cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5441020.v1
title: Extracellular DNA and lipoteichoic acids interact with exopolysaccharides in the extracellular matrix of <i>Streptococcus mutans</i> biofilms

description: <i>Streptococcus mutans</i>-derived exopolysaccharides are virulence determinants in the matrix of biofilms that cause caries. Extracellular DNA (eDNA) and lipoteichoic acid (LTA) are found in cariogenic biofilms, but their functions are unclear. Therefore, strains of <i>S. mutans</i> carrying single deletions that would modulate matrix components were used: eDNA – ∆<i>lytS</i> and ∆<i>lytT</i>; LTA – ∆<i>dltA</i> and ∆<i>dltD</i>; and insoluble exopolysaccharide – Δ<i>gtfB</i>. Single-species (parental strain <i>S. mutans</i> UA159 or individual mutant strains) and mixed-species (UA159 or mutant strain, <i>Actinomyces naeslundii</i> and <i>Streptococcus gordonii</i>) biofilms were evaluated. Distinct amounts of matrix components were detected, depending on the inactivated gene. eDNA was found to be cooperative with exopolysaccharide in early phases, while LTA played a larger role in the later phases of biofilm development. The architecture of mutant strains biofilms was distinct (<i>vs</i> UA159), demonstrating that eDNA and LTA influence exopolysaccharide distribution and microcolony organization. Thus, eDNA and LTA may shape exopolysaccharide structure, affecting strategies for controlling pathogenic biofilms.
DOI: 10.6084/m9.figshare.5441017.v1
title: A quality assessment of the soil water index by the propagation of ASCAT soil moisture error estimates through an exponential filter

description: Soil moisture data from remote-sensing measurements are used extensively and error characterization is critical in assessing their utility for specific applications. In hydrological monitoring and forecast applications, an estimate of the root-zone soil moisture is often required, and the exponential filter constitutes a common approach to obtaining a soil water index (SWI), i.e. the profile soil moisture from the remotely-sensed surface states. Advanced Scatterometer (ASCAT) surface soil moisture (SSM) time series include error estimates as ancillary data, however their effects are rarely considered in SWI computations. In this study, we introduced a simple error propagation scheme in parallel to exponential filter computation, aimed at estimating a SWI noise, which implicitly takes into account both errors and availability of the input SSM data actually used for each single SWI estimation. Integrating a control on SWI noise within quality check procedures was analysed by comparing <i>in situ</i> measurements available at different depths, up to 60 cm, for the period 2007–2014 in 10 stations located in Italy. The capacity of ASCAT-derived SWI to capture the same processes observed in the root-zone by <i>in situ</i> sensors, was evaluated by computing standard statistics (the correlation coefficient <i>r</i> and the root mean square difference [RMSD]) for different ‘a priori’ data masking procedures on SSM data, based on several indicators (processing flag, orbit direction, SSM noise) available for the ASCAT product. The effects of using the information contained in SSM noise and in the proposed SWI noise were also investigated. Removing data according to ‘a posteriori’ control on SWI noise rather than a priori masking SSM data, with the exponential filter <i>T</i> value and the percentage of removed data being equal, was found to generally improve the statistics of the resulting SWI time series. In addition, evaluating <i>T</i> on the SWI time series screened according to the SWI noise, outperforms other approaches analysed in almost every test case.
DOI: 10.6084/m9.figshare.5440984
title: Dataset for: Accommodating the ecological fallacy in disease mapping in the absence of individual exposures

description: In health exposure modeling, in particular, disease mapping, the ecological fallacy arises because the relationship between aggregated disease incidence on areal units and \emph{average} exposure on those units differs from the relationship between the event of individual incidence and the associated individual exposure. This article presents a novel modeling approach to address the ecological fallacy in the least informative data setting. We assume the known population at risk with an observed incidence for a collection of areal units and, separately, environmental exposure recorded during the period of incidence at a collection of monitoring stations. We do not assume any partial individual level information or random allocation of individuals to observed exposures. We specify a conceptual incidence surface over the study region as a function of an exposure surface resulting in a stochastic integral of the block average disease incidence. The true block level incidence is an unavailable Monte Carlo integration for this stochastic integral. We propose an alternative manageable Monte Carlo integration for the integral. Modeling in this setting is immediately hierarchical and we fit our model within a Bayesian framework. To alleviate the resulting computational burden, we offer two strategies for efficient model fitting: one is through modularization, the other is through sparse or dimension-reduced Gaussian processes. We illustrate the performance of our model with simulations based on a heat-related mortality dataset in Ohio and then analyze associated real data.
DOI: 10.6084/m9.figshare.5440984.v1
title: Dataset for: Accommodating the ecological fallacy in disease mapping in the absence of individual exposures

