The proliferation of digital cameras co-located with eddy covariance instrumentation provides new opportunities to better understand the relationship between canopy phenology and the seasonality of ...canopy photosynthesis. In this paper we analyze the abilities and limitations of canopy color metrics measured by digital repeat photography to track seasonal canopy development and photosynthesis, determine phenological transition dates, and estimate intra-annual and interannual variability in canopy photosynthesis. We used 59 site-years of camera imagery and net ecosystem exchange measurements from 17 towers spanning three plant functional types (deciduous broadleaf forest, evergreen needleleaf forest, and grassland/crops) to derive color indices and estimate gross primary productivity (GPP). GPP was strongly correlated with greenness derived from camera imagery in all three plant functional types. Specifically, the beginning of the photosynthetic period in deciduous broadleaf forest and grassland/crops and the end of the photosynthetic period in grassland/crops were both correlated with changes in greenness; changes in redness were correlated with the end of the photosynthetic period in deciduous broadleaf forest. However, it was not possible to accurately identify the beginning or ending of the photosynthetic period using camera greenness in evergreen needleleaf forest. At deciduous broadleaf sites, anomalies in integrated greenness and total GPP were significantly correlated up to 60 days after the mean onset date for the start of spring. More generally, results from this work demonstrate that digital repeat photography can be used to quantify both the duration of the photosynthetically active period as well as total GPP in deciduous broadleaf forest and grassland/crops, but that new and different approaches are required before comparable results can be achieved in evergreen needleleaf forest.
Abstract
In October, 1865, Paul Bogle and a few hundred Black residents of rural Jamaica rebelled against the vagaries of an overly zealous magistrate. They set the courthouse at Morant Bay on fire ...and killed over a dozen people, mostly white. In the savage government reprisals that followed, over 430 Black Jamaicans were executed. Here, I observe how biblical language played a central role in public discourse about the rebellion. I focus on the rebellion’s slogan: skin for skin. I trace the interpretive history of this phrase drawn from the book of Job, showing how it became associated with advocacy for Black rights. And I examine the social context of Bogle’s use of the phrase to call for a Black alliance that crossed ethnic, religious, and class lines. I thus further a critical trajectory that has recognized the importance of biblical language to race talk in the age of emancipation.
Rising atmospheric carbon dioxide (CO ₂) conditions are driving unprecedented changes in seawater chemistry, resulting in reduced pH and carbonate ion concentrations in the Earth’s oceans. This ocean ...acidification has negative but variable impacts on individual performance in many marine species. However, little is known about the adaptive capacity of species to respond to an acidified ocean, and, as a result, predictions regarding future ecosystem responses remain incomplete. Here we demonstrate that ocean acidification generates striking patterns of genome-wide selection in purple sea urchins (Strongylocentrotus purpuratus) cultured under different CO ₂ levels. We examined genetic change at 19,493 loci in larvae from seven adult populations cultured under realistic future CO ₂ levels. Although larval development and morphology showed little response to elevated CO ₂, we found substantial allelic change in 40 functional classes of proteins involving hundreds of loci. Pronounced genetic changes, including excess amino acid replacements, were detected in all populations and occurred in genes for biomineralization, lipid metabolism, and ion homeostasis—gene classes that build skeletons and interact in pH regulation. Such genetic change represents a neglected and important impact of ocean acidification that may influence populations that show few outward signs of response to acidification. Our results demonstrate the capacity for rapid evolution in the face of ocean acidification and show that standing genetic variation could be a reservoir of resilience to climate change in this coastal upwelling ecosystem. However, effective response to strong natural selection demands large population sizes and may be limited in species impacted by other environmental stressors.
Right ventricular failure from increased pulmonary vascular loading is a major cause of morbidity and mortality, yet its modulation by disease remains poorly understood. We tested the hypotheses ...that, unlike the systemic circulation, pulmonary vascular resistance (R(PA)) and compliance (C(PA)) are consistently and inversely related regardless of age, pulmonary hypertension, or interstitial fibrosis and that this relation may be changed by elevated pulmonary capillary wedge pressure, augmenting right ventricular pulsatile load.
Several large clinical databases with right heart/pulmonary catheterization data were analyzed to determine the R(PA)-C(PA) relationship with pulmonary hypertension, pulmonary fibrosis, patient age, and varying pulmonary capillary wedge pressure. Patients with suspected or documented pulmonary hypertension (n=1009) and normal pulmonary capillary wedge pressure displayed a consistent R(PA)-C(PA) hyperbolic (inverse) dependence, C(PA)=0.564/(0.047+R(PA)), with a near-constant resistance-compliance product (0.48±0.17 seconds). In the same patients, the systemic resistance-compliance product was highly variable. Severe pulmonary fibrosis (n=89) did not change the R(PA)-C(PA) relation. Increasing patient age led to a very small but statistically significant change in the relation. However, elevation of the pulmonary capillary wedge pressure (n=8142) had a larger impact, significantly lowering C(PA) for any R(PA) and negatively correlating with the resistance-compliance product (P<0.0001).
