Digital automated RSA compared to manually operated RSA

The accuracy of digital Roentgen stereophotogrammetric analysis (RSA) was compared to the accuracy of a manually operated RSA system. For this purpose, we used radiographs of a phantom and radiographs of patients. The radiographs of the patients consisted of double examinations of 12 patients that had a tibial osteotomy and of double examinations of 12 patients that received a total hip prosthesis. First, the radiographs were measured manually with an accurate measurement table. Subsequently, the images were digitized by a film scanner at 150 DPI and 300 DPI resolutions and analyzed with the RSA-CMS software. In the phantom experiment, the manually operated system produced significantly better results than the digital system, although the maximum difference between the median values of the manually operated system and the digital system was as low as 0.013 mm for translations and 0.033° for rotations. In the radiographs of the patients, the manually operated system and the digital system produced equally accurate results: no significant differences in translations and rotations were found. We conclude that digital RSA is an accurate, fast, and user friendly alternative for manually operated RSA. Currently, digital RSA systems are being used in a growing number of clinical RSA-studies.     

The Chromosome‐centric Human Proteome Project at FEBS Congress

In the summer of 2013, distinguished global representatives of proteome science gathered to discuss the futuristic visions of the chromosome‐centric human proteome project (C‐HPP) (Cochairs: Y. K. Paik, G. Omenn; hosted by A. Archakov, Institute of Biomedical Chemistry, Russia) that was broadcast to the annual Federation of European Biochemical Societies Congress (St. Petersburg, Russia, July 10–11, 2013). Technology breakthroughs presented included a new ultra‐sensitive Tribrid mass‐spectrometer from Thermo and SOMAmers—Slow Off‐rate Modified Aptamers (SOMAlogic, USA), a new type of protein capture reagents. Professor Archakov's group introduced the “rectangle” concept of proteome size as a product of proteome width and depth. The discussion on proteome width culminated with the introduction of digital biomarkers—low‐copied aberrant proteins that differ from their typical forms by PTMs, alternative splicing, or single amino acid polymorphisms. The aberrant proteoforms, a complement to whole‐genome proteomic surveys, were presented as an ultimate goal for the proteomic community.     

Using topographic wetness index in vegetation ecology: does the algorithm matter?

Questions: How important is the choice of flow routing algorithm with respect to application of topographic wetness index (TWI) in vegetation ecology? Which flow routing algorithms are preferable for application in vegetation ecology? Location: Forests in three different regions of the Czech Republic. Methods: We used vegetation data from 521 georeferenced plots, recently sampled in a wide range of forest communities. From a digital elevation model, we calculated 11 variations of TWI for each plot with 11 different flow routing algorithms. We evaluated the performance of differently calculated TWI by (1) Spearman rank correlation with average Ellenberg indicator values for soil moisture, (2) Mantel correlation coefficient between dissimilarities of species composition and dissimilarities of TWI and (3) the amount of variation in species composition explained by canonical correspondence analysis. Results: The choice of flow routing algorithm had a considerable effect on the performance of TWI. Correlation with Ellenberg indicator values for soil moisture, Mantel correlation coefficient and explained variation doubled when the appropriate algorithm was used. In all regions, multiple flow routing algorithms performed best, while single flow routing algorithms performed worst. Conclusions: We recommend the multiple flow routing algorithms of Quinn et al. and Freeman for application in vegetation ecology.     

Optical fiber tips for biological applications: From light confinement,biosensing to bioparticles manipulation

Background

The tip of an optical fiber has been considered an attractive platform in Biology. The simple cleaved end of an optical fiber can be machined, patterned and/or functionalized, acquiring unique properties enabling the exploitation of novel optical phenomena. Prompted by the constant need to measure and manipulate nanoparticles, the invention of the Scanning Near-field Optical Microscopy (SNOM) triggered the optimization and development of novel fiber tip microfabrication methods. In fact, the fiber tip was soon considered a key element in SNOM by confining light to sufficiently small extensions, challenging the diffraction limit. As result and in consequence of the newly proposed “Lab On Tip” concept, several geometries of fiber tips were applied in three main fields: imaging (in Microscopy/Spectroscopy), biosensors and micromanipulation (Optical Fiber Tweezers, OFTs). These are able to exert forces on microparticles, trap and manipulate them for relevant applications, as biomolecules mechanical study or protein aggregates unfolding.

Formats of image data files that can be used in routine digital light micrography. Part two

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.     

Musculoskeletal modeling of user groups for virtual product and process development

Abstract

Although biomechanical digital human models find their way into virtual engineering processes, biomechanical considerations are currently still unrecognized to a large extent. One major obstacle lies in the fact that even though subject-specific modeling procedures are developed, virtual user groups or populations are still missing. The objective of this contribution is to create such groups of musculoskeletal models. Therefore, a modeling procedure based upon population data is described. First of all, two generic three-dimensional models, one with female and one with male average anthropometric dimensions, were obtained. These models constitute the starting point for the following model adjustment phases. Evenly distributed dimensionless values for gender, age, height, mass, range of motion and strength are sampled and translated into more expressive parameters for the mentioned modeling domains serving as input data for the creation of each individual model of the desired population or user group. The most sophisticated step of the adaption is the strength mapping aiming to create models matching arbitrary target joint torques. Finally, the models’ maximal strength is assessed in a manual material handling task and compared to empirical strength data. The approach is shown using the example of the German population.     

Fine-scale vertical position as an indicator of vegetation in alkali grasslands – Case study based on remotely sensed data

Vertical position is an important driver of vegetation zonation at multiple scales, via determining abiotic environmental parameters, such as climate, soil properties and water balance. In inland alkali landscapes, elevation is a key factor for understanding patterns of salt accumulation and water table which is therefore considered a good indicator of alkali vegetation types. Remote sensing techniques offer viable solutions for linking elevation data to vegetation patterns by providing an elevation model of extended areas. Our goal was to test the relationships between fine-scale differences in vertical position and vegetation patterns in inland alkali landscapes by vegetation data collected in the field and elevation data generated using airborne laser scanning (ALS). We studied whether vertical position influences vegetation patterns at the level of main vegetation groups (based on alliances) or even at the level of associations. Our study sites were situated in a lowland alkali landscape in Hortobágy National Park (East-Hungary). We grouped the associations into four main vegetation groups: loess grasslands, alkali steppes, open alkali swards and alkali meadows. Even though we detected a very limited range (121 cm) in the vertical position of the main vegetation groups, they were well separated by their vertical positions. At the level of associations, a more detailed elevation-based distinction was also possible in many cases. The revealed elevation–vegetation correlations show that high-resolution mapping based on ALS remote sensing techniques is an ideal solution in complex lowland areas, such as alkali landscapes. Our findings suggest that in other types of lowland landscapes, characterised by elevation differences, the applied method might hold a great potential as a supporting tool for vegetation mapping.