JDLL: A library to run Deep Learning models on Java bioimage informatics platforms

We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the functions required to consume DL models seamlessly, without being burdened by the configuration of the Python-based DL frameworks, within Java bioimage informatics platforms. Moreover, it allows the deployment of pre-trained models in the Bioimage Model Zoo (BMZ) by shipping the logic to connect to the BMZ website, download and run a selected model inference

Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH

International audienceAdvances in single-cell RNA sequencing have allowed for the identification of cellular subtypes on the basis of quantification of the number of transcripts in each cell. However, cells might also differ in the spatial distribution of molecules, including RNAs. Here, we present DypFISH, an approach to quantitatively investigate the subcellular localization of RNA and protein. We introduce a range of analytical techniques to interrogate single-molecule RNA fluorescence in situ hybridization (smFISH) data in combination with protein immunolabeling. DypFISH is suited to study patterns of clustering of molecules, the association of mRNA-protein subcellular localization with microtubule organizing center orientation, and interdependence of mRNA-protein spatial distributions. We showcase how our analytical tools can achieve biological insights by utilizing cell micropatterning to constrain cellular architecture, which leads to reduction in subcellular mRNA distribution variation, allowing for the characterization of their localization patterns. Furthermore, we show that our method can be applied to physiological systems such as skeletal muscle fibers

Predictive Importance of Blood Pressure Characteristics With Increasing Age in Healthy Men and Women:The MORGAM Project

It remains unclear which blood pressure (BP) characteristics best predict cardiovascular risk in different age groups and between sexes. We leveraged data from the MORGAM (MONICA [Monitoring of Trends and Determinants in Cardiovascular Disease], Risk, Genetics, Archiving and Monograph) Project to investigate determinants of BP characteristics and their prognostic importance, in younger and older (</≥50 years) men and women. The study population comprised 107 599 individuals (53% men) aged 19 to 97 years without established cardiovascular disease, not on antihypertensive treatment, recruited between 1982 and 2008 in 38 cohorts. Covariates of BP characteristics were explored using multivariable linear regression. Prognostic importance was examined using multivariable Cox proportional-hazards regression, area under the receiver operating characteristic curve, and net reclassification improvement. The primary end point was a composite cardiovascular end point (CEP), defined as fatal or nonfatal stroke, death from coronary heart disease or nonfatal myocardial infarction. The positive association between age and systolic BP was more pronounced among individuals ≥50 years while the same was true for diastolic BP in those <50 years ( P interaction <0.001). Higher systolic BP and mean BP were significantly associated with cardiovascular end point, irrespective of age group ( P <0.001), but diastolic BP only demonstrated an independent relationship in the younger group ( P <0.001). Brachial pulse pressure was associated with cardiovascular end point in the older age group ( P <0.001). In subjects <50 years, diastolic BP significantly improved area under the receiver operating characteristic curve compared with Systematic Coronary Risk Evaluation variables (including systolic BP) alone (0.842 versus 0.840, P =0.03), enhanced continuous net reclassification improvement (0.150 [95% CI, 0.087–0.215]) and improved the prognostic value of the European Society of Cardiology/European Society of Hypertension hypertension definition (categorical net reclassification improvement=0.0255, P =0.005). In conclusion, diastolic BP may provide additional prognostic utility beyond systolic BP, in predicting composite cardiovascular events among younger individuals

Does Estimated Pulse Wave Velocity Add Prognostic Information?:MORGAM Prospective Cohort Project

The Reference Values for Arterial Stiffness Collaboration has derived an equation using age and mean blood pressure to estimated pulse wave velocity (ePWV), which predicted cardiovascular events independently of Systematic COoronary Risk Evaluation (SCORE) and Framingham Risk Score. The study aim was to investigate the independent association between ePWV and clinical outcomes in 107 599 apparently healthy subjects (53% men) aged 19 to 97 years from the MORGAM Project who were included between 1982 and 2002 in 38 cohorts from 11 countries. Using multiple Cox-regression analyses, the predictive value of ePWV was calculated adjusting for country of inclusion and either SCORE, Framingham Risk Score, or traditional cardiovascular risk factors (age, sex, smoking, systolic blood pressure, body mass index [BMI], total and high-density lipoprotein cholesterol). Cardiovascular mortality consisted of fatal stroke, fatal myocardial infarction, or coronary death, and the composite cardiovascular end point consisted of stroke, myocardial infarction, or coronary death. Model discrimination was assessed using Harrell's C-statistic. Adjusting for country and logSCORE or Framingham Risk Score, ePWV was associated with all-cause mortality (hazard ratio, 1.23 [95% CI 1.20-1.25] per m/s or 1.32 [1.29-1.34]), cardiovascular mortality (1.26 [1.21-1.32] or 1.35 [1.31-1.40]), and composite cardiovascular end point (1.19 [1.16-1.22] or 1.23 [1.20-1.25]; all P<0.001). However, after adjusting for traditional cardiovascular risk factors, ePWV was only associated with all-cause mortality (1.15 [1.08-1.22], P<0.001) and not with cardiovascular mortality (0.97 [0.91-1.03]) nor composite cardiovascular end point (1.10 [0.97-1.26]). The areas under the last 3 receiver operator characteristic curves remained unchanged when adding ePWV. Elevated ePWV was associated with subsequent mortality and cardiovascular morbidity independently of systematic coronary risk evaluation and Framingham Risk Score but not independently of traditional cardiovascular risk factors