The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

Background: Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective: To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods: The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results: To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions: The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms.

Commentary on Olvera et al.’s Article Entitled, “Physical Activity in Latino Children: Research and Its Implications”

The following is a commentary on an article discussing physical activity in Latino children. It is clear that research is needed to determine the causes of inactivity and develop effective strategies for promoting physical activity in this population. Approaches involving numerous community entities (faith-based, businesses) and the implementation of policies that enhance physical activity participation appear very promising.

Physical Activity in Latino Children: Research and Its Implications

Childhood obesity affects children across all ages and genders. However, Latino children and adolescents are at an increased risk, with one out of three Latino children (ages 2-19) being classified as overweight. Physical inactivity is deemed a major factor contributing to the energy imbalance that leads to excess adiposity. The aims of this study are twofold: 1) to present relevant research regarding Latino children’s physical patterns, influences on their physical activity, and interventions designed to promote physical activity and fitness in this population; and 2) to discuss implications derived from this research to help health educators, practitioners, and policy makers increase awareness, and to motivate and enable Latino children to adopt an active lifestyle. Research reveals that Latino children and adolescents are consistently less active than their white counterparts. Latino girls are, in particular, at an increased risk for inactivity. Few studies have investigated the factors that contribute to low levels of physical activity among Latino children. Moreover, few physical activity interventions have involved Latino children. Some of our recent research studies have filled some gaps, including providing information on what physical activities Latino children like, what they intend to do, what they are actually doing, and where and when they do physical activity. Based on our research and review of related literature, we made specific physical activity recommendations for researchers, practitioners, and policy makers. These individual points should be applied and integrated within a broad framework and used in combinations to develop multi-component, coordinated approaches to enhancing physical activity among Latino youth.

Race and discourse analysis: Building a dialogue in health service research and health care settings

Using a framework for discourse analysis developed by Van Dijk, the investigator will pinpoint the pathological forms of discourse on race, defined as 'race talk' in three professional domains: health services research, public health provider organizations, and literature on multiculturalism. Attention will then turn to developing an analytical strategy for building more meaningful dialogue on race. The retrieval of potential resources for dialogue will be drawn from the third domain. Analysis will focus on enhancing the prospects of converting 'race talk' into dialogue. This will be accomplished by characterizing the normative preconditions as formal procedural requirements for dialogue and then supplementing these conditions with others related specifically to race. From here, the practical implications of combining procedural requirements and resources in each of the domains will be considered. Finally, the author will attempt to determine how these selected resources might be employed to transform 'race talk' in practice and lay the groundwork for a dialogue of understanding. ^

Academic cooperation to foster research and advocacy competences in the occupied Palestinian territory (West Bank)

Palestinians living in the West Bank, a territory occupied by the State of Israel according to International Law, face deprived access to land and a limited ability to move freely which pertains to the presence of Israeli settlements and other infrastructure (closures, restricted or forbidden roads, etc.). This confinement has significant impacts on their economic and social livelihoods, and it is even worsening with the on-going construction of a 709 km long Barrier which mainly runs inside the West Bank. With regard to this situation, there is a clear need to strengthen the capacity of civil society and its representatives to apply sound research processes as a basis for improved advocacy for Palestinian human rights. Monitoring processes and tools are needed to assess the impacts of the Palestinians’ confinement, particularly in relation to the Barrier’s construction. Reliable data has also to be collected, managed, and above all, shared. These challenges have been addressed within the Academic Cooperation Palestine Project (ACPP) that brings together academic partners from the occupied Palestinian territory (oPt) West Bank (WB), and Switzerland as well as other international academic institutions and Palestinian governmental and non-governmental agencies. ACPP started in early 2011 and is designed as a large cooperation networking platform involving researchers, students, public servants and experts from the oPt WB. A large set of actions have already been developed during the first year of the project, including courses, training, and research actions. First relevant results and impacts of the different actions are presented in this paper. Taken as a whole, the project produces valuable results for all partners: useful advocacy material for the Palestinian partners, and a unique “real-scale laboratory” where investigations are jointly conducted to develop novel confinement and change indicators.

Casting materials and their application in research and teaching

From a biological point of view, casting refers to filling of anatomical and/or pathological spaces with extraneous material that reproduces a three-dimensional replica of the space. Casting may be accompanied by additional procedures such as corrosion, in which the soft tissue is digested out, leaving a clean cast, or the material may be mixed with radiopaque substances to allow x-ray photography or micro computed topography (µCT) scanning. Alternatively, clearing of the surrounding soft tissue increases transparency and allows visualization of the casted cavities. Combination of casting with tissue fixation allows anatomical dissection and didactic surgical procedures on the tissue. Casting materials fall into three categories namely, aqueous substances (India ink, Prussian blue ink), pliable materials (gelatins, latex, and silicone rubber), or hard materials (methyl methacrylates, polyurethanes, polyesters, and epoxy resins). Casting has proved invaluable in both teaching and research and many phenomenal biological processes have been discovered through casting. The choice of a particular material depends inter alia on the targeted use and the intended subsequent investigative procedures, such as dissection, microscopy, or µCT. The casting material needs to be pliable where anatomical and surgical manipulations are intended, and capillary-passable for ultrastructural investigations.

Influence of microphysical schemes on atmospheric water in the Weather Research and Forecasting model

This study examines how different microphysical parameterization schemes influence orographically induced precipitation and the distributions of hydrometeors and water vapour for midlatitude summer conditions in the Weather Research and Forecasting (WRF) model. A high-resolution two-dimensional idealized simulation is used to assess the differences between the schemes in which a moist air flow is interacting with a bell-shaped 2 km high mountain. Periodic lateral boundary conditions are chosen to recirculate atmospheric water in the domain. It is found that the 13 selected microphysical schemes conserve the water in the model domain. The gain or loss of water is less than 0.81% over a simulation time interval of 61 days. The differences of the microphysical schemes in terms of the distributions of water vapour, hydrometeors and accumulated precipitation are presented and discussed. The Kessler scheme, the only scheme without ice-phase processes, shows final values of cloud liquid water 14 times greater than the other schemes. The differences among the other schemes are not as extreme, but still they differ up to 79% in water vapour, up to 10 times in hydrometeors and up to 64% in accumulated precipitation at the end of the simulation. The microphysical schemes also differ in the surface evaporation rate. The WRF single-moment 3-class scheme has the highest surface evaporation rate compensated by the highest precipitation rate. The different distributions of hydrometeors and water vapour of the microphysical schemes induce differences up to 49 W m−2 in the downwelling shortwave radiation and up to 33 W m−2 in the downwelling longwave radiation.

Therapeutic drug monitoring of once daily aminoglycoside dosing: comparison of two methods and investigation of the optimal blood sampling strategy.

PURPOSE Therapeutic drug monitoring of patients receiving once daily aminoglycoside therapy can be performed using pharmacokinetic (PK) formulas or Bayesian calculations. While these methods produced comparable results, their performance has never been checked against full PK profiles. We performed a PK study in order to compare both methods and to determine the best time-points to estimate AUC0-24 and peak concentrations (C max). METHODS We obtained full PK profiles in 14 patients receiving a once daily aminoglycoside therapy. PK parameters were calculated with PKSolver using non-compartmental methods. The calculated PK parameters were then compared with parameters estimated using an algorithm based on two serum concentrations (two-point method) or the software TCIWorks (Bayesian method). RESULTS For tobramycin and gentamicin, AUC0-24 and C max could be reliably estimated using a first serum concentration obtained at 1 h and a second one between 8 and 10 h after start of the infusion. The two-point and the Bayesian method produced similar results. For amikacin, AUC0-24 could reliably be estimated by both methods. C max was underestimated by 10-20% by the two-point method and by up to 30% with a large variation by the Bayesian method. CONCLUSIONS The ideal time-points for therapeutic drug monitoring of once daily administered aminoglycosides are 1 h after start of a 30-min infusion for the first time-point and 8-10 h after start of the infusion for the second time-point. Duration of the infusion and accurate registration of the time-points of blood drawing are essential for obtaining precise predictions.

Pile-dwellings of the Neolithic and the Bronze Age in Switzerland. Long-term research and future tasks

Swiss lake-side settlements dating between 4300 and 800 BC were first recognized in the early 19th century and between 1854 and 1880 early research boomed due to the first scientific studies and the artificial lowering of lakes in Western Switzerland. In the 20th century underwater and wetland archaeology experienced an enormous surge not only because of large rescue excavations, due to extensive motorway construction projects but also due to the evolution of modern IT technology in the 1970s. For the first time huge quantities of ancient wooden structures could be dated by dendrochronology. This produced a quantum leap in the 150 years of pile-dwelling research. In 2011, the UNESCO World Heritage Committee recognized the outstanding universal value of these sites. This article presents an overview about Swiss pile-dwellings of the Neolithic and the Bronze Age and the results of two recent diploma works (case study Sutz-Lattrigen Haupstation innen and case study Seedorf Lobsigensee) as examples of research and cooperation between universities and government agencies for cultural heritage management.

IMRT credentialing for prospective trials using institutional virtual phantoms: results of a joint European Organization for the Research and Treatment of Cancer and Radiological Physics Center project.

BACKGROUND AND PURPOSE Intensity-modulated radiotherapy (IMRT) credentialing for a EORTC study was performed using an anthropomorphic head phantom from the Radiological Physics Center (RPC; RPC(PH)). Institutions were retrospectively requested to irradiate their institutional phantom (INST(PH)) using the same treatment plan in the framework of a Virtual Phantom Project (VPP) for IMRT credentialing. MATERIALS AND METHODS CT data set of the institutional phantom and measured 2D dose matrices were requested from centers and sent to a dedicated secure EORTC uploader. Data from the RPC(PH) and INST(PH) were thereafter centrally analyzed and inter-compared by the QA team using commercially available software (RIT; ver.5.2; Colorado Springs, USA). RESULTS Eighteen institutions participated to the VPP. The measurements of 6 (33%) institutions could not be analyzed centrally. All other centers passed both the VPP and the RPC ±7%/4 mm credentialing criteria. At the 5%/5 mm gamma criteria (90% of pixels passing), 11(92%) as compared to 12 (100%) centers pass the credentialing process with RPC(PH) and INST(PH) (p = 0.29), respectively. The corresponding pass rate for the 3%/3 mm gamma criteria (90% of pixels passing) was 2 (17%) and 9 (75%; p = 0.01), respectively. CONCLUSIONS IMRT dosimetry gamma evaluations in a single plane for a H&N prospective trial using the INST(PH) measurements showed agreement at the gamma index criteria of ±5%/5 mm (90% of pixels passing) for a small number of VPP measurements. Using more stringent, criteria, the RPC(PH) and INST(PH) comparison showed disagreement. More data is warranted and urgently required within the framework of prospective studies.