cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3470555
title: Fileset: Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

description: OTU tables in biom and tabular format, taxa profiles, and bioinformatic protocols used for the manuscript: <br><br> <b>Exploring the cockatiel (</b><i><b>Nymphicus hollandicus</b></i><b>) fecal microbiome, bacterial inhabitants of a worldwide pet</b><br>Authors: Luis David Alcaraz<sup>a</sup>, Apolinar M. Hernández<sup>b</sup>, and Mariana Peimbert<sup>b</sup>,*<sup>a </sup>Laboratorio Nacional de Ciencias de la Sostenibilidad. Instituto de Ecología. Universidad Nacional Autónoma de México. AP 70-275, Ciudad Universitaria, UNAM, 04510, Cd. Mx., México.<sup>b</sup> Departamento de Ciencias Naturales. Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Cd. Mx., México. <br>Corresponding authorMariana PeimbertE-mail address: mpeimbert@correo.cua.uam.mx Tel.: (5255) 5814 6500 ext. 3878<br>
DOI: 10.6084/m9.figshare.3470555.v1
title: Fileset: Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

description: OTU tables in biom and tabular format, taxa profiles, and bioinformatic protocols used for the manuscript: <br><br> <b>Exploring the cockatiel (</b><i><b>Nymphicus hollandicus</b></i><b>) fecal microbiome, bacterial inhabitants of a worldwide pet</b><br>Authors: Luis David Alcaraz<sup>a</sup>, Apolinar M. Hernández<sup>b</sup>, and Mariana Peimbert<sup>b</sup>,*<sup>a </sup>Laboratorio Nacional de Ciencias de la Sostenibilidad. Instituto de Ecología. Universidad Nacional Autónoma de México. AP 70-275, Ciudad Universitaria, UNAM, 04510, Cd. Mx., México.<sup>b</sup> Departamento de Ciencias Naturales. Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Cd. Mx., México. <br>Corresponding authorMariana PeimbertE-mail address: mpeimbert@correo.cua.uam.mx Tel.: (5255) 5814 6500 ext. 3878<br>
DOI: 10.6084/m9.figshare.3470534
title: Dataset.S1_RecordsParamuriceaClavataFor ENM

description: Dataset of presence records used for Ecological Niche Modelling of <i>Paramuricea clavata</i>.
DOI: 10.6084/m9.figshare.3470501
title: Small compact polymer HPG for peritoneal dialysis

description: Impact of chronic exposure to HPG on peritoneal membrane<br>
DOI: 10.6084/m9.figshare.3470501.v1
title: Small compact polymer HPG for peritoneal dialysis

description: Impact of chronic exposure to HPG on peritoneal membrane<br>
DOI: 10.6084/m9.figshare.3470498
title: Vegetation dynamics after experimental fire disturbance in the arid Succulent Karoo, South Africa

description: Disturbance by fire in the Succulent Karoo is rare but fire events could increase as a result of an increase in grassiness (alien and indigenous species). This study assessed the effects of fire eight years after an experimentally induced burn in Succulent Karoo vegetation. Post-fire monitoring was conducted using the line intercept method and species counts per plot (1 m<sup>2</sup>) for each of three fire disturbance treatments: control/unburnt, high and low fuel load. Vegetation cover and abundance were compared across treatments and growth forms. Vegetation cover and abundance on fire-disturbed plots had not returned to pre-fire levels after eight years. Resprouters exhibited a rapid recovery and early dominance on burnt plots. Succulent seedlings established slower, but after eight years occurred at higher densities on the burnt than control plots. Recovery after disturbance of density and cover of long-lived, woody non-resprouter non-succulents was slow relative to resprouting non-succulents and reseeding succulents. This study of vegetation change following fire disturbance in an arid system highlights the slow return of canopy cover, immediate regrowth of only two resprouter species and slower re-establishment by seed of non-resprouter species. In addition, fire disturbance led to the numerical dominance of succulents within the first decade after the fire.
DOI: 10.6084/m9.figshare.3470498.v1
title: Vegetation dynamics after experimental fire disturbance in the arid Succulent Karoo, South Africa

