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  • Open Access
    Authors: 
    Polly L. Arnold; Michał S. Dutkiewicz; Markus Zegke; Olaf Walter; Christos Apostolidis; Emmalina Hollis; Anne-Frédérique Pécharman; Nicola Magnani; Jean-Christophe Griveau; Eric Colineau; +4 more
    Publisher: Wiley
    Country: United Kingdom
    Project: UKRI | Actinide Polyoxo Chemistr... (EP/M010554/1), NSERC

    A dramatic difference in the ability of the reducing An(III) center in AnCp3 (An=U, Np, Pu; Cp=C5 H5 ) to oxo-bind and reduce the uranyl(VI) dication in the complex [(UO2 )(THF)(H2 L)] (L="Pacman" Schiff-base polypyrrolic macrocycle), is found and explained. These are the first selective functionalizations of the uranyl oxo by another actinide cation. At-first contradictory electronic structural data are explained by combining theory and experiment. Complete one-electron transfer from Cp3 U forms the U(IV) -uranyl(V) compound that behaves as a U(V) -localized single molecule magnet below 4 K. The extent of reduction by the Cp3 Np group upon oxo-coordination is much less, with a Np(III) -uranyl(VI) dative bond assigned. Solution NMR and NIR spectroscopy suggest Np(IV) U(V) but single-crystal X-ray diffraction and SQUID magnetometry suggest a Np(III) -U(VI) assignment. DFT-calculated Hirshfeld charge and spin density analyses suggest half an electron has transferred, and these explain the strongly shifted NMR spectra by spin density contributions at the hydrogen nuclei. The Pu(III) -U(VI) interaction is too weak to be observed in THF solvent, in agreement with calculated predictions.

  • Open Access English
    Authors: 
    Choptuik, Matthew; Santos, Jorge E.; Way, Benson;
    Project: UKRI | Particles, Fields and Ext... (ST/P000681/1), NSERC

    We propose the existence of an infinite-parameter family of solutions in AdS that oscillate on any number of non-commensurate frequencies. Some of these solutions appear stable when perturbed, and we suggest that they can be used to map out the AdS "islands of stability". By numerically constructing two-frequency solutions and exploring their parameter space, we find that both collapse and non-collapse are generic scenarios near AdS. Unlike other approaches, our results are valid on any timescale and do not rely on perturbation theory.

  • Open Access
    Authors: 
    Lorenzo Bianchi; Shira Chapman; Xi Dong; Damián A. Galante; Marco Meineri; Robert C. Myers;
    Publisher: Springer Science and Business Media LLC
    Countries: United Kingdom, Netherlands, Italy
    Project: NSERC

    We present a holographic method for computing the response of Rényi entropies in conformal field theories to small shape deformations around a flat (or spherical) entangling surface. Our strategy employs the stress tensor one-point function in a deformed hyperboloid background and relates it to the coefficient in the two-point function of the displacement operator. We obtain explicit numerical results for d = 3 , · · · , 6 spacetime dimensions, and also evaluate analytically the limits where the Rényi index approaches 1 and 0 in general dimensions. We use our results to extend the work of 1602.08493 and disprove a set of conjectures in the literature regarding the relation between the Rényi shape dependence and the conformal weight of the twist operator. We also extend our analysis beyond leading order in derivatives in the bulk theory by studying Gauss-Bonnet gravity.

  • Open Access
    Authors: 
    Kristen K. Beck; Michael-Shawn Fletcher; Patricia Gadd; Henk Heijnis; Krystyna M. Saunders; Gavin Simpson; Atun Zawadzki;
    Publisher: American Geophysical Union (AGU)
    Country: United Kingdom
    Project: ARC | Tracking the response of ... (DI110100019), ARC | Discovery Indigenous - Gr... (IN140100050), NSERC

