Development of a genotyping microarray for Usher syndrome

BACKGROUND: Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons. METHODS: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele-specific oligonucleotides corresponding to all 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. RESULTS: Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of >98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. CONCLUSION: The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.

A pain assessment scale for population-based studies: Development and validation of the Pain Module of the Standard Evaluation Questionnaire

The objectives of this study were to develop and validate a tool for assessing pain in population-based observational studies and to develop three subscales for back/neck, upper extremity and lower extremity pain. Based on a literature review, items were extracted from validated questionnaires and reviewed by an expert panel. The initial questionnaire consisted of a pain manikin and 34 items relating to (i) intensity of pain in different body regions (7 items), (ii) pain during activities of daily living (18 items) and (iii) various pain modalities (9 items). Psychometric validation of the initial questionnaire was performed in a random sample of the German-speaking Swiss population. Analyses included tests for reliability, correlation analysis, principal components factor analysis, tests for internal consistency and validity. Overall, 16,634 of 23,763 eligible individuals participated (70%). Test-retest reliability coefficients ranged from 0.32 to 0.97, but only three coefficients were below 0.60. Subscales were constructed combining four items for each of the subscales. Item-total coefficients ranged from 0.76 to 0.86 and Cronbach's alpha were 0.75 or higher for all subscales. Correlation coefficients between subscales and three validated instruments (WOMAC, SPADI and Oswestry) ranged from 0.62 to 0.79. The final Pain Standard Evaluation Questionnaire (SEQ Pain) included 28 items and the pain manikin and accounted for the multidimensionality of pain by assessing pain location and intensity, pain during activity, triggers and time of onset of pain and frequency of pain medication. It was found to be reliable and valid for the assessment of pain in population-based observational studies.

Development of a highly sensitive and specific assay to detect Staphylococcus aureus in bovine mastitic milk

Diagnosis of udder infections with Staphylococcus aureus by bacteriological milk testing of quarter milk samples is often not satisfactory. To get reliable results, repeated sampling is necessary, which is normally too expensive. Therefore, we developed a test that allows the highly specific detection of Staph. aureus in bovine milk samples at very low concentrations. It is based on a fast procedure to prepare bacteria from milk, followed by DNA extraction and quantitative PCR. The whole analysis is done within 5 h. For clinical milk samples, the analytical sensitivity of the assay was 50.7 times and 507 times higher than conventional bacteriology with 100 and 10 microL, respectively. The diagnostic specificity was 100%. The test is further characterized by a low intra- and interassay variability as well as by a good recovery of Staph. aureus from raw milk. Furthermore, a high correlation (R = 0.925) between the agar plate counts and the quantitative PCR methodology over the whole range of measurement was found. In addition, our test revealed considerably more positive results than bacteriology. Due to its favorable properties, the assay might become an important diagnostic tool in the context of bovine mastitis caused by Staph. aureus.

Follicle-forming cat thyroid cell lines synthesizing extracellular matrix and basal membrane components: a new tool for the study of thyroidal morphogenesis

Interactions between follicular epithelial cells and extracellular matrix (ECM) are supposed to play an important role in the development and maintenance of thyroid tissue architecture. In the present study we have therefore investigated the synthesis of ECM components by a feline thyroid cell line which is able to form follicle-like structures in vitro, and also in v-ras-transfected and control-transfected sublines. Transfections were performed by lipofection with pZSR (viral Harvey ras gene; neo) and pSV2-neo (control, neo only) plasmids. We have adapted a semisolid culture system composed exclusively of polymerized alginate and therefore devoid of ECM components. Feline cells embedded in alginate gels as single cells and cultured for up to 90 days formed cell clusters within 10 days. Follicle-like structures were formed in the original cell lines and also in the v-ras- and control-transfected cells. Differences in proliferation rates were observed, the v-ras-transfected cells growing up to two to three times faster than the non-transfected cells. Immunostaining was done using rabbit first antibodies directed against mouse collagen IV, human fibronectin, laminin (tumor Engelbreth-Holm-Swarm laminin), perlecan and other ECM components. For comparison, immunostaining was also performed on cryosections of nodular goiters of six hyperthyroid cats. The cell lines and their transfected clones stained strongly positive for collagen IV and fibronectin, and positively but less strongly for laminin and perlecan. The cat goiter tissue stained positively for collagen IV, laminin, perlecan, and fibronectin, and positive staining for S-laminin (containing the beta2-chain) was seen in blood vessel walls in this tissue. In conclusion, cat cell lines grow three-dimensionally in alginate beads over several weeks, they form follicle-like structures and express the same ECM components as the native cat goiter tissue. Transfection with v-ras does increase proliferation rate, but does not fundamentally alter formation of follicle-like structures and ECM expression. Alginate gel culture is a promising new tool for the study of follicular morphogenesis, polarity, the expression pattern of ECM components and of the interaction between thyrocytes and ECM. It avoids interference caused by gels composed of ECM components.

