cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6938516
title: Iterative Proportional Scaling Revisited: A Modern Optimization Perspective

description: This article revisits the classic iterative proportional scaling (IPS) from a modern optimization perspective. In contrast to the criticisms made in the literature, we show that based on a coordinate descent characterization, IPS can be slightly modified to deliver coefficient estimates, and from a majorization-minimization standpoint, IPS can be extended to handle log-affine models with features not necessarily binary-valued or nonnegative. Furthermore, some state-of-the-art optimization techniques such as block-wise computation, randomization, and momentum-based acceleration can be employed to provide more scalable IPS algorithms, as well as some regularized variants of IPS for concurrent feature selection. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6938525.v1
title: Detecting Structural Differences in Tail Dependence of Financial Time Series

description: An accurate assessment of tail inequalities and tail asymmetries of financial returns is key for risk management and portfolio allocation. We propose a new test procedure for detecting the full extent of such structural differences in the dependence of bivariate extreme returns. We decompose the testing problem into piecewise multiple comparisons of Cramér–von Mises distances of tail copulas. In this way, tail regions that cause differences in extreme dependence can be located and consequently be targeted by financial strategies. We derive the asymptotic properties of the test and provide a bootstrap approximation for finite samples. Moreover, we account for the multiplicity of the piecewise tail copula comparisons by adjusting individual <i>p</i>-values according to multiple testing techniques. Monte Carlo simulations demonstrate the test’s superior finite-sample properties for common financial tail risk models, both in the iid and the sequentially dependent case. During the last 90 years in U.S. stock markets, our test detects up to 20% more tail asymmetries than competing tests. This can be attributed to the presence of nonstandard tail dependence structures. We also find evidence for diminishing tail asymmetries during every major financial crisis—except for the 2007–2009 crisis—reflecting a risk-return trade-off for extreme returns. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6938516.v1
title: Iterative Proportional Scaling Revisited: A Modern Optimization Perspective

description: This article revisits the classic iterative proportional scaling (IPS) from a modern optimization perspective. In contrast to the criticisms made in the literature, we show that based on a coordinate descent characterization, IPS can be slightly modified to deliver coefficient estimates, and from a majorization-minimization standpoint, IPS can be extended to handle log-affine models with features not necessarily binary-valued or nonnegative. Furthermore, some state-of-the-art optimization techniques such as block-wise computation, randomization, and momentum-based acceleration can be employed to provide more scalable IPS algorithms, as well as some regularized variants of IPS for concurrent feature selection. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6938498
title: The treatment of refractory angle-closure glaucoma in a patient with X-linked juvenile retinoschisis

description: X-Linked Retinoschisis (XLRS) is a common genetically determined form of macular degeneration affecting young males. XLRS is due to mutations in the RS1 gene located on chromosome Xp22 which codes for retinoschisin and is estimated to affect between 1:5000 to 1:20000 individuals worldwide. We report a case of refractory angle-closure glaucoma in a thirty-nine-year-old Caucasian man with atypical XLRS. The patient presented with a two-day history of left eye pain, acutely reduced vision and a nine-month history of hemicranial pain. Examination identified left intraocular pressure (IOP) of 52mmHg. Gonioscopy confirmed complete angle closure. Following failure of medical management and persistently raised left IOP (43-46mmHg), the patient underwent left phacoemulsification and intraocular lens insertion without complication. After surgery, his IOP reduced to 10-14mmHg on all follow up examinations without the need for glaucoma drops. His iridocorneal angle remained open and vision improved to 20/100. Our case demonstrates the additional role of lens surgery in the treatment of secondary angle-closure glaucoma in the presence of an inherited retinal dystrophy. All patients with inherited retinopathy presenting with a headache or eye pain should undergo gonioscopic examination to exclude angle-closure glaucoma.
DOI: 10.6084/m9.figshare.6938498.v1
title: The treatment of refractory angle-closure glaucoma in a patient with X-linked juvenile retinoschisis