    Critical transitions in ecosystem states are often sudden and unpredictable. Consequently, there is a concerted effort to identify measurable early warning signals (EWS) for these important events. Aquatic ecosystems provide an opportunity to observe critical transitions due to their high sensitivity and rapid response times. Using palaeoecological techniques, we can measure properties of time series data to determine if critical transitions are preceded by any measurable ecosystem metrics, that is, identify EWS. Using a suite of palaeoenvironmental data spanning the last 2,400 years (diatoms, pollen, geochemistry, and charcoal influx), we assess whether a critical transition in diatom community structure was preceded by measurable EWS. Lake Vera, in the temperate rain forest of western Tasmania, Australia, has a diatom community dominated by Discostella stelligera and undergoes an abrupt compositional shift at ca. 820 cal yr BP that is concomitant with increased fire disturbance of the local vegetation. This shift is manifest as a transition from less oligotrophic acidic diatom flora (Achnanthidium minutissimum, Brachysira styriaca, and Fragilaria capucina) to more oligotrophic acidic taxa (Frustulia elongatissima, Eunotia diodon, and Gomphonema multiforme). We observe a marked increase in compositional variance and rate-of-change prior to this critical transition, revealing these metrics are useful EWS in this system. Interestingly, vegetation remains complacent to fire disturbance until after the shift in the diatom community. Disturbance taxa invade and the vegetation system experiences an increase in both compositional variance and rate-of-change. These trends imply an approaching critical transition in the vegetation and the probable collapse of the local rain forest system.

  • Open Access
    Authors: 
    Tyler K. Ambrose; David Wallis; Lars N. Hansen; D. J. Waters; Michael P. Searle;
    Publisher: Elsevier BV
    Countries: United Kingdom, Netherlands, United Kingdom
    Project: UKRI | A new method for mapping ... (NE/M000966/1), NSERC

    Abstract Studies of experimentally deformed rocks and small-scale natural shear zones have demonstrated that volumetrically minor phases can control strain localisation by limiting grain growth and promoting grain-size sensitive deformation mechanisms. These small-scale studies are often used to infer a critical role for minor phases in the development of plate boundaries. However, the role of minor phases in strain localisation at an actual plate boundary remains to be tested by direct observation. In order to test the hypothesis that minor phases control strain localisation at plate boundaries, we conducted microstructural analyses of peridotite samples collected along a ∼1 km transect across the base of the Oman-United Arab Emirates (UAE) ophiolite. The base of the ophiolite is marked by the Semail thrust, which represents the now exhumed contact between subducted oceanic crust and the overlying mantle wedge. As such, the base of the ophiolite provides the opportunity to directly examine a former plate boundary. Our results demonstrate that the mean olivine grain size is inversely proportional to the abundance of minor phases (primarily orthopyroxene, as well as clinopyroxene, hornblende, and spinel), consistent with suppression of grain growth by grain-boundary pinning. Our results also reveal that mean olivine grain size is proportional to CPO strength (both of which generally decrease towards the metamorphic sole), suggesting that the fraction of strain produced by different deformation mechanisms varied spatially. Experimentally-derived flow laws indicate that under the inferred deformation conditions, the viscosity of olivine was grain-size sensitive. As such, grain size, and thereby the abundance of minor phases, influenced viscosity during subduction-related deformation along the base of the mantle wedge. We calculate an order of magnitude decrease in the viscosity of olivine towards the base of the ophiolite, which suggests strain was localised near the subduction interface. Our data indicate that this rheological weakening was primarily the result of more abundant minor phases near the base of the ophiolite. Our interpretations are consistent with those of previous studies on experimentally deformed rocks and smaller-scale natural shear zones that indicate minor phases can exert the primary control on strain localisation. However, our study demonstrates for the first time that minor phases can control strain localisation at the scales relevant to a major plate boundary.