description: Disturbance by fire in the Succulent Karoo is rare but fire events could increase as a result of an increase in grassiness (alien and indigenous species). This study assessed the effects of fire eight years after an experimentally induced burn in Succulent Karoo vegetation. Post-fire monitoring was conducted using the line intercept method and species counts per plot (1 m<sup>2</sup>) for each of three fire disturbance treatments: control/unburnt, high and low fuel load. Vegetation cover and abundance were compared across treatments and growth forms. Vegetation cover and abundance on fire-disturbed plots had not returned to pre-fire levels after eight years. Resprouters exhibited a rapid recovery and early dominance on burnt plots. Succulent seedlings established slower, but after eight years occurred at higher densities on the burnt than control plots. Recovery after disturbance of density and cover of long-lived, woody non-resprouter non-succulents was slow relative to resprouting non-succulents and reseeding succulents. This study of vegetation change following fire disturbance in an arid system highlights the slow return of canopy cover, immediate regrowth of only two resprouter species and slower re-establishment by seed of non-resprouter species. In addition, fire disturbance led to the numerical dominance of succulents within the first decade after the fire.
DOI: 10.6084/m9.figshare.3470495
title: Impact of <i>Prosopis</i> (mesquite) invasion and clearing on vegetation species composition and diversity in semi-arid Nama-Karoo rangeland, South Africa

description: The Nama-Karoo biome occupies 28% of South Africa’s land area. Alien leguminous trees of the genus <i>Prosopis</i> have invaded large tracts of Nama-Karoo rangeland. We evaluated the impact of <i>Prosopis</i> invasion and clearing on vegetation species composition and diversity (alien and indigenous species richness and cover) in Nama-Karoo rangeland on two sheep farms in the Beaufort West district of the Western Cape province of South Africa. Our results suggest that <i>Prosopis</i> invasion and clearing can significantly change Nama-Karoo rangeland species composition. Invasion and clearing appear to have no effect on alien species richness. Invasion, however, increases alien species cover, while clearing restores it to pre-invasion levels. In contrast, invasion reduces indigenous species richness while clearing restores it to pre-invasion levels. Invasion appears to have no effect on indigenous species cover. This lack of effect appears to be the serendipitous result of a site-specific trade-off between a decline in cover of grasses that are negatively affected by <i>Prosopis</i> invasion and a concomitant increase in the cover of positively affected grasses. Clearing increases indigenous species cover to above pre-invasion levels. The higher than usual indigenous species cover after clearing could be a transient legacy of <i>Prosopis</i> soil nutrient enrichment.
DOI: 10.6084/m9.figshare.3470495.v1
title: Impact of <i>Prosopis</i> (mesquite) invasion and clearing on vegetation species composition and diversity in semi-arid Nama-Karoo rangeland, South Africa

description: The Nama-Karoo biome occupies 28% of South Africa’s land area. Alien leguminous trees of the genus <i>Prosopis</i> have invaded large tracts of Nama-Karoo rangeland. We evaluated the impact of <i>Prosopis</i> invasion and clearing on vegetation species composition and diversity (alien and indigenous species richness and cover) in Nama-Karoo rangeland on two sheep farms in the Beaufort West district of the Western Cape province of South Africa. Our results suggest that <i>Prosopis</i> invasion and clearing can significantly change Nama-Karoo rangeland species composition. Invasion and clearing appear to have no effect on alien species richness. Invasion, however, increases alien species cover, while clearing restores it to pre-invasion levels. In contrast, invasion reduces indigenous species richness while clearing restores it to pre-invasion levels. Invasion appears to have no effect on indigenous species cover. This lack of effect appears to be the serendipitous result of a site-specific trade-off between a decline in cover of grasses that are negatively affected by <i>Prosopis</i> invasion and a concomitant increase in the cover of positively affected grasses. Clearing increases indigenous species cover to above pre-invasion levels. The higher than usual indigenous species cover after clearing could be a transient legacy of <i>Prosopis</i> soil nutrient enrichment.
DOI: 10.6084/m9.figshare.3470492
title: Further evidence that in African acacia, white is a warning colour to herbivores: the white pseudo-galls of <i>Vachellia seyal</i>

