HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes

Gene duplication is an important evolutionary mechanism capable of providing new genetic material for adaptive and nonadaptive evolution. However, bioinformatics tools for identifying duplicate genes are often limited to the detection of paralogs in multiple species or to specific types of gene duplicates, such as retrocopies. Here, we present a user-friendly, BLAST-based web tool, called HSDFinder, which can identify, annotate, categorize, and visualize highly similar duplicate genes (HSDs) in eukaryotic nuclear genomes. HSDFinder includes an online heatmap plotting option, allowing users to compare HSDs among different species and visualize the results in different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional categories. The external software requirements are BLAST, InterProScan, and KEGG. The utility of HSDFinder was tested on various model eukaryotic species, including Chlamydomonas reinhardtii, Arabidopsis thaliana, Oryza sativa, and Zea mays as well as the psychrophilic green alga Chlamydomonas sp. UWO241, and was proven to be a practical and accurate tool for gene duplication analyses. The web tool is free to use at http://hsdfinder.com. Documentation and tutorials can be found via the GitHub: https://github.com/zx0223winner/HSDFinder.

VueBox® for quantitative analysis of contrast-enhanced ultrasound in liver tumors

Dynamic contrast-enhanced ultrasound (DCE-US) enables quantification of tumor perfusion. VueBox is a platform independent external software using DICOM cine loops which objectively provides various DCE-US parameters of tumor vascularity. This review summaries its use for diagnosis and treatment monitoring of liver tumors. The existing literature provides evidence on the successful application of Vuebox based DCE-US for characterization and differential diagnosis of focal liver lesions, as well as on its use for monitoring of local ablative therapies and of modern systemic treatment in oncology.

Petri Net-Based Semi-Compiled Code Generation for Programmable Logic Controllers

Industrial discrete event dynamic systems (DEDSs) are commonly modeled by means of Petri nets (PNs). PNs have the capability to model behaviors such as concurrency, synchronization, and resource sharing, compared to a step transition function chart or GRAphe Fonctionnel de Commande Etape Transition (GRAFCET) which is a particular case of a PN. However, there is not an effective systematic way to implement a PN in a programmable logic controller (PLC), and so the implementation of such a controller outside a PLC in some external software that will communicate with the PLC is very common. There have been some attempts to implement PNs within a PLC, but they are dependent on how the logic of places and transitions is programmed for each application. This work proposes a novel application-independent and platform-independent PN implementation methodology. This methodology is a systematic way to implement a PN controller within industrial PLCs. A great portion of the code will be validated automatically prior to PLC implementation. Net structure and marking evolution will be checked on the basis of PN model structural analysis, and only net interpretation will be manually coded and error-prone. Thus, this methodology represents a systematic and semi-compiled PN implementation method. A use case supported by a digital twin (DT) is shown where the automated solution required by a manufacturing system is carried out and executed in two different devices for portability testing, and the scan cycle periods are compared for both approaches.

Petri Net-Based Semi-Compiled Code Generation for Programmable Logic Controllers

Industrial discrete event dynamic systems (DEDSs) are commonly modelled by means of Petri nets (PNs). PNs have the capability to model behaviours such as concurrency, synchronization, and resource sharing, compared to a GRAphe Fonctionnel de Commande Etape Transition (GRAFCET) which is a particular case of a PN. However, there is not a systematic way to implement a PN in a programmable logic controller (PLC), and so it is very common the implementation of such a controller outside a PLC, in some external software that will communicate with the PLC. There have been some attempts to implement PNs within a PLC, but they are dependent on how the logic of places and transitions is programmed for each application. This work proposes a novel application-independent and platform-independent PN implementation methodology. This methodology is a systematic way to implement a PN controller within industrial PLCs. A great portion of the code will be validated automatically prior to PLC implementation. Net structure and marking evolution will be checked on the basis of PN model structural analysis, and only net interpretation will be manually coded and error-prone. Thus, this methodology represents a systematic and semi-compiled PN implementation method. A use case supported by a digital twin (DT) is shown where the automated solution required by a manufacturing system is carried out and executed in two different devices for portability testing, and the scan cycle periods are compared for both approaches.

