cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1581633.v1
title: How much information does dependence between wavelet coefficients contain?

description: Motivated by several papers which propose statistical inference assuming independence of wavelet coefficients for both short- as well as long-range dependent time series, we focus exemplary on the sample variance and investigate the influence of the dependence between wavelet coefficients to this statistic. To this end, we derive asymptotic distributional properties of the sample variance for a time series which is synthesized ignoring some or all dependence between wavelet coefficients. We show that the second order properties differ from the ones of the true time series whose wavelet coefficients have the same marginal distribution except in the independent Gaussian case. This holds true even if the dependency is correct within each level and only the dependence between levels is ignored. For the example of sample autocovariances and sample autocorrelations at lag one, we indicate that already first order properties are erroneous in these cases. In a second step, several non-parametric bootstrap schemes in the wavelet domain are investigated which take more and more dependence into account until finally the full dependency is mimicked. We obtain very similar results, where only a bootstrap mimicking the full covariance structure correctly can be valid asymptotically. A simulation study supports our theoretical findings for the wavelet domain bootstraps. For long-range dependent time series with long-memory parameter <i>d</i> &gt; 1/4, we show that some additional problems occur which cannot be solved easily without using additional information for the bootstrap.
DOI: 10.6084/m9.figshare.1581632.v2
title: Inference for Monotone Functions Under Short- and Long-Range Dependence: Confidence Intervals and New Universal Limits

description: We introduce new point-wise confidence interval estimates for monotone functions observed with additive, dependent noise. Our methodology applies to both short- and long-range dependence regimes for the errors. The interval estimates are obtained via the method of inversion of certain discrepancy statistics. This approach avoids the estimation of nuisance parameters such as the derivative of the unknown function, which previous methods are forced to deal with. The resulting estimates are therefore more accurate, stable, and widely applicable in practice under minimal assumptions on the trend and error structure. The dependence of the errors especially long-range dependence leads to new phenomena, where new universal limits based on convex minorant functionals of drifted fractional Brownian motion emerge. Some extensions to uniform confidence bands are also developed. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581626
title: Modeling Probability Forecasts via Information Diversity

description: Randomness in scientific estimation is generally assumed to arise from unmeasured or uncontrolled factors. However, when combining subjective probability estimates, heterogeneity stemming from people’s cognitive or information diversity is often more important than measurement noise. This article presents a novel framework that uses partially overlapping information sources. A specific model is proposed within that framework and applied to the task of aggregating the probabilities given by a group of forecasters who predict whether an event will occur or not. Our model describes the distribution of information across forecasters in terms of easily interpretable parameters and shows how the optimal amount of <i>extremizing</i> of the average probability forecast (shifting it closer to its nearest extreme) varies as a function of the forecasters’ information overlap. Our model thus gives a more principled understanding of the historically ad hoc practice of extremizing average forecasts. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.1581632.v4
title: Inference for Monotone Functions Under Short- and Long-Range Dependence: Confidence Intervals and New Universal Limits

description: We introduce new point-wise confidence interval estimates for monotone functions observed with additive, dependent noise. Our methodology applies to both short- and long-range dependence regimes for the errors. The interval estimates are obtained via the method of inversion of certain discrepancy statistics. This approach avoids the estimation of nuisance parameters such as the derivative of the unknown function, which previous methods are forced to deal with. The resulting estimates are therefore more accurate, stable, and widely applicable in practice under minimal assumptions on the trend and error structure. The dependence of the errors especially long-range dependence leads to new phenomena, where new universal limits based on convex minorant functionals of drifted fractional Brownian motion emerge. Some extensions to uniform confidence bands are also developed. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581632.v3
title: Inference for Monotone Functions Under Short- and Long-Range Dependence: Confidence Intervals and New Universal Limits

description: We introduce new point-wise confidence interval estimates for monotone functions observed with additive, dependent noise. Our methodology applies to both short- and long-range dependence regimes for the errors. The interval estimates are obtained via the method of inversion of certain discrepancy statistics. This approach avoids the estimation of nuisance parameters such as the derivative of the unknown function, which previous methods are forced to deal with. The resulting estimates are therefore more accurate, stable, and widely applicable in practice under minimal assumptions on the trend and error structure. The dependence of the errors especially long-range dependence leads to new phenomena, where new universal limits based on convex minorant functionals of drifted fractional Brownian motion emerge. Some extensions to uniform confidence bands are also developed. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581618
title: The AMPK-PPARGC1A pathway is required for antimicrobial host defense through activation of autophagy

