A DNA Polymerase Variant Senses the Epigenetic Marker 5-Methylcytosine by Increased Misincorporation.

Dysregulation of DNA methylation is associated with human disease, particularly cancer, and the assessment of aberrant methylation patterns holds great promise for clinical diagnostics. However, DNA polymerases do not effectively discriminate between processing 5-methylcytosine (5 mC) and unmethylated cytosine, resulting in the silencing of methylation information during amplification or sequencing. As a result, current detection methods require multi-step DNA conversion treatments or careful analysis of sequencing data to decipher individual 5 mC bases.

SciJava Ops: an improved algorithms framework for Fiji and beyond.

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many "bridge" layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits.

A New Mass Spectroscopy-Based Method for Assessing the Periodontal-Endodontic Interface after Intracanal Placement of Biomaterials In Vitro.

Optimizing the interface between biomaterials and dental hard tissues can prevent leakage of bacteria or inflammatory mediators into periapical tissues and thus avoid alveolar bone inflammation. In this study, an analysis system for testing the periodontal-endodontic interface using gas leakage and subsequent mass spectrometry was developed and validated using the roots of 15 single-rooted teeth in four groups: (I) roots without root canal filling, (II) roots with an inserted gutta-percha post without sealer, (III) roots with gutta-percha post and sealer, (IV) roots filled with sealer only, and (V) adhesively covered roots. Helium was used as the test gas, and its leakage rate was found by measuring the rising ion current using mass spectrometry.

Impact of thermal photodynamic disinfection on root dentin temperature in vitro.

Background: Thermal photodynamic disinfection procedures have been proposed for adjunctive endodontic treatment. This study assessed photothermal disinfection relative to root dentin temperature and the thermal effects of simulated periodontal blood flow.

Methods: Thirty freshly extracted human single-rooted teeth were prepared endodontically using a 45/.

Integration of the ImageJ Ecosystem in the KNIME Analytics Platform.

Open-source software tools are often used for analysis of scientific image data due to their flexibility and transparency in dealing with rapidly evolving imaging technologies. The complex nature of image analysis problems frequently requires many tools to be used in conjunction, including image processing and analysis, data processing, machine learning and deep learning, statistical analysis of the results, visualization, correlation to heterogeneous but related data, and more. However, the development, and therefore application, of these computational tools is impeded by a lack of integration across platforms.

Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances.

The first in vitro tests for developmental toxicity made use of rodent cells. Newer teratology tests, e.g.

Whither systems medicine?

New technologies to generate, store and retrieve medical and research data are inducing a rapid change in clinical and translational research and health care. Systems medicine is the interdisciplinary approach wherein physicians and clinical investigators team up with experts from biology, biostatistics, informatics, mathematics and computational modeling to develop methods to use new and stored data to the benefit of the patient. We here provide a critical assessment of the opportunities and challenges arising out of systems approaches in medicine and from this provide a definition of what systems medicine entails.

Efficiency of soft tissue incision with a novel 445-nm semiconductor laser.

Using a 445-nm semiconductor laser for tissue incision, an effective cut is expected due to the special absorption properties of blue laser light in soft tissues. The aim of the present study was the histological evaluation of tissue samples after incision with a 445-nm diode laser. Forty soft tissue specimens were obtained from pork oral mucosa and mounted on a motorized linear translation stage.

KNIME for reproducible cross-domain analysis of life science data.

Experiments in the life sciences often involve tools from a variety of domains such as mass spectrometry, next generation sequencing, or image processing. Passing the data between those tools often involves complex scripts for controlling data flow, data transformation, and statistical analysis. Such scripts are not only prone to be platform dependent, they also tend to grow as the experiment progresses and are seldomly well documented, a fact that hinders the reproducibility of the experiment.

Automated workflows for modelling chemical fate, kinetics and toxicity.

Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA).

Complications with allogeneic, cancellous bone blocks in vertical alveolar ridge augmentation: prospective clinical case study and review of the literature.

Objectives: Vertical bone augmentation in dental implantology is an indication for cancellous allogeneic bone blocks (ABB). However, these materials may lead to adverse reactions, which are known well in orthopedics but rarely published. Therefore, in this study, we performed an evaluation of the use of ABB in vertical bone augmentation in clinical dental implantology.