  • Open Access
    Authors: 
    Gabriel Ethier-Majcher; Dorian Gangloff; Robert Stockill; Edmund Clarke; Maxime Hugues; C. Le Gall; Mete Atatüre;
    Publisher: American Physical Society (APS)
    Country: United Kingdom
    Project: UKRI | UK Quantum Technology Hub... (EP/M013243/1), EC | PHOENICS (617985), NSERC

    A controlled quantum system can alter its environment by feedback, leading to reduced-entropy states of the environment and to improved system coherence. Here, using a quantum-dot electron spin as a control and probe, we prepare the quantum-dot nuclei under the feedback of coherent population trapping and observe their evolution from a thermal to a reduced-entropy state, with the immediate consequence of extended qubit coherence. Via Ramsey interferometry on the electron spin, we directly access the nuclear distribution following its preparation and measure the emergence and decay of correlations within the nuclear ensemble. Under optimal feedback, the inhomogeneous dephasing time of the electron, T_{2}^{*}, is extended by an order of magnitude to 39 ns. Our results can be readily exploited in quantum information protocols utilizing spin-photon entanglement and represent a step towards creating quantum many-body states in a mesoscopic nuclear-spin ensemble. We acknowledge financial support from the European Research Council ERC Consolidator Grant Agreement No. 617985 and the EPSRC National Quantum Technologies Program NQIT EP/M013243/1. G.E-M. acknowledges financial support from NSERC.

  • Open Access
    Authors: 
    Andrew C. Mason;
    Publisher: Frontiers Media SA
    Project: NSERC

    Insects are often small relative to the wavelengths of sounds they need to localize, which presents a fundamental biophysical problem. Understanding novel solutions to this limitation can provide insights for biomimetic technologies. Such an approach has been successful using the fly Ormia ochracea (Diptera: Tachinidae) as a model. O. ochracea is a parasitoid species whose larvae develop as internal parasites within crickets (Gryllidae). In nature, female flies find singing male crickets by phonotaxis, despite severe constraints on directional hearing due to their small size. A physical coupling between the two tympanal membranes allows the flies to obtain information about sound source direction with high accuracy because it generates interaural time-differences (ITD) and interaural level differences (ILD) in tympanal vibrations that are exaggerated relative to the small arrival-time difference at the two ears, that is the only cue available in the sound stimulus. In this study, I demonstrate that pure time-differences in the neural responses to sound stimuli are sufficient for auditory directionality in O. ochracea.

  • Open Access
    Authors: 
    K. Abe; C. Bronner; Yoshinari Hayato; M. Ikeda; K. Iyogi; J. Kameda; Y. Kato; Yasuhiro Kishimoto; Ll. Marti; M. Miura; +153 more
    Publisher: American Astronomical Society
    Countries: United Kingdom, United Kingdom, Italy, France, Italy
    Project: EC | SKPLUS (641540), NSERC

    We report the results of a neutrino search in Super-Kamiokande for coincident signals with the first detected gravitational wave produced by a binary neutron star merger, GW170817, which was followed by a short gamma-ray burst, GRB170817A, and a kilonova/macronova. We searched for coincident neutrino events in the range from 3.5 MeV to $\sim$100 PeV, in a time window $\pm$500 seconds around the gravitational wave detection time, as well as during a 14-day period after the detection. No significant neutrino signal was observed for either time window. We calculated 90% confidence level upper limits on the neutrino fluence for GW170817. From the upward-going-muon events in the energy region above 1.6 GeV, the neutrino fluence limit is $16.0^{+0.7}_{-0.6}$ ($21.3^{+1.1}_{-0.8}$) cm$^{-2}$ for muon neutrinos (muon antineutrinos), with an error range of $\pm5^{\circ}$ around the zenith angle of NGC4993, and the energy spectrum is under the assumption of an index of $-2$. The fluence limit for neutrino energies less than 100 MeV, for which the emission mechanism would be different than for higher-energy neutrinos, is also calculated. It is $6.6 \times 10^7$ cm$^{-2}$ for anti-electron neutrinos under the assumption of a Fermi-Dirac spectrum with average energy of 20 MeV. 8 pages, 4 figures

  • Open Access
    Authors: 
    Shenheng Guan; Paul Taylor; Ziwei Han; Michael F. Moran; Bin Ma;
    Publisher: American Chemical Society (ACS)
    Project: NSERC

