Browse Articles

Tomato disease identification with shallow convolutional neural networks

Trinh et al. | Mar 03, 2023

Tomato disease identification with shallow convolutional neural networks

Plant diseases can cause up to 50% crop yield loss for the popular tomato plant. A mobile device-based method to identify diseases from photos of symptomatic leaves via computer vision can be more effective due to its convenience and accessibility. To enable a practical mobile solution, a “shallow” convolutional neural networks (CNNs) with few layers, and thus low computational requirement but with high accuracy similar to the deep CNNs is needed. In this work, we explored if such a model was possible.

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Employee resignation study in Fairfax County

Zhang et al. | Mar 03, 2023

Employee resignation study in Fairfax County

In this study, the authors address potential reasons why employees may voluntarily resign. This is in response to the currently observed economic trend The Great Resignation. Through analysis of federal and local government data along with survey results from Fairfax County, they concluded that adding additional benefits will help companies retain talented empolyees.

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Using machine learning to develop a global coral bleaching predictor

Madireddy et al. | Feb 21, 2023

Using machine learning to develop a global coral bleaching predictor
Image credit: Madireddy, Bosch, and McCalla

Coral bleaching is a fatal process that reduces coral diversity, leads to habitat loss for marine organisms, and is a symptom of climate change. This process occurs when corals expel their symbiotic dinoflagellates, algae that photosynthesize within coral tissue providing corals with glucose. Restoration efforts have attempted to repair damaged reefs; however, there are over 360,000 square miles of coral reefs worldwide, making it challenging to target conservation efforts. Thus, predicting the likelihood of bleaching in a certain region would make it easier to allocate resources for conservation efforts. We developed a machine learning model to predict global locations at risk for coral bleaching. Data obtained from the Biological and Chemical Oceanography Data Management Office consisted of various coral bleaching events and the parameters under which the bleaching occurred. Sea surface temperature, sea surface temperature anomalies, longitude, latitude, and coral depth below the surface were the features found to be most correlated to coral bleaching. Thirty-nine machine learning models were tested to determine which one most accurately used the parameters of interest to predict the percentage of corals that would be bleached. A random forest regressor model with an R-squared value of 0.25 and a root mean squared error value of 7.91 was determined to be the best model for predicting coral bleaching. In the end, the random model had a 96% accuracy in predicting the percentage of corals that would be bleached. This prediction system can make it easier for researchers and conservationists to identify coral bleaching hotspots and properly allocate resources to prevent or mitigate bleaching events.

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Machine learning-based enzyme engineering of PETase for improved efficiency in plastic degradation

Gupta et al. | Jan 31, 2023

 Machine learning-based enzyme engineering of PETase for improved efficiency in plastic degradation
Image credit: Markus Spiske

Here, recognizing the recognizing the growing threat of non-biodegradable plastic waste, the authors investigated the ability to use a modified enzyme identified in bacteria to decompose polyethylene terephthalate (PET). They used simulations to screen and identify an optimized enzyme based on machine learning models. Ultimately, they identified a potential mutant PETases capable of decomposing PET with improved thermal stability.

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Spectrophotometric comparison of 4-Nitrophenyl carbonates & carbamates as base-labile protecting groups

Kocalar et al. | Dec 12, 2022

Spectrophotometric comparison of 4-Nitrophenyl carbonates & carbamates as base-labile protecting groups

In organic synthesis, protecting groups are derivatives of reactive functionalities that play a key role in ensuring chemoselectivity of chemical transformations. To protect alcohols and amines, acid-labile tert-butyloxycarbonyl protecting groups are often employed but are avoided when the substrate is acid-sensitive. Thus, orthogonal base-labile protecting groups have been in demand to enable selective deprotection and to preserve the reactivity of acid-sensitive substrates. To meet this demand, we present 4-nitrophenyl carbonates and carbamates as orthogonal base-labile protecting group strategies.

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The presence of Wolbachia in Brood X cicadas

Hasan et al. | Oct 15, 2022

The presence of <em>Wolbachia</em> in Brood X cicadas

Here, seeking to understand a possible cause of the declining popluations of Brood X cicadas in Ohio and Indiana, the authors investigated the presence of Wolbachia, an inherited bacterial symbiont that lives in the reproductive cells of approximately 60% of insect species in these cicadas. Following their screening of one-hundred 17-year periodical cicadas, they only identified the presence of Wolbachia infection in less than 2%, suggesting that while Wolbachia can infect cicadas it appears uncommon in the Brood X cicadas they surveyed.

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Refinement of Single Nucleotide Polymorphisms of Atopic Dermatitis related Filaggrin through R packages

Naravane et al. | Oct 12, 2022

Refinement of Single Nucleotide Polymorphisms of Atopic Dermatitis related Filaggrin through R packages

In the United States, there are currently 17.8 million affected by atopic dermatitis (AD), commonly known as eczema. It is characterized by itching and skin inflammation. AD patients are at higher risk for infections, depression, cancer, and suicide. Genetics, environment, and stress are some of the causes of the disease. With the rise of personalized medicine and the acceptance of gene-editing technologies, AD-related variations need to be identified for treatment. Genome-wide association studies (GWAS) have associated the Filaggrin (FLG) gene with AD but have not identified specific problematic single nucleotide polymorphisms (SNPs). This research aimed to refine known SNPs of FLG for gene editing technologies to establish a causal link between specific SNPs and the diseases and to target the polymorphisms. The research utilized R and its Bioconductor packages to refine data from the National Center for Biotechnology Information's (NCBI's) Variation Viewer. The algorithm filtered the dataset by coding regions and conserved domains. The algorithm also removed synonymous variations and treated non-synonymous, frameshift, and nonsense separately. The non-synonymous variations were refined and ordered by the BLOSUM62 substitution matrix. Overall, the analysis removed 96.65% of data, which was redundant or not the focus of the research and ordered the remaining relevant data by impact. The code for the project can also be repurposed as a tool for other diseases. The research can help solve GWAS's imprecise identification challenge. This research is the first step in providing the refined databases required for gene-editing treatment.

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An efficient approach to automated geometry diagram parsing

Date et al. | Oct 02, 2022

An efficient approach to automated geometry diagram parsing

Here, beginning from an initial interest in the possibility to use a computer to automatically solve a geometry diagram parser, the authors developed their own Fast Geometry Diagram Parser (FastGDP) that uses clustering and corner information. They compared their own methods to a more widely available, method, GeoSolver, finding their own to be an order of magnitude faster in most cases that they considered.

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Tap water quality analysis in Ulaanbaatar City

Munkhbat et al. | Sep 25, 2022

Tap water quality analysis in Ulaanbaatar City

There have been several issues concerning the water quality in Ulaanbaatar, Mongolia in the past few years. This study, we collected 28 samples from 6 districts of Ulaanbaatar to check if the water supply quality met the standards of the World Health Organization, the Environmental Protection Agency, and a Mongolian National Standard. Only three samples fully met all the requirements of the global standards. Samples in Zaisan showed higher hardness (>120 ppm) and alkalinity levels (20–200 ppm) over the other districts in the city. Overall, the results show that it is important to ensure a safe and accessible water supply in Ulaanbaatar to prevent future water quality issues.

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