Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning.

Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers' access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses.

GuPPy, a Python toolbox for the analysis of fiber photometry data.

Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for new users, especially those with a limited programming background. Here, we present Guided Photometry Analysis in Python (GuPPy), a free and open-source FP analysis tool. GuPPy is designed to operate across computing platforms and can accept data from a variety of FP data acquisition systems. The program presents users with a set of graphic user interfaces (GUIs) to load data and provide input parameters. Graphs are produced that can be easily exported for integration into scientific figures. As an open-source tool, GuPPy can be modified by users with knowledge of Python to fit their specific needs.

Feasibility of Photo-Optical Transcutaneous Oxygen Tension Measurement During Revascularization of the Lower Extremity.

OBJECTIVES: A novel approach in the evaluation of peripheral arterial disease is the photo-optical oxygen tension measurement (pTCpO2). This modality is suggested to be more practical in use in comparison to standard electro-chemical oxygen tension measurement. Hence, pTCpO2 might be of added value to evaluate revascularization of the lower extremities peri-procedural. We conducted a preliminary feasibility study to analyze the potential of pTCpO2 during revascularization. METHODS: Ten patients scheduled for revascularization of the lower extremities were enrolled. pTCpO2 values of the affected lower extremity were measured pre-operatively, during revascularization and after revascularization. Results were compared to the pre- and postoperative ankle-brachial index (ABI) and to perioperative angiography. Primary endpoint was the feasibility of perioperative pTCpO2 measurement. Secondary endpoints were concordance between pTCpO2, ABI, angiography and clinical outcome. RESULTS: Two out of twelve measurements were unsuccessful. Eight out of ten patients experienced significant clinical improvement and pTCpO2 increase. Two patients that did not experience clinical improvement corresponded with no changes in intraoperative angiography and without increase in ABI or pTCpO2. A significant and strong correlation was found between prior and after revascularization ABI and pTCpO2 measurements (r = 0.82 P = 0.04). CONCLUSIONS: Photo-optical transcutaneous oxygen tension measurement may serve as an intraoperative tool to evaluate the success of revascularization. pTCpO2 could be an alternative for the ABI to determine the success of lower extremity revascularization.

Cholesteric liquid crystal mirror-based imaging Stokes polarimeter.

We have developed a cholesteric liquid crystal (CLC) mirror-based innovative model for detection and visualization of images in turbid media. Due to its unique optical-polarization properties, the CLC mirror is suggested as the basic element of the imaging Stokes polarimeter. The particular design of the proposed polarimeter, coupled with its distinguished operational simplicity, reliability, and real-time operational facilities, promises to fabricate a new generation of the imaging Stokes polarimeter, which can find applications in areas such as diagnostics, biology, astronomy, and remote sensing.

Biosensor based on two-dimensional gradient guided-mode resonance filter.

A novel biosensor based on a two-dimensional gradient (TDG) guided-mode resonance (GMR) filter was introduced in this study. The TDG-GMR is demarcated in terms of the gradient grating period (GGP) in one dimension and gradient waveguide thickness (GWT) in the other dimension. A single compact sensor can combine these two features to simultaneously provide a broad detection range through GGP and high resolution through GWT. A detection range of 0.109 RIU (0%-60% sucrose content) with a limit of detection of 5.62 × 10-4 was demonstrated in this study by using a TDG-GMR with a size of 140.8 × 125.4 µm2. This value cannot be achieved using one dimensional gradient GMR sensor. Label-free (LF) biomolecule detection through TDG-GMR was also experimentally demonstrated in a model assay of albumin. The result confirms that the GWT-GMR provides a better resolution, whereas the GGP-GMR provides a broader detection range. A device for multiplex measurement could be easily implemented with a compact sensor chip and a simple readout directly from a charge-coupled device. This system would require a narrow-band source such as a light emitting diode or a laser diode, in addition to a limited number of other components such as a polarizer and a collimator. The proposed TDG-GMR could easily be integrated with smartphones and portable devices.

Remote photonic sensing of blood oxygen saturation via tracking of anomalies in micro-saccades patterns.

