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Figure 6 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty

Figure 6. Ventral view of the head scales of Death Adder specimens from Melbourne Museum, and close up of Gerard Krefft's illustration of the ventral head scales of the Death Adder collected at Lake Boga in 1857 (bottom right). Top left is specimen D3579. Top right is D51857. Bottom left is D4349.

Figure 1 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty

Figure 1. South-eastern Australia, showing records of the death adder Acanthophis antarcticus (black dots; Atlas of Living Australia, year) and key localities discussed in the text.

Figure 2. Specimen D4349, a in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty

Figure 2. Specimen D4349, a death adder Acanthophis antarcticus in the collection of Museums Victoria.

Figure 5 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty

Figure 5. Illustration by Gerard Krefft of the death adder collected at Lake Boga in north-western Victoria on the 8 March 1857. (Photograph by Rebecca Carland; Museum of Natural History Berlin. Historical collection of pictures and writings. [Sigel: MfN, HBSB.] Bestand: Zool. Mus. Signatur: B VIII/56.)

opencc-by-4.0Apr 2023View details →

Figure 1 in Acanthodian fauna from the Early Devonian (Emsian) of Death Valley, California

Figure 1. Map showing the position and geology of the fossil locality (Elliott and Ilyes 1996, fig. 1).

opencc-by-4.0Apr 2023View details →

Figure 2. Ischnacanthiform acanthodian dermal elements. A in Acanthodian fauna from the Early Devonian (Emsian) of Death Valley, California

Figure 2. Ischnacanthiform acanthodian dermal elements. A, fin spine FMNH-PF14560; B, fin spine fragment FMNH-PF14561. C, D, dentigerous jaw bone FMNH-PF14562, labial view; boxed area in C is enlarged in D. Scale bars=0.5 mm in A–C, 0.1 mm in D. Arrow indicates rostral direction.

opencc-by-4.0Apr 2023View details →

Figure 3. Acanthodian fin spines and scapulocoracoid. A-C in Acanthodian fauna from the Early Devonian (Emsian) of Death Valley, California

Figure 3. Acanthodian fin spines and scapulocoracoid. A-C, Bryantonchus peracutus: A, B complete spine FMNH-PF14564; C, proximal end of spine FMNH-PF14568. D, E, Machaeracanthus sp.: D, incomplete spine FMNH-PF14573, lateral view; E, abraded spine FMNH-PF14574, dorsoventrally compressed. F-H, acanthodian indet. scapulocoracoid: F, counterpart FMNH-PF14575; G, part FMNH-PF14576; H, outline sketch. Abbreviations: IEB, insertion-exsertion boundary; k/w, worn keel or wing; plac, placoderm plate; le, leading edge; te, trailing edge; teg, trailing edge groove. Scale bars=0.5 mm in A, C–E, 0.1 mm in B, F–H.

opencc-by-4.0Nov 2021View details →

Incidents of death and missing people on migratory routes around the world

<pre>Dataset with data on incidents of people dead or missing on international migratory routes in different regions, from the website https://missingmigrants.iom.int/, from the Missing Migrants Project of the International Organisation for Migration (IOM). </pre>

opencc-by-4.0Nov 2021View details →

Outdoor air pollution impacts chronic obstructive pulmonary disease deaths in South Asia and China: a systematic review and meta-analysis

Background: Chronic obstructive pulmonary disease (COPD) is among leading causes of death globally. Exposure to outdoor pollution is an important cause for increased mortality and morbidity. This study presents a systemic review regarding the impact of outdoor pollution on COPD mortality in South Asia and China. Methods: A systematic search was conducted from 1990 to June 30th 2020 in English electronic databases: PubMed, Google Scholar and CDSR (Cochrane Database of Systematic Reviews) following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The following terms were used: Chronic Obstructive Pulmonary disease OR COPD OR Chronic Bronchitis OR Emphysema OR COPD Deaths OR Chronic Obstructive Lung Disease OR Airflow Obstruction OR Chronic Airflow Obstruction OR Airflow Obstruction, Chronic OR Bronchitis, Chronic AND Mortality OR Death OR Deceased AND Outdoor pollution, ambient pollution was conducted. Results: Out of 1899 papers screened only 17 were found eligible to be included. Subjects with COPD exposed to higher levels of outdoor air pollution had a 49% higher risk of death as compared to COPD subjects exposed to lower levels of outdoor air pollution. When taking common air pollutants individually into consideration, PM10 had an odds ratio (OR) of 1.99 respectively at CI 95%, whereas SO2 had OR of 1.8 at 95% CI, and NO2 had an OR of 1.23 OR at 95% CI. These values suggest that there is an effect of outdoor pollution on COPD but not to a significant level. Conclusion: Despite heterogeneity across selected studies, individuals exposed to outdoor pollutants were found to be at risk of COPD mortality. Though it appears to have risk, COPD mortality was not significantly associated with outdoor pollutants. Controlling air pollution can substantially decrease the risk of COPD in South Asia and China. Further researches including more prospective and longitudinal studies are urgently needed in COPD sub-groups.

opencc-zeroDec 2021View details →

Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of "total-evidence" analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct the past number of lineages. Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the COVID-19 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.

opencc-by-4.0Dec 2020View details →

[Data from:] Genetic Analysis Reveals Three Novel QTLs Underpinning a Butterfly Egg-Induced Hypersensitive Response-Like Cell Death in Brassica Rapa

Background Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa. Results A germplasm screening of B. rapa 56 accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 contains also LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract. Conclusions This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.