description: AMP-activated protein kinase (AMPK) is a crucial energy sensor and plays a key role in integration of cellular functions to maintain homeostasis. Despite this, it is largely unknown whether targeting the AMPK pathway can be used as a therapeutic strategy for infectious diseases. Herein, we show that AMPK activation robustly induces antibacterial autophagy, which contributes to antimicrobial defense against <i>Mycobacterium tuberculosis</i> (Mtb). AMPK activation led to inhibition of Mtb-induced phosphorylation of the mechanistic target of rapamycin (MTOR) in macrophages. In addition, AMPK activation increased the genes involved in oxidative phosphorylation, mitochondrial ATP production, and biogenesis in Mtb-infected macrophages. Notably, peroxisome proliferator-activated receptor-gamma, coactivator 1α (PPARGC1A) was required for AMPK-mediated antimicrobial activity, as well as enhancement of mitochondrial function and biogenesis, in macrophages. Further, the AMPK-PPARGC1A pathway was involved in the upregulation of multiple autophagy-related genes via CCAAT/enhancer binding protein (C/EBP), β (CEBPB). PPARGC1A knockdown inhibited the AMPK-mediated induction of autophagy and impaired the fusion of phagosomes with MAP1LC3B (LC3B) autophagosomes in Mtb-infected macrophages. The link between autophagy, mitochondrial function, and antimicrobial activity was further demonstrated by studying LysMCre-mediated knockout of <i>atg7</i>, demonstrating mitochondrial ultrastructural defects and dysfunction, as well as blockade of antimicrobial activity against mycobacteria. Collectively, our results identify the AMPK-PPARGC1A axis as contributing to autophagy activation leading to an antimicrobial response, as a novel host defense mechanism.
DOI: 10.6084/m9.figshare.1581626.v2
title: Modeling Probability Forecasts via Information Diversity

description: Randomness in scientific estimation is generally assumed to arise from unmeasured or uncontrolled factors. However, when combining subjective probability estimates, heterogeneity stemming from people’s cognitive or information diversity is often more important than measurement noise. This article presents a novel framework that uses partially overlapping information sources. A specific model is proposed within that framework and applied to the task of aggregating the probabilities given by a group of forecasters who predict whether an event will occur or not. Our model describes the distribution of information across forecasters in terms of easily interpretable parameters and shows how the optimal amount of <i>extremizing</i> of the average probability forecast (shifting it closer to its nearest extreme) varies as a function of the forecasters’ information overlap. Our model thus gives a more principled understanding of the historically ad hoc practice of extremizing average forecasts. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.1581626.v1
title: Modeling Probability Forecasts via Information Diversity

description: Randomness in scientific estimation is generally assumed to arise from unmeasured or uncontrolled factors. However, when combining subjective probability estimates, heterogeneity stemming from people’s cognitive or information diversity is often more important than measurement noise. This article presents a novel framework that uses partially overlapping information sources. A specific model is proposed within that framework and applied to the task of aggregating the probabilities given by a group of forecasters who predict whether an event will occur or not. Our model describes the distribution of information across forecasters in terms of easily interpretable parameters and shows how the optimal amount of <i>extremizing</i> of the average probability forecast (shifting it closer to its nearest extreme) varies as a function of the forecasters’ information overlap. Our model thus gives a more principled understanding of the historically ad hoc practice of extremizing average forecasts. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.1581602
title: Conditional Sure Independence Screening

description: Independence screening is powerful for variable selection when the number of variables is massive. Commonly used independence screening methods are based on marginal correlations or its variants. When some prior knowledge on a certain important set of variables is available, a natural assessment on the relative importance of the other predictors is their conditional contributions to the response given the known set of variables. This results in conditional sure independence screening (CSIS). CSIS produces a rich family of alternative screening methods by different choices of the conditioning set and can help reduce the number of false positive and false negative selections when covariates are highly correlated. This article proposes and studies CSIS in generalized linear models. We give conditions under which sure screening is possible and derive an upper bound on the number of selected variables. We also spell out the situation under which CSIS yields model selection consistency and the properties of CSIS when a data-driven conditioning set is used. Moreover, we provide two data-driven methods to select the thresholding parameter of conditional screening. The utility of the procedure is illustrated by simulation studies and analysis of two real datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581569
title: Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community

