Multi-modal microscopy imaging with the OpenFlexure Delta Stage.

Microscopes are vital pieces of equipment in much of biological research and medical diagnostics. However, access to a microscope can represent a bottleneck in research, especially in lower-income countries. 'Smart' computer controlled motorized microscopes, which can perform automated routines or acquire images in a range of modalities are even more expensive and inaccessible. Developing low-cost, open-source, smart microscopes enables more researchers to conceive and execute optimized or more complex experiments. Here we present the OpenFlexure Delta Stage, a 3D-printed microscope designed for researchers. Powered by the OpenFlexure software stack, it is capable of performing automated experiments. The design files and assembly instructions are freely available under an open licence. Its intuitive and modular design-along with detailed documentation-allows researchers to implement a variety of imaging modes with ease. The versatility of this microscope is demonstrated by imaging biological and non-biological samples (red blood cells with Plasmodium parasites and colloidal particles in brightfield, epi-fluorescence, darkfield, Rheinberg and differential phase contrast. We present the design strategy and choice of tools to develop devices accessible to researchers from lower-income countries, as well as the advantages of an open-source project in this context. This microscope, having been open-source since its conception, has already been built and tested by researchers around the world, promoting a community of expertise and an environment of reproducibility in science.

Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope.

The OpenFlexure Microscope is a 3D-printed, low-cost microscope capable of automated image acquisition through the use of a motorised translation stage and a Raspberry Pi imaging system. This automation has applications in research and healthcare, including in supporting the diagnosis of malaria in low-resource settings. The plasmodium parasites that cause malaria require high magnification imaging, which has a shallow depth of field, necessitating the development of an accurate and precise autofocus procedure. We present methods of identifying the focal plane of the microscope, and procedures for reliably acquiring a stack of focused images on a system affected by backlash and drift. We also present and assess a method to verify the success of autofocus during the scan. The speed, reliability and precision of each method are evaluated, and the limitations discussed in terms of the end users' requirements.

A low-dose rituximab regimen for first-line treatment of acquired haemophilia A.

A low-dose rituximab regimen for first-line treatment of acquired haemophilia A. INTRODUCTION: Acquired haemophilia A (AHA) is a rare disease caused by the development of autoantibodies against FVIII. Diagnosis involves confirmation of FVIII deficiency and the presence of an inhibitor via the Bethesda assay. Severe bleeding is often managed with bypassing agents such as recombinant factor VII. This is then followed by eradication of the inhibitor with immunosuppression which typically includes a corticosteroid backbone. AIM: Review the current management and outcomes of AHA in Queensland, Australia. Determine the incidence, demographics and clinical characteristics of AHA patients. METHODS: Retrospective case series of AHA diagnosed between May 2014 and August 2018. Data were derived from the Australian Bleeding Disorders Registry and state-wide pathology database. Data collection proforma was completed by the treating haematologist and reviewed/compiled centrally. RESULTS: 24 patients were identified (incidence 1 in 1.27 million). The median age was 76.5 years. Median follow-up was 20 months. Index bleed was atraumatic and skin/soft tissue in the majority of patients. Recombinant FVIIa was the most commonly used haemostatic therapy and effective in 85% of patients. Immunosuppression and steroid usage were uniform. Upfront second agent was used in 75% of patients and was most commonly rituximab. 87.5% of patients achieved a complete remission in a median time of 48 days. Low-dose rituximab was frequently used and equally as efficacious as standard dose. CONCLUSION: Immunosuppression with combination therapy, notably rituximab, appears to be non-inferior and has a favourable side effect profile.

Loss of TaIRX9b gene function in wheat decreases chain length and amount of arabinoxylan in grain but increases cross-linking.

