Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering

While technologies for multiplexed imaging have provided an unprecedented understanding of tissue composition in health and disease, interpreting this data remains a significant computational challenge. To understand the spatial organization of tissue and how it relates to disease processes, imaging studies typically focus on cell-level phenotypes. However, images can capture biologically important objects that are outside of cells, such as the extracellular matrix. Here, we describe a pipeline, Pixie, that achieves robust and quantitative annotation of pixel-level features using unsupervised clustering and show its application across a variety of biological contexts and multiplexed imaging platforms. Furthermore, current cell phenotyping strategies that rely on unsupervised clustering can be labor intensive and require large amounts of manual cluster adjustments. We demonstrate how pixel clusters that lie within cells can be used to improve cell annotations. We comprehensively evaluate pre-processing steps and parameter choices to optimize clustering performance and quantify the reproducibility of our method. Importantly, Pixie is open source and easily customizable through a user-friendly interface

Long term outcome in patients with silent versus symptomatic ischaemia during dobutamine stress echocardiography

OBJECTIVES: To compare the long term prognosis of patients having silent versus symptomatic ischaemia during dobutamine stress echocardiography (DSE). DESIGN: Observational study. SETTING: Tertiary referral centre. PATIENTS: 931 patients who experienced stress induced myocardial ischaemia during DSE. RESULTS: Silent ischaemia was present in 643 of 931 patients (69%). The number of dysfunctional segments at rest (mean (SD) 9.6 (5.1) v 8.8 (5.0), p = 0.1) and of ischaemic segments (3.5 (2.2) v 3.8 (2.1), p = 0.2) was comparable in both groups. During a mean (SD) follow up of 5.5 (3.3) years, there were 169 (18%) cardiac deaths and 86 (9%) non-fatal infarctions. Multivariable Cox regression analysis showed age (hazard ratio (HR) 1.1, 95% confidence interval (CI) 1.02 to 1.05), previous myocardial infarction (HR 1.4, 95% CI 1.1 to 2.0), and number of ischaemic segments during the test (HR 2.0, 95% CI 1.0 to 3.7) as independent predictors of cardiac death and myocardial infarction. For every additional ischaemic segment there was a twofold increment in risk of late cardiac events. The annual cardiac death or myocardial infarction rate was 3.0% in patients with symptomatic ischaemia and 4.6% in patients with silent ischaemia (p < 0.01). Silent induced ischaemia was an independent predictor of cardiac death and myocardial infarction (HR 1.7, 95% CI 1.1 to 2.0). During follow up symptomatic patients were treated more often with cardioprotective therapy (p < 0.01) and coronary revascularisation (145 of 288 (50%) v 174 of 643 (27%), p < 0.001). CONCLUSIONS: Patients with silent ischaemia had a similar extent of myocardial ischaemia during DSE compared to patients with symptomatic ischaemia but received less cardioprotective treatment and coronary revascularisation and experienced a higher cardiac event rate

Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats

Based on nine microsatellite loci, the aim of this study was to appraise the genetic diversity of 42 cassava (Manihot esculenta) landraces from selected regions in Brazil, and examine how this variety is distributed according to origin in several municipalities in the states of Minas Gerais, São Paulo, Mato Grosso do Sul, Amazonas and Mato Grosso. High diversity values were found among the five above-mentioned regions, with 3.3 alleles per locus on an average, a high percentage of polymorphic loci varying from 88.8% to 100%, an average of 0.265 for observed heterozygosity and 0.570 for gene diversity. Most genetic diversity was concentrated within the regions themselves (HS = 0.52). Cluster analysis and principal component based scatter plotting showed greater similarity among landraces from São Paulo, Mato Grosso do Sul and Amazonas, whereas those from Minas Gerais were clustered into a sub-group within this group. The plants from Mato Grosso, mostly collected in the municipality of General Carneiro, provided the highest differentiation. The migration of human populations is one among the possible reasons for this closer resemblance or greater disparity among plants from the various regions

Atomistic calculations on interfaces: Bridging the length and time scales

Phase field simulations suitable to describe interfacial phenomena at the mesoscale require as input parameters accurate interfacial energies as well as the interface mobilities. However, this information is not directly accessible by experiment. Furthermore, phenomena such as impurity segregation cannot be decoupled and their independent role in interfacial cohesion and mobility cannot be deduced. On the other hand ab-initio calculations and/or classical interatomic potentials are suitable tools which can provide an on-atomic-scale description of the interfaces. However, there are a number of challenges that one encounters: multidimensional phase space of the interfacial misorientation degrees of freedom, suitable driving forces, and large length and time scales just to mention a few. In the present report we provide an extended review on the atomistic calculations and the simulation strategies proposed to tackle the corresponding problems

A multi-centre, non-inferiority, randomised controlled trial to compare a cervical pessary with a cervical cerclage in the prevention of preterm delivery in women with short cervical length and a history of preterm birth - PC study

Background Preterm birth is in quantity and in severity the most important contributor of perinatal morbidity and mortality both in well- and low-resource countries. Cervical pessary and cervical cerclage are both considered as preventive treatments in women at risk for preterm birth. We aim to evaluate whether a cervical pessary can replace cervical cerclage for preventing recurrent preterm birth in women with a prior preterm birth due to cervical insufficiency or in women with a prior preterm birth and a short cervix in the current pregnancy. Methods/design A nationwide open-label multicentre randomised clinical trial will be set up to study women with a singleton pregnancy and a prior preterm birth before 34 weeks of gestation. Women are eligible in case of previous preterm birth based on cervical insufficiency (primary intervention, <16 weeks) or in case of previous preterm birth and a short cervical length in current pregnancy ≤25 mm (secondary intervention, <24 weeks). Eligible women will be randomised to either cervical pessary or cervical cerclage. Both interventions will be removed at labour or at 36 weeks of gestational age, whatever comes first. The primary outcome will be delivery before 32 weeks. Secondary outcomes will be gestational age at birth, preterm birth rate before 24, 28, 34 and 37 weeks of gestation (overall and stratified by spontaneous or indicated delivery), premature rupture of membranes, use of tocolysis and/or corticosteroids during pregnancy, mode of delivery, maternal infections, maternal side effects, neonatal and maternal hospital admissions, and a composite of adverse perinatal outcomes including both morbidity and mortality. We assume an event rate of 20% preterm birth before 32 weeks for cerclage and use a non-inferiority margin of 10% for the cervical pessary. Using an alpha of 0.05 and power of 0.80 we need 2 groups of 200 women each. Discussion The outcome of this study will indicate the effectiveness and the cost-effectiveness of a cervical cerclage and of a cervical pessary