cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8187005
title: The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

description: Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.
DOI: 10.5281/zenodo.8187026
title: The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

description: Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.
DOI: 10.5281/zenodo.10059360
title: The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

description: Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.
DOI: 10.5281/zenodo.8187004
title: The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

description: Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.
DOI: 10.5281/zenodo.8191971
title: The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

description: Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.
DOI: 10.5517/ccdc.csd.cc2b9n0b
title: CCDC 2154221: Experimental Crystal Structure Determination

description: Related Article: Joschua Helmer, Alexander Hepp, Raphael J. F. Berger, Felicitas Lips|2023|Dalton Trans.|52|14949|doi:10.1039/D2DT03952D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c23zk
title: CCDC 2176788: Experimental Crystal Structure Determination

description: Related Article: Junro Yoshino, Yoshito Hirono, Ayako Kaneda, Naoto Hayashi|2023|Dalton Trans.|52|15017|doi:10.1039/D3DT02332J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c24l6
title: CCDC 2176807: Experimental Crystal Structure Determination

description: Related Article: Junro Yoshino, Yoshito Hirono, Ayako Kaneda, Naoto Hayashi|2023|Dalton Trans.|52|15017|doi:10.1039/D3DT02332J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c24tf
title: CCDC 2176814: Experimental Crystal Structure Determination

description: Related Article: Junro Yoshino, Yoshito Hirono, Ayako Kaneda, Naoto Hayashi|2023|Dalton Trans.|52|15017|doi:10.1039/D3DT02332J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c6jvz
title: CCDC 2181031: Experimental Crystal Structure Determination

description: Related Article: Tao Guo, Penghua Hu, Yu Liu, Panke Zhang, Yunhui Zhao, Congjun Zhu|2023|Chem.Commun.|59|12455|doi:10.1039/D3CC03850E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dm0wy
title: CCDC 2222820: Experimental Crystal Structure Determination

description: Related Article: Rafael Contreras-Montoya, James P. Smith, Stephen C. Boothroyd, Juan A. Aguilar, Marzieh Mirzamani, Martin A. Screen, Dmitry S. Yufit, Mark Robertson, Lilin He, Shuo Qian, Harshita Kumari, Jonathan W. Steed|2023|Chemical Science|14|11389|doi:10.1039/D3SC03841F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dm0xz
title: CCDC 2222821: Experimental Crystal Structure Determination

description: Related Article: Rafael Contreras-Montoya, James P. Smith, Stephen C. Boothroyd, Juan A. Aguilar, Marzieh Mirzamani, Martin A. Screen, Dmitry S. Yufit, Mark Robertson, Lilin He, Shuo Qian, Harshita Kumari, Jonathan W. Steed|2023|Chemical Science|14|11389|doi:10.1039/D3SC03841F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dm0y0
title: CCDC 2222822: Experimental Crystal Structure Determination

description: Related Article: Rafael Contreras-Montoya, James P. Smith, Stephen C. Boothroyd, Juan A. Aguilar, Marzieh Mirzamani, Martin A. Screen, Dmitry S. Yufit, Mark Robertson, Lilin He, Shuo Qian, Harshita Kumari, Jonathan W. Steed|2023|Chemical Science|14|11389|doi:10.1039/D3SC03841F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dm0z1
title: CCDC 2222823: Experimental Crystal Structure Determination

description: Related Article: Rafael Contreras-Montoya, James P. Smith, Stephen C. Boothroyd, Juan A. Aguilar, Marzieh Mirzamani, Martin A. Screen, Dmitry S. Yufit, Mark Robertson, Lilin He, Shuo Qian, Harshita Kumari, Jonathan W. Steed|2023|Chemical Science|14|11389|doi:10.1039/D3SC03841F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dm103
title: CCDC 2222824: Experimental Crystal Structure Determination

description: Related Article: Rafael Contreras-Montoya, James P. Smith, Stephen C. Boothroyd, Juan A. Aguilar, Marzieh Mirzamani, Martin A. Screen, Dmitry S. Yufit, Mark Robertson, Lilin He, Shuo Qian, Harshita Kumari, Jonathan W. Steed|2023|Chemical Science|14|11389|doi:10.1039/D3SC03841F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dxwx4
title: CCDC 2232307: Experimental Crystal Structure Determination

description: Related Article: Yu Li, Mei Wang, Rongrong Ma, Rui Niu, Haodong Wang, Yantu Zhang, Jun-Bing Lin|2023|Org.Biomol.Chem.|21|8263|doi:10.1039/D3OB01317K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6073/pasta/95adf6e90b2ba0e032c480c23e2ca1b8
title: Soil moisture, temperature, and electrical conductivity data from the black sand extended growing season length experiment, 2018 - ongoing, hourly.

