The use of workflows for macromolecular crystallography experiments at the ESRF

The high performance of modern synchrotron facilities means there is an increasing reliance on automated data analysis and collection methods. The EMBL and ESRF are actively involved in designing and implementing such automated methods. However, as these methods are evolving there is also a need to continually integrate newer and more sophisticated data analysis and collection protocols with experimental control. This integration often poses a challenge, requiring a high level software environment to automatically coordinate beamline control with data acquisition and analysis. This is why we have extended the Eclipse RCP version of the workflow tool Passerelle into a user friendly GUI for experiment design by scientists and programmers [1], which is now part of the Data Analysis WorkbeNch (DAWN) collaboration (http://www.dawnsci.org). The execution of several complex workflows using this technology are now fully integrated in the new version of MxCuBE [2] and deployed on the ESRF macromolecular crystallography beamlines. Here, I will present their current implementation and the data quality improvements that can be achieved. In particular we have developed automated crystal re-orientation workflows that can improve the success of ab initio phasing experiments and help mitigate against radiation damage effect [3]. Other protocols implemented include a 3D diffraction based centring routine, a dehydration protocol and the automated measurement of a crystals radiation sensitivity. Lastly I will present our future plans for other new advanced diffraction based workflow routines, including automated crystal screening and data collection protocols.

Management of impacted wisdom teeth: teaching of undergraduate students in UK dental schools

INTRODUCTION

Wisdom tooth removal is one of the most common oral surgical procedures performed across the world. The aim of this study was to gauge the teaching and training of impacted wisdom teeth in undergraduate dental programmes across the UK. The objectives were to identify consistencies and variations in theoretical instructions and clinical training as well as approaches to management of impacted wisdom teeth.

METHODS

This was a cross-sectional survey utilising an online questionnaire. A purposefully designed pro forma with open- as well as closed-ended questions was used. The questionnaire was hosted online on the school's blackboard academic suite (Emily). Prior to conducting the study, approval was gained from the Research and Ethics Committee, and all the ethical principles pertaining to data protection were strictly followed. E-mail invitations were sent to oral surgery leads in all dental schools in the UK. The participants were provided with an information sheet, and an informed consent was obtained. The participants were invited by e-mail to complete the questionnaire online voluntarily.

RESULTS

A total of 16 dental schools offering an undergraduate course in dentistry in the UK, 13 responded positively. (response rate = 81.25%). In majority of dental schools, this subject is taught in the 4th and 5th years. A pre-clinical competency on phantom heads is a requirement in six schools, whilst only one school requires the students to pass a clinical competency. The clinical exposure of students to wisdom tooth surgery is quite variable. Although the dental schools are fairly consistent in their teaching with regard to the indications for surgical intervention, diagnostic/treatment modalities as well as the post-operative care, interesting variations were also observed.

CONCLUSIONS

This study, perhaps the first of its kind, provides useful insights into management of impacted wisdom teeth, as taught in the undergraduate dental programmes across the UK.

Summary of recommendations on malaria issues in special hosts

BACKGROUND

On behalf of the Public Health Agency of Canada, the Committee to Advise on Tropical Medicine and Travel (CATMAT) developed the Canadian Recommendations for the Prevention and Treatment of Malaria Among International Travellers for Canadian health care providers who are preparing patients for travel to malaria-endemic areas and treating travellers who have returned ill.

OBJECTIVE

To provide guidelines on malaria issues related to special hosts.

METHODS

CATMAT reviewed all major sources of information on malaria prevention, as well as recent research and national and international epidemiological data, to tailor guidelines to the Canadian context. The evidence-based medicine recommendations were developed with associated rating scales for the strength and quality of the evidence.

RECOMMENDATIONS

All people visiting malaria endemic regions should use effective personal protective measures (PPM; topical repellants, bed nets, behavioural choices) and the prescribed chemoprophylaxis. Chemoprophylaxis for pregnant and breastfeeding women and for children requires careful consideration in the context of the pregnancy trimester, the age or size of the infant/child as well as their glucose-6-phosphate dehydrogenase (G6PD) status. Recommendations for long-term travellers, expatriates and people visiting friends and relatives (VFRs) do not differ markedly from those for short-term travellers. Some underlying medical conditions may make individuals more vulnerable to malaria. In addition, some conditions or their treatment may preclude the use of one or more antimalarial medications.

Summary of recommendations for the prevention of malaria by the Committee to Advise on Tropical Medicine and Travel (CATMAT)

BACKGROUND

On behalf of the Public Health Agency of Canada, the Committee to Advise on Tropical Medicine and Travel (CATMAT) developed the Canadian Recommendations for the Prevention and Treatment of Malaria Among International Travellers for Canadian health care providers who are preparing patients for travel to malaria-endemic areas and treating travellers who have returned ill.

