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Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics.
Decker, Jared E,Pires, J Chris,Conant, Gavin C,McKay, Stephanie D,Heaton, Michael P,Chen, Kefei,Cooper, Alan,Vilkki, Johanna,Seabury, Christopher M,Caetano, Alexandre R,Johnson, Gary S,Brenneman, Rick National Academy of Sciences 2009 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.106 No.44
<P>The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.</P>
Decker, Zachary C. J.,Zarzana, Kyle J.,Coggon, Matthew,Min, Kyung-Eun,Pollack, Ilana,Ryerson, Thomas B.,Peischl, Jeff,Edwards, Pete,Dubé,, William P.,Markovic, Milos Z.,Roberts, James M.,Veres, American Chemical Society 2019 Environmental science & technology Vol.53 No.5
<P>Biomass burning (BB) is a large source of reactive compounds in the atmosphere. While the daytime photochemistry of BB emissions has been studied in some detail, there has been little focus on nighttime reactions despite the potential for substantial oxidative and heterogeneous chemistry. Here, we present the first analysis of nighttime aircraft intercepts of agricultural BB plumes using observations from the NOAA WP-3D aircraft during the 2013 Southeast Nexus (SENEX) campaign. We use these observations in conjunction with detailed chemical box modeling to investigate the formation and fate of oxidants (NO<SUB>3</SUB>, N<SUB>2</SUB>O<SUB>5</SUB>, O<SUB>3</SUB>, and OH) and BB volatile organic compounds (BBVOCs), using emissions representative of agricultural burns (rice straw) and western wildfires (ponderosa pine). Field observations suggest NO<SUB>3</SUB> production was approximately 1 ppbv hr<SUP>-1</SUP>, while NO<SUB>3</SUB> and N<SUB>2</SUB>O<SUB>5</SUB> were at or below 3 pptv, indicating rapid NO<SUB>3</SUB>/N<SUB>2</SUB>O<SUB>5</SUB> reactivity. Model analysis shows that >99% of NO<SUB>3</SUB>/N<SUB>2</SUB>O<SUB>5</SUB> loss is due to BBVOC + NO<SUB>3</SUB> reactions rather than aerosol uptake of N<SUB>2</SUB>O<SUB>5</SUB>. Nighttime BBVOC oxidation for rice straw and ponderosa pine fires is dominated by NO<SUB>3</SUB> (72, 53%, respectively) but O<SUB>3</SUB> oxidation is significant (25, 43%), leading to roughly 55% overnight depletion of the most reactive BBVOCs and NO<SUB>2</SUB>.</P> [FIG OMISSION]</BR>
Sebastian Decker,Renaud Lafage,Christian Krettek,Robert Hart,Christopher Ames,Justin S. Smith,Douglas Burton,Eric Klineberg,Shay Bess,Frank J. Schwab,Virginie Lafage,International Spine Study Group 대한척추외과학회 2020 Asian Spine Journal Vol.14 No.2
Study Design: Retrospective cohort study. Purpose: To investigate the role of sacral extension (SE) for the development of proximal junctional kyphosis (PJK) in adult spinal deformity (ASD) surgery. Overview of Literature: The development of PJK is multifactorial and different risk factors have been identified. Of these, there is some evidence that SE also affects the development of PJK, but data are insufficient. Methods: Using a combined database comprising two propensity-matched groups of fusions following ASD surgery, one with fixation to S1 or S1 and the ilium (SE) and one without SE but with a lower instrumented vertebra of L5 or higher (lumbar fixation, LF), PJK and the role of further parameters were analyzed. The propensity-matched variables included age, the upper-most instrumented vertebra (UIV), preoperative sagittal alignment, and the baseline to 1 year change of the sagittal alignment. Results: Propensity matching led to two groups of 89 patients each. The UIV, pelvic incidence minus lumbar lordosis, sagittal vertical axis, pelvic tilt, age, and body mass index were similar in both groups (p>0.05). The incidence of PJK at postoperative 1 year was similar for SE (30.3%) and LF (22.5%) groups (p=0.207). The PJK angle was comparable (p=0.963) with a change of −8.2° (SE) and −8.3° (LF) from the preoperative measures (p=0.954). A higher rate of PJK after SE (p=0.026) was found only in the subgroup of patients with UIV levels between T9 and T12. Conclusions: Instrumentation to the sacrum with or without iliac extension did not increase the overall risk of PJK. However, an increased risk for PJK was found after SE with UIV levels between T9 and T12.
Jilyan Decker,Amanda Cavanaugh,Megan Brown,Saverio Ligato,Oscar Kenneth Serrano 한국간담췌외과학회 2021 Annals of hepato-biliary-pancreatic surgery Vol.25 No.4
Intraductal tubulopapillary neoplasms (ITPNs) of the pancreas and biliary tract are rare pre-malignant entities of the biliary tract and pancreas that are difficult to diagnose preoperatively. While there are imaging characteristics that can differentiate these lesions from more common entities like adenocarcinoma or intraductal papillary mucinous neoplasms (IPMN), ITPNs are not always distinctive. Herein we present two cases of ITPN, one of biliary and the other of pancreatic origin, which had a preoperative diagnosis of cholangiocarcinoma and IPMN, respectively. We discuss our findings in these cases, patient presentation and course, review the radiographic and pathologic findings, and propose a more effective approach to the preoperative workup and diagnosis of ITPN based on our review of the contemporary literature.
Clocking the Evolution of Post-starburst Galaxies: Methods and First Results
French, K. Decker,Yang, Yujin,Zabludoff, Ann I.,Tremonti, Christy A. American Astronomical Society 2018 The Astrophysical journal Vol.862 No.1
<P>Detailed modeling of the recent star formation histories (SFHs) of post-starburst (or 'E+A') galaxies is impeded by the degeneracy between the time elapsed since the starburst ended (post-burst age), the fraction of stellar mass produced in the burst (burst strength), and the burst duration. To resolve this issue, we combine GALEX ultraviolet photometry, SDSS photometry and spectra, and new stellar population synthesis models to fit the SFHs of 532 post-starburst galaxies. In addition to an old stellar population and a recent starburst, 48% of the galaxies are best fit with a second recent burst. Lower stellar mass galaxies (log M-*/M-circle dot<10.5) are more likely to experience two recent bursts, and the fraction of their young stellar mass is more strongly anticorrelated with their total stellar mass. Applying our methodology to other, younger post-starburst samples, we identify likely progenitors to our sample and examine the evolutionary trends of molecular gas and dust content with post-burst age. We discover a significant (4 sigma) decline, with a 117-230 Myr characteristic depletion time, in the molecular gas to stellar mass fraction with the post-burst age. The implied rapid gas depletion rate of 2-150 M(circle dot)yr(-1) cannot be due to current star formation, given the upper limits on the current star formation rates in these post-starbursts. Nor are stellar winds or supernova feedback likely to explain this decline. Instead, the decline points to the expulsion or destruction of molecular gas in outflows, a possible smoking gun for active galactic nucleus feedback.</P>