Wheat contains abundant xylan in cell walls of all tissues, but in endosperm, there is an unusual form of xylan substituted only by arabinose (arabinoxylan; AX) that has long chains and low levels of feruloylation, a fraction of which is extractable in water (WE-AX). WE-AX acts as soluble dietary fibre but also gives rise to viscous extracts from grain, a detrimental trait for some non-food uses of wheat. Here, we show that a glycosyl transferase family 43 wheat gene abundantly expressed in endosperm complements the Arabidopsis irx9 mutant and so name the three homoeologous genes TaIRX9b. We generated wheat lines with a constitutive knockout of TaIRX9b by stacking loss-of-function alleles for these homeologues from a mutagenized hexaploid wheat population resulting in decreases in grain extract viscosity of 50%-80%. The amount and chain length of WE-AX molecules from grain of these triple-stack lines was decreased accounting for the changes in extract viscosity. Imaging of immature wheat grain sections of triple-stacks showed abolition of immunolabelling in endosperm with LM11 antibody that recognizes epitopes in AX, but also showed apparently normal cell size and shape in all cell types, including endosperm. We identified differentially expressed genes from endosperm of triple-stacks suggesting that compensatory changes occur to maintain this endosperm cell wall integrity. Consistent with this, we observed increased ferulate dimerization and increased cross-linking of WE-AX molecules in triple-stacks. These novel wheat lines lacking functional TaIRX9b therefore provide insight into control of wheat endosperm cell walls.

Pembrolizumab-induced thrombotic thrombocytopenic purpura.

INTRODUCTION: Pembrolizumab is a humanised monoclonal antibody targeting the receptor programmed cell death protein-1 (PD-1), with anti-tumour activity demonstrated for many malignancies. Such immune checkpoint inhibitors are associated with many immune-related adverse events including rash, colitis, hepatitis, pneumonitis, endocrinopathy and, rarely, haematological adverse events, including immune-related thrombocytopenia. CASE REPORT: We report a 60-year-old female with metastatic non-small cell lung cancer treated with pembrolizumab every three weeks. Following her fifth cycle, she presented to our hospital with community-acquired pneumonia. Thrombocytopenia developed the next day and, after detailed investigations, thrombotic thrombocytopenic purpura was diagnosed. MANAGEMENT AND OUTCOME: Pembrolizumab was immediately ceased and plasma exchange commenced along with IV methylprednisolone 250 mg daily for three days followed by oral prednisolone. After five days of plasma exchange, platelet counts normalised and haemolytic anaemia resolved. DISCUSSION: Acquired thrombotic thrombocytopenic purpura is an autoimmune disorder caused by an inhibitory autoantibody against ADAMTS-13. While most cases of acquired thrombotic thrombocytopenic purpura are idiopathic, certain conditions (e.g. bacterial infection, autoimmune disorders, malignancies) and medications are associated with thrombotic thrombocytopenic purpura. Other potential causes were eliminated in our patient. As acquired thrombotic thrombocytopenic purpura is an autoimmune disorder, pembrolizumab, given its unique mechanism of action and association with immune-related adverse events, is believed to be implicated in the development of thrombotic thrombocytopenic purpura. This case is one of only two linking anti-PD-1 therapy to thrombotic thrombocytopenic purpura development (the other occurring in a patient on nivolumab plus ipilimumab). Thrombotic thrombocytopenic purpura is life-threatening and clinicians are advised to be aware of its possible occurrence in immune checkpoint inhibitor-treated patients.

Using old laboratory equipment with modern Web-of-Things standards: a smart laboratory with LabThings Retro.

There has been an increasing, and welcome, open hardware trend towards science teams building and sharing their designs for new instruments. These devices, often built upon low-cost microprocessors and microcontrollers, can be readily connected to enable complex, automated and smart experiments. When designed to use open communication web standards, devices from different laboratories and manufacturers can be controlled using a single protocol and even communicate with each other. However, science labs still have a majority of old, perfectly functional equipment which tends to use older, and sometimes proprietary, standards for communications. In order to encourage the continued and integrated use of this equipment in modern automated experiments, we develop and demonstrate LabThings Retro. This allows us to retrofit old instruments to use modern Web-of-Things standards, which we demonstrate with closed-loop feedback involving an optical microscope, digital imaging and fluid pumping.

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications.

