Full characterization of vibrational coherence in a porphyrin chromophore by two-dimensional electronic spectroscopy

In this work we present experimental and calculated two-dimensional electronic spectra for a 5,15-bisalkynyl porphyrin chromophore. The lowest energy electronic Qy transition couples mainly to a single 380 cm–1 vibrational mode. The two-dimensional electronic spectra reveal diagonal and cross peaks which oscillate as a function of population time. We analyze both the amplitude and phase distribution of this main vibronic transition as a function of excitation and detection frequencies. Even though Feynman diagrams provide a good indication of where the amplitude of the oscillating components are located in the excitation-detection plane, other factors also affect this distribution. Specifically, the oscillation corresponding to each Feynman diagram is expected to have a phase that is a function of excitation and detection frequencies. Therefore, the overall phase of the experimentally observed oscillation will reflect this phase dependence. Another consequence is that the overall oscillation amplitude can show interference patterns resulting from overlapping contributions from neighboring Feynman diagrams. These observations are consistently reproduced through simulations based on third order perturbation theory coupled to a spectral density described by a Brownian oscillator model

'Treatment of the Sportsman's groin': British Hernia Society's 2014 position statement based on the Manchester Consensus Conference

<b>Introduction</b> The aim was to produce a multidisciplinary consensus to determine the current position on the nomenclature, definition, diagnosis, imaging modalities and management of Sportsman's groin (SG).<p></p> <b>Methods</b> Experts in the diagnosis and management of SG were invited to participate in a consensus conference held by the British Hernia Society in Manchester, UK on 11–12 October 2012. Experts included a physiotherapist, a musculoskeletal radiologist and surgeons with a proven track record of expertise in this field. Presentations detailing scientific as well as outcome data from their own experiences were given. Records were made of the presentations with specific areas debated openly.<p></p> <b>Results</b> The term ‘inguinal disruption’ (ID) was agreed as the preferred nomenclature with the term ‘Sportsman's hernia’ or ‘groin’ rejected, as no true hernia exists. There was an overwhelming agreement of opinion that there was abnormal tension in the groin, particularly around the inguinal ligament attachment. Other common findings included the possibility of external oblique disruption with consequent small tears noted as well as some oedema of the tissues. A multidisciplinary approach with tailored physiotherapy as the initial treatment was recommended with any surgery involving releasing the tension in the inguinal canal by various techniques and reinforcing it with a mesh or suture repair. A national registry should be developed for all athletes undergoing surgery.<p></p> <b>Conclusions</b> ID is a common condition where no true hernia exists. It should be managed through a multidisciplinary approach to ensure consistent standards and outcomes are achieved

Switched-current filter structure for synthesizing arbitrary characteristics based on follow-the-leader feedback configuration

This document is the Accepted Manuscript version of the following article: Wenshan Zhao, Yigang He, and Yichuang Sun, ‘Switched-current filter structure for synthesizing arbitrary characteristics based on follow-the-leader feedback configuration’, Analog Integrated Circuits and Signal Processing, (2015), Vol. 82 (2): 479-486. The version of record is available online at doi: 10.1007/s10470-014-0477-8 © Springer Science+Business Media New York 2015Peer reviewedFinal Accepted Versio

Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

Peer reviewe

Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

Peer reviewe

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance

The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein–DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 complexes from the protein–DNA docking benchmark. We show that HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s). Our DNA analysis and modelling procedure captures the bend and twist motions occurring upon complex formation and uses these to generate custom-built DNA structural models, more closely resembling the bound form, for use in a second docking round. We achieve throughout the benchmark an overall success rate of 94% of one-star solutions or higher (interface root mean square deviation ≤4 Å and fraction of native contacts >10%) according to CAPRI criteria. Our improved protocol successfully predicts even the challenging protein–DNA complexes in the benchmark. Finally, our method is the first to readily dock multiple molecules (N > 2) simultaneously, pushing the limits of what is currently achievable in the field of protein–DNA docking

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

<p>Abstract</p> <p>Background</p> <p>Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene-based selection. Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows.</p> <p>Results</p> <p>Genome-wide association analysis identified a number of candidate genes and chromosome regions associated with 31 dairy traits in contemporary U.S. Holstein cows. Highly significant genes and chromosome regions include: BTA13's <it>GNAS </it>region for milk, fat and protein yields; BTA7's <it>INSR </it>region and BTAX's <it>LOC520057 </it>and <it>GRIA3 </it>for daughter pregnancy rate, somatic cell score and productive life; BTA2's <it>LRP1B </it>for somatic cell score; BTA14's <it>DGAT1-NIBP </it>region for fat percentage; <it>BTA1</it>'s <it>FKBP2 </it>for protein yields and percentage, BTA26's <it>MGMT </it>and BTA6's <it>PDGFRA </it>for protein percentage; BTA18's 53.9-58.7 Mb region for service-sire and daughter calving ease and service-sire stillbirth; BTA18's <it>PGLYRP1</it>-<it>IGFL1 </it>region for a large number of traits; BTA18's <it>LOC787057 </it>for service-sire stillbirth and daughter calving ease; BTA15's <it>CD82</it>, BTA23's <it>DST </it>and the <it>MOCS1</it>-<it>LRFN2 </it>region for daughter stillbirth; and BTAX's <it>LOC520057 </it>and <it>GRIA3 </it>for daughter pregnancy rate. For body conformation traits, BTA11, BTAX, BTA10, BTA5, and BTA26 had the largest concentrations of SNP effects, and <it>PHKA2 </it>of BTAX and <it>REN </it>of BTA16 had the most significant effects for body size traits. For body shape traits, BTAX, BTA19 and BTA3 were most significant. Udder traits were affected by BTA16, BTA22, BTAX, BTA2, BTA10, BTA11, BTA20, BTA22 and BTA25, teat traits were affected by BTA6, BTA7, BTA9, BTA16, BTA11, BTA26 and BTA17, and feet/legs traits were affected by BTA11, BTA13, BTA18, BTA20, and BTA26.</p> <p>Conclusions</p> <p>Genome-wide association analysis identified a number of genes and chromosome regions associated with 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. The results provide useful information for annotating phenotypic effects on the dairy genome and for building consensus of dairy QTL effects.</p

Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer

Early in F plasmid conjugative transfer, the F relaxase, TraI, cleaves one plasmid strand at a site within the origin of transfer called nic. The reaction covalently links TraI Tyr16 to the 5′-ssDNA phosphate. Ultimately, TraI reverses the cleavage reaction to circularize the plasmid strand. The joining reaction requires a ssDNA 3′-hydroxyl; a second cleavage reaction at nic, regenerated by extension from the plasmid cleavage site, may generate this hydroxyl. Here we confirm that TraI is transported to the recipient during transfer. We track the secondary cleavage reaction and provide evidence it occurs in the donor and F ssDNA is transferred to the recipient with a free 3′-hydroxyl. Phe substitutions for four Tyr within the TraI active site implicate only Tyr16 in the two cleavage reactions required for transfer. Therefore, two TraI molecules are required for F plasmid transfer. Analysis of TraI translocation on various linear and circular ssDNA substrates supports the assertion that TraI slowly dissociates from the 3′-end of cleaved F plasmid, likely a characteristic essential for plasmid re-circularization

Chemistry and Sr–Nd isotope signature of amphiboles of the magnesio-hastingsite-pargasite-kaersutite series in Cenozoic volcanic rocks: Insight into lithospheric mantle beneath the Bohemian Massif

Amphibole phenocrysts and xenocrysts from Cenozoic volcanic rocks of the Bohemian Massif (BM) belong to the magnesio-hastingsite-pargasite-kaersutite series. Their host rocks are mostly basaltic lavas, dykes and breccia pipe fills, less commonly also felsic rocks from rift zones along lithospheric block boundaries of the BM. The calculated p–T conditions suggest that almost all amphiboles crystallized in a relatively narrow temperature range (1020–1100 °C) at depths of 20–45 km (0.7–1.2 GPa) during the magma ascent. The initial 143Nd/144Nd and 87Sr/86Sr ratios of amphiboles (0.51266–0.51281 and 0.70328–0.70407, respectively) are similar to those of their whole rocks (0.51266–0.51288 and 0.70341–0.70462, respectively). This testifies to locally elevated proportions of recycled Variscan crustal material during melting of mantle peridotites rich in clinopyroxene–amphibole veins. These veins were formed by metasomatic fluids enriched in High Field Strength Elements and are isotopically similar to EM-1 mantle type.Fenokrysty a xenokrysty amfibolů kenozoických vulkanických hornin Českého masivu (ČM) náleží svým složením do magnesiohastingsit-pargasit-kaersutitové série. Jejich hostitelské horniny jsou především bazaltické lávy, žíly nebo brekciovité výplně komínů, méně často také felsické horniny z riftových zón podél hranic litosférických bloků ČM. Vypočtené p-T podmínky ukazují, že téměř všechny amfiboly krystalizovaly v relativně úzkém teplotním rozmezí (1020–1100 °C) v hloubkách 20–45 km (0,7–1,2 GPa) během výstupu magmatu. Iniciální izotopové poměry 143Nd/144Nd a 87Sr/86Sr v amfibolech jsou v rozmezí 0,51266–0,51281 a 0,70328–0,70407. To vypovídá o lokálně zvýšeném množství recyklovaného variského korového materiálu během tavení plášťového peridotitu bohatého na klinopyroxen-amfibolové žíly. Tyto žíly vznikly z metasomatických fluid obohacených o prvky s velkým iontovým potenciálem a jsou izotopově podobné obohacenému plášti typu 1 (EM-1)

The structural and geochemical evolution of the continental crust: Support for the oceanic plateau model of continental growth

The problem of the origin of the continental crust can be resolved into two fundamental questions: (1) the location and mechanisms of initial mantle extraction of the primitive crust and (2) the processes by which this primitive crust is converted into the continental crust that presently exists. We know that Archean continental crust is compositionally distinct from younger continental crust. Archean magmatism was dominantly bimodal, mafic thoeleiitic plus dacitic, heavy rare earth element depleted, in contrast to the dominantly unimodal, roughly andesitic calc-alkaline magmatism on younger crust [Taylor and McLennan, 1985; Condie, 1989]. The problem is whether these compositional differences are primarily due to different mechanisms of crustal extraction from the mantle or to different mechanisms of differentiation and alteration of newly formed continental crust