2,968 research outputs found
Detecting Large Concept Extensions for Conceptual Analysis
When performing a conceptual analysis of a concept, philosophers are
interested in all forms of expression of a concept in a text---be it direct or
indirect, explicit or implicit. In this paper, we experiment with topic-based
methods of automating the detection of concept expressions in order to
facilitate philosophical conceptual analysis. We propose six methods based on
LDA, and evaluate them on a new corpus of court decision that we had annotated
by experts and non-experts. Our results indicate that these methods can yield
important improvements over the keyword heuristic, which is often used as a
concept detection heuristic in many contexts. While more work remains to be
done, this indicates that detecting concepts through topics can serve as a
general-purpose method for at least some forms of concept expression that are
not captured using naive keyword approaches
Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency
The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PK and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.National Institutes of Health, Cancer Research UK Program Grant IDs: C6/A11224, C6946/A14492), Wellcome Trust (Grant IDs: WT092096, WT093167
Band edge evolution of transparent Zn M2III O4 (MIII=Co, Rh, Ir) spinels
ZnMIII
2 O4 (MIII = Co, Rh, Ir) spinels have been recently identified as promising p-type semiconductors for
transparent electronics. However, discrepancies exist in the literature regarding their fundamental optoelectronic
properties. In this paper, the electronic structures of these spinels are directly investigated using soft/hard x-ray
photoelectron and x-ray absorption spectroscopies in conjunction with density functional theory calculations.
In contrast to previous results, ZnCo2O4 is found to have a small electronic band gap with forbidden optical
transitions between the true band edges, allowing for both bipolar doping and high optical transparency.
Furthermore, increased d-d splitting combined with a concomitant lowering of Zn s/p conduction states is
found to result in a ZnCo2O4 (ZCO) < ZnRh2O4 (ZRO) ≈ ZnIr2O4 (ZIO) band gap trend, finally resolving
long-standing discrepancies in the literature
Advanced engineering of third-generation lysins and formulation strategies for clinical applications
One of the possible solutions for the current antibiotic resistance crisis may be found in (often bacteriophage-derived) peptidoglycan hydrolases. The first clinical trials of these natural enzymes, coined here as first-generation lysins, are currently ongoing. Moving beyond natural endolysins with protein engineering established the second generation of lysins. In second-generation lysins, the focus lies on improving antibacterial and biochemical properties such as antimicrobial activity and stability, as well as expanding their activities towards Gram-negative pathogens. However, solutions to particular key challenges regarding clinical applications are only beginning to emerge in the third generation of lysins, in which protein and biochemical engineering efforts focus on improving properties relevant under clinical conditions. In addition, increasingly advanced formulation strategies are developed to increase the bioavailability, antibacterial activity, and half-life, and to reduce pro-inflammatory responses. This review focuses on third-generation and advanced formulation strategies that are developed to treat infections, ranging from topical to systemic applications. Together, these efforts may fully unlock the potential of lysin therapy and will propel it as a true antibiotic alternative or supplement
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Spectral reflectance of whale skin above the sea surface: a proposed measurement protocol
Great whales have been detected using very-high-resolution satellite imagery, suggesting this technology could be used to monitor whales in remote areas. However, the application of this method to whale studies is at an early developmental stage and several technical factors need to be addressed, including capacity for species differentiation and the maximum depth of detection in the water column. Both require knowledge of the spectral reflectance of the various whale species just above the sea surface, as when whales bodies break the surface of the water to breath, log or breach, there is, theoretically, no sea water between the whale’s skin and the satellite sensor. Here we tested whether such reflectance could be measured on dead whale tissue. We measured the spectral reflectance of fresh integument collected during the bowhead subsistence harvest, and of thawed integument samples from various species obtained following strandings and stored at -20°C. We show that fresh and thawed samples of whale integument have different spectral properties. The reflectance of fresh samples was higher than the reflectance of thawed samples, as integument appears to darken after death and with time, even under frozen conditions. In this study, we present the first whale reflectance estimates (without the influence of sea water and for dead tissue). These provide a baseline for additional work, needed to advance the use of satellite imagery to monitor whales and facilitate their conservation.MAVA Foundation, B B Roberts Fund, Cambridge Philosophical Society, Prescott Stranding Grants
Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games
Biodiversity is essential to the viability of ecological systems. Species
diversity in ecosystems is promoted by cyclic, non-hierarchical interactions
among competing populations. Such non-transitive relations lead to an evolution
with central features represented by the `rock-paper-scissors' game, where rock
crushes scissors, scissors cut paper, and paper wraps rock. In combination with
spatial dispersal of static populations, this type of competition results in
the stable coexistence of all species and the long-term maintenance of
biodiversity. However, population mobility is a central feature of real
ecosystems: animals migrate, bacteria run and tumble. Here, we observe a
critical influence of mobility on species diversity. When mobility exceeds a
certain value, biodiversity is jeopardized and lost. In contrast, below this
critical threshold all subpopulations coexist and an entanglement of travelling
spiral waves forms in the course of temporal evolution. We establish that this
phenomenon is robust, it does not depend on the details of cyclic competition
or spatial environment. These findings have important implications for
maintenance and evolution of ecological systems and are relevant for the
formation and propagation of patterns in excitable media, such as chemical
kinetics or epidemic outbreaks.Comment: Final submitted version; the printed version can be found at
http://dx.doi.org/10.1038/nature06095 Supplementary movies are available at
http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie1.AVI
and
http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie2.AV
Endogenous endophthalmitis caused by Pseudomonas aeruginosa in a preterm infant: a case report
Endophthalmitis is an infection of the vitreous or aqueous humor of the eye. Although it rarely occurs in the neonatal period it has been previously diagnosed in preterm infants
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