Structured training in intraosseous infusion to improve potentially life saving skills in pediatric emergencies - Results of an open prospective national quality development project over 3 years

BACKGROUND: Children in emergencies need peripheral intravenous (IV) access in order to receive drugs or fluids. The success of IV access is associated with the age of patients and fails in up to 50% of children younger than 6 years. In such situations, it is essential that physicians and paramedics have a tool and easily learnable skills with a high chance of success. According to international guidelines intraosseous (IO) access would be the next step after failed IV access. Our hypothesis was that the success rate in IO puncturing can be improved by standardizing the training; so we developed an IO workshop. METHODS: Twenty-eight hospitals and ambulance services participated in an evaluation process over 3 years. IO workshops and the distribution of standardized IO sets were coordinated by the study group of the University Hospital of Berne. Any attempted or successful IO punctures were evaluated with a standardized interview. RESULTS: We investigated 35 applications in 30 patients (a total of 49 punctures) between November 2001 and December 2004. IO puncture was not successful in 5 patients. The success rate depended neither on the occupation nor the experience of users. Attendance at a standardized IO workshop increased the overall success rate from 77% to 100%, which was statistically not significant (P = 0.074). CONCLUSIONS: Standardized training in IO puncturing seems to improve success more than previous experience and occupation of providers. However, we could not show a significant increase in success rate after this training. Larger supranational studies are needed to show a significant impact of teaching on rarely used emergency skills.

Learning for sustainability - LforS: Simulation games - a creative tool for interactive learning

Description of simulation and training games as tool for awareness and capacity development in multi steakeholder processes

Development of two real-time PCR assays for the detection of Mycoplasma hyopneumoniae in clinical samples

In order to improve the diagnosis of enzootic pneumonia (EP) in pigs two real-time polymerase chain reaction (rtPCR) assays for the detection of Mycoplasma hyopneumoniae in bronchial swabs from lung necropsies were established and validated in parallel. As a gold standard, the current "mosaic diagnosis" was taken, including epidemiological tracing, clinical signs, macro- and histopathological lesions of the lungs and immunofluorescence. One rtPCR is targeting a repeated DNA element of the M. hyopneumoniae genome (REP assay), the other a putative ABC transporter gene (ABC assay). Both assays were shown to be specific for M. hyopneumoniae and did not cross react with other bacteria and mollicutes from pig. With material from pigs of defined EP-negative farms the two assays showed to be 100% specific. When testing lungs from pig farms with EP, the REP assay detected 50% and the ABC assay 90% of the farms as positive. Both tests together detected all positive farms. Within a positive herd the two assays tested similarly with on average over 90% of the lung samples analysed from a single farm showing positive scores. A series of samples with suspicion of EP and samples from pigs with diseases other than respiratory taken from current routine diagnostic was assayed. None of the assays showed false positive results. The sensitivities in this sample group were 50% for the REP and 70% for the ABC assays and for both assays together 85%. The two assays run in parallel are therefore a valuable tool for the improvement of the current diagnosis of EP.

