Phase Variation of LPS and Capsule Is Responsible for Stochastic Biofilm Formation in Francisella tularensis

Biofilms have been established as an important lifestyle for bacteria in nature as these structured communities often enable survivability and persistence in a multitude of environments. Francisella tularensis is a facultative intracellular Gram-negative bacterium found throughout much of the northern hemisphere. However, biofilm formation remains understudied and poorly understood in F. tularensis as non-substantial biofilms are typically observed in vitro by the clinically relevant subspecies F. tularensis subsp. tularensis and F. tularensis subsp. holarctica (Type A and B, respectively). Herein, we report conditions under which robust biofilm development was observed in a stochastic, but reproducible manner in Type A and B isolates. The frequency at which biofilm was observed increased temporally and appeared switch-like as progeny from the initial biofilm quickly formed biofilm in a predictable manner regardless of time or propagation with fresh media. The Type B isolates used for this study were found to more readily switch on biofilm formation than Type A isolates. Additionally, pH was found to function as an environmental checkpoint for biofilm initiation independently of the heritable cellular switch. Multiple colony morphologies were observed in biofilm positive cultures leading to the identification of a particular subset of grey variants that constitutively produce biofilm. Further, we found that constitutive biofilm forming isolates delay the onset of a viable non-culturable state. In this study, we demonstrate that a robust biofilm can be developed by clinically relevant F. tularensis isolates, provide a mechanism for biofilm initiation and examine the potential role of biofilm formation.

X-ray absorption spectroscopy and actinide electrochemistry: a setup dedicated to radioactive samples applied to neptunium chemistry

A spectroelectrochemical setup has been developed to investigate radioactive elements in small volumes (0.7 to 2 ml) under oxidation–reduction (redox) controlled conditions by X-ray absorption spectroscopy (XAS). The cell design is presented together with in situ XAS measurements performed during neptunium redox reactions. Cycling experiments on the NpO2 2+/NpO2 + redox couple were applied to qualify the cell electrodynamics using XANES measurements and its ability to probe modifications in the neptunyl hydration shell in a 1 mol l−1 HNO3 solution. The XAS results are in agreement with previous structural studies and the NpO2 2+/NpO2 + standard potential, determined using Nernst methods, is consistent with measurements based on other techniques. Subsequently, the NpO2 +, NpO2 2+ and Np4+ ion structures in solution were stabilized and measured using EXAFS. The resulting fit parameters are again compared with other results from the literature and with theoretical models in order to evaluate how this spectroelectrochemistry experiment succeeds or fails to stabilize the oxidation states of actinides. The experiment succeeded in: (i) implementing a robust and safe XAS device to investigate unstable radioactive species, (ii) evaluate in a reproducible manner the NpO2 2+/NpO2 + standard potential under dilute conditions and (iii) clarify mechanistic aspects of the actinyl hydration sphere in solution. In contrast, a detailed comparison of EXAFS fit parameters shows that this method is less appropriate than the majority of the previously reported chemical methods for the stabilization of the Np4+ ion.

Histopathological Analysis of Cerebrovascular Lesions Associated With Aging

Cerebrovascular disease (CVD) has been associated with cognitive impairment. Yet, our understanding of vascular contribution to cognitive decline has been limited by heterogeneity of definitions and assessment, as well as its occurrence in cognitively healthy aging. Therefore, we aimed to establish the natural progression of CVD associated with aging. We conducted a retrospective observational study of 63 cognitively healthy participants aged 19–84 years selected through the histological archives of the CHU de Québec. Assessment of CVD lesions was performed independently by 3 observers blinded to clinical data using the Vascular Cognitive Impairment Neuropathology Guidelines (VCING). We found moderate to almost perfect interobserver agreement for most regional CVD scores. Atherosclerosis (ρ = 0.758) and arteriolosclerosis (ρ = 0.708) showed the greatest significant association with age, followed by perivascular hemosiderin deposits (ρ = 0.432) and cerebral amyloid angiopathy (CAA; ρ = 0.392). Amyloid and tau pathologies were both associated with higher CVD load, but only CAA remained significantly associated with amyloid plaques after controlling for age. Altogether, these findings support the presence of multiple CVD lesions in the brains of cognitively healthy adults, the burden of which increases with age and can be quantified in a reproducible manner using standardized histological scales such as the VCING.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.

The eWaterCycle platform for Open and FAIR Hydrological collaboration

Hutton (2016) argued that computational hydrology can only be a proper science if the hydrological community makes sure that hydrological model studies are executed and presented in a reproducible manner. We replied that to achieve this, hydrologists shouldn't ‘re-invent the water wheel’ but rather use existing technology from other fields (such as containers and ESMValTool) and open interfaces (such as BMI) to do their computational science (Hut, 2017). With this paper and the associated release of the eWaterCycle platform and software package1 we are putting our money where our mouth is and provide the hydrological community with a ‘FAIR by design’ platform to do our science. eWaterCycle is a platform that separates the experiment done on the model from the model code. In eWaterCycle hydrological models are accessed through a common interface (BMI) in Python and run inside of software containers. In this way all models are accessed in a similar manner facilitating easy switching of models, model comparison and model coupling. Currently the following models are available through eWaterCycle: PCR-GLOBWB 2.0, wflow, Hype, LISFLOOD, TopoFlex HBV, MARRMoT and WALRUS. While these models are written in different programming languages they can all be run and interacted with from the Jupyter notebook environment within eWaterCycle. Furthermore, the pre-processing of input data for these models has been streamlined by making use of ESMValTool. Forcing for the models available in eWaterCycle from well known datasets such as ERA5 can be generated with a single line of code. To illustrate the type of research that eWaterCycle facilitates this manuscript includes five case studies: from a simple ‘Hello World’ where only a hydrograph is generated to a complex coupling of models in different languages. In this manuscript we stipulate the design choices made in building eWaterCycle and provide all the technical details to understand and work with the platform. For system administrators who want to install eWaterCycle on their infrastructure we offer a separate installation guide. For computational hydologist who want to work with eWaterCycle we also provide a video explaining the platform from a users point of view. With the eWaterCycle platform we are providing the hydrological community with a platform to conduct their research fully compatible with the principles of Open Science as well as FAIR science.1available on Zenodo: doi.org/10.5281/zenodo.5119389

