VARiD: A variation detection framework for color-space and letter-space platforms

Motivation: High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together

Apprehending Joule Thieves with Cinder

Energy is the critical limiting resource to mobile computing devices. Correspondingly, an operating system must track, provision, and ration how applications consume energy. The emergence of third-party application stores and marketplaces makes this concern even more pressing. A third-party application must not deny service through excessive, unforeseen energy expenditure, whether accidental or malicious. Previous research has shown promise in tracking energy usage and rationing it to meet device lifetime goals, but such mechanisms and policies are still nascent, especially regarding user interaction. We argue for a new operating system, called Cinder, which builds on top of the HiStar OS. Cinder's energy awareness is based on hierarchical capacitors and task profiles. We introduce and explore these abstractions, paying particular attention to the ways in which policies could be generated and enforced in a dynamic system

Energy management in mobile devices with the cinder operating system

We argue that controlling energy allocation is an increasingly useful and important feature for operating systems, especially on mobile devices. We present two new low-level abstractions in the Cinder operating system, reserves and taps, which store and distribute energy for application use. We identify three key properties of control -- isolation, delegation, and subdivision -- and show how using these abstractions can achieve them. We also show how the architecture of the HiStar information-flow control kernel lends itself well to energy control. We prototype and evaluate Cinder on a popular smartphone, the Android G1.National Science Foundation (U.S.) (grant #0831163)National Science Foundation (U.S.) (grant #0846014)Natural Sciences and Engineering Research Council of Canada (NSERC)King Abdullah University of Science and TechnologyMicrosoft ResearchNational Science Foundation (U.S.) (Cybertrust award CNS-0716806)National Science Foundation (U.S.) (POMI (Programmable Open Mobile Internet) 2020 Expedition Grant #0832820)T-Mobile US

Welcome to Zombieland: Practical and Energy-efficient Memory Disaggregation in a Datacenter

In this paper, we propose an effortless way for disaggregating the CPU-memory couple, two of the most important resources in cloud computing. Instead of redesigning each resource board, the disaggregation is done at the power supply domain level. In other words, CPU and memory still share the same board, but their power supply domains are separated. Besides this disaggregation, we make the two following contributions: (1) the prototyping of a new ACPI sleep state (called zombie and noted Sz) which allows to suspend a server (thus save energy) while making its memory remotely accessible; and (2) the prototyping of a rack-level system software which allows the transparent utilization of the entire rack resources (avoiding resource waste). We experimentally evaluate the effectiveness of our solution and show that it can improve the energy efficiency of state-of-the-art consolidation techniques by up to 86%, with minimal additional complexity

Adjuvant and Salvage Radiotherapy After Prostatectomy: American Society of Clinical Oncology Clinical Practice Guideline Endorsement

PURPOSE: To endorse the American Urological Association (AUA)/American Society for Radiation Oncology (ASTRO) guideline on adjuvant and salvage radiotherapy after prostatectomy. The American Society of Clinical Oncology (ASCO) has a policy and set of procedures for endorsing clinical practice guidelines developed by other professional organizations. METHODS: The guideline on adjuvant and salvage radiotherapy after prostatectomy was reviewed for developmental rigor by methodologists. An ASCO endorsement panel then reviewed the content and recommendations. RESULTS: The panel determined that the guideline recommendations on adjuvant and salvage radiotherapy after prostatectomy, published in August 2013, are clear, thorough, and based on the most relevant scientific evidence. ASCO endorsed the guideline on adjuvant and salvage radiotherapy after prostatectomy, adding one qualifying statement that not all candidates for adjuvant or salvage radiotherapy have the same risk of recurrence or disease progression, and thus, risk-benefit ratios are not the same for all men. Those at the highest risk for recurrence after radical prostatectomy include men with seminal vesicle invasion, Gleason score 8 to 10, extensive positive margins, and detectable postoperative prostate-specific antigen (PSA). RECOMMENDATIONS: Physicians should discuss adjuvant radiotherapy with patients with adverse pathologic findings at prostatectomy (ie, seminal vesicle invasion, positive surgical margins, extraprostatic extension) and salvage radiotherapy with patients with PSA or local recurrence after prostatectomy. The discussion of radiotherapy should include possible short- and long-term adverse effects and potential benefits. The decision to administer radiotherapy should be made by the patient and multidisciplinary treatment team, keeping in mind that not all men are at equal risk of recurrence or clinically meaningful disease progression. Thus, the risk-benefit ratio will differ for each patient

SHRiMP: Accurate Mapping of Short Color-space Reads

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp

RPCValet: NI-Driven Tail-Aware Balancing of µs-Scale RPCs

Modern online services come with stringent quality requirements in terms of response time tail latency. Because of their decomposition into fine-grained communicating software layers, a single user request fans out into a plethora of short, μs-scale RPCs, aggravating the need for faster inter-server communication. In reaction to that need, we are witnessing a technological transition characterized by the emergence of hardware-terminated user-level protocols (e.g., InfiniBand/RDMA) and new architectures with fully integrated Network Interfaces (NIs). Such architectures offer a unique opportunity for a new NI-driven approach to balancing RPCs among the cores of manycore server CPUs, yielding major tail latency improvements for μs-scale RPCs. We introduce RPCValet, an NI-driven RPC load-balancing design for architectures with hardware-terminated protocols and integrated NIs, that delivers near-optimal tail latency. RPCValet's RPC dispatch decisions emulate the theoretically optimal single-queue system, without incurring synchronization overheads currently associated with single-queue implementations. Our design improves throughput under tight tail latency goals by up to 1.4x, and reduces tail latency before saturation by up to 4x for RPCs with μs-scale service times, as compared to current systems with hardware support for RPC load distribution. RPCValet performs within 15% of the theoretically optimal single-queue system

Historic landscape character and sense of place

This is an Author's Accepted Manuscript of an article published in Landscape Research, 2013, Vol. 38, Issue 2 pp.179-202, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/01426397.2012.672642.Most studies of landscape character within archaeology and historical geography have focused on morphological features such as whether settlement patterns were nucleated or dispersed, but this paper discusses how adding depth to this, for example by studying place-names, vernacular architecture, and the territorial structures within which a landscape was managed in the past, gives us a far greater understanding of its texture and meaning to local communities. In two case-studies in southern Essex, for example, it is shown how the connections that once existed between inland and coastal communities can be used today to promote public access to the countryside. A further case study, in southwest England, shows how field-/place-names and vernacular architecture also make an important contribution to our appreciation of the time depth and complexity of landscape character.Arts and Humanities Research Council (AHRC)Southend-on-Sea Borough Counci