Clinical validation of an open-access SARS-COV-2 antigen detection lateral flow assay, compared to commercially available assays.

Rapid tests for SARS-COV-2 infection are important tools for pandemic control, but current rapid tests are based on proprietary designs and reagents. We report clinical validation results of an open-access lateral flow assay (OA-LFA) design using commercially available materials and reagents, along with RT-qPCR and commercially available comparators (BinaxNOW® and Sofia®). Adult patients with suspected COVID-19 based on clinical signs and symptoms, and with symptoms ≤7 days duration, underwent anterior nares (AN) sampling for the OA-LFA, Sofia®, BinaxNOW ™, and RT-qPCR, along with nasopharyngeal (NP) RT-qPCR. Results indicate a positive predictive agreement with NP sampling as 69% (60% -78%) OA-LFA, 74% (64% - 82%) Sofia®, and 82% (73% - 88%) BinaxNOW™. The implication for these results is that we provide an open-access LFA design that meets the minimum WHO target product profile for a rapid test, that virtually any diagnostic manufacturer could produce.

Optical tracking and laser-induced mortality of insects during flight.

Addressing the need for novel insect observation and control tools, the Photonic Fence detects and tracks mosquitoes and other flying insects and can apply lethal doses of laser light to them. Previously, we determined lethal exposure levels for a variety of lasers and pulse conditions on anesthetized Anopheles stephensi mosquitoes. In this work, similar studies were performed while the subjects were freely flying within transparent cages two meters from the optical system; a proof-of-principle demonstration of a 30 m system was also performed. From the dose-response curves of mortality data created as a function of various beam diameter, pulse width, and power conditions at visible and near-infrared wavelengths, the visible wavelengths required significantly lower laser exposure than near infrared wavelengths to disable subjects, though near infrared sources remain attractive given their cost and retina safety. The flight behavior of the subjects and the performance of the tracking system were found to have no impact on the mortality outcomes for pulse durations up to 25 ms, which appears to be the ideal duration to minimize required laser power. The results of this study affirm the practicality of using optical approaches to protect people and crops from pestilent flying insects.

Decoy exosomes provide protection against bacterial toxins.

The production of pore-forming toxins that disrupt the plasma membrane of host cells is a common virulence strategy for bacterial pathogens such as methicillin-resistant Staphylococcus aureus (MRSA)1-3. It is unclear, however, whether host species possess innate immune mechanisms that can neutralize pore-forming toxins during infection. We previously showed that the autophagy protein ATG16L1 is necessary for protection against MRSA strains encoding α-toxin4-a pore-forming toxin that binds the metalloprotease ADAM10 on the surface of a broad range of target cells and tissues2,5,6. Autophagy typically involves the targeting of cytosolic material to the lysosome for degradation. Here we demonstrate that ATG16L1 and other ATG proteins mediate protection against α-toxin through the release of ADAM10 on exosomes-extracellular vesicles of endosomal origin. Bacterial DNA and CpG DNA induce the secretion of ADAM10-bearing exosomes from human cells as well as in mice. Transferred exosomes protect host cells in vitro by serving as scavengers that can bind multiple toxins, and improve the survival of mice infected with MRSA in vivo. These findings indicate that ATG proteins mediate a previously unknown form of defence in response to infection, facilitating the release of exosomes that serve as decoys for bacterially produced toxins.

Autophagy and microbial pathogenesis.

Autophagy is a cell biological process that promotes resilience in the face of environmental perturbations. Given that infectious agents represent a major type of environmental threat, it follows that the autophagy pathway is central to the outcome of host-microbe interactions. Detailed molecular studies have revealed intricate ways in which autophagy suppresses or enhances the fitness of infectious agents, particularly intracellular pathogens such as viruses that require the host cell machinery for replication. Findings in animal models have reinforced the importance of these events that occur within individual cells and have extended the role of autophagy to extracellular microbes and immunity at the whole organism level. These functions impact adaptation to bacteria that are part of the gut microbiota, which has implications for the etiology of chronic disorders such as inflammatory bowel disease. Despite major advances in how autophagy regulates inflammatory reactions toward microbes, many challenges remain, including distinguishing autophagy from closely related pathways such as LC3-associated phagocytosis. Here, we review the role of autophagy in microbial pathogenesis at the level of organismal biology. In addition to providing an overview of the prominent function of autophagy proteins in host-microbe interactions, we highlight how observations at the cellular level are informing pathogenesis studies and offer our perspective on the future directions of the field.

