Strengthening the food systems governance evidence base: Supporting commensurability of research through a systematic review of methods

Governance of food systems is a poorly understood determinant of food security. Much scholarship on food systems governance is non-empirical, while existing research is often case study-based and theoretically and methodologically incommensurable. This frustrates aggregation of evidence and generalisation. We undertook a systematic review of methods used in food systems governance research with a view to identifying a core set of indicators for future research. We gathered literature through a structured consultation and sampling from recent reviews. Indicators were identified and classified according to the levels and sectors they investigate. We found a concentration of indicators in food production at local to national levels and a sparseness in distribution and consumption. Unsurprisingly, many indicators of institutional structure were found, while agency-related indicators are moderately represented. We call for piloting and validation of these indicators and for methodological development to fill gaps identified. These efforts are expected to support a more consolidated future evidence base and eventual meta-analysis.

Methods to convert continuous outcomes into odds ratios of treatment response and numbers needed to treat: meta-epidemiological study

Clinicians find standardized mean differences (SMDs) calculated from continuous outcomes difficult to interpret. Our objective was to determine the performance of methods in converting SMDs or means to odds ratios of treatment response and numbers needed to treat (NNTs) as more intuitive measures of treatment effect.

B-type natriuretic peptide for diagnosis and treatment of congestive heart failure

BACKGROUND Prognostic classification of congestive heart failure (CHF) is difficult and only possible with the help of additional diagnostic tools. B-type natriuretic peptide (BNP) has been used as a diagnostic and prognostic marker for patients (pts) with CHF. In this study, the clinical value of BNP for stratification and treatment of pts with CHF was evaluated. PATIENTS AND METHODS 33 out-pts with CHF (age 57 +/- 12 years) were included. Left-ventricular (LV) ejection fraction (EF) was 27 +/- 8% (mean +/- SD) and NYHA-class 2.4 +/- 0.7. Following parameters were measured: BNP and sodium from blood samples, exercise performance from 6-minute walking test (6MWT, meters) (n = 18), LV end-diastolic diameter (LVEDD) and LV mass (LVM) from 2D-echocardiography (n = 33), as well as LV end-diastolic pressure (LVEDP, n = 23) and systemic vascular resistance (SVR, n = 20) from heart-catheterisation. Ten pts were hospitalised in the preceding 6 months because of worsening CHF or for optimisation of medical therapy. BNP was measured at the beginning and end of the hospital-stay. Follow-up was for 1 year. RESULTS Pts with a high NYHA-class had a higher BNP (pg/ml) than those with a low NYHA- class: NYHA I 51 +/- 20, II 281 +/- 223, III 562+/-346 and IV 1061 +/- 126 pg/ml (p = 0.002). BNP correlated with LVEDP (r = 0.50, p <0.02), SVR (r =0.49, p <0.03) and inversely with 6MWT (r =-0.60, p <0.009), LVEF (r = -0.49, p <0.004) and sodium (r = -0.36, p = 0.04). In the hospitalised pts, mean BNP (pg/ml) was 881 +/- 695 at admission,and 532 +/- 435 at discharge (n.s.). Decrease in BNPduring hospitalisation paralleled weight-loss and was significantly greater in patients with >1000 pg/ml BNP at admission (n = 5) as compared to the 5 patients with BNP <1000 (p <0.03). Patients with an adverse event during 1-year follow-up had significantly higher BNP both at steady-state (603 +/-359 pg/ml) and at time of decompensation than patients with a favourable outcome (227 +/- 218 pg/ml,p <0.001). CONCLUSIONS BNP correlates well with the clinical severity of CHF (NYHA-class) and is directly related to filling pressure (LVEDP), LV function(LVEF) and exercise performance (6 MWT). Furthermore, BNP has prognostic impact with regard to adverse clinical events.

