A Review of the fossil record of turtles of the clade Pan-Kinosternoidea

Turtles of the total clade Pan-Kinosternoidea have a relatively poor fossil record that extends back to the Late Cretaceous (Campanian). The clade is found only in North America during its early history, but dispersed to Central America no later than the Miocene and to South America no later than the Pleistocene. Ancestral pan-kinosternoids were likely aquatic, bottom-walking omnivores or carnivores that preferred low-energy freshwater habitats. The Pan-Dermatemys lineage is often recovered in more fluvial habitats, and some are specialized to feed on aquatic vegetation. Alternatively, many representatives of Kinosternon evolved specializations (e.g., plastral lobe kinesis) that allowed them to successfully inhabit and disperse across more terrestrial habitats such as savannas and floodplains. A taxonomic review of the group concludes that of 42 named taxa, 27 are nomina valida (including two species of the controversial taxon Planetochelys), 14 are nomina invalida and only one a nomen dubium

Effect of the COVID-19 Pandemic on Patient Volumes, Acuity, and Outcomes in Pediatric Emergency Departments: A Nationwide Study

Objectives The aim of this study was to quantify the effect of the COVID-19 pandemic on pediatric emergency department (ED) utilization and outcomes. Methods This study is an interrupted-Time-series observational study of children presenting to 11 Canadian tertiary-care pediatric EDs. Data were grouped into weeks in 3 study periods: prepandemic (January 1, 2018-January 27, 2020), peripandemic (January 28, 2020-March 10, 2020), and early pandemic (March 11, 2020-April 30, 2020). These periods were compared with the same time intervals in the 2 preceding calendar years. Primary outcomes were number of ED visits per week. The secondary outcomes were triage acuity, hospitalization, intensive care unit (ICU) admission, mortality, length of hospital stay, ED revisits, and visits for trauma and mental health concerns. Results There were 577,807 ED visits (median age, 4.5 years; 52.9% male). Relative to the prepandemic period, there was a reduction [-58%; 95% confidence interval (CI),-63% to-51%] in the number of ED visits during the early-pandemic period, with concomitant higher acuity. There was a concurrent increase in the proportion of ward [odds ratio (OR), 1.39; 95% CI, 1.32-1.45] and intensive care unit (OR, 1.20; 95% CI, 1.01-1.42) admissions, and trauma-related ED visits among children less than 10 years (OR, 1.51; 95% CI, 1.45-1.56). Mental health-related visits in children declined in the early-pandemic period (in \u3c10 years,-60%; 95% CI,-67% to-51%; in children ≥10 years:-56%; 95% CI,-63% to-47%) relative to the pre-COVID-19 period. There were no differences in mortality or length of stay; however, ED revisits within 72 hours were reduced during the early-pandemic period (percent change:-55%; 95% CI,-61% to-49%; P \u3c 0.001). Conclusions After the declaration of the COVID-19 pandemic, dramatic reductions in pediatric ED visits occurred across Canada. Children seeking ED care were sicker, and there was an increase in trauma-related visits among children more than 10 years of age, whereas mental health visits declined during the early-pandemic period. When faced with a future pandemic, public health officials must consider the impact of the illness and the measures implemented on children\u27s health and acute care needs

Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes

Large numbers of sequence elements have been identified to be highly conserved among vertebrate genomes. These highly conserved elements (HCEs) are often located in or around genes that are involved in transcription regulation and early development. They have been shown to be involved in cis-regulatory activities through both in vivo and additional computational studies. We have investigated the structural relationships between such elements and genes in six vertebrate genomes human, mouse, rat, chicken, zebrafish and tetraodon and detected several thousand cases of conserved HCE-gene associations, and also cases of HCEs with no common target genes. A few examples underscore the potential significance of our findings about several individual genes. We found that the conserved association between HCE/HCEs and gene/genes are not restricted to elements by their absolute distance on the genome. Notably, long-range associations were identified and the molecular functions of the associated genes do not show any particular overrepresentation of the functional categories previously reported. HCEs in close proximity are found to be linked with different set of gene/genes. The results reflect the highly complex correlation between HCEs and their putative target genes

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Data from: New mud turtles (Kinosternidae, Kinosternon) from the Middle-Late Miocene of the United States

Kinosternon Spix, 1824, was widespread in xeric to savanna associated paleowetlands across North America during the middle–late Miocene and steadily diversified following its first occurrences in the Hemingfordian. In the middle Miocene, Kinosternon rincon n. sp. occurred in the late Barstovian Cerro Conejo Formation of north central New Mexico, perhaps concurrently with Kinosternon pojoaque Bourque 2012a from the Tesuque Formation. Subsequent late Miocene kinosternine fossils indicate that at least three potentially contemporaneous species existed throughout the Clarendonian. These are Kinosternon pannekollops n. sp., from the Ogallala Formation of northern Texas; Kinosternon wakeeniense, n. sp., from the Ogallala Formation of northwestern Kansas and Ash Hollow Formation of south-central Nebraska; and Kinosternon notolophus n. sp., from the Alachua and Statenville formations of northern Florida. Kinosternon rincon is phylogenetically nested between the Kinosternon flavescens (Agassiz, 1857) group (=Platythyra Agassiz, 1857) and more derived Kinosternon including the Kinosternon subrubrum (Lacépède, 1788) group (=Thyrosternum Agassiz, 1857). Kinosternon pannekollops is recovered on the stem of the K. subrubrum group and is the oldest and largest member of that lineage. Kinosternon notolophus is readily differentiated from other Miocene Kinosternon in possessing a distinct dorsomedial keel on the nuchal and faint dorsolateral costal carination. The K. subrubrum group probably originated in the late Miocene savannas of the Great Plains and dispersed eastward via the Gulf Coastal Plain. An unnamed kinosternine taxon existed in the coastal plains of the eastern and southeastern United States during the Middle Miocene Climatic Optimum (with fossils from ~18 to 15 Ma), and disappeared from the region coincident with the end of that megathermal event

Bourque Appendix 2 Revision2

character/taxon matrix used in phylogenetic analysis (in Excel format

Bourque Appendix 1 Revision2

description of characters used in phylogenetic analysi

Bourque matrix Revision2

character/taxon matrix used in phylogenetic analysi