description: X-Linked Retinoschisis (XLRS) is a common genetically determined form of macular degeneration affecting young males. XLRS is due to mutations in the RS1 gene located on chromosome Xp22 which codes for retinoschisin and is estimated to affect between 1:5000 to 1:20000 individuals worldwide. We report a case of refractory angle-closure glaucoma in a thirty-nine-year-old Caucasian man with atypical XLRS. The patient presented with a two-day history of left eye pain, acutely reduced vision and a nine-month history of hemicranial pain. Examination identified left intraocular pressure (IOP) of 52mmHg. Gonioscopy confirmed complete angle closure. Following failure of medical management and persistently raised left IOP (43-46mmHg), the patient underwent left phacoemulsification and intraocular lens insertion without complication. After surgery, his IOP reduced to 10-14mmHg on all follow up examinations without the need for glaucoma drops. His iridocorneal angle remained open and vision improved to 20/100. Our case demonstrates the additional role of lens surgery in the treatment of secondary angle-closure glaucoma in the presence of an inherited retinal dystrophy. All patients with inherited retinopathy presenting with a headache or eye pain should undergo gonioscopic examination to exclude angle-closure glaucoma.
DOI: 10.6084/m9.figshare.6938486
title: Multiresolution Network Models

description: Many existing statistical and machine learning tools for social network analysis focus on a single level of analysis. Methods designed for clustering optimize a global partition of the graph, whereas projection-based approaches (e.g., the latent space model in the statistics literature) represent in rich detail the roles of individuals. Many pertinent questions in sociology and economics, however, span multiple scales of analysis. Further, many questions involve comparisons across disconnected graphs that will, inevitably be of different sizes, either due to missing data or the inherent heterogeneity in real-world networks. We propose a class of network models that represent network structure on multiple scales and facilitate comparison across graphs with different numbers of individuals. These models differentially invest modeling effort within subgraphs of high density, often termed communities, while maintaining a parsimonious structure between said subgraphs. We show that our model class is projective, highlighting an ongoing discussion in the social network modeling literature on the dependence of inference paradigms on the size of the observed graph. We illustrate the utility of our method using data on household relations from Karnataka, India. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6938486.v1
title: Multiresolution network models

description: Many existing statistical and machine learning tools for social network analysis focus on a single level of analysis. Methods designed for clustering optimize a global partition of the graph, whereas projection based approaches (e.g. the latent space model in the statistics literature) represent in rich detail the roles of individuals. Many pertinent questions in sociology and economics, however, span multiple scales of analysis. Further, many questions involve comparisons across disconnected graphs that will, inevitably be of different sizes, either due to missing data or the inherent heterogeneity in real-world networks. We propose a class of network models that represent network structure on multiple scales and facilitate comparison across graphs with different numbers of individuals. These models differentially invest modeling effort within subgraphs of high density, often termed communities, while maintaining a parsimonious structure between said subgraphs. We show that our model class is projective, highlighting an ongoing discussion in the social network modeling literature on the dependence of inference paradigms on the size of the observed graph. We illustrate the utility of our method using data on household relations from Karnataka, India.
DOI: 10.6084/m9.figshare.6938486.v2
title: Multiresolution Network Models

description: Many existing statistical and machine learning tools for social network analysis focus on a single level of analysis. Methods designed for clustering optimize a global partition of the graph, whereas projection-based approaches (e.g., the latent space model in the statistics literature) represent in rich detail the roles of individuals. Many pertinent questions in sociology and economics, however, span multiple scales of analysis. Further, many questions involve comparisons across disconnected graphs that will, inevitably be of different sizes, either due to missing data or the inherent heterogeneity in real-world networks. We propose a class of network models that represent network structure on multiple scales and facilitate comparison across graphs with different numbers of individuals. These models differentially invest modeling effort within subgraphs of high density, often termed communities, while maintaining a parsimonious structure between said subgraphs. We show that our model class is projective, highlighting an ongoing discussion in the social network modeling literature on the dependence of inference paradigms on the size of the observed graph. We illustrate the utility of our method using data on household relations from Karnataka, India. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6938486.v3
title: Multiresolution Network Models