Development of a Rasch homogenous short form of the Pathological Narcissism Inventory

During the last decades, the narcissistic personality inventory (npi) was the most widely used questionnaire to measure narcissism as a personality trait. But the npi assesses grandiose narcissism only, while recent discussions emphasize the existence of vulnerable narcissism. The pathological narcissism inventory (pni, pincus et al., 2009) is a new questionnaire assessing these different aspects of narcissism. However, with 54 items on seven subscales, the pni is quite long to serve as a screening tool for narcissistic traits. We therefore developed a short form to facilitate its application in research and practice. Even though the pni covers different symptoms of narcissism, they are all expressions of the same underlying construct. We therefore used the rasch model to guide the item selection. Method and results: a sample of 1837 participants (67.5% female, mean age 26.8 years) was used to choose the items for the short form. Two criteria were adopted: all aspects, represented by the seven subscales in the original, should be retained, and items should be rasch homogenous. In a step-by-step procedure we excluded items successively until reaching a homogenous pool of 22 items. All remaining items had satisfactory fit indices and fitstatistics for the model were good. characteristics of the resulting short form were tested using a new independent validation sample (n=104, mean age = 32.8, 45% female). Correlations of the short pni with different validation measures were comparable to the correlations obtained with the original form, indicating that the two forms were equivalent. Conclusion: the resulting one-dimensional measure can be used as a screening questionnaire for pathological narcissism. The rasch homogeneity facilitates the comparison of narcissism scores among a variety of samples.

The additional facet of immunoscore: immunoprofiling as a possible predictive tool for cancer treatment

Recent investigations of the tumor microenvironment have shown that many tumors are infiltrated by inflammatory and lymphocytic cells. Increasing evidence suggests that the number, type and location of these tumor-infiltrating lymphocytes in primary tumors has prognostic value, and this has led to the development of an 'immunoscore. As well as providing useful prognostic information, the immunoscore concept also has the potential to help predict response to treatment, thereby improving decision- making with regard to choice of therapy. This predictive aspect of the tumor microenvironment forms the basis for the concept of immunoprofiling, which can be described as 'using an individual's immune system signature (or profile) to predict that patient's response to therapy' The immunoprofile of an individual can be genetically determined or tumor-induced (and therefore dynamic). Ipilimumab is the first in a series of immunomodulating antibodies and has been shown to be associated with improved overall survival in patients with advanced melanoma. Other immunotherapies in development include anti-programmed death 1 protein (nivolumab), anti-PD-ligand 1, anti-CD137 (urelumab), and anti-OX40. Biomarkers that can be used as predictive factors for these treatments have not yet been clinically validated. However, there is already evidence that the tumor microenvironment can have a predictive role, with clinical activity of ipilimumab related to high baseline expression of the immune-related genes FoxP3 and indoleamine 2,3-dioxygenase and an increase in tumor-infiltrating lymphocytes. These biomarkers could represent the first potential proposal for an immunoprofiling panel in patients for whom anti-CTLA-4 therapy is being considered, although prospective data are required. In conclusion, the evaluation of systemic and local immunological biomarkers could offer useful prognostic information and facilitate clinical decision making. The challenge will be to identify the individual immunoprofile of each patient and the consequent choice of optimal therapy or combination of therapies to be used.

Development of a bead-based multiplex assay for the simultaneous detection of porcine inflammation markers using xMAP technology

Commercially available assays for the simultaneous detection of multiple inflammatory and cardiac markers in porcine blood samples are currently lacking. Therefore, this study was aimed at developing a bead-based, multiplexed flow cytometric assay to simultaneously detect porcine cytokines [interleukin (IL)-1β, IL-6, IL-10, and tumor necrosis factor alpha], chemokines (IL-8 and monocyte chemotactic protein 1), growth factors [basic fibroblast growth factor (bFGF), vascular endothelial growth factor, and platelet-derived growth factor-bb], and injury markers (cardiac troponin-I) as well as complement activation markers (C5a and sC5b-9). The method was based on the Luminex xMAP technology, resulting in the assembly of a 6- and 11-plex from the respective individual singleplex situation. The assay was evaluated for dynamic range, sensitivity, cross-reactivity, intra-assay and interassay variance, spike recovery, and correlation between multiplex and commercially available enzyme-linked immunosorbent assay as well as the respective singleplex. The limit of detection ranged from 2.5 to 30,000 pg/ml for all analytes (6- and 11-plex assays), except for soluble C5b-9 with a detection range of 2-10,000 ng/ml (11-plex). Typically, very low cross-reactivity (<3% and <1.4% by 11- and 6-plex, respectively) between analytes was found. Intra-assay variances ranged from 4.9 to 7.4% (6-plex) and 5.3 to 12.9% (11-plex). Interassay variances for cytokines were between 8.1 and 28.8% (6-plex) and 10.1 and 26.4% (11-plex). Correlation coefficients with singleplex assays for 6-plex as well as for 11-plex were high, ranging from 0.988 to 0.997 and 0.913 to 0.999, respectively. In this study, a bead-based porcine 11-plex and 6-plex assay with a good assay sensitivity, broad dynamic range, and low intra-assay variance and cross-reactivity was established. These assays therefore represent a new, useful tool for the analysis of samples generated from experiments with pigs.

