Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

The validation of Fibit ZipTM physical activity monitor as a measure of free-living physical activity

BACKGROUND: The new generation of activity monitors allow users to upload their data to the internet and review progress. The aim of this study is to validate the Fitbit Zip as a measure of free-living physical activity.

FINDINGS: Participants wore a Fitbit Zip, ActiGraph GT3X accelerometer and a Yamax CW700 pedometer for seven days. Participants were asked their opinion on the utility of the Fitbit Zip. Validity was assessed by comparing the output using Spearman's rank correlation coefficients, Wilcoxon signed rank tests and Bland-Altman plots. 59.5% (25/47) of the cohort were female. There was a high correlation in steps/day between the Fitbit Zip and the two reference devices (r = 0.91, p < 0.001). No statistically significant difference between the Fitbit and Yamax steps/day was observed (Median (IQR) 7477 (3597) vs 6774 (3851); p = 0.11). The Fitbit measured significantly more steps/day than the Actigraph (7477 (3597) vs 6774 (3851); p < 0.001). Bland-Altman plots revealed no systematic differences between the devices.

CONCLUSIONS: Given the high level of correlation and no apparent systematic biases in the Bland Altman plots, the use of Fitbit Zip as a measure of physical activity. However the Fitbit Zip recorded a significantly higher number of steps per day than the Actigraph.

Using postal questionnaires to evaluate physical activity and diet behaviour change: case study exploring implications of valid responder characteristics in interpreting intervention outcomes.

Background: Patient reported outcome measures (PROMs) are used to evaluate lifestyle interventions but littleis known about differences between patients returning valid and invalid responses, or of potential for bias inevaluations. We aimed to examine the characteristics of patients who returned valid responses to lifestylequestionnaires compared to those whose responses were invalid for evaluating lifestyle change. 
Methods: We conducted a secondary data analysis from the SPHERE Study, a trial of an intervention to improveoutcomes for patients with coronary heart disease in primary care. Postal questionnaires were used to assessphysical activity (Godin) and diet (DINE) among study participants at baseline and 18 month follow-up. Three binaryresponse variables were generated for analysis: (1) valid Godin score; (2) valid DINE Fibre score; and (3) validDINE Total Fat score. Multivariate analysis comprised generalised estimating equation regression to examine theassociation of patients’ characteristics with their return of valid responses at both timepoints. 
Results: Overall, 92.1% of participants (832/903) returned questionnaires at both baseline and 18 months. Relativelyfewer valid Godin scores were returned by those who left school aged <15 years (36.5%) than aged 18 and over(50.5%), manual workers (39.5%) than non-manual (49.5%) and those with an elevated cholesterol (>5 mmol)(34.7%) than those with a lower cholesterol (44.4%) but multivariate analysis identified that only school leaving age(p = 0.047) was of statistical significance.Relatively fewer valid DINE scores were returned by manual than non-manual workers (fibre: 80.8% v 86.8%;fat: 71.2% v 80.0%), smokers (fibre: 72.6% v 84.7%; fat: 67.5% v 76.9%), patients with diabetes (fibre: 75.9% v 82.9%;fat: 66.9% v 75.8%) and those with cholesterol >5 mmol (fat: 68.2% v 76.2%) but multivariate analysis showedstatistical significance only for smoking (fibre: p = 0.013; fat: p = 0.045), diabetes (fibre: p = 0.039; fat: p = 0.047), andcholesterol (fat: p = 0.039). 
Conclusions: Our findings illustrate the importance of detailed reporting of research methods, with clearinformation about response rates, respondents and valid outcome data. Outcome measures which are relevant to astudy population should be chosen carefully. The impact of methods of outcome measurement and valid responserates in evaluating healthcare requires further study.

International inter-school competition to encourage children to walk to school: a mixed methods feasibility study.

