cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4214502.v3
title: Adaptive Shrinkage in Bayesian Vector Autoregressive Models

description: Vector autoregressive (VAR) models are frequently used for forecasting and impulse response analysis. For both applications, shrinkage priors can help improving inference. In this article, we apply the Normal-Gamma shrinkage prior to the VAR with stochastic volatility case and derive its relevant conditional posterior distributions. This framework imposes a set of normally distributed priors on the autoregressive coefficients and the covariance parameters of the VAR along with Gamma priors on a set of local and global prior scaling parameters. In a second step, we modify this prior setup by introducing another layer of shrinkage with scaling parameters that push certain regions of the parameter space to zero. Two simulation exercises show that the proposed framework yields more precise estimates of model parameters and impulse response functions. In addition, a forecasting exercise applied to U.S. data shows that this prior performs well relative to other commonly used specifications in terms of point and density predictions. Finally, performing structural inference suggests that responses to monetary policy shocks appear to be reasonable.
DOI: 10.6084/m9.figshare.4214502.v2
title: Adaptive Shrinkage in Bayesian Vector Autoregressive Models

description: Vector autoregressive (VAR) models are frequently used for forecasting and impulse response analysis. For both applications, shrinkage priors can help improving inference. In this article, we apply the Normal-Gamma shrinkage prior to the VAR with stochastic volatility case and derive its relevant conditional posterior distributions. This framework imposes a set of normally distributed priors on the autoregressive coefficients and the covariance parameters of the VAR along with Gamma priors on a set of local and global prior scaling parameters. In a second step, we modify this prior setup by introducing another layer of shrinkage with scaling parameters that push certain regions of the parameter space to zero. Two simulation exercises show that the proposed framework yields more precise estimates of model parameters and impulse response functions. In addition, a forecasting exercise applied to U.S. data shows that this prior performs well relative to other commonly used specifications in terms of point and density predictions. Finally, performing structural inference suggests that responses to monetary policy shocks appear to be reasonable.
DOI: 10.5281/zenodo.4013302
title: Perl et al 2020 Substantial variability in morphological scaling among bumblebee colonies

description: Data and R code for the submitted manuscript Perl et al 2020 Substantial variability in morphological scaling among bumblebee colonies
DOI: 10.6084/m9.figshare.4214400
title: Genomics of a revived breed case study of the Belgian Campine cattle

description: Genotypes and breed information for the study "Genomics of a revived breed case study of the Belgian Campine cattle"
DOI: 10.6084/m9.figshare.4214400.v1
title: Genomics of a revived breed case study of the Belgian Campine cattle

description: Genotypes and breed information for the study "Genomics of a revived breed case study of the Belgian Campine cattle"
DOI: 10.6084/m9.figshare.4214376
title: Data from Zebrafish embryonic development is induced by carp sperm

description: Data collected during the experiments described
DOI: 10.6084/m9.figshare.4214373
title: Supplementary Data from Bacteria facilitate prey retention by the pitcher plant <i>Darlingtonia californica</i>

description: Statistical results and raw data used in experiment
DOI: 10.6084/m9.figshare.4214340
title: Discovery of Lower Cretaceous hydrothermal vent complexes in a late rifting setting, southern North Sea: insights from 3D imaging

description: Tables of seismic attributes and the geometry of the vent complexes as well as a 3D visualisation of the vents.
DOI: 10.6084/m9.figshare.4214340.v1
title: Discovery of Lower Cretaceous hydrothermal vent complexes in a late rifting setting, southern North Sea: insights from 3D imaging

description: Tables of seismic attributes and the geometry of the vent complexes as well as a 3D visualisation of the vents.
DOI: 10.6084/m9.figshare.4214334
title: Learning new meanings for known words: biphasic effects of prior knowledge

description: Long after knowing the meaning of roller-“skate”, one may learn that “skate” is also a kind of fish. Such learning of new meanings for familiar words involves two potentially contrasting processes: form-based familiarity may facilitate the learning, and meaning-based interference may be inhibitory. We had native speakers learn new meanings for familiar and less familiar words, as well as for unfamiliar (novel) words. Tracking learning at several points revealed a biphasic pattern: higher learning rates and greater learning efficiency for familiar words relative to novel words early in learning and a reversal of this pattern later. After meaning learning, lexical access to familiar, but not to less familiar, words became faster than exposure controls. Overall, the results suggest that form-based familiarity facilitates learning earlier, while meaning-based interference becomes more influential later. The co-activation of new and old meanings during learning may play a role in lexicalisation of new meanings.
DOI: 10.6084/m9.figshare.4214334.v1
title: Learning new meanings for known words: biphasic effects of prior knowledge

