Data management for prospective research studies using SAS® software

<p>Abstract</p> <p>Background</p> <p>Maintaining data quality and integrity is important for research studies involving prospective data collection. Data must be entered, erroneous or missing data must be identified and corrected if possible, and an audit trail created.</p> <p>Methods</p> <p>Using as an example a large prospective study, the Missouri Lower Respiratory Infection (LRI) Project, we present an approach to data management predominantly using SAS software. The Missouri LRI Project was a prospective cohort study of nursing home residents who developed an LRI. Subjects were enrolled, data collected, and follow-ups occurred for over three years. Data were collected on twenty different forms. Forms were inspected visually and sent off-site for data entry. SAS software was used to read the entered data files, check for potential errors, apply corrections to data sets, and combine batches into analytic data sets. The data management procedures are described.</p> <p>Results</p> <p>Study data collection resulted in over 20,000 completed forms. Data management was successful, resulting in clean, internally consistent data sets for analysis. The amount of time required for data management was substantially underestimated.</p> <p>Conclusion</p> <p>Data management for prospective studies should be planned well in advance of data collection. An ongoing process with data entered and checked as they become available allows timely recovery of errors and missing data.</p

Comparing counselling alone versus counselling supplemented with guided use of a well-being app for university students experiencing anxiety or depression (CASELOAD): protocol for a feasibility trial.

BACKGROUND: University counselling services face a unique challenge to offer short-term therapeutic support to students presenting with complex mental health needs and in a setting which suits the academic timetable. The recent availability of mobile phone applications (apps) offers an opportunity to supplement face-to-face therapy and has the potential to reach a wider audience, maintain engagement between therapy sessions, and enhance therapeutic outcomes. The present study, entitled Counselling plus Apps for Students Experiencing Levels of Anxiety or Depression (CASELOAD), aims to explore the feasibility of supplementing counselling with guided use of a well-being app. METHODS/DESIGN: Forty help-seeking university students (aged 18 years and over) with symptoms of moderate anxiety or depression will be recruited from a University Counselling Service (UCS) in the United Kingdom (UK). Participants will be recruited via counsellors who provide the initial clinical assessment and who determine treatment allocation to one of two treatments on the basis of client-treatment fit. The two conditions comprise (1) counselling alone (treatment as usual/TAU) or (2) counselling supplemented with guided use of a well-being app (enhanced intervention). Trained counsellors will deliver up to six counselling sessions in each treatment arm across a 6-month period, and the session frequency will be decided by client-counsellor discussion. Assessments will occur at baseline, every counselling session, post-intervention (3 months after consent) and follow-up (6 months after consent). Assessments will include clinical measures of anxiety, depression, psychological functioning, specific mental health concerns (e.g. academic distress and substance misuse), resilience and therapeutic alliance. The usage, acceptability, feasibility and potential implications of combining counselling with guided use of the well-being app will be assessed through audio recordings of counselling sessions, telephone interviews with participants, focus groups with counsellors and counsellor notes. DISCUSSION: This study will inform the design of a randomised pilot trial and a definitive trial which aim to improve therapy engagement, reduce dropout and enhance clinical outcomes of student counselling. TRIAL REGISTRATION: ISRCTN55102899

Advances in prevention and therapy of neonatal dairy calf diarrhoea : a systematical review with emphasis on colostrum management and fluid therapy

Neonatal calf diarrhoea remains the most common cause of morbidity and mortality in preweaned dairy calves worldwide. This complex disease can be triggered by both infectious and non-infectious causes. The four most important enteropathogens leading to neonatal dairy calf diarrhoea are Escherichia coli, rota-and coronavirus, and Cryptosporidium parvum. Besides treating diarrhoeic neonatal dairy calves, the veterinarian is the most obvious person to advise the dairy farmer on prevention and treatment of this disease. This review deals with prevention and treatment of neonatal dairy calf diarrhoea focusing on the importance of a good colostrum management and a correct fluid therapy

From father to son: transgenerational effect of tetracycline on sperm viability

The broad-spectrum antibiotic tetracycline is used in animal production, antimicrobial therapy, and for curing arthropods infected with bacterial endosymbionts such as Wolbachia. Tetracycline inhibits mitochondrial translation, and recent evidence indicates that male reproductive traits may be particularly sensitive to this antibiotic. Here, we report the first multi-generation investigation of tetracycline's effects on ejaculate traits. In a study of the pseudoscorpion, Cordylochernes scorpioides, in which siblings were randomly assigned to control and tetracycline treatments across replicate full-sibling families, tetracycline did not affect body size in either sex, female reproduction or sperm number. However, tetracycline-treated males exhibited significantly reduced sperm viability compared to control males, and transmitted this toxic effect of tetracycline on sperm to their untreated sons but not to their F2 grandsons. These results are consistent with tetracycline-induced epigenetic changes in the male germline, and suggest the need for further investigation of transgenerational effects of tetracycline on male reproductive function

Gastric cancer surgery: Billroth I or Billroth II for distal gastrectomy?

