BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies

Background The software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing. Results Here we describe BactImAS – a modular, multi- platform, open- source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time- lapse movies. BactImAS uses a semi- automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to- segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10- fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree. Conclusions The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software

Unexpectedly small empirical vector strangeness of nucleons predicted in a baryon model

Most of model considerations of the hidden nucleon strangeness, as well as some preliminary experimental evidence, led to the expectations of relatively sizeable strange vector form factors of the proton. For example, it seemed that the contribution of the fluctuating strange quark-antiquark pairs accounts for as much as one tenth of the proton's magnetic moment. By the same token, baryon models which failed to produce the "vector strangeness" of the nucleon seemed disfavoured. Recently, however, more accurate measurements and more sophisticated data analysis, as well as lattice simulations, revealed that the form factors associated with the vector strangeness of the nucleon are much smaller than thought previously; in fact, due to the experimental uncertainties, the measured strange vector-current proton form factors may be consistent with zero. In the light of that, we re-asses the merit of the baryon models leading to little or no vector strangeness of the nucleon. It is done on the concrete example of the baryon model which essentially amounts to the MIT bag enriched by the diluted instanton liquid

Unexpectedly small empirical vector strangeness of nucleons predicted in a baryon model

Most of model considerations of the hidden nucleon strangeness, as well as some preliminary experimental evidence, led to the expectations of relatively sizeable strange vector form factors of the proton. For example, it seemed that the contribution of the fluctuating strange quark-antiquark pairs accounts for as much as one tenth of the proton's magnetic moment. By the same token, baryon models which failed to produce the "vector strangeness" of the nucleon seemed disfavoured. Recently, however, more accurate measurements and more sophisticated data analysis, as well as lattice simulations, revealed that the form factors associated with the vector strangeness of the nucleon are much smaller than thought previously; in fact, due to the experimental uncertainties, the measured strange vector-current proton form factors may be consistent with zero. In the light of that, we re-asses the merit of the baryon models leading to little or no vector strangeness of the nucleon. It is done on the concrete example of the baryon model which essentially amounts to the MIT bag enriched by the diluted instanton liquid

Intense desert dust event in the northern Adriatic (March 2020); insights from the numerical model application and chemical characterization results.

The untypically extreme and sudden particulate matter outbreak set stage over Balkan region from 27 to 30 March 2020. The available observations at air quality stations in Croatia recorded the hourly PM10 concentrations up to 412 μgm-3. Meteorological analysis shows the PM10 concentrations increase was primarily affected by advection of mineral dust from the desert area east to the Caspian Sea. The anticyclone north of Croatia and cyclone over Anatolia formed a strong pressure gradient driving a transport from the east. The backward trajectories as well as satellite products indicated the dry Aral Sea as a major source of dust. A dust plume affected the PM10 increase observed in Croatia, starting at Osijek and easternmost air quality stations . Modeling study shows the vertical extension of a plume was up to ~2 km. However, the PM10 chemical (Pb, Cd, Cu, Zn, Fe, Mn, PAHs) and morphological (SEM analyses) composition at the site in the northeastern Adriatic revealed mainly the presence of the Saharan dust. Preceding the Asian dust advection, the Saharan dust transport towards Balkan driven by Sharav cyclone was observed in PM10 at several stations in the Adriatic and continental Croatia on 26 March 2020. Modeling results showed the Saharan dust transport was at levels below ~ 8 km. The mixing of the Asian and Saharan dust plumes over Balkan was favored by subsidence due to anticyclonic high pressure conditions, and it is the most likely explanation for the observed PMs chemical and morphological results