Evaluating Low-Cost Optical Spectrometers for the Detection of Simulated Substandard and Falsified Medicines.

Distribution of substandard and falsified (SF) medicines is on the rise, and its impact on public health, particularly in low-resource countries, is becoming increasingly significant. Portable, nondestructive screening devices can support regulatory authorities in their defense against the spread of SF medicines. Vibrational spectroscopy is an ideal candidate due to its sampling ease and speed. In this work, five portable, among which four are considered low-cost, spectroscopic devices based on near-infrared (NIR), Raman, and mid-infrared (MIR) were evaluated to quantify active pharmaceutical ingredients (APIs) and formulation accuracy within simulated authentic, falsified, and substandard medicines. Binary sample mixtures containing a typical API in antimalarial, antiretroviral, or anti-tuberculosis medicines were assessed. In both univariate and multivariate analyses, the API quantification performance of the digital light processing (DLP) NIR spectrometer and a handheld Raman device consistently matched or exceeded that of the other NIR spectrometers and a scientific grade MIR spectrometer. In the formulation accuracy tests, data from all devices, other than the silicon photodiode array NIR spectrometer, were able to create regression models with less than 6% error. From this exploratory study, we conclude that certain portable NIR devices hold significant promise as cost-effective screening tools for falsified and potentially substandard medicines, and they warrant further investigation and development.

DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling.

Although the majority of patients with acute myeloid leukemia (AML) initially respond to chemotherapy, many of them subsequently relapse, and the mechanistic basis for AML persistence following chemotherapy has not been determined. Recurrent somatic mutations in DNA methyltransferase 3A (DNMT3A), most frequently at arginine 882 (DNMT3AR882), have been observed in AML and in individuals with clonal hematopoiesis in the absence of leukemic transformation. Patients with DNMT3AR882 AML have an inferior outcome when treated with standard-dose daunorubicin-based induction chemotherapy, suggesting that DNMT3AR882 cells persist and drive relapse. We found that Dnmt3a mutations induced hematopoietic stem cell expansion, cooperated with mutations in the FMS-like tyrosine kinase 3 gene (Flt3ITD) and the nucleophosmin gene (Npm1c) to induce AML in vivo, and promoted resistance to anthracycline chemotherapy. In patients with AML, the presence of DNMT3AR882 mutations predicts minimal residual disease, underscoring their role in AML chemoresistance. DNMT3AR882 cells showed impaired nucleosome eviction and chromatin remodeling in response to anthracycline treatment, which resulted from attenuated recruitment of histone chaperone SPT-16 following anthracycline exposure. This defect led to an inability to sense and repair DNA torsional stress, which resulted in increased mutagenesis. Our findings identify a crucial role for DNMT3AR882 mutations in driving AML chemoresistance and highlight the importance of chromatin remodeling in response to cytotoxic chemotherapy.

Laser induced mortality of Anopheles stephensi mosquitoes.

Small, flying insects continue to pose great risks to both human health and agricultural production throughout the world, so there remains a compelling need to develop new vector and pest control approaches. Here, we examined the use of short (<25 ms) laser pulses to kill or disable anesthetized female Anopheles stephensi mosquitoes, which were chosen as a representative species. The mortality of mosquitoes exposed to laser pulses of various wavelength, power, pulse duration, and spot size combinations was assessed 24 hours after exposure. For otherwise comparable conditions, green and far-infrared wavelengths were found to be more effective than near- and mid-infrared wavelengths. Pulses with larger laser spot sizes required lower lethal energy densities, or fluence, but more pulse energy than for smaller spot sizes with greater fluence. Pulse duration had to be reduced by several orders of magnitude to significantly lower the lethal pulse energy or fluence required. These results identified the most promising candidates for the lethal laser component in a system being designed to identify, track, and shoot down flying insects in the wild.

Loss of BAP1 function leads to EZH2-dependent transformation.

