Genome sequence data of the contemporary fresh-market tomatoes.

OBJECTIVE: The fresh-market tomato (Solanum lycopersicum) is bred for direct human consumption. It is selected for specific traits to meet market demands and production systems, and unique genetic variations underlying fresh-market tomato yields have been recently identified. However, DNA sequence variant-trait associations are not yet fully examined even for major traits. To provide a rich genome sequence resource for various genetics and breeding goals for fresh-market tomato traits, we report whole genome sequence data of a pool of contemporary U.S. fresh-market tomatoes. DATA DESCRIPTION: Eighty-one tomatoes were nominated by academic tomato breeding programs in the U.S. Of the 81 tomatoes, 68 were contemporary fresh-market tomatoes, whereas the remaining 13 were relevant fresh-market tomato breeding and germplasm accessions. Whole genome sequencing (WGS) of the 81 tomatoes was conducted using the Illumina next-generation sequencing technology. The polymerase chain reaction (PCR)-free, paired-end sequencing libraries were sequenced on an average depth per sequenced base of 24 × for each tomato. This data note enhances visibility and potential for use of the more diverse, freely accessible whole genome sequence data of contemporary fresh-market tomatoes.

Whole genome sequence data of 516 F2 plants of tomato (Solanum lycopersicum).

The large-fruited fresh-market tomato cultivated in the U.S. represents a unique fruit market class of contemporary (modern) tomatoes for direct consumption. The genomes of F2 plants from crosses between inbred contemporary U.S. large-fruited fresh-market tomatoes were sequenced. 516 F2 individual plants randomly selected from five different biparental segregating populations were used for DNA extraction. The polymerase chain reaction (PCR)-free, paired-end (2 × 150 bp) sequencing libraries (350 bp DNA fragment length) were prepared, and sequenced on average 5 Gb for each plant using the Illumina next-generation sequencing technologies [1,2]. Raw Illumina reads with adapter contamination and/or uncertain nucleotides constitute (Ns, >10 % of either read; Q-score 5 or lower, >50 % of either read) were removed. This data article will contribute to improving our knowledge of the genetic recombination and variation in tomato.

Protein codes promote selective subcellular compartmentalization.

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.

Cartoon Animation Outpainting With Region-Guided Motion Inference.

Cartoon animation video is a popular visual entertainment form worldwide, however many classic animations were produced in a 4:3 aspect ratio that is incompatible with modern widescreen displays. Existing methods like cropping lead to information loss while retargeting causes distortion. Animation companies still rely on manual labor to renovate classic cartoon animations, which is tedious and labor-intensive, but can yield higher-quality videos. Conventional extrapolation or inpainting methods tailored for natural videos struggle with cartoon animations due to the lack of textures in anime, which affects the motion estimation of the objects. In this paper, we propose a novel framework designed to automatically outpaint 4:3 anime to 16:9 via region-guided motion inference. Our core concept is to identify the motion correspondences between frames within a sequence in order to reconstruct missing pixels. Initially, we estimate optical flow guided by region information to address challenges posed by exaggerated movements and solid-color regions in cartoon animations. Subsequently, frames are stitched to produce a pre-filled guide frame, offering structural clues for the extension of optical flow maps. Finally, a voting and fusion scheme utilizes learned fusion weights to blend the aligned neighboring reference frames, resulting in the final outpainting frame. Extensive experiments confirm the superiority of our approach over existing methods.

Using machine learning and partial dependence to evaluate robustness of best linear unbiased prediction (BLUP) for phenotypic values.

Best linear unbiased prediction (BLUP) is widely used in plant research to address experimental variation. For phenotypic values, BLUP accuracy is largely dependent on properly controlled experimental repetition and how variable components are outlined in the model. Thus, determining BLUP robustness implies the need to evaluate contributions from each repetition. Here, we assessed the robustness of BLUP values for simulated or empirical phenotypic datasets, where the BLUP value and each experimental repetition served as dependent and independent (feature) variables, respectively. Our technique incorporated machine learning and partial dependence. First, we compared the feature importance estimated with the neural networks. Second, we compared estimated average marginal effects of individual repetitions, calculated with a partial dependence analysis. We showed that contributions of experimental repetitions are unequal in a phenotypic dataset, suggesting that the calculated BLUP value is likely to be influenced by some repetitions more than others (such as failing to detect simulated true positive associations). To resolve disproportionate sources, variable components in the BLUP model must be further outlined.

