VDNA: The virtual DNA plug-in for VMD

Summary: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason, we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, bent and circular DNA, and models of the nucleosome superhelix, chromatin, thermal motion and nucleosome unwrapping

Fundamental Conditions for N-th Order Accurate Lattice Boltzmann Models

In this paper, we theoretically prove a set of fundamental conditions pertaining discrete velocity sets and corresponding weights. These conditions provide sufficient conditions for a priori formulation of lattice Boltzmann models that automatically admit correct hydrodynamic moments up to any given N-th order

Alien species of <i>Bugula</i> (Bryozoa) along the Atlantic coasts of Europe

Three apparently non-native species of Bugula occur in marinas and harbours in Atlantic Europe. The most common, B. neritina, was known from a few sites in southern Britain and northern France during the 20th century, following its discovery at Plymouth by 1911. During the 1950-60s it was abundant in a dock heated by power station effluent at Swansea, south Wales, where it flourished until the late 1960s, while water temperatures were 7-10°C above ambient. It disappeared after power generation ceased, when summer temperatures probably became insufficient to support breeding. Details of disappearances have not been recorded but B. neritina was not seen in Britain between c1970 and 1999. Since 2000, it has been recorded along the south coast of England, and subsequently in marinas in the southern North Sea, Ireland and southern Scotland, well to the north of its former range, as well as along the Atlantic coast from Spain to The Netherlands. It has also been introduced to outlying localities such as the Azores and Tristan da Cunha. We report that this rapidly spreading form has the same COI haplotype as B. neritina currently invasive elsewhere in the world. B. simplex has been reported less, with 1950s records from settlement panels in some Welsh docks. It has not been targeted in most recent marina surveys but has been observed in southwest England, Belgium and The Netherlands. There are almost no recent records of B. stolonifera, though it was probably introduced to a few British and Irish ports prior to the 1950s. Its current status in most of western Europe is unknown but it has been reported as expanding throughout most of the world during the last 60 years. Having poorly known distributions, B. simplex and B. stolonifera should be recorded during future monitoring of alien species in Atlantic Europe. Illustrations to aid identification are included for all three species

Nuclear receptors in vascular biology

Nuclear receptors sense a wide range of steroids and hormones (estrogens, progesterone, androgens, glucocorticoid, and mineralocorticoid), vitamins (A and D), lipid metabolites, carbohydrates, and xenobiotics. In response to these diverse but critically important mediators, nuclear receptors regulate the homeostatic control of lipids, carbohydrate, cholesterol, and xenobiotic drug metabolism, inflammation, cell differentiation and development, including vascular development. The nuclear receptor family is one of the most important groups of signaling molecules in the body and as such represent some of the most important established and emerging clinical and therapeutic targets. This review will highlight some of the recent trends in nuclear receptor biology related to vascular biology

Formal Firewall Conformance Testing: An Application of Test and Proof Techniques

Firewalls are an important means to secure critical ICT infrastructures. As configurable off-the-shelf prod\-ucts, the effectiveness of a firewall crucially depends on both the correctness of the implementation itself as well as the correct configuration. While testing the implementation can be done once by the manufacturer, the configuration needs to be tested for each application individually. This is particularly challenging as the configuration, implementing a firewall policy, is inherently complex, hard to understand, administrated by different stakeholders and thus difficult to validate. This paper presents a formal model of both stateless and stateful firewalls (packet filters), including NAT, to which a specification-based conformance test case gen\-eration approach is applied. Furthermore, a verified optimisation technique for this approach is presented: starting from a formal model for stateless firewalls, a collection of semantics-preserving policy transformation rules and an algorithm that optimizes the specification with respect of the number of test cases required for path coverage of the model are derived. We extend an existing approach that integrates verification and testing, that is, tests and proofs to support conformance testing of network policies. The presented approach is supported by a test framework that allows to test actual firewalls using the test cases generated on the basis of the formal model. Finally, a report on several larger case studies is presented