    Data dependent acquisition (DDA) and data independent acquisition (DIA) are traditionally separate experimental paradigms in bottom-up proteomics. In this work, we developed a strategy combining the two experimental methods into a single LC-MS/MS run. We call the novel strategy data dependent-independent acquisition proteomics, or DDIA for short. Peptides identified from DDA scans by a conventional and robust DDA identification workflow provide useful information for interrogation of DIA scans. Deep learning based LC-MS/MS property prediction tools, developed previously, can be used repeatedly to produce spectral libraries facilitating DIA scan extraction. A complete DDIA data processing pipeline, including the modules for iRT vs RT calibration curve generation, DIA extraction classifier training, and false discovery rate control, has been developed. Compared to another spectral library-free method, DIA-Umpire, the DDIA method produced a similar number of peptide identifications, but nearly twice as many protein group identifications. The primary advantage of the DDIA method is that it requires minimal information for processing its data.

  • Closed Access
    Authors: 
    Scott C. Sibole; Eng Kuan Moo; Salvatore Federico; Walter Herzog;
    Publisher: ASME International
    Project: EC | MADE-TEC (890936), NSERC

    Abstract The deformation of articular cartilage and its cells at the micro-scale during dynamic activities such as gait has high mechanoregulatory importance. Measuring the cellular geometries during such dynamics has been limited by the rate of microscopic image acquisition. The introduction of resonating mirrors for image rasterization (resonant scanning), rather than the conventional servo control (galvano scanning), has significantly improved the scanning rate by more than 100×. However, the high scanning rate comes at the cost of image quality, thereby posing challenges in image processing. Here, resonance-driven 3-D laser microscopy is used to observe the transient, micro-scale deformation of articular cartilage and its cells under osmotic challenge conditions. Custom image segmentation and deformable registration software were implemented for analysis of the resonance-scanned microscopy data. The software exhibited robust and accurate performance on the osmotic swelling measurements, as well as quantitative validation testing. The resonance-scanning protocol and developed analysis software allow for simultaneous strain calculation of both the local tissue and cells, and are thus a valuable tool for real-time probing of the cell–matrix interactions that are highly relevant in the fields of orthopedic biomechanics, cell mechanobiology, and functional tissue engineering.

Include:
19,414 Research products, page 1 of 1,942
  • Open Access
    Authors: 
    Polly L. Arnold; Michał S. Dutkiewicz; Markus Zegke; Olaf Walter; Christos Apostolidis; Emmalina Hollis; Anne-Frédérique Pécharman; Nicola Magnani; Jean-Christophe Griveau; Eric Colineau; +4 more
    Publisher: Wiley
    Country: United Kingdom
    Project: UKRI | Actinide Polyoxo Chemistr... (EP/M010554/1), NSERC

    A dramatic difference in the ability of the reducing An(III) center in AnCp3 (An=U, Np, Pu; Cp=C5 H5 ) to oxo-bind and reduce the uranyl(VI) dication in the complex [(UO2 )(THF)(H2 L)] (L="Pacman" Schiff-base polypyrrolic macrocycle), is found and explained. These are the first selective functionalizations of the uranyl oxo by another actinide cation. At-first contradictory electronic structural data are explained by combining theory and experiment. Complete one-electron transfer from Cp3 U forms the U(IV) -uranyl(V) compound that behaves as a U(V) -localized single molecule magnet below 4 K. The extent of reduction by the Cp3 Np group upon oxo-coordination is much less, with a Np(III) -uranyl(VI) dative bond assigned. Solution NMR and NIR spectroscopy suggest Np(IV) U(V) but single-crystal X-ray diffraction and SQUID magnetometry suggest a Np(III) -U(VI) assignment. DFT-calculated Hirshfeld charge and spin density analyses suggest half an electron has transferred, and these explain the strongly shifted NMR spectra by spin density contributions at the hydrogen nuclei. The Pu(III) -U(VI) interaction is too weak to be observed in THF solvent, in agreement with calculated predictions.