AnimeDiffusion: Anime Diffusion Colorization.

Being essential in animation creation, colorizing anime line drawings is usually a tedious and time-consuming manual task. Reference-based line drawing colorization provides an intuitive way to automatically colorize target line drawings using reference images. The prevailing approaches are based on generative adversarial networks (GANs), yet these methods still cannot generate high-quality results comparable to manually-colored ones. In this paper, a new AnimeDiffusion approach is proposed via hybrid diffusions for the automatic colorization of anime face line drawings. This is the first attempt to utilize the diffusion model for reference-based colorization, which demands a high level of control over the image synthesis process. To do so, a hybrid end-to-end training strategy is designed, including phase 1 for training diffusion model with classifier-free guidance and phase 2 for efficiently updating color tone with a target reference colored image. The model learns denoising and structure-capturing ability in phase 1, and in phase 2, the model learns more accurate color information. Utilizing our hybrid training strategy, the network convergence speed is accelerated, and the colorization performance is improved. Our AnimeDiffusion generates colorization results with semantic correspondence and color consistency. In addition, the model has a certain generalization performance for line drawings of different line styles. To train and evaluate colorization methods, an anime face line drawing colorization benchmark dataset, containing 31,696 training data and 579 testing data, is introduced and shared. Extensive experiments and user studies have demonstrated that our proposed AnimeDiffusion outperforms state-of-the-art GAN-based methods and another diffusion-based model, both quantitatively and qualitatively.

3DSN-Net: A 3-D Scale-Aware convNet With Nonlocal Context Guidance for Kidney and Tumor Segmentation From CT Volumes.

Automatic kidney and tumor segmentation from CT volumes is a critical prerequisite/tool for diagnosis and surgical treatment (such as partial nephrectomy). However, it remains a particularly challenging issue as kidneys and tumors often exhibit large-scale variations, irregular shapes, and blurring boundaries. We propose a novel 3-D network to comprehensively tackle these problems; we call it 3DSN-Net. Compared with existing solutions, it has two compelling characteristics. First, with a new scale-aware feature extraction (SAFE) module, the proposed 3DSN-Net is capable of adaptively selecting appropriate receptive fields according to the sizes of targets instead of indiscriminately enlarging them, which is particularly essential for improving the segmentation accuracy of the tumor with large scale variation. Second, we propose a novel yet efficient nonlocal context guidance (NCG) mechanism to capture global dependencies to tackle irregular shapes and blurring boundaries of kidneys and tumors. Instead of directly harnessing a 3-D NCG mechanism, which makes the number of parameters exponentially increase and hence the network difficult to be trained under limited training data, we develop a 2.5D NCG mechanism based on projections of feature cubes, which achieves a tradeoff between segmentation accuracy and network complexity. We extensively evaluate the proposed 3DSN-Net on the famous KiTS dataset with many challenging kidney and tumor cases. Experimental results demonstrate our solution consistently outperforms state-of-the-art 3-D networks after being equipped with scale aware and NCG mechanisms, particularly for tumor segmentation.

Data-Driven Linear Quadratic Optimization for Controller Synthesis With Structural Constraints.

For various typical cases and situations where the formulation results in an optimal control problem, the linear quadratic regulator (LQR) approach and its variants continue to be highly attractive. In certain scenarios, it can happen that some prescribed structural constraints on the gain matrix would arise. Consequently then, the algebraic Riccati equation (ARE) is no longer applicable in a straightforward way to obtain the optimal solution. This work presents a rather effective alternative optimization approach based on gradient projection. The utilized gradient is obtained through a data-driven methodology, and then projected onto applicable constrained hyperplanes. Essentially, this projection gradient determines a direction of progression and computation for the gain matrix update with a decreasing functional cost; and then the gain matrix is further refined in an iterative framework. With this formulation, a data-driven optimization algorithm is summarized for controller synthesis with structural constraints. This data-driven approach has the key advantage that it avoids the necessity of precise modeling which is always required in the classical model-based counterpart; and thus the approach can additionally accommodate various model uncertainties. Illustrative examples are also provided in the work to validate the theoretical results.

Adaptive Safe Reinforcement Learning With Full-State Constraints and Constrained Adaptation for Autonomous Vehicles.

