New Poisson denoising method for pulse-count STEM imaging.

With the recent progress in the development of detectors in electron microscopy, it has become possible to directly count the number of electrons per pixel, even with a scintillator-type detector, by incorporating a pulse-counting module. To optimize a denoising method for electron counting imaging, in this study, we propose a Poisson denoising method for atomic-resolution scanning transmission electron microscopy images. Our method is based on the Markov random field model and Bayesian inference, and we can reduce the electron dose by a factor of about 15 times or further below. Moreover, we showed that the method of reconstruction from multiple images without integrating them performs better than that from an integrated image.

Coprocessed heterogeneous near-infrared lasers on thin-film lithium niobate.

Thin-film lithium niobate (TFLN) is an attractive platform for photonic applications on account of its wide bandgap, its large electro-optic coefficient, and its large nonlinearity. Since these characteristics are used in systems that require a coherent light source, size, weight, power, and cost can be reduced and reliability enhanced by combining TFLN processing and heterogeneous laser fabrication. Here, we report the fabrication of laser devices on a TFLN wafer and also the coprocessing of five different GaAs-based III-V epitaxial structures, including InGaAs quantum wells and InAs quantum dots. Lasing is observed at wavelengths near 930, 1030, and 1180 nm, which, if frequency-doubled using TFLN, would produce blue, green, and orange visible light. A single-sided power over 25 mW is measured with an integrating sphere.

Multimodality integrated microresonators using the Moiré speedup effect.

High-Q microresonators are indispensable components of photonic integrated circuits and offer several useful operational modes. However, these modes cannot be reconfigured after fabrication because they are fixed by the resonator's physical geometry. In this work, we propose a Moiré speedup dispersion tuning method that enables a microresonator device to operate in any of three modes. Electrical tuning of Vernier coupled rings switches operating modality to Brillouin laser, bright microcomb, and dark microcomb operation on demand using the same hybrid-integrated device. Brillouin phase matching and microcomb operation across the telecom C-band is demonstrated. Likewise, by using a single-pump wavelength, the operating mode can be switched. As a result, one universal design can be applied across a range of applications. The device brings flexible mixed-mode operation to integrated photonic circuits.

mRNA vaccine quality analysis using RNA sequencing.

The success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.

Targeting ryanodine receptor type 2 to mitigate chemotherapy-induced neurocognitive impairments in mice.

Chemotherapy-induced cognitive dysfunction (chemobrain) is an important adverse sequela of chemotherapy. Chemobrain has been identified by the National Cancer Institute as a poorly understood problem for which current management or treatment strategies are limited or ineffective. Here, we show that chemotherapy treatment with doxorubicin (DOX) in a breast cancer mouse model induced protein kinase A (PKA) phosphorylation of the neuronal ryanodine receptor/calcium (Ca2+) channel type 2 (RyR2), RyR2 oxidation, RyR2 nitrosylation, RyR2 calstabin2 depletion, and subsequent RyR2 Ca2+ leakiness. Chemotherapy was furthermore associated with abnormalities in brain glucose metabolism and neurocognitive dysfunction in breast cancer mice. RyR2 leakiness and cognitive dysfunction could be ameliorated by treatment with a small molecule Rycal drug (S107). Chemobrain was also found in noncancer mice treated with DOX or methotrexate and 5-fluorouracil and could be prevented by treatment with S107. Genetic ablation of the RyR2 PKA phosphorylation site (RyR2-S2808A) also prevented the development of chemobrain. Chemotherapy increased brain concentrations of the tumor necrosis factor-α and transforming growth factor-ß signaling, suggesting that increased inflammatory signaling might contribute to oxidation-driven biochemical remodeling of RyR2. Proteomics and Gene Ontology analysis indicated that the signaling downstream of chemotherapy-induced leaky RyR2 was linked to the dysregulation of synaptic structure-associated proteins that are involved in neurotransmission. Together, our study points to neuronal Ca2+ dyshomeostasis via leaky RyR2 channels as a potential mechanism contributing to chemobrain, warranting further translational studies.

Electron counting detectors in scanning transmission electron microscopy via hardware signal processing.

Transmission electron microscopy is a pivotal instrument in materials and biological sciences due to its ability to provide local structural and spectroscopic information on a wide range of materials. However, the electron detectors used in scanning transmission electron microscopy are often unable to provide quantified information, that is the number of electrons impacting the detector, without exhaustive calibration and processing. This results in arbitrary signal values with slow response times that cannot be used for quantification or comparison to simulations. Here we demonstrate and optimise a hardware signal processing approach to augment electron detectors to perform single electron counting.

