Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis [preprint]

The proposed Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines described here aim to deliver a set of rules representing the minimal information required to report and support interpretation and assessment of data arising from intracellular multiple particle tracking (MPT) experiments. Examples of such experiments are those tracking viral particles as they move from the site of entry to the site of replication within an infected cell, or those following vesicular dynamics during secretion, endocytosis, or exocytosis. By promoting development of community standards, we hope that MIAPTE will contribute to making MPT data FAIR (Findable Accessible Interoperable and Reusable). Ultimately, the goal of MIAPTE is to promote and maximize data access, discovery, preservation, re-use, and repurposing through efficient annotation, and ultimately to enable reproducibility of particle tracking experiments. This document introduces MIAPTE v0.2, which updates the version that was posted to Fairsharing.org in October 2016. MIAPTE v0.2 is presented with the specific intent of soliciting comments from the particle tracking community with the purpose of extending and improving the model. The MIAPTE guidelines are intended for different categories of users: 1) Scientists with the desire to make new results available in a way that can be interpreted unequivocally by both humans and machines. For this class of users, MIAPTE provides data descriptors to define data entry terms and the analysis workflow in a unified manner. 2) Scientists wishing to evaluate, replicate and re-analyze results published by others. For this class of users MIAPTE provides descriptors that define the analysis procedures in a manner that facilitates its reproduction. 3) Developers who want to take advantage of the schema of MIAPTE to produce MIAPTE compatible tools. MIAPTE consists of a list of controlled vocabulary (CV) terms that describe elements and properties for the minimal description of particle tracking experiments, with a focus on viral and vesicular traffic within cells. As part of this submission we provide entity relationship (ER) diagrams that show the relationship between terms. Finally, we also provide documents containing the MIAPTE-compliant XML schema describing the data model used by Open Microscopy Environment inteGrated Analysis (OMEGA), our novel particle tracking data analysis and management tool, which is reported in a separate manuscript. MIAPTE is structured in two sub-sections: 1) Section 1 contains elements, attributes and data structures describing the results of particle tracking, namely: particles, links, trajectories and trajectory segments. 2) Section 2 contains elements that provide details about the algorithmic procedure utilized to produce and analyze trajectories as well as the results of trajectory analysis. In addition MIAPTE includes those OME-XML elements that are required to capture the acquisition parameters and the structure of images to be subjected to particle tracking

Sulphate and Chloride-Dependent Potassium Transport in Human Erythrocytes are Affected by Crude Venom from Nematocysts of the Jellyfish Pelagia noctiluca

Background: It has been reported that biologically active compounds extracted from Cnidaria venom may induce damage by oxidative stress. Erythrocytes are constantly exposed to oxidative stresses, which can contribute to sulphydril (SH-) group oxidation and cell membrane deformability accompanied with activation of K-Cl co-transport and inhibition of anion transport. In this regard, Band 3 protein is responsible for mediating the electroneutral exchange of chloride (Cl-) for bicarbonate (HCO3-), particularly in erythrocytes, where it is the most abundant membrane protein. The aim of this study was to elucidate the effect of crude venom extracted from Pelagia noctiluca nematocysts on Band 3 -mediated anion transport in human erythrocytes. Methods: Erythrocytes were tested for SO42- uptake, K+ efflux, glutathione (GSH) levels and concentration of SH- groups. Results: The rate constant of SO42- uptake decreased progressively to 58% of control with increasing venom doses, and showed a 28% decrease after 2 mM NEM treatment. These effects can be explained by oxidative stress, which was reflected by decreased GSH levels in venom-treated erythrocytes. Hence, the decreased efficiency of anion transport may be due to changes in Band 3 structure caused by SH-group oxidation and reduced GSH concentration. In addition, an increased Cl--dependent K+ efflux was observed in venom-treated erythrocytes. Conclusion: Our results suggest that crude venom from Pelagia noctiluca alters cell membrane transport in human erythrocytes

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control [preprint]