The number of samples in biological experiments is continuously increasing, but complex protocols and human error in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments, and due to the lack of open application programming interfaces (APIs), they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, automated, high-throughput experiments are demonstrated for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools OpenFlexure, Opentrons, ImJoy, and UC2. This automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on the analysis of previously acquired images, enables the realization of fully autonomous "smart" microscopy experiments. All documents and source files are publicly available to prove the concept of smart lab automation using inexpensive, open tools. It is believed this democratizes access to the power and repeatability of automated experiments.

Case study of thrombosis and thrombocytopenia syndrome following administration of the AstraZeneca COVID-19 vaccine.

Cerebral venous sinus thrombosis is a complication of the ChAdOx1 nCoV-19 vaccine that should elicit a high index of suspicion when patients present with persistent headache post vaccination.

Simplifying the OpenFlexure microscope software with the web of things.

We present the OpenFlexure Microscope software stack which provides computer control of our open source motorised microscope. Our diverse community of users needs both graphical and script-based interfaces. We split the control code into client and server applications interfaced via a web API conforming to the W3C Web of Things standard. A graphical interface is viewed either in a web browser or in our cross-platform Electron application, and gives basic interactive control including common operations such as Z stack acquisition and tiled scanning. Automated control is possible from Python and Matlab, or any language that supports HTTP requests. Network control makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment. Graphical and script-based clients can run simultaneously, making it easier to monitor ongoing experiments. We have included an extension mechanism to add functionality, for example controlling additional hardware components or adding automation routines. Using a Web of Things approach has resulted in a user-friendly and extremely versatile software control solution for the OpenFlexure Microscope, and we believe this approach could be generalized in the future to make automated experiments involving several instruments much easier to implement.

Concurrent lipidomics and proteomics on malignant plasma cells from multiple myeloma patients: Probing the lipid metabolome.

BACKGROUND: Multiple myeloma (MM) is a hematological malignancy characterized by the clonal expansion of malignant plasma cells. Though durable remissions are possible, MM is considered incurable, with relapse occurring in almost all patients. There has been limited data reported on the lipid metabolism changes in plasma cells during MM progression. Here, we evaluated the feasibility of concurrent lipidomics and proteomics analyses from patient plasma cells, and report these data on a limited number of patient samples, demonstrating the feasibility of the method, and establishing hypotheses to be evaluated in the future. METHODS: Plasma cells were purified from fresh bone marrow aspirates using CD138 microbeads. Proteins and lipids were extracted using a bi-phasic solvent system with methanol, methyl tert-butyl ether, and water. Untargeted proteomics, untargeted and targeted lipidomics were performed on 7 patient samples using liquid chromatography-mass spectrometry. Two comparisons were conducted: high versus low risk; relapse versus newly diagnosed. Proteins and pathways enriched in the relapsed group was compared to a public transcriptomic dataset from Multiple Myeloma Research Consortium reference collection (n = 222) at gene and pathways level. RESULTS: From one million purified plasma cells, we were able to extract material and complete untargeted (~6000 and ~3600 features in positive and negative mode respectively) and targeted lipidomics (313 lipids), as well as untargeted proteomics analysis (~4100 reviewed proteins). Comparative analyses revealed limited differences between high and low risk groups (according to the standard clinical criteria), hence we focused on drawing comparisons between the relapsed and newly diagnosed patients. Untargeted and targeted lipidomics indicated significant down-regulation of phosphatidylcholines (PCs) in relapsed MM. Although there was limited overlap of the differential proteins/transcripts, 76 significantly enriched pathways in relapsed MM were common between proteomics and transcriptomics data. Further evaluation of transcriptomics data for lipid metabolism network revealed enriched correlation of PC, ceramide, cardiolipin, arachidonic acid and cholesterol metabolism pathways to be exclusively correlated among relapsed but not in newly-diagnosed patients. CONCLUSIONS: This study establishes the feasibility and workflow to conduct integrated lipidomics and proteomics analyses on patient-derived plasma cells. Potential lipid metabolism changes associated with MM relapse warrant further investigation.

Robotic microscopy for everyone: the OpenFlexure microscope.

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi- illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.

Atomic dispensers for thermoplasmonic control of alkali vapor pressure in quantum optical applications.

Alkali metal vapors enable access to single electron systems, suitable for demonstrating fundamental light-matter interactions and promising for quantum logic operations, storage and sensing. However, progress is hampered by the need for robust and repeatable control over the atomic vapor density and over the associated optical depth. Until now, a moderate improvement of the optical depth was attainable through bulk heating or laser desorption - both time-consuming techniques. Here, we use plasmonic nanoparticles to convert light into localized thermal energy and to achieve optical depths in warm vapors, corresponding to a ~16 times increase in vapor pressure in less than 20 ms, with possible reload times much shorter than an hour. Our results enable robust and compact light-matter devices, such as efficient quantum memories and photon-photon logic gates, in which strong optical nonlinearities are crucial.

Second-Harmonic Generation Optical Rotation Solely Attributable to Chirality in Plasmonic Metasurfaces.

Chiral plasmonic nanostructures, those lacking mirror symmetry, can be designed to manipulate the polarization of incident light resulting in chiroptical (chiral optical) effects such as circular dichroism (CD) and optical rotation (OR). Due to high symmetry sensitivity, corresponding effects in second-harmonic generation (SHG-CD and SHG-OR) are typically much stronger in comparison. These nonlinear effects have long been used for chiral molecular analysis and characterization; however both linear and nonlinear optical rotation can occur even in achiral structures, if the structure is birefringent due to anisotropy. Crucially, chiroptical effects resulting from anisotropy typically exhibit a strong dependence on structural orientation. Here we report a large second-harmonic generation optical rotation of ±45°, due to intrinsic chirality in a highly anisotropic helical metamaterial. The SHG intensity is found to strongly relate to the structural anisotropy; however, the angle of SHG-OR is invariant under sample rotation. We show that by tuning the geometry of anisotropic nanostructures, the interaction between anisotropy, chirality, and experimental geometry can allow even greater control over the chiroptical properties of plasmonic metamaterials.

Successful use of oseltamivir prophylaxis in managing a nosocomial outbreak of influenza A in a hematology and allogeneic stem cell transplant unit.

AIM: To describe a nosocomial outbreak of H1N1 influenza A in an inpatient hematology and allogeneic stem cell transplant unit and outcomes of universal oseltamivir prophylaxis. METHODS: Medical records of all patients admitted to the unit were reviewed to define the nosocomial outbreak, commencing 1 week prior to the index case until 4 weeks following institution of oseltamivir prophylaxis. Timelines for clinical symptoms, viral spread, management, patient outcomes and follow up testing were constructed. All cases of influenza were confirmed on nasopharyngeal swabs and/or bronchoalveolar lavages collected for polymerase chain reaction testing. RESULTS: In addition to the index case, further 11 patients were diagnosed with influenza A during the outbreak. Six patients (50%) had influenza-like-illness, five (42%) had respiratory symptoms only and one (8%) was asymptomatic. In total, five patients died, including four (33%) patients who were admitted to intensive care. A clustering of seven cases led to recognition of the outbreak and subsequent commencement of universal prophylaxis with oseltamivir 75 mg/day in all inpatients within the unit. Strict infection control processes were reinforced concurrently. There were no further cases of influenza A linked to the outbreak after the implementation of universal oseltamivir prophylaxis. Three later cases were linked to H1N1 exposure during the original outbreak. CONCLUSION: H1N1 influenza infection is associated with significant mortality in hematology patients. Universal prophylaxis with oseltamivir during a nosocomial outbreak appeared to be effective in controlling spread of the virus. We recommend early institution of infection control and universal prophylaxis in any nosocomial outbreak of influenza.

Strong Rotational Anisotropies Affect Nonlinear Chiral Metamaterials.

Masked by rotational anisotropies, xthe nonlinear chiroptical response of a metamaterial is initially completely inaccessible. Upon rotating the sample the chiral information emerges. These results highlight the need for a general method to extract the true chiral contributions to the nonlinear optical signal, which would be hugely valuable in the present context of increasingly complex chiral meta/nanomaterials.

