Detection of grapevine yellows symptoms in Vitis vinifera L. with artificial intelligence

Grapevine yellows (GY) are a significant threat to grapes due to the severe symptoms and lack of treatments. Conventional diagnosis of the phytoplasmas associated to GYs relies on symptom identification, due to sensitivity limits of diagnostic tools (e.g. real time PCR) in asymptomatic vines, where the low concentration of the pathogen or its erratic distribution can lead to a high rate of false-negatives. GY's primary symptoms are leaf discoloration and irregular wood ripening, which can be easily confused for symptoms of other diseases making recognition a difficult task. Herein, we present a novel system, utilizing convolutional neural networks, for end-to-end detection of GY in red grape vine (cv. Sangiovese), using color images of leaf clippings. The diagnostic test detailed in this work does not require the user to be an expert at identifying GY. Data augmentation strategies make the system robust to alignment errors during data capture. When applied to the task of recognizing GY from digital images of leaf clippings—amongst many other diseases and a healthy control—the system has a sensitivity of 98.96% and a specificity of 99.40%. Deep learning has 35.97% and 9.88% better predictive value (PPV) when recognizing GY from sight, than a baseline system without deep learning and trained humans respectively. We evaluate six neural network architectures: AlexNet, GoogLeNet, Inception v3, ResNet-50, ResNet-101 and SqueezeNet. We find ResNet-50 to be the best compromise of accuracy and training cost. The trained neural networks, code to reproduce the experiments, and data of leaf clipping images are available on the internet. This work will advance the frontier of GY detection by improving detection speed, enabling a more effective response to the disease

p53 accumulation following cytokinesis failure in the absence of caspase-2

Abstract not availableYoon Lim, Dylan De Bellis, Loretta Dorstyn, Sharad Kuma

Gigwa v2—Extended and improved genotype investigator

The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community

Increased ventral striatal volume in college-aged binge drinkers

BACKGROUND Binge drinking is a serious public health issue associated with cognitive, physiological, and anatomical differences from healthy individuals. No studies, however, have reported subcortical grey matter differences in this population. To address this, we compared the grey matter volumes of college-age binge drinkers and healthy controls, focusing on the ventral striatum, hippocampus and amygdala. METHOD T1-weighted images of 19 binge drinkers and 19 healthy volunteers were analyzed using voxel-based morphometry. Structural data were also covaried with Alcohol Use Disorders Identification Test (AUDIT) scores. Cluster-extent threshold and small volume corrections were both used to analyze imaging data. RESULTS Binge drinkers had significantly larger ventral striatal grey matter volumes compared to controls. There were no between group differences in hippocampal or amygdalar volume. Ventral striatal, amygdalar, and hippocampal volumes were also negatively related to AUDIT scores across groups. CONCLUSIONS Our findings stand in contrast to the lower ventral striatal volume previously observed in more severe forms of alcohol use disorders, suggesting that college-age binge drinkers may represent a distinct population from those groups. These findings may instead represent early sequelae, compensatory effects of repeated binge and withdrawal, or an endophenotypic risk factor

Comment on the narrow structure reported by Amaryan et al

The CLAS Collaboration provides a comment on the physics interpretation of the results presented in a paper published by M. Amaryan et al. regarding the possible observation of a narrow structure in the mass spectrum of a photoproduction experiment.Comment: to be published in Physical Review

Differential cross section and recoil polarization measurements for the gamma p to K+ Lambda reaction using CLAS at Jefferson Lab

We present measurements of the differential cross section and Lambda recoil polarization for the gamma p to K+ Lambda reaction made using the CLAS detector at Jefferson Lab. These measurements cover the center-of-mass energy range from 1.62 to 2.84 GeV and a wide range of center-of-mass K+ production angles. Independent analyses were performed using the K+ p pi- and K+ p (missing pi -) final-state topologies; results from these analyses were found to exhibit good agreement. These differential cross section measurements show excellent agreement with previous CLAS and LEPS results and offer increased precision and a 300 MeV increase in energy coverage. The recoil polarization data agree well with previous results and offer a large increase in precision and a 500 MeV extension in energy range. The increased center-of-mass energy range that these data represent will allow for independent study of non-resonant K+ Lambda photoproduction mechanisms at all production angles.Comment: 22 pages, 16 figure

Absorption of the ω\omega and ϕ\phi Mesons in Nuclei

Due to their long lifetimes, the $\omega$ and $\phi$ mesons are the ideal candidates for the study of possible modifications of the in-medium meson-nucleon interaction through their absorption inside the nucleus. During the E01-112 experiment at the Thomas Jefferson National Accelerator Facility, the mesons were photoproduced from $^{2}$H, C, Ti, Fe, and Pb targets. This paper reports the first measurement of the ratio of nuclear transparencies for the $e^{+}e^{-}$ channel. The ratios indicate larger in-medium widths compared with what have been reported in other reaction channels.Comment: 6 pages, 4 figure

Near-threshold Photoproduction of Phi Mesons from Deuterium

We report the first measurement of the differential cross section on $\phi$-meson photoproduction from deuterium near the production threshold for a proton using the CLAS detector and a tagged-photon beam in Hall B at Jefferson Lab. The measurement was carried out by a triple coincidence detection of a proton, $K^+$ and $K^-$ near the theoretical production threshold of 1.57 GeV. The extracted differential cross sections $\frac{d\sigma}{dt}$ for the initial photon energy from 1.65-1.75 GeV are consistent with predictions based on a quasifree mechanism. This experiment establishes a baseline for a future experimental search for an exotic $\phi$-N bound state from heavier nuclear targets utilizing subthreshold/near-threshold production of $\phi$ mesons

Differential cross sections and recoil polarizations for the reaction gamma p -> K+ Sigma0

High-statistics measurements of differential cross sections and recoil polarizations for the reaction $\gamma p \rightarrow K^+ \Sigma^0$ have been obtained using the CLAS detector at Jefferson Lab. We cover center-of-mass energies ($\sqrt{s}$) from 1.69 to 2.84 GeV, with an extensive coverage in the $K^+$ production angle. Independent measurements were made using the $K^{+}p\pi^{-}$($\gamma$) and $K^{+}p$($\pi^-, \gamma$) final-state topologies, and were found to exhibit good agreement. Our differential cross sections show good agreement with earlier CLAS, SAPHIR and LEPS results, while offering better statistical precision and a 300-MeV increase in $\sqrt{s}$ coverage. Above $\sqrt{s} \approx 2.5$ GeV, $t$- and $u$-channel Regge scaling behavior can be seen at forward- and backward-angles, respectively. Our recoil polarization ($P_\Sigma$) measurements represent a substantial increase in kinematic coverage and enhanced precision over previous world data. At forward angles we find that $P_\Sigma$ is of the same magnitude but opposite sign as $P_\Lambda$, in agreement with the static SU(6) quark model prediction of $P_\Sigma \approx -P_\Lambda$. This expectation is violated in some mid- and backward-angle kinematic regimes, where $P_\Sigma$ and $P_\Lambda$ are of similar magnitudes but also have the same signs. In conjunction with several other meson photoproduction results recently published by CLAS, the present data will help constrain the partial wave analyses being performed to search for missing baryon resonances.Comment: 23 pages, 17 figure