An investigation of routes to cancer diagnosis in 10 international jurisdictions, as part of the International Cancer Benchmarking Partnership: survey development and implementation

Objectives This paper describes the methods used in the International Cancer Benchmarking Partnership Module 4 Survey (ICBPM4) which examines time intervals and routes to cancer diagnosis in 10 jurisdictions. We present the study design with defining and measuring time intervals, identifying patients with cancer, questionnaire development, data management and analyses.
Design and setting Recruitment of participants to the ICBPM4 survey is based on cancer registries in each jurisdiction. Questionnaires draw on previous instruments and have been through a process of cognitive testing and piloting in three jurisdictions followed by standardised translation and adaptation. Data analysis focuses on comparing differences in time intervals and routes to diagnosis in the jurisdictions.
Participants Our target is 200 patients with symptomatic breast, lung, colorectal and ovarian cancer in each jurisdiction. Patients are approached directly or via their primary care physician (PCP). Patients’ PCPs and cancer treatment specialists (CTSs) are surveyed, and ‘data rules’ are applied to combine and reconcile conflicting information. Where CTS information is unavailable, audit information is sought from treatment records and databases.
Main outcomes Reliability testing of the patient questionnaire showed that agreement was complete (κ=1) in four items and substantial (κ=0.8, 95% CI 0.333 to 1) in one item. The identification of eligible patients is sufficient to meet the targets for breast, lung and colorectal cancer. Initial patient and PCP survey response rates from the UK and Sweden are comparable with similar published surveys. Data collection was completed in early 2016 for all cancer types.
Conclusion An international questionnaire-based survey of patients with cancer, PCPs and CTSs has been developed and launched in 10 jurisdictions. ICBPM4 will help to further understand international differences in cancer survival by comparing time intervals and routes to cancer diagnosis.

Secure 5G Wireless Communications: A Joint Relay Selection and Wireless Power Transfer Approach

In this paper, we investigate the secrecy performance of an energy harvesting relay system, where a legitimate source communicates with a legitimate destination via the assistance of multiple trusted relays. In the considered system, the source and relays deploy the time-switching-based radio frequency energy harvesting technique to harvest energy from a multi-antenna beacon. Different antenna selection and relay selection schemes are applied to enhance the security of the system. Specifically, two relay selection schemes based on the partial and full knowledge of channel state information, i.e., optimal relay selection and partial relay selection, and two antenna selection schemes for harvesting energy at source and relays, i.e., maximizing energy harvesting channel for the source and maximizing energy harvesting channel for the selected relay, are proposed. The exact and asymptotic expressions of secrecy outage probability in these schemes are derived. We demonstrate that applying relay selection approaches in the considered energy harvesting system can enhance the security performance. In particular, optimal relay selection scheme outperforms partial relay selection scheme and achieves full secrecy diversity order, regardless of energy harvesting scenarios.

Design and Implementation of a Low Cost Virtual Rugby Decision Making Interactive

The paper describes the design and implementation of a novel low cost virtual rugby decision making interactive for use in a visitor centre. Original laboratory-based experimental work in decision making in rugby, using a virtual reality headset [1] is adapted for use in a public visitor centre, with consideration given to usability, costs, practicality and health and safety. Movement of professional rugby players was captured and animated within a virtually recreated stadium. Users then interact with these virtual representations via use of a lowcost sensor (Microsoft Kinect) to attempt to block them. Retaining the principles of perception and action, egocentric viewpoint, immersion, sense of presence, representative design and game design the system delivers an engaging and effective interactive to illustrate the underlying scientific principles of deceptive movement. User testing highlighted the need for usability, system robustness, fair and accurate scoring, appropriate level of difficulty and enjoyment.

Design and implementation of a non-destructive defect detection technique based on UWB-SAR imaging

In the last twenty years aerospace and automotive industries started working widely with composite materials, which are not easy to test using classic Non-Destructive Inspection (NDI) techniques. Pairwise, the development of safety regulations sets higher and higher standards for the qualification and certification of those materials. In this thesis a new concept of a Non-Destructive defect detection technique is proposed, based on Ultrawide-Band (UWB) Synthetic Aperture Radar (SAR) imaging. Similar SAR methods are yet applied either in minefield [22] and head stroke [14] detection. Moreover feasibility studies have already demonstrated the validity of defect detection by means of UWB radars [12, 13]. The system was designed using a cheap commercial off-the-shelf radar device by Novelda and several tests of the developed system have been performed both on metallic specimen (aluminum plate) and on composite coupon (carbon fiber). The obtained results confirm the feasibility of the method and highlight the good performance of the developed system considered the radar resolution. In particular, the system is capable of discerning healthy coupons from damaged ones, and correctly reconstruct the reflectivity image of the tested defects, namely a 8 x 8 mm square bulge and a 5 mm drilled holes on metal specimen and a 5 mm drilled hole on composite coupon.

