Phy-X/ZeXTRa: a software for robust calculation of effective atomic numbers for photon,electron, proton,alpha particle,and carbon ion interactions

The purpose of the present work is robust calculation of effective atomic numbers ($${Z}_{text{eff}}$$s) for photon, electron, proton, alpha particle and carbon ion interactions through the newly developed software, Phy-X/ZeXTRa (Zeff of materials for X-Type Radiation attenuation). A pool of total mass attenuation and energy absorption coefficients (for photons) and total mass stopping powers (for charged particles) for elements was constructed first. Then, a matrix of interaction cross sections for elements Z = 1–92 was constructed. Finally, effective atomic numbers were calculated for any material by interpolating adjacent cross sections through a linear logarithmic interpolation formula. The results for $${Z}_{text{eff}}$$ for photon interaction were compared with those calculated through Mayneord’s formula, which suggests a single-valued $${Z}_{text{eff}}$$ for any material for low-energy photons for which photoelectric absorption is the dominant interaction process. The single-valued $${Z}_{text{eff}}$$ was found to agree well with that obtained by other methods, in the low-energy region. In addition, $${Z}_{text{eff}}$$ values of various materials of biological interest were compared with those obtained experimentally at 59.54 keV. In general, the agreement between values calculated with Phy-X/ZeXTRa and Auto-Zeff and those measured were satisfactory. A comparison of $${Z}_{text{eff}}$$ values for photon energy absorption calculated with Phy-X/ZeXTRa and literature values for a nucleotide base, adenine, was made, and the relative difference (RD) in $${Z}_{text{eff}}$$ between Phy-X/ZeXTRa and literature values was found to be 2% < RD < 11%, at low photon energies (1–100 keV), while it was less than 1% at energies higher than 100 keV. Highest $${Z}_{text{eff}}$$ values were observed at low photon energies, where photoelectric absorption dominates photon interaction. For electrons, corresponding RD(%) values in $${Z}_{text{eff}}$$ were found to be in the range 0.4 ≤ RD(%) ≤ 1.7, while for heavy charged particle interactions it was 2.4 ≤ RD(%) ≤ 4.2 for total proton interaction and 0 ≤ RD(%) ≤ 8 for total alpha particle interaction. In view of the importance of $${Z}_{text{eff}}$$ for identifying and differentiating tissues in diagnostic imaging as well as for estimating accurate dose in radiotherapy and particle-beam therapy, Phy-X/ZeXTRa could be used for fast and accurate calculation of $${Z}_{text{eff}}$$ in a wide energy range for both photon and charged particle (electrons, protons, alpha particles and C ions) interactions.     

ISD: a software package for Bayesian NMR structure calculation

Summary: The conventional approach to calculating biomolecularstructures from nuclear magnetic resonance (NMR) data is oftenviewed as subjective due to its dependence on rules of thumbfor deriving geometric constraints and suitable values for theoryparameters from noisy experimental data. As a result, it canbe difficult to judge the precision of an NMR structure in anobjective manner. The inferential Structure determination (ISD)framework, which has been introduced recently, addresses thisproblem by using Bayesian inference to derive a probabilitydistribution that represents both the unknown structure andits uncertainty. It also determines additional unknowns, suchas theory parameters, that normally need to be chosen empirically.Here we give an overview of the ISD software package, whichimplements this methodology. Availability: http://www.bioc.cam.ac.uk/isd Contact: wolfgang.rieping{at}bioc.cam.ac.uk, michael.habeck{at}tuebingen.mpg.de Associate Editor: Alfonso Valencia     

Dosimetric validation of a redundant independent calculation software for VMAT fields

A redundant independent dosimetric calculation (RIDC) prior to treatment has become a basic part of the QA process for 3D conventional radiotherapy, and is strongly recommended in several international publications. On the other hand, the rapid growth in the number of intensity modulated treatments has led to a significant increase in the workflow associated with QA treatments. Diamond (“K&S Associates”) is RIDC software which is capable of calculating VMAT (Volumetric Modulated Arc Therapy) fields. Modeling, validation and commissioning are necessary steps thereby making it a useful tool for VMAT QA. In this paper, a procedure for the validation of the calculation algorithm is demonstrated. A set 3D conventional field was verified in two ways: firstly, a comparison was made between Diamond calculations and experimental measures obtaining an average deviation of ?0.1 ± 0.7%(1SD), and secondly, a comparison made between Diamond and the treatment planning system (TPS) Eclipse, obtaining an average deviation of 0.4 ± 0.8%(1SD). For both steps, a plastic slab phantom was used. VMAT validation was carried out by analyzing 59 VMAT plans in two ways: first, Diamond calculation versus experimental measurement with an average deviation of ?0.2 ± 1.7%(1SD), and second, Diamond calculation versus TPS calculation with an average deviation of 0.0 ± 1.6%(1SD). In this phase a homogeneous cylindrical phantom was used. These results led us to consider this calculation algorithm validated for use in VMAT verifications.     