High-performance learning-based control for the typical safety-critical autonomous vehicles invariably requires that the full-state variables are constrained within the safety region even during the learning process. To solve this technically critical and challenging problem, this work proposes an adaptive safe reinforcement learning (RL) algorithm that invokes innovative safety-related RL methods with the consideration of constraining the full-state variables within the safety region with adaptation. These are developed toward assuring the attainment of the specified requirements on the full-state variables with two notable aspects. First, thus, an appropriately optimized backstepping technique and the asymmetric barrier Lyapunov function (BLF) methodology are used to establish the safe learning framework to ensure system full-state constraints requirements. More specifically, each subsystem's control and partial derivative of the value function are decomposed with asymmetric BLF-related items and an independent learning part. Then, the independent learning part is updated to solve the Hamilton-Jacobi-Bellman equation through an adaptive learning implementation to attain the desired performance in system control. Second, with further Lyapunov-based analysis, it is demonstrated that safety performance is effectively doubly assured via a methodology of a constrained adaptation algorithm during optimization (which incorporates the projection operator and can deal with the conflict between safety and optimization). Therefore, this algorithm optimizes system control and ensures that the full set of state variables involved is always constrained within the safety region during the whole learning process. Comparison simulations and ablation studies are carried out on motion control problems for autonomous vehicles, which have verified superior performance with smaller variance and better convergence performance under uncertain circumstances. The effectiveness of the safe performance of overall system control with the proposed method accordingly has been verified.

Distinct chemical environments in biomolecular condensates.

Diverse mechanisms have been described for selective enrichment of biomolecules in membrane-bound organelles, but less is known about mechanisms by which molecules are selectively incorporated into biomolecular assemblies such as condensates that lack surrounding membranes. The chemical environments within condensates may differ from those outside these bodies, and if these differed among various types of condensate, then the different solvation environments would provide a mechanism for selective distribution among these intracellular bodies. Here we use small molecule probes to show that different condensates have distinct chemical solvating properties and that selective partitioning of probes in condensates can be predicted with deep learning approaches. Our results demonstrate that different condensates harbor distinct chemical environments that influence the distribution of molecules, show that clues to condensate chemical grammar can be ascertained by machine learning and suggest approaches to facilitate development of small molecule therapeutics with optimal subcellular distribution and therapeutic benefit.

Precise sensorimotor control impacts reproductive fitness of C. elegans in 3D environments.

The ability of animals to sense and navigate towards relevant cues in complex and elaborate habitats is paramount for their survival and reproductive success. The nematode Caenorhabditis elegans uses a simple and elegant sensorimotor program to track odors in its environments. Whether this allows the worm to effectively navigate a complex environment and increase its evolutionary success has not been tested yet. We designed an assay to test whether C. elegans can track odors in a complex 3D environment. We then used a previously established 3D cultivation system to test whether defect in tracking odors to find food in a complex environment affected their brood size. We found that wild-type worms can accurately migrate toward a variety of odors in 3D. However, mutants of the muscarinic acetylcholine receptor GAR-3 which have a sensorimotor integration defect that results in a subtle navigational defect steering towards attractive odors, display decreased chemotaxis to the odor butanone not seen in the traditional 2D assay. We also show that the decreased ability to locate appetitive stimuli in 3D leads to reduced brood size not observed in the standard 2D culture conditions. Our study shows that mutations in genes previously overlooked in 2D conditions can have a significant impact in the natural habitat, and highlights the importance of considering the evolutionary selective pressures that have shaped the behavior, as well as the underlying genes and neural circuits.

Comparative Evaluation of the Efficacy of Combined Intramedullary Pinning with K-Wires Pinning in the Treatment of Fifth Metacarpal Neck Fractures versus Conventional Techniques-K-Wires Pinning and Intramedullary Pinning.

