Managing open access workflows at the University of St Andrews: challenges and Pathfinder solutions

Presentation of Janet Aucock, at the FinELib Consortium Seminar (Aineistopäivä), April 16, 2015 in Helsinki.

Identification of characteristics for successful university-company partnership development

The importance of university-company collaboration has increased during the last decades. The drivers for that are, on the one hand, changes in business logic of companies and on the other hand the decreased state funding of universities. Many companies emphasize joint research with universities as an enabling input to their development processes, which aim at creating new innovations, products and wealth. These factors have changed universities’ operations and they have adopted several practices of dynamic business organizations, such as strategic planning, monitoring and controlling methods of internal processes etc. The objective of this thesis is to combine different characteristics of successful university-company partnership and its development. The development process starts with identifying potential partners in the university’s interest group, which requires understanding the role of different partners in the innovation system. Next, in order to find a common development basis, matching the policy and strategy between partners is needed. The third phase is to combine the academic and industrial objectives of a joint project, which is a typical form of university-company collaboration. The optimum is a win-win situation where both partners, universities and companies, can get addedvalue. For the companies added value typically means access to new research results before their competitors. For the universities added value offers a possibility to carry on high level scientific work. The research output in the form of published scientific articles is evaluated by the international science community. Because the university-company partnership is often executed by joint projects, the different forms of this kind of projects is discussed in this study. The most challenging form of collaboration is a semi-open project model, which is not based on bilateral activities between universities and companies but on a consortium of several universities, research institutes and companies. The universities and companies are core actors in the innovation system. Thus the discussion of their roles and relations to public operators like publicly funded financiers is important. In the Finnish innovation system there are at least the following doers executing strategies and policies: EU, Academy of Finland and TEKES. In addition to these, Strategic Centres for Science, Technology and Innovation which are owned jointly by companies, universities and research organizations have a very important role in their fields of business. They transfer research results into commercial actions to generate wealth. The thesis comprises two parts. The first part consists of an overview of the study including introduction, literature review, research design, synthesis of findings and conclusions. The second part introduces four original research publications.

Comparison of the effectiveness of initial combined antiretroviral therapy with nelfinavir or efavirenz at a university-based outpatient service in Brazil

Since there are some concerns about the effectiveness of highly active antiretroviral therapy in developing countries, we compared the initial combination antiretroviral therapy with zidovudine and lamivudine plus either nelfinavir or efavirenz at a university-based outpatient service in Brazil. This was a retrospective comparative cohort study carried out in a tertiary level hospital. A total of 194 patients receiving either nelfinavir or efavirenz were identified through our electronic database search, but only 126 patients met the inclusion criteria. Patients were included if they were older than 18 years old, naive for antiretroviral therapy, and had at least 1 follow-up visit after starting the antiretroviral regimen. Fifty-one of the included patients were receiving a nelfinavir-based regimen and 75 an efavirenz-based regimen as outpatients. Antiretroviral therapy was prescribed to all patients according to current guidelines. By intention-to-treat (missing/switch = failure), after a 12-month period, 65% of the patients in the efavirenz group reached a viral load <400 copies/mL compared to 41% of the patients in the nelfinavir group (P = 0.01). The mean CD4 cell count increase after a 12-month period was also greater in the efavirenz group (195 x 10(6) cells/L) than in the nelfinavir group (119 x 10(6) cells/L; P = 0.002). The efavirenz-based regimen was superior compared to the nelfinavir-based regimen. The low response rate in the nelfinavir group might be partially explained by the difficulty of using a regimen requiring a higher patient compliance (12 vs 3 pills a day) in a developing country.

Vancomycin-dependent Enterococcus faecium vanA: characterization of the first case isolated in a university hospital in Brazil

In this study, we report the characterization of a strain of Enterococcus faecium vanA, which grows only in the presence of vancomycin (VDEfm-UEL). The bacterium was isolated from the feces of a female patient who had undergone surgical treatment of Reinke’s edema and was receiving intravenous vancomycin therapy for infection with methicillin/oxacillin-resistant Staphylococcus aureus, a postoperative complication. Antimicrobial dependence was further confirmed by the vancomycin E-test. VDEfm-UEL was also shown to be resistant to ampicillin, ciprofloxacin, chloramphenicol, erythromycin, levofloxacin, penicillin, rifampicin, and teicoplanin. The putative virulence genes efaA, gelE and esp were detected by PCR. The ddl gene from VDEfm-UEL was cloned and sequenced. Vancomycin dependence seems to be associated with the insertion of a nucleotide in that sequence, which results in a frame-shift mutation, introducing a premature stop codon. This is the first report of vancomycin-dependent E. faecium isolation in a university hospital in Brazil.

