Selected reading from Treatise on Friendship

Course reading ebook, adapted by Ian D. Dunkle from Project Gutenberg’s Treatises on Friendship and Old Age, by Marcus Tullius Cicero, translated by E.S. Shuckburgh: http://www.gutenberg.org/ebooks/2808Cicero describes the necessary features, the value, and the limits of friendship through a short dialogue

Deuterated nucleotides as chemical probes of RNA structure: a detailed protocol for the enzymatic synthesis of a complete set of nucleotides specifically deuterated at ribose carbons

We describe here a detailed protocol for the synthesis of ribonucleotides specifically deuterated at each ribose carbon atom. We synthesized 20 specifically deuterated ribonucleotides: ATP, CTP, GTP, and UTP, each of which contained one of five deuterated riboses (either 1′-D, 2″-D, 3′-D, 4′-D, or 5′,5″-D2). Our synthetic approach is inspired by the pioneering work of Tolbert and Williamson, who developed a method for the convenient one-pot enzymatic synthesis of nucleotides (Tolbert, T. J. and Williamson, J. R. (1996) J. Am. Chem. Soc. 118, 7929–7940). Our protocol consists of a comprehensive list of required chemical and enzymatic reagents and equipment, detailed procedures for enzymatic assays and nucleotide synthesis, and chromatographic procedures for purification of deuterated nucleotides. As an example of the utility of specifically deuterated nucleotides, we used them to synthesize specifically deuterated sarcin/ricin loop (SRL) RNA and measured the deuterium kinetic isotope effect on hydroxyl radical cleavage of the SRL.https://www.scienceopen.com/document/read?vid=eb44f1b0-c408-4336-a2c0-aed203250898Published versio

Accelerated Discontinuous Galerkin Solvers with the Chebyshev Iterative Method on the Graphics Processing Unit

This work demonstrates implementations of the discontinuous Galerkin (DG) method on graphics processing units (GPU), which deliver improved computational time compared to the conventional central processing unit (CPU). The linear system developed when applying the DG method to an elliptic problem is solved using the GPU. The conjugate gradient (CG) method and the Chebyshev iterative method are the linear system solvers that are compared, to see which is more efficient when computing with the CPU's parallel architecture. When applying both methods, computational times decreased for large problems executed on the GPU compared to CPU; however, CG is the more efficient method compared to the Chebyshev iterative method. In addition, a constant-free upper bound for the DC spectrum applied to the elliptic problem is developed. Few previous works combine the DG method and the GPU. This thesis will provide useful guidelines for the numerical solution of elliptic problems using DG on the GPU

Where Is Waldo? Visual search behavior in "Wimmelpictures"

In order to explore an image, the human eye functions like a spotlight, scanning the content from one object to the next. This visual search behavior is implemented with the help of attention control. The following work surveys the visual search behavior in "Wimmelpictures", a special type of busy pictures. The research objective is to analyze different search strategies and to work out possible differences concerning age and gender. The university experiment is carried out by an eye tracker that records the fixations and saccades of the test persons. The results indicate three forms of search strategy: based on a pattern, based on feature selection, or a mixture of both. Our data shows the search for special features of the target is the most successful. Furthermore there are no differences concerning gender but some concerning age. All age groups need more time to locate the target with an increasing number of distractors in the image. The size of the target is also relevant as a larger target is found more quickly than the smaller one

Informatics Inside : Grenzen überwinden - Virtualität erweitert Realität : Informatik-Konferenz an der Hochschule Reutlingen, 11. Mai 2011

Die Informatics Inside-Konferenz findet in diesem Jahr zum dritten Mal statt. Mit dem Thema "Grenzen überwinden – Virtualität erweitert Realität" stellt sich die Veranstaltung einem aktuellen Schwerpunkt, der viele Interessierte aus Wirtschaft, Wissenschaft und Forschung anzieht. Die Konferenz hat sich von einer Veranstaltung für die Masterstudenten des Studiengangs Medien- und Kommunikationsinformatik zu einer offenen Studentenkonferenz entwickelt. Um die Qualität weiter zu steigern wurde parallel dazu ein zweistufiges Review-Verfahren für Beiträge dieses Tagungsbandes eingeführt

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations

Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein–DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein–DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein–DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.National Institutes of Health [R01GM106056 to R.R., T.D.T.; U54CA121852 in part to T.D.T.]; Boston University Undergraduate Research Opportunities Program [Faculty Matching Grants to D.O. and Y.J.]; USC Graduate School [Research Enhancement Fellowship and Manning Endowed Fellowship to T.P.C.]. R.R. is an Alfred P. Sloan Research Fellow. Funding for open access charge: Boston University. (R01GM106056 - National Institutes of Health; U54CA121852 - National Institutes of Health; Boston University Undergraduate Research Opportunities Program; USC Graduate School; Boston University)https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1Published versio

Flow characteristics and heat transfer performance in a Y-Fractal mini/microchannel heat sink

This article presents a combined experimental and computational study to investigate the flow and heat transfer in a Y-fractal microchannel. Experimental apparatus was newly built to investigate the effect of three different control factors, i.e., fluid flow rate, inlet temperature and heat flux, on the heat transfer characteristics of the microchannel. A standard k-Ɛ turbulence computational fluid dynamics (CFD) model was developed, validated and further employed to simulate the flow and heat transfer microchannel. A comparison between simulated results and the obtained experimental data was presented and discussed. Results showed that good agreement was achieved between the current simulated results and experimental data. Furthermore, an improved new design was suggested to further increase the heat transfer performance and create uniformity of temperature distribution.Peer reviewe

Current status of vascularized composite tissue allotransplantation

Vascularized composite tissue allotransplantation (VCA) offers treatment options of complex functional deficiencies that cannot be repaired with conventional reconstructive methods. VCAs consist of blocks of functional units comprising different tissue types such as skin, bone, muscle, nerves, blood vessels, tendons, ligaments and others, and are thus substantially different from the composition of organ transplants. The field of VCA has made fascinating progresses in the recent past. Among other VCAs, numerous successful hand, face and limb transplants have been performed in the world. At the same time, specific questions in regard to innate and adaptive immunity, consequences of ischemia/reperfusion injury, immunosuppression, preservation, and regenerative capacity remain. In spite of this, the field is poised to make significant advances in the near future

Dezentralisierung, Vermarktlichung und diskursive Koordinierung: neue Rationalisierungstrategien und deren Auswirkungen auf die unteren Produktionsvorgesetzten ; eine Fallstudie aus der Automobilindustrie

Technologische und vor allem organisatorische Veränderungen verbunden mit neuen Strategien der Kapitalverwertung führen seit einigen Jahren zu einer Rationalisierungsdynamik, die sich in veränderten Mustern betrieblicher Steuerung und Kontrolle niederschlägt. Diese Rationalisierungsstrategien sind nicht frei von Widersprüchen, sondern erzeugen neue Probleme und Dysfunktionalitäten. Bei deren Bewältigung spielt die Ebene der unteren Führungskräfte, vor allem der Meister, so die im Beitrag diskutierte These, eine Schlüsselrolle. Der Text stellt zunächst die Kernprinzipien der gegenwärtigen Rationalisierungspolitik in der bundesdeutscchen Industrie dar, um dann die neue Rolle und Funktion der unteren Führungskräfte am Beispiel eines Automobilbetriebs zu überprüfen. Der Beitrag schließt mit Überlegungen und Schlußfolgerungen zu einem 'neuen' Meistertyp. (pre