Qualitative methods: An alternative view

Are qualitative and quantitative research really based on different philosophies? John Paley and Richard Lilford argue that the idea that qualitative research is constructivist should not be allowed to diffuse into medical literature unopposed

An anthropometric model to estimate neonatal fat mass using air displacement plethysmography

<p>Abstract</p> <p>Background</p> <p>Current validated neonatal body composition methods are limited/impractical for use outside of a clinical setting because they are labor intensive, time consuming, and require expensive equipment. The purpose of this study was to develop an anthropometric model to estimate neonatal fat mass (kg) using an air displacement plethysmography (PEA POD^®Infant Body Composition System) as the criterion.</p> <p>Methods</p> <p>A total of 128 healthy term infants, 60 females and 68 males, from a multiethnic cohort were included in the analyses. Gender, race/ethnicity, gestational age, age (in days), anthropometric measurements of weight, length, abdominal circumference, skin-fold thicknesses (triceps, biceps, sub scapular, and thigh), and body composition by PEA POD^®were collected within 1-3 days of birth. Backward stepwise linear regression was used to determine the model that best predicted neonatal fat mass.</p> <p>Results</p> <p>The statistical model that best predicted neonatal fat mass (kg) was: -0.012 -0.064*gender + 0.024*day of measurement post-delivery -0.150*weight (kg) + 0.055*weight (kg)²+ 0.046*ethnicity + 0.020*sum of three skin-fold thicknesses (triceps, sub scapular, and thigh); R²= 0.81, MSE = 0.08 kg.</p> <p>Conclusions</p> <p>Our anthropometric model explained 81% of the variance in neonatal fat mass. Future studies with a greater variety of neonatal anthropometric measurements may provide equations that explain more of the variance.</p

Spinal cord compression secondary to cancer : disability and rehabilitation

Introduction This thesis describes a research study designed to examine the consequences of disability arising out of spinal cord compression secondary to cancer, and to examine the rehabilitation services available to patients. Research aims and questions The study was intended to achieve the following: 1. To ascertain what might constitute effective rehabilitation interventions for patients with metastatic spinal cord compression. 2. To identify the conditions in which these intervention might be delivered. 3. To ground proposals in spinal cord compression patients’ experience of disability. The following research questions were posed: 1. What are the consequences of disability for patients with metastatic spinal cord compression? 2. What strategies do patients themselves use to manage disability? 3. What do health care staff, particularly rehabilitation professionals, understand to be the consequences of disability for this patient group, and correspondingly, what are their views on the significance and provision of rehabilitation? 4. To what extent is rehabilitation being provided to these patients, and with what effect? 5. Where rehabilitation is not being provided, why is this the case? Study design The study had two components: • A series of nine in-depth interview-based case studies, which involved talking to patients about their experiences of living with spinal cord compression, as well as gaining the perspectives of family members and the health professionals who provided care and services. • A retrospective audit of the medical records of 73 spinal cord compression patients admitted to a radiotherapy in-patient unit (the Frank Ellis Unit at the Churchill Hospital in Oxford) over a two year period (July 2003 – June 2005), identifying disability-related problems and the measures taken to address them. This was a Phase I modelling study in terms of the Medical Research Council’s framework for evaluating complex interventions, with Pawson and Tilley’s (1997) Context-Mechanism-Outcome configuration adopted as a conceptual basis for data collection. Within-case analysis was informed by George and Bennett’s (2004) account of process tracing, and between-case analysis was modelled on the constant comparative method of Glaser and Strauss (1967) with an analysis of narrative as a variation on that theme. Results Disability is a serious problem for patients with spinal cord compression, but it is one problem among many others, not the least of which are the physical and emotional consequences of life-threatening illness. In response to disability, patients ‘twin-track’ their attitudes to it, acknowledging but also resisting the idea of themselves as disabled, and adopting a series of psychological devices to manage the tension. In effect, patients recognise that something significant has changed and that, as a consequence, new self-management skills must be learned, functional boundaries must be explored, useful information must be sought. At the same time, they display a determination to hold on to an established identity, associated with a sense of normality. This identity embraces the idea of competence and resourcefulness, the events, activities and pleasures that one looks forward to, and the wish to avoid burdening others. It is not a ‘disabled’ identity. To some extent, these two attitudes are in tension, as one acknowledges disability while the other, implicitly or explicitly, resists it. Consequently, patients try to find ways of resolving this tension, by ‘revising downwards’ their expectations, by constantly deferring the anticipated pleasures, and by avoiding situations in which their abilities might be put to the test, or the sense of normality be disconfirmed. Health care professionals are likely to construe the patient’s response as indicative of a certain type of character – ‘realistic’ on one hand, and ‘unrealistic’ on the other. They do not see ‘acknowledging / not acknowledging’ as twin facets of a complex response to circumstances, or as something which every patient engages in to one degree or another. Patients are motivated not to recognise rehabilitation as something they need, a view which is confirmed by the cursory form of rehabilitation experienced in hospital, and by the marginal significance attributed to it by nursing and medical staff. On discharge, hospital staff assume that rehabilitation needs will be identified in the community, although the way in which community rehabilitation services are organised virtually guarantees that this will not happen, unless a specific referral is made (as it is in only 5% of cases). The patient, meanwhile, remains unaware of the potential value of rehabilitation, and has no incentive to request rehabilitation if no-one offers it. They are consequently unprepared for life post-discharge, and assume that they (and their families) must manage on their own. Conclusions Like the patients, health care professionals may have to ‘twin-track’ if they are to provide rehabilitation in a way that is acceptable to patients with metastatic spinal cord compression. Instead of categorising patients as ‘realistic’ or ‘unrealistic’, they should work towards sustaining patients’ ‘positive illusions’, while at the same time taking whatever opportunities arise to enhance the patient’s day-to-day ability to function in a ‘safe’ space. This entails revising some deeply entrenched ideas about working with patients who have a disability: patient-centredness, the importance of goal setting, and the need for adjustment.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

EcoCyc: a comprehensive database resource for Escherichia coli

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions

MetaCyc: a multiorganism database of metabolic pathways and enzymes

MetaCyc is a database of metabolic pathways and enzymes located at . Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the website. These PGDBs also include predicted operons and pathway hole fillers

The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon

Genetic resistance to infectious pancreatic necrosis virus (IPNV) in Atlantic salmon is a rare example of a trait where a single locus (QTL) explains almost all of the genetic variation. Genetic marker tests based on this QTL on salmon chromosome 26 have been widely applied in selective breeding to markedly reduce the incidence of the disease. In the current study, whole genome sequencing and functional annotation approaches were applied to characterise genes and variants in the QTL region. This was complemented by an analysis of differential expression between salmon fry of homozygous resistant and homozygous susceptible genotypes challenged with IPNV. These analyses pointed to the NEDD-8 activating enzyme 1 (nae1) gene as a putative functional candidate underlying the QTL effect. The role of nae1 in IPN resistance was further assessed via CRISPR-Cas9 knockout of the nae1 gene and chemical inhibition of the nae1 protein activity in Atlantic salmon cell lines, both of which resulted in highly significant reduction in productive IPNV replication. In contrast, CRISPR-Cas9 knockout of a candidate gene previously purported to be a cellular receptor for the virus (cdh1) did not have a major impact on productive IPNV replication. These results suggest that nae1 is the causative gene underlying the major QTL affecting resistance to IPNV in salmon, provide further evidence for the critical role of neddylation in host-pathogen interactions, and highlight the value in combining high-throughput genomics approaches with targeted genome editing to understand the genetic basis of disease resistance

Multidimensional annotation of the Escherichia coli K-12 genome

The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure