Single-protein detection in crowded molecular environments in cryo-EM images

We present an approach to study macromolecular assemblies by detecting component proteins' characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and in the presence of protein background a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material

Optimum Small Optical Beam Displacement Measurement

We derive the quantum noise limit for the optical beam displacement of a TEM00 mode. Using a multimodal analysis, we show that the conventional split detection scheme for measuring beam displacement is non-optimal with 80% efficiency. We propose a new displacement measurement scheme that is optimal for small beam displacement. This scheme utilises a homodyne detection setup that has a TEM10 mode local oscillator. We show that although the quantum noise limit to displacement measurement can be surpassed using squeezed light in appropriate spatial modes for both schemes, the TEM10 homodyning scheme out-performs split detection for all values of squeezing.Comment: 13 pages, 7 figure

Nano-displacement measurements using spatially multimode squeezed light

We demonstrate the possibility of surpassing the quantum noise limit for simultaneous multi-axis spatial displacement measurements that have zero mean values. The requisite resources for these measurements are squeezed light beams with exotic transverse mode profiles. We show that, in principle, lossless combination of these modes can be achieved using the non-degenerate Gouy phase shift of optical resonators. When the combined squeezed beams are measured with quadrant detectors, we experimentally demonstrate a simultaneous reduction in the transverse x- and y- displacement fluctuations of 2.2 dB and 3.1 dB below the quantum noise limit.Comment: 21 pages, 9 figures, submitted to "Special Issue on Fluctuations & Noise in Photonics & Quantum Optics" of J. Opt.

Toward the use of temporary tattoo electrodes for impedancemetric respiration monitoring and other electrophysiological recordings on skin

The development of dry, ultra-conformable and unperceivable temporary tattoo electrodes (TTEs), based on the ink-jet printing of poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) on top of commercially available temporary tattoo paper, has gained increasing attention as a new and promising technology for electrophysiological recordings on skin. In this work, we present a TTEs epidermal sensor for real time monitoring of respiration through transthoracic impedance measurements, exploiting a new design, based on the application of soft screen printed Ag ink and magnetic interlink, that guarantees a repositionable, long-term stable and robust interconnection of TTEs with external “docking” devices. The efficiency of the TTE and the proposed interconnection strategy under stretching (up to 10%) and over time (up to 96 h) has been verified on a dedicated experimental setup and on humans, fulfilling the proposed specific application of transthoracic impedance measurements. The proposed approach makes this technology suitable for large-scale production and suitable not only for the specific use case presented, but also for real time monitoring of different bio-electric signals, as demonstrated through specific proof of concept demonstrators

Perturbation theory of the space-time non-commutative real scalar field theories

The perturbative framework of the space-time non-commutative real scalar field theory is formulated, based on the unitary S-matrix. Unitarity of the S-matrix is explicitly checked order by order using the Heisenberg picture of Lagrangian formalism of the second quantized operators, with the emphasis of the so-called minimal realization of the time-ordering step function and of the importance of the $\star$-time ordering. The Feynman rule is established and is presented using $\phi^4$ scalar field theory. It is shown that the divergence structure of space-time non-commutative theory is the same as the one of space-space non-commutative theory, while there is no UV-IR mixing problem in this space-time non-commutative theory.Comment: Latex 26 pages, notations modified, add reference

5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind‐pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi‐copy, potentially multi‐locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra‐genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high‐throughput sequencing (HTS) of the 5S intergenic spacers (5S‐IGS) for a lineage of wind‐pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S‐IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra‐genomic competition between two or more paralogous‐homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years

The quest for companions to post-common envelope binaries. II. NSVS14256825 and HS0705+6700

We report new mid-eclipse times of the two close binaries NSVS14256825 and HS0705+6700, harboring an sdB primary and a low-mass main-sequence secondary. Both objects display clear variations in the measured orbital period, which can be explained by the action of a third object orbiting the binary. If this interpretation is correct, the third object in NSVS14256825 is a giant planet with a mass of roughly 12 M_Jup. For HS0705+6700, we provide evidence that strengthens the case for the suggested periodic nature of the eclipse time variation and reduces the uncertainties in the parameters of the brown dwarf implied by that model. The derived period is 8.4 yr and the mass is 31 M_Jup, if the orbit is coplanar with the binary. This research is part of the PlanetFinders project, an ongoing collaboration between professional astronomers and student groups at high schools.Comment: Accepted by Astron. and Astrophy

Cynomolgus monkey's choroid reference database derived from hybrid deep learning optical coherence tomography segmentation.

Cynomolgus monkeys exhibit human-like features, such as a fovea, so they are often used in non-clinical research. Nevertheless, little is known about the natural variation of the choroidal thickness in relation to origin and sex. A combination of deep learning and a deterministic computer vision algorithm was applied for automatic segmentation of foveolar optical coherence tomography images in cynomolgus monkeys. The main evaluation parameters were choroidal thickness and surface area directed from the deepest point on OCT images within the fovea, marked as the nulla with regard to sex and origin. Reference choroid landmarks were set underneath the nulla and at 500 µm intervals laterally up to a distance of 2000 µm nasally and temporally, complemented by a sub-analysis of the central bouquet of cones. 203 animals contributed 374 eyes for a reference choroid database. The overall average central choroidal thickness was 193 µm with a coefficient of variation of 7.8%, and the overall mean surface area of the central bouquet temporally was 19,335 µm2 and nasally was 19,283 µm2. The choroidal thickness of the fovea appears relatively homogeneous between the sexes and the studied origins. However, considerable natural variation has been observed, which needs to be appreciated

Sub-wavelength lithography over extended areas

We demonstrate a systematic approach to sub-wavelength resolution lithographic image formation on films covering areas larger than a wavelength squared. For example, it is possible to make a lithographic pattern with a feature size resolution of $\lambda/[2(N+1)]$ by using a particular $2 M$-photon, multi-mode entangled state, where $N < M$, and banks of birefringent plates. By preparing a statistically mixed such a state one can form any pixel pattern on a $(N+1) 2^{M-N} \times (N+1) 2^{M-N}$ pixel grid occupying a square with a side of $L=2^{M-N-1}$ wavelengths. Hence, there is a trade-off between the exposed area, the minimum lithographic feature size resolution, and the number of photons used for the exposure. We also show that the proposed method will work even under non-ideal conditions, albeit with somewhat poorer performance.Comment: 8 pages, 8 figures, 1 table. Written in RevTe

Surface Resonant Raman Scattering from Cu 110

We report the first evidence of Raman scattering from surface phonons of a pristine metal surface. Our study reveals a Raman active surface vibrational resonance on Cu 110 with a surprisingly large scattering efficiency. With the incident photon energy close to the energy of the Cu 110 surface state electronic transition, the Raman scattering from the surface optical resonance can be significantly enhanced, while any contribution from bulk phonons is absen