Diagnosis of focal liver lesions from ultrasound using deep learning

PURPOSE: The purpose of this study was to create an algorithm that simultaneously detects and characterizes (benign vs. malignant) focal liver lesion (FLL) using deep learning. MATERIALS AND METHODS: We trained our algorithm on a dataset proposed during a data challenge organized at the 2018 Journées Francophones de Radiologie. The dataset was composed of 367 two-dimensional ultrasound images from 367 individual livers, captured at various institutions. The algorithm was guided using an attention mechanism with annotations made by a radiologist. The algorithm was then tested on a new data set from 177 patients. RESULTS: The models reached mean ROC-AUC scores of 0.935 for FLL detection and 0.916 for FLL characterization over three shuffled three-fold cross-validations performed with the training data. On the new dataset of 177 patients, our models reached a weighted mean ROC-AUC scores of 0.891 for seven different tasks. CONCLUSION: This study that uses a supervised-attention mechanism focused on FLL detection and characterization from liver ultrasound images. This method could prove to be highly relevant for medical imaging once validated on a larger independent cohort

Solution Counting for CSP and SAT with Large Tree-Width

Рассмотрена проблема подсчета количества решений задачи совместимости ограничений (Constraint Satisfaction Problem). Для ее решения был адаптирован метод обратного прослеживания с ацикличным представлением графа ограничений (Backtracking with Tree-Decomposition). Предложен точный алгоритм, сложность которого экспоненциально зависит от ширины дерева, и приближенный алгоритм, экспоненциально зависящий от размера максимальной клики.The problem of counting the number of solutions of a CSP is considered. For solving the problem the Backtracking with a Tree-Decomposition method was adapted. The exact algorithm is suggested which has the worst-time complexity exponential in a tree width, as well as iterative algorithm that has computational complexity exponential in a maximum clique size.Розглянуто проблему підрахунку кількості розв’язків задачі сумісності обмежень (Constraint Satisfaction Problem). Для її розв’язку було адаптовано метод зворотного простеження з ациклічним поданням графа обмежень (Backtracking with Tree-Decomposition). Запропоновано точний алгоритм, складність якого експоненційно залежить від ширини дерева, і наближений алгоритм, експоненційно залежний від розміру максимальної кліки

Cr cluster characterization in Cu-Cr-Zr alloy after ECAP processing and aging using SANS and HAADF-STEM

International audienceThe precipitation of nano-sized Cr clusters was investigated in a commercial Cu-1Cr-0.1Zr (wt.%) alloy processed by Equal-Channel Angular Pressing (ECAP) and subsequent aging at 550 °C for 4 hours using small angle neutron scattering (SANS) measurements and high-angle annular dark-field-scanning transmission electron microscopy (HAADF-STEM). The size and volume fraction of nano-sized Cr clusters were estimated using both techniques. These parameters assessed from SANS (d~3.2 nm, Fv~1.1 %) agreed reasonably with those from HAADF-STEM (d ~2.5 nm, Fv~2.3%). Besides nano-sized Cr clusters, HAADF-STEM technique evidenced the presence of rare cuboid and spheroid sub-micronic Cr particles about 380-620 nm mean size. Both techniques did not evidence the presence of intermetallic CuxZry phases within the aging conditions

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

© 2019, The Author(s). Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers

Evaluating Multimedia Features and Fusion for Example-Based Event Detection

Multimedia event detection (MED) is a challenging problem because of the heterogeneous content and variable quality found in large collections of Internet videos. To study the value of multimedia features and fusion for representing and learning events from a set of example video clips, we created SESAME, a system for video SEarch with Speed and Accuracy for Multimedia Events. SESAME includes multiple bag-of-words event classifiers based on single data types: low-level visual, motion, and audio features; high-level semantic visual concepts; and automatic speech recognition. Event detection performance was evaluated for each event classifier. The performance of low-level visual and motion features was improved by the use of difference coding. The accuracy of the visual concepts was nearly as strong as that of the low-level visual features. Experiments with a number of fusion methods for combining the event detection scores from these classifiers revealed that simple fusion methods, such as arithmetic mean, perform as well as or better than other, more complex fusion methods. SESAME’s performance in the 2012 TRECVID MED evaluation was one of the best reported

Parallel assessment of male reproductive function in workers and wild rats exposed to pesticides in banana plantations in Guadeloupe