Speckle pattern analysis has been found by many researchers to be applicable to remote sensing of various biomedical parameters. This paper shows how analysis of dynamic differential speckle patterns scattered from subjects' sclera illuminated by a laser beam allows extraction of micro-saccades movement in the human eye. Analysis of micro-saccades movement using advanced machine learning techniques based on convolutional neural networks offers a novel approach for non-contact assessment of human blood oxygen saturation level (SpO2). Early stages of hypoxia can rapidly progress into pneumonia and death, and lives can be saved by advance remote detection of reduced blood oxygen saturation.

A layered single-side readout depth of interaction time-of-flight-PET detector.

We are exploring a scintillator-based PET detector with potential of high sensitivity, depth of interaction (DOI) capability, and timing resolution, with single-side readout. Our design combines two previous concepts: (1) multiple scintillator arrays stacked with relative offset, yielding inherent DOI information, but good timing performance has not been demonstrated with conventional light sharing readout. (2) Single crystal array with one-to-one coupling to the photodetector, showing superior timing performance compared to its light sharing counterparts, but lacks DOI. The combination, where the first layer of a staggered design is coupled one-to-one to a photodetector array, may provide both DOI and timing resolution and this concept is here evaluated through light transport simulations. Results show that: (1) unpolished crystal pixels in the staggered configuration yield better performance across all metrics compared to polished pixels, regardless of readout scheme. (2) One-to-one readout of the first layer allows for accurate DOI extraction using a single threshold. The number of multi pixel photon counter (MPPC) pixels with signal amplitudes exceeding the threshold corresponds to the interaction layer. This approach was not possible with conventional light sharing readout. (3) With a threshold of 2 optical photons, the layered approach with one-to-one coupled first layer improves timing close to the MPPC compared to the conventional one-to-one coupling non-DOI detector, due to effectively reduced crystal thickness. Single detector timing resolution values of 91, 127, 151 and 164 ps were observed per layer in the 4-layer design, to be compared to 148 ps for the single array with one-to-one coupling. (4) For the layered design with light sharing readout, timing improves with increased MPPC pixel size due to higher signal per channel. In conclusion, the combination of straightforward DOI determination, good timing performance, and relatively simple design makes the proposed concept promising for DOI-Time-of-Flight PET detectors.

Evaluation of pasting and gelling properties of commercial flours under high heating temperatures using Rapid Visco Analyzer 4800.

In this study, pasting and gelling behaviors of flours were investigated at heating temperatures of 95-140 °C. Overall, both peak and breakdown viscosities of the flours were positively correlated with starch contents (p < 0.01) but inversely correlated with protein (p < 0.01) and fiber contents (p < 0.05) at 95-140 °C. When the heating temperature increased, pasting temperatures and peak viscosities of most waxy and normal flours largely remained the same, but their holding strengths and final viscosities gradually decreased. However, pulse and high-amylose maize flours required a holding temperature above 95 °C to achieve the highest peak and final viscosities. Normal maize and pulse flours formed hard gels after cooking at 120 °C, and high-amylose maize flour developed the firmest gel after cooking at 140 °C. Chemical compositions, particle sizes, and thermal properties of the studied flours influenced their pasting and gelling properties to certain levels under the different heating temperatures.

In Vivo Optogenetics with Stimulus Calibration.

Optogenetic reagents allow for depolarization and hyperpolarization of cells with light. This provides unprecedented spatial and temporal resolution to the control of neuronal activity both in vitro and in vivo. In the intact animal this requires strategies to deliver light deep into the highly scattering tissue of the brain. A general approach that we describe here is to implant optical fibers just above brain regions targeted for light delivery. In part due to the fact that expression of optogenetic proteins is accomplished by techniques with inherent variability (e.g., viral expression levels), it also requires strategies to measure and calibrate the effect of stimulation. Here we describe general procedures that allow one to simultaneously stimulate neurons and use photometry with genetically encoded activity indicators to precisely calibrate stimulation.

Image edge detection with a photonic spiking VCSEL-neuron.