Background: Active travel to school can be an important contributor to the total physical activity of children but levels have declined and more novel approaches are required to stimulate this as an habitual behaviour. The aim of this mixed methods study was to investigate the feasibility of an international walk to school competition supported by novel swipecard technology to increase children's walking to/from school. Methods: Children aged 9-13 years old participated in an international walk to school competition to win points for themselves, their school and their country over a 4-week period. Walks to and from school were recorded using swipecard technology and a bespoke website. For each point earned by participants, 1 pence (£0.01) was donated to the charity of the school's choice. The primary outcome was number of walks to/from school objectively recorded using the swipecard tracking system over the intervention period. Other measures included attitudes towards walking collected at baseline and week 4 (post-intervention). A qualitative sub-study involving focus groups with children, parents and teachers provided further insight. Results: A total of 3817 children (mean age 11.5±SD 0.7) from 12 schools in three cities (London and Reading, England and Vancouver, Canada) took part in the intervention, representing a 95% intervention participation rate. Results show a gradual decline in the average number of children walking to and from school over the 4-week period (week 1 mean 29%±SD2.5; week 2 mean 18%±SD3.6; week 3 mean 14%±SD4.0; week 4 mean 12%±SD1.1). Post intervention, 97% of children felt that walking to school helped them stay healthy, feel happy (81%) and stay alert in class (76%). These results are supported by qualitative findings from children, parents and teachers. Key areas for improvement include the need to incorporate strategies for maintenance of behaviour change into the intervention and also to adopt novel methods of data collection to increase follow-up rates. Conclusions: This mixed methods study suggests that an international walk to school competition using innovative technology can be feasibly implemented and offers a novel way of engaging schools and motivating children to walk to school.

Femoral exostosis causing vastus medialis pain in an active young lady: a case report.

BACKGROUND:
Musculoskeletal conditions are a common reason for consultation to General Practitioners (GPs)/family physicians in primary care. Osteochondromas are the most common benign bone tumours and usually occur in the metaphyseal region of long bones. Despite the distal femur being the commonest location to find these benign bone tumours, this is the first case report in the literature specifically describing vastus medialis muscle pain as the presenting symptom due to underlying bursa formation secondary to local pressure effects.

CASE PRESENTATION:
Twenty nine year old female of white British ethnic origin, presenting to a primary care clinic with a three year history of intermittent left distal medial thigh pain.

CONCLUSION:
The benign bone tumour, femoral exostosis/osteochondroma, was diagnosed via Magnaetic Resonance Imaging (MRI) and treated conservatively, with surgical excision an option if not resolving. GPs/family physicians need to be aware of this diagnosis and that femoral exostosis/osteochondroma can present to primary care physicians, particularly within the second decade of life.

Failure of a numerical quality assessment scale to identify potential risk of bias in a systematic review: a comparison study

BACKGROUND: Assessing methodological quality of primary studies is an essential component of systematic reviews. Following a systematic review which used a domain based system [United States Preventative Services Task Force (USPSTF)] to assess methodological quality, a commonly used numerical rating scale (Downs and Black) was also used to evaluate the included studies and comparisons were made between quality ratings assigned using the two different methods. Both tools were used to assess the 20 randomized and quasi-randomized controlled trials examining an exercise intervention for chronic musculoskeletal pain which were included in the review. Inter-rater reliability and levels of agreement were determined using intraclass correlation coefficients (ICC). Influence of quality on pooled effect size was examined by calculating the between group standardized mean difference (SMD).

RESULTS: Inter-rater reliability indicated at least substantial levels of agreement for the USPSTF system (ICC 0.85; 95% CI 0.66, 0.94) and Downs and Black scale (ICC 0.94; 95% CI 0.84, 0.97). Overall level of agreement between tools (ICC 0.80; 95% CI 0.57, 0.92) was also good. However, the USPSTF system identified a number of studies (n = 3/20) as "poor" due to potential risks of bias. Analysis revealed substantially greater pooled effect sizes in these studies (SMD -2.51; 95% CI -4.21, -0.82) compared to those rated as "fair" (SMD -0.45; 95% CI -0.65, -0.25) or "good" (SMD -0.38; 95% CI -0.69, -0.08).

CONCLUSIONS: In this example, use of a numerical rating scale failed to identify studies at increased risk of bias, and could have potentially led to imprecise estimates of treatment effect. Although based on a small number of included studies within an existing systematic review, we found the domain based system provided a more structured framework by which qualitative decisions concerning overall quality could be made, and was useful for detecting potential sources of bias in the available evidence.

“They should stay at their desk until the work’s done”: a qualitative study examining perceptions of sedentary behaviour in a desk-based occupational setting

Background: Workplace sedentary behaviour is a priority target for health promotion. However, little is known about how to effect change. We aimed to explore desk-based office workers’ perceptions of factors that influenced sedentary behaviour at work and to explore the feasibility of using a novel mobile phone application to track their behaviours.

Methods: We invited office employees (n = 12) and managers (n = 2) in a software engineering company to participate in semi-structured interviews to explore perceived barriers and facilitators affecting workplace sedentary behaviour. We assessed participants’ sedentary behaviours using an accelerometer before and after they used a mobile phone application to record their activities at self-selected time intervals daily for 2 weeks. Interviews were analysed using a thematic framework.

