AP/Linux - initial implementation

The AP1000+ is a distributed-memory parallel computer based on SuperSPARC processors, which incorporates message-passing hardware which can be accessed safely from user mode. We are in the process of porting the Linux kernel to this machine and extending it to support execution of parallel programs. This report outlines the motivation and background of this effort, and describes the current status and future directions for the work. The reader may also refer to our WWW page at http://cap.anu.edu.au/cap/projects/linux for up to date information on the progress of the port

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.https://doi.org/10.1186/1471-2105-12-35

AP/Linux - A modern OS for the AP1000+

AP/Linux is an ongoing effort to develop a new operating system environment for the Fujitsu AP1000+ and successor machines. Based on the popular Linux operating system, AP/Linux provides modern operating system capabilities, such as virtual memory and multi-user support, as well as efficient communication facilities for parallel programs. Users can develop parallel programs using MPI or the CellOS-compatible APlib library. This paper describes the progress achieved thus far in developing the system, and presents results from some simple parallel benchmark programs showing that there is no loss of performance for parallel programs running under AP/Linux, compared with the standard CellOS environment. 1 Introduction The standard operating system provided with the Fujitsu AP1000+[2, 1] is CellOS. CellOS supports the execution of a single program at any given time. The CellOS kernel is short-lived in the sense that the machine is reset and the CellOS kernel is reloaded anew each time a pr..

Novel therapeutic option for orbital atypical lymphoid hyperplasia

Ocular lymphoid tumours represent a spectrum of lymphoproliferative disease and can be subdivided into benign or reactive lymphoid hyperplasia, indeterminate or atypical lymphoid proliferations and malignant lymphoma. Treatment options include a wait an

Acute hyperglycemia impairs IL‐6 expression in humans

Normal glucose metabolism is critical to immune function but the effects of short‐term hyperglycemia on immunity are not well described. To study this phenomenon, we induced hyperglycemia in healthy subjects for 2 h with intravenous dextrose and octreotide. An RNA‐seq analysis of whole blood RNA demonstrated alterations in multiple immune pathways and transcripts during acute hyperglycemia including decreased transcription of IL‐6, an important component of both innate and adaptive immune responses. Additional in vitro studies of human peripheral blood mononuclear cells (PBMCs) exposed to high glucose confirmed decreased IL‐6 expression, most prominently in CD14(+)CD16(+) intermediate monocytes. Hyperglycemia also reduced IL‐17A expression suggesting further impairment of immune responses during acute hyperglycemia. These findings demonstrate multiple defective immune responses in acute hyperglycemia and suggest a novel role for intermediate monocytes as metabolically sensitive innate immune cells

Acute hyperglycemia impairs IL-6 expression in humans.

Normal glucose metabolism is critical to immune function but the effects of short-term hyperglycemia on immunity are not well described. To study this phenomenon, we induced hyperglycemia in healthy subjects for 2 h with intravenous dextrose and octreotide. An RNA-seq analysis of whole blood RNA demonstrated alterations in multiple immune pathways and transcripts during acute hyperglycemia including decreased transcription of IL-6, an important component of both innate and adaptive immune responses. Additional in vitro studies of human peripheral blood mononuclear cells (PBMCs) exposed to high glucose confirmed decreased IL-6 expression, most prominently in CD14(+)CD16(+) intermediate monocytes. Hyperglycemia also reduced IL-17A expression suggesting further impairment of immune responses during acute hyperglycemia. These findings demonstrate multiple defective immune responses in acute hyperglycemia and suggest a novel role for intermediate monocytes as metabolically sensitive innate immune cells