description: In health exposure modeling, in particular, disease mapping, the ecological fallacy arises because the relationship between aggregated disease incidence on areal units and \emph{average} exposure on those units differs from the relationship between the event of individual incidence and the associated individual exposure. This article presents a novel modeling approach to address the ecological fallacy in the least informative data setting. We assume the known population at risk with an observed incidence for a collection of areal units and, separately, environmental exposure recorded during the period of incidence at a collection of monitoring stations. We do not assume any partial individual level information or random allocation of individuals to observed exposures. We specify a conceptual incidence surface over the study region as a function of an exposure surface resulting in a stochastic integral of the block average disease incidence. The true block level incidence is an unavailable Monte Carlo integration for this stochastic integral. We propose an alternative manageable Monte Carlo integration for the integral. Modeling in this setting is immediately hierarchical and we fit our model within a Bayesian framework. To alleviate the resulting computational burden, we offer two strategies for efficient model fitting: one is through modularization, the other is through sparse or dimension-reduced Gaussian processes. We illustrate the performance of our model with simulations based on a heat-related mortality dataset in Ohio and then analyze associated real data.
DOI: 10.6084/m9.figshare.5440978
title: Dataset for: Plant resistance to drought depends on timely stomatal closure

description: Stomata play a significant role in the Earth's water and carbon cycles, by regulating gaseous exchanges between the plant and the atmosphere. Under drought conditions, stomatal control of transpiration has long been thought to be closely coordinated with the decrease in hydraulic capacity (hydraulic failure due to xylem embolism). We tested this hypothesis, by coupling a meta-analysis of functional traits related to the stomatal response to drought and embolism resistance with simulations from a soil-plant hydraulic model. We report here a previously unreported phenomenon: the existence of an absolute limit by which stomata closure must occur to avoid rapid death in drought conditions. The water potential causing stomatal closure and the xylem pressure at the onset of embolism formation were equal for only a small number of species, and the difference between these two traits (i.e. safety margins) increased continuously with increasing embolism resistance. Our findings demonstrate the need to revise current views about the functional coordination between stomata and lead to a mechanistic framework allowing to model plant mortality under drought conditions with leaf and xylem traits.
DOI: 10.6084/m9.figshare.5440978.v1
title: Dataset for: Plant resistance to drought depends on timely stomatal closure

description: Stomata play a significant role in the Earth's water and carbon cycles, by regulating gaseous exchanges between the plant and the atmosphere. Under drought conditions, stomatal control of transpiration has long been thought to be closely coordinated with the decrease in hydraulic capacity (hydraulic failure due to xylem embolism). We tested this hypothesis, by coupling a meta-analysis of functional traits related to the stomatal response to drought and embolism resistance with simulations from a soil-plant hydraulic model. We report here a previously unreported phenomenon: the existence of an absolute limit by which stomata closure must occur to avoid rapid death in drought conditions. The water potential causing stomatal closure and the xylem pressure at the onset of embolism formation were equal for only a small number of species, and the difference between these two traits (i.e. safety margins) increased continuously with increasing embolism resistance. Our findings demonstrate the need to revise current views about the functional coordination between stomata and lead to a mechanistic framework allowing to model plant mortality under drought conditions with leaf and xylem traits.
DOI: 10.5281/zenodo.4010383
title: causal knowledge rules

description: The rules we learned from our rule learning framework. It can also be seen as a causal knowledge graph.
DOI: 10.5281/zenodo.4010382
title: causal knowledge rules

description: The rules we learned from our rule learning framework. It can also be seen as a causal knowledge graph.
DOI: 10.25442/hku.12859622
title: Supporting data for "Molecular characterization of herbal medicine formulation Qi-Fu-Yin for the treatment of neuroinflammation in Alzheimer’s Disease"

description: This dataset contains the supporting data and/or raw data for the results present in this MPhil thesis, signed data management plan submitted in August 2019 and a README text file describing each data file.
DOI: 10.25442/hku.12859622.v1
title: Supporting data for "Molecular characterization of herbal medicine formulation Qi-Fu-Yin for the treatment of neuroinflammation in Alzheimer’s Disease"

description: This dataset contains the supporting data and/or raw data for the results present in this MPhil thesis, signed data management plan submitted in August 2019 and a README text file describing each data file.
DOI: 10.1184/r1/5440198
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160427140455_Experiment 1

description: 160427140455 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><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/r1/5440204
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160510164658_Experiment 1

description: 160510164658 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/r1/5440204.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160510164658_Experiment 1

description: 160510164658 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/r1/5440186
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160421091747_Experiment 1

description: 160421091747 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/r1/5440198.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160427140455_Experiment 1

description: 160427140455 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><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/r1/5440174
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160310120847_Experiment 1

description: 160310120847 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/r1/5440177
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160420131627_Experiment 1

description: 160420131627 nii filesPart 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/r1/5440186.v1
title: The large-scale organization of shape processing in the ventral and dorsal pathways: Subject 160421091747_Experiment 1

description: 160421091747 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.