Laser scanning microscopy combined with image restoration to analyse a 3D model of the human epithelial airway barrier

A laser scanning microscope collects information from a thin, focal plane and ignores out of focus information. During the past few years it has become the standard imaging method to characterise cellular morphology and structures in static as well as in living samples. Laser scanning microscopy combined with digital image restoration is an excellent tool for analysing the cellular cytoarchitecture, expression of specific proteins and interactions of various cell types, thus defining valid criteria for the optimisation of cell culture models. We have used this tool to establish and evaluate a three dimensional model of the human epithelial airway wall.

Mortality and morbidity in the city of Bern, Switzerland, 1805-1815 with special emphasis on infant, child and maternal deaths

This article contributes to the research on demographics and public health of urban populations of preindustrial Europe. The key source is a burial register that contains information on the deceased, such as age and sex, residence and cause of death. This register is one of the earliest compilations of data sets of individuals with this high degree of completeness and consistency. Critical assessment of the register's origin, formation and upkeep promises high validity and reliability. Between 1805 and 1815, 4,390 deceased inhabitants were registered. Information concerning these individuals provides the basis for this study. Life tables of Bern's population were created using different models. The causes of death were classified and their frequency calculated. Furthermore, the susceptibility of age groups to certain causes of death was established. Special attention was given to causes of death and mortality of newborns, infants and birth-giving women. In comparison to other cities and regions in Central Europe, Bern's mortality structure shows low rates for infants (q0=0.144) and children (q1-4=0.068). This could have simply indicated better living conditions. Life expectancy at birth was 43 years. Mortality was high in winter and spring, and decreased in summer to a low level with a short rise in August. The study of the causes of death was inhibited by difficulties in translating early 19th century nomenclature into the modern medical system. Nonetheless, death from metabolic disorders, illnesses of the respiratory system, and debilitation were the most prominent causes in Bern. Apparently, the worst killer of infants up to 12 months was the "gichteren", an obsolete German term for lethal spasmodic convulsions. The exact modern identification of this disease remains unclear. Possibilities such as infant tetanus or infant epilepsy are discussed. The maternal death rate of 0.72% is comparable with values calculated from contemporaneous sources. Relevance of childbed fever in the early 1800s was low. Bern's data indicate that the extent of deaths related to childbirth in this period is overrated. This research has an explicit interdisciplinary value for various fields including both the humanities and natural sciences, since information reported here represents the complete age and sex structure of a deceased population. Physical anthropologists can use these data as a true reference group for their palaeodemographic studies of preindustrial Central Europe of the late 18th and early 19th century. It is a call to both historians and anthropologists to use our resources to a better effect through combination of methods and exchange of knowledge.

Everolimus-based, calcineurin-inhibitor-free regimen in recipients of de-novo kidney transplants: an open-label, randomised, controlled trial

Non-nephrotoxic immunosuppressive strategies that allow reduction of calcineurin-inhibitor exposure without compromising safety or efficacy remain a goal in kidney transplantation. Immunosuppression based on the mammalian-target-of-rapamycin inhibitor everolimus was assessed as a strategy for elimination of calcineurin-inhibitor exposure and optimisation of renal-graft function while maintaining efficacy.

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Prevention and control of surgical site infections: review of the Basel Cohort Study

