P20-16. Ultra-deep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in SIV-infected macaques

Background A complex population of viral variants exists within each individual infected with immunodeficiency virus. Deciphering the breadth and frequency of accruing viral mutations provides insight into immune responses, drug resistance, and potential vaccine targets. Contemporary sequencing methods are limited to detection of high frequency variants, leading to an incomplete assessment of the overall viral population. Here, we use ultra-deep pyrosequencing to create a comprehensive picture of CD8+ T-lymphocyte (CD8-TL) escape in two epitopes in SIV-infected rhesus and cynomolgus macaques, revealing a complex pattern of viral variants previously undetected. Methods Plasma was collected from SIV-infected rhesus and cynomolgus macaques at multiple timepoints between weeks 1 and 20 post-infection. Viral RNA was isolated and amplicons spanning the epitopes of interest were generated by RT-PCR, using primers that incorporated a unique 10 bp molecular barcode into each sample. Amplicons were pooled and sequenced on a Roche Genome Sequencer FLX instrument and analyzed using Roche Amplicon Variant Analyzer software. Results The increased sensitivity of ultra-deep pyrosequencing enabled detection of acute CD8-TL escape as early as 17 days post-infection, representing the earliest published example of CD8-TL escape in intrarectally infected macaques. Conversely, we observed the continued presence of a complex viral population well into chronic infection, indicating that viral mutations deemed ''fixed'' by Sanger sequencing are instead complemented by a broad array of viral variants. Additionally, we show that these methods can be applied to sequencing of the entire SIVmac239 genome, supporting the continued use of pyrosequencing in comprehensive SIV infection studies. Conclusion Overall, these findings demonstrate that pyrosequencing can be used to study viral evolution during HIV/SIV infection with an unprecedented degree of sensitivity. Utilizing newly emerging molecular tools is essential and will further our understanding of how viral pathogens evade the immune system

Pain and Sickness Behavior Associated with Corneal Lesions in Dairy Calves

Infectious bovine keratoconjunctivitis (IBK) is a common corneal disease of calves that adversely affects animal welfare by causing pain and weight loss. Identifying behavioral indicators of pain and sickness in calves with IBK is necessary for designing studies that aim to identify effective means of pain mitigation. Consistent with principles of the 3Rs for animal use in research, data from a randomized blinded challenge study was used to identify and describe variation of behaviors that could serve as reliable indicators of pain and sickness in calves with corneal injuries. Behavioral observations were collected from 29 Holstein calves 8 to 12 weeks of age randomly allocated to one of three treatments: (1) corneal scarification only, (2) corneal scarification with inoculation with Moraxella bovoculi and (3) corneal scarification with inoculation with Moraxella bovis. Behavior was continuously observed between time 1230 - 1730 h on day -1 (baseline time period) and day 0 (scarification time period). Corneal scarification and inoculation occurred between 0800 - 1000 h on day 0. Frequency of head-directed behaviors (head shaking, head rubbing, head scratching) and durations of head rubbing, feeding, standing with head lifted, lying with head lifted and sleeping were compared between study days and groups. Following scarification, the frequency of head-directed behavior significantly increased (p = 0.0001), as did duration of head rubbing (p=0.02). There was no significant effect of trial, trial day, treatment or treatment-day interaction on other behaviors studied. Our study demonstrated that head-directed behavior, such as head shaking, rubbing and scratching, was associated with scarification of eyes using an IBK challenge model, but sickness behavior was not observed

Quality of life with conservative care compared with assisted peritoneal dialysis and haemodialysis