Validation of cervical lesion proportion measure using a gridded imaging techique to assess cervical pathology in women with genital schistosomiasis

Female genital schistosomiasis (FGS) is characterized by a pattern of lesions which manifest at the cervix and the vagina, such as homogeneous and grainy sandy patches, rubbery papules in addition to neovascularization. A tool for quantification of the lesions is needed to improve FGS research and control programs. Hitherto, no tools are available to quantify clinical pathology at the cervix in a standardized and reproducible manner. This study aimed to develop and validate a cervical lesion proportion (CLP) measure for quantification of cervical pathology in FGS. A digital imaging technique was applied in which a grid containing 424 identical squares was positioned on high resolution digital images from the cervix of 70 women with FGS. A CLP was made for each image by counting the total number of squares containing at least one type of pathognomonic lesions. For validation of inter- and intra-observer reliability, three different observers estimated CLP independently. In addition, a rubbery papule count (RPC) was determined in a similar manner. The intraclass correlation coefficient was 0.94 (excellent) for the CLP inter-rater reliability and 0.90 (good) for intra-rater reliability and the coefficients for the RPC were 0.88 and 0.80 (good), respectively. The CLP facilitated a reliable and reproducible quantification of the surface of the cervix affected by FGS pathognomonic lesions. Grading of cervical pathology by CLP can provide insight into the natural course of schistosome egg-induced pathology of the cervix. Moreover, CLP provides a measure for the efficacy of treatment.

Using RMarkdown to Present Your Findings

This chapter covers how to utilize RMarkdown to present SSD for R findings in a well-ordered and reproducible manner. RMarkdown is a plain text formatting syntax that makes writing research reports simple. The language provides a simple syntax that formats text such as headers, lists, boldface, and so on. This language is popular, and you will find many apps that are compatible with it. For example, combined with other packages, like SSD for R, users can easily create tables and graphics to present their research findings. Another important feature of this markdown language is that it will make your findings reproducible in that all of your files are connected. Thus, if there are changes to your data, rerunning the analysis is simple.

Quantification of Lipid Area within Thermogenic Mouse Perivascular Adipose Tissue Using Standardized Image Analysis in FIJI

Quantification of adipocyte size and number is routinely performed for white adipose tissues using existing image analysis software. However, thermogenic adipose tissue has multilocular adipocytes, making it difficult to distinguish adipocyte cell borders and to analyze lipid proportion using existing methods. We developed a simple, standardized method to quantify lipid content of mouse thermogenic adipose tissue. This method, using FIJI analysis of hematoxylin/eosin stained sections, was highly objective and highly reproducible, with ∼99% inter-rater reliability. The method was compared to direct lipid staining of adipose tissue, with comparable results. We used our method to analyze perivascular adipose tissue (PVAT) from C57BL/6 mice on a normal chow diet, compared to calorie restriction or a high fat diet, where lipid storage phenotypes are known. Results indicate that lipid content can be estimated within mouse PVAT in a quantitative and reproducible manner, and shows correlation with previously studied molecular and physiological measures.

Selection of a High-Affinity DNA Aptamer for the Recognition of Cadmium Ions

Cadmium ions as toxic metallic pollutants have been dramatically risen due to industrial production, which causes serious environmental damages and potential health risks. Thus, developing sensitive and specific probes to recognize cadmium ions is vital for human and environmental safety. In this work, the aptamer as a capture probe was selected for the identification of cadmium ions. The modified SELEX method based on immobilizing ssDNA libraries on streptavidin magnetic beads was used to the high-affinity aptamer selection for binding cadmium ions. After 9 rounds of selection, 4 ssDNA sequences with the highest enrichment were obtained, and the Cd-1 aptamer exhibited the highest affinity to cadmium ions. The dissociation constant Kd value of the Cd-1 aptamer was 81.39 μM for cadmium ions. Later, we also investigated the binding specificity of Cd-1 aptamer toward other heavy metal ions. Given the availability of immobilizing ssDNA library on matrix, we believe the strategy also applies to discover other ions in a reproducible manner.

Sustainable Packaging of Quantum Chemistry Software with the Nix Package Manager

The installation of quantum chemistry software packages is commonly done manually and can be a time-consuming and complicated process. An update of the underlying Linux system requires a reinstallation in many cases and can quietly break software installed on the system. In this paper, we present an approach that allows for an easy installation of quantum chemistry software packages, which is also independent of operating system updates. The use of the Nix package manager allows building software in a reproducible manner, which allows for a reconstruction of the software for later reproduction of scientific results. The build recipes that are provided can be readily used by anyone to avoid complex installation procedures.