Using Phylogeny to Improve Genome-Wide Distant Homology Recognition

The gap between the number of known protein sequences and structures continues to widen, particularly as a result of sequencing projects for entire genomes. Recently there have been many attempts to generate structural assignments to all genes on sets of completed genomes using fold-recognition methods. We developed a method that detects false positives made by these genome-wide structural assignment experiments by identifying isolated occurrences. The method was tested using two sets of assignments, generated by SUPERFAMILY and PSI-BLAST, on 150 completed genomes. A phylogeny of these genomes was built and a parsimony algorithm was used to identify isolated occurrences by detecting occurrences that cause a gain at leaf level. Isolated occurrences tend to have high e-values, and in both sets of assignments, a sudden increase in isolated occurrences is observed for e-values >10(−8) for SUPERFAMILY and >10(−4) for PSI-BLAST. Conditions to predict false positives are based on these results. Independent tests confirm that the predicted false positives are indeed more likely to be incorrectly assigned. Evaluation of the predicted false positives also showed that the accuracy of profile-based fold-recognition methods might depend on secondary structure content and sequence length. We show that false positives generated by fold-recognition methods can be identified by considering structural occurrence patterns on completed genomes; occurrences that are isolated within the phylogeny tend to be less reliable. The method provides a new independent way to examine the quality of fold assignments and may be used to improve the output of any genome-wide fold assignment method

Charge frustration in complex fluids and in electronic systems

The idea of charge frustration is applied to describe the properties of such diverse physical systems as oil-water-surfactant mixtures and metal-ammonia solutions. The minimalist charge-frustrated model possesses one energy scale and two length scales. For oil-water-surfactant mixtures, these parameters have been determined starting from the microscopic properties of the physical systems under study. Thus microscopic properties are successfully related to the observed mesoscopic structure.Comment: latex type, 13 page

The Belle II Physics Book

We present the physics program of the Belle II experiment, located on the intensity frontier SuperKEKB $e^+e^-$ collider. Belle II collected its first collisions in 2018, and is expected to operate for the next decade. It is anticipated to collect 50/ab of collision data over its lifetime. This book is the outcome of a joint effort of Belle II collaborators and theorists through the Belle II theory interface platform (B2TiP), an effort that commenced in 2014. The aim of B2TiP was to elucidate the potential impacts of the Belle II program, which includes a wide scope of physics topics: B physics, charm, tau, quarkonium, electroweak precision measurements and dark sector searches. It is composed of nine working groups (WGs), which are coordinated by teams of theorist and experimentalists conveners: Semileptonic and leptonic B decays, Radiative and Electroweak penguins, phi_1 and phi_2 (time-dependent CP violation) measurements, phi_3 measurements, Charmless hadronic B decay, Charm, Quarkonium(like), tau and low-multiplicity processes, new physics and global fit analyses. This book highlights "golden- and silver-channels", i.e. those that would have the highest potential impact in the field. Theorists scrutinised the role of those measurements and estimated the respective theoretical uncertainties, achievable now as well as prospects for the future. Experimentalists investigated the expected improvements with the large dataset expected from Belle II, taking into account improved performance from the upgraded detector.Comment: 689 page

[Zirconia in removable prosthodontics. A case report]

Zirconia as a framework material is well established in fixed prosthodontics. However, for its application for removable dentures little experience exists. Zirkonzahn® has developed a copy-milling unit, that is a manually operated machine for the manufacture not only of frameworks but also of complete removable dentures. The aim of this case report is to show the step-by-step clinical and technical fabrication of a zirconia bar on implants and of a corresponding zirconia complete denture. The advantages and disadvantages of the system are presented and problems are critically discussed

[The interdisciplinary fixed restoration of an edentulous maxilla with a marked resorption of the alveolar crest. A case report. Part II: the definitive restoration]

Different materials and methods can be used for edentulous maxillae rehabilitations. A precise fit between the implant and the framework is assumed. Hence, often implant suprastructures made by conventional lost wax techniques lack such a fit and a secondary modification is necessary. Alternatively the CNC-milling technique provides implant frameworks with a passive fit made of titanium and recently also of zirconia. This article describes the fabrication of a fixed complete dental prosthesis supported by seven implants in an edentulous maxilla. Two prostheses were fabricated, one made of a titanium framework veneered with resin and one made experimentally of a zirconia framework veneered with ceramics. The clinical and technical steps are documented and discussed

[Low-cost simple anchorage systems in the removable hybrid prosthesis. Locator Root Attachment and Würzburg post]

For a simple and provisional retention of a removable prosthesis, less expensive direct retainers are an option compared to indirect cast gold copings with attachment. The Dalbo-Rotex-retainer and the Ticap-system are clinically established. The Locator Root attachment and the Würzburger Stift were recently introduced. The Locator Root attachment uses a massive profiled cylindrical post as a radicular anchorage. The Würzburger Stift has a small endodontic part which is retained by four spreadable lamellae in a convergent cavity. They further differ in the design of the male and female part. Depending on the clinical situation these characteristics can offer benefits and disadvantages. Both systems are documented and their indication, advantages and restrictions are discussed with clinical relevance

[Navigated implant placement using a bone supported CT-guided surgical template. Case report]

Surgical navigation allows precise implant placement and minimizes the risk of interferences with anatomical structures. Computerized implant planning based on tomographic data can be clinically realized by surgical templates. These are normally produced by stereo lithographic rapid prototyping. Accurate placement of virtually planned dental implants depends on a precise fabrication and positioning of the surgical template. Bone-, tooth-, implant-, and/or soft tissue-supported surgical templates allow for different micromovements. This report documents the diagnostics and surgical procedures of implant placement in an edentulous patient. Implant fixed complete dentures in the maxilla and mandible were planned. In the maxilla implants were inserted with the aid of a conventional surgical template. In the mandible a bone supported CT-guided surgical template was used

e-Value Distributions for SUPERFAMILY (SF) and PSI-BLAST (PB) Assignments and Occurrences

<div><p>(A) e-Value distribution of all assignments.</p><p>(B) e-Value distribution of occurrences. The e-value of an occurrence is defined as the lowest e-value of all assignments to a superfamily on a genome.</p><p>(C) e-Value distribution of occurrences that cause a gain at leaf level (i.e., predicted false positives). Arrows indicate local minima in the distribution, which might indicate the point where false positive assignments become more dominant.</p></div

Ranked e-Value Distributions for Occurrences without Isolated Occurrences

<p>The predicted false positives are calculated through a base pattern created from assignments with an e-value below the threshold. If an occurrence lies on a genome with either a gain at leaf level in the base pattern or a potential gain at leaf level, it is here defined as an isolated occurrence. A clear overprediction of isolated occurrences is only seen in the set with a base pattern cutoff of 10⁻²⁰.</p