Caloric restriction and cardiovascular aging in cynomolgus monkeys (Macaca fascicularis): metabolic, physiologic, and atherosclerotic measures from a 4-year intervention trial.

Caloric restriction (CR) retards aging processes, extends maximal life span, and consistently improves insulin resistance in lower species. Insulin resistance is associated with cardiovascular disease, but data is lacking demonstrating that increased insulin sensitivity reduces atherosclerosis progression. We initiated a study in 32 adult cynomolgus monkeys to evaluate increased insulin sensitivity secondary to CR on atherosclerosis extent. Following pretrial determinations, animals were randomized to a moderately atherogenic (0.25 mg cholesterol/Cal containing 30% of calories from fat)-fed control group or CR group (30% reduction) with equivalent dietary cholesterol intake. CR significantly improved insulin sensitivity and reduced intraabdominal fat over the 4-year intervention, while no significant differences were seen for the lipid profile between groups. Despite improved insulin sensitivity with CR, atherosclerosis extent did not differ between the ad libitum-fed or CR groups. These studies demonstrate that CR significantly improves insulin sensitivity, but when elevated plasma cholesterol concentrations were held similar, there was no effect on atherosclerosis extent. However, the composition of these lesions and changes in endothelial function may have been improved but were not evaluated in this study. Thus, further studies are needed to determine if improved insulin sensitivity might decrease arterial inflammation and improve endothelial function, despite no changes in atherosclerosis extent.

Rosiglitazone treatment improves insulin regulation and dyslipidemia in type 2 diabetic cynomolgus monkeys.

Impairment of peroxisome proliferator-activated receptor-gamma (PPAR-gamma), a nuclear receptor that regulates genes involved in lipid and glucose metabolism, may contribute to the onset of metabolic disorders such as diabetes and the accompanying dyslipidemia. Fat-derived tumor necrosis factor alpha (TNF-alpha) and the acute-phase response protein, C-reactive protein (CRP), may also have a role in the development of obesity-related insulin resistance and type 2 diabetes mellitus. In this study, a group of 14 naturally occurring, insulin-requiring, type 2 diabetic cynomolgus monkeys were used to evaluate the effects of the PPAR-gamma agonist, rosiglitazone, on glycemic and lipid parameters and serum levels of TNF-alpha and CRP. The animals were randomized into 2 groups of 7. One group was treated with 0.5 mg/kg rosiglitazone orally once a day for 7 weeks. Blood was collected for evaluation at baseline, at 2 and 7 weeks during the treatment period, and at 7 and 13 weeks after treatment. Daily insulin requirements were recorded during the entire study. Results showed daily exogenous insulin requirements were significantly reduced (P <.01) in those treated with rosiglitazone, while glycemic control was maintained. Plasma triglyceride concentrations were significantly lower (P <.01) whereas plasma cholesterol levels tended to be lower and high-density lipoprotein (HDL) concentrations tended to be higher after treatment. No significant differences were noted in TNF-alpha and CRP serum levels during the treatment period. Body weights remained steady in both groups during the study. These results suggest overall improvement in insulin regulation and lipid profiles during treatment with rosiglitazone.

Olopatadine 0.6% nasal spray protects from vasomotor challenge in patients with severe vasomotor rhinitis.

BACKGROUND: Vasomotor rhinitis (VMR) is a hypersensitivity syndrome with heightened reactivity to environmental triggers. METHODS: Twenty-two patients with severe VMR were treated nasally with either normal saline or 0.6% olopatadine and challenged nasally with a hyperosmolar mannitol solution. RESULTS: Treatment with 0.6% olopatadine resulted in an improvement in instantaneous nasal symptom scores at 5 and 30 minutes (p < 0.01) compared with baseline and at 30 minutes after hyperosmolar challenge compared with saline-pretreated individuals (p < 0.01). There was also an improvement in nasal peak inspiratory flow rate at 30 minutes after hyperosmolar challenge compared with saline-pretreated individuals (p < 0.01). CONCLUSION: In this patient population 0.6% olopatadine appears to be efficacious in symptom reduction in VMR and protects from hyperosmolar challenge.