Design and implementation of BIRDY satellite data and Radiation Payload simulators

Numerical modelling and simulations are needed to develop and test specific analysis methods by providing test data before BIRDY would be launched. This document describes the "satellite data simulator" which is a multi-sensor, multi-spectral satellite simulator produced especially for the BIRDY mission which could be used as well to analyse data from other satellite missions providing energetic particles data in the Solar system.

Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Selection and Floral Evolution in Platanthera bifolia and P. chlorantha (Orchidaceae)

Natural selection mediated by pollinators has influenced the evolution of floral diversity of the flowering plants (angiosperms). The scope of this thesis was to study: 1) phenotypic selection, 2) mating systems, and 3) floral shifts involved in plant speciation. Model plant species were Platanthera bifolia and P. chlorantha (Orchidaceae). These orchids are moth-pollinated, strictly co-sexual (bisexual flowers), and produce a spike that displays 10-20 white flowers. I explored the influence of characters on plant fitness by using multiple linear regressions. Pollen removal (male fitness) and fruit set (female fitness) increased with more flowers per plant in three P. bifolia populations. There was selection towards longer spurs in a dry year when average spur length was shorter than in normal-wet years. Female function was sensitive to drought, which enabled an application of the male function hypothesis of floral evolution (Bateman's principle). The results show that selection may vary between populations, years, and sex-functions. I examined inbreeding by estimating levels of geitonogamy (self-pollination between flowers of an individual) with an emasculation method in two P. bifolia populations. Geitonogamy did not vary with inflorescence size. Levels of geitonogamy was 20-40% in the smaller, but non-significant in the larger population. This may relate to lower number of possible mates and pollinator activity in the smaller population. Platanthera bifolia exhibits the ancestral character state of tongue-attachment of pollinia on the pollinator. Its close relative P. chlorantha attaches its pollinia onto the pollinator's eyes. To explore the mechanism of a floral shift, pollination efficiency and speed was compared between the two species. The results showed no differences in pollination efficiency, but P. chlorantha had faster pollen export and import. Efficiency of pollination in terms of speed may cause floral shifts, and thus speciation.

The politics of negotiation and implementation: a reciprocal water access agreement in the Himalayan foothills, India

In this paper, we examine the on-the-ground realities of upstream-downstream negotiations and transactions over ecosystem services. We explore the engagement, negotiation, implementation, and postimplementation phases of a “reciprocal water access” (RWA) agreement between village communities and municipal water users at Palampur, Himachal Pradesh, India. We aim to highlight how external actors drove the payments for ecosystem services agenda through a series of facilitation and research engagements, which were pivotal to the RWA’s adoption, and how the agreement fared once external agents withdrew. In the postimplementation period, the RWA agreement continues to be upheld by upstream communities amidst evolving, competing land-use changes and claims. The introduction of cash payments for environmental services for forest-water relationships has given rise to multifaceted difficulties for the upstream hamlets, which has impeded the functionality of their forest management committee. Upstream communities’ formal rights and abilities to control and manage their resources are dynamic and need strengthening and assurance; these developments result in fluctuating transaction and opportunity costs not originally envisaged by the RWA agreement. The paper demonstrates the importance of an explicit understanding of the local politics of negotiation and implementation to determine the effectiveness of compensation-based mechanisms for the supply of ecosystem services.

An appraisal of adaptive management planning and implementation in ecological restoration: case studies from the San Francisco Bay Delta, USA

Adaptive management has been defined and redefined in the context of natural resource management, yet there are few examples of its successful application in ecological restoration. Although the 2009 Delta Reform Act now legally requires adaptive management for all restoration efforts in the Sacramento-San Joaquin Delta, in California, USA, projects in this region still encounter problems with implementation. We used a comparative case study analysis to examine adaptive management planning and implementation both in and around the Delta, assessing not only why adaptive management is not yet well implemented, but also what changes can be made to facilitate the adaptive management approach without sacrificing scientific rigor. Adaptive management seems to be directly and indirectly affected by a variety of challenges and convoluted by ambiguity in both planning documents and practitioner’s interpretations of the concept. Addressing these challenges and ambiguities at the project level may facilitate the adaptive management process and help make it more accessible to practitioners.

