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Establishing reliable correspondences is essential for registration tasks such as 3D and 2D3D registration. Existing methods commonly leverage geometric or semantic point features to generate potential correspondences. However, these features may face challenges such as large deformation, scale inconsistency, and ambiguous matching problems (e.g., symmetry). Additionally, many previous methods, which rely on single-pass prediction, may struggle with local minima in complex scenarios. To mitigate these challenges, we introduce a diffusion matching model for robust correspondence construction. Our approach treats correspondence estimation as a denoising diffusion process within the doubly stochastic matrix space, which gradually denoises (refines) a doubly stochastic matching matrix to the ground-truth one for high-quality correspondence estimation. It involves a forward diffusion process that gradually introduces Gaussian noise into the ground truth matching matrix and a reverse denoising process that iteratively refines the noisy matching matrix. In particular, the feature extraction from the backbone occurs only once during the inference phase. Our lightweight denoising module utilizes the same feature at each reverse sampling step. Evaluation of our method on both 3D and 2D3D registration tasks confirms its effectiveness., Comment: arXiv admin note: text overlap with arXiv:2401.00436

Point Cloud Registration is a fundamental and challenging problem in 3D computer vision. Recent works often utilize the geometric structure information in point feature embedding or outlier rejection for registration while neglecting to consider explicitly isometry-preserving constraint ($e.g.,$ point pair linked edge's length preserving after transformation) in training. We claim that the explicit isometry-preserving constraint is also important for improving feature representation abilities in the feature training stage. To this end, we propose a \underline{G}raph \underline{M}atching \underline{O}ptimization based \underline{Net}work (GMONet for short), which utilizes the graph-matching optimizer to explicitly exert the isometry preserving constraints in the point feature training to improve the point feature representation. Specifically, we exploit a partial graph-matching optimizer to optimize the super point ($i.e.,$ down-sampled key points) features and a full graph-matching optimizer to optimize fine-level point features in the overlap region. Meanwhile, we leverage the inexact proximal point method and the mini-batch sampling technique to accelerate these two graph-matching optimizers. Given high discriminative point features in the evaluation stage, we utilize the RANSAC approach to estimate the transformation between the scanned pairs. The proposed method has been evaluated on the 3DMatch/3DLoMatch benchmarks and the KITTI benchmark. The experimental results show that our method performs competitively compared to state-of-the-art baselines.

Image guidance is an effective strategy for depth super-resolution. Generally, most existing methods employ hand-crafted operators to decompose the high-frequency (HF) and low-frequency (LF) ingredients from low-resolution depth maps and guide the HF ingredients by directly concatenating them with image features. However, the hand-designed operators usually cause inferior HF maps (e.g., distorted or structurally missing) due to the diverse appearance of complex depth maps. Moreover, the direct concatenation often results in weak guidance because not all image features have a positive effect on the HF maps. In this paper, we develop a recurrent structure attention guided (RSAG) framework, consisting of two important parts. First, we introduce a deep contrastive network with multi-scale filters for adaptive frequency-domain separation, which adopts contrastive networks from large filters to small ones to calculate the pixel contrasts for adaptive high-quality HF predictions. Second, instead of the coarse concatenation guidance, we propose a recurrent structure attention block, which iteratively utilizes the latest depth estimation and the image features to jointly select clear patterns and boundaries, aiming at providing refined guidance for accurate depth recovery. In addition, we fuse the features of HF maps to enhance the edge structures in the decomposed LF maps. Extensive experiments show that our approach obtains superior performance compared with state-of-the-art depth super-resolution methods., Comment: Accepted by AAAI-2023

Real depth super-resolution (DSR), unlike synthetic settings, is a challenging task due to the structural distortion and the edge noise caused by the natural degradation in real-world low-resolution (LR) depth maps. These defeats result in significant structure inconsistency between the depth map and the RGB guidance, which potentially confuses the RGB-structure guidance and thereby degrades the DSR quality. In this paper, we propose a novel structure flow-guided DSR framework, where a cross-modality flow map is learned to guide the RGB-structure information transferring for precise depth upsampling. Specifically, our framework consists of a cross-modality flow-guided upsampling network (CFUNet) and a flow-enhanced pyramid edge attention network (PEANet). CFUNet contains a trilateral self-attention module combining both the geometric and semantic correlations for reliable cross-modality flow learning. Then, the learned flow maps are combined with the grid-sampling mechanism for coarse high-resolution (HR) depth prediction. PEANet targets at integrating the learned flow map as the edge attention into a pyramid network to hierarchically learn the edge-focused guidance feature for depth edge refinement. Extensive experiments on real and synthetic DSR datasets verify that our approach achieves excellent performance compared to state-of-the-art methods., Comment: Accepted by AAAI-2023

Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier feature representations. In this paper, we develop a novel variational non-local network-based outlier rejection framework for robust alignment. By reformulating the non-local feature learning with variational Bayesian inference, the Bayesian-driven long-range dependencies can be modeled to aggregate discriminative geometric context information for inlier/outlier distinction. Specifically, to achieve such Bayesian-driven contextual dependencies, each query/key/value component in our non-local network predicts a prior feature distribution and a posterior one. Embedded with the inlier/outlier label, the posterior feature distribution is label-dependent and discriminative. Thus, pushing the prior to be close to the discriminative posterior in the training step enables the features sampled from this prior at test time to model high-quality long-range dependencies. Notably, to achieve effective posterior feature guidance, a specific probabilistic graphical model is designed over our non-local model, which lets us derive a variational low bound as our optimization objective for model training. Finally, we propose a voting-based inlier searching strategy to cluster the high-quality hypothetical inliers for transformation estimation. Extensive experiments on 3DMatch, 3DLoMatch, and KITTI datasets verify the effectiveness of our method., Comment: Accepted by CVPR2023

Efficiently finding optimal correspondences between point clouds is crucial for solving both rigid and non-rigid point cloud registration problems. Existing methods often rely on geometric or semantic feature embedding to establish correspondences and estimate transformations or flow fields. Recently, state-of-the-art methods have employed RAFT-like iterative updates to refine the solution. However, these methods have certain limitations. Firstly, their iterative refinement design lacks transparency, and their iterative updates follow a fixed path during the refinement process, which can lead to suboptimal results. Secondly, these methods overlook the importance of refining or optimizing correspondences (or matching matrices) as a precursor to solving transformations or flow fields. They typically compute candidate correspondences based on distances in the point feature space. However, they only project the candidate matching matrix into some matrix space once with Sinkhorn or dual softmax operations to obtain final correspondences. This one-shot projected matching matrix may be far from the globally optimal one, and these approaches do not consider the distribution of the target matching matrix. In this paper, we propose a novel approach that exploits the Denoising Diffusion Model to predict a searching gradient for the optimal matching matrix within the Doubly Stochastic Matrix Space. During the reverse denoising process, our method iteratively searches for better solutions along this denoising gradient, which points towards the maximum likelihood direction of the target matching matrix. Our method offers flexibility by allowing the search to start from any initial matching matrix provided by the online backbone or white noise. Experimental evaluations on the 3DMatch/3DLoMatch and 4DMatch/4DLoMatch datasets demonstrate the effectiveness of our newly designed framework.

In this paper, we introduce an SE(3) diffusion model-based point cloud registration framework for 6D object pose estimation in real-world scenarios. Our approach formulates the 3D registration task as a denoising diffusion process, which progressively refines the pose of the source point cloud to obtain a precise alignment with the model point cloud. Training our framework involves two operations: An SE(3) diffusion process and an SE(3) reverse process. The SE(3) diffusion process gradually perturbs the optimal rigid transformation of a pair of point clouds by continuously injecting noise (perturbation transformation). By contrast, the SE(3) reverse process focuses on learning a denoising network that refines the noisy transformation step-by-step, bringing it closer to the optimal transformation for accurate pose estimation. Unlike standard diffusion models used in linear Euclidean spaces, our diffusion model operates on the SE(3) manifold. This requires exploiting the linear Lie algebra $\mathfrak{se}(3)$ associated with SE(3) to constrain the transformation transitions during the diffusion and reverse processes. Additionally, to effectively train our denoising network, we derive a registration-specific variational lower bound as the optimization objective for model learning. Furthermore, we show that our denoising network can be constructed with a surrogate registration model, making our approach applicable to different deep registration networks. Extensive experiments demonstrate that our diffusion registration framework presents outstanding pose estimation performance on the real-world TUD-L, LINEMOD, and Occluded-LINEMOD datasets., Comment: Accepted by NeurIPS-2023

