Ten quick tips for getting the most scientific value out of numerical data

Most studies in the life sciences and other disciplines involve generating and analyzing numerical data of some type as the foundation for scientific findings. Working with numerical data involves multiple challenges. These include reproducible data acquisition, appropriate data storage, computationally correct data analysis, appropriate reporting and presentation of the results, and suitable data interpretation. Finding and correcting mistakes when analyzing and interpreting data can be frustrating and time-consuming. Presenting or publishing incorrect results is embarrassing but not uncommon. Particular sources of errors are inappropriate use of statistical methods and incorrect interpretation of data by software. To detect mistakes as early as possible, one should frequently check intermediate and final results for plausibility. Clearly documenting how quantities and results were obtained facilitates correcting mistakes. Properly understanding data is indispensable f or reaching well-founded conclusions from experimental results. Units are needed to make sense of numbers, and uncertainty should be estimated to know how meaningful results are. Descriptive statistics and significance testing are useful tools for interpreting numerical results if applied correctly. However, blindly trusting in computed numbers can also be misleading, so it is worth thinking about how data should be summarized quantitatively to properly answer the question at hand. Finally, a suitable form of presentation is needed so that the data can properly support the interpretation and findings. By additionally sharing the relevant data, others can access, understand, and ultimately make use of the results. These quick tips are intended to provide guidelines for correctly interpreting, efficiently analyzing, and presenting numerical data in a useful way

Composite Finite Element simulation of radio frequency ablation and bone elasticity

Biomedical simulations often involve interfaces of geometrically complex shapes which are described by 3D image data. For this purpose, Composite Finite Elements (CFEs) for complicated domains, discontinuous coefficients, and their combination can be used. Their efficiency is due to the uniformly structured hexahedral grid given by the image data. The geometric complexity is treated by adapted FE basis functions without introducing additional degrees of freedom. The treatment of boundary conditions is not straight-forward in this context because geometrically complicated boundaries are not resolved by the computational grid. We here describe how Dirichlet and Neumann boundary conditions can be incorporated in the CFE context. We moreover show that our approach numerically achieves the expected orders of convergence of the CFE approximation for increasing grid resolution, also in combination with discontinuous coefficients. The methods explained here are used for two bio medical applications. First, radio-frequency ablation is an example where two scalar problems with complicated domains and discontinuous coefficients are considered. Second, a linearly elastic deformation of a vertebral disk is simulated in a two-scale model geometry also involving both a complicated domain and a discontinuous coefficient. The coefficient for the trabecular interior is obtained from numerical homogenization

Impact of the vegetation on the lignin pyrolytic signature of soil humic acids from Mediterranean soils

Humic acids (HAs) from 16 soils in Continental Mediterranean areas under potential vegetation consisting of sclerophyllic, mesophyllic or conifer forests in Madrid (Spain) were studied by Curie-Point pyrolysis. Statistical analyses based on the absolute and the relative abundances of the whole compound assemblages released by pyrolysis suggested that a considerable portion of the variance (inertia) associated with the vegetation was accounted for the lignin-derived compounds. In the studied samples, a set of 12 index-methoxyphenols was considered to have a discriminating potential comparable to that of the classical index phenols released from sedimentary organic matter by wet CuO alkaline oxidation. The ecological features most accurately reflected by the methoxyphenolic patterns consisted of: (i) the expected lack of syringol derivatives in HAs formed in soils under Gymnosperm plants, (ii) the diagnostic patterns of guaiacols in the HAs from soils under different species of Angiosperms (Quercus spp., Fraxinus, Castanea, grasses); (iii) the responsivity of the methoxyphenols to the extent of some types of soil perturbations: the highest environmental impact on the HA structure was found in soil after severe burning, not in the soil affected by medium-intensity fire.This research has been supported by the Spanish CICyT under grants AMB99- 0907 and AMB99-0226-02.Peer Reviewe

Variability of intrahepatic vascular anatomy in rodents & their surgical implications

Background: The need for precise experimental surgical procedures parallels the development of clinical hepatobiliary surgery rising. The intra-hepatic vascular anatomy in rodents, its variations and corresponding supplying and draining territories in respect to the lobar structure of the liver have not been described. We performed a detailed anatomical imaging study in rats and mice to allow for further refinement of experimental-surgical approaches. Methods: LEWIS-Rats & C57Bl/6N-Mice were subjected to ex-vivo & in-vivo imaging using CT & MRI. Underlying vascular anatomy was reconstructed, analysed and used for volume-determination of the dependent territories. Results: Variations in hepatic vascular anatomy were observed in terms of branching pattern and of distance of branches to each other. Most liver lobes have their own portal supply and their hepatic drainage. In contrast the paracaval liver is supplied by various branches from other lobar portal vein and drains directly into the vena cava. Surgically relevant variations were primarily observed in portal venous supply of right lobe and the distance between branching in left median and left lateral portal vein in rats, but not in mice. Small differences of the volume were observed according to the vascular territory which is used for calculation. Conclusions: It was demonstrated that lobar borders of the liver are not always matching territorial borders. Determination of small differences in liver volume during liver regeneration or in livers undergoing atrophy can only be detected when the liver lobe respectively the calculation of the liver lobe volume is anatomically defined. This is of importance for the development of surgicall planning prior to experimental surgery