  • Open Access English
    Authors: 
    Choptuik, Matthew; Santos, Jorge E.; Way, Benson;
    Project: UKRI | Particles, Fields and Ext... (ST/P000681/1), NSERC

    We propose the existence of an infinite-parameter family of solutions in AdS that oscillate on any number of non-commensurate frequencies. Some of these solutions appear stable when perturbed, and we suggest that they can be used to map out the AdS "islands of stability". By numerically constructing two-frequency solutions and exploring their parameter space, we find that both collapse and non-collapse are generic scenarios near AdS. Unlike other approaches, our results are valid on any timescale and do not rely on perturbation theory.

  • Open Access
    Authors: 
    Lorenzo Bianchi; Shira Chapman; Xi Dong; Damián A. Galante; Marco Meineri; Robert C. Myers;
    Publisher: Springer Science and Business Media LLC
    Countries: United Kingdom, Netherlands, Italy
    Project: NSERC

    We present a holographic method for computing the response of Rényi entropies in conformal field theories to small shape deformations around a flat (or spherical) entangling surface. Our strategy employs the stress tensor one-point function in a deformed hyperboloid background and relates it to the coefficient in the two-point function of the displacement operator. We obtain explicit numerical results for d = 3 , · · · , 6 spacetime dimensions, and also evaluate analytically the limits where the Rényi index approaches 1 and 0 in general dimensions. We use our results to extend the work of 1602.08493 and disprove a set of conjectures in the literature regarding the relation between the Rényi shape dependence and the conformal weight of the twist operator. We also extend our analysis beyond leading order in derivatives in the bulk theory by studying Gauss-Bonnet gravity.

  • Open Access
    Authors: 
    Kristen K. Beck; Michael-Shawn Fletcher; Patricia Gadd; Henk Heijnis; Krystyna M. Saunders; Gavin Simpson; Atun Zawadzki;
    Publisher: American Geophysical Union (AGU)
    Country: United Kingdom
    Project: ARC | Tracking the response of ... (DI110100019), ARC | Discovery Indigenous - Gr... (IN140100050), NSERC

    Critical transitions in ecosystem states are often sudden and unpredictable. Consequently, there is a concerted effort to identify measurable early warning signals (EWS) for these important events. Aquatic ecosystems provide an opportunity to observe critical transitions due to their high sensitivity and rapid response times. Using palaeoecological techniques, we can measure properties of time series data to determine if critical transitions are preceded by any measurable ecosystem metrics, that is, identify EWS. Using a suite of palaeoenvironmental data spanning the last 2,400 years (diatoms, pollen, geochemistry, and charcoal influx), we assess whether a critical transition in diatom community structure was preceded by measurable EWS. Lake Vera, in the temperate rain forest of western Tasmania, Australia, has a diatom community dominated by Discostella stelligera and undergoes an abrupt compositional shift at ca. 820 cal yr BP that is concomitant with increased fire disturbance of the local vegetation. This shift is manifest as a transition from less oligotrophic acidic diatom flora (Achnanthidium minutissimum, Brachysira styriaca, and Fragilaria capucina) to more oligotrophic acidic taxa (Frustulia elongatissima, Eunotia diodon, and Gomphonema multiforme). We observe a marked increase in compositional variance and rate-of-change prior to this critical transition, revealing these metrics are useful EWS in this system. Interestingly, vegetation remains complacent to fire disturbance until after the shift in the diatom community. Disturbance taxa invade and the vegetation system experiences an increase in both compositional variance and rate-of-change. These trends imply an approaching critical transition in the vegetation and the probable collapse of the local rain forest system.

  • Open Access
    Authors: 
    Tyler K. Ambrose; David Wallis; Lars N. Hansen; D. J. Waters; Michael P. Searle;
    Publisher: Elsevier BV
    Countries: United Kingdom, Netherlands, United Kingdom
    Project: UKRI | A new method for mapping ... (NE/M000966/1), NSERC