description: Pseudo-galls of three East African acacia (<i>Vachellia</i>) species were compared to determine the correlates of gall colour and their potential defensive functions. Although all three species produce white thorns, the pseudo-galls of <i>V. gerrardii</i> and <i>V. drepanolobium</i> are dark coloured. In contrast, pseudo-galls of <i>V. seyal</i> var. <i>fistula</i> are white. Associated with this, they are thin-walled and poorly used by aggressive mutualistic ants. We suggest that this weak functionality is compensated for by the highly visible white colour. This aposematism may also involve mimicry as only the <i>fistula</i> variety of <i>V. seyal</i> has galls and only this variety co-occurs with other <i>Vachellia</i> species that have functional galls. <i>Vachellia seyal seyal</i> does not have pseudo-galls and this variety does not occur with other <i>Vachellia</i> species that have pseudo-galls.
DOI: 10.6084/m9.figshare.3470492.v1
title: Further evidence that in African acacia, white is a warning colour to herbivores: the white pseudo-galls of <i>Vachellia seyal</i>

description: Pseudo-galls of three East African acacia (<i>Vachellia</i>) species were compared to determine the correlates of gall colour and their potential defensive functions. Although all three species produce white thorns, the pseudo-galls of <i>V. gerrardii</i> and <i>V. drepanolobium</i> are dark coloured. In contrast, pseudo-galls of <i>V. seyal</i> var. <i>fistula</i> are white. Associated with this, they are thin-walled and poorly used by aggressive mutualistic ants. We suggest that this weak functionality is compensated for by the highly visible white colour. This aposematism may also involve mimicry as only the <i>fistula</i> variety of <i>V. seyal</i> has galls and only this variety co-occurs with other <i>Vachellia</i> species that have functional galls. <i>Vachellia seyal seyal</i> does not have pseudo-galls and this variety does not occur with other <i>Vachellia</i> species that have pseudo-galls.
DOI: 10.6084/m9.figshare.3470489
title: Standard Deviation from Ensemble Niche Model

description: Standard deviation from the ensemble of the best models. Algorithm: Boosted Regression Trees. Species: Paramuricea clavata.
DOI: 10.6084/m9.figshare.3470489.v1
title: Standard Deviation from Ensemble Niche Model

description: Standard deviation from the ensemble of the best models. Algorithm: Boosted Regression Trees. Species: Paramuricea clavata.
DOI: 10.6084/m9.figshare.3470468
title: JH Survey 2 20160701 Tascam wav files

description: <br>Panshanger Barbastelle Survey 2<br>1 July 2016<br>21:25-23:00<br>Justin A T Halls<br>Tascam DR05 96ksps 16bit<br>MEMS SPM0408UD5<br>Luton 9:50pm 12C 77% 1008hPa 6.7m/s WSW light cloud51.798956 -0.145018Pleasant, clear evening with base camp at the junction of two large and one smaller <br>ride through the coniferous part of the Panshanger woods. Quite breezy in open<br>areas at times. Mainly Common Pips with one or two Sopranos and a nyctalus,<br>probably Leislers. No confirmed Barbstelles at this location although we thought<br>we had a pair of Barbies fly past at 22:21, observed flying about waist height from the <br>northern ride and departing down the southern ride.<br>On analysis looks like BLE's, sweeping 50-25kHz with some second harmonic. Area<br>at the junction quite open so not likely to be Barbastelle clutter type calls.<br>The Tascam was located about a 100yards down the ride to the south and did not pick up<br>the 35kHz bat at all.
DOI: 10.6084/m9.figshare.3470468.v1
title: JH Survey 2 20160701 Tascam wav files

description: <br>Panshanger Barbastelle Survey 2<br>1 July 2016<br>21:25-23:00<br>Justin A T Halls<br>Tascam DR05 96ksps 16bit<br>MEMS SPM0408UD5<br>Luton 9:50pm 12C 77% 1008hPa 6.7m/s WSW light cloud51.798956 -0.145018Pleasant, clear evening with base camp at the junction of two large and one smaller <br>ride through the coniferous part of the Panshanger woods. Quite breezy in open<br>areas at times. Mainly Common Pips with one or two Sopranos and a nyctalus,<br>probably Leislers. No confirmed Barbstelles at this location although we thought<br>we had a pair of Barbies fly past at 22:21, observed flying about waist height from the <br>northern ride and departing down the southern ride.<br>On analysis looks like BLE's, sweeping 50-25kHz with some second harmonic. Area<br>at the junction quite open so not likely to be Barbastelle clutter type calls.<br>The Tascam was located about a 100yards down the ride to the south and did not pick up<br>the 35kHz bat at all.
DOI: 10.6084/m9.figshare.3470447
title: Evolution of my CV

description: A file containing many of my cv drafts. <br><br>
DOI: 10.6084/m9.figshare.3470447.v1
title: Evolution of my CV