description: Many existing statistical and machine learning tools for social network analysis focus on a single level of analysis. Methods designed for clustering optimize a global partition of the graph, whereas projection-based approaches (e.g., the latent space model in the statistics literature) represent in rich detail the roles of individuals. Many pertinent questions in sociology and economics, however, span multiple scales of analysis. Further, many questions involve comparisons across disconnected graphs that will, inevitably be of different sizes, either due to missing data or the inherent heterogeneity in real-world networks. We propose a class of network models that represent network structure on multiple scales and facilitate comparison across graphs with different numbers of individuals. These models differentially invest modeling effort within subgraphs of high density, often termed communities, while maintaining a parsimonious structure between said subgraphs. We show that our model class is projective, highlighting an ongoing discussion in the social network modeling literature on the dependence of inference paradigms on the size of the observed graph. We illustrate the utility of our method using data on household relations from Karnataka, India. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6938477.v1
title: Quantile-Regression Inference With Adaptive Control of Size

description: Regression quantiles have asymptotic variances that depend on the conditional densities of the response variable given regressors. This article develops a new estimate of the asymptotic variance of regression quantiles that leads any resulting Wald-type test or confidence region to behave as well in large samples as its infeasible counterpart in which the true conditional response densities are embedded. We give explicit guidance on implementing the new variance estimator to control adaptively the size of any resulting Wald-type test. Monte Carlo evidence indicates the potential of our approach to deliver powerful tests of heterogeneity of quantile treatment effects in covariates with good size performance over different quantile levels, data-generating processes, and sample sizes. We also include an empirical example. Supplementary material is available online.
DOI: 10.6084/m9.figshare.6938459
title: Adaptive evolution of synchronous egg-hatching in compensation for the loss of parental care

description: Data for the paper "Adaptive evolution of synchronous egg-hatching in compensation for the loss of parental care". alldat.csv contains the data on the skew found in the experimental evolution populations, and skew.csv contains the data for the experimental manipulation of skew.
DOI: 10.6084/m9.figshare.6938459.v1
title: Adaptive evolution of synchronous egg-hatching in compensation for the loss of parental care

description: Data for the paper "Adaptive evolution of synchronous egg-hatching in compensation for the loss of parental care". alldat.csv contains the data on the skew found in the experimental evolution populations, and skew.csv contains the data for the experimental manipulation of skew.
DOI: 10.6084/m9.figshare.6938456
title: Cost effectiveness of short term medical service trips - Data

description: CSV files of pre/post surveys of health science students volunteering on a medical service trip. Data on costs and changes in cultural competence.
DOI: 10.6084/m9.figshare.6938438
title: Nonparametric change point detection in multivariate piecewise stationary time series

description: Detecting change points in multivariate time series is an important problem with numerous applications. We develop a nonparametric method to detect multiple change points in multivariate piecewise stationary processes when the locations and number of change points are unknown. Based on a test statistic that measures differences in the spectral density matrices through the norm, we sequentially identify points of local maxima in the test statistic and test for the significance of each of them being change points. In addition, the components responsible for the change in the covariance structure at each detected change point are identified. The asymptotic properties of the test for significant change points under the null and alternative hypothesis are derived. We illustrate the better performance of our method in comparison to some of the recent methods through a few simulation examples and discuss applications of our method in seismology and finance.
DOI: 10.6084/m9.figshare.6938438.v1
title: Nonparametric change point detection in multivariate piecewise stationary time series

description: Detecting change points in multivariate time series is an important problem with numerous applications. We develop a nonparametric method to detect multiple change points in multivariate piecewise stationary processes when the locations and number of change points are unknown. Based on a test statistic that measures differences in the spectral density matrices through the norm, we sequentially identify points of local maxima in the test statistic and test for the significance of each of them being change points. In addition, the components responsible for the change in the covariance structure at each detected change point are identified. The asymptotic properties of the test for significant change points under the null and alternative hypothesis are derived. We illustrate the better performance of our method in comparison to some of the recent methods through a few simulation examples and discuss applications of our method in seismology and finance.
DOI: 10.6084/m9.figshare.6938372
title: ttc9_tt9b alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938366
title: picalm_snap91 alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938369
title: rhoub_rhov alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938372.v1
title: ttc9_tt9b alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938369.v1
title: rhoub_rhov alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938360
title: fut4_fut9 alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938363
title: itpka_itpkb_itpkc alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938366.v1
title: picalm_snap91 alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938360.v1
title: fut4_fut9 alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938363.v1
title: itpka_itpkb_itpkc alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938354
title: aadacl1_aadacl2_nceh1a alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938357
title: fndc3a_fndc3b alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938357.v1
title: fndc3a_fndc3b alignment

