Reconstitution of recombination-associated DNA synthesis with human proteins.

The repair of DNA breaks by homologous recombination is a high-fidelity process, necessary for the maintenance of genome integrity. Thus, DNA synthesis associated with recombinational repair must be largely error-free. In this report, we show that human DNA polymerase delta (δ) is capable of robust DNA synthesis at RAD51-mediated recombination intermediates dependent on the processivity clamp PCNA. Translesion synthesis polymerase eta (η) also extends these substrates, albeit far less processively. The single-stranded DNA binding protein RPA facilitates recombination-mediated DNA synthesis by increasing the efficiency of primer utilization, preventing polymerase stalling at specific sequence contexts, and overcoming polymerase stalling caused by topological constraint allowing the transition to a migrating D-loop. Our results support a model whereby the high-fidelity replicative DNA polymerase δ performs recombination-associated DNA synthesis, with translesion synthesis polymerases providing a supportive role as in normal replication

Nicalon/siliconoxycarbide ceramic composites

A series of silsesquioxane copolymers was synthesized by acid hydrolysis and condensation of trimethoxysilanes of the form RSi(OCH3)3, where R = methyl or phenyl. By varying pH, water/methoxy and methyl/phenyl ratios, the molecular structure, polymer rheology and ceramic composition can be controlled. The polymers form an amorphous siliconoxycarbide on pyrolysis. Composites of Nicalon/siliconoxycarbide were fractured in four-point flexure and in tension to evaluate the influence of matrix composition, final fabrication temperature and use of filler on composite mode of failure, modulus, strain capability and strength. Incorporation of filler was found to increase matrix compressive strength. Employment of processing temperatures of 1375 to 1400 C enhanced strain to failure and reduced the tendency toward brittle fracture. Mixed mode (compression/shear and tension/shear) failures were observed in flexural samples processed to the higher temperatures, giving rise to nonlinear stress-strain curves. Tensile samples pyrolyzed to 1400 C showed linear-elastic behavior and failed by fracture of fiber bundles. Matrix material was found to be adherent to the fiber surface after failure. These results demonstrate the need for tensile testing to establish composite behavior

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them.National Science Foundation [1640775]Open access journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Detecting hardware damage using a resistive grid

Dropping a mobile phone or other electronic device can damage not only the enclosure but also internal components, e.g., batteries, printed circuit boards, etc. Sometimes the damage is only internal, with no apparent damage to the casing. Continued use of damaged internal components can result in further damage, e.g., continued use of a damaged USB bridge or battery can result in short circuits or explosions. Per techniques of this disclosure, a variable resistive matrix is embedded within the casing of the electronic device. If the casing is dented or otherwise damaged, even invisibly, the resistance of corresponding rows and columns of the matrix changes enabling localization of the damage. Components near the damage can be disabled, and the user can be notified to take the device in for service

User account suggestions for access-restricted online resources

Mobile device users often have multiple account credentials, e.g., personal accounts, corporate accounts, etc., stored on their devices. A given webpage, document, or URL may be configured with permission for access via one user account but not for other user accounts. This disclosure describes techniques that automatically use or recommend credentials stored on a device to gain access to protected content

Distribution of interference in random quantum algorithms

We study the amount of interference in random quantum algorithms using a recently derived quantitative measure of interference. To this end we introduce two random circuit ensembles composed of random sequences of quantum gates from a universal set, mimicking quantum algorithms in the quantum circuit representation. We show numerically that these ensembles converge to the well--known circular unitary ensemble (CUE) for general complex quantum algorithms, and to the Haar orthogonal ensemble (HOE) for real quantum algorithms. We provide exact analytical formulas for the average and typical interference in the circular ensembles, and show that for sufficiently large numbers of qubits a random quantum algorithm uses with probability close to one an amount of interference approximately equal to the dimension of the Hilbert space. As a by-product, we offer a new way of efficiently constructing random operators from the Haar measures of CUE or HOE in a high dimensional Hilbert space using universal sets of quantum gates.Comment: 14 pages revtex, 11 eps figure

Multi-camera arrays to detect posture

This disclosure describes techniques that, with user permission, automatically detect the posture of a user of a personal computer. The user’s posture is detected using hardware typically found on a desktop or laptop PC, e.g., cameras, without requiring extra sensors or other additional hardware. If the detected posture is determined to be poor, the user is alerted. By detecting and alerting the user of poor posture, the techniques can help forestall health problems. The techniques are implemented with user permission. Users are provided with options to turn off posture detection

Tumor bed brachytherapy for locally advanced laryngeal cancer: a feasibility assessment of combination with ferromagnetic hyperthermia

Purpose. To assess the feasibility of adding hyperthermia to an original method of organ-preserving brachytherapy treatment for locally advanced head and neck tumors. Methods and materials. The method involves organ-preserving tumor resection and adjunctive high-dose-rate (HDR) brachytherapy delivered via afterloading catheters. These catheters are embedded in a polymeric implant prepared intraoperatively to fill the resection cavity, allowing precise computer planning of dose distribution in the surrounding at-risk tumor bed tissue. Theoretical and experimental analyzes address the feasibility of heating the tumor bed implant by coupling energy from a 100 kHz magnetic field applied externally into ferromagnetic particles, which are uniformly distributed within the implant. The goal is to combine adjuvant hyperthermia (40 °C–45 °C) to at-risk tissue within 5 mm of the resection cavity for thermal enhancement of radiation and chemotherapy response. Results. A five-year relapse free survival rate of 95.8% was obtained for a select group of 48 male patients with T3N0M0 larynx tumors, when combining organ-preserving surgery with HDR brachytherapy from a tumor bed implant. Anticipating the need for additional treatment in patients with more advanced disease, a theoretical analysis demonstrates the ability to heat at-risk tissue up to 10 mm from the surface of an implant filled with magnetically coupled ferromagnetic balls. Using a laboratory induction heating system, it takes just over 2 min to increase the target tissue temperature by 10 °C using a 19% volume fraction of ferromagnetic spheres in a 2 cm diameter silicone implant. Conclusion. The promising clinical results of a 48 patient pilot study demonstrate the feasibility of a new organ sparing treatment for laryngeal cancer. Anticipating the need for additional therapy, theoretical estimations of potential implant heating are confirmed with laboratory experiments, preparing the way for future implementation of a thermobrachytherapy implant approach for organ-sparing treatment of locally advanced laryngeal cancer