The isochore theory depicts the genomes of warm-blooded vertebrates as a mosaic of long genomic regions that are characterized by relatively homogeneous GC content. In the absence of genomic data, the GC content at third-codon positions of protein-coding genes (GC3) was commonly used as a proxy for the GC content of isochores. Oddly, in the postgenomic era, GC3 is still sometimes used as a proxy f

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a

The GC content in the third codon position (GC(3)) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC(3) was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC(3) from 5' to 3'. Moreover, GC(3)-rich genes are predom

BACKGROUND: The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up t

While Datalog provides a high-level language for expressing static program analyses, it depends on external tooling to extract the input facts from the analyzed programs. To remove this dependency, we present MetaDL. The MetaDL system consists of a Datalog language extension for source-level program analysis and tools for generating the language extension from a description of the analyzed languag

Hepatic fibrosis can result as a pathological response to nonalcoholic steatohepatitis (NASH). Cirrhosis, the late stage of fibrosis, has been linked to poor survival and an increased risk of developing hepatocellular carcinoma, with limited treatment options available. Therefore, there is an unmet need for novel effective antifibrotic compounds. Cyclophilins are peptidyl-prolyl cis-trans isomeras

While the study of building types is a well-known and relatively active research field, the topic of room types is less explored. This article takes a broad approach to spatial categorization, enabling the examination of different types of spaces over longer periods. How do different room types evolve and die? How do the different residential room types relate to each other? Do they act alone or d

Software-defined networks are being widely adopted and used in large and complex networks supporting critical operations. Their increasing importance highlights the need for effective validation of SDN topologies and routing policies both prior and during operation. The policies that configure an SDN deployment come from several, possibly conflicting sources. This may lead to undesired effects suc

Astronomical spectroscopy has recently expanded into the near-infrared (nIR) wavelength region, raising the demands on atomic transition data. The interpretation of the observed spectra largely relies on theoretical results, and progress towards the production of accurate theoretical data must continuously be made. Spectrum calculations that target multiple atomic states at the same time are by no

Over the past ten years, significant industry, policy, and scientific attention has been given to the ‘circular economy’, which aims to create a more sustainable society by decoupling economic growth from resource consumption. Firms are expected to play a significant role in the shift to a circular economy model by implementing circular business models that encourage prolonged use of products, com

Diffusion MRI may enable non-invasive mapping of axonal microstructure. Most approaches infer axon diameters from effects of time-dependent diffusion on the diffusion-weighted MR signal by modeling axons as straight cylinders. Axons do not, however, propagate in straight trajectories, and so far the impact of the axonal trajectory on diameter estimation has been insufficiently investigated. Here,

Atmospheric inverse modeling is a method for reconstructing historical fluxes of green-house gas between land and atmosphere, using observed atmospheric concentrations and an atmospheric tracer transport model. The small number of observed atmospheric concentrations in relation to the number of unknown flux components makes the inverse problem ill-conditioned, and assumptions on the fluxes are nee

The present paper argues that experimental phenomenology has an important role to play in research on mindfulness. Experimental phenomenology is defined as a subcategory of phenomenology (defined as the science of our subjective experience of being in the world), which explores the effects of intentional variations of subjective experiencing (direction of attention and choice of attitude) on subse

We argue that the two temporal cognition systems are conceptually too confined to be helpful in understanding the evolution of temporal cognition. In fact, we doubt there are two systems. In relation to this, we question that the authors did not describe the results of our planning study on ravens correctly, as this is of consequence to their theory.

Local governments have come to play an increasingly active role in addressing current environmental challenges. In addition to improving the environmental performance of a specific city, such initiatives can potentially spur policy change at other levels of government and thereby contribute to the addressing of global environmental challenges. This type of interplay between local and higher levels

This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required