description: As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how changes in growing season length may affect biotic and abiotic components, NWT LTER researchers established 5 experimental sites each containing a pair 10 x 40m rectangular plots. These blocks include north and south facing aspects, subalpine and alpine tundra meadows in a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot of each block by adding chemically inert black sand, while keeping the second plot as an unmanipulated control (black sand was added to these plots after snow had naturally melted). This dataset includes measurements of soil temperature, moisture, and electrical conductivity.
DOI: 10.6084/m9.figshare.24417277
title: Supplementary Materials for Chapter 4

description: Abstract: Cyanobacteria are crucial primary producers in many ecosystems, transforming light into chemical energy. Their death plays a vital role in releasing organic carbon and nitrogen into the environment for heterotrophs, creating a pathway from the atmosphere to the sediment. With warming waters, algal blooms are becoming more common and larger in size, highlighting the need to understand the underlying mechanisms of death of these blooms. Although the lysis of Cyanobacteria through viral predation is well-documented in marine environments, there has been less exploration of other mechanisms of death, including programmed cell death and its various (a)biotic triggers. In this study, we investigated a sudden and rapid mechanism of cell lysis in an alkaliphilic, filamentous, mat-forming cyanobacterium, Candidatus Sodalinema alkaliphilum, cultivated, with its associated heterotrophs, from alkaline soda lakes.
DOI: 10.6084/m9.figshare.24417277.v1
title: Supplementary Materials for Chapter 4

description: Abstract: Cyanobacteria are crucial primary producers in many ecosystems, transforming light into chemical energy. Their death plays a vital role in releasing organic carbon and nitrogen into the environment for heterotrophs, creating a pathway from the atmosphere to the sediment. With warming waters, algal blooms are becoming more common and larger in size, highlighting the need to understand the underlying mechanisms of death of these blooms. Although the lysis of Cyanobacteria through viral predation is well-documented in marine environments, there has been less exploration of other mechanisms of death, including programmed cell death and its various (a)biotic triggers. In this study, we investigated a sudden and rapid mechanism of cell lysis in an alkaliphilic, filamentous, mat-forming cyanobacterium, Candidatus Sodalinema alkaliphilum, cultivated, with its associated heterotrophs, from alkaline soda lakes.
DOI: 10.18112/openneuro.ds003037.v2.1.0
title: SUDMEX_TMS
DOI: 10.17632/5pp6thh5zd.1
title: ICCB Grid

description: These videos show comparisons between the interlocking between sand and the proposed Isometric Cogged Biaxial Grid, which is denoted as ICBG. The interlocking of the cogs and sand aggregates, besides the confinement within the grid apertures, are compared with the confinement of the Biaxial grid apertures of sand aggregates. The videos show the end of the pull-out tests when the surcharge and pull-out loads were released in each case of soil reinforcement.
DOI: 10.17632/vb8fxrhjt9.1
title: Multidimensional poverty and growth: Evidence from India 1998–2021

description: Data for the paper "Multidimensional poverty and growth: Evidence from India 1998–2021"
DOI: 10.17632/6ss7f276mb.2
title: upload test

description: it's a test upload
DOI: 10.17632/kgf5fhrwjm.1
title: baseline hematological parameters - influenza vaccination

description: This data contain characteristics of study's subjects and also 3 hematological parameters (neutrophils, lymphocytes, monocytes)
DOI: 10.17632/8sxf8tvwgm.1
title: European consensus for the diagnosis of MCI _QUADAS-II assessment

description: Using a modified Delphi procedure, a European task force is defining a diagnostic workflow for etiologicical and biomarker-based diagnosis of neurocognitive disorders, in which expert expertise fills evidence gaps for validity and prioritization of biomarkers. The panel of experts is asked to answer a Delphi questionnaire and justify their answers with evidence from the literature. We then provided the experts with data on the diagnostic accuracy of biomarkers (MRI, amyloid PET, tau and FDG, MIBG scintigraphy, DaT-SPECT, EEG and polysomnography) in predicting clinical progression from prodromal stages to mild dementia in neurocognitive disorders.  We assessed the quality of evidence from the included literature using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). The data were recorded in the attached Excel sheet.