Robust obstacle avoidance is one of the critical steps for successful goal-driven indoor navigation tasks.Due to the obstacle missing in the visual image and the possible missed detection issue, visual image-based obstacle avoidance techniques still suffer from unsatisfactory robustness. To mitigate it, in this paper, we propose a novel implicit obstacle map-driven indoor navigation framework for robust obstacle avoidance, where an implicit obstacle map is learned based on the historical trial-and-error experience rather than the visual image. In order to further improve the navigation efficiency, a non-local target memory aggregation module is designed to leverage a non-local network to model the intrinsic relationship between the target semantic and the target orientation clues during the navigation process so as to mine the most target-correlated object clues for the navigation decision. Extensive experimental results on AI2-Thor and RoboTHOR benchmarks verify the excellent obstacle avoidance and navigation efficiency of our proposed method. The core source code is available at https://github.com/xwaiyy123/object-navigation., Comment: 9 pages, 7 figures, 43 references. This paper has been accepted for ACM MM 2023

Learning robust feature matching between the template and search area is crucial for 3D Siamese tracking. The core of Siamese feature matching is how to assign high feature similarity on the corresponding points between the template and search area for precise object localization. In this paper, we propose a novel point cloud registration-driven Siamese tracking framework, with the intuition that spatially aligned corresponding points (via 3D registration) tend to achieve consistent feature representations. Specifically, our method consists of two modules, including a tracking-specific nonlocal registration module and a registration-aided Sinkhorn template-feature aggregation module. The registration module targets at the precise spatial alignment between the template and search area. The tracking-specific spatial distance constraint is proposed to refine the cross-attention weights in the nonlocal module for discriminative feature learning. Then, we use the weighted SVD to compute the rigid transformation between the template and search area, and align them to achieve the desired spatially aligned corresponding points. For the feature aggregation model, we formulate the feature matching between the transformed template and search area as an optimal transport problem and utilize the Sinkhorn optimization to search for the outlier-robust matching solution. Also, a registration-aided spatial distance map is built to improve the matching robustness in indistinguishable regions (e.g., smooth surface). Finally, guided by the obtained feature matching map, we aggregate the target information from the template into the search area to construct the target-specific feature, which is then fed into a CenterPoint-like detection head for object localization. Extensive experiments on KITTI, NuScenes and Waymo datasets verify the effectiveness of our proposed method.

Contrastive learning has shown great promise in the field of graph representation learning. By manually constructing positive/negative samples, most graph contrastive learning methods rely on the vector inner product based similarity metric to distinguish the samples for graph representation. However, the handcrafted sample construction (e.g., the perturbation on the nodes or edges of the graph) may not effectively capture the intrinsic local structures of the graph. Also, the vector inner product based similarity metric cannot fully exploit the local structures of the graph to characterize the graph difference well. To this end, in this paper, we propose a novel adaptive subgraph generation based contrastive learning framework for efficient and robust self-supervised graph representation learning, and the optimal transport distance is utilized as the similarity metric between the subgraphs. It aims to generate contrastive samples by capturing the intrinsic structures of the graph and distinguish the samples based on the features and structures of subgraphs simultaneously. Specifically, for each center node, by adaptively learning relation weights to the nodes of the corresponding neighborhood, we first develop a network to generate the interpolated subgraph. We then construct the positive and negative pairs of subgraphs from the same and different nodes, respectively. Finally, we employ two types of optimal transport distances (i.e., Wasserstein distance and Gromov-Wasserstein distance) to construct the structured contrastive loss. Extensive node classification experiments on benchmark datasets verify the effectiveness of our graph contrastive learning method., Comment: ECCV 2022

Cross-spectrum depth estimation aims to provide a depth map in all illumination conditions with a pair of dual-spectrum images. It is valuable for autonomous vehicle applications when the vehicle is equipped with two cameras of different modalities. However, images captured by different-modality cameras can be photometrically quite different. Therefore, cross-spectrum depth estimation is a very challenging problem. Moreover, the shortage of large-scale open-source datasets also retards further research in this field. In this paper, we propose an unsupervised visible-light image guided cross-spectrum (i.e., thermal and visible-light, TIR-VIS in short) depth estimation framework given a pair of RGB and thermal images captured from a visible-light camera and a thermal one. We first adopt a base depth estimation network using RGB-image pairs. Then we propose a multi-scale feature transfer network to transfer features from the TIR-VIS domain to the VIS domain at the feature level to fit the trained depth estimation network. At last, we propose a cross-spectrum depth cycle consistency to improve the depth result of dual-spectrum image pairs. Meanwhile, we release a large dual-spectrum depth estimation dataset with visible-light and far-infrared stereo images captured in different scenes to the society. The experiment result shows that our method achieves better performance than the compared existing methods. Our datasets is available at https://github.com/whitecrow1027/VIS-TIR-Datasets.

