DISTRIBUTED REPRODUCIBLE RESEARCH USING CACHED COMPUTATIONS

The ability to make scientific findings reproducible is increasingly important in areas where substantive results are the product of complex statistical computations. Reproducibility can allow others to verify the published findings and conduct alternate analyses of the same data. A question that arises naturally is how can one conduct and distribute reproducible research? This question is relevant from the point of view of both the authors who want to make their research reproducible and readers who want to reproduce relevant findings reported in the scientific literature. We present a framework in which reproducible research can be conducted and distributed via cached computations and describe specific tools for both authors and readers. As a prototype implementation we introduce three software packages written in the R language. The cacheSweave and stashR packages together provide tools for caching computational results in a key-value style database which can be published to a public repository for readers to download. The SRPM package provides tools for generating and interacting with "shared reproducibility packages" (SRPs) which can facilitate the distribution of the data and code. As a case study we demonstrate the use of the toolkit on a national study of air pollution exposure and mortality.

Potassium transporters in plants--involvement in K+ acquisition, redistribution and homeostasis

Potassium is a major plant nutrient which has to be accumulated in great quantity by roots and distributed throughout the plant and within plant cells. Membrane transport of potassium can be mediated by potassium channels and secondary potassium transporters. Plant potassium transporters are present in three families of membrane proteins: the K(+) uptake permeases (KT/HAK/KUP), the K(+) transporter (Trk/HKT) family and the cation proton antiporters (CPA). This review will discuss the contribution of members of each family to potassium acquisition, redistribution and homeostasis.

Diagnostic workup of patients with acute transverse myelitis: spectrum of clinical presentation, neuroimaging and laboratory findings

STUDY DESIGN: Retrospective 9-year survey. OBJECTIVES: Clinical presentation of acute myelitis syndromes is variable, and neuroimaging and laboratory findings are not specific enough to establish the diagnosis with certainty. We evaluated the spectrum clinical features and paraclinical findings encountered during diagnostic workup and aiding the diagnosis. SETTING: Department of Neurology, Inselspital Bern, Switzerland. MATERIAL: Charts and magnetic resonance imaging (MRI) of 63 patients discharged with the diagnosis of acute transverse myelitis. RESULTS: The diagnosis was supported by abnormal MRI and cerebrospinal fluid (CSF) findings in 52 patients (82.5%) and suspected in the remaining either because of a spinal cord MRI lesion suggestive of myelitis (n=5), or abnormal CSF findings (n=4), or electrophysiological evidence of a spinal cord dysfunction (n=2). Clinical impairment was mild (ASIA D) in the majority. All patients had sensory disturbances, whereas motor deficit and autonomic dysfunction were less frequent. Neurological levels were mainly located in cervical or thoracic dermatomes. Spinal cord lesions were visualized by MRI in 90.4% of the patients and distributed either in the cervical or thoracic cord, or both. Multiple lesions were present in more than half of the patients, and lateral, centromedullary and posterior locations were most common. A high percentage of multiple sclerosis (MS)-typical brain lesions and CSF findings suggested a substantial number of MS-related myelitis in our cohort. CONCLUSION: The diagnostic workup of acute myelitis discloses a broad spectrum of CSF or MRI findings, and may be associated with diagnostic uncertainty due to lack of specific CSF or MRI features, or pathological findings.

DISTRIBUTED APPROACH FOR SOLVING OPTIMAL POWER FLOW PROBLEMS IN THREE-PHASE UNBALANCED DISTRIBUTION NETWORK

The objective of this report is to study distributed (decentralized) three phase optimal power flow (OPF) problem in unbalanced power distribution networks. A full three phase representation of the distribution networks is considered to account for the highly unbalance state of the distribution networks. All distribution network’s series/shunt components, and load types/combinations had been modeled on commercial version of General Algebraic Modeling System (GAMS), the high-level modeling system for mathematical programming and optimization. The OPF problem has been successfully implemented and solved in a centralized approach and distributed approach, where the objective is to minimize the active power losses in the entire system. The study was implemented on the IEEE-37 Node Test Feeder. A detailed discussion of all problem sides and aspects starting from the basics has been provided in this study. Full simulation results have been provided at the end of the report.