OBJECTIVE

To provide guidelines on risk assessment and prevention of malaria.

METHODS

CATMAT reviewed all major sources of information on malaria prevention, as well as recent research and national and international epidemiological data, to tailor guidelines to the Canadian context. The evidence-based medicine recommendations were developed with associated rating scales for the strength and quality of the evidence.

RECOMMENDATIONS

Used together and correctly, personal protective measures (PPM) and chemoprophylaxis very effectively protect against malaria infection. PPM include protecting accommodation areas from mosquitoes, wearing appropriate clothing, using bed nets pre-treated with insecticide and applying topical insect repellant (containing 20%-30% DEET or 20% icaridin) to exposed skin. Selecting the most appropriate chemoprophylaxis involves assessment of the traveller's itinerary to establish his/her malaria risk profile as well as potential drug resistance issues. Antimalarials available on prescription in Canada include chloroquine (or hydroxychloroquine), atovaquone-proguanil, doxycycline, mefloquine and primaquine.

Summary of recommendations for the diagnosis and treatment of malaria by the Committee to Advise on Tropical Medicine and Travel (CATMAT)

BACKGROUND

On behalf of the Public Health Agency of Canada, the Committee to Advise on Tropical Medicine and Travel (CATMAT) developed the Canadian Recommendations for the Prevention and Treatment of Malaria Among International Travellers for Canadian health care providers who are preparing patients for travel to malaria-endemic areas and treating travellers who have returned ill. These recommendations aim to achieve appropriate diagnosis and management of malaria, a disease that is still uncommon in Canada.

OBJECTIVE

To provide recommendations on the appropriate diagnosis and treatment of malaria.

METHODS

CATMAT reviewed all major sources of information on malaria diagnosis and treatment, as well as recent research and national and international epidemiological data, to tailor guidelines to the Canadian context. The evidence-based medicine recommendations were developed with associated rating scales for the strength and quality of the evidence.

RECOMMENDATIONS

Malarial management depends on rapid identification of the disease, as well as identification of the malaria species and level of parasitemia. Microscopic identification of blood samples is both rapid and accurate but can be done only by trained laboratory technicians. Rapid diagnostic tests are widely available, are simple to use and do not require specialized laboratory equipment or training; however, they do not provide the level of parasitemia and do require verification. Polymerase chain reaction (PCR), although still limited in availability, is emerging as the gold standard for high sensitivity and specificity in identifying the species.

A novel, automated nutrition screening system as a predictor of nutritional risk in an oncology day treatment unit (ODTU)

PURPOSE

Paper-based nutrition screening tools can be challenging to implement in the ambulatory oncology setting. The aim of this study was to determine the validity of the Malnutrition Screening Tool (MST) and a novel, automated nutrition screening system compared to a 'gold standard' full nutrition assessment using the Patient-Generated Subjective Global Assessment (PG-SGA).

METHODS

An observational, cross-sectional study was conducted in an outpatient oncology day treatment unit (ODTU) within an Australian tertiary health service. Eligibility criteria were as follows: ≥ 18 years, receiving outpatient anticancer treatment and English literate. Patients self-administered the MST. A dietitian assessed nutritional status using the PG-SGA, blinded to the MST score. Automated screening system data were extracted from an electronic oncology prescribing system. This system used weight loss over 3 to 6 weeks prior to the most recent weight record or age-categorised body mass index (BMI) to identify nutritional risk. Sensitivity and specificity against PG-SGA (malnutrition) were calculated using contingency tables and receiver operating curves.

RESULTS

There were a total of 300 oncology outpatients (51.7% male, 58.6 ± 13.3 years). The area under the curve (AUC) for weight loss alone was 0.69 with a cut-off value of ≥ 1% weight loss yielding 63% sensitivity and 76.7% specificity. MST (score ≥ 2) resulted in 70.6% sensitivity and 69.5% specificity, AUC 0.77.

CONCLUSIONS

Both the MST and the automated method fell short of the accepted professional standard for sensitivity (~≥ 80%) derived from the PG-SGA. Further investigation into other automated nutrition screening options and the most appropriate parameters available electronically is warranted to support targeted service provision.

Evaluation of an innovative recruitment initiative on the attitudes of medical students

Some medical specialties struggle to recruit sufficient trainees to their postgraduate programmes. In many countries including Ireland, psychiatry is one of these specialties. A psychiatric summer school was developed by the trainee committee of the College of Psychiatry of Ireland as a recruitment initiative. All applicants were invited to complete a questionnaire prior, on the day of and three months after the summer school assessing their attitudes to a career in psychiatry. The mean score on the modified Nielson questionnaire in the pre-summer school group was 26.7 (SD +/- 3.8) and this rose significantly 28.3 (SD +/- 3.2) after completion of the summer school. 64% (n = 31) of applicants to the Summer school expressed an interest in a career in psychiatry. This rose to 88% (n = 32) of those who attended. The findings of this study have national and international interest for all specialties who are struggling to recruit to their field.