description: Long after knowing the meaning of roller-“skate”, one may learn that “skate” is also a kind of fish. Such learning of new meanings for familiar words involves two potentially contrasting processes: form-based familiarity may facilitate the learning, and meaning-based interference may be inhibitory. We had native speakers learn new meanings for familiar and less familiar words, as well as for unfamiliar (novel) words. Tracking learning at several points revealed a biphasic pattern: higher learning rates and greater learning efficiency for familiar words relative to novel words early in learning and a reversal of this pattern later. After meaning learning, lexical access to familiar, but not to less familiar, words became faster than exposure controls. Overall, the results suggest that form-based familiarity facilitates learning earlier, while meaning-based interference becomes more influential later. The co-activation of new and old meanings during learning may play a role in lexicalisation of new meanings.
DOI: 10.6084/m9.figshare.4214292
title: Metallogenesis and hydrothermal evolution of Middle Jurassic porphyry Mo deposits in the southern Zhangguangcai Range, NE China: evidence from fluid inclusions, H–O–S isotopes, and Re–Os geochronology

description: A major metallogenic belt with substantial resources of gold, lead, zinc, copper, and molybdenum is present in the southern Zhangguangcai Range, NE China. Several large porphyry Mo deposits are located in this belt, as for example at Jidetun, Fu’anpu, and Daheishan. Five molybdenite samples from the Jidetun deposit yielded an Re–Os isochron age of 168.6 ± 2.1 Ma (mean standard weighted deviation = 0.20), and this is consistent with the Re–Os isochron ages of the other Mo deposits in the southern Zhangguangcai Range, giving a Middle Jurassic age for metallogenesis. The Jidetun, Fu’anpu, and Daheishan deposits all tend to have weakly enriched <sup>34</sup>S values of 0.80‰–3.20‰ and relatively low Re contents ranging from 3.073 to 43.567 ppm, which indicates the ore-forming materials were derived mainly from granitic magmas that had an origin in the mixture of crust and mantle. Three stages of mineralization can be identified in the deposits at Jidetun, Fu’anpu, and Daheishan. The original ore-forming fluids in stage I were characterized by high-temperature magmatic hydrothermal fluids that were most likely derived by exsolution from the Middle Jurassic ore-bearing magmas. However, two different fluid systems, NaCl–H<sub>2</sub>O–CO<sub>2</sub> fluids and NaCl–H<sub>2</sub>O fluids, were widespread in stage I of porphyry Mo deposits in the southern Zhangguangcai Range. Taking into account the regional geological characteristics and tectonic setting, we suggest that two different emplacement modes of the ore-bearing magmas explain the different fluid systems in stage I: the first magmas were emplaced along the contact zones between the strata and earlier granitoids, whereas the second magmas were emplaced entirely within the earlier granitoid intrusions. The stage II and III fluids were characterized by relatively lower temperatures and low H–O isotopic values, indicating a gradual evolution from magmatic to meteoric sources.
DOI: 10.6084/m9.figshare.4214295
title: Probing binding mechanism of interleukin-6 and olokizumab: <i>in silico</i> design of potential lead antibodies for autoimmune and inflammatory diseases

description: Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated <i>in silico</i> to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag − Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag − Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.
DOI: 10.6084/m9.figshare.4214295.v1
title: Probing binding mechanism of interleukin-6 and olokizumab: <i>in silico</i> design of potential lead antibodies for autoimmune and inflammatory diseases

description: Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated <i>in silico</i> to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag − Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag − Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.
DOI: 10.6084/m9.figshare.4214292.v1
title: Metallogenesis and hydrothermal evolution of Middle Jurassic porphyry Mo deposits in the southern Zhangguangcai Range, NE China: evidence from fluid inclusions, H–O–S isotopes, and Re–Os geochronology