We report both experimentally and in theory on the detection of edge features in digital images with an artificial optical spiking neuron based on a vertical-cavity surface-emitting laser (VCSEL). The latter delivers fast (< 100 ps) neuron-like optical spikes in response to optical inputs pre-processed using convolution techniques; hence representing image feature information with a spiking data output directly in the optical domain. The proposed technique is able to detect target edges of different directionalities in digital images by applying individual kernel operators and can achieve complete image edge detection using gradient magnitude. Importantly, the neuromorphic (brain-like) spiking edge detection of this work uses commercially sourced VCSELs exhibiting responses at sub-nanosecond rates (many orders of magnitude faster than biological neurons) and operating at the important telecom wavelength of 1300 nm; hence making our approach compatible with optical communication and data-centre technologies.

Adenosine A2A receptor blockade improves neuroprosthetic learning by volitional control of population calcium signal in M1 cortical neurons.

Volitional control is at the core of brain-machine interfaces (BMI) adaptation and neuroprosthetic-driven learning to restore motor function for disabled patients, but neuroplasticity changes and neuromodulation underlying volitional control of neuroprosthetic learning are largely unexplored. To better study volitional control at annotated neural population, we have developed an operant neuroprosthetic task with closed-loop feedback system by volitional conditioning of population calcium signal in the M1 cortex using fiber photometry recording. Importantly, volitional conditioning of the population calcium signal in M1 neurons did not improve within-session adaptation, but specifically enhanced across-session neuroprosthetic skill learning with reduced time-to-target and the time to complete 50 successful trials. With brain-behavior causality of the neuroprosthetic paradigm, we revealed that proficiency of neuroprosthetic learning by volitional conditioning of calcium signal was associated with the stable representational (plasticity) mapping in M1 neurons with the reduced calcium peak. Furthermore, pharmacological blockade of adenosine A2A receptors facilitated volitional conditioning of neuroprosthetic learning and converted an ineffective volitional conditioning protocol to be the effective for neuroprosthetic learning. These findings may help to harness neuroplasticity for better volitional control of neuroprosthetic training and suggest a novel pharmacological strategy to improve neuroprosthetic learning in BMI adaptation by targeting striatal A2A receptors.

Highly sensitive eight-channel light sensing system for biomedical applications.

We demonstrate the potential of an eight-channel light sensing platform system, named Black Box I (BBI), for rapid and highly sensitive measurement of low-level light using a nonradioactive optical readout. We developed, normalized, and characterized the photon sensitivities of the eight channels of the BBI using placental alkaline phosphatase (PLAP) as a model imaging reporter. We found that the BBI system had a statistically strong linear correlation with the reference IVIS Lumina II system. When we applied normalization constants, we were able to optimize the photomultiplier tubes (PMT) of all eight channels of the BBI (up to r2 = 0.998). We investigated the biomedical utilities of BBI by: (i) determining alkaline phosphatase activities in mouse plasma samples as a diagnostic secretory biomarker of cancer, and (ii) diagnosing cancer metastases in the organs of mice bearing triple negative breast cancer. We provide an important new addition to low-cost biomedical instruments intended for pre-clinical diagnostic imaging with high sensitivity, high sample throughput, portability, and rapid on-site analysis of low-level light.

Wireless, battery-free subdermally implantable photometry systems for chronic recording of neural dynamics.

Recording cell-specific neuronal activity while monitoring behaviors of freely moving subjects can provide some of the most significant insights into brain function. Current means for monitoring calcium dynamics in genetically targeted populations of neurons rely on delivery of light and recording of fluorescent signals through optical fibers that can reduce subject mobility, induce motion artifacts, and limit experimental paradigms to isolated subjects in open, two-dimensional (2D) spaces. Wireless alternatives eliminate constraints associated with optical fibers, but their use of head stages with batteries adds bulk and weight that can affect behaviors, with limited operational lifetimes. The systems introduced here avoid drawbacks of both types of technologies, by combining highly miniaturized electronics and energy harvesters with injectable photometric modules in a class of fully wireless, battery-free photometer that is fully implantable subdermally to allow for the interrogation of neural dynamics in freely behaving subjects, without limitations set by fiber optic tethers or operational lifetimes constrained by traditional power supplies. The unique capabilities of these systems, their compatibility with magnetic resonant imaging and computed tomography and the ability to manufacture them with techniques in widespread use for consumer electronics, suggest a potential for broad adoption in neuroscience research.

