Advanced Denoising for X-ray Ptychography

The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for parasitic noise and sample smoothness to achieve a thorough characterization and removal of structured and random noise. We present a formal description of the proposed algorithm and prove its convergence under mild conditions. Numerical experiments from simulations and real data (both soft and hard X-ray beamlines) demonstrate that the proposed algorithms produce better results when compared to state-of-the-art methods.Comment: 24 pages, 9 figure

Focused ultrasound excites neurons via mechanosensitive calcium accumulation and ion channel amplification

Ultrasonic neuromodulation has the unique potential to provide non-invasive control of neural activity in deep brain regions with high spatial precision and without chemical or genetic modification. However, the biomolecular and cellular mechanisms by which focused ultrasound excites mammalian neurons have remained unclear, posing significant challenges for the use of this technology in research and potential clinical applications. Here, we show that focused ultrasound excites neurons through a primarily mechanical mechanism mediated by specific calcium-selective mechanosensitive ion channels. The activation of these channels results in a gradual build-up of calcium, which is amplified by calcium- and voltage-gated channels, generating a burst firing response. Cavitation, temperature changes, large-scale deformation, and synaptic transmission are not required for this excitation to occur. Pharmacological and genetic inhibition of specific ion channels leads to reduced responses to ultrasound, while over-expressing these channels results in stronger ultrasonic stimulation. These findings provide a critical missing explanation for the effect of ultrasound on neurons and facilitate the further development of ultrasonic neuromodulation and sonogenetics as unique tools for neuroscience research

Field Theory for a Deuteron Quantum Liquid

Based on general symmetry principles we study an effective Lagrangian for a neutral system of condensed spin-1 deuteron nuclei and electrons, at greater-than-atomic but less-than-nuclear densities. We expect such matter to be present in thin layers within certain low-mass brown dwarfs. It may also be produced in future shock-wave-compression experiments as an effective fuel for laser induced nuclear fusion. We find a background solution of the effective theory describing a net spin zero condensate of deuterons with their spins aligned and anti-aligned in a certain spontaneously emerged preferred direction. The spectrum of low energy collective excitations contains two spin waves with linear dispersions -- like in antiferromagnets -- as well as gapped longitudinal and transverse modes related to the Meissner effect -- like in superconductors. We show that counting of the Nambu-Goldstone modes of spontaneously broken internal and space-time symmetries obeys, in a nontrivial way, the rules of the Goldstone theorem for Lorentz non-invariant systems. We discuss thermodynamic properties of the condensate, and its potential manifestation in the low-mass brown dwarfs.Comment: 19 LaTeX pages; v2: 2 refs added, JHEP versio

In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ

Directed evolution continues to expand the capabilities of complex biomolecules for a range of applications, such as adeno-associated virus vectors for gene therapy; however, advances in library design and selection strategies are key to develop variants that overcome barriers to clinical translation. To address this need, we applied structure-guided SCHEMA recombination of the multimeric adeno-associated virus (AAV) capsid to generate a highly diversified chimeric library with minimal structural disruption. A stringent in vivo Cre-dependent selection strategy was implemented to identify variants that transduce adult neural stem cells (NSCs) in the subventricular zone. A novel variant, SCH9, infected 60% of NSCs and mediated 24-fold higher GFP expression and a 12-fold greater transduction volume than AAV9. SCH9 utilizes both galactose and heparan sulfate as cell surface receptors and exhibits increased resistance to neutralizing antibodies. These results establish the SCHEMA library as a valuable tool for directed evolution and SCH9 as an effective gene delivery vector to investigate subventricular NSCs

The Effects of Nutrient Concentration, Addition of Thickeners, and Agitation Speed on Liquid Fermentation of Steinernema feltiae

Entomopathogenic nematode production in liquid fermentation still requires improvements to maximize efficiency, yield, and nematode quality. Therefore, this study was aimed at developing a more suitable liquid medium for mass production of Steinernema feltiae, by assessing the effects of nutrient concentration, thickeners (primarily agar), and agitation speed on infective juvenile (IJ) yield. Base medium (BM) contained yeast extract (2.3%), egg yolk (1.25%), NaCl (0.5%), and corn oil (4%). All media were inoculated with Xenorhabdus bovienii, and 2 d later, with 2-d-old S. feltiae juveniles. For the nutrient concentration experiment, we evaluated the base medium versus a modified base medium containing all the components, but with 33 concentrations of yeast extract (6.9%), egg yolk (3.75%), and corn oil (12%). The nematodes and bacteria were cultured in 150-ml Erlenmeyer flasks containing 50 ml of liquid medium at (258C) and 180 rpm on a rotary shaker incubator. To assess the effect of thickeners, IJs were inoculated in BM with agar (0.2%), carrageen (0.2%), and carboxymethyl cellulose (0.2% and 0.5%). The addition of 33 more nutrients relative to the BM resulted in a significantly lower yield of nematodes. For agar and agitation speed experiments, five levels of agar in the BM (0%, 0.2%, 0.4%, 0.6%, and 0.8% agar) and two agitation speeds (180 and 280 rpm) were evaluated for production. Increasing agitation speed from 180 to 280 rpm and higher levels of agar in the medium (. 0.2%) significantly increased the yield of bacteria. At the lower agitation speed, media amended with 0.4% and 0.6% agar produced higher nematode yields compared to media without agar. Media with 0.2% and 0.8% agar resulted in intermediate levels of nematode production. At the higher agitation speed, media supplemented with 0.8% agar resulted in the lowest yield of nematodes when compared to the other media tested.Results indicated that increasing nutrient concentration levels was detrimental to nematode production. Also, media containing agar (0.4% and 0.6%) increased nematode yields when cultures were grown at low agitation speed. When IJs were used as the inoculum,0.2% agar also enhanced recovery and nematode yield at the higher agitation speed