N<sub>e</sub></i> ≈ 107) and evidence of a genetic bottleneck. Taken together, the results of this study show that although rare, kokanee in Alaska are not ephemeral and can persist in isolation for hundreds of generations despite the colder temperatures and shorter growing season, that are thought to limit their sustainability in Alaska. Received April 26, 2017; accepted July 25, 2017 Published online September 25, 2017
DOI: 10.6084/m9.figshare.5439787.v1
title: The Time of Origin and Genetic Diversity of Three Isolated Kokanee Populations in Southwest Alaska

description: We examined the time of origin and genetic diversity of native kokanee, the nonanadromous ecotype of Sockeye Salmon <i>Oncorhynchus nerka</i>, from three isolated lakes in the Katmai National Park and Preserve in southwest Alaska. These kokanee evolved independently from Sockeye Salmon when migration barriers arose, blocking ocean access. We used information about the relative age of each barrier to hypothesize the relative time of origin for kokanee in each lake. In addition, we used data from 13 microsatellite loci to test our time of origin hypotheses and assess genetic diversity of kokanee from these three lakes and proximate Sockeye Salmon populations. Coalescent-based estimates of the time of origin for kokanee in Jo-Jo Lake (170 years before present [ybp]) and Devil’s Cove Lake (6,583 ybp) were consistent with the relative age of barriers isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested that the barrier was older than hypothesized. Indices of intrapopulation diversity were lower for kokanee than for Sockeye Salmon. Estimates for kokanee population divergence (<i>R</i><sub>ST</sub>; the <i>F</i><sub>ST</sub> analog for microsatellites) among the three lakes were consistent with time of origin estimates. Furthermore, the most recently isolated kokanee (Jo-Jo Lake population) were most closely related to neighboring Sockeye Salmon. Only the kokanee from Jo-Jo Lake exhibited a relatively low historical effective population size (<i>N<sub>e</sub></i> ≈ 107) and evidence of a genetic bottleneck. Taken together, the results of this study show that although rare, kokanee in Alaska are not ephemeral and can persist in isolation for hundreds of generations despite the colder temperatures and shorter growing season, that are thought to limit their sustainability in Alaska. Received April 26, 2017; accepted July 25, 2017 Published online September 25, 2017