Shortcomings of current fish transfer functions and a proposal for a new transfer function

One important component of almost all theoretical models in fishery is a fish transfer function. However, most of the current fish transfer functions have significant shortcomings. This paper contributes to the literature on fishery management by (1) showing some of shortcomings of commonly used fish transfer functions and proposing a new fish transfer function that is more appropriate to model net amount of fish transfer from one marine area to another; and (2) applying the proposed transfer function in an optimal harvest problem to assess the economic payoff from a switching reserve versus a fixed marine reserve. The findings indicate that a switching marine reserve appears to provide fishers with higher economic benefits than a fixed marine reserve. The payoff gain from a switching reserve appears to increase when the fish move less because of bio-ecological and territorial factors that impede the fish dispersal between marine areas.     

Validation of a dose tracking software for skin dose map calculation in interventional radiology

PurposeValidate the skin dose software within the radiation dose index monitoring system NEXO[DOSE]® (Bracco Injeneering S.A., Lausanne, Switzerland). It provides the skin dose distribution in interventional radiology (IR) procedures.MethodsTo determine the skin dose distribution and the Peak Skin Dose (PSD) in IR procedures, the software uses exposure and geometrical parameters taken from the radiation dose structured report and additional information specific to each angiographic system. To test the accuracy of the software, GafChromic® XR-RV3 films, wrapped under a cylindrical PMMA phantom, were irradiated with different setups. Calculations and films results are compared in terms of absolute dose and geometric accuracy, using two angiographic systems (Philips Integris Allura FD20, Siemens AXIOM-ArtisZeego).ResultsCalculated and film measured PSD values agree with an average difference of 7% ± 5%. The discrepancies in dose evaluation increase up to 33% in lower dose regions, because the algorithm does not consider the out-of-field scatter contribution of the neighboring fields, which is more significant in these areas. Regarding the geometric accuracy, the differences between the simulated dose spatial distributions and the measured ones are<3 mm (4%) in simple tests and 5 mm (5%) in setups closer to clinical practice. Moreover, similar results are obtained for the two studied angiographic system vendors.ConclusionsNEXO[DOSE]® provides an accurate skin dose distribution and PSD estimate. It will allow faster and more accurate monitoring of patient follow-up in the future.     

“Omnidia”: software for taxonomy,calculation of diatom indices and inventories management

Software for calculation of 6 diatom indices and diversity indices has been created for both Macintosh and IBM compatible computers. This software runs with the data base Omnis 5 under Windows 3.0. It includes three taxonomic files: families, genera and species, and an inventories file. Four types of data inputs are possible. It is always possible to operate simulations and to carry out investigations with simple or combined characters. All files and results of investigations can be listed in different ways. This data base is compatible with both word processing and spreadsheet systems.     

GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits

Background

In designing genome-wide association (GWA) studies it is important to calculate statistical power. General statistical power calculation procedures for quantitative measures often require information concerning summary statistics of distributions such as mean and variance. However, with genetic studies, the effect size of quantitative traits is traditionally expressed as heritability, a quantity defined as the amount of phenotypic variation in the population that can be ascribed to the genetic variants among individuals. Heritability is hard to transform into summary statistics. Therefore, general power calculation procedures cannot be used directly in GWA studies. The development of appropriate statistical methods and a user-friendly software package to address this problem would be welcomed.

Results

This paper presents GWAPower, a statistical software package of power calculation designed for GWA studies with quantitative traits, where genetic effect is defined as heritability. Based on several popular one-degree-of-freedom genetic models, this method avoids the need to specify the non-centrality parameter of the F-distribution under the alternative hypothesis. Therefore, it can use heritability information directly without approximation. In GWAPower, the power calculation can be easily adjusted for adding covariates and linkage disequilibrium information. An example is provided to illustrate GWAPower, followed by discussions.

Conclusions

GWAPower is a user-friendly free software package for calculating statistical power based on heritability in GWA studies with quantitative traits. The software is freely available at: http://dl.dropbox.com/u/10502931/GWAPower.zip     

Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function

Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called contrast transfer function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.     