description: A file containing many of my cv drafts. <br><br>
DOI: 10.6084/m9.figshare.3470444
title: NSFGRF Unfunded Applications

description: Fileset contains files associated with my 2013 and 2014 NSF GRF applications. <br><br>
DOI: 10.6084/m9.figshare.3470444.v2
title: NSFGRF Unfunded Applications

description: Fileset contains files associated with my 2013 and 2014 NSF GRF applications. <br><br>
DOI: 10.6084/m9.figshare.3470435
title: JH Survey 2 20160701 Tascam wav files

description: <br>Panshanger Barbastelle Survey 2<br>1 July 2016<br>21:25-23:00<br>Justin A T Halls<br>Tascam DR05 96ksps 16bit<br>MEMS SPM0408UD5<br>Luton 9:50pm 12C 77% 1008hPa 6.7m/s WSW light cloud51.798956 -0.145018Pleasant, clear evening with base camp at the junction of two large and one smaller <br>ride through the coniferous part of the Panshanger woods. Quite breezy in open<br>areas at times. Mainly Common Pips with one or two Sopranos and a nyctalus,<br>probably Leislers. No confirmed Barbstelles at this location although we thought<br>we had a pair of Barbies fly past at 22:21, observed flying about waist height from the <br>northern ride and departing down the southern ride.<br>On analysis looks like BLE's, sweeping 50-25kHz with some second harmonic. Area<br>at the junction quite open so not likely to be Barbastelle clutter type calls.<br>The Tascam was located about a 100yards down the ride to the south and did not pick up<br>the 35kHz bat at all.<br>
DOI: 10.6084/m9.figshare.3470435.v1
title: JH Survey 2 20160701 Tascam wav files

description: <br>Panshanger Barbastelle Survey 2<br>1 July 2016<br>21:25-23:00<br>Justin A T Halls<br>Tascam DR05 96ksps 16bit<br>MEMS SPM0408UD5<br>Luton 9:50pm 12C 77% 1008hPa 6.7m/s WSW light cloud51.798956 -0.145018Pleasant, clear evening with base camp at the junction of two large and one smaller <br>ride through the coniferous part of the Panshanger woods. Quite breezy in open<br>areas at times. Mainly Common Pips with one or two Sopranos and a nyctalus,<br>probably Leislers. No confirmed Barbstelles at this location although we thought<br>we had a pair of Barbies fly past at 22:21, observed flying about waist height from the <br>northern ride and departing down the southern ride.<br>On analysis looks like BLE's, sweeping 50-25kHz with some second harmonic. Area<br>at the junction quite open so not likely to be Barbastelle clutter type calls.<br>The Tascam was located about a 100yards down the ride to the south and did not pick up<br>the 35kHz bat at all.<br>
DOI: 10.6084/m9.figshare.3470426
title: Application to Center for Great Plains Studies (2015)

description: My 2015 application to the Center for Great Plains Studies (Univ. of Nebraska-Lincoln).<br>Application resulted in an invitation to become a graduate fellow (2016-2018).<br><br>
DOI: 10.6084/m9.figshare.3470426.v1
title: Application to Center for Great Plains Studies (2015)

description: My 2015 application to the Center for Great Plains Studies (Univ. of Nebraska-Lincoln).<br>Application resulted in an invitation to become a graduate fellow (2016-2018).<br><br>
DOI: 10.6084/m9.figshare.3470411.v3
title: Spatial Frequency and Emotion: The Functional Role of the Subcortical Route to the Amygdala

description: This presentation was given at an invited talk in the Université de Grenoble on the 4th of July, 2016. Transcript of speech can be found in the slide notes of the PowerPoint file.
DOI: 10.6084/m9.figshare.3470399
title: Data From: A Bayesian approach to sequential meta-analysis

description: As evidence accumulates within a meta-analysis, it is desirable to determine when the results could be considered conclusive to guide systematic review updates and future trial designs. Adapting sequential testing methodology from clinical trials for application to pooled meta-analytic effect size estimates appears well suited for this objective. In this paper we describe a Bayesian sequential meta-analysis method, in which an informative heterogeneity prior is employed and stopping rule criteria are applied directly to the posterior distribution for the treatment effect parameter. Using simulation studies, we examine how well this approach performs under different parameter combinations by monitoring the proportion of sequential meta-analyses that reach incorrect conclusions (to yield error rates), the number of studies required to reach conclusion, and the resulting parameter estimates. By adjusting the stopping rule thresholds, the overall error rates can be controlled within the target levels and are no higher than those of alternative frequentist and semi-Bayes methods for the majority of the simulation scenarios. To illustrate the potential application of this method, we consider two contrasting meta-analyses using data from the Cochrane Library and compare the results of employing different sequential methods, while examining the effect of the heterogeneity prior in the proposed Bayesian approach.
DOI: 10.6084/m9.figshare.3470399.v1
title: Data From: A Bayesian approach to sequential meta-analysis

