Patterns of rural settlement in Sierra Leone: methods of geographical analysis in a tropical environment

The debate between classical empiricists and those who favour deductive and theoretical research methods is a feature of modern geography. This thesis aims to show that these approaches are complementary rather than mutually exclusive. It also hopes to demonstrate new methods and applications of location analysis in an underdeveloped area where base line information is uneven in quality. The dissertation is divided into four main parts. In the first, a model settlement pattern for Sierra Leone is devised. This model is based on a stylised subsistence village and the arguments of central place theory. The second part deals with the uses made of aerial photographs, topographical maps, pilot surveys and random sampling procedures in constructing an accurate base map of rural settlement distribution for the whole country, the first of its kind for any West African state. The third part of the work uses purely qualitative and empirical methods, A system of settlement regions is devised and described, and the settlement model is compared with the actual pattern, and with overall changes in settlement structures between 1927 and 1964. An account of rural settlement evolution using historical sources and comparative mapping is also presented. In the fourth part, a range of parametric and nonparametric tests and techniques of location analysis (e. g. set theory and nearest-neighbour analysis) is used to establish indices of settlement density and nucleation and to test the hypotheses presented in earlier sections of the work

Holderness: land drainage and the evolution of a landscape

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MHC-linked and un-linked class I genes in the wallaby

Background: MHC class I antigens are encoded by a rapidly evolving gene family comprising classical and non-classical genes that are found in all vertebrates and involved in diverse immune functions. However, there is a fundamental difference between the organization of class I genes in mammals and non-mammals. Non-mammals have a single classical gene responsible for antigen presentation, which is linked to the antigen processing genes, including TAP. This organization allows co-evolution of advantageous class Ia/ TAP haplotypes. In contrast, mammals have multiple classical genes within the MHC, which are separated from the antigen processing genes by class III genes. It has been hypothesized that separation of classical class I genes from antigen processing genes in mammals allowed them to duplicate. We investigated this hypothesis by characterizing the class I genes of the tammar wallaby, a model marsupial that has a novel MHC organization, with class I genes located within the MHC and 10 other chromosomal locations. Results: Sequence analysis of 14 BACs containing 15 class I genes revealed that nine class I genes, including one to three classical class I, are not linked to the MHC but are scattered throughout the genome. Kangaroo Endogenous Retroviruses (KERVs) were identified flanking the MHC un-linked class I. The wallaby MHC contains four non-classical class I, interspersed with antigen processing genes. Clear orthologs of non-classical class I are conserved in distant marsupial lineages. Conclusion: We demonstrate that classical class I genes are not linked to antigen processing genes in the wallaby and provide evidence that retroviral elements were involved in their movement. The presence of retroviral elements most likely facilitated the formation of recombination hotspots and subsequent diversification of class I genes. The classical class I have moved away from antigen processing genes in eutherian mammals and the wallaby independently, but both lineages appear to have benefited from this loss of linkage by increasing the number of classical genes, perhaps enabling response to a wider range of pathogens. The discovery of non-classical orthologs between distantly related marsupial species is unusual for the rapidly evolving class I genes and may indicate an important marsupial specific function

Survey of ultrasound practice amongst podiatrists in the UK

Background: Ultrasound in podiatry practice encompasses musculoskeletal ultrasound imaging, vascular hand-held Doppler ultrasound and therapeutic ultrasound. Sonography practice is not regulated by the Health and Care Professions Council (HCPC), with no requirement to hold a formal qualification. The College of Podiatry does not currently define ultrasound training and competencies. This study aimed to determine the current use of ultrasound, training received and mentorship received and/or provided by podiatrists using ultrasound. Methods: A quantitative study utilising a cross-sectional, on-line, single-event survey was undertaken within the UK. Results: Completed surveys were received from 284 podiatrists; 173 (70%) use ultrasound as part of their general practice, 139 (49%) for musculoskeletal problems, 131 (46%) for vascular assessment and 39 (14%) to support their surgical practice. Almost a quarter (n=62) worked for more than one organisation; 202 (71%) were employed by the NHS and/or private sector (n=118, 41%). Nearly all (93%) respondents report using a hand-held vascular Doppler in their daily practice; 216 (82%) to support decisions regarding treatment options, 102 (39%) to provide diagnostic reports for other health professionals, and 34 (13%) to guide nerve blocks. Ultrasound imaging was used by 104 (37%) respondents primarily to aid clinical decision making (n=81) and guide interventions (steroid injections n=67; nerve blocks n=39). Ninety-three percent stated they use ultrasound imaging to treat their own patients, while others scan at the request of other podiatrists (n=28) or health professionals (n=18). Few use ultrasound imaging for research (n=7) or education (n=2). Only 32 (11%) respondents (n=20 private sector) use therapeutic ultrasound to treat patients presenting with musculoskeletal complaints, namely tendon pathologies. Few respondents (18%) had completed formal post-graduate CASE (Consortium for the Accreditation of Sonographic Education) accredited ultrasound courses. Forty (14%) respondents receive ultrasound mentorship; the majority from fellow podiatrists (n=17) or medical colleagues (n=15). Over half (n=127) who do not have ultrasound mentorship indicated they would like a mentor predominantly for ultrasound imaging. Fifty-five (19%) report they currently provide ultrasound mentorship for others. Conclusions: Understanding the scope of ultrasound practice, the training undertaken and the requirements for mentorship will underpin the development of competencies and recommendations defined by the College of Podiatry to support professional development and ensure safe practice.</p