2-(1,3-Benzoxazol-2-yl)guanidinium chloride

The non-H atoms of the cation of the title salt, C8H9N4O+·Cl−, are approximately co-planar (r.m.s. deviation = 0.024 Å) with one amino group forming an intra­molecular hydrogen bond to the tertiary N atom of the benzoxazole fused-ring system. The cations and anions are linked by cyclic R 2 1(6) N—H⋯Cl hydrogen-bonding associations, generating linear chains running along the a-axis direction

Characteristic Evolution and Matching

I review the development of numerical evolution codes for general relativity based upon the characteristic initial value problem. Progress in characteristic evolution is traced from the early stage of 1D feasibility studies to 2D axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to extend such simulations to null infinity where the waveform from the binary inspiral and merger can be unambiguously computed. This has now been accomplished by Cauchy-characteristic extraction, where data for the characteristic evolution is supplied by Cauchy data on an extraction worldtube inside the artificial outer boundary. The ultimate application of characteristic evolution is to eliminate the role of this outer boundary by constructing a global solution via Cauchy-characteristic matching. Progress in this direction is discussed.Comment: New version to appear in Living Reviews 2012. arXiv admin note: updated version of arXiv:gr-qc/050809

Image analysis of cutaneous melanoma histology: a systematic review and meta-analysis

The current subjective histopathological assessment of cutaneous melanoma is challenging. The application of image analysis algorithms to histological images may facilitate improvements in workflow and prognostication. To date, several individual algorithms applied to melanoma histological images have been reported with variations in approach and reported accuracies. Histological digital images can be created using a camera mounted on a light microscope, or through whole slide image (WSI) generation using a whole slide scanner. Before any such tool could be integrated into clinical workflow, the accuracy of the technology should be carefully evaluated and summarised. Therefore, the objective of this review was to evaluate the accuracy of existing image analysis algorithms applied to digital histological images of cutaneous melanoma. Database searching of PubMed and Embase from inception to 11th March 2022 was conducted alongside citation checking and examining reports from organisations. All studies reporting accuracy of any image analysis applied to histological images of cutaneous melanoma, were included. The reference standard was any histological assessment of haematoxylin and eosin-stained slides and/or immunohistochemical staining. Citations were independently deduplicated and screened by two review authors and disagreements were resolved through discussion. The data was extracted concerning study demographics; type of image analysis; type of reference standard; conditions included and test statistics to construct 2 × 2 tables. Data was extracted in accordance with our protocol and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Diagnostic Test Accuracy (PRISMA-DTA) Statement. A bivariate random-effects meta-analysis was used to estimate summary sensitivities and specificities with 95% confidence intervals (CI). Assessment of methodological quality was conducted using a tailored version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. The primary outcome was the pooled sensitivity and specificity of image analysis applied to cutaneous melanoma histological images. Sixteen studies were included in the systematic review, representing 4,888 specimens. Six studies were included in the meta-analysis. The mean sensitivity and specificity of automated image analysis algorithms applied to melanoma histological images was 90% (CI 82%, 95%) and 92% (CI 79%, 97%), respectively. Based on limited and heterogeneous data, image analysis appears to offer high accuracy when applied to histological images of cutaneous melanoma. However, given the early exploratory nature of these studies, further development work is necessary to improve their performance

Ipl1/aurora kinase suppresses S-CDK-driven spindle formation during prophase I to ensure chromosome integrity during meiosis

Cells coordinate spindle formation with DNA repair and morphological modifications to chromosomes prior to their segregation to prevent cell division with damaged chromosomes. Here we uncover a novel and unexpected role for Aurora kinase in preventing the formation of spindles by Clb5-CDK (S-CDK) during meiotic prophase I and when the DDR is active in budding yeast. This is critical since S-CDK is essential for replication during premeiotic S-phase as well as double-strand break induction that facilitates meiotic recombination and, ultimately, chromosome segregation. Furthermore, we find that depletion of Cdc5 polo kinase activity delays spindle formation in DDR-arrested cells and that ectopic expression of Cdc5 in prophase I enhances spindle formation, when Ipl1 is depleted. Our findings establish a new paradigm for Aurora kinase function in both negative and positive regulation of spindle dynamics