description: A major metallogenic belt with substantial resources of gold, lead, zinc, copper, and molybdenum is present in the southern Zhangguangcai Range, NE China. Several large porphyry Mo deposits are located in this belt, as for example at Jidetun, Fu’anpu, and Daheishan. Five molybdenite samples from the Jidetun deposit yielded an Re–Os isochron age of 168.6 ± 2.1 Ma (mean standard weighted deviation = 0.20), and this is consistent with the Re–Os isochron ages of the other Mo deposits in the southern Zhangguangcai Range, giving a Middle Jurassic age for metallogenesis. The Jidetun, Fu’anpu, and Daheishan deposits all tend to have weakly enriched <sup>34</sup>S values of 0.80‰–3.20‰ and relatively low Re contents ranging from 3.073 to 43.567 ppm, which indicates the ore-forming materials were derived mainly from granitic magmas that had an origin in the mixture of crust and mantle. Three stages of mineralization can be identified in the deposits at Jidetun, Fu’anpu, and Daheishan. The original ore-forming fluids in stage I were characterized by high-temperature magmatic hydrothermal fluids that were most likely derived by exsolution from the Middle Jurassic ore-bearing magmas. However, two different fluid systems, NaCl–H<sub>2</sub>O–CO<sub>2</sub> fluids and NaCl–H<sub>2</sub>O fluids, were widespread in stage I of porphyry Mo deposits in the southern Zhangguangcai Range. Taking into account the regional geological characteristics and tectonic setting, we suggest that two different emplacement modes of the ore-bearing magmas explain the different fluid systems in stage I: the first magmas were emplaced along the contact zones between the strata and earlier granitoids, whereas the second magmas were emplaced entirely within the earlier granitoid intrusions. The stage II and III fluids were characterized by relatively lower temperatures and low H–O isotopic values, indicating a gradual evolution from magmatic to meteoric sources.
DOI: 10.6084/m9.figshare.4214271
title: World Health Organization disability assessment schedule 2.0: An international systematic review

description: <b>Purpose:</b> This systematic review examines research and practical applications of the World Health Organization Disability Assessment Schedule (WHODAS 2.0) as a basis for establishing specific criteria for evaluating relevant international scientific literature. The aims were to establish the extent of international dissemination and use of WHODAS 2.0 and analyze psychometric research on its various translations and adaptations. In particular, we wanted to highlight which psychometric features have been investigated, focusing on the factor structure, reliability, and validity of this instrument. <b>Method:</b> Following Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) methodology, we conducted a search for publications focused on “whodas” using the ProQuest, PubMed, and Google Scholar electronic databases. <b>Results:</b> We identified 810 studies from 94 countries published between 1999 and 2015. WHODAS 2.0 has been translated into 47 languages and dialects and used in 27 areas of research (40% in psychiatry). <b>Conclusions:</b> The growing number of studies indicates increasing interest in the WHODAS 2.0 for assessing individual functioning and disability in different settings and individual health conditions. The WHODAS 2.0 shows strong correlations with several other measures of activity limitations; probably due to the fact that it shares the same disability latent variable with them. Implications for RehabilitationWHODAS 2.0 seems to be a valid, reliable self-report instrument for the assessment of disability.The increasing interest in use of the WHODAS 2.0 extends to rehabilitation and life sciences rather than being limited to psychiatry.WHODAS 2.0 is suitable for assessing health status and disability in a variety of settings and populations.A critical issue for rehabilitation is that a single “minimal clinically important .difference” score for the WHODAS 2.0 has not yet been established. WHODAS 2.0 seems to be a valid, reliable self-report instrument for the assessment of disability. The increasing interest in use of the WHODAS 2.0 extends to rehabilitation and life sciences rather than being limited to psychiatry. WHODAS 2.0 is suitable for assessing health status and disability in a variety of settings and populations. A critical issue for rehabilitation is that a single “minimal clinically important .difference” score for the WHODAS 2.0 has not yet been established.
DOI: 10.6084/m9.figshare.4214283.v2
title: UMA Fall Detection Dataset

description: The files contain the mobility traces generated by a group of 17 experimental subjects that emulated a set of predetermined ADL (Activities of Daily Life) and falls. The traces are aimed at evaluating fall detection algorithms.Several video clips describing the performed movements are also included.
DOI: 10.6084/m9.figshare.4214271.v1
title: World Health Organization disability assessment schedule 2.0: An international systematic review