3D integration enables ultralow-noise isolator-free lasers in silicon photonics.

Photonic integrated circuits are widely used in applications such as telecommunications and data-centre interconnects1-5. However, in optical systems such as microwave synthesizers6, optical gyroscopes7 and atomic clocks8, photonic integrated circuits are still considered inferior solutions despite their advantages in size, weight, power consumption and cost. Such high-precision and highly coherent applications favour ultralow-noise laser sources to be integrated with other photonic components in a compact and robustly aligned format-that is, on a single chip-for photonic integrated circuits to replace bulk optics and fibres. There are two major issues preventing the realization of such envisioned photonic integrated circuits: the high phase noise of semiconductor lasers and the difficulty of integrating optical isolators directly on-chip. Here we challenge this convention by leveraging three-dimensional integration that results in ultralow-noise lasers with isolator-free operation for silicon photonics. Through multiple monolithic and heterogeneous processing sequences, direct on-chip integration of III-V gain medium and ultralow-loss silicon nitride waveguides with optical loss around 0.5 decibels per metre are demonstrated. Consequently, the demonstrated photonic integrated circuit enters a regime that gives rise to ultralow-noise lasers and microwave synthesizers without the need for optical isolators, owing to the ultrahigh-quality-factor cavity. Such photonic integrated circuits also offer superior scalability for complex functionalities and volume production, as well as improved stability and reliability over time. The three-dimensional integration on ultralow-loss photonic integrated circuits thus marks a critical step towards complex systems and networks on silicon.

Interlacing in Atomic Resolution Scanning Transmission Electron Microscopy.

Fast frame rates are desirable in scanning transmission electron microscopy for a number of reasons: controlling electron beam dose, capturing in situ events, or reducing the appearance of scan distortions. While several strategies exist for increasing frame rates, many impact image quality or require investment in advanced scan hardware. Here, we present an interlaced imaging approach to achieve minimal loss of image quality with faster frame rates that can be implemented on many existing scan controllers. We further demonstrate that our interlacing approach provides the best possible strain precision for a given electron dose compared with other contemporary approaches.

How Fast is Your Detector? The Effect of Temporal Response on Image Quality.

With increasing interest in high-speed imaging, there should be an increased interest in the response times of our scanning transmission electron microscope detectors. Previous works have highlighted and contrasted the performance of various detectors for quantitative compositional or structural studies, but here, we shift the focus to detector temporal response, and the effect this has on captured images. The rise and decay times of eight detectors' single-electron response are reported, as well as measurements of their flatness, roundness, smoothness, and ellipticity. We develop and apply a methodology for incorporating the temporal detector response into simulations, showing that a loss of resolution is apparent in both the images and their Fourier transforms. We conclude that the solid-state detector outperforms the photomultiplier tube-based detectors in all areas bar a slightly less elliptical central hole and is likely the best detector to use for the majority of applications. However, using the tools introduced here, we encourage users to effectively evaluate which detector is most suitable for their experimental needs.

Sinus tarsi and sinus tarsi syndrome: An imaging review.

The sinus tarsi is a funnel-shaped region at the junction of mid-foot and hind-foot which contains fat, vessels, nerves and ligaments. The ligaments help stabilise the subtalar joint and maintain the longitudinal arch of the foot. The nerve endings contain proprioceptive fibres indicating a role for the sinus tarsi in movement of the foot. Sinus tarsi syndrome is a clinical entity characterised by lateral hind-foot pain with worsening on palpation and weight-bearing, and perceived instability. It is associated with both traumatic and non-traumatic causes. Magnetic resonance imaging is the imaging modality of choice for assessment of the sinus tarsi and sinus tarsi syndrome. In this review article, we review the anatomy and various aetiologies of sinus tarsi syndrome, along with the imaging appearances.

The Role of the Trapezius in Stabilization of the Acromioclavicular Joint: A Biomechanical Evaluation.

