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BINding ANAlyzer (BINANA) is an algorithm for identifying and characterizing protein/ligand interactions and other factors that contribute to binding. We recently updated BINANA to make the algorithm more accessible to a broader audience. We have also ported the Python3 codebase to JavaScript, thus enabling BINANA analysis in the web browser. As proof of principle, we created a web-browser application so students and chemical-biology researchers can quickly visualize receptor/ligand complexes and their unique binding interactions.

Monitoring harmful algal blooms (HABs) in freshwater over regional scales has been implemented through mapping chlorophyll-a (Chl-a) concentrations using multi-sensor satellite remote sensing data. Cloud-free satellite measurements and a sufficient number of matched-up ground samples are critical for constructing a predictive model for Chl-a concentration. This paper presents a methodological framework for automatically pairing surface reflectance values from multi-sensor satellite observations with ground water quality samples in time and space to form match-up points, using the Google Earth Engine cloud computing platform. A support vector machine model was then trained using the match-up points, and the prediction accuracy of the model was evaluated and compared with traditional image processing results. This research demonstrates that the integration of multi-sensor satellite observations through Google Earth Engine enables accurate and fast Chl-a prediction at a large regional scale over multiple years. The challenges and limitations of using and calibrating multi-sensor satellite image data and current and potential solutions are discussed.

In light of rising textbook prices, open education resources (OER) have been shown to decrease non-tuition costs, while simultaneously increasing academic access, student performance, and time-to-graduation rates. Yet very little research to date has explored OER’s specific impact on those who are presumed to benefit most from this potential: historically underserved students. This reality has left a significant gap of understanding in the current body of literature, resulting in calls for more empirically-based examinations of OER through a social justice lens. For each of these reasons, this study explored the impact of OER and textbook pricing among racial/ethnic minority students, low-income students, and first-generation college students at a four-year Hispanic Serving Institution (HSI) in Southern California. Drawing upon more than 700 undergraduate surveys, our univariate, bivariate and multivariate results revealed textbook costs to be a substantial barrier for the vast majority of students. However, those barriers were even more significant among historically underserved college students; thus, confirming textbook affordability as a redistributive justice issue, and positing OER as a potential avenue for realizing a more socially just college experience.

This study evaluated the performances of twenty-nine algorithms that use satellite-based spectral imager data to derive estimates of chlorophyll-a concentrations that, in turn, can be used as an indicator of the general status of algal cell densities and the potential for a harmful algal bloom (HAB). The performance assessment was based on making relative comparisons between two temperate inland lakes: Harsha Lake (7.99 km2) in Southwest Ohio and Taylorsville Lake (11.88 km2) in central Kentucky. Of interest was identifying algorithm-imager combinations that had high correlation with coincident chlorophyll-a surface observations for both lakes, as this suggests portability for regional HAB monitoring. The spectral data utilized to estimate surface water chlorophyll-a concentrations were derived from the airborne Compact Airborne Spectral Imager (CASI) 1500 hyperspectral imager, that was then used to derive synthetic versions of currently operational satellite-based imagers using spatial resampling and spectral binning. The synthetic data mimics the configurations of spectral imagers on current satellites in earth’s orbit including, WorldView-2/3, Sentinel-2, Landsat-8, Moderate-resolution Imaging Spectroradiometer (MODIS), and Medium Resolution Imaging Spectrometer (MERIS). High correlations were found between the direct measurement and the imagery-estimated chlorophyll-a concentrations at both lakes. The results determined that eleven out of the twenty-nine algorithms were considered portable, with r2 values greater than 0.5 for both lakes. Even though the two lakes are different in terms of background water quality, size and shape, with Taylorsville being generally less impaired, larger, but much narrower throughout, the results support the portability of utilizing a suite of certain algorithms across multiple sensors to detect potential algal blooms through the use of chlorophyll-a as a proxy. Furthermore, the strong performance of the Sentinel-2 algorithms is exceptionally promising, due to the recent launch of the second satellite in the constellation, which will provide higher temporal resolution for temperate inland water bodies. Additionally, scripts were written for the open-source statistical software R that automate much of the spectral data processing steps. This allows for the simultaneous consideration of numerous algorithms across multiple imagers over an expedited time frame for the near real-time monitoring required for detecting algal blooms and mitigating their adverse impacts.

We analyzed 37 satellite reflectance algorithms and 321 variants for five satellites for estimating turbidity in a freshwater inland lake in Ohio using coincident real hyperspectral aircraft imagery converted to relative reflectance and dense coincident surface observations. This study is part of an effort to develop simple proxies for turbidity and algal blooms and to evaluate their performance and portability between satellite imagers for regional operational turbidity and algal bloom monitoring. Turbidity algorithms were then applied to synthetic satellite images and compared to in situ measurements of turbidity, chlorophyll-a (Chl-a), total suspended solids (TSS) and phycocyanin as an indicator of cyanobacterial/blue green algal (BGA) abundance. Several turbidity algorithms worked well with real Compact Airborne Spectrographic Imager (CASI) and synthetic WorldView-2, Sentinel-2 and Sentinel-3/MERIS/OLCI imagery. A simple red band algorithm for MODIS imagery and a new fluorescence line height algorithm for Landsat-8 imagery had limited performance with regard to turbidity estimation. Blue-Green Algae/Phycocyanin (BGA/PC) and Chl-a algorithms were the most widely applicable algorithms for turbidity estimation because strong co-variance of turbidity, TSS, Chl-a, and BGA made them mutual proxies in this experiment.