description: Halite endoliths (salt rocks) in the Atacama Desert represent one of the most extreme environments on Earth. We obtained a 9.6 Gb high quality shotgun metagenome from halite nodules collected in the Salar Grande area. Our metagenome is unique because it has high sequencing depth, low diversity, and representative members from all 3 domains of life and from viruses. Taxonomic assignment of the metagenomic reads confirmed that the community was dominated by members of the Archaea, including Nanohaloarchaea, and also comprised members of the Bacteria and Eukarya. The functional annotation of the metagenome revealed that the cyanobacterium Halothece was responsible for most of the CO2 fixed in the community and that a number of archaea and bacteria carried out photoheterotrophy, via light-driven proton pumps, increasing the energy budget of the community from light. Our analysis predicted that the alga identified in the community has one of the lowest protein isoelectric point (pI) distributions of any reported eukaryote. Its pI profile was similar to that of halophiles using a “salt-in” strategy. Our genome assembly produced a nanohaloarchaeon genome of 1.2 Mbp. We have named this new microorganism Candidatus Nanopetramus SG9. Analysis of its genome sequence revealed a photoheterotrophic life style, a low median isoelectric point for all its predicted proteins, suggesting a “salt-in” strategist, and the presence of a unique CRISPR/Cas system in its genome; one of the spacers from this unique CRISPR/Cas system matched a partial viral genome from the metagenome. We developed new methods to identify viral genomic content from metagenome data, resulting in the identification of over 30 complete or near complete viral or proviral genomes in the halite metagenome. These viral genomes were diverse in genome structure, gene content, host, and genome size. Putative hosts for these viruses included Halobacteriaceae, Nanohaloarchaea, and Cyanobacteria. Despite the dependence on deliquescence of the halite community for liquid water availability, this study revealed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses, and a predominant “salt-in” strategy to balance the high osmotic pressure of the environment.
DOI: 10.6084/m9.figshare.1581602.v1
title: Conditional Sure Independence Screening

description: Independence screening is powerful for variable selection when the number of variables is massive. Commonly used independence screening methods are based on marginal correlations or its variants. When some prior knowledge on a certain important set of variables is available, a natural assessment on the relative importance of the other predictors is their conditional contributions to the response given the known set of variables. This results in conditional sure independence screening (CSIS). CSIS produces a rich family of alternative screening methods by different choices of the conditioning set and can help reduce the number of false positive and false negative selections when covariates are highly correlated. This article proposes and studies CSIS in generalized linear models. We give conditions under which sure screening is possible and derive an upper bound on the number of selected variables. We also spell out the situation under which CSIS yields model selection consistency and the properties of CSIS when a data-driven conditioning set is used. Moreover, we provide two data-driven methods to select the thresholding parameter of conditional screening. The utility of the procedure is illustrated by simulation studies and analysis of two real datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581569.v1
title: Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community

description: Halite endoliths (salt rocks) in the Atacama Desert represent one of the most extreme environments on Earth. We obtained a 9.6 Gb high quality shotgun metagenome from halite nodules collected in the Salar Grande area. Our metagenome is unique because it has high sequencing depth, low diversity, and representative members from all 3 domains of life and from viruses. Taxonomic assignment of the metagenomic reads confirmed that the community was dominated by members of the Archaea, including Nanohaloarchaea, and also comprised members of the Bacteria and Eukarya. The functional annotation of the metagenome revealed that the cyanobacterium Halothece was responsible for most of the CO2 fixed in the community and that a number of archaea and bacteria carried out photoheterotrophy, via light-driven proton pumps, increasing the energy budget of the community from light. Our analysis predicted that the alga identified in the community has one of the lowest protein isoelectric point (pI) distributions of any reported eukaryote. Its pI profile was similar to that of halophiles using a “salt-in” strategy. Our genome assembly produced a nanohaloarchaeon genome of 1.2 Mbp. We have named this new microorganism Candidatus Nanopetramus SG9. Analysis of its genome sequence revealed a photoheterotrophic life style, a low median isoelectric point for all its predicted proteins, suggesting a “salt-in” strategist, and the presence of a unique CRISPR/Cas system in its genome; one of the spacers from this unique CRISPR/Cas system matched a partial viral genome from the metagenome. We developed new methods to identify viral genomic content from metagenome data, resulting in the identification of over 30 complete or near complete viral or proviral genomes in the halite metagenome. These viral genomes were diverse in genome structure, gene content, host, and genome size. Putative hosts for these viruses included Halobacteriaceae, Nanohaloarchaea, and Cyanobacteria. Despite the dependence on deliquescence of the halite community for liquid water availability, this study revealed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses, and a predominant “salt-in” strategy to balance the high osmotic pressure of the environment.
DOI: 10.6084/m9.figshare.1581590
title: Molecular organization of the 5S rDNA gene type II in elasmobranchs

