SUMMARY: The Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships. AVAILABILITY AND IMPLEMENTATION: The project is available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions and comments).

Infections of stratified epithelia contribute to a large group of common diseases, such as dermatological conditions and sexually transmitted diseases. To investigate how epithelial structure affects infection dynamics, we develop a general ecology-inspired model for stratified epithelia. Our model allows us to simulate infections, explore new hypotheses and estimate parameters that are difficult to measure with tissue cell cultures. We focus on two contrasting pathogens: Chlamydia trachomatis and Human papillomaviruses (HPV). Using cervicovaginal parameter estimates, we find that key infection symptoms can be explained by differential interactions with the layers, while clearance and pathogen burden appear to be bottom-up processes. Cell protective responses to infections (e.g. mucus trapping) generally lowered pathogen load but there were specific effects based on infection strategies. Our modeling approach opens new perspectives for 3D tissue culture experimental systems of infections and, more generally, for developing and testing hypotheses related to infections of stratified epithelia.

A majority of digital logic devices receives stimulus from an external system clock and sends information out on bus pins which are synchronized to the system clock. During functional testing of such devices, ATE architectures supply the clock and input data signals. The output signals generated by these devices are synchronous to the tester and are sampled accurately by the test equipment's strobe circuits. With the emergence of wide data busses in memories and high speed communication protocols implemented to transfer data between the CPU and peripherals, it has become necessary to forward a clock along with a group of bus pins to maintain skew across the high speed bus pins to an acceptable value for system design. This has resulted in a class of devices which have source synchronous busses where output signals are sent out relative to their strobe (output clock) signals. This work describes the challenges associated with testing this class of devices with the classical automatic test equipment (ATE) architecture and presents a unique hardware solution implemented on a contemporary tester architecture to meet the test challenge. This work also compares this implementation with other solutions available in the ATE domain.