Equivalence of pathologists' and rule-based parser's annotations of Dutch pathology reports

Introduction: In the Netherlands, pathology reports are annotated using a nationwide pathology network (PALGA) thesaurus. Annotations must address topography, procedure, and diagnosis. The Pathology Report Annotation Module (PRAM) can be used to annotate the report conclusion with PALGA-compliant code series. The equivalence of these generated annotations to manual annotations is unknown. We assess the equivalence of annotations by authoring pathologists, pathologists participating in this study, and PRAM. Methods: New annotations were created for one thousand histopathology reports by the PRAM and a pathologist panel. We calculated dissimilarity of annotations using a semantic distance measure, Minimal Transition Cost (MTC). In absence of a gold standard, we compared dissimilarity scores having one common annotator. The resulting comparisons yielded a measure for the coding dissimilarity between PRAM, the pathologist panel and the authoring pathologist. To compare the comprehensiveness of the coding methods, we assessed number and length of the annotations. Results: Eight of the twelve comparisons of dissimilarity scores were significantly equivalent. Non-equivalent score pairs involved dissimilarity between the code series by the original pathologist and the panel pathologists. Coding dissimilarity was lowest for procedures, highest for diagnoses: MTC overall = 0.30, topographies = 0.22, procedures = 0.13, diagnoses = 0.33. Both number and length of annotations per report increased with report conclusion length, mostly in PRAM-annotated conclusions: conclusion length ranging from 2 to 373 words, number of annotations ranged from 1 to 10 for pathologists, 1–19 for PRAM, annotation length ranged from 3 to 43 codes for pathologists, 4–123 for PRAM. Conclusions: We measured annotation similarity among PRAM, authoring pathologists and panel pathologists. Annotating by PRAM, the panel pathologists and to a lesser extent by the authoring pathologist was equivalent. Therefore, the use of annotations by PRAM in a practical setting is justified. PRAM annotations are equivalent to study-setting annotations, and more comprehensive than routine coding. Further research on annotation quality is needed

Arctic cut-off high drives the poleward shift of a new Greenland melting record

Large-scale atmospheric circulation controls the mass and energy balance of the Greenland ice sheet through its impact on radiative budget, runoff and accumulation. Here, using reanalysis data and the outputs of a regional climate model, we show that the persistence of an exceptional atmospheric ridge, centred over the Arctic Ocean, was responsible for a poleward shift of runoff, albedo and surface temperature records over the Greenland during the summer of 2015. New records of monthly mean zonal winds at 500 hPa and of the maximum latitude of ridge peaks of the 5,700±50 m isohypse over the Arctic were associated with the formation and persistency of a cutoff high. The unprecedented (1948–2015) and sustained atmospheric conditions promoted enhanced runoff, increased the surface temperatures and decreased the albedo in northern Greenland, while inhibiting melting in the south, where new melting records were set over the past decade

A comparative study of different model families for the constitutive simulation of viscous clays

The simulation of the viscous behavior of some clays is of high importance in many geotechnical problems. The literature offers a vast amount of constitutive models able to simulate the rate dependence observed on these materials. Although most of thesemodels are calibrated to very similar experimental observations and share similar definitions ofmaterial parameters, some discrepancies of their response have been detected, which are related to their mathematical formulations. In this work, the causes of these discrepancies are carefully studied. To that end, four different model families are analyzed, namely, nonstationary flow surface (NSFS) models, viscoplasticity with overstress function (OVP), viscoplasticity with Norton\u27s power law (NVP), and visco-hypoplasticity (VHP). For the sake of a fair comparison, single constitutive models using the same set of material parameters, and following other requirements, are developed for each model family. Numerical implementations of the four resulting models are performed. Their response at different tests are carefully analyzed through simulation examples and direct examination of their constitutive equations. The set includes some basic tests at isotropic stress states and others as responses envelopes, undrained creep rupture, and an oedometer test with loading, unloading-reloading, creep, and relaxation. The article is concluded with some remarks about the observed discrepancies of these model families

CCN2/Connective Tissue Growth Factor Is Essential for Pericyte Adhesion and Endothelial Basement Membrane Formation during Angiogenesis

CCN2/Connective Tissue Growth Factor (CTGF) is a matricellular protein that regulates cell adhesion, migration, and survival. CCN2 is best known for its ability to promote fibrosis by mediating the ability of transforming growth factor β (TGFβ) to induce excess extracellular matrix production. In addition to its role in pathological processes, CCN2 is required for chondrogenesis. CCN2 is also highly expressed during development in endothelial cells, suggesting a role in angiogenesis. The potential role of CCN2 in angiogenesis is unclear, however, as both pro- and anti-angiogenic effects have been reported. Here, through analysis of Ccn2-deficient mice, we show that CCN2 is required for stable association and retention of pericytes by endothelial cells. PDGF signaling and the establishment of the endothelial basement membrane are required for pericytes recruitment and retention. CCN2 induced PDGF-B expression in endothelial cells, and potentiated PDGF-B-mediated Akt signaling in mural (vascular smooth muscle/pericyte) cells. In addition, CCN2 induced the production of endothelial basement membrane components in vitro, and was required for their expression in vivo. Overall, these results highlight CCN2 as an essential mediator of vascular remodeling by regulating endothelial-pericyte interactions. Although most studies of CCN2 function have focused on effects of CCN2 overexpression on the interstitial extracellular matrix, the results presented here show that CCN2 is required for the normal production of vascular basement membranes