Results: Software engineers (5 employees; 2 managers) were interviewed; 13 tested the mobile phone application; 8 returned feedback. Major barriers to reducing workplace sedentary behaviour included the pressure of ‘getting the job done’, the nature of their work requiring sitting at a computer, personal preferences for the use of time at and after work, and a lack of facilities, such as a canteen, to encourage moving from their desks. Facilitators for reduced sedentariness included having a definite reason to leave their desks, social interaction and relief of physical and mental symptoms of prolonged sitting. The findings were similar for participants with different levels of overall physical activity. Valid accelerometer data were tracked for four participants: all reduced their sedentary behaviour. Participants stated that recording data using the phone application added to their day’s work but the extent to which individuals perceived this as a burden varied and was counter-balanced by its perceived value in increasing awareness of sedentary behaviour. Individuals expressed a wish for flexibility in its configuration.

Conclusions: These findings indicate that employers’ and employees’ perceptions of the cultural context and physical environment of their work, as well as personal factors, must be considered in attempting to effect changes that reduce workplace sedentary behaviour. Further research should investigate appropriate individually tailored approaches to this challenge, using a framework of behaviour change theory which takes account of specific work practices, preferences and settings.

The spectrum of paediatric cardiac disease presenting to an outpatient clinic in Malawi

BACKGROUND: As progress is made towards attaining Millennium Development Goal 4, further reductions in paediatric mortality will only be achieved by concentrating on the burden of non-communicable or neglected diseases. The literature relating to paediatric cardiac disease in sub-Saharan Africa is sparse. There are no published descriptions of paediatric cardiac disease from Malawi, making it impossible to estimate the contribution it makes to childhood morbidity and mortality.

FINDINGS: In 2008, a paediatric cardiac clinic with echocardiogram scanning was established in Blantyre, southern Malawi. Between January 2009 and February 2011, the age and cardiac diagnosis of every child with an abnormal echocardiogram was recorded in a database. Of 250 children, 139 (55.6%) had congenital heart disease, and 111 (44.4%) acquired heart disease. Ventricular septal defect (VSD) (24%), Tetralogy of Fallot (10%) and patent ductus arteriousus (7.2%) were the commonest forms of congenital heart disease. Rheumatic heart disease (RHD) (22.4%) and dilated cardiomyopathy (13.6%) were the commonest acquired diseases. The mean age of presentation was 3 years 2 months for VSD and 11 years 6 months for RHD.

CONCLUSIONS: In this cohort of children from one centre in Malawi, acquired heart disease - in particular rheumatic heart disease was almost as common as congenital heart disease. Most presented late. It is likely that untreated cardiac disease causes a large number of childhood deaths in Malawi. In addition to renewing secondary preventative efforts against rheumatic heart disease, adequate and accessible cardiothoracic surgical services should be established at a regional level.

Physical Education or Playtime: which is more effective at promoting physical activity in primary school children?

Background School physical education (PE) and playtime provide important opportunities for physical activity (PA). However, little research has assessed PA during primary school PE using accelerometry or compared PA during different lesson types. There is also a lack of research comparing PA during PE and playtime, despite suggestions that playtime promotes more PA. The primary aim of this study was to determine which types of PE lesson are most facilitative of PA. The secondary aim was to determine whether children are more active during PE or playtime. Methods Descriptive and fitness data were assessed in 20 children aged 8-9years from a single school. Over eight consecutive weeks PA was assessed during PE lessons, which were classified as either team games or movement activities. At the mid-week of data collection playtime PA was also assessed. PA was assessed using accelerometry and the percentage of time spent in moderate to vigorous PA (MVPA) calculated. Paired t-tests were used to compare MVPA during movement lessons and team games lessons and during PE and playtime. Results Children spent 9.5% of PE lessons in MVPA and engaged in significantly more MVPA during team games (P < 0.001). MVPA was also significantly higher during PE than playtime (P < 0.01). Conclusions Children do not engage in sufficient PA during PE, but are most active during team games lessons; whilst PA during playtime is lower than PE. Interventions to increase PA during both PE and playtime are therefore required. PE interventions should target games lessons as they dominate the curriculum, encourage most PA and present the greatest potential for change. Playtime interventions should encourage participation in active games through the provision of playground equipment and markings.

Spectrum of digoxin-induced ocular toxicity: a case report and literature review.