Developing diatom-based transfer functions for Central Mexican lakes

This paper is the first attempt to produce diatom-based transfer functions for the northern tropical Americas. A dataset of 53 modern diatom samples and associated hydrochemical variables from 31 sites in the volcanic highlands of central Mexico is presented. The relationship between diatom species distribution and water chemistry is explored using canonical correspondence analysis (CCA) and partial CCA. Variance partitioning indicates that ionic strength and ion type both account for significant and independent portions of this variation. Transfer functions are developed for electrical conductivity (r ² = 0.91) and alkalinity (as a percentage of total anions) (r ² = 0.90), reflecting ionic strength and ionic composition respectively. Prediction errors, estimated using jack-knifing, are low for the conductivity model, but the carbonate transfer function performs less well. This study highlights the potential for diatom-based quantitative palaeoenvironmental reconstructions in central Mexico. However, a number of key diatom species found in fossil material are not represented in the modern flora. Sampling of additional sites may resolve this, but it is thought that the lack of modern analogues may reflect the high degree of anthropogenic disturbance in many of the catchments. This highlights the problem of trying to reconstruct pre-disturbance environmental changes in highly modified ecosystems. One possible solution is to merge the central Mexican data with the African dataset, which includes sites of similar chemical composition, but which have not suffered the same degree of disturbance.     

Review of skin dose calculation software in interventional cardiology

PurposeIn interventional cardiology, patients may be exposed to high doses to the skin resulting in skin burns following single or multiple procedures. Reviewing and analysing available software (online or offline) may help medical physicists assessing the maximum skin dose to the patient together with the dose distribution during (or after) these procedures.Method and resultsCapabilities and accuracy of available software were analysed through an extensive bibliography search and contacts with both vendor and authors. Their markedly differed among developers.In total, 22 software were identified and reviewed according to their algorithms and their capabilities. Special attention was dedicated to their main features and limitations of interest for the intended clinical use.While the accuracy of the 12 software products validated with measurements on phantoms was acceptable (within ± 25%), the agreement was poor for the two products validated on patients (within ± 43% and ± 76%, respectively). In addition, no software has been validated on angiographic units from all manufacturers, though several software developers claimed vendor-independent transportability. Only one software allows for multiple procedures dose calculation.ConclusionLarge differences among vendors made it clear that work remains to be done before an accurate and reliable skin dose mapping is available for all patients.     

StarD10, a START domain protein overexpressed in breast cancer, functions as a phospholipid transfer protein

We originally identified StarD10 as a protein overexpressed in breast cancer that cooperates with the ErbB family of receptor tyrosine kinases in cellular transformation. StarD10 contains a steroidogenic acute regulatory protein (StAR/StarD1)-related lipid transfer (START) domain that is thought to mediate binding of lipids. We now provide evidence that StarD10 interacts with phosphatidylcholine (PC) and phosphatidylethanolamine (PE) by electron spin resonance measurement. Interaction with these phospholipids was verified in a fluorescence resonance energy transfer-based assay with 7-nitro-2,1,3-benzoxadiazol-4-yl-labeled lipids. Binding was not restricted to lipid analogs since StarD10 selectively extracted PC and PE from small unilamellar vesicles prepared with endogenous radiolabeled lipids from Vero monkey kidney cells. Mass spectrometry revealed that StarD10 preferentially selects lipid species containing a palmitoyl or stearoyl chain on the sn-1 and an unsaturated fatty acyl chain (18:1 or 18:2) on the sn-2 position. StarD10 was further shown to bind lipids in vivo by cross-linking of protein expressed in transfected HEK-293T cells with photoactivable phosphatidylcholine. In addition to a lipid binding function, StarD10 transferred PC and PE between membranes. Interestingly, these lipid binding and transfer specificities distinguish StarD10 from the related START domain proteins Pctp and CERT, suggesting a distinct biological function.     

Testing the stability of transfer functions

In dendroclimatology, testing the stability of transfer functions using cross-calibration verification (CCV) statistics is a common procedure. However, the frequently used statistics reduction of error (RE) and coefficient of efficiency (CE) merely assess the skill of reconstruction for the validation period, which does not necessarily reflect possibly instable regression parameters. Furthermore, the frequently used rigorous threshold of zero which sharply distinguishes between valid and invalid transfer functions is prone to an underestimation of instability. To overcome these drawbacks, we here introduce a new approach – the Bootstrapped Transfer Function Stability test (BTFS). BTFS relies on bootstrapped estimates of the change of model parameters (intercept, slope, and r²) between calibration and verification period as well as the bootstrapped significance of corresponding models. A comparison of BTFS, CCV and a bootstrapped CCV approach (BCCV) applied to 42,000 pseudo-proxy datasets with known properties revealed that BTFS responded more sensitively to instability compared to CCV and BCCV. BTFS performance was significantly affected by sample size (length of calibration period) and noise (explained variance between predictor and predictand). Nevertheless, BTFS performed superior with respect to the detection of instable transfer functions in comparison to CCV.     