Background and Objectives: Since the neck is the weakest part of the metacarpals, the most common metacarpal fracture is a neck fracture, a type which accounts for 38% of all hand fractures. Such fractures can be fixed using a variety of conventional techniques, including intramedullary pinning and K-wire pinning. However, conventional techniques involve complications, such as angulation, stiffness, and rotational deformity. The purpose of this study was to compare the usefulness of our new technique, combined intramedullary pinning with K-wire pinning (IPKP), with those of intramedullary pinning (IP) and K-wire pinning (KP). Materials and Methods: This was a single-center, randomized controlled trial conducted between January 2005 and April 2023. A total of 158 patients with acute displaced fractures of the fifth-metacarpal neck were randomly assigned to either the IPKP group (n = 48), the KP group (n = 60), or the IP group (n = 50). We radiographically evaluated angulation and shortening in three visits: pre-operatively, post-operatively, and at a 1-year follow-up. We clinically evaluated the ranges of motion and Quick-DASH scores to assess daily living performance and the cosmetic scores, using the SBSES score, to assess patients' satisfaction with their cosmetic outcomes. Results: The IPKP group was superior to the KP group and the IP group regarding radiographical and clinical assessments at the 1-year follow-up visit. The angulation was 15.7° (±7.7) in the KP group, 17.0° (±5.9) in the IP group, and 12.6° (±2.5) in the IPKP group (p < 0.001) at the 1-year follow-up visit. The shortening was 0.9 mm (±0.3) in the KP group, 1.4 mm (±0.2) in the IP group, and 0.4 mm (±0.1) in the IPKP group (m < 0.001) at the 1-year follow-up visit. The TAM was 272.6° (±17.5) in the KP group, 271.1° (±18.0) in the IP group, and 274.1° (±14.9) in the IPKP group (p = 0.42). Four patients (6.6%) in the KP group and two patients (4%) in the IP group were reported as having stiffness, while no patients were found to have stiffness in the IPKP group. The average Quick-DASH score was 2.3 (±0.5) in the KP group, 2.5 (±0.4) in the IP group, and 1.9 (±0.4) in the IPKP group (p > 0.05). The average cosmetic score was 3.7 (±1.2) in the KP group, 3.8 (±0.9) in the IP group, and 4.7 (±0.8) in the IPKP group (p < 0.001). A complication involving nonunion occurred in one case (1.6%) in the KP group, while there were three cases (6%) of rotational deformity in the IP groups. Conclusions: With the IPKP technique, accurate reduction can be achieved to improve hand function and cosmetic outcomes.

Retargeting video with an end-to-end framework.

Video holds significance in computer graphics applications. Because of the heterogeneous of digital devices, retargeting videos becomes an essential function to enhance user viewing experience in such applications. In the research of video retargeting, preserving the relevant visual content in videos, avoiding flicking, and processing time are the vital challenges. Extending image retargeting techniques to the video domain is challenging due to the high running time. Prior work of video retargeting mainly utilizes time-consuming preprocessing to analyze frames. Plus, being tolerant of different video content, avoiding important objects from shrinking, and the ability to play with arbitrary ratios are the limitations that need to be resolved in these systems requiring investigation. In this paper, we present an end-to-end RETVI method to retarget videos to arbitrary aspect ratios. We eliminate the computational bottleneck in the conventional approaches by designing RETVI with two modules, content feature analyzer (CFA) and adaptive deforming estimator (ADE). The extensive experiments and evaluations show that our system outperforms previous work in quality and running time.

Transcription factors interact with RNA to regulate genes.

Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

MeshWGAN: Mesh-to-Mesh Wasserstein GAN With Multi-Task Gradient Penalty for 3D Facial Geometric Age Transformation.

As the metaverse develops rapidly, 3D facial age transformation is attracting increasing attention, which may bring many potential benefits to a wide variety of users, e.g., 3D aging figures creation, 3D facial data augmentation and editing. Compared with 2D methods, 3D face aging is an underexplored problem. To fill this gap, we propose a new mesh-to-mesh Wasserstein generative adversarial network (MeshWGAN) with a multi-task gradient penalty to model a continuous bi-directional 3D facial geometric aging process. To the best of our knowledge, this is the first architecture to achieve 3D facial geometric age transformation via real 3D scans. As previous image-to-image translation methods cannot be directly applied to the 3D facial mesh, which is totally different from 2D images, we built a mesh encoder, decoder, and multi-task discriminator to facilitate mesh-to-mesh transformations. To mitigate the lack of 3D datasets containing children's faces, we collected scans from 765 subjects aged 5-17 in combination with existing 3D face databases, which provided a large training dataset. Experiments have shown that our architecture can predict 3D facial aging geometries with better identity preservation and age closeness compared to 3D trivial baselines. We also demonstrated the advantages of our approach via various 3D face-related graphics applications. Our project will be publicly available at: https://github.com/Easy-Shu/MeshWGAN.

Image Collage on Arbitrary Shape via Shape-Aware Slicing and Optimization.