The Clinicians’ Skills, Capability, and Organisational Research Readiness (SCORR) Tool

A research-active healthcare workforce contributes to improved quality of care. Clinicians may be unaware that they are applying early research skills during their everyday practice. Greater understanding of their level of research attainment may improve their awareness and confidence in their research skills. This article describes the development of the Clinicians Skills, Capability, and Organisational Research Readiness (SCORR) Tool, a simple innovation that assesses and captures research skills and attainment at 1) clinician, and 2) organisational level. The SCORR Tool was initially developed to assess levels of research attainment and to promote discussion during annual appraisals for podiatrists working across secondary and community care in a northern region of England. The levels (1 to 5) of attainment recognise UK Health and Care Professions Council (HCPC) registration requirements for chiropodists/podiatrists (Standards 12 to 14). Following testing and feedback, research levels were adapted (Levels 0 to 5) to accommodate all healthcare professionals (with the exception of doctors and dentists). The SCORR Tool may be used individually by clinicians, or in collaboration with their manager, to better understand the level of research attainment and to prompt discussion to increase research activity. It may also be used across a workforce (e.g. during an appraisal) to understand the organisational research readiness. The SCORR Tool requires additional testing and evaluation to validate it as a tool for use across a variety of organisational environments

Visualization of Patient Behavior from Natural Language Recommendations

The visualization of procedural knowledge from textual documents using 3D animation may be a way to improve understanding. We are interested in applying this approach to documents relating to patient education for bariatric surgery: a domain with challenging textual documents describing behavior recommendations that contain few procedural steps and leave much commonsense knowledge unspecified. In this work we look at how to automatically capture knowledge from a range of differently phrased recommendations and use that with implicit knowledge about compliance and violation, such that the recommendations can be visualized using 3D animations. Our solution is an end-to-end system that automates this process via: analysis of input recommendations to uncover their conditional structure; the use of commonsense knowledge and deontic logic to generate compliance and violation rules; and mapping of this knowledge to update a default knowledge base, which is used to generate appropriate sequences of visualizations. In this paper we overview this approach and demonstrate its potential

The tammar wallaby major histocompatibility complex shows evidence of past genomic instability

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The major histocompatibility complex (MHC) is a group of genes with a variety of roles in the innate and adaptive immune responses. MHC genes form a genetically linked cluster in eutherian mammals, an organization that is thought to confer functional and evolutionary advantages to the immune system. The tammar wallaby (Macropus eugenii), an Australian marsupial, provides a unique model for understanding MHC gene evolution, as many of its antigen presenting genes are not linked to the MHC, but are scattered around the genome. Results Here we describe the 'core' tammar wallaby MHC region on chromosome 2q by ordering and sequencing 33 BAC clones, covering over 4.5 MB and containing 129 genes. When compared to the MHC region of the South American opossum, eutherian mammals and non-mammals, the wallaby MHC has a novel gene organization. The wallaby has undergone an expansion of MHC class II genes, which are separated into two clusters by the class III genes. The antigen processing genes have undergone duplication, resulting in two copies of TAP1 and three copies of TAP2. Notably, Kangaroo Endogenous Retroviral Elements are present within the region and may have contributed to the genomic instability. Conclusions The wallaby MHC has been extensively remodeled since the American and Australian marsupials last shared a common ancestor. The instability is characterized by the movement of antigen presenting genes away from the core MHC, most likely via the presence and activity of retroviral elements. We propose that the movement of class II genes away from the ancestral class II region has allowed this gene family to expand and diversify in the wallaby. The duplication of TAP genes in the wallaby MHC makes this species a unique model organism for studying the relationship between MHC gene organization and function.Peer Reviewe