<p>Abstract</p> <p>Background</p> <p>The selection of an anastomosis method after a distal gastrectomy is a highly debatable topic; however, the available documentation lacks the necessary research based on a comparison of early postoperative complications. This study was conducted to investigate the difference of early postoperative complications between Billroth I and Billroth II types of anastomosis for distal gastrectomies.</p> <p>Methods</p> <p>A total of 809 patients who underwent distal gastrectomies for gastric cancer during four years were included in the study. The only study endpoint was analysis of in-patients' postoperative complications. The risk adjusted complication rate was compared by POSSUM (Physiological and operative severity score for enumeration of morbidity and mortality) and the severity of complications was compared by Rui Jin Hospital classification of complication.</p> <p>Results</p> <p>Complication rate of Billroth II type of anastomosis was almost double of that in Billroth I (P = 0.000). Similarly, the risk adjusted complication rate was also higher in Billroth II group. More severe complications were observed and the postoperative duration was significantly longer in Billroth II type (P = 0.000). Overall expenditure was significantly higher in Billroth II type (P = 0.000).</p> <p>Conclusion</p> <p>Billroth II method of anastomosis was associated with higher rate of early postoperative complications. Therefore, we conclude that the Billroth I method should be the first choice after a distal gastrectomy as long as the anatomic and oncological environment of an individual patient allows us to perform it. However more prospective studies should be designed to compare the overall surgical outcomes of both anastomosis methods.</p

Real-time PCR assay and rapid diagnostic tests for the diagnosis of clinically suspected malaria patients in Bangladesh

<p>Abstract</p> <p>Background</p> <p>More than 95% of total malaria cases in Bangladesh are reported from the 13 high endemic districts. <it>Plasmodium falciparum </it>and <it>Plasmodium vivax </it>are the two most abundant malaria parasites in the country. To improve the detection and management of malaria patients, the National Malaria Control Programme (NMCP) has been using rapid diagnostic test (RDT) in the endemic areas. A study was conducted to establish a SYBR Green-based modified real-time PCR assay as a gold standard to evaluate the performance of four commercially-available malaria RDTs, along with the classical gold standard- microscopy.</p> <p>Methods</p> <p>Blood samples were collected from 338 febrile patients referred for the diagnosis of malaria by the attending physician at Matiranga</p> <p>Upazila Health Complex (UHC) from May 2009 to August 2010. Paracheck RDT and microscopy were performed at the UHC. The blood samples were preserved in EDTA tubes. A SYBR Green-based real-time PCR assay was performed and evaluated. The performances of the remaining three RDTs (Falcivax, Onsite Pf and Onsite Pf/Pv) were also evaluated against microscopy and real-time PCR using the stored blood samples.</p> <p>Result</p> <p>In total, 338 febrile patients were enrolled in the study. Malaria parasites were detected in 189 (55.9%) and 188 (55.6%) patients by microscopy and real-time PCR respectively. Among the RDTs, the highest sensitivity for the detection of <it>P. falciparum </it>(including mixed infection) was obtained by Paracheck [98.8%, 95% confidence interval (CI) 95.8-99.9] and Falcivax (97.6%, 95% CI 94.1-99.4) compared to microscopy and real-time PCR respectively. Paracheck and Onsite Pf/Pv gave the highest specificity (98.8%, 95% CI 95.7-99.9) compared to microscopy and Onsite Pf/Pv (98.8, 95% CI 95.8-99.9) compared to real-time PCR respectively for the detection of <it>P. falciparum</it>. On the other hand Falcivax and Onsite Pf/Pv had equal sensitivity (90.5%, 95% CI 69.6-98.8) and almost 100% specificity compared to microscopy for the detection of <it>P. vivax</it>. However, compared to real-time PCR assay RDTs and microscopy gave low sensitivity (76.9%, 95% CI 56.4-91) in detecting of <it>P. vivax </it>although a very high specificity was obtained (99- 100%).</p> <p>Conclusion</p> <p>The results of this study suggest that the SYBR Green-based real-time PCR assay could be used as an alternative gold standard method in a reference setting. Commercially-available RDTs used in the study are quite sensitive and specific in detecting <it>P. falciparum</it>, although their sensitivity in detecting <it>P. vivax </it>was not satisfactory compared to the real-time PCR assay.</p

Age and sex influence marmot antipredator behavior during periods of heightened risk

Animals adjust their antipredator behavior according to environmental variation in risk, and to account for their ability to respond to threats. Intrinsic factors that influence an animal’s ability to respond to predators (e.g., age, body condition) should explain variation in antipredator behavior. For example, a juvenile might allocate more time to vigilance than an adult because mortality as a result of predation is often high for this age class; however, the relationship between age/vulnerability and antipredator behavior is not always clear or as predicted. We explored the influence of intrinsic factors on yellow-bellied marmot (Marmota flaviventris) antipredator behavior using data pooled from 4 years of experiments. We hypothesized that inherently vulnerable animals (e.g., young, males, and individuals in poor condition) would exhibit more antipredator behavior prior to and immediately following conspecific alarm calls. As expected, males and yearlings suppressed foraging more than females and adults following alarm call playbacks. In contrast to predictions, animals in better condition respond more than animals in below average condition. Interestingly, these intrinsic properties did not influence baseline time budgets; animals of all ages, sexes, and condition levels devoted comparable amounts of time to foraging prior to alarm calls. Our results support the hypothesis that inherent differences in vulnerability influence antipredator behavior; furthermore, it appears that a crucial, but poorly acknowledged, interaction exists between risk and state-dependence. Elevated risk may be required to reveal the workings of state-dependent behavior, and studies of antipredator behavior in a single context may draw incomplete conclusions about age- or sex-specific strategies