Characterization and analysis of the outcome of adults with acute myeloid leukemia treated in a Brazilian University hospital over three decades

We evaluated the outcome of 227 patients with acute myeloid leukemia during three decades (period 1 - 1980’s, N = 89; period 2 - 1990’s, N = 73; period 3 - 2000’s, N = 65) at a single institution. Major differences between the three groups included a higher median age, rates of multilineage dysplasia and co-morbidities, and a lower rate of clinical manifestations of advanced leukemia in recent years. The proportion of patients who received induction remission chemotherapy was 66, 75, and 85% for periods 1, 2, and 3, respectively (P = 0.04). The median survival was 40, 77, and 112 days, and the 5-year overall survival was 7, 13, and 22%, respectively (P = 0.01). The median disease-free survival was 266, 278, and 386 days (P = 0.049). Survival expectation for patients with acute myeloid leukemia has substantially improved during this 30-year period, due to a combination of lower tumor burden and a more efficient use of chemotherapy and supportive care.

Study of the comprehension of the scientific method by members of a university health research laboratory

In Brazil, scientific research is carried out mainly at universities, where professors coordinate research projects with the active participation of undergraduate and graduate students. However, there is no formal program for the teaching/learning of the scientific method. The objective of the present study was to evaluate the comprehension of the scientific method by students of health sciences who participate in scientific projects in an academic research laboratory. An observational descriptive cross-sectional study was conducted using Edgar Morin complexity as theoretical reference. In a semi-structured interview, students were asked to solve an abstract logical puzzle - TanGram. The collected data were analyzed using the hermeneutic-dialectic analysis method proposed by Minayo and discussed in terms of the theoretical reference of complexity. The students’ concept of the scientific method is limited to participation in projects, stressing the execution of practical procedures as opposed to scientific thinking. The solving of the TanGram puzzle revealed that the students had difficulties in understanding questions and activities focused on subjects and their processes. Objective answers, even when dealing with personal issues, were also reflected on the students’ opinions about the characteristics of a successful researcher. Students’ difficulties concerning these issues may affect their scientific performance and result in poorly designed experiments. This is a preliminary study that should be extended to other centers of scientific research.

Clinical outcome of protein-energy malnourished patients in a Brazilian university hospital

Protein-energy malnutrition (PEM) is a treatable disease with high prevalence among hospitalized patients. It can cause significant increases in the duration of hospitalization and costs. PEM is especially important for health systems since malnourished patients present higher morbidity and mortality. The objective of the present study was to assess the evolution of nutritional status (NS) and the effect of malnutrition on clinical outcome of patients at a public university hospital of high complexity in Brazil. Patients hospitalized in internal medicine (n = 54), oncology (n = 43), and infectious diseases (n = 12) wards were included. NS was evaluated using subjective global assessment up to 48 h after admission, and thereafter at intervals of 4-6 days. On admission, patients (n = 109) were classified as well-nourished (n = 73), moderately malnourished or at risk of malnutrition (n = 28), and severely malnourished (n = 8). During hospitalization, malnutrition developed or worsened in 11 patients. Malnutrition was included in the clinical diagnosis of only 5/36 records (13.9% of the cases, P = 0.000). Nutritional therapy was administered to only 22/36 of the malnourished patients; however, unexpectedly, 6/73 well-nourished patients also received commercial enteral diets. Complications were diagnosed in 28/36 malnourished and 9/73 well-nourished patients (P = 0.000). Death occurred in 12/36 malnourished and 3/73 well-nourished patients (P = 0.001). A total of 24/36 malnourished patients were discharged regardless of NS. In summary, malnutrition remains a real problem, often unrecognized, unappreciated, and only sporadically treated, even though its effects can be detrimental to the clinical course and prognosis of patients. The amount of public and private funds unnecessarily dispersed because of hospital malnutrition is significant.