INTRODUCTION: Surgical site infections (SSI) are the most common hospital-acquired infections among surgical patients, with significant impact on patient morbidity and health care costs. The Basel SSI Cohort Study was performed to evaluate risk factors and validate current preventive measures for SSI. The objective of the present article was to review the main results of this study and its implications for clinical practice and future research. SUMMARY OF METHODS OF THE BASEL SSI COHORT STUDY: The prospective observational cohort study included 6,283 consecutive general surgery procedures closely monitored for evidence of SSI up to 1 year after surgery. The dataset was analysed for the influence of various potential SSI risk factors, including timing of surgical antimicrobial prophylaxis (SAP), glove perforation, anaemia, transfusion and tutorial assistance, using multiple logistic regression analyses. In addition, post hoc analyses were performed to assess the economic burden of SSI, the efficiency of the clinical SSI surveillance system, and the spectrum of SSI-causing pathogens. REVIEW OF MAIN RESULTS OF THE BASEL SSI COHORT STUDY: The overall SSI rate was 4.7% (293/6,283). While SAP was administered in most patients between 44 and 0 minutes before surgical incision, the lowest risk of SSI was recorded when the antibiotics were administered between 74 and 30 minutes before surgery. Glove perforation in the absence of SAP increased the risk of SSI (OR 2.0; CI 1.4-2.8; p <0.001). No significant association was found for anaemia, transfusion and tutorial assistance with the risk of SSI. The mean additional hospital cost in the event of SSI was CHF 19,638 (95% CI, 8,492-30,784). The surgical staff documented only 49% of in-hospital SSI; the infection control team registered the remaining 51%. Staphylococcus aureus was the most common SSI-causing pathogen (29% of all SSI with documented microbiology). No case of an antimicrobial-resistant pathogen was identified in this series. CONCLUSIONS: The Basel SSI Cohort Study suggested that SAP should be administered between 74 and 30 minutes before surgery. Due to the observational nature of these data, corroboration is planned in a randomized controlled trial, which is supported by the Swiss National Science Foundation. Routine change of gloves or double gloving is recommended in the absence of SAP. Anaemia, transfusion and tutorial assistance do not increase the risk of SSI. The substantial economic burden of in-hospital SSI has been confirmed. SSI surveillance by the surgical staff detected only half of all in-hospital SSI, which prompted the introduction of an electronic SSI surveillance system at the University Hospital of Basel and the Cantonal Hospital of Aarau. Due to the absence of multiresistant SSI-causing pathogens, the continuous use of single-shot single-drug SAP with cefuroxime (plus metronidazole in colorectal surgery) has been validated.

[Pathways-to-Care for First-Episode psychotic patients--an overview of international studies]

A longer duration of untreated psychosis (DUP) as well as of untreated illness (DUI) was found to be associated with a negative course of psychosis. Thus, increasing efforts are made to reduce the DUP and provide adequate treatment as early as possible. But, in order to overcome obstacles to early help-seeking, these have to be identified first. Thus, an overview on initial help-seeking behaviour and predictors of DUP is given. Across 25 identified studies, the DUP, at about one year on average, is still unfavourably long and includes on average of three help-seeking contacts prior to the initiation of adequate treatment. Since negative factors in pathways-to-care involve features on all relevant levels (patient, social environment and health-care system), an optimisation of pathways-to-care will require the integration of services and continuous awareness programmes targeting the general population and mental health-care professionals.

A qualitative study on the role of cultural background in patients perspectives on rehabilitation

Background Low back pain (LBP) is one of the major concerns in health care. In Switzerland, musculoskeletal problems represent the third largest illness group with 9.4 million consultations per year. The return to work rate is increased by an active treatment program and saves societal costs. However, results after rehabilitation are generally poorer in patients with a Southeast European cultural background than in other patients. This qualitative research about the rehabilitation of patients with LBP and a Southeast European cultural background, therefore, explores possible barriers to successful rehabilitation. Methods We used a triangulation of methods combining three qualitative methods of data collection: 13 semi-structured in-depth interviews with patients who have a Southeast European cultural background and live in Switzerland, five semi-structured in-depth interviews and two focus groups with health professionals, and a literature review. Between June and December 2008, we recruited participants at a Rehabilitation Centre in the German-speaking part of Switzerland. Results To cope with pain, patients prefer passive strategies, which are not in line with recommended coping strategies. Moreover, the families of patients tend to support passive behaviour and reduce the autonomy of patients. Health professionals and researchers propagate active strategies including activity in the presence of pain, yet patients do not consider psychological factors contributing to LBP. The views of physicians and health professionals are in line with research evidence demonstrating the importance of psychosocial factors for LBP. Treatment goals focusing on increasing daily activities and return to work are not well understood by patients partly due to communication problems, which is something that patients and health professionals are aware of. Additional barriers to returning to work are caused by poor job satisfaction and other work-related factors. Conclusions LBP rehabilitation can be improved by addressing the following points. Early management of LBP should be activity-centred instead of pain-centred. It is mandatory to implement return to work management early, including return to adapted work, to improve rehabilitation for patients. Rehabilitation has to start when patients have been off work for three months. Using interpreters more frequently would improve communication between health professionals and patients, and reduce misunderstandings about treatment procedures. Special emphasis must be put on the process of goal-formulation by spending more time with patients in order to identify barriers to goal attainment. Information on the return to work process should also include the financial aspects of unemployment and disability.

