Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals

We compare calcium ion signaling ($\mathrm {Ca}^{2+}$) between two exposures; the data are present as movies, or, more prosaically, time series of images. This paper describes novel uses of singular value decompositions (SVD) and weighted versions of them (WSVD) to extract the signals from such movies, in a way that is semi-automatic and tuned closely to the actual data and their many complexities. These complexities include the following. First, the images themselves are of no interest: all interest focuses on the behavior of individual cells across time, and thus, the cells need to be segmented in an automated manner. Second, the cells themselves have 100$+$ pixels, so that they form 100$+$ curves measured over time, so that data compression is required to extract the features of these curves. Third, some of the pixels in some of the cells are subject to image saturation due to bit depth limits, and this saturation needs to be accounted for if one is to normalize the images in a reasonably unbiased manner. Finally, the $\mathrm {Ca}^{2+}$ signals have oscillations or waves that vary with time and these signals need to be extracted. Thus, our aim is to show how to use multiple weighted and standard singular value decompositions to detect, extract and clarify the $\mathrm {Ca}^{2+}$ signals. Our signal extraction methods then lead to simple although finely focused statistical methods to compare $\mathrm {Ca}^{2+}$ signals across experimental conditions.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS253 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Multiplex sorting of foodborne pathogens by on-chip free-flow magnetophoresis

This study reports multiplex sorting of Salmonella typhimurium and Escherichia coli 0157, from broth cultures and from pathogen-spiked skinned chicken breast enrichment broths by employing microfluidic free-flow magnetophoresis. Magnetic beads of different sizes and magnetite content, namely Dynabeads anti-salmonella and Hyglos-Streptavidin beads together with the corresponding pathogen-specific biotinylated recombinant phages, were utilised as affinity solid phases for the capture and concentration of viable S. typhimurium and E. coli 0157. Following optimisation, the protocol was used to demonstrate continuous magnetophoretic sorting of the two pathogen-bound magnetic bead populations from mixed cultures and from pathogen-spiked chicken pre-enrichment broths under the influence of a Halbach magnet array. For example, in the la tter case, a pure population of S. typhimurium-bound Dynabeads (72% recovery) was sorted from a 100 μL mixture containing E. coli 0157-bound Hyglos beads (67% recovery) within 1.2 min in the presence of 0.1% Tween 20. This proof-of-principle study demonstrates how more than one pathogen type can be simultaneously isolated/enriched from a single food pre-enrichment broth (e.g. Universal food enrichment broth)

Using Abrupt Changes in Magnetic Susceptibility within Type-II Superconductors to Explore Global Decoherence Phenomena

A phenomenon of a periodic staircase of macroscopic jumps in the admitted magnetic field has been observed, as the magnitude of an externally applied magnetic field is smoothly increased or decreased upon a superconducting (SC) loop of type II niobium-titanium wire which is coated with a non-superconducting layer of copper. Large temperature spikes were observed to occur simultaneously with the jumps, suggesting brief transitions to the normal state, caused by en masse motions of Abrikosov vortices. An experiment that exploits this phenomenon to explore the global decoherence of a large superconducting system will be discussed, and preliminary data will be presented. Though further experimentation is required to determine the actual decoherence rate across the superconducting system, multiple classical processes are ruled out, suggesting that jumps in magnetic flux are fully quantum mechanical processes which may correspond to large group velocities within the global Cooper pair wavefunction.Comment: 13 pages, 4 figures, part of proceedings for FQMT 2011 conference in Prague, Czech Republi

On-chip acoustophoretic isolation of microflora including S. typhimurium from raw chicken, beef and blood samples

Pathogen analysis in food samples routinely involves lengthy growth-based pre-enrichment and selective enrichment of food matrices to increase the ratio of pathogen to background flora. Similarly, for blood culture analysis, pathogens must be isolated and enriched from large excess of blood cells to allow further analysis. Conventional techniques of centrifugation and filtration are cumbersome, suffer from low sample throughput, are not readily amenable to automation and carry a risk of damaging biological samples. We report on-chip acoustophoresis as a pre-analytical technique for the resolution of total microbial flora from food and blood samples. The resulting ‘clarified’ sample is expected to increase the performance of downstream systems for the specific detection of the pathogens. A microfluidic chip with three inlets, a central separation channel and three outlets was utilized. Samples were introduced through the side inlets, buffer through the central inlet. Upon ultrasound actuation, large debris particles (10–100 μm) from meat samples were continuously partitioned into the central buffer channel, leaving the “clarified” outer sample streams containing both, the pathogenic cells and the background flora (ca. 1 μm) to be collected over a 30 min operation cycle before further analysis. The system was successfully tested with Salmonella typhimurium-spiked (ca. 103 CFU mL⁻¹) samples of chicken and minced beef, demonstrating a high level of the pathogen recovery (60–90%). When applied to S. typhimurium contaminated blood samples (107 CFU mL⁻¹), acoustophoresis resulted in a high depletion of the red blood cells (99.8%) which partitioned in the buffer stream, whilst sufficient numbers of the viable S. typhimurium remained in the outer channels for further analysis. These results indicate that the technology may provide a generic approach for pre-analytical sample preparation prior to integrated and automated downstream detection of bacterial pathogens