A pragmatic randomised controlled trial to compare antidepressants with a community-based psychosocial intervention for the treatment of women with postnatal depression: the RESPOND trial

OBJECTIVES

To evaluate clinical effectiveness at 4 weeks of antidepressant therapy for mothers with postnatal depression (PND) compared with general supportive care; to compare outcome at 18 weeks of those randomised to antidepressant therapy with those randomised to listening visits as the first intervention (both groups were to be allowed to receive the alternative intervention after 4 weeks if the woman or her doctor so decided); and to assess acceptability of antidepressants and listening visits to users and health professionals.

DESIGN

A pragmatic two-arm individually randomised controlled trial.

SETTING

Participants were recruited from 77 general practices: 21 in Bristol, 21 in south London and 35 in Manchester.

PARTICIPANTS

A total of 254 women who fulfilled International Classification of Diseases version 10 criteria for major depression in the first 6 postnatal months were recruited and randomised.

INTERVENTIONS

Women were randomised to receive either an antidepressant, usually a selective serotonin reuptake inhibitor prescribed by their general practitioner (GP), or non-directive counselling (listening visits) from a specially trained research health visitor (HV). The trial was designed to compare antidepressants with general supportive care for the first 4 weeks, after which women allocated to listening visits commenced their sessions. It allowed for women to receive the alternative intervention if they had not responded to their allocated intervention or wished to change to, or add in, the alternative intervention at any time after 4 weeks.

MAIN OUTCOME MEASURES

The duration of the trial was 18 weeks. Primary outcome, measured at 4 weeks and 18 weeks post randomisation, was the proportion of women improved on the Edinburgh Postnatal Depression Scale (EPDS), that is scoring < 13. Secondary outcomes were the EPDS measured as a continuous variable at 4 and 18 weeks, and scores on various other questionnaires.

RESULTS

At 4 weeks, women were more than twice as likely to have improved if they had been randomised to antidepressants compared with listening visits, which started after the 4-week follow-up, i.e. after 4 weeks of general supportive care [primary intention-to-treat (ITT), 45% versus 20%; odds ratio (OR) 3.4, 95% confidence interval (CI) 1.8 to 6.5, p < 0.001]. Explanatory analyses emphasised these findings. At 18 weeks, ITT analysis revealed that the proportion of women improving was 11% greater in the antidepressant group, but logistic regression analysis showed no clear benefit for one group over the other [62% versus 51%, OR 1.5 (95% CI 0.8 to 2.6), p = 0.19]. Overall, there was a difference between the groups in favour of the antidepressant group of about 25 percentage points at 4 weeks, which reduced at 18 weeks. No statistical support existed for a benefit of antidepressants at 18 weeks, but 95% CIs could not rule out a clinically important benefit. It was difficult for GPs not to prescribe antidepressants to women randomised to listening visits after the initial 4 weeks, so many women received both interventions in both groups by 18 weeks and consequently power was reduced. Qualitative interviews with women revealed a preference for listening visits but an acceptance that antidepressants might be necessary. They wished to be reassured that their GP and HV were offering continuity of care focusing on their particular set of circumstances. Interviews with GPs and HVs revealed lack of collaboration in managing care for women with PND; neither professional group was willing to assume responsibility.

CONCLUSIONS

At 4 weeks, antidepressants were significantly superior to general supportive care. Trial design meant that by 18 weeks many of the women initially randomised to listening visits were also receiving antidepressants, and more vice versa. The lack of evidence for differences at 18 weeks is likely to reflect a combination of reduced power and the considerable degree of switching across the two interventions. Qualitative study revealed that women found both antidepressants and listening visits effective depending on their circumstances and preferences. The trial indicates that early treatment with antidepressants leads to clinical benefit for women with PND.

Primary adenoid cystic carcinoma of the bronchus in a female teenager

Primary adenoid cystic carcinoma (ACC) of the lung is an extremely rare malignant lung neoplasm. ACC of salivary glands of the head and neck, lachrymal glands, breast, skin, vulva and trachea have been frequently reported disease patterns in the literature, but it is unique to see this rare lung tumour in a patient as young as 14 years old. No double blind placebo, multicentre treatment data are available. Surgery is considered as the cornerstone of the treatment. Prognosis is variable and adjuvant radiotherapy has been found beneficial for prolonged survival. Our report of primary lung ACC in a young girl is a complex case due to young age, a different way of presentation and staging on diagnosis. It has been a quite challenging clinical scenario for the multidisciplinary lung cancer treating team involved in the clinical care. Prognosis remains unpredictable and uncertain despite the best present day evidence-based treatment.