Determining the optical properties of a gelatin-TiO2 phantom at 780 nm

Tissue phantoms play a central role in validating biomedical imaging techniques. Here we employ a series of methods that aim to fully determine the optical properties, i.e., the refractive index n, absorption coefficient μa, transport mean free path ℓ∗, and scattering coefficient μs of a TiO2 in gelatin phantom intended for use in optoacoustic imaging. For the determination of the key parameters μa and ℓ∗, we employ a variant of time of flight measurements, where fiber optodes are immersed into the phantom to minimize the influence of boundaries. The robustness of the method was verified with Monte Carlo simulations, where the experimentally obtained values served as input parameters for the simulations. The excellent agreement between simulations and experiments confirmed the reliability of the results. The parameters determined at 780 nm are n=1.359(±0.002), μ′s=1/ℓ∗=0.22(±0.02) mm-1, μa= 0.0053(+0.0006-0.0003) mm-1, and μs=2.86(±0.04) mm-1. The asymmetry parameter g obtained from the parameters ℓ∗ and μ′s is 0.93, which indicates that the scattering entities are not bare TiO2 particles but large sparse clusters. The interaction between the scattering particles and the gelatin matrix should be taken into account when developing such phantoms.

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Principles and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies.

Improved effectiveness of partner notification for patients with sexually transmitted infections: systematic review

OBJECTIVE: To examine the effectiveness of methods to improve partner notification by patient referral (index patient has responsibility for informing sex partners of their exposure to a sexually transmitted infection). DESIGN: Systematic review of randomised trials of any intervention to supplement simple patient referral. DATA SOURCES: Seven electronic databases searched (January 1990 to December 2005) without language restriction, and reference lists of retrieved articles. REVIEW METHODS: Selection of trials, data extraction, and quality assessment were done by two independent reviewers. The primary outcome was a reduction of incidence or prevalence of sexually transmitted infections in index patients. If this was not reported data were extracted according to a hierarchy of secondary outcomes: number of partners treated; number of partners tested or testing positive; and number of partners notified, located, or elicited. Random effects meta-analysis was carried out when appropriate. RESULTS: 14 trials were included with 12 389 women and men diagnosed as having gonorrhoea, chlamydia, non-gonococcal urethritis, trichomoniasis, or a sexually transmitted infection syndrome. All studies had methodological weaknesses that could have biased their results. Three strategies were used. Six trials examined patient delivered partner therapy. Meta-analysis of five of these showed a reduced risk of persistent or recurrent infection in patients with chlamydia or gonorrhoea (summary risk ratio 0.73, 95% confidence interval 0.57 to 0.93). Supplementing patient referral with information for partners was as effective as patient delivered partner therapy. Neither strategy was effective in women with trichomoniasis. Two trials found that providing index patients with chlamydia with sampling kits for their partners increased the number of partners who got treated. CONCLUSIONS: Involving index patients in shared responsibility for the management of sexual partners improves outcomes. Health professionals should consider the following strategies for the management of individual patients: patient delivered partner therapy, home sampling for partners, and providing additional information for partners.

Preparation of soluble extracts from adenovirus-infected cells for studies of RNA splicing

Here we describe a collection of methods that have been adapted to produce highly efficient nuclear and cytoplasmic extracts from adenovirus-infected HeLa cells. We describe how to produce extracts from virus-infected cells and how to analyze RNA splicing in vitro using T7 RNA polymerase-derived splicing substrate RNAs.