description: As evidence accumulates within a meta-analysis, it is desirable to determine when the results could be considered conclusive to guide systematic review updates and future trial designs. Adapting sequential testing methodology from clinical trials for application to pooled meta-analytic effect size estimates appears well suited for this objective. In this paper we describe a Bayesian sequential meta-analysis method, in which an informative heterogeneity prior is employed and stopping rule criteria are applied directly to the posterior distribution for the treatment effect parameter. Using simulation studies, we examine how well this approach performs under different parameter combinations by monitoring the proportion of sequential meta-analyses that reach incorrect conclusions (to yield error rates), the number of studies required to reach conclusion, and the resulting parameter estimates. By adjusting the stopping rule thresholds, the overall error rates can be controlled within the target levels and are no higher than those of alternative frequentist and semi-Bayes methods for the majority of the simulation scenarios. To illustrate the potential application of this method, we consider two contrasting meta-analyses using data from the Cochrane Library and compare the results of employing different sequential methods, while examining the effect of the heterogeneity prior in the proposed Bayesian approach.
DOI: 10.6084/m9.figshare.3470384
title: Data From: Prior Event Rate Ratio Adjustment for Hidden Confounding in Observational Studies of Treatment Effectiveness: A Pairwise Cox Likelihood Approach

description: Observational studies provide a rich source of information for assessing effectiveness of treatment interventions in many situations where it is not ethical or practical to perform randomized controlled trials. However, such studies are prone to bias from hidden (unmeasured) confounding. A promising approach to identifying and reducing the impact of unmeasured confounding is Prior Event Rate Ratio (PERR) adjustment, a quasi-experimental analytic method proposed in the context of electronic medical record database studies. In this paper we present a statistical framework for using a pairwise approach to PERR adjustment that removes bias inherent in the original PERR method. A flexible pairwise Cox likelihood function is derived and used to demonstrate the consistency of the simple and convenient PERR-ALT estimator. We show how to estimate standard errors and confidence intervals for treatment effect estimates based on the observed information, and provide R code to illustrate how to implement the method. Assumptions required for the pairwise approach (as well as PERR) are clarified, and the consequences of model misspecification are explored. Our results confirm the need for researchers to consider carefully the suitability of the method in the context of each problem. Extensions of the pairwise likelihood to more complex designs involving time-varying covariates or more than two periods are considered. We illustrate the application of the method using data from a longitudinal cohort study of enzyme replacement therapy for lysosomal storage disorders.
DOI: 10.6084/m9.figshare.3470384.v1
title: Data From: Prior Event Rate Ratio Adjustment for Hidden Confounding in Observational Studies of Treatment Effectiveness: A Pairwise Cox Likelihood Approach

description: Observational studies provide a rich source of information for assessing effectiveness of treatment interventions in many situations where it is not ethical or practical to perform randomized controlled trials. However, such studies are prone to bias from hidden (unmeasured) confounding. A promising approach to identifying and reducing the impact of unmeasured confounding is Prior Event Rate Ratio (PERR) adjustment, a quasi-experimental analytic method proposed in the context of electronic medical record database studies. In this paper we present a statistical framework for using a pairwise approach to PERR adjustment that removes bias inherent in the original PERR method. A flexible pairwise Cox likelihood function is derived and used to demonstrate the consistency of the simple and convenient PERR-ALT estimator. We show how to estimate standard errors and confidence intervals for treatment effect estimates based on the observed information, and provide R code to illustrate how to implement the method. Assumptions required for the pairwise approach (as well as PERR) are clarified, and the consequences of model misspecification are explored. Our results confirm the need for researchers to consider carefully the suitability of the method in the context of each problem. Extensions of the pairwise likelihood to more complex designs involving time-varying covariates or more than two periods are considered. We illustrate the application of the method using data from a longitudinal cohort study of enzyme replacement therapy for lysosomal storage disorders.