Parametric Oscillation of a Moving Mirror Driven by Radiation Pressure in a Superconducting Fabry-Perot Resonating System

A moving pellicle superconducting mirror, which is driven by radiation pressure on its one side, and by the Coulomb force on its other side, can become a parametric oscillator that can generate microwaves when placed within a high-Q superconducting Fabry-Perot resonator system. A paraxial-wave analysis shows that the fundamental resonator eigenmode needed for parametric oscillation is the TM011 mode. A double Fabry-Perot structure is introduced to resonate the pump and the idler modes, but to reject the parasitic anti-Stokes mode. The threshold for oscillation is estimated based on the radiation-pressure coupling of the pump to the signal and idler modes, and indicates that the experiment is feasible to perform.Comment: 30 pages, 6 figures, part of proceedings of FQMT 2011 conference in Prague, Czech Republi

Filtration efficiency of air conditioner filters and face masks to limit exposure to aerosolized algal toxins

Harmful algal blooms (HABs) can generate toxins that can be aerosolized and negatively impact human health through inhalation. HABs are often found in waterways near residences, therefore, aerosolized HAB toxins can potentially affect both indoor and outdoor air quality. Given that HABs are predicted to increase worldwide, effective mitigation strategies are needed to prevent the inhalation of aerosolized HAB toxins. In this work, we characterized both the particle filtration efficiency using particle sizing instruments as well as the mass concentration of different congeners of aerosolized microcystin (MC) toxins that penetrate through commercially available face masks and air conditioner (AC) filters. Particles were generated from cultures of the toxin-producing cyanobacteria Microcystis aeruginosa. Hydrophobic congeners of microcystin including MC-LF and MC-LW were enriched in aerosols compared to water, with MC-LR being the most abundant, which has implications for the toxicity of inhalable particles generated from HAB-contaminated waters. Particle transmission efficiencies and toxin filtration efficiencies scaled with the manufacturer-provided filter performance ratings. Up to 80% of small, microcystin-containing aerosols were transmitted through AC filters with low filter performance ratings. In contrast, both face masks as well as AC filters with high filter performance ratings efficiently removed toxin-containing particles to below limits of quantification. Our findings suggest that face masks and commercially available AC filters with high filtration efficiency ratings are suitable mitigation strategies to avoid indoor and outdoor air exposure to aerosolized HAB toxins. This work also has relevance for reducing airborne exposure to other HAB toxins, non-HAB toxins, pathogens, and viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic

High-affinity anti-Arc nanobodies provide tools for structural and functional studies

Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is poorly understood. Arc has an N-terminal domain (NTD) involved in membrane binding and a C-terminal domain (CTD) that binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerisation, including assembly of retrovirus-like capsids involved in intercellular signalling. To obtain new tools for studies on Arc structure and function, we produced and characterised six high-affinity anti-Arc nanobodies (Nb). The CTD of rat and human Arc were both crystallised in ternary complexes with two Nbs. One Nb bound deep into the stargazin-binding pocket of Arc CTD and suggested competitive binding with Arc ligand peptides. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. The collapsed conformation closely resembles Drosophila Arc in capsids, suggesting that we have trapped a capsid-like conformation of the human Arc CTD. Our data obtained with the help of anti-Arc Nbs suggest that structural dynamics of the CTD and dimerisation of the NTD may promote the formation of capsids. Taken together, the recombinant high-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function, as well as mechanisms of Arc capsid formation, both in vitro and in vivo. For example, the Nbs could serve as a genetically encoded tools for inhibition of endogenous Arc interactions in the study of neuronal function and plasticity.publishedVersio

A Study of Mexican Free-Tailed Bat Chirp Syllables: Bayesian Functional Mixed Models for Nonstationary Acoustic Time Series