Evaluation of two lyophilized molecular assays to rapidly detect foot-and-mouth disease virus directly from clinical samples in field settings

Accurate, timely diagnosis is essential for the control, monitoring and eradication of foot‐and‐mouth disease (FMD). Clinical samples from suspect cases are normally tested at reference laboratories. However, transport of samples to these centralized facilities can be a lengthy process that can impose delays on critical decision making. These concerns have motivated work to evaluate simple‐to‐use technologies, including molecular‐based diagnostic platforms, that can be deployed closer to suspect cases of FMD. In this context, FMD virus (FMDV)‐specific reverse transcription loop‐mediated isothermal amplification (RT‐LAMP) and real‐time RT‐PCR (rRT‐PCR) assays, compatible with simple sample preparation methods and in situ visualization, have been developed which share equivalent analytical sensitivity with laboratory‐based rRT‐PCR. However, the lack of robust ‘ready‐to‐use kits’ that utilize stabilized reagents limits the deployment of these tests into field settings. To address this gap, this study describes the performance of lyophilized rRT‐PCR and RT‐LAMP assays to detect FMDV. Both of these assays are compatible with the use of fluorescence to monitor amplification in real‐time, and for the RT‐LAMP assays end point detection could also be achieved using molecular lateral flow devices. Lyophilization of reagents did not adversely affect the performance of the assays. Importantly, when these assays were deployed into challenging laboratory and field settings within East Africa they proved to be reliable in their ability to detect FMDV in a range of clinical samples from acutely infected as well as convalescent cattle. These data support the use of highly sensitive molecular assays into field settings for simple and rapid detection of FMDV

Development and Validation of the Geriatric Anxiety Inventory

Background: Anxiety symptoms and anxiety disorders are highly prevalent among elderly people, although infrequently the subject of systematic research in this age group. One important limitation is the lack of a widely accepted instrument to measure dimensional anxiety in both normal old people and old people with mental health problems seen in various settings. Accordingly, we developed and tested of a short scale to measure anxiety in older people. Methods:We generated a large number of potential items de novo and by reference to existing anxiety scales, and then reduced the number of items to 60 through consultation with a reference group consisting of psychologists, psychiatrists and normal elderly people. We then tested the psychometric properties of these 60 items in 452 normal old people and 46 patients attending a psychogeriatric service. We were able to reduce the number of items to 20. We chose a 1-week perspective and a dichotomous response scale. Results: Cronbach's alpha for the 20-item Geriatric Anxiety Inventory (GAI) was 0.91 among normal elderly people and 0.93 in the psychogeriatric sample. Concurrent validity with a variety of other measures was demonstrated in both the normal sample and the psychogeriatric sample. Inter-rater and test-retest reliability were found to be excellent. Receiver operating characteristic analysis indicated a cut-point of 10/11 for the detection of DSM-IV Generalized Anxiety Disorder (GAD) in the psychogeriatric sample, with 83% of patients correctly classified with a specificity of 84% and a sensitivity of 75%. Conclusions: The GAI is a new 20-item self-report or nurse-administered scale that measures dimensional anxiety in elderly people. It has sound psychometric properties. Initial clinical testing indicates that it is able to discriminate between those with and without any anxiety disorder and between those with and without DSM-IV GAD

Assimilative real-time models of HF absorption at high latitudes

Improved real-time HF communications frequency management is required for aircraft on trans-polar routes. Polar cap absorption (PCA) models have therefore been adapted to assimilate real-time measurements of zenithal cosmic radio noise absorption (~ 30 MHz) from a large network of online riometers in Canada and Finland. Two types of PCA model have been developed and improvements to model accuracy following optimisation are quantified. Real-time optimisation is performed by age-weighting riometer measurements in a non-linear regression. This reduces root-mean-square errors (RMSE) from 2-3 dB to less than 1 dB and mean errors to within ±0.2 dB over a wide latitude range. This paper extends previous work by further optimising the models’ dependences on solar-zenith angle to account for differences in the ionospheric response at sunrise and sunset (the Twilight Anomaly). Two models of the rigidity cutoff latitudes are compared and one is optimised in real time by regression to riometer measurements. Whilst measurements from the NASA POES satellites may provide a direct measurement of the rigidity cut-off, it is observed that proton flux measurements from POES often need correcting for relativistic electron contamination for several hours at the start of a PCA event. An optimised real-time absorption model will be integrated into HF ray-tracing propagation predictions relating to measurements of HF signal strengths on a network of HF transmitters and receivers in the high northern latitudes