KNIME for Open-Source Bioimage Analysis: A Tutorial.

The open analytics platform KNIME is a modular environment that enables easy visual assembly and interactive execution of workflows. KNIME is already widely used in various areas of research, for instance in cheminformatics or classical data analysis. In this tutorial the KNIME Image Processing Extension is introduced, which adds the capabilities to process and analyse huge amounts of images.

A KNIME-Based Analysis of the Zebrafish Photomotor Response Clusters the Phenotypes of 14 Classes of Neuroactive Molecules.

Recently, the photomotor response (PMR) of zebrafish embryos was reported as a robust behavior that is useful for high-throughput neuroactive drug discovery and mechanism prediction. Given the complexity of the PMR, there is a need for rapid and easy analysis of the behavioral data. In this study, we developed an automated analysis workflow using the KNIME Analytics Platform and made it freely accessible.

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses.

Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling.

Functional assays, such as the "migration inhibition of neural crest cells" (MINC) developmental toxicity test, can identify toxicants without requiring knowledge on their mode of action (MoA). Here, we were interested, whether (i) inhibition of migration by structurally diverse toxicants resulted in a unified signature of transcriptional changes; (ii) whether statistically-identified transcript patterns would inform on compound grouping even though individual genes were little regulated, and (iii) whether analysis of a small group of biologically-relevant transcripts would allow the grouping of compounds according to their MoA. We analyzed transcripts of 35 'migration genes' after treatment with 16 migration-inhibiting toxicants.

MARK-AGE data management: Cleaning, exploration and visualization of data.

Databases are an organized collection of data and necessary to investigate a wide spectrum of research questions. For data evaluation analyzers should be aware of possible data quality problems that can compromise results validity. Therefore data cleaning is an essential part of the data management process, which deals with the identification and correction of errors in order to improve data quality.

The MARK-AGE phenotypic database: Structure and strategy.

In the context of the MARK-AGE study, anthropometric, clinical and social data as well as samples of venous blood, buccal mucosal cells and urine were systematically collected from 3337 volunteers. Information from about 500 standardised questions and about 500 analysed biomarkers needed to be documented per individual. On the one hand handling with such a vast amount of data necessitates the use of appropriate informatics tools and the establishment of a database.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

MS-based proteomics and metabolomics are rapidly evolving research fields driven by the development of novel instruments, experimental approaches, and analysis methods. Monolithic analysis tools perform well on single tasks but lack the flexibility to cope with the constantly changing requirements and experimental setups. Workflow systems, which combine small processing tools into complex analysis pipelines, allow custom-tailored and flexible data-processing workflows that can be published or shared with collaborators.

From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects.

The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transcriptome changes could describe altered differentiation states as indirect consequence of drug exposure.

Effect of simulated pulpal fluid circulation on intrapulpal temperature following irradiation with an Nd:YVO4 laser.

It is suggested that pulpal fluid circulation has an impact on pulp temperature increase during heat-generating dental treatment procedures. Thus, the aim of the study was to assess the effect of a simulated pulpal fluid circulation on temperature changes inside the pulp chamber following laser irradiation of the tooth surface. Twenty freshly extracted human multirooted teeth were included and cross-sectioned along the long axis exposing two root canals each.

KNIME-CDK: Workflow-driven cheminformatics.

Background: Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in.

Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation.

In cellular systems environmental and metabolic signals are integrated for the conditional control of gene expression. On the other hand, artificial manipulation of gene expression is of high interest for metabolic and genetic engineering. Especially the reprogramming of gene expression patterns to orchestrate cellular responses in a predictable fashion is considered to be of great importance.

Biological imaging software tools.

Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data.

The impact of antimicrobial photodynamic therapy in an artificial biofilm model.

The susceptibility of bacterial cultures in biofilm formations is important for a variety of clinical treatment procedures. Therefore, the aim of the study was to assess the impact of laser-induced antimicrobial photodynamic therapy on the viability of Streptococcus mutans cells employing an artificial biofilm model. Using sterile chambered coverglasses, a salivary pellicle layer was formed in 40 chambers.