A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes

The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron–exon structure and by unique codomain architectures. We identified many new genes belonging to previously defined classes (HD-ZIP I to IV, BEL, KNOX, PLINC, WOX). Other newly identified genes allowed us to characterize PHD, DDT, NDX, and LD genes as members of four new evolutionary classes and to define two additional classes, which we named SAWADEE and PINTOX. Our comprehensive analysis allowed us to identify several newly characterized conserved motifs, including novel zinc finger motifs in SAWADEE and DDT. Members of the BEL and KNOX classes were found in Chlorobionta (green plants) and in Rhodophyta. We found representatives of the DDT, WOX, and PINTOX classes only in green plants, including unicellular green algae, moss, and vascular plants. All 14 homeobox gene classes were represented in flowering plants, Selaginella, and moss, suggesting that they had already differentiated in the last common ancestor of moss and vascular plants

A population-specific material model for sagittal craniosynostosis to predict surgical shape outcomes

Sagittal craniosynostosis consists of premature fusion (ossification) of the sagittal suture during infancy, resulting in head deformity and brain growth restriction. Spring-assisted cranioplasty (SAC) entails skull incisions to free the fused suture and insertion of two springs (metallic distractors) to promote cranial reshaping. Although safe and effective, SAC outcomes remain uncertain. We aimed hereby to obtain and validate a skull material model for SAC outcome prediction. Computed tomography data relative to 18 patients were processed to simulate surgical cuts and spring location. A rescaling model for age matching was created using retrospective data and validated. Design of experiments was used to assess the effect of different material property parameters on the model output. Subsequent material optimization—using retrospective clinical spring measurements—was performed for nine patients. A population-derived material model was obtained and applied to the whole population. Results showed that bone Young’s modulus and relaxation modulus had the largest effect on the model predictions: the use of the population-derived material model had a negligible effect on improving the prediction of on-table opening while significantly improved the prediction of spring kinematics at follow-up. The model was validated using on-table 3D scans for nine patients: the predicted head shape approximated within 2 mm the 3D scan model in 80% of the surface points, in 8 out of 9 patients. The accuracy and reliability of the developed computational model of SAC were increased using population data: this tool is now ready for prospective clinical application

High-Level Language Tools for Reconfigurable Computing

In the past decade or so we have witnessed a steadily increasing interest in FPGAs as hardware accelerators: they provide an excellent mid-point between the reprogrammability of software devices (CPUs, DSPs, and GPUs) and the performance and low energy consumption of ASICs. However, the programmability of FPGA-based accelerators remains one of the biggest obstacles to their wider adoption. Developing FPGA programs requires extensive familiarity with hardware design and experience with a tedious and complex tool chain. For half a century, layers of abstractions have been developed that simplify the software development process: languages, compilers, dynamically linked libraries, operating systems, APIs, etc. Very little, if any, such abstractions exist in the development of FPGA programs. In this paper, we review the history of using FPGAs as hardware accelerators and summarize the challenges facing the raising of the programming abstraction layers. We survey five High-Level Language tools for the development of FPGA programs: Xilinx Vivado, Altera OpenCL, BluespecBSV, ROCCC, and LegUp to provide an overview of their tool flow, the optimizations they provide, and a qualitative analysis of their hardware implementations of high level code

An open-source compiler and PCB synthesis tool for digital microfluidic biochips

This paper describes a publicly available, open source software framework designed to support research efforts on algorithms and control for digital microfluidic biochips (DMFBs), an emerging laboratory-on-a-chip (LoC) technology. The framework consists of two parts: a compiler, which converts an assay, specified using the BioCoder language, into a sequence of electrode activations that execute out the assay on the DMFB; and a printed circuit board (PCB) layout tool, which includes algorithms to reduce the number of control pins and PCB layers required to drive the chip from an external source. The framework also includes a suite of visualization tools for debugging, and a collection of front-end algorithms that generate mixing/dilution trees for sample preparation

Adapted cognitive behavior therapy for obsessive compulsive disorder with co-occuring autism spectrum disorder: A clinical effectiveness study

Obsessive-compulsive disorder (OCD) and autism spectrum disorder (ASD) commonly co-occur. Adapted CBT for OCD in adults with ASD has not previously been evaluated outside the United Kingdom. In this study, 19 adults with OCD and ASD were treated using an adapted CBT protocol that consisted of 20 sessions focused on exposure with response prevention. The primary outcome was the clinician-rated Yale-Brown Obsessive-Compulsive Scale (YBOCS). Participants were assessed up to 3 months after treatment. There were significant reductions on the YBOCS at post-treatment (d=1.5), and improvements were sustained at follow-up (d=1.2). Self-rated OCD symptoms and depressive symptoms showed statistically significant reductions. Improvements in general functioning and quality of life were statistically non-significant. Three participants (16%) were responders at post-treatment and four (21%) were in remission from OCD. At follow-up, three participants (16%) were responders and one (5%) was in full remission. Adapted CBT for OCD in adults with co-occurring ASD is associated with reductions in obsessive-compulsive symptoms and depressive symptoms. However, outcomes are modest; few patients were completely symptom free, and treatment engagement was low with few completed exposures and low adherence to homework assignments. We identify and discuss the need for further treatment refinement for this vulnerable group