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"Letts, J."
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Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata
The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III2’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III2. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.Cryogenic electron microscopy structure of respiratory supercomplex I + III2 from mung bean reveals interfaces, a new complex I subunit and differences in complex III2 versus other supercomplexes. Resting complex I adopts an intermediate conformational state and a non-canonical active/deactive response.
Journal Article
How much higher can HTCondor fly?
The HTCondor high throughput computing system is heavily used in the high energy physics (HEP) community as the batch system for several Worldwide LHC Computing Grid (WLCG) resources. Moreover, it is the backbone of GlidelnWMS, the pilot system used by the computing organization of the Compact Muon Solenoid (CMS) experiment. To prepare for LHC Run 2, we probed the scalability limits of new versions and configurations of HTCondor with a goal of reaching 200,000 simultaneous running jobs in a single internationally distributed dynamic pool. In this paper, we first describe how we created an opportunistic distributed testbed capable of exercising runs with 200,000 simultaneous jobs without impacting production. This testbed methodology is appropriate not only for scale testing HTCondor, but potentially for many other services. In addition to the test conditions and the testbed topology, we include the suggested configuration options used to obtain the scaling results, and describe some of the changes to HTCondor inspired by our testing that enabled sustained operations at scales well beyond previous limits.
Journal Article
A Scoping Review of the Use of Theory in Studies of Knowledge Translation
Background.
Advancing the science of knowledge translation (KT) in occupational therapy is critical. Explicit application of theory can advance this science; yet, how theory is applied and the degree to which it can guide research remain poorly defined.
Purpose.
To understand how theory is applied within KT research.
Methods.
A scoping review was conducted to examine and summarize the extent, range, and nature of the application of three specific KT theories: Diffusion of Innovations, Promoting Action on Research Implementation in Health Services framework, and Theory of Planned Behaviour.
Findings.
Theory use was seen most frequently in medicine and nursing. Only 3 of 90 articles were in rehabilitation. Five approaches to theory application were found, the most common being the use of to predict success of KT (57/90).
Implications.
In-depth study of the importance and methods of theory application in KT research is needed, in particular in occupational therapy.
Journal Article
Optimal Positioning of Occupational Therapy
Background. Occupation is central to occupational therapy. Although occupation is a universal experience, occupational therapists need to consider the risks and opportunities of exploring new roles and maintaining existing services.
Purpose. I propose three questions to guide the optimal positioning of occupational therapy services. First, how proximal is occupation in the role? Second, how strong is the evidence to support occupational therapy in the role? Third, is the timing right for change? These questions are applied to the role of occupational therapy in primary health care.
Key Issues. Occupation is proximal and the evidence is emerging to support an occupational therapy role in primary health care. Reforms make timing ideal.
Implications. If we focus on the underlying principles of primary health care reform, the potential for an emerging role in primary health care is optimal. The same three questions can be used to transform and optimally position occupational therapy.
Journal Article
Assessment Tools for Evaluating Fitness to Drive: A Critical Appraisal of Evidence
Background. Many office-based assessment tools are used by occupational therapists to predict fitness to drive. Purpose. To appraise psychometric properties of such tools, specifically predictive validity for on-road performance. Methods. A literature search was conducted to identify assessment tools and studies involving on-road outcomes (behind-the-wheel evaluation, crashes, traffic violations). Using a standardized appraisal process, reviewers rated each tool's psychometrric properties, including its predictive validity with on-road performance. Findings. Seventeen measures met the inclusion criteria. Evidence suggests many tools do not have cut-off scores linked with on-road outcomes, although some had stronger evidence than others. Implications. When making a determination regarding driver fitness, clinicians should consider the psychometric properties of the tool as well as existing evidence concerning its utility in predicting on-road performance. Caution is warranted in using any one office-based tool to predict driving fitness; rather, a multifactorial-based assessment approach that includes physical, cognitive, and visual-perceptual components, is recommended.
Journal Article
CMS Connect
The CMS experiment collects and analyzes large amounts of data coming from high energy particle collisions produced by the Large Hadron Collider (LHC) at CERN. This involves a huge amount of real and simulated data processing that needs to be handled in batch-oriented platforms. The CMS Global Pool of computing resources provide +100K dedicated CPU cores and another 50K to 100K CPU cores from opportunistic resources for these kind of tasks and even though production and event processing analysis workflows are already managed by existing tools, there is still a lack of support to submit final stage condor-like analysis jobs familiar to Tier-3 or local Computing Facilities users into these distributed resources in an integrated (with other CMS services) and friendly way. CMS Connect is a set of computing tools and services designed to augment existing services in the CMS Physics community focusing on these kind of condor analysis jobs. It is based on the CI-Connect platform developed by the Open Science Grid and uses the CMS GlideInWMS infrastructure to transparently plug CMS global grid resources into a virtual pool accessed via a single submission machine. This paper describes the specific developments and deployment of CMS Connect beyond the CI-Connect platform in order to integrate the service with CMS specific needs, including specific Site submission, accounting of jobs and automated reporting to standard CMS monitoring resources in an effortless way to their users.
Journal Article
Effective HTCondor-based monitoring system for CMS
The CMS experiment at the LHC relies on HTCondor and glideinWMS as its primary batch and pilot-based Grid provisioning systems, respectively. Given the scale of the global queue in CMS, the operators found it increasingly difficult to monitor the pool to find problems and fix them. The operators had to rely on several different web pages, with several different levels of information, and sift tirelessly through log files in order to monitor the pool completely. Therefore, coming up with a suitable monitoring system was one of the crucial items before the beginning of the LHC Run 2 in order to ensure early detection of issues and to give a good overview of the whole pool. Our new monitoring page utilizes the HTCondor ClassAd information to provide a complete picture of the whole submission infrastructure in CMS. The monitoring page includes useful information from HTCondor schedulers, central managers, the glideinWMS frontend, and factories. It also incorporates information about users and tasks making it easy for operators to provide support and debug issues.
Journal Article
CMS readiness for multi-core workload scheduling
In the present run of the LHC, CMS data reconstruction and simulation algorithms benefit greatly from being executed as multiple threads running on several processor cores. The complexity of the Run 2 events requires parallelization of the code to reduce the memory-per- core footprint constraining serial execution programs, thus optimizing the exploitation of present multi-core processor architectures. The allocation of computing resources for multi-core tasks, however, becomes a complex problem in itself. The CMS workload submission infrastructure employs multi-slot partitionable pilots, built on HTCondor and GlideinWMS native features, to enable scheduling of single and multi-core jobs simultaneously. This provides a solution for the scheduling problem in a uniform way across grid sites running a diversity of gateways to compute resources and batch system technologies. This paper presents this strategy and the tools on which it has been implemented. The experience of managing multi-core resources at the Tier-0 and Tier-1 sites during 2015, along with the deployment phase to Tier-2 sites during early 2016 is reported. The process of performance monitoring and optimization to achieve efficient and flexible use of the resources is also described.
Journal Article