The tumor suppressors BAP1 and ASXL1 interact to form a polycomb deubiquitinase complex that removes monoubiquitin from histone H2A lysine 119 (H2AK119Ub). However, BAP1 and ASXL1 are mutated in distinct cancer types, consistent with independent roles in regulating epigenetic state and malignant transformation. Here we demonstrate that Bap1 loss in mice results in increased trimethylated histone H3 lysine 27 (H3K27me3), elevated enhancer of zeste 2 polycomb repressive complex 2 subunit (Ezh2) expression, and enhanced repression of polycomb repressive complex 2 (PRC2) targets. These findings contrast with the reduction in H3K27me3 levels seen with Asxl1 loss. Conditional deletion of Bap1 and Ezh2 in vivo abrogates the myeloid progenitor expansion induced by Bap1 loss alone. Loss of BAP1 results in a marked decrease in H4K20 monomethylation (H4K20me1). Consistent with a role for H4K20me1 in the transcriptional regulation of EZH2, expression of SETD8-the H4K20me1 methyltransferase-reduces EZH2 expression and abrogates the proliferation of BAP1-mutant cells. Furthermore, mesothelioma cells that lack BAP1 are sensitive to EZH2 pharmacologic inhibition, suggesting a novel therapeutic approach for BAP1-mutant malignancies.

CHZ868, a Type II JAK2 Inhibitor, Reverses Type I JAK Inhibitor Persistence and Demonstrates Efficacy in Myeloproliferative Neoplasms.

Although clinically tested JAK inhibitors reduce splenomegaly and systemic symptoms, molecular responses are not observed in most myeloproliferative neoplasm (MPN) patients. We previously demonstrated that MPN cells become persistent to type I JAK inhibitors that bind the active conformation of JAK2. We investigated whether CHZ868, a type II JAK inhibitor, would demonstrate activity in JAK inhibitor persistent cells, murine MPN models, and MPN patient samples. JAK2 and MPL mutant cell lines were sensitive to CHZ868, including type I JAK inhibitor persistent cells. CHZ868 showed significant activity in murine MPN models and induced reductions in mutant allele burden not observed with type I JAK inhibitors. These data demonstrate that type II JAK inhibition is a viable therapeutic approach for MPN patients.

Human mesenchymal stromal cells attenuate graft-versus-host disease and maintain graft-versus-leukemia activity following experimental allogeneic bone marrow transplantation.

We sought to define the effects and underlying mechanisms of human, marrow-derived mesenchymal stromal cells (hMSCs) on graft-versus-host disease (GvHD) and graft-versus-leukemia (GvL) activity. Irradiated B6D2F1 mice given C57BL/6 BM and splenic T cells and treated with hMSCs had reduced systemic GvHD, donor T-cell expansion, and serum TNFα and IFNγ levels. Bioluminescence imaging demonstrated that hMSCs redistributed from lungs to abdominal organs within 72 hours, and target tissues harvested from hMSC-treated allogeneic BMT (alloBMT) mice had less GvHD than untreated controls. Cryoimaging more precisely revealed that hMSCs preferentially distributed to splenic marginal zones and regulated T-cell expansion in the white pulp. Importantly, hMSCs had no effect on in vitro cytotoxic T-cell activity and preserved potent GvL effects in vivo. Mixed leukocyte cultures containing hMSCs exhibited decreased T-cell proliferation, reduced TNFα, IFNγ, and IL-10 but increased PGE2 levels. Indomethacin and E-prostanoid 2 (EP2) receptor antagonisms both reversed while EP2 agonism restored hMSC-mediated in vitro T-cell suppression, confirming the role for PGE2 . Furthermore, cyclo-oxygenase inhibition following alloBMT abrogated the protective effects of hMSCs. Together, our data show that hMSCs preserve GvL activity and attenuate GvHD and reveal that hMSC biodistribute to secondary lymphoid organs wherein they attenuate alloreactive T-cell proliferation likely through PGE2 induction.

Genetic studies reveal an unexpected negative regulatory role for Jak2 in thrombopoiesis.