    Abstract Studies of experimentally deformed rocks and small-scale natural shear zones have demonstrated that volumetrically minor phases can control strain localisation by limiting grain growth and promoting grain-size sensitive deformation mechanisms. These small-scale studies are often used to infer a critical role for minor phases in the development of plate boundaries. However, the role of minor phases in strain localisation at an actual plate boundary remains to be tested by direct observation. In order to test the hypothesis that minor phases control strain localisation at plate boundaries, we conducted microstructural analyses of peridotite samples collected along a ∼1 km transect across the base of the Oman-United Arab Emirates (UAE) ophiolite. The base of the ophiolite is marked by the Semail thrust, which represents the now exhumed contact between subducted oceanic crust and the overlying mantle wedge. As such, the base of the ophiolite provides the opportunity to directly examine a former plate boundary. Our results demonstrate that the mean olivine grain size is inversely proportional to the abundance of minor phases (primarily orthopyroxene, as well as clinopyroxene, hornblende, and spinel), consistent with suppression of grain growth by grain-boundary pinning. Our results also reveal that mean olivine grain size is proportional to CPO strength (both of which generally decrease towards the metamorphic sole), suggesting that the fraction of strain produced by different deformation mechanisms varied spatially. Experimentally-derived flow laws indicate that under the inferred deformation conditions, the viscosity of olivine was grain-size sensitive. As such, grain size, and thereby the abundance of minor phases, influenced viscosity during subduction-related deformation along the base of the mantle wedge. We calculate an order of magnitude decrease in the viscosity of olivine towards the base of the ophiolite, which suggests strain was localised near the subduction interface. Our data indicate that this rheological weakening was primarily the result of more abundant minor phases near the base of the ophiolite. Our interpretations are consistent with those of previous studies on experimentally deformed rocks and smaller-scale natural shear zones that indicate minor phases can exert the primary control on strain localisation. However, our study demonstrates for the first time that minor phases can control strain localisation at the scales relevant to a major plate boundary.

  • Open Access
    Authors: 
    Gabriel Ethier-Majcher; Dorian Gangloff; Robert Stockill; Edmund Clarke; Maxime Hugues; C. Le Gall; Mete Atatüre;
    Publisher: American Physical Society (APS)
    Country: United Kingdom
    Project: UKRI | UK Quantum Technology Hub... (EP/M013243/1), EC | PHOENICS (617985), NSERC

    A controlled quantum system can alter its environment by feedback, leading to reduced-entropy states of the environment and to improved system coherence. Here, using a quantum-dot electron spin as a control and probe, we prepare the quantum-dot nuclei under the feedback of coherent population trapping and observe their evolution from a thermal to a reduced-entropy state, with the immediate consequence of extended qubit coherence. Via Ramsey interferometry on the electron spin, we directly access the nuclear distribution following its preparation and measure the emergence and decay of correlations within the nuclear ensemble. Under optimal feedback, the inhomogeneous dephasing time of the electron, T_{2}^{*}, is extended by an order of magnitude to 39 ns. Our results can be readily exploited in quantum information protocols utilizing spin-photon entanglement and represent a step towards creating quantum many-body states in a mesoscopic nuclear-spin ensemble. We acknowledge financial support from the European Research Council ERC Consolidator Grant Agreement No. 617985 and the EPSRC National Quantum Technologies Program NQIT EP/M013243/1. G.E-M. acknowledges financial support from NSERC.

  • Open Access
    Authors: 
    Andrew C. Mason;
    Publisher: Frontiers Media SA
    Project: NSERC

    Insects are often small relative to the wavelengths of sounds they need to localize, which presents a fundamental biophysical problem. Understanding novel solutions to this limitation can provide insights for biomimetic technologies. Such an approach has been successful using the fly Ormia ochracea (Diptera: Tachinidae) as a model. O. ochracea is a parasitoid species whose larvae develop as internal parasites within crickets (Gryllidae). In nature, female flies find singing male crickets by phonotaxis, despite severe constraints on directional hearing due to their small size. A physical coupling between the two tympanal membranes allows the flies to obtain information about sound source direction with high accuracy because it generates interaural time-differences (ITD) and interaural level differences (ILD) in tympanal vibrations that are exaggerated relative to the small arrival-time difference at the two ears, that is the only cue available in the sound stimulus. In this study, I demonstrate that pure time-differences in the neural responses to sound stimuli are sufficient for auditory directionality in O. ochracea.