BACKGROUND: Digoxin intoxication results in predominantly digestive, cardiac and neurological symptoms. This case is outstanding in that the intoxication occurred in a nonagenarian and induced severe, extensively documented visual symptoms as well as dysphagia and proprioceptive illusions. Moreover, it went undiagnosed for a whole month despite close medical follow-up, illustrating the difficulty in recognizing drug-induced effects in a polymorbid patient. CASE PRESENTATION: Digoxin 0.25 mg qd for atrial fibrillation was prescribed to a 91-year-old woman with an estimated creatinine clearance of 18 ml/min. Over the following 2-3 weeks she developed nausea, vomiting and dysphagia, snowy and blurry vision, photopsia, dyschromatopsia, aggravated pre-existing formed visual hallucinations and proprioceptive illusions. She saw her family doctor twice and visited the eye clinic once until, 1 month after starting digoxin, she was admitted to the emergency room. Intoxication was confirmed by a serum digoxin level of 5.7 ng/ml (reference range 0.8-2 ng/ml). After stopping digoxin, general symptoms resolved in a few days, but visual complaints persisted. Examination by the ophthalmologist revealed decreased visual acuity in both eyes, 4/10 in the right eye (OD) and 5/10 in the left eye (OS), decreased color vision as demonstrated by a score of 1/13 in both eyes (OU) on Ishihara pseudoisochromatic plates, OS cataract, and dry age-related macular degeneration (ARMD). Computerized static perimetry showed non-specific diffuse alterations suggestive of either bilateral retinopathy or optic neuropathy. Full-field electroretinography (ERG) disclosed moderate diffuse rod and cone dysfunction and multifocal ERG revealed central loss of function OU. Visual symptoms progressively improved over the next 2 months, but multifocal ERG did not. The patient was finally discharged home after a 5 week hospital stay. CONCLUSION: This case is a reminder of a complication of digoxin treatment to be considered by any treating physician. If digoxin is prescribed in a vulnerable patient, close monitoring is mandatory. In general, when facing a new health problem in a polymorbid patient, it is crucial to elicit a complete history, with all recent drug changes and detailed complaints, and to include a drug adverse reaction in the differential diagnosis.

Margaret Glassford fonds, 1941, 1951, 1961, 1971, 1973-1975, 1977-1984, 1986-2000, 2002, 2005, n.d.

Margaret was an only child who grew up on a farm just east of Cayuga, Ontario. After high school, Margaret attended Hamilton Teacher’s College and took a position with Grantham Public School Board and taught at Power Glen school. Margaret was married in 1962 and had 2 children, a daughter and a son in 1963 and 1964, respectively. Margaret left her teaching job to raise her children. Margaret was very creative and artistic and during this time, focused on these talents, which included painting, graphic arts and sewing. Margaret was also an accomplished pianist. In her 40’s, Margaret enrolled at Brock University and in 1989 obtained a Honors Bachelor of Arts degree with First-Class Honors in Sociology. In partial fulfillment of her Honors B.A. she completed her thesis that is entitled ; The State and Liberal Feminism: The Ontario Government’s “Business Ownership For Women Program”. While living in St. Catharines, Margaret attended York University and graduated with a Master of Arts in Sociology in 1992 where her studies focused on women’s issues. Margaret received a scholarship from York University and was a teaching assistant. Margaret stayed on at York University and completed her academic requirements for a Doctorate degree in Sociology. Her dissertation was on self employed women in St. Catharines at the beginning of WWII -- not the” Rosie the Riveters” who took over jobs formerly held by men who had to go off to fight World War II, but women who ran their own businesses when that was still unusual. Margaret completed the research for her thesis but did not complete her written thesis as she made a difficult decision to put her academic work on hold in the mid-1990’s and she returned to her love for the arts, although she always remained a voracious reader and interested in women’s issues. In the last decade of her life, she took up quilting with a passion, which she referred to as fabric arts. Margaret loved colour and being non-traditional. Margaret had been a quilting instructor at the Flemington College for Fine Arts in Haliburton. In 1997, Margaret founded Project Smile in the St. Catharines region, a non-profit group who make quilts for children with cancer. Margaret was also the President of the Niagara Heritage Quilters’ Guild in 2006-2007 and was very involved with the Local Council of Women.