Background: Acromioclavicular joint (ACJ) injuries are common, and many are adequately treated nonoperatively. Biomechanical studies have mainly focused on static ligamentous stabilizers. Few studies have quantified ACJ stabilization provided by the trapezius. Purpose/Hypothesis: To elucidate the stabilization provided by the trapezius to the ACJ during scapular internal and external rotation (protraction and retraction). It was hypothesized that sequential trapezial resection would result in increasing ACJ instability. Study Design: Controlled laboratory study. Methods: A biomechanical approach was pursued, with 10 cadaveric shoulders with the trapezius anatomically force loaded to normal. The trapezius was then serially transected over 8 trials, which alternated between clavicular defects (CD) and scapular defects (SD); each sequential defect consisted of 25% of the clavicular or scapular trapezial attachment. After each defect, specimens were tested with angle-controlled scapular internal and external rotation (12°) with rotary torque measurements to evaluate ACJ stability. Results: The mean resistance in rotary torque for 12° of scapular internal rotation (protraction) with native specimens was 7.0 ± 2.0 N·m. Overall, internal rotation demonstrated a significant decrease in ACJ stability with trapezial injury (P < .001). Eight sequential defects resulted in the following significant percentage decreases in rotary torque from native internal rotation: 1.5% (25% CD; 0% SD), 5.6% (25% CD; 25% SD), 5.1% (50% CD; 25% SD), 6.5% (50% CD; 50% SD), 3.8% (75% CD; 50% SD), 7.1% (75% CD; 75% SD), 6.7% (100% CD; 75% SD), and 12.3% (100% CD 100% SD) (P < .001). The mean resistance in rotary torque for 12° of scapular external rotation (retraction) with native specimens was 7.1 ± 1.7 N·m. External rotation did not demonstrate a significant decrease in ACJ stability with trapezial injury (P = .596). The 8 sequential defects resulted in decreases in rotary torque from native external rotation of 0%, 3.8%, 4.0%, 3.2%, 3.5%, 3.4%, 4.2%, and 0.7%. Conclusion: Trapezial injury resulted in increased instability in the setting of scapular internal rotation (protraction) of the ACJ. Clinical Relevance: These findings validate the inclusion of deltotrapezial fascial injury consideration in the modified Rockwood classification system. Repair of the trapezial insertion on the ACJ may provide improved outcomes in the setting of ACJ reconstruction.

Tissue engineered cancer metastases as cancer vaccine to improve cancer immunotherapy.

Radiotherapy is often used to improve cancer immunotherapy outcomes. While there are both pre-clinical and clinical data supporting this approach, there are also significant challenges. One key challenge is that not all patients have tumors that can be easily treated with radiotherapy due to potential normal tissue toxicity and prior treatment. In addition, it is difficult to control the tumor microenvironment to promote the immune response after radiosurgery. To overcome these challenges, we hypothesize that we can engineer cancer metastasis and utilize irradiated engineered tumor cells as a personalized cancer vaccine to improve cancer immunotherapy. Herein, we report the development of engineered lung metastasis using decellularized rat lung tissue. Using the B16F10 melanoma tumor model, we showed that radiotherapy-treated engineered metastases are highly effective in improving cancer immunotherapy responses and more effective than in vivo metastasis. Our work has demonstrated the potential of applying tissue engineering to cancer immunotherapy. STATEMENT OF SIGNIFICANCE: Combination of radiation and immunotherapy are an effective way to treat metastasis. Despite their success, long term response still remains low. Tumor microenvironment evading the immune response, normal tissue toxicity to radiation and inaccessibility to radiosurgery are some of the limitations. To overcome these challenges, in this paper we present with data supporting the use of high dose radiation treated ex vivo engineered B16F10 metastasis model using decellularized lung scaffolds. These engineered metastases closely mimic the in vivo tumors and when given into tumor bearing mice along with check point inhibitors are highly effective in improving the cancer immunotherapy response.

Tospoviruses Induce Small Interfering RNAs Targeting Viral Sequences and Endogenous Transcripts in Solanaceous Plants.

Tospoviruses infect numerous crop species worldwide, causing significant losses throughout the supply chain. As a defence mechanism, plants use RNA interference (RNAi) to generate virus-derived small-interfering RNAs (vsiRNAs), which target viral transcripts for degradation. Small RNA sequencing and in silico analysis of capsicum and N. benthamiana infected by tomato spotted wilt virus (TSWV) or capsicum chlorosis virus (CaCV) demonstrated the presence of abundant vsiRNAs, with host-specific differences evident for each pathosystem. Despite the biogenesis of vsiRNAs in capsicum and N. benthamiana, TSWV and CaCV viral loads were readily detectable. In response to tospovirus infection, the solanaceous host species also generated highly abundant virus-activated small interfering RNAs (vasiRNAs) against many endogenous transcripts, except for an N. benthamiana accession lacking a functional RDR1 gene. Strong enrichment for ribosomal protein-encoding genes and for many genes involved in protein processing in the endoplasmic reticulum suggested co-localisation of viral and endogenous transcripts as a basis for initiating vasiRNA biogenesis. RNA-seq and RT-qPCR-based analyses of target transcript expression revealed an inconsistent role for vasiRNAs in modulating gene expression in N. benthamiana, which may be characteristic of this tospovirus-host pathosystem.