  • Open Access
    Authors: 
    K. Abe; C. Bronner; Yoshinari Hayato; M. Ikeda; K. Iyogi; J. Kameda; Y. Kato; Yasuhiro Kishimoto; Ll. Marti; M. Miura; +153 more
    Publisher: American Astronomical Society
    Countries: United Kingdom, United Kingdom, Italy, France, Italy
    Project: EC | SKPLUS (641540), NSERC

    We report the results of a neutrino search in Super-Kamiokande for coincident signals with the first detected gravitational wave produced by a binary neutron star merger, GW170817, which was followed by a short gamma-ray burst, GRB170817A, and a kilonova/macronova. We searched for coincident neutrino events in the range from 3.5 MeV to $\sim$100 PeV, in a time window $\pm$500 seconds around the gravitational wave detection time, as well as during a 14-day period after the detection. No significant neutrino signal was observed for either time window. We calculated 90% confidence level upper limits on the neutrino fluence for GW170817. From the upward-going-muon events in the energy region above 1.6 GeV, the neutrino fluence limit is $16.0^{+0.7}_{-0.6}$ ($21.3^{+1.1}_{-0.8}$) cm$^{-2}$ for muon neutrinos (muon antineutrinos), with an error range of $\pm5^{\circ}$ around the zenith angle of NGC4993, and the energy spectrum is under the assumption of an index of $-2$. The fluence limit for neutrino energies less than 100 MeV, for which the emission mechanism would be different than for higher-energy neutrinos, is also calculated. It is $6.6 \times 10^7$ cm$^{-2}$ for anti-electron neutrinos under the assumption of a Fermi-Dirac spectrum with average energy of 20 MeV. 8 pages, 4 figures

  • Open Access
    Authors: 
    Shenheng Guan; Paul Taylor; Ziwei Han; Michael F. Moran; Bin Ma;
    Publisher: American Chemical Society (ACS)
    Project: NSERC

    Data dependent acquisition (DDA) and data independent acquisition (DIA) are traditionally separate experimental paradigms in bottom-up proteomics. In this work, we developed a strategy combining the two experimental methods into a single LC-MS/MS run. We call the novel strategy data dependent-independent acquisition proteomics, or DDIA for short. Peptides identified from DDA scans by a conventional and robust DDA identification workflow provide useful information for interrogation of DIA scans. Deep learning based LC-MS/MS property prediction tools, developed previously, can be used repeatedly to produce spectral libraries facilitating DIA scan extraction. A complete DDIA data processing pipeline, including the modules for iRT vs RT calibration curve generation, DIA extraction classifier training, and false discovery rate control, has been developed. Compared to another spectral library-free method, DIA-Umpire, the DDIA method produced a similar number of peptide identifications, but nearly twice as many protein group identifications. The primary advantage of the DDIA method is that it requires minimal information for processing its data.

  • Closed Access
    Authors: 
    Scott C. Sibole; Eng Kuan Moo; Salvatore Federico; Walter Herzog;
    Publisher: ASME International
    Project: EC | MADE-TEC (890936), NSERC

    Abstract The deformation of articular cartilage and its cells at the micro-scale during dynamic activities such as gait has high mechanoregulatory importance. Measuring the cellular geometries during such dynamics has been limited by the rate of microscopic image acquisition. The introduction of resonating mirrors for image rasterization (resonant scanning), rather than the conventional servo control (galvano scanning), has significantly improved the scanning rate by more than 100×. However, the high scanning rate comes at the cost of image quality, thereby posing challenges in image processing. Here, resonance-driven 3-D laser microscopy is used to observe the transient, micro-scale deformation of articular cartilage and its cells under osmotic challenge conditions. Custom image segmentation and deformable registration software were implemented for analysis of the resonance-scanned microscopy data. The software exhibited robust and accurate performance on the osmotic swelling measurements, as well as quantitative validation testing. The resonance-scanning protocol and developed analysis software allow for simultaneous strain calculation of both the local tissue and cells, and are thus a valuable tool for real-time probing of the cell–matrix interactions that are highly relevant in the fields of orthopedic biomechanics, cell mechanobiology, and functional tissue engineering.