opencc-by-4.0Feb 2022View details →

Diabetes-related excess mortality in Mexico: a comparative analysis of national death registries between 2017-2019 and 2020

Dataset to replicate the article "Diabetes-related excess mortality in Mexico: a comparative analysis of national death registries between 2017-2019 and 2020" available in MedRxiv at: https://www.medrxiv.org/content/10.1101/2022.02.24.22271337v1 Code available at: https://github.com/oyaxbell/diabetes_excess

opencc-by-4.0Feb 2022View details →

Sphingolipids are involved in Pieris brassicae egg-induced cell death in Arabidopsis thaliana

This table contains mean + SEM values of sphingolipid levels by LC-MS analysis in Arabidopsis thaliana (wild-type and mutant lines) and Brassica nigra (wild-type) in response to egg extract of Pieris brassicae, as well as P-values for selected comparisons by Welsch t-test. These data were used for Fig. 7 and Fig. 8 of Groux et al. 2022

opencc-zeroApr 2022View details →

Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating

Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)". For two specific datasets, involving divergence time estimation for the early radiations of ants, bees and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme, and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed, or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of the Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach available currently for addressing DRA in total-evidence dating.

opencc-zeroJul 2022View details →

The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2

Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process which gives rise to the phylogeny. Existing birth-death diversification models include a wide range of features, for instance lineage-specific variations in speciation and extinction rates. While across-lineage variation in speciation and extinction rates is widespread in empirical datasets, few heterogeneous rate models have been implemented as tree priors for Bayesian phylogenetic inference. As a consequence, rate heterogeneity is typically ignored when reconstructing phylogenies, and rate heterogeneity is usually investigated on fixed trees. In this paper, we present a new BEAST2 package implementing the cladogenetic diversification rate shift (ClaDS) model as a tree prior. ClaDS is a birth-death diversification model designed to capture small progressive variations in birth and death rates along a phylogeny. Unlike previous implementations of ClaDS, which were designed to be used with fixed, user-chosen phylogenies, our package is implemented in the BEAST2 framework and thus allows full phylogenetic inference, where the phylogeny and model are co-estimated from a molecular alignment. Our package provides all necessary components of the inference, including a new tree object and operators to propose moves to the MCMC. It also includes a graphical interface through BEAUti. We validate our implementation of the package by comparing the produced distributions to simulated data, and show an empirical example of the full inference, using a cetaceans dataset.

opencc-zeroOct 2022View details →

Species-specific effects and the ecological role of Programmed cell Death in the microalgae Ankistrodesmus (Sphaeropleales, Selenastraceae)

Reports of programmed cell death (PCD) in phytoplankton raise questions about the ecological evolutionary role of cell death in these organisms. We induced PCD by nitrogen deprivation and unregulated cell death (non-PCD) in one strain of the green microalga Ankistrodesmus densus and investigated the effects of the cell death supernatants on phylogenetically related co-occurring organisms using growth rates and maximum biomass as proxies of fitness. PCD-released materials from A. densus CCMA-UFSCar-3 significantly increased growth rates of two conspecific strains compared to healthy culture (HC) supernatants and improved the maximum biomass of all A. densus strains compared to related species. Although growth rates of non-A. densus with PCD supernatants were not statistically different from HC treatment, biomass gain was significantly reduced. Thus, the organic substances released by PCD, possibly nitrogenous compounds, could promote conspecific growth. These results support the argument that PCD may differentiate species or subtypes and increases inclusive fitness in this model unicellular chlorophyte. Further research, however, is needed to identify the responsible molecules and how they interact with cells to provide the PCD benefits.

opencc-by-4.0May 2024View details →

DEATH IN "LIVE BROADCAST"

Supplementary Table S1 Valid ethological categories of trace fossils (based on Vallon et al. 2016, related references inside).   Supplementary Table S2 Overview of published specimens of trace fossils with preserved tracemaker (related references inside).

opencc-by-4.0Feb 2020View details →

Рис. 1. Птицы, погибшие от стоΛкновений с оконными стекΛами в г. Уссурийске осенью 2019 г. Фото Δ. А. БеΛяева Fig. 1. Birds that died as a result of window collisions in Ussuriysk in the autumn of 2019. Photo by D. A. Belyaev in Deaths Resulting From Bird Window Collisions In Ussuriysk (Primorsky Krai)

Рис. 1. Птицы, погибшие от стоΛкновений с оконными стекΛами в г. Уссурийске осенью 2019 г. Фото Δ. А. БеΛяева Fig. 1. Birds that died as a result of window collisions in Ussuriysk in the autumn of 2019. Photo by D. A. Belyaev

opencc-by-4.0May 2024View details →

Dataset of molecular structures of PNAS article " Ca2+ permeation through C-terminal cleaved, but not full-length human Pannexin1 hemichannels, mediates cell death"

The PMFWT_91_80.tar.gz file contains the WT molecular system described in the cited article. Briefly, the package contains the structure and topology files for AMBER software, along with configuration files to run Umbrella Sampling method and calculation of PMF of a Ca+2 ion traslocating the human pannexin channel (WT).  The TRUCWT_91_80.tar.gz file contains the truncated molecular system described in the cited article. Briefly, the package contains the structure and topology files for AMBER software, along with configuration files to run Umbrella Sampling method and calculation of PMF of a Ca+2 ion traslocating the truncated human pannexin channel as described in the article. Two NetCDF trajectories (*.nc) of a single PMF window are provided for each system.