PICDI,a simple program for codon bias calculation

PICDI is a very simple program designed to calculate the Intrinsic Codon Deviation Index (ICDI). The program is available in Macintosh as well a PC format. Requirements for correct input of the sequences have been kept to a minimum and the analysis of sequences up to 2000 codons is very quick. The ICDI is very useful for estimation of codon bias of genes from species in which optimal codons are not known. The availability of a computer program for its calculation will increase its usefulness in the fields of Molecular Biology and Biotechnology.     

HitKeeper, a generic software package for hit list management

Background  

The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provide a wealth of biological "knowledge", for example manually validated annotations (features) that are located on the sequences, but mining the sequence annotations and especially the predicted and curated features requires dedicated tools. Due to the heterogeneity and diversity of the biological information, it is difficult to handle redundancy, frequent updates, taxonomic information and "private" data together with computational algorithms in a common workflow.     

Phospholipid transfer proteins from lung, properties and possible physiological functions

Phospholipid transfer proteins have been found in lung just as they have in tissues throughout the body. There is speculation that the proteins are involved in membrane biogenesis and in determining the phospholipid composition of membranes. For this reason the lung, which contains subcellular organelles of distinct phospholipid composition, is of interest in terms of its complement of phospholipid transfer proteins. The lamellar bodies of pulmonary type II alveolar cells have a phospholipid composition unique in terms of the proportions of dipalmitoyl phosphatidylcholine and phosphatidylglycerol. Studies of the phospholipid transfer proteins in lung have demonstrated two molecular species of the transfer proteins that differ significantly from those found in liver and other tissues. These proteins show specificity for the transfer of dipalmitoyl phosphatidylcholine and phosphatidylglycerol.     

Development and functions of seed transfer cells

In secretion or absorption processes, solutes are transported across the plasmalemma between the symplastic and apoplastic compartments. For this purpose, certain plant cells have developed a specialised transfer cell morphology characterised by wall ingrowths, which amplify the associated plasmalemma surface area up to 20-fold. Detailed studies on the function and development of transfer cells in the context of seed filling have been carried out mainly in cereal endosperm, and for the cotyledon and seed coat cells of legumes. The major solutes transferred are amino acids, sucrose and monosaccharides. The contributions of recently identified symporter proteins to solute transfer are reviewed here, as is the role of apoplastic invertases in promoting solute assimilation. Expression of invertase and monosaccharide transporters early in both cereal and legume seed development orchestrates the distribution of free sugars which play an important role in regulating transfer cell function and determining final endosperm or embryo cell number. Transfer cell differentiation is subject to developmental control, and may also be modulated by sugar levels. The most abundant genes specifically expressed in the transfer layer of maize endosperm encode small antipathogenic proteins, pointing to a role for these cells in protecting the developing endosperm against pathogen ingress. The functional characterisation of the corresponding transfer layer-specific promoters has provided a tool for dissecting transfer cell functions. Transfer cells are highly polar in their organisation, the characteristic cell wall ingrowths developing on one face only. The presence of cytoskeletal components bordering wall ingrowths is documented, but their role in establishing transfer cell morphology remains to be established.     

The large,diverse, and robust arsenal of Ralstonia solanacearum type III effectors and their in planta functions

The type III secretion system with its delivered type III effectors (T3Es) is one of the main virulence determinants of Ralstonia solanacearum, a worldwide devastating plant pathogenic bacterium affecting many crop species. The pan-effectome of the R. solanacearum species complex has been exhaustively identified and is composed of more than 100 different T3Es. Among the reported strains, their content ranges from 45 to 76 T3Es. This considerably large and varied effectome could be considered one of the factors contributing to the wide host range of R. solanacearum. In order to understand how R. solanacearum uses its T3Es to subvert the host cellular processes, many functional studies have been conducted over the last three decades. It has been shown that R. solanacearum effectors, as those from other plant pathogens, can suppress plant defence mechanisms, modulate the host metabolism, or avoid bacterial recognition through a wide variety of molecular mechanisms. R. solanacearum T3Es can also be perceived by the plant and trigger immune responses. To date, the molecular mechanisms employed by R. solanacearum T3Es to modulate these host processes have been described for a growing number of T3Es, although they remain unknown for the majority of them. In this microreview, we summarize and discuss the current knowledge on the characterized R. solanacearum species complex T3Es.     

Properties of the transfer functions of compartmental models

This paper is concerned with the nonlinear system of algebraic equations relating the positive parameters of a linear time-invariant compartmental model to its transfer function coefficients. The general form that these equations must take is shown, and simple necessary conditions for the existence of positive solutions are given. An immediate use of these conditions is the development of necessary conditions for a polynomial with positive coefficients to have negative roots. A method is then outlined which triangularizes the system and reduces the complete solution problem to one of finding and counting roots of a polynomial. Sufficient conditions for the existence of real and positive solutions are demonstrated.