description: This alignment has been used to reconstruct the phylogeny shown in Fig. S1 of the manuscript.
DOI: 10.6084/m9.figshare.6938348
title: Bmp16 alignment

description: This alignment has been used as input file for phylogenetic tree inference using PhyloBayes (Fig. 3A in the manuscript).
DOI: 10.6084/m9.figshare.6938348.v1
title: Bmp16 alignment

description: This alignment has been used as input file for phylogenetic tree inference using PhyloBayes (Fig. 3A in the manuscript).
DOI: 10.6084/m9.figshare.6938333
title: Bmp2/4/16 alignment

description: This alignment has been used as input file for phylogenetic tree inference using PhyloBayes (Fig. 1 in the manuscript).
DOI: 10.6084/m9.figshare.6938333.v1
title: Bmp2/4/16 alignment

description: This alignment has been used as input file for phylogenetic tree inference using PhyloBayes (Fig. 1 in the manuscript).
DOI: 10.6084/m9.figshare.6938270
title: First microbial-archaeocyathan boundstone record from early Cambrian erratic cobbles in glacial diamictite deposits of Namibia (Dwyka Group, Carboniferous)

description: This study records the first occurrence of a lower Cambrian archaeocyathan fauna in limestone cobbles from Carboniferous glacigenic deposits of the Dwyka Group of the Aranos Basin in Namibia. Petrographic and microfacies analysis of 17 large, middle and standard thin sections reveals two distinctive limestone cobble facies: (a) bioclastic wackestone-packstone (hyoliths, trilobites, chancelloriids, crinoids and archaeocyaths); and (b) microbial-archaeocyathan boundstone dominated by calcimicrobes (<i>Epiphyton</i> and <i>Renalcis</i>), neomorphosed microbial crusts and crypto-fibrous calcite crusts around mainly regular archaeocyaths such as <i>Polycoscinus scutatus</i>, where encrusting ?sponges are accessory. The published stratigraphical and palaeocurrent data from the Dwyka Group, as well as published ages and the tectonothermal history of the underlying Nama Group, have been used in this study to establish the provenance of these lower Cambrian cobbles. The archaeocyaths from the Aranos Basin are: <i>Favilynthus contractus</i>, <i>Ajacicyathus aequitriens</i>, <i>Kisasacyathus subacutus</i>, <i>Plicocyathus</i> sp., <i>Erismacoscinus endutus</i>, <i>Erismacoscinus ganigobisensis</i> sp. nov., <i>Erismacoscinus</i> cf. <i>stephensoni</i>, <i>Polycoscinus scutatus</i>, <i>Chabakovicyathus</i> sp., Loculicyathidae gen. et sp. indet., <i>Dictyocyathus aranosensis</i> sp. nov., <i>Graphoscyphia</i> sp., <i>Archaeopharetra irregularis</i> and <i>Syringocnema favus</i>. The presence of <i>Syringocnema favus</i> and other species allows us to determine a precise upper Stage 3 or early-mid Botoman age for the erratic cobbles of the Dwyka Group from the Aranos Basin. The Namibian fauna reported here provides a key record in Cambrian palaeobiogeography based on archaeocyathan assemblages. The archaeocyath faunal assemblage from the Dwyka cobbles is diverse and has an analogous richness to allochthonous assemblages from Permo-Carboniferous glacigenic deposits of other localities in south-western Gondwana. Thus, the archaeocyath-bearing cobbles from the Dwyka Group of Namibia could provide a better understanding of the different palaeo-ice flow direction models of the Permo-Carboniferous glacial deposits in future palaeogeographical reconstructions of south-western Gondwana. http://zoobank.org/urn:lsid:zoobank.org:pub:0365EE4C-D7FA-4C09-89DF-27C9E1F55511
DOI: 10.6084/m9.figshare.6938252
title: JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

description: The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.