We compared 10 established and 2 new satellite reflectance algorithms for estimating chlorophyll- a (Chl- a ) in a temperate reservoir in southwest Ohio using coincident hyperspectral aircraft imagery and dense coincident surface observations collected within 1 h of image acquisition to develop simple proxies for algal blooms in water bodies sensitive to algal blooms (especially toxic or harmful algal blooms (HABs)) and to facilitate portability between multispectral satellite imagers for regional algal bloom monitoring. All algorithms were compared with narrow band hyperspectral aircraft images. These images were subsequently upscaled spectrally and spatially to simulate 5 current and near future satellite imaging systems. Established and new Chl- a algorithms were then applied to the synthetic satellite images and compared to coincident surface observations of Chl- a collected from 44 sites within 1 h of aircraft acquisition of the imagery. We found several promising algorithm/satellite imager combinations for routine Chl- a estimation in smaller inland water bodies with operational and near-future satellite systems. The CI, MCI, FLH, NDCI, 2BDA and 3 BDA Chl- a algorithms worked well with CASI imagery. The NDCI, 2BDA, and 3BDA Chl- a algorithms worked well with simulated WorldView-2 and 3, Sentinel-2, and MERIS-like imagery. NDCI was the most widely applicable Chl- a algorithm with good performance for CASI, WorldView 2 and 3, Sentinel-2 and MERIS-like imagery and limited performance with MODIS imagery. A new fluorescence line height “greenness” algorithm yielded the best Chl- a estimates with simulated Landsat-8 imagery.

Introduction: High-grade glioma (HGG) is the most common subtype of primary brain tumors with high recurrence rate and poor survival. The emergence of targeted molecular and cellular therapies (e.g., pembrolizumab, Chimeric Antigen Receptor [CAR] T-cell therapy) are potentially promising in improving overall survival. Due to increased intratumor heterogeneity and inhomogeneous treatment response, there is an unmet need of imaging biomarkers predictive of treatment response and survival. Radiomics using machine learning methods have shown promise in predicting treatment response in various solid tumors, including HGG. In this study, we compare the survival prediction performance using machine learning models with different radiomic features individually derived from T1- and T2-weighted MR images in patients suffering from HGG treated with CAR-T cell therapy. Methods: In this IRB-approved phase 1 clinical trial, 61 patients (39 males, median age = 49) suffering from recurrent HGG underwent surgical resection and CAR T-cell therapy1. All patients underwent baseline MRI scans prior to both surgical resection and CAR T-cell administration in the resection cavity. For patients with a complete set of T1- and T2-weighted MRIs (n = 50), we generated segmentations in a semi-automated manner, labeling with each tumorous voxel as either contrast-enhanced tumor (ET), non-enhancing tumor (NET) and edema. From each tumor label, we extracted shape-based, texture-based and image-filtered radiomic features2. We utilized gradient-boosted tree models (lightGBM) to classify whether survival is above or below group median (188 days) by using two nested loops of 10-fold cross validations each. For the inner validation loop, we determined the optimal model from hyper-parameters including regularization. For the outer validation loop, we tested this model on the hold-out data and the predictions were used as radiomic risk scores. Results: For each of the ET, NET, and edema tumor ROIs, we extracted 1313 radiomic features for predictive modeling. The outer validation loop Area Under the Receiver Operating Characteristic Curve (AUC) for ET, NET and edema were 0.55, 0.70, and 0.46, respectively, suggesting that radiomic features calculated from NET voxels are the most predictive of survival compared to features from ET and edema voxels. We also stratified the patients into two distinct prognostic sub-groups (25 patients each group) using the NET radiomic risk scores obtained from the outer validation loop, with a log-rank test p-value of 0.01. Conclusions: In patients suffering from recurrent HGG who were treated with CAR T-cell therapy, we found that radiomic features derived from NET voxels are predictive of survival while the other two tumorous voxel types (ET and edema) are not. Further work is needed to incorporate clinical and molecular features that also may be predictive of survival. 1N Engl J Med 2016; 375:2561-2569. 2Cancer Research, 77(21), e104-e107 Citation Format: Chi Wah Wong, Sohaib Naim, Vincent La, Seth Michael Hilliard, Eemon Tizpa, Rashi Ranjan, Hannah Jade Young, Kimberly Jane Bonjoc, Aleksandr Filippov, Saman Tabassum Khan, Christine Brown, Behnam Badie, Ammar Ahmed Chaudhry. Radiomic prediction of survival in recurrent high-grade glioma patients treated with CAR T-cell therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 866.

We analyzed 27 established and new simple and therefore perhaps portable satellite phycocyanin pigment reflectance algorithms for estimating cyanobacterial values in a temperate 8.9 km2 reservoir in southwest Ohio using coincident hyperspectral aircraft imagery and dense coincident water surface observations collected from 44 sites within 1 h of image acquisition. The algorithms were adapted to real Compact Airborne Spectrographic Imager (CASI), synthetic WorldView-2, Sentinel-2, Landsat-8, MODIS and Sentinel-3/MERIS/OLCI imagery resulting in 184 variants and corresponding image products. Image products were compared to the cyanobacterial coincident surface observation measurements to identify groups of promising algorithms for operational algal bloom monitoring. Several of the algorithms were found useful for estimating phycocyanin values with each sensor type except MODIS in this small lake. In situ phycocyanin measurements correlated strongly (r2 = 0.757) with cyanobacterial sum of total biovolume (CSTB) allowing us to estimate both phycocyanin values and CSTB for all of the satellites considered except MODIS in this situation.