Instrument-based Tests for Measuring Anterior Chamber Cells in Uveitis: A Systematic Review.

PURPOSE: New instrument-based techniques for anterior chamber (AC) cell counting can offer automation and objectivity above clinician assessment. This review aims to identify such instruments and its correlation with clinician estimates. METHODS: Using standard systematic review methodology, we identified and tabulated the outcomes of studies reporting reliability and correlation between instrument-based measurements and clinician AC cell grading. RESULTS: From 3470 studies, 6 reported correlation between an instrument-based AC cell count to clinician grading. The two instruments were optical coherence tomography (OCT) and laser flare-cell photometry (LFCP). Correlation between clinician grading and LFCP was 0.66-0.87 and 0.06-0.97 between clinician grading and OCT. OCT volume scans demonstrated correlation between 0.75 and 0.78. Line scans in the middle AC demonstrated higher correlation (0.73-0.97) than in the inferior AC (0.06-0.56). CONCLUSION: AC cell count by OCT and LFP can achieve high levels of correlation with clinician grading, whilst offering additional advantages of speed, automation, and objectivity.

A quantitative cross-sectional analysis of the melanin index in the skin of preterm newborns and its association with gestational age at birth.

BACKGROUND: Estimation of gestational age (GA) is important to make timely decisions and provide appropriate neonatal care. Clinical maturity scales to estimate GA have used skin texture and color to assess maturity at birth facing situations of the uncertainty of pregnancy dating. The size and darkness of the areola around the nipple to grade skin characteristics are based on visual appearance. The melanin index (M-Index) is an optical skin parameter related to the melanin content in the tissue. This study is aimed to associate the M-Index of the skin with the GA. METHODS: A cross-sectional study evaluated 80 newborns at birth. A photometer device quantified the skin pigmentation on the areolae, forearms, and soles. Paired average differences of M-Index were compared among the three body sites. The skin M-Indexes were compared between subgroups of newborns until 34 weeks or with 34 and more. RESULTS: The skin over the areola had the highest values of M-Index compared with the forearm or sole areas (P < .001 for both). Infants with a GA between 34 and <37 weeks had higher M-Index values over the areola than the group with a GA with 24 to <34 weeks: 41.7 (8.9) and 38.3 (10.5) median (IQR), P = .005. CONCLUSIONS: The measurable M-Index values have the potential to improve physical evaluation in assessing GA at birth.

Automatic multicommuted flow-batch setup for photometric determination of mercury in drinking water at ppb level.

Herein, a multicommuted flow-batch setup and a photometric procedure for the determination of mercury at the ppb level in aqueous samples are described. The setup was designed to implement a versatile solvent extraction and pre-concentration strategy by combining flow-batch and multicommuted flow analysis approaches. The photometric method was based on Hg(II) reaction with dithizone in a chloroform medium, which was also used as the extracting organic solvent. The flow analysis system was composed of a homemade syringe pump module, a set of solenoid valves, two Aquarius mini-pumps, and a flow-batch chamber. The homemade photometer was comprised of a light emitting diode (LED), photodiode, and homemade flow cell (50 mm length). The flow system and photometer were controlled using an Arduino Due board, running custom-written software. After optimizing the operational conditions, the effectiveness of the developed system was evaluated for the determination of the mercury concentration in drinking water. For accuracy assessment, samples were analyzed using a spiking methodology and an independent method, yielding a recovery ranging from 92% to 108%. Other important characteristics of the proposed method were found as follows: linear response range, 0.5-10.0 µg L-1 (r = 0.9984); limit of detection 0.38 µg L-1 Hg(II); consumption of dithizone and chloroform, 1.85 µg L-1 and 0.8 mL per analysis, respectively; coefficient of variation, 2% (n = 10); sampling throughput, 20 determinations per h.

Open source silicon microprobes for high throughput neural recording.