Automating Laboratory Processes by Connecting Biotech and Robotic Devices—An Overview of the Current Challenges, Existing Solutions and Ongoing Developments

The constantly growing interest and range of applications of advanced cell, gene and regenerative therapies raise the need for efficient production of biological material and novel treatment technologies. Many of the production and manipulation processes of such materials are still manual and, therefore, need to be transferred to a fully automated execution. Developers of such systems face several challenges, one of which is mechanical and communication interfaces in biotechnological devices. In the present state, many devices are still designed for manual use and rarely provide a connection to external software for receiving commands and sending data. However, a trend towards automation on the device market is clearly visible, and the communication protocol, Open Platform Communications Data Access (OPC DA), seems to become established as a standard in biotech devices. A rising number of vendors offer software for device control and automated processing, some of which even allow the integration of devices from multiple manufacturers. The high, application-specific need in functionalities, flexibility and adaptivity makes it difficult to find the best solution and, in many cases, leads to the creation of new custom-designed software. This report shall give an overview of existing technologies, devices and software for laboratory automation of biotechnological processes. Furthermore, it presents an outlook for possible future developments and standardizations.

Decentralized Digital Health Services Caught Between the Pressure for Innovation and the Burden of Regulations

Multiple challenges await third-party digital health services when trying to enter the health market. Prominent examples of such services are clinical decision support systems provided as external software. Uncertainty about their challenges, technical as well as legal, pose serious hurdles for many innovations to be adopted early on. There are many options and trade-offs to provide digital healthcare solutions as a third-party service. This paper discusses them by referring to a pharmacogenetic decision support service. By providing best-practices, scenario descriptions and templates designed for third-party services with respect to legal and technical issues, obstacles and uncertainties can be reduced, which will have an impact on better diagnoses and treatments in the healthcare system.

Single molecule tracking and analysis framework including theory-predicted parameter settings

Imaging, tracking and analyzing individual biomolecules in living systems is a powerful technology to obtain quantitative kinetic and spatial information such as reaction rates, diffusion coefficients and localization maps. Common tracking tools often operate on single movies and require additional manual steps to analyze whole data sets or to compare different experimental conditions. We report a fast and comprehensive single molecule tracking and analysis framework (TrackIt) to simultaneously process several multi-movie data sets. A user-friendly GUI offers convenient tracking visualization, multiple state-of-the-art analysis procedures, display of results, and data im- and export at different levels to utilize external software tools. We applied our framework to quantify dissociation rates of a transcription factor in the nucleus and found that tracking errors, similar to fluorophore photobleaching, have to be considered for reliable analysis. Accordingly, we developed an algorithm, which accounts for both tracking losses and suggests optimized tracking parameters when evaluating reaction rates. Our versatile and extensible framework facilitates quantitative analysis of single molecule experiments at different experimental conditions.

Monitoring of Erosive Tooth Wear with Intraoral Scanners In vitro

Intraoral scanners (IOS) have been used to quantify tooth wear, but so far they have not been systematically validated for monitoring of tissue loss. The aim of this in vitro study was to investigate whether progression of tissue loss can be detected with an IOS and whether IOS values agree with those obtained with noncontacting profilometry (PRO) serving as a standard method. Model jaws were mounted in a phantom head positioned in a dental chair. Flattened areas were prepared on the non-load-bearing cusps of the first molars (model teeth; n = 16) in order to fix flat enamel samples with an experimental area and a reference area. After baseline PRO and IOS, the experimental enamel area was stepwise etched with 35% H3PO4 gel (4 × 30 s and 4 × 15 s). After each etching, PRO and IOS was performed and the vertical tissue loss between the reference and experimental areas was measured, each at the same 3 measurement points. Furthermore, cupped cusps were simulated by stepwise preparation of the load-bearing cusps of the model teeth with a spherical diamond bur, and the maximum vertical depth after each preparation step was measured only by IOS. Trios3 (3Shape, Denmark), Carestream CS3600 (Carestream, USA) and an optical profilometer (MicroProf, Fries, Germany) were used to measure the flat areas of the enamel samples, whereas only IOS were used to measure curved surfaces on the load-bearing cupped cusps of the model teeth. The IOS data were analyzed with an external software (GOM Inspect, Germany) and with the respective internal IOS software. PRO revealed a mean (±SD) tissue loss of 17.1 ± 4.7 µm after 30-s etching steps and 10.1 ± 5.1 µm after the 15-s etching steps. IOS and software types were able to detect the progression of tissue loss after each etching step (p ≤ 0.001 each); Bland-Altmann plots revealed good agreement with PRO regardless of the order of tissue loss, and no systematic difference was found. Increasing cupped lesion depths were detected by all IOS, with no significant differences between IOS and analysis methods. IOS were able to detect small amounts of tissue loss under simulated clinical conditions and seem to be a promising tool for monitoring even initial erosive tooth wear.

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.