Verification and Implementation of Call Sequence Analysing Algorithm

Työssä arvioidaan ja verifioidaan puheluiden luokitteluun suunniteltu Call Sequence Analysing Algorithm (CSA-algoritmi). Algoritmin tavoitteena on luokitella riittävän samankaltaiset puhelut ryhmiksi tarkempaa vika-analyysia varten. Työssä esitellään eri koneoppimisalgoritmien pääluokitukset ja niiden tyypilliset eroavaisuudet, eri luokitteluprosesseille ominaiset datatyypit, sekä toimintaympäristöt, joissa kyseinen toteutus on suunniteltu toimivaksi. CSA-algoritmille syötetään verkon ylläpitoviesteistä koostuvia viestisarjoja, joiden sisällön perusteella samankaltaiset sarjat ryhmitellään kokonaisuuksiksi. Algoritmin suorituskykyä arvioidaan 94 käsin luokitellun verrokkisarjan avulla. Sarjat on kerätty toimivasta 3G-verkon kontrollerista. Kahta sarjaa vertailemalla sarjaparille muodostetaan keskinäinen tunnusluku: sarjojen samanlaisuutta kuvaava etäisyys. Tässä työssä keskitytään erityisesti Hamming-etäisyyteen. Etäisyyden avulla sarjat koostetaan ryhmiksi. Muuttamalla hyväksyttävää maksimietäisyyttä, jonka perusteella kaksi sarjaa lasketaan kuuluvaksi samaan ryhmään, saadaan aikaiseksi alaryhmiä, joihin kuuluu ainoastaan samankaltaisia sarjoja. Hyväksyttävän etäisyyden kasvaessa, myös virheluokitusten määrä kasvaa. Oikeiden lajittelutulosten vertailukohteena toimii käsin luokiteltu ryhmittely. CSA-algoritmin luokittelutuloksen tarkkuus esitetään prosentuaalisena osuutena tavoiteryhmittelystä maksimietäisyyden funktiona. Työssä osoitetaan, miten etäisyysattribuutiksi valittu Hamming-etäisyys ei sovellu tämän datan luokitteluun. Työn lopussa ehdotetaan menetelmää ja työkalua, joiden avulla useampaa eri lajittelija-algoritmia voidaan testata nopealla kehityssyklillä.

The Design and Implementation of a SD Card File System

SD card (Secure Digital Memory Card) is widely used in portable storage medium. Currently, latest researches on SD card, are mainly SD card controller based on FPGA (Field Programmable Gate Array). Most of them are relying on API interface (Application Programming Interface), AHB bus (Advanced High performance Bus), etc. They are dedicated to the realization of ultra high speed communication between SD card and upper systems. Studies about SD card controller, really play a vital role in the field of high speed cameras and other sub-areas of expertise. This design of FPGA-based file systems and SD2.0 IP (Intellectual Property core) does not only exhibit a nice transmission rate, but also achieve the systematic management of files, while retaining a strong portability and practicality. The file system design and implementation on a SD card covers the main three IP innovation points. First, the combination and integration of file system and SD card controller, makes the overall system highly integrated and practical. The popular SD2.0 protocol is implemented for communication channels. Pure digital logic design based on VHDL (Very-High-Speed Integrated Circuit Hardware Description Language), integrates the SD card controller in hardware layer and the FAT32 file system for the entire system. Secondly, the document management system mechanism makes document processing more convenient and easy. Especially for small files in batch processing, it can ease the pressure of upper system to frequently access and process them, thereby enhancing the overall efficiency of systems. Finally, digital design ensures the superior performance. For transmission security, CRC (Cyclic Redundancy Check) algorithm is for data transmission protection. Design of each module is platform-independent of macro cells, and keeps a better portability. Custom integrated instructions and interfaces may facilitate easily to use. Finally, the actual test went through multi-platform method, Xilinx and Altera FPGA developing platforms. The timing simulation and debugging of each module was covered. Finally, Test results show that the designed FPGA-based file system IP on SD card can support SD card, TF card and Micro SD with 2.0 protocols, and the successful implementation of systematic management for stored files, and supports SD bus mode. Data read and write rates in Kingston class10 card is approximately 24.27MB/s and 16.94MB/s.

Design and implementation of a floating point unit for rigel, a massively parallel accelerator

Scientific applications rely heavily on floating point data types. Floating point operations are complex and require complicated hardware that is both area and power intensive. The emergence of massively parallel architectures like Rigel creates new challenges and poses new questions with respect to floating point support. The massively parallel aspect of Rigel places great emphasis on area efficient, low power designs. At the same time, Rigel is a general purpose accelerator and must provide high performance for a wide class of applications. This thesis presents an analysis of various floating point unit (FPU) components with respect to Rigel, and attempts to present a candidate design of an FPU that balances performance, area, and power and is suitable for massively parallel architectures like Rigel.