description: <b>Purpose:</b> This systematic review examines research and practical applications of the World Health Organization Disability Assessment Schedule (WHODAS 2.0) as a basis for establishing specific criteria for evaluating relevant international scientific literature. The aims were to establish the extent of international dissemination and use of WHODAS 2.0 and analyze psychometric research on its various translations and adaptations. In particular, we wanted to highlight which psychometric features have been investigated, focusing on the factor structure, reliability, and validity of this instrument. <b>Method:</b> Following Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) methodology, we conducted a search for publications focused on “whodas” using the ProQuest, PubMed, and Google Scholar electronic databases. <b>Results:</b> We identified 810 studies from 94 countries published between 1999 and 2015. WHODAS 2.0 has been translated into 47 languages and dialects and used in 27 areas of research (40% in psychiatry). <b>Conclusions:</b> The growing number of studies indicates increasing interest in the WHODAS 2.0 for assessing individual functioning and disability in different settings and individual health conditions. The WHODAS 2.0 shows strong correlations with several other measures of activity limitations; probably due to the fact that it shares the same disability latent variable with them. Implications for RehabilitationWHODAS 2.0 seems to be a valid, reliable self-report instrument for the assessment of disability.The increasing interest in use of the WHODAS 2.0 extends to rehabilitation and life sciences rather than being limited to psychiatry.WHODAS 2.0 is suitable for assessing health status and disability in a variety of settings and populations.A critical issue for rehabilitation is that a single “minimal clinically important .difference” score for the WHODAS 2.0 has not yet been established. WHODAS 2.0 seems to be a valid, reliable self-report instrument for the assessment of disability. The increasing interest in use of the WHODAS 2.0 extends to rehabilitation and life sciences rather than being limited to psychiatry. WHODAS 2.0 is suitable for assessing health status and disability in a variety of settings and populations. A critical issue for rehabilitation is that a single “minimal clinically important .difference” score for the WHODAS 2.0 has not yet been established.
DOI: 10.6084/m9.figshare.4214283.v3
title: UMAFall: Fall Detection Dataset (Universidad de Malaga)

description: The files contain the mobility traces generated by a group of 17 experimental subjects that emulated a set of predetermined ADL (Activities of Daily Life) and falls. The traces are aimed at evaluating fall detection algorithms.Several video clips describing the performed movements are also included.
DOI: 10.6084/m9.figshare.4214208
title: File name: Nicholson_et_al_manual_splits_9Myr_splits_ESM Title: Time binsDescription: File containing temporal bin information for use in Shareholder Quorum Subsampling analyses from Latitudinal diversity gradients in Mesozoic non-marine turtles

description: The latitudinal biodiversity gradient (LBG)–the pattern of increasing taxonomic richness with decreasing latitude–is prevalent in the structure of the modern biota. However, some freshwater taxa show peak richness at mid-latitudes; for example, extant Testudines (turtles, terrapins and tortoises) exhibit their greatest diversity at 25° N, a pattern sometimes attributed to recent bursts of climatically mediated species diversification. Here, we test whether this pattern also characterizes the Mesozoic distribution of turtles, to determine whether it was established during either their initial diversification or as a more modern phenomenon. Using global occurrence data for non-marine testudinate genera, we find that subsampled richness peaks at palaeolatitudes of 15 – 30° N in the Jurassic, 30 – 45° N through the Cretaceous to the Campanian, and from 30° to 60° N in the Maastrichtian. The absence of a significant diversity peak in southern latitudes is consistent with results from climatic models and turtle niche modelling that demonstrate a dearth of suitable turtle habitat in Gondwana during the Jurassic and Late Cretaceous. Our analyses confirm that the modern testudinate LBG has a deep-time origin and further demonstrate that LBGs are not always expressed as a smooth, equator-to-pole distribution.
DOI: 10.6084/m9.figshare.4214205
title: File name: Nicholson_et_al_Dataset_2_ESM.xlsx Title: Dataset 2Description: Calculations for palaeo-non-marine area at 15 degree palaeolatitudinal bands for Jurassic, Lower Cretaceous and Upper Cretaceous time bins used in GLS analyses from Latitudinal diversity gradients in Mesozoic non-marine turtles

description: The latitudinal biodiversity gradient (LBG)–the pattern of increasing taxonomic richness with decreasing latitude–is prevalent in the structure of the modern biota. However, some freshwater taxa show peak richness at mid-latitudes; for example, extant Testudines (turtles, terrapins and tortoises) exhibit their greatest diversity at 25° N, a pattern sometimes attributed to recent bursts of climatically mediated species diversification. Here, we test whether this pattern also characterizes the Mesozoic distribution of turtles, to determine whether it was established during either their initial diversification or as a more modern phenomenon. Using global occurrence data for non-marine testudinate genera, we find that subsampled richness peaks at palaeolatitudes of 15 – 30° N in the Jurassic, 30 – 45° N through the Cretaceous to the Campanian, and from 30° to 60° N in the Maastrichtian. The absence of a significant diversity peak in southern latitudes is consistent with results from climatic models and turtle niche modelling that demonstrate a dearth of suitable turtle habitat in Gondwana during the Jurassic and Late Cretaceous. Our analyses confirm that the modern testudinate LBG has a deep-time origin and further demonstrate that LBGs are not always expressed as a smooth, equator-to-pole distribution.