Image collage is a very useful tool for visualizing an image collection. Most of the existing methods and commercial applications for generating image collages are designed on simple shapes, such as rectangular and circular layouts. This greatly limits the use of image collages in some artistic and creative settings. Although there are some methods that can generate irregularly-shaped image collages, they often suffer from severe image overlapping and excessive blank space. This prevents such methods from being effective information communication tools. In this paper, we present a shape slicing algorithm and an optimization scheme that can create image collages of arbitrary shapes in an informative and visually pleasing manner given an input shape and an image collection. To overcome the challenge of irregular shapes, we propose a novel algorithm, called Shape-Aware Slicing, which partitions the input shape into cells based on medial axis and binary slicing tree. Shape-Aware Slicing, which is designed specifically for irregular shapes, takes human perception and shape structure into account to generate visually pleasing partitions. Then, the layout is optimized by analyzing input images with the goal of maximizing the total salient regions of the images. To evaluate our method, we conduct extensive experiments and compare our results against previous work. The evaluations show that our proposed algorithm can efficiently arrange image collections on irregular shapes and create visually superior results than prior work and existing commercial tools.

Regenerating Arbitrary Video Sequences with Distillation Path-Finding.

If the video has long been mentioned as a widespread visualization form, the animation sequence in the video is mentioned as storytelling for people. Producing an animation requires intensive human labor from skilled professional artists to obtain plausible animation in both content and motion direction, incredibly for animations with complex content, multiple moving objects, and dense movement. This paper presents an interactive framework to generate new sequences according to the users' preference on the starting frame. The critical contrast of our approach versus prior work and existing commercial applications is that novel sequences with arbitrary starting frame are produced by our system with a consistent degree in both content and motion direction. To achieve this effectively, we first learn the feature correlation on the frameset of the given video through a proposed network called RSFNet. Then, we develop a novel path-finding algorithm, SDPF, which formulates the knowledge of motion directions of the source video to estimate the smooth and plausible sequences. The extensive experiments show that our framework can produce new animations on the cartoon and natural scenes and advance prior works and commercial applications to enable users to obtain more predictable results.

Genetic architecture of fresh-market tomato yield.

BACKGROUND: The fresh-market tomato (Solanum lycopersicum) is bred for direct consumption and is selected for a high yield of large fruits. To understand the genetic variations (distinct types of DNA sequence polymorphism) that influence the yield, we collected the phenotypic variations in the yields of total fruit, extra-large-sized fruit, small-sized fruit, or red-colored fruit from 68 core inbred contemporary U.S. fresh-market tomatoes for three consecutive years and the genomic information in 8,289,741 single nucleotide polymorphism (SNP) positions from the whole-genome resequencing of these tomatoes. RESULTS: Genome-wide association (GWA) mapping using the SNP data with or without SNP filtering steps using the regularization methods, validated with quantitative trait loci (QTL) linkage mapping, identified 18 significant association signals for traits evaluated. Among them, 10 of which were not located within genomic regions previously identified as being associated with fruit size/shape. When mapping-driven association signals [558 SNPs associated with 28 yield (component) traits] were used to calculate genomic estimated breeding values (GEBVs) of evaluated traits, the prediction accuracies of the extra-large-sized fruit and small-sized fruit yields were higher than those of the total and red-colored fruit yields, as we tested the generated breeding values in inbred tomatoes and F2 populations. Improved accuracy in GEBV calculation of evaluated traits was achieved by using 364 SNPs identified using the regularization methods. CONCLUSIONS: Together, these results provide an understanding of the genetic variations underlying the heritable phenotypic variability in yield in contemporary tomato breeding and the information necessary for improving such economically important and complex quantitative trait through breeding.

Balance-Aware Grid Collage for Small Image Collections.

Grid collages (GClg) of small image collections are popular and useful in many applications, such as personal album management, online photo posting, and graphic design. In this article, we focus on how visual effects influence individual preferences through various arrangements of multiple images under such scenarios. A novel balance-aware metric is proposed to bridge the gap between multi-image joint presentation and visual pleasure. The metric merges psychological achievements into the field of grid collage. To capture user preference, a bonus mechanism related to a user-specified special location in the grid and uniqueness values of the subimages is integrated into the metric. An end-to-end reinforcement learning mechanism empowers the model without tedious manual annotations. Experiments demonstrate that our metric can evaluate the GClg visual balance in line with human subjective perception, and the model can generate visually pleasant GClg results, which is comparable to manual designs.