MOTIVATION: Particle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al, 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would eliminate the need for manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analysis standards. RESULTS: Here, we present Open Microscopy Environment inteGrated Analysis (OMEGA), a cross-platform data management, analysis, and visualization system, for particle tracking data, with particular emphasis on results from viral and vesicular trafficking experiments. OMEGA provides easy to use graphical interfaces to implement integrated particle tracking and motion analysis workflows while keeping track of error propagation and data provenance. Specifically, OMEGA: 1) imports image data and metadata from data management tools such as Open Microscopy Environment Remote Objects (OMERO; Allan et al., 2012); 2) tracks intracellular particles moving across time series of image planes; 3) facilitates parameter optimization and trajectory results inspection and validation; 4) performs downstream trajectory analysis and motion type classification; 5) estimates the uncertainty associated with motion analysis; and, 6) facilitates storage and dissemination of analysis results, and analysis definition metadata, on the basis of our newly proposed Minimum Information About Particle Tracking Experiments (MIAPTE; Rigano & Strambio-De-Castillia, 2016; 2017) guidelines in combination with the OME-XML data model (Goldberg et al, 2005)

Salicylic acid and melatonin alleviate the effects of heat stress on essential oil composition and antioxidant enzyme activity in Mentha × piperita and Mentha arvensis L

The aim of this study was to evaluate changes in the chemical profile of essential oils and antioxidant enzymes activity (catalase CAT, superoxide dismutase SOD, Glutathione S-transferases GST, and Peroxidase POX) in Mentha × piperita L. (Mitcham variety) and Mentha arvensis L. (var. piperascens), in response to heat stress. In addition, we used salicylic acid (SA) and melatonin (M), two brassinosteroids that play an important role in regulating physiological processes, to assess their potential to mitigate heat stress. In both species, the heat stress caused a variation in the composition of the essential oils and in the antioxidant enzymatic activity. Furthermore both Salicylic acid (SA) and melatonin (M) alleviated the effect of heat stress

Longitudinal study of computerised cardiotocography in early fetal growth restriction.

OBJECTIVES: To explore if in early fetal growth restriction (FGR) the longitudinal pattern of short-term fetal heart rate (FHR) variation (STV) can be used for identifying imminent fetal distress and if abnormalities of FHR registration associate with two-year infant outcome. METHODS: The original TRUFFLE study assessed if in early FGR the use of ductus venosus Doppler pulsatility index (DVPI), in combination with a safety-net of very low STV and / or recurrent decelerations, could improve two-year infant survival without neurological impairment in comparison to computerised cardiotocography (cCTG) with STV calculation only. For this secondary analysis we selected women, who delivered before 32 weeks, and who had consecutive STV data for more than 3 days before delivery, and known infant two-year outcome data. Women who received corticosteroids within 3 days of delivery were excluded. Individual regression line algorithms of all STV values except the last one were calculated. Life table analysis and Cox regression analysis were used to calculate the day by day risk for a low STV or very low STV and / or FHR decelerations (DVPI group safety-net) and to assess which parameters were associated to this risk. Furthermore, it was assessed if STV pattern, lowest STV value or recurrent FHR decelerations were associated with two-year infant outcome. RESULTS: One hundred and fourty-nine women matched the inclusion criteria. Using the individual STV regression lines prediction of a last STV below the cCTG-group cut-off had a sensitivity of 0.42 and specificity of 0.91. For each day after inclusion the median risk for a low STV(cCTG criteria) was 4% (Interquartile range (IQR) 2% to 7%) and for a very low STV and / or recurrent decelerations (DVPI safety-net criteria) 5% (IQR 4 to 7%). Measures of STV pattern, fetal Doppler (arterial or venous), birthweight MoM or gestational age did not improve daily risk prediction usefully. There was no association of STV regression coefficients, a last low STV or /and recurrent decelerations with short or long term infant outcomes. CONCLUSION: The TRUFFLE study showed that a strategy of DVPI monitoring with a safety-net delivery indication of very low STV and / or recurrent decelerations could increase infant survival without neurological impairment at two years. This post-hoc analysis demonstrates that in early FGR the day by day risk of an abnormal cCTG as defined by the DVPI protocol safety-net criteria is 5%, and that prediction of this is not possible. This supports the rationale for cCTG monitoring more often than daily in these high-risk fetuses. Low STV and/or recurrent decelerations were not associated with adverse infant outcome and it appears safe to delay intervention until such abnormalities occur, as long as DVPI is in the normal range

OmegaProject/Omega: Omega public beta release 0.47

This public beta release of OMEGA is described in details in the following preprint manuscript: OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, Jeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, Caterina Strambio-De-Castillia bioRxiv 251850; doi: https://doi.org/10.1101/251850, which can be found at: https://www.biorxiv.org/content/early/2018/02/27/251850