Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird ...species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
For COVID-19, it is vital to understand if quarantines shorter than 14 days can be equally effective with judiciously deployed testing. Here, we develop a mathematical model that quantifies the ...probability of post-quarantine transmission incorporating testing into travel quarantine, quarantine of traced contacts with an unknown time of infection, and quarantine of cases with a known time of exposure. We find that testing on exit (or entry and exit) can reduce the duration of a 14-day quarantine by 50%, while testing on entry shortens quarantine by at most one day. In a real-world test of our theory applied to offshore oil rig employees, 47 positives were obtained with testing on entry and exit to quarantine, of which 16 had tested negative at entry; preventing an expected nine offshore transmission events that each could have led to outbreaks. We show that appropriately timed testing can make shorter quarantines effective.
A
bstract
The generic scale-invariant theory of an axion and a dilaton coupled to gravity in
d
-dimensions is generalized to a ‘universal’ one-axion model with two dilatons that reproduces itself ...under consistent dimensional-reduction/truncation. Flat FLRW cosmologies are shown to correspond to trajectories of a three-dimensional autonomous dynamical system, which we analyse with a focus on accelerated cosmic expansion, deriving the precise swampland bounds that exclude eternal acceleration. We also show that for two sets of values of its three independent parameters, the model is a consistent truncation of maximal ‘massive’ supergravity theories arising from string/M-theory; for these maximal-supergravity parameter values the FLRW cosmologies include some with a transient de Sitter-like phase, but not the recurring de Sitter-like phase or eternal cosmic acceleration that is possible for other parameter values.
Strategies for containing Ebola in West Africa Pandey, Abhishek; Atkins, Katherine E.; Medlock, Jan ...
Science (American Association for the Advancement of Science),
11/2014, Letnik:
346, Številka:
6212
Journal Article
Recenzirano
Odprti dostop
The ongoing Ebola outbreak poses an alarming risk to the countries of West Africa and beyond. To assess the effectiveness of containment strategies, we developed a stochastic model of Ebola ...transmission between and within the general community, hospitals, and funerals, calibrated to incidence data from Liberia. We find that a combined approach of case isolation, contact-tracing with quarantine, and sanitary funeral practices must be implemented with utmost urgency in order to reverse the growth of the outbreak. As of 19 September, under status quo, our model predicts that the epidemic will continue to spread, generating a predicted 224 (134 to 358) daily cases by 1 December, 280 (184 to 441) by 15 December, and 348 (249 to 545) by 30 December.
Among the most consequential unknowns of the devastating COVID-19 pandemic are the durability of immunity and time to likely reinfection. There are limited direct data on SARS-CoV-2 long-term immune ...responses and reinfection. The aim of this study is to use data on the durability of immunity among evolutionarily close coronavirus relatives of SARS-CoV-2 to estimate times to reinfection by a comparative evolutionary analysis of related viruses SARS-CoV, MERS-CoV, human coronavirus (HCoV)-229E, HCoV-OC43, and HCoV-NL63.
We conducted phylogenetic analyses of the S, M, and ORF1b genes to reconstruct a maximum-likelihood molecular phylogeny of human-infecting coronaviruses. This phylogeny enabled comparative analyses of peak-normalised nucleocapsid protein, spike protein, and whole-virus lysate IgG antibody optical density levels, in conjunction with reinfection data on endemic human-infecting coronaviruses. We performed ancestral and descendent states analyses to estimate the expected declines in antibody levels over time, the probabilities of reinfection based on antibody level, and the anticipated times to reinfection after recovery under conditions of endemic transmission for SARS-CoV-2, as well as the other human-infecting coronaviruses.
We obtained antibody optical density data for six human-infecting coronaviruses, extending from 128 days to 28 years after infection between 1984 and 2020. These data provided a means to estimate profiles of the typical antibody decline and probabilities of reinfection over time under endemic conditions. Reinfection by SARS-CoV-2 under endemic conditions would likely occur between 3 months and 5·1 years after peak antibody response, with a median of 16 months. This protection is less than half the duration revealed for the endemic coronaviruses circulating among humans (5–95% quantiles 15 months to 10 years for HCoV-OC43, 31 months to 12 years for HCoV-NL63, and 16 months to 12 years for HCoV-229E). For SARS-CoV, the 5–95% quantiles were 4 months to 6 years, whereas the 95% quantiles for MERS-CoV were inconsistent by dataset.
The timeframe for reinfection is fundamental to numerous aspects of public health decision making. As the COVID-19 pandemic continues, reinfection is likely to become increasingly common. Maintaining public health measures that curb transmission—including among individuals who were previously infected with SARS-CoV-2—coupled with persistent efforts to accelerate vaccination worldwide is critical to the prevention of COVID-19 morbidity and mortality.
