Reliability of environmental sampling culture results using the negative binomial intraclass correlation coefficient.

The Intraclass Correlation Coefficient (ICC) is commonly used to estimate the similarity between quantitative measures obtained from different sources. Overdispersed data is traditionally transformed so that linear mixed model (LMM) based ICC can be estimated. A common transformation used is the natural logarithm. The reliability of environmental sampling of fecal slurry on freestall pens has been estimated for Mycobacterium avium subsp. paratuberculosis using the natural logarithm transformed culture results. Recently, the negative binomial ICC was defined based on a generalized linear mixed model for negative binomial distributed data. The current study reports on the negative binomial ICC estimate which includes fixed effects using culture results of environmental samples. Simulations using a wide variety of inputs and negative binomial distribution parameters (r; p) showed better performance of the new negative binomial ICC compared to the ICC based on LMM even when negative binomial data was logarithm, and square root transformed. A second comparison that targeted a wider range of ICC values showed that the mean of estimated ICC closely approximated the true ICC

TITER: predicting translation initiation sites by deep learning.

MotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning-based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames on gene expression and the mutational effects influencing translation initiation efficiency.Availability and implementationTITER is available as an open-source software and can be downloaded from https://github.com/zhangsaithu/titer [email protected] or [email protected] informationSupplementary data are available at Bioinformatics online

Retinal vascular segmentation using superpixel-based line operator and its application to vascular topology estimation

Purpose: Automatic methods of analyzing of retinal vascular networks, such as retinal blood vessel detection, vascular network topology estimation, and arteries / veins classi cation are of great assistance to the ophthalmologist in terms of diagnosis and treatment of a wide spectrum of diseases. Methods: We propose a new framework for precisely segmenting retinal vasculatures, constructing retinal vascular network topology, and separating the arteries and veins. A non-local total variation inspired Retinex model is employed to remove the image intensity inhomogeneities and relatively poor contrast. For better generalizability and segmentation performance, a superpixel based line operator is proposed as to distinguish between lines and the edges, thus allowing more tolerance in the position of the respective contours. The concept of dominant sets clustering is adopted to estimate retinal vessel topology and classify the vessel network into arteries and veins. Results: The proposed segmentation method yields competitive results on three pub- lic datasets (STARE, DRIVE, and IOSTAR), and it has superior performance when com- pared with unsupervised segmentation methods, with accuracy of 0.954, 0.957, and 0.964, respectively. The topology estimation approach has been applied to ve public databases 1 (DRIVE,STARE, INSPIRE, IOSTAR, and VICAVR) and achieved high accuracy of 0.830, 0.910, 0.915, 0.928, and 0.889, respectively. The accuracies of arteries / veins classi cation based on the estimated vascular topology on three public databases (INSPIRE, DRIVE and VICAVR) are 0.90.9, 0.910, and 0.907, respectively. Conclusions: The experimental results show that the proposed framework has e ectively addressed crossover problem, a bottleneck issue in segmentation and vascular topology recon- struction. The vascular topology information signi cantly improves the accuracy on arteries / veins classi cation

Population Projection and Development of the Mythimna loreyi (Lepidoptera: Noctuidae) as Affected by Temperature: Application of an Age-Stage, Two-Sex Life Table

The Mythimna (=Leucania) loreyi (Duponchel) has recently emerged as a major pest of grain crops in China. Little is known about its basic biology and ecology, making it difficult to predict its population dynamics. An age-stage, two-sex life table was constructed for this insect when reared on maize in the laboratory at five constant temperatures (18, 21, 24, 27, and 30 °C). Both the intrinsic rate of increase (r) and finite rate increase (λ) increased as temperature significantly increased and mean generation time (T) decreased significantly with increasing temperature. The highest values for net reproductive rate (R0) and fecundity were observed at 24 °C. However, M. loreyi was able to develop, survive, and lay eggs at all temperatures tested (18–30 °C). Development rates at different temperatures for the egg, larval, pupal, as well as for a total preoviposition period, fit a linear equation. The lower threshold temperatures of egg, larval, pupal, preoviposition, and total preoviposition period were 8.83, 10.95, 11.67, 9.30, and 9.65 °C, respectively. And their effective accumulated temperatures were 87.64, 298.51, 208.33, 66.47, and 729.93 degree-days, respectively. This study provides insight into the temperature-based phenology and population ecology in M. loreyi. The results will benefit population dynamics monitoring, prediction, and management of this insect pest in the field