Background. There is little information about quality of life (QoL) for patients with end-stage kidney disease (ESKD) choosing conservative kidney management (CKM). The Frail and Elderly Patients on Dialysis (FEPOD) study demonstrated that frailty was associated with poorer QoL outcomes with little difference between dialysis modalities [assisted peritoneal dialysis (aPD) or haemodialysis (HD)]. We therefore extended the FEPOD study to include CKM patients with estimated glomerular filtration rate ⌉10 mL/min/1.73m2 (i.e. individuals with ESKD otherwise likely to be managed with dialysis). Methods. CKM patients were propensity matched to HD and aPD patients by age, gender, ethnicity, diabetes status and index of deprivation. QoL outcomes measured were Short Form-12 (SF12), Hospital Anxiety and Depression Scale depression score, symptom score, Illness Intrusiveness Rating Scale (IIRS) and Renal Treatment Satisfaction Questionnaire. Frailty was assessed using the Clinical Frailty Scale. Generalized linear modelling was used to assess the impact of treatment modality on QoL outcomes, adjusting for baseline characteristics. Results. In total, 84 (28 CKM, 28 HD and 28 PD) patients were included. Median age for the cohort was 82 (79-88) years. Compared with CKM, aPD was associated with higher SF12 physical component score (PCS) [Exp B (95% confidence interval)=1.20 (1.00-1.45), P<0.05] and lower symptom score [Exp B=0.62 (0.43-0.90), P=0.01]; depression score was lower in HD compared with CKM [Exp B=0.70 (0.52-0.92), P=0.01]. Worsening frailty was associated with higher depression scores [Exp B=2.59 (1.45-4.62), P<0.01], IIRS [Exp B=1.20 (1.12-1.28), P<0.01] and lower SF12 PCS [Exp B=0.87 (0.83-0.93), P<0.01]. Conclusion. Treatment by dialysis, both with aPD and HD, improved some QoL measures. Overall, aPD was equal to or slightly better than the other modalities in this elderly population. However, as in the primary FEPOD study, frailty was associated with worse QoL measures irrespective of CKD modality. These findings highlight the need for an individualized approach to the management of ESKD in older people.Peer reviewedFinal Published versio

Student voice in work integrated learning scholarship: a review of teacher education and geographical sciences

Work integrated learning is an umbrella term that refers to the opportunities provided to university students to integrate knowledge of theory and practice as part of their degree program. As the role of students in higher education is evolving, we sought to develop our understanding of the role of students in the work integrated learning (WIL) space through exploring current literature on student voice. In this paper, we consider what has been reported about WIL in relation to student voice, how it has been represented, and how this has influenced practice. We undertook a systematic literature review for two different disciplines, one which represented an example of a professionally accredited undergraduate degree program (teacher education), and the other an example of a program with no professional accreditation (geographical sciences). The teacher education literature demonstrated more clearly the use of student voice to inform WIL within curriculum design. However, the geographical sciences literature did include examples of student voice being incorporated within the design of collaborative community-based forms of WIL. A role for students as researchers, who lead research and initiate curriculum change into WIL, was noticeably absent in both disciplinary sets of literature. The lack of evidence of the inclusion of students in the design, conduct, and analysis of WIL provides an invitation for SoTL scholars to redefine the role of students in this space

Student voice in work integrated learning scholarship: A review of teacher education and geographical sciences

Work integrated learning is an umbrella term that refers to the opportunities provided to university students to integrate knowledge of theory and practice as part of their degree program. As the role of students in higher education is evolving, we sought to develop our understanding of the role of students in the work integrated learning (WIL) space through exploring current literature on student voice. In this paper, we consider what has been reported about WIL in relation to student voice, how it has been represented, and how this has influenced practice. We undertook a systematic literature review for two different disciplines, one which represented an example of a professionally accredited undergraduate degree program (teacher education), and the other an example of a program with no professional accreditation (geographical sciences). The teacher education literature demonstrated more clearly the use of student voice to inform WIL within curriculum design. However, the geographical sciences literature did include examples of student voice being incorporated within the design of collaborative community-based forms of WIL. A role for students as researchers, who lead research and initiate curriculum change into WIL, was noticeably absent in both disciplinary sets of literature. The lack of evidence of the inclusion of students in the design, conduct, and analysis of WIL provides an invitation for SoTL scholars to redefine the role of students in this space

Understanding regional scale structural uncertainty: The onshore Gulf of Corinth Rift as a hydrocarbon exploration analogue