Initializing a National Grid Infrastructure: Lessons Learned from the Swiss National Grid Association Seed Project

In addition to multi-national Grid infrastructures, several countries operate their own national Grid infrastructures to support science and industry within national borders. These infrastructures have the benefit of better satisfying the needs of local, regional and national user communities. Although Switzerland has strong research groups in several fields of distributed computing, only recently a national Grid effort was kick-started to integrate a truly heterogeneous set of resource providers, middleware pools, and users. In the following. article we discuss our efforts to start Grid activities at a national scale to combine several scientific communities and geographical domains. We make a strong case for the need of standards that have to be built on top of existing software systems in order to provide support for a heterogeneous Grid infrastruc

Generisches Framework Studi-App

Mit der Idee eines generischen, an vielfältige Hochschulanforderungen anpassbaren Studierenden-App-Frameworks haben sich innerhalb des Arbeitskreises Web der ZKI ca. 30 Hochschulen zu einem Entwicklungsverbund zusammengefunden. Ziel ist es, an den beteiligten Einrichtungen eine umfassende Zusammenstellung aller elektronischen Studienservices zu evaluieren, übergreifende Daten- und Metadatenmodelle für die Beschreibung dieser Dienste zu erstellen und Schnittstellen zu den gängigen Campusmanagementsystemen sowie zu Infrastrukturen der elektronischen Lehre (LMS, Druckdienste, elektronischen Katalogen usw.) zu entwickeln. In einem abschließenden Schritt werden auf dieser Middleware aufsetzende Studienmanagement-Apps für Studierende erstellt, die die verschiedenen Daten- und Kommunikationsströme der standardisierten Dienste und Kommunikationskanäle bündeln und in eine für den Studierenden leicht zu durchschauende, navigationsfreundliche Aufbereitung kanalisiert. Mit der Konzeption eines dezentralen, über eine Vielzahl von Hochschulen verteilten Entwicklungsprojektes unter einer zentralen Projektleitung wird sichergestellt, dass redundante Entwicklungen vermieden, bundesweit standardisierte Serviceangebote angeboten und Wissenstransferprozesse zwischen einer Vielzahl von Hochschulen zur Nutzung mobiler Devices (Smartphones, Tablets und entsprechende Apps) angeregt werden können. Die Unterstützung der Realisierung klarer Schnittstellenspezifikationen zu Campusmanagementsystemen durch deren Anbieter kann durch diese breite Interessensgemeinschaft ebenfalls gestärkt werden. Weiterhin zentraler Planungsinhalt ist ein Angebot für den App-Nutzer zum Aufbau eines datenschutzrechtlich integeren, persönlichen E-Portfolios. Details finden sich im Kapitel Projektziele weiter unten.

Semantic Methods for Intelligent Distributed Design Environments

Continuous advancements in technology have led to increasingly comprehensive and distributed product development processes while in pursuit of improved products at reduced costs. Information associated with these products is ever changing, and structured frameworks have become integral to managing such fluid information. Ontologies and the Semantic Web have emerged as key alternatives for capturing product knowledge in both a human-readable and computable manner. The primary and conclusive focus of this research is to characterize relationships formed within methodically developed distributed design knowledge frameworks to ultimately provide a pervasive real-time awareness in distributed design processes. Utilizing formal logics in the form of the Semantic Web’s OWL and SWRL, causal relationships are expressed to guide and facilitate knowledge acquisition as well as identify contradictions between knowledge in a knowledge base. To improve the efficiency during both the development and operational phases of these “intelligent” frameworks, a semantic relatedness algorithm is designed specifically to identify and rank underlying relationships within product development processes. After reviewing several semantic relatedness measures, three techniques, including a novel meronomic technique, are combined to create AIERO, the Algorithm for Identifying Engineering Relationships in Ontologies. In determining its applicability and accuracy, AIERO was applied to three separate, independently developed ontologies. The results indicate AIERO is capable of consistently returning relatedness values one would intuitively expect. To assess the effectiveness of AIERO in exposing underlying causal relationships across product development platforms, a case study involving the development of an industry-inspired printed circuit board (PCB) is presented. After instantiating the PCB knowledge base and developing an initial set of rules, FIDOE, the Framework for Intelligent Distributed Ontologies in Engineering, was employed to identify additional causal relationships through extensional relatedness measurements. In a conclusive PCB redesign, the resulting “intelligent” framework demonstrates its ability to pass values between instances, identify inconsistencies amongst instantiated knowledge, and identify conflicting values within product development frameworks. The results highlight how the introduced semantic methods can enhance the current knowledge acquisition, knowledge management, and knowledge validation capabilities of traditional knowledge bases.