Dynamic Gradient Reactivation for Backward Compatible Person Re-identification

We study the backward compatible problem for person re-identification (Re-ID), which aims to constrain the features of an updated new model to be comparable with the existing features from the old model in galleries. Most of the existing works adopt distillation-based methods, which focus on pushing new features to imitate the distribution of the old ones. However, the distillation-based methods are intrinsically sub-optimal since it forces the new feature space to imitate the inferior old feature space. To address this issue, we propose the Ranking-based Backward Compatible Learning (RBCL), which directly optimizes the ranking metric between new features and old features. Different from previous methods, RBCL only pushes the new features to find best-ranking positions in the old feature space instead of strictly alignment, and is in line with the ultimate goal of backward retrieval. However, the sharp sigmoid function used to make the ranking metric differentiable also incurs the gradient vanish issue, therefore stems the ranking refinement during the later period of training. To address this issue, we propose the Dynamic Gradient Reactivation (DGR), which can reactivate the suppressed gradients by adding dynamic computed constant during forward step. To further help targeting the best-ranking positions, we include the Neighbor Context Agents (NCAs) to approximate the entire old feature space during training. Unlike previous works which only test on the in-domain settings, we make the first attempt to introduce the cross-domain settings (including both supervised and unsupervised), which are more meaningful and difficult. The experimental results on all five settings show that the proposed RBCL outperforms previous state-of-the-art methods by large margins under all settings.Comment: Submitted to Pattern Recognition on Dec 06, 2021. Under Revie

Retinal Vascular Network Topology Reconstruction and Artery/Vein Classification via Dominant Set Clustering

The estimation of vascular network topology in complex networks is important in understanding the relationship between vascular changes and a wide spectrum of diseases. Automatic classification of the retinal vascular trees into arteries and veins is of direct assistance to the ophthalmologist in terms of diagnosis and treatment of eye disease. However, it is challenging due to their projective ambiguity and subtle changes in appearance, contrast and geometry in the imaging process. In this paper, we propose a novel method that is capable of making the artery/vein (A/V) distinction in retinal color fundus images based on vascular network topological properties. To this end, we adapt the concept of dominant set clustering and formalize the retinal blood vessel topology estimation and the A/V classification as a pairwise clustering problem. The graph is constructed through image segmentation, skeletonization and identification of significant nodes. The edge weight is defined as the inverse Euclidean distance between its two end points in the feature space of intensity, orientation, curvature, diameter, and entropy. The reconstructed vascular network is classified into arteries and veins based on their intensity and morphology. The proposed approach has been applied to five public databases, INSPIRE, IOSTAR, VICAVR, DRIVE and WIDE, and achieved high accuracies of 95.1%, 94.2%, 93.8%, 91.1%, and 91.0%, respectively. Furthermore, we have made manual annotations of the blood vessel topologies for INSPIRE, IOSTAR, VICAVR, and DRIVE datasets, and these annotations are released for public access so as to facilitate researchers in the community

The Ginger-shaped Asteroid 4179 Toutatis: New Observations from a Successful Flyby of Chang'e-2

On 13 December 2012, Chang'e-2 conducted a successful flyby of the near-Earth asteroid 4179 Toutatis at a closest distance of 770 $\pm$ 120 meters from the asteroid's surface. The highest-resolution image, with a resolution of better than 3 meters, reveals new discoveries on the asteroid, e.g., a giant basin at the big end, a sharply perpendicular silhouette near the neck region, and direct evidence of boulders and regolith, which suggests that Toutatis may bear a rubble-pile structure. Toutatis' maximum physical length and width are (4.75 $\times$ 1.95 km) $\pm$10$\%$, respectively, and the direction of the +$z$ axis is estimated to be (250$\pm$5$^\circ$, 63$\pm$5$^\circ$) with respect to the J2000 ecliptic coordinate system. The bifurcated configuration is indicative of a contact binary origin for Toutatis, which is composed of two lobes (head and body). Chang'e-2 observations have significantly improved our understanding of the characteristics, formation, and evolution of asteroids in general.Comment: 21 pages, 3 figures, 1 tabl