cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6448010.v5
title: On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations

description: R code and associated data for a comment on a paper by Christopher Swan and Bryan Brown titled "Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration." <br><br>Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). This is due to issues with experimental design, improper use of statistical analyses, and discrepancies between written methods and what was actually conducted. Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, metacommunity, and restoration ecology. <br>These are the corrected data provided by Christopher M. Swan and Bryan L. Brown (Swan and Brown 2017), and are deposited here for ease of the reader. <br> If the data are re-used, please cite the proper source: Swan, C. M., and B. L. Brown. 2017. Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 27:2209-2219.<br>
DOI: 10.6084/m9.figshare.6448010.v7
title: On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations

description: R code and associated data for a comment on a paper by Christopher Swan and Bryan Brown titled "Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration." <br><br>Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). This is due to issues with experimental design, improper use of statistical analyses, and discrepancies between written methods and what was actually conducted. Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, metacommunity, and restoration ecology. <br>These are the corrected data provided by Christopher M. Swan and Bryan L. Brown (Swan and Brown 2017), and are deposited here for ease of the reader. <br> If the data are re-used, please cite the proper source: Swan, C. M., and B. L. Brown. 2017. Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 27:2209-2219.<br>This is the final version uploaded after recommendation by PCI Ecology.<br>
DOI: 10.6084/m9.figshare.6448010.v6
title: On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations

description: R code and associated data for a comment on a paper by Christopher Swan and Bryan Brown titled "Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration." <br><br>Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). This is due to issues with experimental design, improper use of statistical analyses, and discrepancies between written methods and what was actually conducted. Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, metacommunity, and restoration ecology. <br>These are the corrected data provided by Christopher M. Swan and Bryan L. Brown (Swan and Brown 2017), and are deposited here for ease of the reader. <br> If the data are re-used, please cite the proper source: Swan, C. M., and B. L. Brown. 2017. Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 27:2209-2219.<br>
DOI: 10.6084/m9.figshare.6447959.v1
title: Bayesian Regularization for Graphical Models with Unequal Shrinkage

description: We consider a Bayesian framework for estimating a high-dimensional sparse precision matrix, in which adaptive shrinkage and sparsity are induced by a mixture of Laplace priors. Besides discussing our formulation from the Bayesian standpoint, we investigate the MAP (maximum a posteriori) estimator from a penalized likelihood perspective that gives rise to a new non-convex penalty approximating the ℓ<sub>0</sub> penalty. Optimal error rates for estimation consistency in terms of various matrix norms along with selection consistency for sparse structure recovery are shown for the unique MAP estimator under mild conditions. For fast and efficient computation, an EM algorithm is proposed to compute the MAP estimator of the precision matrix and (approximate) posterior probabilities on the edges of the underlying sparse structure. Through extensive simulation studies and a real application to a call center data, we have demonstrated the fine performance of our method compared with existing alternatives.
DOI: 10.34740/kaggle/dsv/1449791
title: COVID-19 cases by Continent
DOI: 10.6084/m9.figshare.6447917
title: Two <i>Mychonastes</i> isolated from freshwater bodies are novel potential feedstocks for biodiesel production

description: Microalgae have been considered as ideal feedstocks for biodiesel production but the potential application is still under investigations. Here, eight kinds of microalgae were identified from water samples based on the morphologic and phylogenetic analyses. Among these eight microalgae, two <i>Mychonastes</i> S4 and S15 exhibited relative faster growth rate in the early culture stage and the highest contents of lipids. The two <i>Mychonastes</i> also showed higher C18:1 contents than the two <i>Chlorella</i> which were traditionally considered to be potential species for biodiesel production. As one kind of less researched microalgae, this study suggests <i>Mychonastes</i> should be a potential feedstock for biodiesel production. The application of the microalgal biodiesel still have some limiting factors, however, it is promising based on better lipid extraction technology and more relevant studies.
DOI: 10.6084/m9.figshare.6447917.v1
title: Two <i>Mychonastes</i> isolated from freshwater bodies are novel potential feedstocks for biodiesel production

description: Microalgae have been considered as ideal feedstocks for biodiesel production but the potential application is still under investigations. Here, eight kinds of microalgae were identified from water samples based on the morphologic and phylogenetic analyses. Among these eight microalgae, two <i>Mychonastes</i> S4 and S15 exhibited relative faster growth rate in the early culture stage and the highest contents of lipids. The two <i>Mychonastes</i> also showed higher C18:1 contents than the two <i>Chlorella</i> which were traditionally considered to be potential species for biodiesel production. As one kind of less researched microalgae, this study suggests <i>Mychonastes</i> should be a potential feedstock for biodiesel production. The application of the microalgal biodiesel still have some limiting factors, however, it is promising based on better lipid extraction technology and more relevant studies.
DOI: 10.6084/m9.figshare.6447914.v1
title: Covariate-adjusted Regression for Distorted Longitudinal Data with Informative Observation Times