Creating a public tool to assess and promote transparency in global land deals: the experience of the Land Matrix

The Beta version of the Land Matrix (Land Matrix 2012) was launched in April 2012 as a tool to promote public participation in building a constantly evolving database on large-scale land deals, and making the data visible and understandable. The aim of the Land Matrix partnership is to promote transparency and open data in decisionmaking over land and investment, as a step towards greater accountability. Since its launch, the Land Matrix has attracted a high degree of attention, and stirred some controversy. It provides valuable lessons on the challenges and benefits of promoting open data on practices that are often shrouded in secrecy. This paper critically examines the ongoing efforts by the Land Matrix partnership to build a public tool to promote greater transparency in decision-making over land and investment at a global level. It intends to provoke discussion of the extent to which such a tool can ultimately promote greater transparency and be a step towards greater accountability and improved decision-making. It will present the Land Matrix and its value addition, before detailing the challenges it encountered related to the measurement of the largescale land acquisition phenomenon. It will then specify how it intends to address these issues in order to establish a dynamic and participatory tool for open development.

Responses to rapid warming at Termination 1a at Gerzensee (Central Europe): Primary succession, albedo, soils, lake development, and ecological interactions

The transition from the Oldest Dryas to the Bølling around 14,685 cal yr BP was a period of extremely rapid climatic warming. From a single core of lake marl taken at Gerzensee (Switzerland) we studied the transition in stable isotopes of oxygen and carbon on bulk sediment and charophyte remains, as well as on monospecific samples of ostracods, after Pisidium a; in addition pollen, chironomids, and Cladocera were analyzed. The δ18O record serves as an estimate of mean air temperature, and by correlation to the one from NGRIP in Greenland it provides a timescale. The timing of responses: The statistically significant zone boundaries of the biostratigraphies are telescoped at the rapid increase of about 3‰ in δ18O at the onset of Bølling. Biotic responses may have occurred within sampling resolution (8 to 16 years), although younger zone boundaries are less synchronous. Gradual and longer-lasting responses include complex processes such as primary or secular succession. During the late-glacial interstadial of Bølling and Allerød, two stronger and two weaker cool phases were found. Biological processes involved in the responses occurred on levels of individuals (e.g. pollen productivity), of populations (increases or decreases, immigration, or extinction), and on the ecosystem level (species interactions such as facilitation or competition). Abiotic and biotic interactions include pedogenesis, nitrogen-fixation, nutrient cycling, catchment hydrology, water chemistry of the lake and albedo (controlled by the transition from tundra to forest). For the Swiss Plateau this major change in vegetation induced a change in the mammal fauna, which in turn led to changes in the tool-making by Paleolithic people.

The Cost-Effectiveness of Monitoring Strategies for Antiretroviral Therapy of HIV Infected Patients in Resource-Limited Settings: Software Tool.