Abstract We describe a new approach to analyze chirp syllables of free-tailed bats from two regions of Texas in which they are predominant: Austin and College Station. Our goal is to characterize any systematic regional differences in the mating chirps and assess whether individual bats have signature chirps. The data are analyzed by modeling spectrograms of the chirps as responses in a Bayesian functional mixed model. Given the variable chirp lengths, we compute the spectrograms on a relative time scale interpretable as the relative chirp position, using a variable window overlap based on chirp length. We use 2D wavelet transforms to capture correlation within the spectrogram in our modeling and obtain adaptive regularization of the estimates and inference for the regions-specific spectrograms. Our model includes random effect spectrograms at the bat level to account for correlation among chirps from the same bat, and to assess relative variability in chirp spectrograms within and between bats. The modeling of spectrograms using functional mixed models is a general approach for the analysis of replicated nonstationary time series, such as our acoustical signals, to relate aspects of the signals to various predictors, while accounting for between-signal structure. This can be done on raw spectrograms when all signals are of the same length, and can be done using spectrograms defined on a relative time scale for signals of variable length in settings where the idea of defining correspondence across signals based on relative position is sensible

Longitudinal Remote SBRT/SRS Training in Latin America: A Prospective Cohort Study

BACKGROUND: Continuing medical education in stereotactic technology are scarcely accessible in developing countries. We report the results of upscaling a longitudinal telehealth training course on stereotactic body radiation therapy (SBRT) and stereotactic radiosurgery (SRS), after successfully developing a pilot course in Latin America. METHODS: Longitudinal training on SBRT and SRS was provided to radiation oncology practitioners in Peru and Colombia at no cost. The program included sixteen weekly 1-hour live conferencing sessions with interactive didactics and a cloud-based platform for case-based learning. Participant-reported confidence was measured in 16 SBRT/SRS practical domains, based on a 1-to-5 Likert scale. Pre- and post-curriculum exams were required for participation credit. Knowledge-baseline, pre- and post-curriculum surveys, overall and single professional-group confidence changes, and exam results were assessed. RESULTS: One hundred and seventy-three radiotherapy professionals participated. An average of 56 (SD ±18) attendees per session were registered. Fifty (29.7%) participants completed the pre- and post-curriculum surveys, of which 30% were radiation oncologists (RO), 26% radiation therapists (RTT), 20% residents, 18% medical physicists and 6% neurosurgeons. Significant improvements were found across all 16 domains with overall mean +0.55 (SD ±0.17, p\u3c0.001) Likert-scale points. Significant improvements in individual competences were most common among medical physicists, RTT and residents. Pre- and post-curriculum exams yielded a mean 16.15/30 (53.8 ± 20.3%) and 23.6/30 (78.7 ± 19.3%) correct answers (p\u3c0.001). CONCLUSION: Longitudinal telehealth training is an effective method for improving confidence and knowledge on SBRT/SRS amongst professionals. Remote continuing medical education should be widely adopted in lower-middle income countries

A human embryonic kidney 293T cell line mutated at the Golgi -mannosidase II locus

Disruption of Golgi -mannosidase II activity can result in type II congenital dyserythropoietic anemia and can induce lupus-like autoimmunity in mice. Here, we isolate a mutant human embryonic kidney (HEK) 293T cell line, called Lec36, that displays sensitivity to ricin that lies between the parental HEK 293T cells, whose secreted and membrane-expressed proteins are dominated by complex-type glycosylation, and 293S Lec1 cells, which only produce oligomannose-type N-linked glycans. The stem cell marker, 19A, was transiently expressed in the HEK 293T Lec36 cells, and in parental HEK 293T cells with and without the potent Golgi -mannosidase II inhibitor, swainsonine. Negative-ion nano-electrospray ionization mass spectra of the 19A N-linked glycans from HEK 293T Lec36 and swainsonine-treated HEK 293T cells were qualitatively indistinguishable and, as shown by collision-induced dissociation spectra, dominated by hybrid-type glycosylation. Nucleotide sequencing revealed mutations in each allele of MAN2A1, the gene encoding Golgi -mannosidase II: a point mutation in one allele mapping to the active site and an in-frame deletion of twelve-nucleotides in the other. Expression of wild-type but not the mutant MAN2A1 alleles in Lec36 cells restored processing of the 19A reporter glycoprotein to complex-type glycosylation. The Lec36 cell line will be useful for expressing therapeutic glycoproteins with hybrid-type glycans and provides a sensitive host for detecting mutations in human MAN2A1 causing type II congenital dyserythropoietic anemia