Human Papillomavirus (HPV) 16 E6 Variants in Tonsillar Cancer in Comparison to Those in Cervical Cancer in Stockholm, Sweden

Background: Human papillomavirus (HPV), especially HPV16, is associated with the development of both cervical and tonsillar cancer and intratype variants in the amino acid sequence of the HPV16 E6 oncoprotein have been demonstrated to be associated with viral persistence and cancer lesions. For this reason the presence of HPV16 E6 variants in tonsillar squamous cell carcinoma (TSCC) in cervical cancer (CC), as well as in cervical samples (CS), were explored. Methods: HPV16 E6 was sequenced in 108 TSCC and 52 CC samples from patients diagnosed 2000–2008 in the County of Stockholm, and in 51 CS from young women attending a youth health center in Stockholm. Results: The rare E6 variant R10G was relatively frequent (19%) in TSCC, absent in CC and infrequent (4%) in CS, while the well-known L83V variant was common in TSCC (40%), CC (31%), and CS (29%). The difference for R10G was significant between TSCC and CC (p = 0.0003), as well as between TSCC and CS (p = 0.009). The HPV16 European phylogenetic lineage and its derivatives dominated in all samples (.90%). Conclusion: The relatively high frequency of the R10G variant in TSCC, as compared to what has been found in CC both in the present study as well as in several other studies in different countries, may indicate a difference between TSCC and CC with regard to tumor induction and development. Alternatively, there could be differences with regard to the oral an

Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles

Gene therapy is an emerging alternative to conventional anti-HIV-1 drugs, and can potentially control the virus while alleviating major limitations of current approaches. Yet, HIV-1's ability to rapidly acquire mutations and escape therapy presents a critical challenge to any novel treatment paradigm. Viral escape is thus a key consideration in the design of any gene-based technique. We develop a computational model of HIV's evolutionary dynamics in vivo in the presence of a genetic therapy to explore the impact of therapy parameters and strategies on the development of resistance. Our model is generic and captures the properties of a broad class of gene-based agents that inhibit early stages of the viral life cycle. We highlight the differences in viral resistance dynamics between gene and standard antiretroviral therapies, and identify key factors that impact long-term viral suppression. In particular, we underscore the importance of mutationally-induced viral fitness losses in cells that are not genetically modified, as these can severely constrain the replication of resistant virus. We also propose and investigate a novel treatment strategy that leverages upon gene therapy's unique capacity to deliver different genes to distinct cell populations, and we find that such a strategy can dramatically improve efficacy when used judiciously within a certain parametric regime. Finally, we revisit a previously-suggested idea of improving clinical outcomes by boosting the proliferation of the genetically-modified cells, but we find that such an approach has mixed effects on resistance dynamics. Our results provide insights into the short- and long-term effects of gene therapy and the role of its key properties in the evolution of resistance, which can serve as guidelines for the choice and optimization of effective therapeutic agents

A study of the relationship between the migration of image silver and perceived yellowing of silver gelatine photographs

Silver gelatine photographs were the most dominant photographic process of the twentieth century from the 1880s until the 1960s. They are prone to yellowing, mirroring and fading which is largely attributed to the effects of pollutants, relative humidity and residual processing chemicals. Experts in the conservation of photographs claim they can determine the causes of deterioration with the naked eye: the effects of humidity result in a more yellowed appearance, whilst the presence of residual chemicals results in a redder appearance. This work aims to investigate if the same deterioration processes can be diagnosed in photographic prints with a spectrophotometer by addressing two questions: (1) In new and artificially aged silver gelatine photographs is it possible to distinguish between discolouration caused by silver migration and that caused by the presence of residual sulfur? (2) What are the complexities of applying these findings to historic photographs? A set of test photographs, some well processed and some insufficiently washed was developed and artificially aged. These were compared to a small collection of historical photographs of different ages, paper types and image colours. Samples were assessed using visual observation, residual silver and hypo spot tests, colour measurements including L*a*b* and reflectance spectra, Fourier transform infra-red (FTIR) spectroscopy and transmission electron microscopy (TEM). After artificial ageing the well processed test photographs were more yellowed, TEM indicated that this was due to colloidal silver formation. The insufficiently washed test photographs were more red but also darker, TEM showed these samples to have more homogeneous silver filaments, thought to be due to silver sulfide formation. The results for the historical photographs were similar but more subtle. A larger sample set is needed to investigate this more extensively. Further investigation on historical samples, with colour measurements and residual silver and fixer spot tests will take place