description: In many longitudinal studies, repeated response and predictors are not directly observed, but can be treated as distorted by unknown functions of a common confounding covariate. Moreover, longitudinal data involve an observation process which may be informative with a longitudinal response process in practice. To deal with such complex data, we propose a class of flexible semiparametric covariate-adjusted joint models. The new models not only allow for the longitudinal response to be correlated with observation times through latent variables and completely unspecified link functions, but they also characterize distorted longitudinal response and predictors by unknown multiplicative factors depending on time and a confounding covariate. For estimation of regression parameters in the proposed models, we develop a novel covariate-adjusted estimating equation approach which does not rely on forms of link functions and distributions of frailties. The asymptotic properties of resulting parameter estimators are established and examined by simulation studies. A longitudinal data example containing calcium adsorption and intake measurements is provided for illustration.
DOI: 10.6084/m9.figshare.6447908
title: Partial Identification of the Average Treatment Effect Using Instrumental Variables: Review of Methods for Binary Instruments, Treatments, and Outcomes

description: Several methods have been proposed for partially or point identifying the average treatment effect (ATE) using instrumental variable (IV) type assumptions. The descriptions of these methods are widespread across the statistical, economic, epidemiologic, and computer science literature, and the connections between the methods have not been readily apparent. In the setting of a binary instrument, treatment, and outcome, we review proposed methods for partial and point identification of the ATE under IV assumptions, express the identification results in a common notation and terminology, and propose a taxonomy that is based on sets of identifying assumptions. We further demonstrate and provide software for the application of these methods to estimate bounds. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6447908.v2
title: Partial Identification of the Average Treatment Effect Using Instrumental Variables: Review of Methods for Binary Instruments, Treatments, and Outcomes

description: Several methods have been proposed for partially or point identifying the average treatment effect (ATE) using instrumental variable (IV) type assumptions. The descriptions of these methods are widespread across the statistical, economic, epidemiologic, and computer science literature, and the connections between the methods have not been readily apparent. In the setting of a binary instrument, treatment, and outcome, we review proposed methods for partial and point identification of the ATE under IV assumptions, express the identification results in a common notation and terminology, and propose a taxonomy that is based on sets of identifying assumptions. We further demonstrate and provide software for the application of these methods to estimate bounds. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6447908.v1
title: Partial Identification of the Average Treatment Effect Using Instrumental Variables: Review of Methods for Binary Instruments, Treatments, and Outcomes

description: Several methods have been proposed for partially or point identifying the average treatment effect (ATE) using instrumental variable (IV) type assumptions. The descriptions of these methods are widespread across the statistical, economic, epidemiologic, and computer science literature, and the connections between the methods have not been readily apparent. In the setting of a binary instrument, treatment, and outcome, we review proposed methods for partial and point identification of the ATE under IV assumptions, express the identification results in a common notation and terminology, and propose a taxonomy that is based on sets of identifying assumptions. We further demonstrate and provide software for the application of these methods to estimate bounds.
DOI: 10.6084/m9.figshare.6447905.v1
title: Skinny Gibbs: A Consistent and Scalable Gibbs Sampler for Model Selection

description: We consider the computational and statistical issues for high-dimensional Bayesian model selection under the Gaussian spike and slab priors. To avoid large matrix computations needed in a standard Gibbs sampler, we propose a novel Gibbs sampler called “Skinny Gibbs” which is much more scalable to high-dimensional problems, both in memory and in computational efficiency. In particular, its computational complexity grows only linearly in <i>p</i>, the number of predictors, while retaining the property of strong model selection consistency even when <i>p</i> is much greater than the sample size <i>n</i>. The present article focuses on logistic regression due to its broad applicability as a representative member of the generalized linear models. We compare our proposed method with several leading variable selection methods through a simulation study to show that Skinny Gibbs has a strong performance as indicated by our theoretical work. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6447881
title: Quantitative Evaluation of the Trade-off of Strengthened Instruments and Sample Size in Observational Studies

description: Weak instruments produce causal inferences that are sensitive to small failures of the assumptions underlying an instrumental variable, so strong instruments are preferred. The possibility of strengthening an instrument at the price of a reduced sample size has been proposed in the statistical literature and used in the medical literature, but there has not been a theoretical study of the trade-off of instrument strength and sample size. This trade-off and related questions are examined using the Bahadur efficiency of a test or a sensitivity analysis. A moderate increase in instrument strength is worth more than an enormous increase in sample size. This is true with a flawless instrument, and the difference is more pronounced when allowance is made for small unmeasured biases in the instrument. A new method of strengthening an instrument is proposed: it discards half the sample to learn empirically where the instrument is strong, then discards part of the remaining half to avoid areas where the instrument is weak; however, the gains in instrument strength can more than compensate for the loss of sample size. The example is drawn from a study of the effectiveness of high-level neonatal intensive care units in saving the lives of premature infants.
DOI: 10.6084/m9.figshare.6447881.v2
title: Quantitative Evaluation of the Trade-off of Strengthened Instruments and Sample Size in Observational Studies