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

Gene expression actualizes the organismal phenotypes encoded within the genome in an environment-dependent manner. Among all encoded phenotypes, cell population growth rate (fitness) is perhaps the most important, since it determines how well-adapted a genotype is in various environments. Traditional biological measurement techniques have revealed the connection between the environment and fitness based on the gene expression mean. Yet, recently it became clear that cells with identical genomes exposed to the same environment can differ dramatically from the population average in their gene expression and division rate (individual fitness). For cell populations with bimodal gene expression, this difference is particularly pronounced, and may involve stochastic transitions between two cellular states that form distinct sub-populations. Currently it remains unclear how a cell population's growth rate and its subpopulation fractions emerge from the molecular-level kinetics of gene networks and the division rates of single cells. To address this question we developed and quantitatively characterized an inducible, bistable synthetic gene circuit controlling the expression of a bifunctional antibiotic resistance gene in Saccharomyces cerevisiae. Following fitness and fluorescence measurements in two distinct environments (inducer alone and antibiotic alone), we applied a computational approach to predict cell population fitness and subpopulation fractions in the combination of these environments based on stochastic cellular movement in gene expression space and fitness space. We found that knowing the fitness and nongenetic (cellular) memory associated with specific gene expression states were necessary for predicting the overall fitness of cell populations in combined environments. We validated these predictions experimentally and identified environmental conditions that defined a “sweet spot” of drug resistance. These findings may provide a roadmap for connecting the molecular-level kinetics of gene networks to cell population fitness in well-defined environments, and may have important implications for phenotypic variability of drug resistance in natural settings

Measurement of the W±Z boson pair-production cross section in pp collisions at √s=13TeV with the ATLAS detector

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Evidence-based Kernels: Fundamental Units of Behavioral Influence

This paper describes evidence-based kernels, fundamental units of behavioral influence that appear to underlie effective prevention and treatment for children, adults, and families. A kernel is a behavior–influence procedure shown through experimental analysis to affect a specific behavior and that is indivisible in the sense that removing any of its components would render it inert. Existing evidence shows that a variety of kernels can influence behavior in context, and some evidence suggests that frequent use or sufficient use of some kernels may produce longer lasting behavioral shifts. The analysis of kernels could contribute to an empirically based theory of behavioral influence, augment existing prevention or treatment efforts, facilitate the dissemination of effective prevention and treatment practices, clarify the active ingredients in existing interventions, and contribute to efficiently developing interventions that are more effective. Kernels involve one or more of the following mechanisms of behavior influence: reinforcement, altering antecedents, changing verbal relational responding, or changing physiological states directly. The paper describes 52 of these kernels, and details practical, theoretical, and research implications, including calling for a national database of kernels that influence human behavior

Charged-particle distributions at low transverse momentum in √s=13 13 TeV pp interactions measured with the ATLAS detector at the LHC

Measurements of distributions of charged particles produced in proton–proton collisions with a centre-of-mass energy of 13 TeV are presented. The data were recorded by the ATLAS detector at the LHC and correspond to an integrated luminosity of 151 μb −1 μb−1 . The particles are required to have a transverse momentum greater than 100 MeV and an absolute pseudorapidity less than 2.5. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity and the dependence of the mean transverse momentum on multiplicity are measured in events containing at least two charged particles satisfying the above kinematic criteria. The results are corrected for detector effects and compared to the predictions from several Monte Carlo event generators

Measurement of the inelastic proton-proton cross section at √s=13 TeV with the ATLAS detector at the LHC

This Letter presents a measurement of the inelastic proton-proton cross section using 60  μb −1 of pp collisions at a center-of-mass energy √s of 13 TeV with the ATLAS detector at the LHC. Inelastic interactions are selected using rings of plastic scintillators in the forward region (2.0710 −6 , where M X is the larger invariant mass of the two hadronic systems separated by the largest rapidity gap in the event. In this ξ range the scintillators are highly efficient. For diffractive events this corresponds to cases where at least one proton dissociates to a system with M X >13  GeV . The measured cross section is compared with a range of theoretical predictions. When extrapolated to the full phase space, a cross section of 78.1±2.9  mb is measured, consistent with the inelastic cross section increasing with center-of-mass energy