Pulmonary hypertension and pulmonary fibrosis do not significantly change the hyperbolic dependence between R(PA) and C(PA), and patient age has only minimal effects. This fixed relationship helps explain the difficulty of reducing total right ventricular afterload by therapies that have a modest impact on mean R(PA). Higher pulmonary capillary wedge pressure appears to enhance net right ventricular afterload by elevating pulsatile, relative to resistive, load and may contribute to right ventricular dysfunction.
DroID (http://droidb.org/), the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and ...experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. Data in DroID is accessible through user-friendly, intuitive interfaces that allow simple or advanced searches and graphical visualization of interaction networks. DroID has been expanded to include interaction types that enable more complete analyses of the genetic networks that underlie biological processes. In addition to protein-protein and genetic interactions, the database now includes transcription factor-gene and regulatory RNA-gene interactions. In addition, DroID now has more gene expression data that can be used to search and filter interaction networks. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans. Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study.
Long polycytidine (polyC) tracts varying in length from 50 to 400 nucleotides were first described in the 5'-noncoding region (NCR) of genomes of picornaviruses belonging to the Cardio- and ...Aphthovirus genera over 50 years ago, but the molecular basis of their function is still unknown. Truncation or complete deletion of the polyC tracts in picornaviruses compromises virulence and pathogenicity but do not affect replicative fitness in vitro, suggesting a role as "viral security" RNA element. The evidence available suggests that the presence of a long polyC tract is required for replication in immune cells, which impacts viral distribution and targeting, and, consequently, pathogenic progression. Viral attenuation achieved by reduction of the polyC tract length has been successfully used for vaccine strategies. Further elucidation of the role of the polyC tract in viral replication cycle and its connection with replication in immune cells has the potential to expand the arsenal of tools in the fight against cancer in oncolytic virotherapy (OV). Here, we review the published data on the biological significance and mechanisms of action of the polyC tract in viral pathogenesis in Cardio- and Aphthoviruses.
Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of ...viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
Reliable and reproducible methods for identifying PD-L1 expression on tumor cells are necessary to identify responders to anti-PD-1 therapy. We tested the reproducibility of the assessment of PD-L1 ...expression in non-small cell lung cancer (NSCLC) tissue samples by pathologists.
NSCLC samples were stained with PD-L1 22C3 pharmDx kit using the Dako Autostainer Link 48 Platform. Two sample sets of 60 samples each were designed to assess inter- and intraobserver reproducibility considering two cut points for positivity: 1% or 50% of PD-L1 stained tumor cells. A randomization process was used to obtain equal distribution of PD-L1 positive and negative samples within each sample set. Ten pathologists were randomly assigned to two subgroups. Subgroup 1 analyzed all samples on two consecutive days. Subgroup 2 performed the same assessments, except they received a 1-hour training session prior to the second assessment.
For intraobserver reproducibility, the overall percent agreement (OPA) was 89.7% 95% confidence interval (CI), 85.7-92.6 for the 1% cut point and 91.3% (95% CI, 87.6-94.0) for the 50% cut point. For interobserver reproducibility, OPA was 84.2% (95% CI, 82.8-85.5) for the 1% cut point and 81.9% (95% CI, 80.4-83.3) for the 50% cut point, and Cohen's κ coefficients were 0.68 (95% CI, 0.65-0.71) and 0.58 (95% CI, 0.55-0.62), respectively. The training was found to have no or very little impact on intra- or interobserver reproducibility.
Pathologists reported good reproducibility at both 1% and 50% cut points. More adapted training could potentially increase reliability, in particular for samples with PD-L1 proportion, scores around 50%.
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Homoepitaxial diamond has been used to demonstrate the RF performance of 50-nm gate length hydrogen-terminated diamond field-effect transistors. An extrinsic cutoff frequency of 53 GHz is achieved ...which we believe to be the highest value reported for a diamond-based transistor. The generation of an RF small signal equivalent circuit is used to extract device elements to better understand variation between intrinsic and extrinsic operation. An intrinsic cutoff frequency of 90 GHz is extracted through this process, verifying the requirement to minimize access resistance to maximize the potential high-frequency performance of this technology.
Evolutionary dynamics of language systems Greenhill, Simon J.; Wu, Chieh-Hsi; Hua, Xia ...
Proceedings of the National Academy of Sciences - PNAS,
10/2017, Letnik:
114, Številka:
42
Journal Article
Recenzirano
Odprti dostop
Understanding how and why language subsystems differ in their evolutionary dynamics is a fundamental question for historical and comparative linguistics. One key dynamic is the rate of language ...change. While it is commonly thought that the rapid rate of change hampers the reconstruction of deep language relationships beyond 6,000–10,000 y, there are suggestions that grammatical structures might retainmore signal over time than other subsystems, such as basic vocabulary. In this study, we use a Dirichlet process mixture model to infer the rates of change in lexical and grammatical data from 81 Austronesian languages. We show that, on average, most grammatical features actually change faster than items of basic vocabulary. The grammatical data show less schismogenesis, higher rates of homoplasy, and more bursts of contact-induced change than the basic vocabulary data. However, there is a core of grammatical and lexical features that are highly stable. These findings suggest that different subsystems of language have differing dynamics and that careful, nuanced models of language change will be needed to extract deeper signal from the noise of parallel evolution, areal readaptation, and contact.
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