JAK inhibitor treatment is limited by the variable development of anemia and thrombocytopenia thought to be due to on-target JAK2 inhibition. We evaluated the impact of Jak2 deletion in platelets (PLTs) and megakaryocytes (MKs) on blood counts, stem/progenitor cells, and Jak-Stat signaling. Pf4-Cre-mediated Jak2 deletion in PLTs and MKs did not compromise PLT formation but caused thrombocytosis, and resulted in expansion of MK progenitors and Lin(-)Sca1(+)Kit+ cells. Serum thrombopoietin (TPO) was maintained at normal levels in Pf4-Cre-positive Jak2(f/f) mice, consistent with reduced internalization/turnover by Jak2-deficient PLTs. These data demonstrate that Jak2 in terminal megakaryopoiesis is not required for PLT production, and that Jak2 loss in PLTs and MKs results in non-autonomous expansion of stem/progenitors and of MKs and PLTs via dysregulated TPO turnover. This suggests that the thrombocytopenia frequently seen with JAK inhibitor treatment is not due to JAK2 inhibition in PLTs and MKs, but rather due to JAK2 inhibition in stem/progenitor cells.

Vocoder simulations of highly focused cochlear stimulation with limited dynamic range and discriminable steps.

OBJECTIVES: There is recent interest in focused stimulation of the cochlea via modalities such as tripolar electrical and infrared neural stimulation to improve speech in noise comprehension and music perception. The purpose of this work was to use vocoder-based simulations to investigate speech recognition for broad stimulation (standard monopolar paradigm) versus more focused stimulation under a variety of signal-to-noise ratios, dynamic ranges, and numbers of discriminable loudness steps. DESIGN: Vocoder simulations were used to assess the intelligibility of sentences, consonants, and vowels that were noise vocoded and presented to 7 normal-hearing listeners for identification. A novel aspect of the simulations presented here was the use of nonuniform quantization steps within the dynamic range to more closely simulate the Weber functions observed in cochlear implant users. Intelligibility was assessed for the different filter slopes under a variety of signal-to-noise ratio levels, dynamic ranges, and numbers of discriminable steps. RESULTS: Speech processed via vocoder simulations representing focused stimulation was found to be substantially more intelligible than speech processed via a monopolar electric vocoder simulation, with differences of up to 60 percentage points. There were no significant differences, however, seen between the two focused approaches (signal attenuations of 10 and 17 dB/mm) for the conditions investigated. Speech processed via the highly focused vocoder (17 dB/mm) was robust to constraints on small envelope dynamic range and small number of discriminable steps within the dynamic range, as high performance was maintained with at least a 5 dB dynamic range and eight or more discriminable steps. Significant drops in intelligibility were noted when the number of steps fell below eight. CONCLUSIONS: Highly focused stimulation-tripolar electrical and infrared neural stimulation-has potential for increased performance in noise compared with monopolar stimulation, but much work remains to bear this potential out and to take full advantage of each modality's strengths.

Analytical approaches for determining heat distributions and thermal criteria for infrared neural stimulation.

Infrared neural stimulation (INS) is becoming an important complementary tool to electrical stimulation. Since the mechanism of INS is photothermal, describing the laser-induced heat distribution is fundamental to determining the relationship between stimulation pulses and neural responses. This work developed both a framework describing the time evolution of the heat distribution induced by optical fluence and a new method to extract thermal criteria (e.g., temperature change and rate of change) for neural activation. To solve the general problem of describing the temperature distribution, a Green's function solution to the heat diffusion equation was determined and convolved with the optical fluence. This provided a solution in the form of a single integral over time, from which closed-form solutions can be determined for special cases. This work also yielded an expression for thermal relaxation time, which provides a rigorous description of thermal confinement for INS. The developed framework was then applied to experimental data from the cochlea to extract the minimum temperature increase and rate of that increase to stimulate the cochlear spiral ganglion. This result, and similar analyses applied to other neural systems, can then shed light on the fundamental mechanism for INS and aid the development of optical neuroprostheses.

Development of a spatially offset Raman spectroscopy probe for breast tumor surgical margin evaluation.

The risk of local recurrence for breast cancers is strongly correlated with the presence of a tumor within 1 to 2 mm of the surgical margin on the excised specimen. Previous experimental and theoretical results suggest that spatially offset Raman spectroscopy (SORS) holds much promise for intraoperative margin analysis. Based on simulation predictions for signal-to-noise ratio differences among varying spatial offsets, a SORS probe with multiple source-detector offsets was designed and tested. It was then employed to acquire spectra from 35 frozen-thawed breast tissue samples in vitro. Spectra from each detector ring were averaged to create a composite spectrum with biochemical information covering the entire range from the tissue surface to ∼2 mm below the surface, and a probabilistic classification scheme was used to classify these composite spectra as "negative" or "positive" margins. This discrimination was performed with 95% sensitivity and 100% specificity, or with 100% positive predictive value and 94% negative predictive value.