A major challenge when exploring for hydrocarbons in frontier areas is a lack of data coverage. Data may be restricted to regional scale 2D seismic lines, from which assumptions of the 3D geometric configuration are drawn. Understanding the limitations and uncertainties when extrapolating 2D data into 3D space is crucial when assessing the requirements for acquiring additional data such as 3D seismic or exploration wells, and of assigning geologically reasonable uncertainty ranges. The Onshore Gulf of Corinth Rift provides an excellent analogue for rift-scale structural uncertainty in the context of hydrocarbon exploration. Here we use seismic forward modelling to explore this area of uncertainty. Synthetic seismic sections have been generated across the rift based upon fault geometries mapped in the field. Comparison of these sections with the mapped geometries allows quantification of uncertainties encountered when extrapolating 2D data into three dimensions. We demonstrate through examples how potential column heights may be both severely over- and under-estimation due to trap integrity, spill point depth and fault seal ambiguities directly related to fault geometric uncertainty. In addition, fault geometries and linkages also control the location of hanging wall syn-rift reservoirs. Hence, gross reservoir volumes and sediment facies distributions are also significantly influenced by how fault geometries are extrapolated along-strike from 2D to 3D

Electrospun nanosized cellulose fibers using ionic liquids at room temperature

Aiming at replacing the noxious solvents commonly employed, ionic-liquid-based solvents have been recently explored as novel non-volatile and non-flammable media for the electrospinning of polymers. In this work, nanosized and biodegradable cellulose fibers were obtained by electrospinning at room temperature using a pure ionic liquid or a binary mixture of two selected ionic liquids. The electrospinning of 8 wt% cellulose in 1-ethyl-3-methylimidazolium acetate medium (a low viscosity and room temperature ionic liquid capable of efficiently dissolving cellulose) showed to produce electrospun fibers with average diameters within (470 ± 110) nm. With the goal of tailoring the surface tension of the spinning dope, a surface active ionic liquid was further added in a 0.10 : 0.90 mole fraction ratio. Electrospun cellulose fibers from the binary mixture composed of 1-ethyl-3-methylimidazolium acetate and 1-decyl-3-methylimidazolium chloride ionic liquids presented average diameters within (120 ± 55) nm. Scanning electron microscopy, X-ray diffraction analysis, nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, and thermogravimetric assays were used as core methods to evaluate the structural integrity, morphology and crystallinity of the raw, electrospun, and regenerated samples of cellulose. Moreover, the photoluminescence spectra of both raw and electrospun fibers were acquired, and compared, indicating that the cellulose emitting centers are not affected by the dissolution of cellulose in ionic liquids. Finally, the use of non-volatile solvents in electrospinning coupled to a water coagulation bath allows the recovery of the ionic fluid, and represents a step forward into the search of environmentally friendly alternatives to the conventional approaches

Physicians' intentions and use of three patient decision aids

<p>Abstract</p> <p>Background</p> <p>Decision aids are evidence based tools that assist patients in making informed values-based choices and supplement the patient-clinician interaction. While there is evidence to show that decision aids improve key indicators of patients' decision quality, relatively little is known about physicians' acceptance of decision aids or factors that influence their decision to use them. The purpose of this study was to describe physicians' perceptions of three decision aids, their expressed intent to use them, and their subsequent use of them.</p> <p>Methods</p> <p>We conducted a cross-sectional survey of random samples of Canadian respirologists, family physicians, and geriatricians. Three decision aids representing a range of health decisions were evaluated. The survey elicited physicians' opinions on the characteristics of the decision aid and their willingness to use it. Physicians who indicated a strong likelihood of using the decision aid were contacted three months later regarding their actual use of the decision aid.</p> <p>Results</p> <p>Of the 580 eligible physicians, 47% (n = 270) returned completed questionnaires. More than 85% of the respondents felt the decision aid was well developed and that it presented the essential information for decision making in an understandable, balanced, and unbiased manner. A majority of respondents (>80%) also felt that the decision aid would guide patients in a logical way, preparing them to participate in decision making and to reach a decision. Fewer physicians (<60%) felt the decision aid would improve the quality of patient visits or be easily implemented into practice and very few (27%) felt that the decision aid would save time. Physicians' intentions to use the decision aid were related to their comfort with offering it to patients, the decision aid topic, and the perceived ease of implementing it into practice. While 54% of the surveyed physicians indicated they would use the decision aid, less than a third followed through with this intention.</p> <p>Conclusion</p> <p>Despite strong support for the format, content, and quality of patient decision aids, and physicians' stated intentions to adopt them into clinical practice, most did not use them within three months of completing the survey. There is a wide gap between intention and behaviour. Further research is required to study the determinants of this intention-behaviour gap and to develop interventions aimed at barriers to physicians' use of decision aids.</p