Accurate Region-of-Interest Recovery Improves the Measurement of the Cell Migration Rate in the In Vitro Wound Healing Assay

The wound healing assay is widely used for the quantitative analysis of highly regulated cellular events. In this essay, a wound is voluntarily produced on a confluent cell monolayer, and then the rate of wound reduction (WR) is characterized by processing images of the same regions of interest (ROIs) recorded at different time intervals. In this method, sharp-image ROI recovery is indispensable to compensate for displacements of the cell cultures due either to the exploration of multiple sites of the same culture or to transfers from the microscope stage to a cell incubator. ROI recovery is usually done manually and, despite a low-magnification microscope objective is generally used (10x), repositioning imperfections constitute a major source of errors detrimental to the WR measurement accuracy. We address this ROI recovery issue by using pseudoperiodic patterns fixed onto the cell culture dishes, allowing the easy localization of ROIs and the accurate quantification of positioning errors. The method is applied to a tumor-derived cell line, and the WR rates are measured by means of two different image processing software. Sharp ROI recovery based on the proposed method is found to improve significantly the accuracy of the WR measurement and the positioning under the microscope.

Bio-EdIP: An automatic approach for in vitro cell confluence images quantification

BACKGROUND AND OBJECTIVES

Cell imaging is a widely-employed technique to analyze multiple biological processes. Therefore, simple, accurate and quantitative tools are needed to understand cellular events. For this purpose, Bio-EdIP was developed as a user-friendly tool to quantify confluence levels using cell culture images.

METHODS

The proposed algorithm combines a pre-processing step with subsequent stages that involve local processing techniques and a morphological reconstruction-based segmentation algorithm. Segmentation performance was assessed in three constructed image sets, comparing F-measure scores and AUC values (ROC analysis) for Bio-EdIP, its previous version and TScratch. Furthermore, segmentation results were compared with published algorithms using eight public benchmarks.

RESULTS

Bio-EdIP automatically segmented cell-free regions from images of in vitro cell culture. Based on mean F-measure scores and ROC analysis, Bio-EdIP conserved a high performance regardless of image characteristics of the constructed dataset, when compared with its previous version and TScratch. Although acquisition quality of the public dataset affected Bio-EdIP segmentation, performance was better in two out of eight public sets.

CONCLUSIONS

Bio-EdIP is a user-friendly interface, which is useful for the automatic analysis of confluence levels and cell growth processes using in vitro cell culture images. Here, we also presented new manually annotated data for algorithms evaluation.

Optimal design of monitoring networks for multiple groundwater quality parameters using a Kalman filter: application to the Irapuato-Valle aquifer

A new method for the optimal design of groundwater quality monitoring networks is introduced in this paper. Various indicator parameters were considered simultaneously and tested for the Irapuato-Valle aquifer in Mexico. The steps followed in the design were (1) establishment of the monitoring network objectives, (2) definition of a groundwater quality conceptual model for the study area, (3) selection of the parameters to be sampled, and (4) selection of a monitoring network by choosing the well positions that minimize the estimate error variance of the selected indicator parameters. Equal weight for each parameter was given to most of the aquifer positions and a higher weight to priority zones. The objective for the monitoring network in the specific application was to obtain a general reconnaissance of the water quality, including water types, water origin, and first indications of contamination. Water quality indicator parameters were chosen in accordance with this objective, and for the selection of the optimal monitoring sites, it was sought to obtain a low-uncertainty estimate of these parameters for the entire aquifer and with more certainty in priority zones. The optimal monitoring network was selected using a combination of geostatistical methods, a Kalman filter and a heuristic optimization method. Results show that when monitoring the 69 locations with higher priority order (the optimal monitoring network), the joint average standard error in the study area for all the groundwater quality parameters was approximately 90 % of the obtained with the 140 available sampling locations (the set of pilot wells). This demonstrates that an optimal design can help to reduce monitoring costs, by avoiding redundancy in data acquisition.

A meta-analysis of published studies of endothelial dysfunction does not support its routine clinical use

BACKGROUND

Endothelial dysfunction is a marker of future cardiovascular disease (CVD) risk, yet epidemiological studies have yielded inconsistent results. We therefore studied the association between endothelial dysfunction and CVD under diverse circumstances.

METHODS AND RESULTS

Literature-based meta-analysis of prospective observational studies with ≥ 12 months of follow-up published in Medline and having information on endothelial function and CVD outcomes. Tabular data on participant characteristics, endothelial function assessments and incident CVD outcomes were abstracted from individual studies. Random-effects meta-analysis was used to quantify pooled associations, and I(2) statistic to evaluate between-study heterogeneity. Potential sources of heterogeneity were explored by subgroup analyses and meta-regression. Thirty five studies involving 17,206 participants met the inclusion criteria. During more than 80,000 person-years of observation, up to 2755 CVD events were accrued, yielding a pooled relative risk (RR) of 1.25 (95% confidence interval 1.15-1.35) for CVD comparing top (i.e. more severe) vs. bottom (less severe) third of endothelial dysfunction. There was significant between-study heterogeneity and evidence of publication bias. RRs varied importantly according to the method used to ascertain endothelial function, and were higher among older individuals and among participants with risk factors for CVD or established CVD at baseline.

CONCLUSIONS

Although endothelial dysfunction is an important determinant of cardiovascular outcomes in people with pre-existing CVD, current evidence base does not support its use as a potentially useful measurement for risk stratification in people at lower risk of CVD.

Middle Miocene closure of the Central American Seaway

Uranium-lead geochronology in detrital zircons and provenance analyses in eight boreholes and two surface stratigraphic sections in the northern Andes provide insight into the time of closure of the Central American Seaway. The timing of this closure has been correlated with Plio-Pleistocene global oceanographic, atmospheric, and biotic events. We found that a uniquely Panamanian Eocene detrital zircon fingerprint is pronounced in middle Miocene fluvial and shallow marine strata cropping out in the northern Andes but is absent in underlying lower Miocene and Oligocene strata. We contend that this fingerprint demonstrates a fluvial connection, and therefore the absence of an intervening seaway, between the Panama arc and South America in middle Miocene times; the Central American Seaway had vanished by that time.

Evaluation of hydrochemical changes due to intensive aquifer exploitation: case studies from Mexico

The impact of intensive aquifer exploitation has been observed in numerous places around the world. Mexico is a representative example of this problem. In 2010, 101 out of the 653 aquifers recognized in the country, showed negative social, economic, and environmental effects related to intensive exploitation. The environmental effects include, among others, groundwater level decline, subsidence, attenuation, and drying up of springs, decreased river flow, and deterioration of water quality. This study aimed at determining the hydrochemical changes produced by intensive aquifer exploitation and highlighting water quality modifications, taking as example the Valle de Toluca, Salamanca, and San Luis Potosi aquifers in Mexico's highlands. There, elements such as fluoride, arsenic, iron, and manganese have been detected, resulting from the introduction of older groundwater with longer residence times and distinctive chemical composition (regional flows). High concentrations of other elements such as chloride, sulfate, nitrate, and vanadium, as well as pathogens, all related to anthropogenic pollution sources (wastewater infiltration, irrigation return flow, and atmospheric pollutants, among others) were also observed. Some of these elements (nitrate, fluoride, arsenic, iron, and manganese) have shown concentrations above Mexican and World Health Organization drinking water standards.