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.

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.

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.

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.

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.

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.

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.

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.