US National Science Foundation.
We investigate the implications of energy conditions on cosmological compactification solutions of the higher-dimensional Einstein field equations. It is known that the strong energy condition ...forbids time-independent compactifications to de Sitter space but allows time-dependent compactifications to other (homogeneous and isotropic) expanding universes that undergo a transient period of acceleration. Here we show that the same assumptions allow compactification to FLRW universes undergoing late-time accelerated expansion; the late-time stress tensor is a perfect fluid but with a lower bound on the pressure/energy-density ratio that excludes de Sitter but allows accelerated power-law expansion. The compact space undergoes a decelerating expansion that leads to decompactification, but on an arbitrarily long timescale.
ABSTRACTAlzheimer's disease (AD) is the most common form of neurodegenerative disorder with dementia in the elderly. The AD brain pathology is characterized by deposits of amyloid‐β (Aβ) peptides and ...neurofibrillary tangles but also (among other aspects) by signs of a chronic inflammatory process. Epidemiological studies have shown that long‐term use of nonsteroidal anti‐inflammatory drugs (NSAIDs) reduces the risk of developing AD and delays its onset. Classical targets of NSAIDs include cycloxygenase, nuclear factor κB, and peroxisome proliferator‐activated receptors. Modulation of these pathways, all of which have been implicated in AD pathogenesis, could explain the NSAID effect on AD progression. However, recent studies indicate that a subset of NSAIDs such as ibuprofen, indomethacin, and flurbiprofen may have direct Aβ‐lowering properties in cell cultures as well as transgenic models of AD‐like amyloidosis. A renewed interest in the old and a discovery of new pharmacological properties of these drugs are providing vital insight for future clinical trials. In this review we will summarize how the combination of traditional (anti‐inflammatory) and new (anti‐amyloidogenic) properties of some NSAIDs is providing unprecedented opportunities for drug discovery and could potentially result in novel therapeutic approaches for the treatment of AD. Townsend K. P., Praticò D. Novel therapeutic opportunities for Alzheimer's disease: focus on nonsteroidal anti‐inflammatory drugs. FASEB J. 19, 1592–1601 (2005)
Many aspects of the evolutionary process of tumorigenesis that are fundamental to cancer biology and targeted treatment have been challenging to reveal, such as the divergence times and genetic ...clonality of metastatic lineages. To address these challenges, we performed tumor phylogenetics using molecular evolutionary models, reconstructed ancestral states of somatic mutations, and inferred cancer chronograms to yield three conclusions. First, in contrast to a linear model of cancer progression, metastases can originate from divergent lineages within primary tumors. Evolved genetic changes in cancer lineages likely affect only the proclivity toward metastasis. Single genetic changes are unlikely to be necessary or sufficient for metastasis. Second, metastatic lineages can arise early in tumor development, sometimes long before diagnosis. The early genetic divergence of some metastatic lineages directs attention toward research on driver genes that are mutated early in cancer evolution. Last, the temporal order of occurrence of driver mutations can be inferred from phylogenetic analysis of cancer chronograms, guiding development of targeted therapeutics effective against primary tumors and metastases.
Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting ...body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The area of North American forests affected by gypsy moth defoliation continues to expand despite efforts to slow the spread. With the increased area of infestation, ecological, environmental and ...economic concerns about gypsy moth disturbance remain significant, necessitating coordinated, repeatable and comprehensive monitoring of the areas affected. In this study, our primary objective was to estimate the magnitude of defoliation using Moderate Resolution Imaging Spectroradiometer (MODIS) imagery for a gypsy moth outbreak that occurred in the US central Appalachian Mountains in 2000 and 2001. We focused on determining the appropriate spectral MODIS indices and temporal compositing method to best monitor the effects of gypsy moth defoliation. We tested MODIS-based Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), Normalized Difference Water Index (NDWI), and two versions of the Normalized Difference Infrared Index (NDIIb6 and NDIIb7, using the channels centered on 1640 nm and 2130 nm respectively) for their capacity to map defoliation as estimated by ground observations. In addition, we evaluated three temporal resolutions: daily, 8-day and 16-day data. We validated the results through quantitative comparison to Landsat based defoliation estimates and traditional sketch maps. Our MODIS based defoliation estimates based on NDIIb6 and NDIIb7 closely matched Landsat defoliation estimates derived from field data as well as sketch maps. We conclude that daily MODIS data can be used with confidence to monitor insect defoliation on an annual time scale, at least for larger patches (>
0.63 km
2). Eight-day and 16-day MODIS composites may be of lesser use due to the ephemeral character of disturbance by the gypsy moth.
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