description: Weak instruments produce causal inferences that are sensitive to small failures of the assumptions underlying an instrumental variable, so strong instruments are preferred. The possibility of strengthening an instrument at the price of a reduced sample size has been proposed in the statistical literature and used in the medical literature, but there has not been a theoretical study of the trade-off of instrument strength and sample size. This trade-off and related questions are examined using the Bahadur efficiency of a test or a sensitivity analysis. A moderate increase in instrument strength is worth more than an enormous increase in sample size. This is true with a flawless instrument, and the difference is more pronounced when allowance is made for small unmeasured biases in the instrument. A new method of strengthening an instrument is proposed: it discards half the sample to learn empirically where the instrument is strong, then discards part of the remaining half to avoid areas where the instrument is weak; however, the gains in instrument strength can more than compensate for the loss of sample size. The example is drawn from a study of the effectiveness of high-level neonatal intensive care units in saving the lives of premature infants.
DOI: 10.6084/m9.figshare.6447881.v1
title: Quantitative Evaluation of the Trade-Off of Strengthened Instruments and Sample Size in Observational Studies

description: Weak instruments produce causal inferences that are sensitive to small failures of the assumptions underlying an instrumental variable, so strong instruments are preferred. The possibility of strengthening an instrument at the price of a reduced sample size has been proposed in the statistical literature and used in the medical literature, but there has not been a theoretical study of the trade-off of instrument strength and sample size. This trade-off and related questions are examined using the Bahadur efficiency of a test or a sensitivity analysis. A moderate increase in instrument strength is worth more than an enormous increase in sample size. This is true with a flawless instrument, and the difference is more pronounced when allowance is made for small unmeasured biases in the instrument. A new method of strengthening an instrument is proposed: it discards half the sample to learn empirically where the instrument is strong, then discards part of the remaining half to avoid areas where the instrument is weak; however, the gains in instrument strength can more than compensate for the loss of sample size. The example is drawn from a study of the effectiveness of high-level neonatal intensive care units in saving the lives of premature infants.
DOI: 10.6084/m9.figshare.6447689
title: Supplementary Data File- Hypophosphataemic osteomalacia in a patient with neurofibromatosis type 1- a role for FGF23?

description: Supplement data file-NF1-FGF23
DOI: 10.5281/zenodo.4005068
title: De novo genome assembly of the Tobacco Hornworm moth (Manduca sexta)

description: <strong>We present the new reference genome for M sexta, JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ~25x more continuous than the original assembly, with scaffold N50 &gt;14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use.</strong>
DOI: 10.6084/m9.figshare.6447266
title: In situ X-ray tomography imaging of soil water and cyanobacteria from biological soil crusts undergoing desiccation

description: AbstractBiological soil crusts (biocrusts) are millimeter-sized microbial communities developing on the topsoils of arid lands that cover some 12% of Earth’s continental area. Biocrusts consist of an assemblage of mineral soil particles consolidated into a crust by microbial organic polymeric substances that are mainly produced by the filamentous bundle-forming cyanobacteria, among which Microcoleus vaginatus is perhaps the most widespread. This cyanobacterium is the primary producer for, and main architect of biocrusts in many arid soils, sustaining the development of a diverse microbial community. Biocrusts are only active when wet, and spend most of their time in a state of desiccated quiescence, from which they can quickly recover upon wetting. Despite their ecological importance for arid ecosystems, little is known about the mechanisms that allow biocrust organisms to endure long periods of dryness while remaining viable for rapid resuscitation upon wetting. We had previously observed the persistence of significant rates of light-dependent carbon fixation in apparently dry biocrusts dominated by M. vaginatus, indicating that it may be able to remain hydrated against a background soil of very low water potential. One potential explanation for this may be that the abundant exopolysaccharide sheaths of M. vaginatus can preferentially retain moisture thus slowing the water equilibration with the surrounding soil allowing for extended activity periods. In order to test this hypothesis we aimed to develop methodologies to visualize and quantify the water dynamics within an undisturbed biocrust undergoing desiccation. We used synchrotron based X-ray microtomography and were able to resolve the distribution of air, liquid water, mineral particles and cyanobacterial bundles at the microscale. We could demonstrate the formation of steep, decreasing gradients of water content from the cyanobacterial bundle surface outward, while the bundle volume remained stable, as the local bulk water content decreased linearly, hence demonstrating a preferential retention of water in the microbes. Our data also suggest a transfer of hydration water from the EPS sheath material into the cyanobacterial filament as desiccation progresses. This work demonstrates the value of X-ray tomography as a tool to study microbe-scale water redistribution in biocrusts.<br><br>