Prophylactic evaluation of verubecestat on disease- and symptom-modifying effects in 5XFAD mice.

Introduction: Alzheimer's disease (AD) is the most common form of dementia. Beta-secretase (BACE) inhibitors have been proposed as potential therapeutic interventions; however, initiating treatment once disease has significantly progressed has failed to effectively stop or treat disease. Whether BACE inhibition may have efficacy when administered prophylactically in the early stages of AD has been under-investigated. The present studies aimed to evaluate prophylactic treatment of the BACE inhibitor verubecestat in an AD mouse model using the National Institute on Aging (NIA) resources of the Model Organism Development for Late-Onset Alzheimer's Disease (MODEL-AD) Preclinical Testing Core (PTC) Drug Screening Pipeline. Methods: 5XFAD mice were administered verubecestat ad libitum in chow from 3 to 6 months of age, prior to the onset of significant disease pathology. Following treatment (6 months of age), in vivo imaging was conducted with 18F-florbetapir (AV-45/Amyvid) (18F-AV45) and 18-FDG (fluorodeoxyglucose)-PET (positron emission tomography)/MRI (magnetic resonance imaging), brain and plasma amyloid beta (Aß) were measured, and the clinical and behavioral characteristics of the mice were assessed and correlated with the pharmacokinetic data. Results: Prophylactic verubecestat treatment resulted in dose- and region-dependent attenuations of 18F-AV45 uptake in male and female 5XFAD mice. Plasma Aß40 and Aß42 were also dose-dependently attenuated with treatment. Across the dose range evaluated, side effects including coat color changes and motor alterations were reported, in the absence of cognitive improvement or changes in 18F-FDG uptake. Discussion: Prophylactic treatment with verubecestat resulted in attenuated amyloid plaque deposition when treatment was initiated prior to significant pathology in 5XFAD mice. At the same dose range effective at attenuating Aß levels, verubecestat produced side effects in the absence of improvements in cognitive function. Taken together these data demonstrate the rigorous translational approaches of the MODEL-AD PTC for interrogating potential therapeutics and provide insight into the limitations of verubecestat as a prophylactic intervention for early-stage AD.

Rationale and design of a randomized controlled clinical trial; Titration of Oxygen Levels (TOOL) during mechanical ventilation.

BACKGROUND: Both hyperoxemia and hypoxemia are deleterious in critically ill patients. Targeted oxygenation is recommended to prevent both of these extremes, however this has not translated to the bedside. Hyperoxemia likely persists more than hypoxemia due to absence of immediate discernible adverse effects, cognitive biases and delay in prioritization of titration. METHODS: We present the methodology for the Titration Of Oxygen Levels (TOOL) trial, an open label, randomized controlled trial of an algorithm-based FiO2 titration with electronic medical record-based automated alerts. We hypothesize that the study intervention will achieve targeted oxygenation by curbing episodes of hyperoxemia while preventing hypoxemia. In the intervention arm, electronic alerts will be used to titrate FiO2 if SpO2 is ≥94% with FiO2 levels ≥0.4 over 45 min. FiO2 will be titrated per standard practice in the control arm. This study is being carried out with deferred consent. The sample size to determine efficacy is 316 subjects, randomized in a 1:1 ratio to the intervention vs. control arm. The primary outcome is proportion of time during mechanical ventilation spent with FiO2 ≥ 0.4 and SpO2 ≥ 94%. We will also assess proportion of time during mechanical ventilation spent with SpO2 < 88%, duration of mechanical ventilation, length of ICU and hospital stay, hospital mortality, and adherence to electronic alerts as secondary outcomes. CONCLUSION: This study is designed to evaluate the efficacy of a high fidelity, bioinformatics-based, electronic medical record derived electronic alert system to improve targeted oxygenation in mechanically ventilated patients by reducing excessive FiO2 exposure.

Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data.