BACKGROUND The cost-effectiveness of routine viral load (VL) monitoring of HIV-infected patients on antiretroviral therapy (ART) depends on various factors that differ between settings and across time. Low-cost point-of-care (POC) tests for VL are in development and may make routine VL monitoring affordable in resource-limited settings. We developed a software tool to study the cost-effectiveness of switching to second-line ART with different monitoring strategies, and focused on POC-VL monitoring. METHODS We used a mathematical model to simulate cohorts of patients from start of ART until death. We modeled 13 strategies (no 2nd-line, clinical, CD4 (with or without targeted VL), POC-VL, and laboratory-based VL monitoring, with different frequencies). We included a scenario with identical failure rates across strategies, and one in which routine VL monitoring reduces the risk of failure. We compared lifetime costs and averted disability-adjusted life-years (DALYs). We calculated incremental cost-effectiveness ratios (ICER). We developed an Excel tool to update the results of the model for varying unit costs and cohort characteristics, and conducted several sensitivity analyses varying the input costs. RESULTS Introducing 2nd-line ART had an ICER of US$1651-1766/DALY averted. Compared with clinical monitoring, the ICER of CD4 monitoring was US$1896-US$5488/DALY averted and VL monitoring US$951-US$5813/DALY averted. We found no difference between POC- and laboratory-based VL monitoring, except for the highest measurement frequency (every 6 months), where laboratory-based testing was more effective. Targeted VL monitoring was on the cost-effectiveness frontier only if the difference between 1st- and 2nd-line costs remained large, and if we assumed that routine VL monitoring does not prevent failure. CONCLUSION Compared with the less expensive strategies, the cost-effectiveness of routine VL monitoring essentially depends on the cost of 2nd-line ART. Our Excel tool is useful for determining optimal monitoring strategies for specific settings, with specific sex-and age-distributions and unit costs.

Development of a novel driving behavior adaptations questionnaire

ABSTRACT Background: Driving a car requires adapting one's behavior to current task demands taking into account one's capacities. With increasing age, driving-relevant cognitive performance may decrease, creating a need for risk-reducing behavioral adaptations. Three different kinds of behavioral adaptations are known: selection, optimization, and compensation. These can occur on the tactical and the strategic level. Risk-reducing behavioral adaptations should be considered when evaluating older drivers' traffic-related risks. Methods: A questionnaire to assess driving-related behavioral adaptations in older drivers was created. The questionnaire was administered to 61 years older (age 65-87 years; mean age = 70.2 years; SD = 5.5 years; 30 female, 31 male) and 31 younger participants (age 22-55 years; mean age = 30.5 years; SD = 6.3 years; 16 female and 15 male) to explore age and gender differences in behavioral adaptations. Results: Two factors were extracted from the questionnaire, a risk-increasing factor and a risk-reducing factor. Group comparisons revealed significantly more risk-reducing behaviors in older participants (t(84.5) = 2.21, p = 0.013) and females (t(90) = 2.52, p = 0.014) compared, respectively, to younger participants and males. No differences for the risk-increasing factor were found (p > 0.05). Conclusions: The questionnaire seems to be a useful tool to assess driving-related behavioral adaptations aimed at decreasing the risk while driving. The possibility to assess driving-related behavioral adaptations in a systematic way enables a more resource-oriented approach in the evaluation of fitness to drive in older drivers.

Development of small molecular tools for the cellular study of adenosine receptors

The adenosine receptors are members of the G-protein coupled receptor (GPCR) family which represents the largest class of cell-surface proteins mediating cellular communication. As a result, GPCRs are formidable drug targets and it is estimated that approximately 30% of the marketed drugs act through members of this receptor class. There are four known subtypes of adenosine receptors: A1, A2A, A2B and A3. The adenosine A1 receptor, which is the subject of this presentation, mediates the physiological effects of adenosine in various tissues including the brain, heart, kidney and adipocytes. In the brain for instance, its role in epilepsy and ischemia has been the focus of many studies. Previous attempts to study the biosynthesis, trafficking and agonist-induced internalisation of the adenosine A1 receptor in neurons using fluorescent protein-receptor fusion constructs have been hampered by the sheer size of the fluorescent protein (GFP) that ultimately affected the function of the receptor. We have therefore initiated a research programme to develop small molecule fluorescent agonists that selectively activate the adenosine A1 receptor. Our probe design is based on the endogenous ligand adenosine and the known unselective adenosine receptor agonist NECA. We have synthesised a small library of non-fluorescent adenosine derivatives that have different cyclic and bicyclic moieties at the 6 position of the purine ring and have evaluated the pharmacology of these compounds using a yeast-based assay. This analysis revealed compounds with interesting behaviour, i.e. exhibiting subtype-selectivity and biased signalling, that can be potentially used as tool compounds in their own right for cellular studies of the adenosine A1 receptor. Furthermore, we have also linked fluorescent dyes to the purine ring and discovered fluorescent compounds that can activate the adenosine A1 receptor.