Robert George Malcomson Papers, 1790s-2009 (non-inclusive)

Materials related to military and naval operations of the 1812 era, research of the late Robert Malcomson, Canadian author and historian. Materials include photocopies of materials relating to the War of 1812, photographs and detailed research notes Malcomson made regarding his approach to research (mainly found in Series VIII). Materials were originally arranged in binders relating to an area of research or a certain publication. Articles were removed from the binders and placed in folders using original titles from the binders as series or sub-series titles. Articles within the binders were separated by tabs indicating what the article related to in the publication or topic of interest. In order to avoid repetition, the writing on the tab was used for folder titles, as each folder would be a part of the Series under which it was grouped. The tab names could be authors, events, accounts etc. of the War. Series and sub-series titles were derived from the original titles on the binders. Original intellectual order was retained, grouping similar subjects into Series and Sub-series. Dates recorded were the publication dates of the articles; however, if no publication date was present the date of retrieval was used if from an academic database (ex. JSTOR). The black and white photos from various repositories are reproductions of paintings, microfilm etc. on photographic paper. The colour photographs from various repositories are actual photographs. All books donated by Malcomson were integrated into the University’s Special Collections book collection. These volumes are noted at the end of the finding aid under separated materials.

Office of the University President Sous fonds: Dr. James A. Gibson

Dr. James A. Gibson was born in Ottawa on January 29, 1912 to John W. and Belle Gibson. At an early age the family moved to Victoria, B.C. where John W. Gibson was a director of the Elementary Agricultural Education Branch, Department of Education. Gibson received his early education in Victoria, receiving a B.A. (honours) at UBC in 1931. In 1931 he was awarded the Rhodes scholarship and received his B.A., M.A., B.Litt and D. Phil at New College, Oxford. This was to be the beginning of a long and dedicated relationship with the Rhodes Scholar Association. Upon his return to Canada, Dr. Gibson lectured in Economics and Government at the University of British Columbia. In 1938 he was married to Caroline Stein in Philadelphia, and the same year joined the staff of the Department of External Affairs as a Foreign Service officer. Within twenty minutes of his arrival he was seconded to the Office of the Prime Minister and Secretary of State for External Affairs, W. L. Mackenzie King in charge of War Records and Liaison Officer. This was a critical time in the history of Canada, and Dr. Gibson experienced firsthand several milestones, including the Royal Visit of King George VI and Queen Elizabeth in 1939. Dr. Gibson was present at the formation of the United Nations in San Francisco in 1945, being part of the Prime Minister’s professional staff as well as attending conferences in Washington, Quebec and London as an advisor to the Canadian delegation. Gibson contributed many articles to the publication bout de papier about his experiences during these years. After his resignation in 1947, Gibson joined the staff of the fledgling Carleton College, as a lecturer. In 1949 he was appointed a professor and in 1951 became Dean of Arts and Sciences. Dr. Gibson acted as President from 1955 to 1956 upon the sudden death of Dr. MacOdrum. In 1963 Dr. Gibson accepted the invitation of the Brock University Founders’ Committee, chaired by Arthur Schmon, to become the founding president. Dr. Gibson guided the new University from a converted refrigeration plant, to an ever expanding University campus on the brow of the Niagara Escarpment. Dr. Gibson remained firmly “attached” to Brock University. Even after official retirement, in 1974, he retained the title President Emeritus. Gibson’s final official contribution was an unpublished ten year history of the University. In retirement Gibson remained active in scholarly pursuits. He was a visiting scholar at the Center of Canadian Studies, University of Edinburgh; continued his ongoing research activities focusing on W. L. Mackenzie King, the Office of the Governor General of Canada, and political prisoners transported to Van Dieman’s Land. He remained active in the Canadian Association of Rhodes Scholars, becoming editor from 1975 to 1994 and was appointed Editor Emeritus and Director for Life in 1995 in honour of his dedicated and outstanding service. In 1993 he was awarded one of Canada’s highest achievements, the Order of Canada. Gibson retained close ties with Brock University and many of its faculty. He maintained an office in the Politics Department where he became a vital part of the department. In 1996 Brock University honoured Gibson by naming the University Library in his honour. James A. Gibson Library staff was instrumental in celebrating the 90th birthday of Gibson in 2002, with a widely attended party in the Pond Inlet where many former students, including Silver Badgers. The attendees also included former and current colleagues from Brock University, Canadian Rhodes Scholars Association, family and friends. Gibson was later to remark that the highlight of this event was the gift of his original academic robe which he had personally designed in 1964. In 2003 Dr. Gibson moved to Ottawa to be near some of his children and the city of his birth and early career. In that year “two visits to Brock ensued: the first, to attend a special celebration of the James A. Gibson Library; his late to attend the 74th Convocation on Saturday, October 18, 2003. A week later, in Ottawa, he went for a long walk, returned to his residence, Rideau Gardens, went into the lounge area, took off his coat and folded it up, put it on the back of his chair, sat down, folded his hands in his lap, closed his eyes, and died”. With sources from: Carleton University The Charlatan, Gibson CV, and Memorial Service Programme