MOTIVATION: With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterization of a sample. The spatially resolved nature of this method lends itself well to histological profiling of complex biological specimens. However, current software can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. RESULTS: To overcome these limitations, we have developed Photizo-an open-source Python library enabling high-throughput spectral data pre-processing, visualization and downstream analysis, including principal component analysis, clustering, macromolecular quantification and mapping. Photizo can be used for analysis of data without a spatial component, as well as spatially resolved data, obtained e.g. by scanning mode IR microspectroscopy and IR imaging by focal plane array detector. AVAILABILITY AND IMPLEMENTATION: The code underlying this article is available at https://github.com/DendrouLab/Photizo with access to example data available at https://zenodo.org/record/6417982#.Yk2O9TfMI6A.

Cost and Capability Compromises in STEM Instrumentation for Low-Voltage Imaging.

Low-voltage transmission electron microscopy (≤80 kV) has many applications in imaging beam-sensitive samples, such as metallic nanoparticles, which may become damaged at higher voltages. To improve resolution, spherical aberration can be corrected for in a scanning transmission electron microscope (STEM); however, chromatic aberration may then dominate, limiting the ultimate resolution of the microscope. Using image simulations, we examine how a chromatic aberration corrector, different objective lenses, and different beam energy spreads each affect the image quality of a gold nanoparticle imaged at low voltages in a spherical aberration-corrected STEM. A quantitative analysis of the simulated examples can inform the choice of instrumentation for low-voltage imaging. We here demonstrate a methodology whereby the optimum energy spread to operate a specific STEM can be deduced. This methodology can then be adapted to the specific sample and instrument of the reader, enabling them to make an informed economical choice as to what would be most beneficial for their STEM in the cost-conscious landscape of scientific infrastructure.

Effects of Elevated Temperature on the Susceptibility of Capsicum Plants to Capsicum Chlorosis Virus Infection.

Capsicum, an important vegetable crop in Queensland, Australia, is vulnerable to both elevated temperatures and capsicum chlorosis virus (CaCV). Thus, it is imperative to understand the genetic responses of capsicum plants (Capsicum annuum) to CaCV under elevated temperature conditions. Here, we challenged susceptible plants (cv. Yolo Wonder) with CaCV and investigated the effects of elevated temperature on symptom expression, the accumulation of virus-derived short interfering RNA (vsiRNA) and viral RNA, and the expression of plant defense-associated genes. CaCV-inoculated plants initially showed more severe symptoms and higher viral concentrations at a higher temperature (HT, 35 °C) than at ambient temperature (AT, 25 °C). However, symptom recovery and reduced viral RNA accumulation were seen in the CaCV-infected plants grown at HT at later stages of infection. We also observed that HT enhanced the accumulation of vsiRNAs and that, concurrently, RNA interference (RNAi)-related genes, including Dicer-like2 (DCL2), DCL4, RNA-dependent RNA polymerase 1 (RdRp1), RdRp6, and Argonaute2 (AGO2), were upregulated early during infection. Moreover, continuous high levels of vsiRNAs were observed during later stages of CaCV infection at HT. Overall, our investigation suggests that HT facilitates CaCV replication during early infection stages. However, this appears to lead to an early onset of antiviral RNA silencing, resulting in a subsequent recovery from CaCV in systemic leaves.

Ferroelectric incommensurate spin crystals.

Ferroics, especially ferromagnets, can form complex topological spin structures such as vortices1 and skyrmions2,3 when subjected to particular electrical and mechanical boundary conditions. Simple vortex-like, electric-dipole-based topological structures have been observed in dedicated ferroelectric systems, especially ferroelectric-insulator superlattices such as PbTiO3/SrTiO3, which was later shown to be a model system owing to its high depolarizing field4-8. To date, the electric dipole equivalent of ordered magnetic spin lattices driven by the Dzyaloshinskii-Moriya interaction (DMi)9,10 has not been experimentally observed. Here we examine a domain structure in a single PbTiO3 epitaxial layer sandwiched between SrRuO3 electrodes. We observe periodic clockwise and anticlockwise ferroelectric vortices that are modulated by a second ordering along their toroidal core. The resulting topology, supported by calculations, is a labyrinth-like pattern with two orthogonal periodic modulations that form an incommensurate polar crystal that provides a ferroelectric analogue to the recently discovered incommensurate spin crystals in ferromagnetic materials11-13. These findings further blur the border between emergent ferromagnetic and ferroelectric topologies, clearing the way for experimental realization of further electric counterparts of magnetic DMi-driven phases.