Analysis of a complete DNA–protein affinity landscape

Properties of biological fitness landscapes are of interest to a wide sector of the life sciences, from ecology to genetics to synthetic biology. For biomolecular fitness landscapes, the information we currently possess comes primarily from two sources: sparse samples obtained from directed evolution experiments; and more fine-grained but less authentic information from ‘in silico’ models (such as NK-landscapes). Here we present the entire protein-binding profile of all variants of a nucleic acid oligomer 10 bases in length, which we have obtained experimentally by a series of highly parallel on-chip assays. The resulting complete landscape of sequence-binding pairs, comprising more than one million binding measurements in duplicate, has been analysed statistically using a number of metrics commonly applied to synthetic landscapes. These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides.     

Structured literature image finder: Parsing text and figures in biomedical literature

The SLIF project combines text-mining and image processing to extract structured information from biomedical literature.SLIF extracts images and their captions from published papers. The captions are automatically parsed for relevant biological entities (protein and cell type names), while the images are classified according to their type (e.g., micrograph or gel). Fluorescence microscopy images are further processed and classified according to the depicted subcellular localization.The results of this process can be queried online using either a user-friendly web-interface or an XML-based web-service. As an alternative to the targeted query paradigm, SLIF also supports browsing the collection based on latent topic models which are derived from both the annotated text and the image data.The SLIF web application, as well as labeled datasets used for training system components, is publicly available at http://slif.cbi.cmu.edu.     

A randomized,double-blind trial on the bioavailability of two CoQ10 formulations

The bioavailability of a single, 100 mg, dose of reduced Coenzyme Q10 (CoQH-CF) and Coenzyme Q10 formulation was compared in individuals of >60 years. Significantly higher (P < 0.001) plasma concentrations were demonstrated for the CoQH-CF formulation at 5, 6, 8, 12, 24, 48 and 72 h post-dose compared to the CoQ10 formulation. The area under the curve (AUC) of reduced and total Coenzyme Q10 was significantly higher (P < 0.001) in subjects administered CoQH-CF resulting in 4.3-fold higher plasma AUC_{0–72 h} (430% increase) in subjects receiving CoQH-CF compared to subjects receiving Coenzyme Q10. Oxidized Coenzyme Q10 in plasma was higher (P < 0.001) in subjects receiving CoQH-CF compared to subjects receiving Coenzyme Q10 resulting in a 3.3-fold higher plasma AUC_{0–72 h} (329% increase). Total CoQ10 reached maximum plasma concentrations 15.5 ± 19.6 h after supplementation with CoQH-CF and 26.5 ± 25.8 h after supplementation with Coenzyme Q10, respectively. Thus, reduced Coenzyme Q10 liquid soft gel formulation was found to be superior to the commercial formulation of Coenzyme Q10 for bioavailability.     

Similarity and assumed similarity in personality reports of well-acquainted persons.

The authors obtained self- and observer reports of personality from pairs of well-acquainted college students. Consistent with previous findings, results of Study 1 showed strong cross-source agreement for all 6 HEXACO personality factors (rs ≈ .55). In addition, the authors found modest levels of similarity (r ≈ .25) between dyad members' self-reports on each of 2 dimensions, Honesty-Humility and Openness to Experience. For these same 2 factors, dyad members' self-reports were correlated with their observer reports of the other dyad member (r ≈ .40), thus indicating moderately high assumed similarity. In Study 2, Honesty-Humility and Openness to Experience were the 2 personality factors most strongly associated with the 2 major dimensions of personal values, which also showed substantial assumed similarity. In Study 3, assumed similarity was considerably stronger for close friends than for nonfriend acquaintances. Results suggest that assumed similarity for Honesty-Humility and Openness to Experience reflects a tendency to overestimate one's similarity to persons with whom one has a close relationship, but only on those personality characteristics whose relevance to values gives them central importance to one's identity. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Glass‐polymer melt hybrids. I: Viscoelastic properties of novel affordable organic‐inorganic polymer hybrids

A novel class of organic‐inorganic polymer hybrids was developed by melt‐blending up to 50 (v/v) % [about 83 (w/w) %] tin‐based polyphosphate glass (Pglass) and low‐density polyethylene (LDPE) in conventional plastics processing equipment. The liquid‐ and solid‐state rheology of the polymer hybrids was studied under oscillatory shear flow and deformation to understand the behavior of these materials and to accelerate efforts to melt process the Pglass with organic polymers. All the materials were found to be linearly viscoelastic in the range of temperature and frequencies examined and their viscoelastic functions increased with increasing Pglass concentration. The Pglass significantly enhanced the shear‐thinning characteristics of the Pglass‐LDPE hybrid, indicating the presence of nonlinear chemical and physical interactions between the hybrid components. Morphological examination of the materials by scanning electron microscopy revealed interesting evolution of microstructure of the Pglass phase from droplets (or round beads) to elongated and interpenetrating network structures as the glass concentration was increased in the Pglass‐LDPE hybrids. Melt viscosities of the materials were well described by a simple power‐law equation and a Maxwellian (Hookean) model with three relaxation times. Time‐temperature superpositioning (TTS) of the complex viscosity versus frequency data was excellent at 170°C < T < 220°C and the temperature dependencies of the shift factors conformed excellently well to predictions from an Arrhenius‐type relation, enabling calculation of the flow‐activation energies (25–285 kj/mol) for the materials. The beneficial function of the Pglass in the hybrid system was significantly enhanced by pre‐treating the glass with coupling agents prior to incorporating them into the Pglass‐LDPE hybrids.     

A landmark‐bounded method for large‐scale underground mine mapping

A practical localization technology for underground drift networks—such as those excavated in the practice of underground mining—has yet to become commercially available. This paper focuses on the problem of mapping GPS‐deprived underground environments with the eventual goal of using these maps for navigation. Recent industry‐directed work in the creation of a landmark‐bounded occupancy grid mapping tool that combines odometry, scanning laser data, and sporadically placed passive RFID tags is described. Unlike other work, the suggested approach holds the philosophy that precise localization of the actual landmark locations is not necessary; rather, landmarks serve as a global means for partitioning the map. Successful field experiments were conducted in two underground environments, with the results used to conduct a basic analysis of the described method. © 2012 Wiley Periodicals, Inc.     

Synthesis, characterization and degradation of biodegradable thermoplastic elastomers from poly(ester urethane)s and renewable soy protein isolate biopolymer

New biodegradable poly(ester urethane)/soy protein isolate (PEU/SPI) hybrids were prepared by in situ polymerization. The chemical incorporation of the SPI into the backbone chain of the PEU was facilitated by the reaction of the amine functional groups of SPI with methylene diphenyl diisocyanate (MDI). X-ray diffraction results showed that the chemical incorporation of SPI into PEU significantly changed the molecular structure of the PEU. The PEU/SPI hybrids exhibited higher thermal decomposition temperature and significant increase in the modulus compared with that of pure PEU. Microscopic examination of the morphology of PEU/SPI hybrids confirmed very fine and homogeneous SPI dispersion in PEU. The hydrolytic degradation of the PEU in a phosphate buffer solution was accelerated by incorporation of SPI, which was confirmed by water absorption and scanning electron microscopy of the samples after up to 10 weeks immersion in the buffer solution. This study provides a facile and innovative method of controlling the biodegradation rate of pure PEU with the additional advantage of environmentally-benign biodegradation of the hybrid PEU/SPI polymer, making the concept potentially widely applicable.