Effect of normal variations on disease classification of Raman spectra from cervical tissue.

In this paper, we examine how variations in normal tissue can influence disease classification of Raman spectra. Raman spectra from normal areas may be affected by previous disease or proximity to areas of dysplasia. Spectra were acquired in vivo from 172 patients and classified into five tissue categories: true normal (no history of disease), previous disease normal (history of disease, current normal diagnosis), adjacent normal (disease on cervix, spectra acquired from visually normal area), low grade, and high grade. Taking into account the various "normal" states of the tissue before statistical analysis led to a disease classification accuracy of 97%. These results indicate that abnormal changes significantly affect Raman spectra, even when areas are histopathologically normal. The sensitivity of Raman spectroscopy to subtle biochemical differences must be considered in order to successfully implement it in a clinical setting for diagnosing cervical dysplasia and cancer.

Monte Carlo model of spatially offset Raman spectroscopy for breast tumor margin analysis.

We have previously demonstrated the discrimination of two layers of soft tissue, specifically normal breast tissue overlying breast tumor, using spatially offset Raman spectroscopy (SORS). In this report, a Monte Carlo code for evaluating SORS in soft tissues has been developed and compared to experimental results. The model was employed to investigate the effects of tissue and probe geometry on SORS measurements and therefore to develop the design strategies of applying SORS for breast tumor surgical margin evaluation. The model was used to predict SORS signals for different tissue geometries difficult to precisely control experimentally, such as varying normal and tumor layer sizes and the addition of a third layer. The results from the model suggest that, using source-detector separations of up to 3.75 mm, SORS can detect sub-millimeter-thick tumors under a 1 mm normal layer, and tumors at least 1 mm thick can be detected under a 2 mm normal layer.

Autofluorescence and diffuse reflectance spectroscopy and spectral imaging for breast surgical margin analysis.

BACKGROUND AND OBJECTIVE: Most women with early stage breast cancer have the option of breast conserving therapy, which involves a partial mastectomy for removal of the primary tumor, usually followed by radiotherapy. The presence of tumor at or near the margin is strongly correlated with the risk of local tumor recurrence, so there is a need for a non-invasive, real-time tool to evaluate margin status. This study examined the use of autofluorescence and diffuse reflectance spectroscopy and spectral imaging to evaluate margin status intraoperatively. MATERIALS AND METHODS: Spectral measurements were taken from the surface of the tissue mass immediately following removal during partial mastectomies and/or from tissues immediately after sectioning by surgical pathology. A total of 145 normal spectra were obtained from 28 patients, and 34 tumor spectra were obtained from 12 patients. RESULTS: After correlation with histopathology, a multivariate statistical algorithm classified the spectra as normal (negative margins) or tumor (positive margins) with 85% sensitivity and 96% specificity. A separate algorithm achieved 100% classification between neo-adjuvant chemotherapy-treated tissues and non-treated tissues. Fluorescence and reflectance-based spectral images were able to demarcate a calcified lesion on the surface of a resected specimen as well. CONCLUSION: Fluorescence and reflectance spectroscopy could be a valuable tool for examining the superficial margin status of excised breast tumor specimens, particularly in the form of spectral imaging to examine entire margins in a single acquisition.

Spatially offset Raman spectroscopy of layered soft tissues.

Raman spectroscopy has been widely used for cancer diagnosis, but conventional forms provide limited depth information. Spatially offset Raman spectroscopy (SORS) can solve the depth issue, but it has only been used to detect hard tissues such as bone. We explore the feasibility of using SORS to discriminate two layers of soft tissue. Measurements were taken with individual source and detector fibers at a number of spatial offsets from samples consisting of various thicknesses of normal human breast tissues overlying breast tumors. Results show that SORS can detect tumors beneath normal tissue, marking, to the best of our knowledge, the first application of SORS for discriminating two layers of soft tissue.