OBJECTIVE: Microfabricated multielectrode arrays are widely used for high throughput recording of extracellular neural activity, which is transforming our understanding of brain function in health and disease. Currently there is a plethora of electrode-based tools being developed at higher education and research institutions. However, taking such tools from the initial research and development phase to widespread adoption by the neuroscience community is often hindered by several obstacles. The objective of this work is to describe the development, application, and open dissemination of silicon microprobes for recording neural activity in vivo. APPROACH: We propose an open source dissemination platform as an alternative to commercialization. This framework promotes recording tools that are openly and inexpensively available to the community. The silicon microprobes are designed in house, but the fabrication and assembly processes are carried out by third party companies. This enables mass production, a key requirement for large-scale dissemination. MAIN RESULTS: We demonstrate the operation of silicon microprobes containing up to 256 electrodes in conjunction with optical fibers for optogenetic manipulations or fiber photometry. These data provide new insights about the relationship between calcium activity and neural spiking activity. We also describe the current state of dissemination of these tools. A file repository of resources related to designing, using, and sharing these tools is maintained online. SIGNIFICANCE: This paper is likely to be a valuable resource for both current and prospective users, as well as developers of silicon microprobes. Based on their extensive usage by a number of labs including ours, these tools present a promising alternative to other types of electrode-based technologies aimed at high throughput recording in head-fixed animals. This work also demonstrates the importance of validating fiber photometry measurements with simultaneous electrophysiological recordings.

Stress experience and hormone feedback tune distinct components of hypothalamic CRH neuron activity.

Stress leaves a lasting impression on an organism and reshapes future responses. However, the influence of past experience and stress hormones on the activity of neural stress circuits remains unclear. Hypothalamic corticotropin-releasing hormone (CRH) neurons orchestrate behavioral and endocrine responses to stress and are themselves highly sensitive to corticosteroid (CORT) stress hormones. Here, using in vivo optical recordings, we find that CRH neurons are rapidly activated in response to stress. CRH neuron activity robustly habituates to repeated presentations of the same, but not novel stressors. CORT feedback has little effect on CRH neuron responses to acute stress, or on habituation to repeated stressors. Rather, CORT preferentially inhibits tonic CRH neuron activity in the absence of stress stimuli. These findings reveal how stress experience and stress hormones modulate distinct components of CRH neuronal activity to mediate stress-induced adaptations.

ISOPT Clinical Hot Topic Panel Discussion on Uveitis and Inflammation.

For this "hot topic" session in uveitis we selected first and foremost an issue that puts our clinical work and research in "holding pattern." The issue is our method of evaluating the severity of uveitis. We posed the following questions to our esteemed panelists: 1.The relative significance of cells vs. flare in following uveitis patients 2.Cells/flare measurements 3.A glance into the future and the relevance of endpoints in clinical studies and their methodologies While there are different opinions in managing and monitoring uveitis patients, there seems to be an agreement on the high need of improving objective mode/s of reliably measuring both cells and flare and better understand their significance.

Differential coupling between subcortical calcium and BOLD signals during evoked and resting state through simultaneous calcium fiber photometry and fMRI.

Task based and resting state fMRI has been widely utilized to study brain functions. As the foundation of fMRI, the underlying neural basis of the BOLD signal has been extensively studied, but the detailed mechanism remains elusive, particularly during the resting state. To examine the neurovascular coupling, it is important to simultaneously record neural and vascular signals. Here we developed a novel setup of camera based, scalable simultaneous calcium fiber photometry and fMRI in rats. Using this setup, we recorded calcium signals of superior colliculus (SC) and lateral geniculate nucleus (LGN) and fMRI simultaneously during visual stimulation and the resting state. Our results revealed robust, region-specific coupling between calcium and BOLD signals in the task state and weaker, whole brain correlation in the resting state. Interestingly, the spatial specificity of such correlation in the resting state was improved upon regression of white matter, ventricle signals and global signals in fMRI data. Overall, our results suggest differential coupling of calcium and BOLD signals for subcortical regions between evoked and resting states, and the coupling relationship in the resting state was related with resting state BOLD preprocessing strategies.