<p>Abstract</p> <p>Background</p> <p>There is increasing evidence that reproductive abnormalities are increasing in frequency in both human population and among wild fauna. This increase is probably related to exposure to toxic contaminants in the environment. The use of sentinel species to raise alarms relating to human reproductive health has been strongly recommended. However, no simultaneous studies at the same site have been carried out in recent decades to evaluate the utility of wild animals for monitoring human reproductive disorders. We carried out a joint study in Guadeloupe assessing the reproductive function of workers exposed to pesticides in banana plantations and of male wild rats living in these plantations.</p> <p>Methods</p> <p>A cross-sectional study was performed to assess semen quality and reproductive hormones in banana workers and in men working in non-agricultural sectors. These reproductive parameters were also assessed in wild rats captured in the plantations and were compared with those in rats from areas not directly polluted by humans.</p> <p>Results</p> <p>No significant difference in sperm characteristics and/or hormones was found between workers exposed and not exposed to pesticide. By contrast, rats captured in the banana plantations had lower testosterone levels and gonadosomatic indices than control rats.</p> <p>Conclusion</p> <p>Wild rats seem to be more sensitive than humans to the effects of pesticide exposure on reproductive health. We conclude that the concept of sentinel species must be carefully validated as the actual nature of exposure may varies between human and wild species as well as the vulnerable time period of exposure and various ecological factors.</p

SPIN90 associates with mDia1 and the Arp2/3 complex to regulate cortical actin organization

Cell shape is controlled by the submembranous cortex, an actomyosin network mainly generated by two actin nucleators: the Arp2/3 complex and the formin mDia1. Changes in relative nucleator activity may alter cortical organization, mechanics and cell shape. Here we investigate how nucleation-promoting factors mediate interactions between nucleators. In vitro, the nucleation-promoting factor SPIN90 promotes formation of unbranched filaments by Arp2/3, a process thought to provide the initial filament for generation of dendritic networks. Paradoxically, in cells, SPIN90 appears to favour a formin-dominated cortex. Our in vitro experiments reveal that this feature stems mainly from two mechanisms: efficient recruitment of mDia1 to SPIN90-Arp2/3 nucleated filaments and formation of a ternary SPIN90-Arp2/3-mDia1 complex that greatly enhances filament nucleation. Both mechanisms yield rapidly elongating filaments with mDia1 at their barbed ends and SPIN90-Arp2/3 at their pointed ends. Thus, in networks, SPIN90 lowers branching densities and increases the proportion of long filaments elongated by mDia1

On the Benefits of Transparent Compression for Cost-Effective Cloud Data Storage

International audienceInfrastructure-as-a-Service (IaaS) cloud computing has revolutionized the way we think of acquiring computational resources: it allows users to deploy virtual machines (VMs) at large scale and pay only for the resources that were actually used throughout the runtime of the VMs. This new model raises new challenges in the design and development of IaaS middleware: excessive storage costs associated with both user data and VM images might make the cloud less attractive, especially for users that need to manipulate huge data sets and a large number of VM images. Storage costs result not only from storage space utilization, but also from bandwidth consumption: in typical deployments, a large number of data transfers between the VMs and the persistent storage are performed, all under high performance requirements. This paper evaluates the trade-off resulting from transparently applying data compression to conserve storage space and bandwidth at the cost of slight computational overhead. We aim at reducing the storage space and bandwidth needs with minimal impact on data access performance. Our solution builds on BlobSeer, a distributed data management service specifically designed to sustain a high throughput for concurrent accesses to huge data sequences that are distributed at large scale. Extensive experiments demonstrate that our approach achieves large reductions (at least 40%) of bandwidth and storage space utilization, while still attaining high performance levels that even surpass the original (no compression) performance levels in several data-intensive scenarios

Male reproductive health and environmental xenoestrogens

EHP is a publication of the U.S. government. Publication of EHP lies in the public domain and is therefore without copyright. Research articles from EHP may be used freely; however, articles from the News section of EHP may contain photographs or figures copyrighted by other commercial organizations and individuals that may not be used without obtaining prior approval from both the EHP editors and the holder of the copyright. Use of any materials published in EHP should be acknowledged (for example, "Reproduced with permission from Environmental Health Perspectives") and a reference provided for the article from which the material was reproduced.Male reproductive health has deteriorated in many countries during the last few decades. In the 1990s, declining semen quality has been reported from Belgium, Denmark, France, and Great Britain. The incidence of testicular cancer has increased during the same time incidences of hypospadias and cryptorchidism also appear to be increasing. Similar reproductive problems occur in many wildlife species. There are marked geographic differences in the prevalence of male reproductive disorders. While the reasons for these differences are currently unknown, both clinical and laboratory research suggest that the adverse changes may be inter-related and have a common origin in fetal life or childhood. Exposure of the male fetus to supranormal levels of estrogens, such as diethlylstilbestrol, can result in the above-mentioned reproductive defects. The growing number of reports demonstrating that common environmental contaminants and natural factors possess estrogenic activity presents the working hypothesis that the adverse trends in male reproductive health may be, at least in part, associated with exposure to estrogenic or other hormonally active (e.g., antiandrogenic) environmental chemicals during fetal and childhood development. An extensive research program is needed to understand the extent of the problem, its underlying etiology, and the development of a strategy for prevention and intervention.Supported by EU Contract BMH4-CT96-0314