Recent developments in Geant4 Allison, J.; Amako, K.; Apostolakis, J. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
11/2016, Letnik:
835, Številka:
C
Journal Article
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Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including ...high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.
•Multithreading resulted in a smaller memory footprint and nearly linear speed-up.•Scoring options, faster geometry primitives, more versatile visualization were added.•Improved electromagnetic and hadronic models and cross sections were developed.•Reverse Monte Carlo and general biasing methods were added.•Physics validation efforts were expanded and new validation tools were added.
Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates ...varying as much as 100-fold. The signals controlling differential translation are poorly understood. Our genome-wide mRNA secondary structure analysis indicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct. ORF translation rate is strongly correlated with its mRNA structure in vivo, and correlation persists, albeit in a reduced form, with its structure when translation is inhibited and with that of in vitro refolded mRNA. These data suggest that intrinsic ORF mRNA structure encodes a rough blueprint for translation efficiency. This structure is then amplified by translation, in a self-reinforcing loop, to provide the structure that ultimately specifies the translation of each ORF.
Background
The diagnosis of dehydration in older patients remains a challenge because clinical and laboratory signs are unspecific. The use of B‑Mode ultrasound of the inferior vena cava is proposed ...to aid in the diagnosis but data concerning diagnostic efficacy of bedside ultrasound are lacking.
Methods
In this study 78 patients ≥65 years old referred to the emergency unit of a university hospital and identified as being dehydrated by applying clinical signs were compared with a reference of 121 patients. The diameter of the inferior vena cava (IVC) was assessed by ultrasound while compressing the IVC during an inspiratory maneuver and the minimum and maximum diameter in M‑Mode.
Results
Significant differences were found concerning compressibility, variability of the diameter assessed by M‑Mode and the diameter during an inspiratory maneuver of the IVC (<0.001); however, a receiver operator characteristics (ROC) showed only moderate values for diagnostic efficacy for all these parameters where the best result was found for the inspiratory maneuver (Area under the curve AUC = 0.73). To reach a specificity of 0.8 to diagnose dehydration, a cut-off value of ≤0.4 cm for IVC diameter was suitable.
Conclusion
Ultrasound of the IVC can easily be applied in a bedside setting and may be helpful in identifying dehydration in older patients; however, this remains challenging and a synopsis covering clinical and technical data is indispensable.
In this paper, polar and spherical Fourier analysis are defined as the decomposition of a function in terms of eigenfunctions of the Laplacian with the eigenfunctions being separable in the ...corresponding coordinates. The proposed transforms provide effective decompositions of an image into basic patterns with simple radial and angular structures. The theory is compactly presented with an emphasis on the analogy to the normal Fourier transform. The relation between the polar or spherical Fourier transform and the normal Fourier transform is explored. As examples of applications, rotation-invariant descriptors based on polar and spherical Fourier coefficients are tested on pattern classification problems.
In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the ...classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.
Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of ...regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti‐σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti‐σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the −35 and −10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti‐σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome‐scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well‐characterized regulatory parts will enable the construction of sophisticated gene expression programs.
The interaction specificities of extracytoplasmic function (ECF) sigma (σ) factors with promoters and their negative regulators (anti‐σs) were mapped to identify non‐crossreacting parts. These orthogonal sets represent a synthetic biology toolbox of genetic switches.
Synopsis
The interaction specificities of extracytoplasmic function (ECF) sigma (σ) factors with promoters and their negative regulators (anti‐σs) were mapped to identify non‐crossreacting parts. These orthogonal sets represent a synthetic biology toolbox of genetic switches.
Part mining was applied to characterize 86 extracytoplasmic function (ECF) σs, their promoters, and 62 anti‐σs identified from the genomes of diverse bacteria.
A subset of 20 σs and promoters were found to be highly orthogonal to each other and can be used to build non‐crossreacting switches in single cells.
The N‐ and C‐terminal domains from σs from different subgroups can be recombined and recognize the corresponding chimeric promoter.
These parts functioned off‐the‐shelf in an E. coli host with minimal re‐engineering and minimally affected host growth and gene expression.
The assessment of the fluid balance as well as the identification of hyperhydration and dehydration often represent a diagnostic challenge, especially in older patients. In principle, various ...diagnostic procedures and approaches are suitable for assessment of the various facets, by which such a disorder can be recognized. The contribution of abdominal ultrasound is described and evaluated in the context of the different diagnostic procedures. An overview of the current situation with respect to assessment of the vena cava is provided. In many respects there is no strict consensus concerning the thresholds of the individual measurements and the value of the different measurements. Currently, an orthograde diameter of the inferior vena cava > 2 cm is accepted as being a good indicator for hyperhydration. Less certain are analogously derived thresholds as indicators for dehydration.
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation, and protein degradation, among other factors. Translation requires the interplay of several RNA ...hybridization processes, which are expected to be temperature-sensitive. We used ribosome profiling to monitor translation in Escherichia coli at 30 °C and to investigate how this changes after 10–20 min of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat-shock response transcriptional program at 30 °C by overexpressing the heat shock σ factor encoded by the rpoH gene. We compared translation efficiency, the ratio of ribosome footprint reads to mRNA reads for each gene, to parameters derived from gene sequences. Genes with stable mRNA structures, non-optimal codon use, and those whose gene product is cotranslationally translocated into the inner membrane are generally less highly translated than other genes. Comparison with other published datasets suggests a role for translational elongation in coupling mRNA structures to translation initiation. Genome-wide calculations of the temperature dependence of mRNA structure predict that relatively few mRNAs show a melting transition between 30 and 42 °C, consistent with the observed lack of changes in translation efficiency. We developed a linear model with six parameters that can predict 38% of the variation in translation efficiency between genes, which may be useful in interpreting transcriptome data.
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