Basic life support knowledge of first-year university students from Brazil

We aimed to evaluate knowledge of first aid among new undergraduates and whether it is affected by their chosen course. A questionnaire was developed to assess knowledge of how to activate the Mobile Emergency Attendance Service - MEAS (Serviço de Atendimento Móvel de Urgência; SAMU), recognize a pre-hospital emergency situation and the first aid required for cardiac arrest. The students were also asked about enrolling in a first aid course. Responses were received from 1038 of 1365 (76.04%) new undergraduates. The questionnaires were completed in a 2-week period 1 month after the beginning of classes. Of the 1038 respondents (59.5% studying biological sciences, 11.6% physical sciences, and 28.6% humanities), 58.5% knew how to activate the MEAS/SAMU (54.3% non-biological vs 61.4% biological, P=0.02), with an odds ratio (OR)=1.39 (95%CI=1.07-1.81) regardless of age, sex, origin, having a previous degree or having a relative with cardiac disease. The majority could distinguish emergency from non-emergency situations. When faced with a possible cardiac arrest, 17.7% of the students would perform chest compressions (15.5% non-biological vs 19.1% biological first-year university students, P=0.16) and 65.2% would enroll in a first aid course (51.1% non-biological vs 74.7% biological, P<0.01), with an OR=2.61 (95%CI=1.98-3.44) adjusted for the same confounders. Even though a high percentage of the students recognized emergency situations, a significant proportion did not know the MEAS/SAMU number and only a minority had sufficient basic life support skills to help with cardiac arrest. A significant proportion would not enroll in a first aid course. Biological first-year university students were more prone to enroll in a basic life support course.

Prevalence of child malnutrition at a university hospital using the World Health Organization criteria and bioelectrical impedance data

Malnutrition constitutes a major public health concern worldwide and serves as an indicator of hospitalized patients’ prognosis. Although various methods with which to conduct nutritional assessments exist, large hospitals seldom employ them to diagnose malnutrition. The aim of this study was to understand the prevalence of child malnutrition at the University Hospital of the Ribeirão Preto Medical School, University of São, Brazil. A cross-sectional descriptive study was conducted to compare the nutritional status of 292 hospitalized children with that of a healthy control group (n=234). Information regarding patients’ weight, height, and bioelectrical impedance (i.e., bioelectrical impedance vector analysis) was obtained, and the phase angle was calculated. Using the World Health Organization (WHO) criteria, 35.27% of the patients presented with malnutrition; specifically, 16.10% had undernutrition and 19.17% were overweight. Classification according to the bioelectrical impedance results of nutritional status was more sensitive than the WHO criteria: of the 55.45% of patients with malnutrition, 51.25% exhibited undernutrition and 4.20% were overweight. After applying the WHO criteria in the unpaired control group (n=234), we observed that 100.00% of the subjects were eutrophic; however, 23.34% of the controls were malnourished according to impedance analysis. The phase angle was significantly lower in the hospitalized group than in the control group (P<0.05). Therefore, this study suggests that a protocol to obtain patients’ weight and height must be followed, and bioimpedance data must be examined upon hospital admission of all children.

Investigation of the effects of peppermint (Mentha piperita) on the biochemical and anthropometric profile of university students

The hypolipidemic effects of several medicinal plants have already been demonstrated, but many plants commonly used to treat diseases still need to be studied. Peppermint (Mentha piperita) is widely consumed by the population for different purposes, but not for the treatment of dyslipidemias. The objective of this study was to examine the effects of this plant on human biochemical and anthropometric profiles and blood pressure, based on the administration of peppermint juice twice daily for 30 days. Blood samples were collected before and after the treatment in order to determine the glycemic and lipid profiles, and the Body Mass Index (BMI) analysis was performed. Results indicated that 41.5% of the subjects showed a reduction in glycemia, 66.9% in total cholesterol levels, 58.5% in triacylglycerides, 52.3% in LDL-c (low-density lipoproteins) indices, 70% in GOT (glutamic-oxaloacetic transaminase) levels, 74.5% in GPT (glutamic-pyruvic transaminase) levels, and that 52% presented an increase in HDL-c (high-density lipoprotein cholesterol) indices. Also, 52.5% showed a decrease in blood pressure and 48.7% in BMI. The use of peppermint by humans can be considered beneficial in the prevention and treatment of risk factors of chronic degenerative diseases.

Application of exploratory factor analysis to assess fish consumption in a university community

The objective of this research was to use the technique of Exploratory Factor Analysis (EFA) for the adequacy of a tool for the assessment of fish consumption and the characteristics involved in this process. Data were collected during a campaign to encourage fish consumption in Brazil with the voluntarily participation of members of a university community. An assessment instrument consisting of multiple-choice questions and a five-point Likert scale was designed and used to measure the importance of certain attributes that influence the choice and consumption of fish. This study sample was composed of of 224 individuals, the majority were women (65.6%). With regard to the frequency of fish consumption, 37.67% of the volunteers interviewed said they consume the product two or three times a month, and 29.6% once a week. The Exploratory Factor Analysis (EFA) was used to group the variables; the extraction was made using the principal components and the rotation using the Quartimax method. The results show clusters in two main constructs, quality and consumption with Cronbach Alpha coefficients of 0.75 and 0.69, respectively, indicating good internal consistency.