Source attribution of human Campylobacter isolates by MLST and fla-typing and association of genotypes with quinolone resistance

Campylobacteriosis is the most frequent zoonosis in developed countries and various domestic animals can function as reservoir for the main pathogens Campylobacter jejuni and Campylobacter coli. In the present study we compared population structures of 730 C. jejuni and C. coli from human cases, 610 chicken, 159 dog, 360 pig and 23 cattle isolates collected between 2001 and 2012 in Switzerland. All isolates had been typed with multi locus sequence typing (MLST) and flaB-typing and their genotypic resistance to quinolones was determined. We used complementary approaches by testing for differences between isolates from different hosts with the proportion similarity as well as the fixation index and by attributing the source of the human isolates with Bayesian assignment using the software STRUCTURE. Analyses were done with MLST and flaB data in parallel and both typing methods were tested for associations of genotypes with quinolone resistance. Results obtained with MLST and flaB data corresponded remarkably well, both indicating chickens as the main source for human infection for both Campylobacter species. Based on MLST, 70.9% of the human cases were attributed to chickens, 19.3% to cattle, 8.6% to dogs and 1.2% to pigs. Furthermore we found a host independent association between sequence type (ST) and quinolone resistance. The most notable were ST-45, all isolates of which were susceptible, while for ST-464 all were resistant.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

Topology and Link quality-aware Geographical opportunistic routing in wireless ad-hoc networks

Opportunistic routing (OR) takes advantage of the broadcast nature and spatial diversity of wireless transmission to improve the performance of wireless ad-hoc networks. Instead of using a predetermined path to send packets, OR postpones the choice of the next-hop to the receiver side, and lets the multiple receivers of a packet to coordinate and decide which one will be the forwarder. Existing OR protocols choose the next-hop forwarder based on a predefined candidate list, which is calculated using single network metrics. In this paper, we propose TLG - Topology and Link quality-aware Geographical opportunistic routing protocol. TLG uses multiple network metrics such as network topology, link quality, and geographic location to implement the coordination mechanism of OR. We compare TLG with well-known existing solutions and simulation results show that TLG outperforms others in terms of both QoS and QoE metrics.

Ontology driven integration platform for clinical and translational research

Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a dynamic and distributed environment. Components of the semantic solution and its overall architecture are described.

MODIFICATION AND IMPLEMENTATION OF THE RPC HETEROGENEOUS THORAX PHANTOM FOR VERIFICATION OF PROTON THERAPY TREATMENT PROCEDURES

The Radiological Physics Center (RPC) provides heterogeneous phantoms that are used to evaluate radiation treatment procedures as part of a comprehensive quality assurance program for institutions participating in clinical trials. It was hypothesized that the existing RPC heterogeneous thorax phantom can be modified to assess lung tumor proton beam therapy procedures involving patient simulation, treatment planning, and treatment delivery, and could confirm agreement between the measured dose and calculated dose within 5%/3mm with a reproducibility of 5%. The Hounsfield Units (HU) for lung equivalent materials (balsa wood and cork) was measured using a CT scanner. The relative linear stopping power (RLSP) of these materials was measured. The linear energy transfer (LET) of Gafchromic EBT2 film was analyzed utilizing parallel and perpendicular orientations in a water tank and compared to ion chamber readings. Both parallel and perpendicular orientations displayed a quenching effect underperforming the ion chamber, with the parallel orientation showing an average 31 % difference and the perpendicular showing an average of 15% difference. Two treatment plans were created that delivered the prescribed dose to the target volume, while achieving low entrance doses. Both treatment plans were designed using smeared compensators and expanded apertures, as would be utilized for a patient in the clinic. Plan 1a contained two beams that were set to orthogonal angles and a zero degree couch kick. Plan 1b utilized two beams set to 10 and 80 degrees with a 15 degree couch kick. EBT2 film and TLD were inserted and the phantom was irradiated 3 times for each plan. Both plans passed the criteria for the TLD measurements where the TLD values were within 7% of the dose calculated by Eclipse. Utilizing the 5%/3mm criteria, the 3 trial average of overall pass rate was 71% for Plan 1a. The 3 trial average for the overall pass rate was 76% for Plan 1b. The trials were then analyzed using RPC conventional lung treatment guidelines set forth by the RTOG: 5%/5mm, and an overall pass rate of 85%. Utilizing these criteria, only Plan 1b passed for all 3 trials, with an average overall pass rate of 89%.