description: The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT<sub>4</sub> sequence as stop signal, however in Rajiformes this signal was doubled in length to dT<sub>8.</sub> This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.
DOI: 10.6084/m9.figshare.1581590.v2
title: Molecular organization of the 5S rDNA gene type II in elasmobranchs

description: The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT<sub>4</sub> sequence as stop signal, however in Rajiformes this signal was doubled in length to dT<sub>8.</sub> This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.
DOI: 10.6084/m9.figshare.1581525
title: Data for "Developing a paired-target apparatus for quantitative testing of nest defense behavior by vespine wasps in response to con- or heterospecific nest defense pheromones"

description: These data are in support of a paper published in Journal of Hymenoptera Research entitled: "Developing a paired-target apparatus for quantitative testing of nest defense behavior by vespine wasps in response to con- or heterospecific nest defense pheromones" available here: http://jhr.pensoft.net/articles.php?id=6585<br><br>Data consists primarily of paired audio files from 10 experiments. For details on how to use the data, see the attached readme.pdf file. <br>Supplemental Video 1 shows the bioassay procedure in use at a Vespula alascensis nest.
DOI: 10.6084/m9.figshare.1581499
title: A new species of baenid turtle from the Kaiparowits Formation (Upper Cretaceous, Campanian) of southern Utah

description: ABSTRACTNewly discovered baenid turtle specimens from the middle Campanian Kaiparowits Formation of southern Utah are described herein as a new taxon, <i>Arvinachelys goldeni</i>, gen. et sp. nov. The holotype consists of a nearly complete articulated skeleton and shell. The skull was scanned using micro-computed tomography (μCT) to gain a better understanding of its internal anatomy. This baenid possesses two distinct external nares almost completely separated by a dorsal projection of the premaxillae and a ventral extension of the nasals, an autapomorphic feature among known baenid taxa. The skull is wedge-shaped with a broad rostrum and laterally expanded nasals. The importance of skull/shell associations is exemplified by <i>Arvinachelys goldeni</i>, because isolated shells attributable to this taxon had previously been assigned to the genus <i>Plesiobaena</i>, whereas phylogenetic analysis of more complete material supports a sister relationship with the Maastrichtian taxon <i>Hayemys latifrons</i>. These taxa are relatively basal within the Baenodda, a nested clade within Baenidae. The general shell morphology exhibited by <i>Plesiobaena antiqua</i>, <i>Peckemys brinkman</i>, and <i>Palatobaena cohen</i> was previously hypothesized to support a monophyletic clade that included those three taxa, along with <i>Cedrobaena putorius</i>, <i>Gamerabaena sonsalla</i>, <i>Palatobaena bairdi</i>, and <i>Palatobaena gaffneyi</i>. However, the inclusion of <i>Arvinachelys goldeni</i>, gen. et sp. nov., in a phylogenetic analysis of Baenidae indicates that the character states exhibited by those taxa are representative of plesiomorphic states within Baenodda, and the phylogenetic relationships within this clade are in need of reevaluation.http://zoobank.org/urn:lsid:zoobank.org:pub:A5C5717C-4962-4056-8563-2C90C3276FDFSUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Lively, J. R. 2015. A new species of baenid turtle from the Kaiparowits Formation (Upper Cretaceous, Campanian) of southern Utah. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1009084.