Double Q-learning is a popular reinforcement learning algorithm in Markov decision process (MDP) problems. Clipped Double Q-learning, as an effective variant of Double Q-learning, employs the clipped double estimator to approximate the maximum expected action value. Due to the underestimation bias of the clipped double estimator, the performance of clipped Double Q-learning may be degraded in some stochastic environments. In this paper, in order to reduce the underestimation bias, we propose an action candidate-based clipped double estimator for Double Q-learning. Specifically, we first select a set of elite action candidates with high action values from one set of estimators. Then, among these candidates, we choose the highest valued action from the other set of estimators. Finally, we use the maximum value in the second set of estimators to clip the action value of the chosen action in the first set of estimators and the clipped value is used for approximating the maximum expected action value. Theoretically, the underestimation bias in our clipped Double Q-learning decays monotonically as the number of action candidates decreases. Moreover, the number of action candidates controls the trade-off between the overestimation and underestimation biases. In addition, we also extend our clipped Double Q-learning to continuous action tasks via approximating the elite continuous action candidates. We empirically verify that our algorithm can more accurately estimate the maximum expected action value on some toy environments and yield good performance on several benchmark problems., Comment: arXiv admin note: substantial text overlap with arXiv:2105.00704

Unsupervised point cloud registration algorithm usually suffers from the unsatisfied registration precision in the partially overlapping problem due to the lack of effective inlier evaluation. In this paper, we propose a neighborhood consensus based reliable inlier evaluation method for robust unsupervised point cloud registration. It is expected to capture the discriminative geometric difference between the source neighborhood and the corresponding pseudo target neighborhood for effective inlier distinction. Specifically, our model consists of a matching map refinement module and an inlier evaluation module. In our matching map refinement module, we improve the point-wise matching map estimation by integrating the matching scores of neighbors into it. The aggregated neighborhood information potentially facilitates the discriminative map construction so that high-quality correspondences can be provided for generating the pseudo target point cloud. Based on the observation that the outlier has the significant structure-wise difference between its source neighborhood and corresponding pseudo target neighborhood while this difference for inlier is small, the inlier evaluation module exploits this difference to score the inlier confidence for each estimated correspondence. In particular, we construct an effective graph representation for capturing this geometric difference between the neighborhoods. Finally, with the learned correspondences and the corresponding inlier confidence, we use the weighted SVD algorithm for transformation estimation. Under the unsupervised setting, we exploit the Huber function based global alignment loss, the local neighborhood consensus loss, and spatial consistency loss for model optimization. The experimental results on extensive datasets demonstrate that our unsupervised point cloud registration method can yield comparable performance., Comment: Accepted by AAAI 2022

In this paper, by modeling the point cloud registration task as a Markov decision process, we propose an end-to-end deep model embedded with the cross-entropy method (CEM) for unsupervised 3D registration. Our model consists of a sampling network module and a differentiable CEM module. In our sampling network module, given a pair of point clouds, the sampling network learns a prior sampling distribution over the transformation space. The learned sampling distribution can be used as a "good" initialization of the differentiable CEM module. In our differentiable CEM module, we first propose a maximum consensus criterion based alignment metric as the reward function for the point cloud registration task. Based on the reward function, for each state, we then construct a fused score function to evaluate the sampled transformations, where we weight the current and future rewards of the transformations. Particularly, the future rewards of the sampled transforms are obtained by performing the iterative closest point (ICP) algorithm on the transformed state. By selecting the top-k transformations with the highest scores, we iteratively update the sampling distribution. Furthermore, in order to make the CEM differentiable, we use the sparsemax function to replace the hard top-$k$ selection. Finally, we formulate a Geman-McClure estimator based loss to train our end-to-end registration model. Extensive experimental results demonstrate the good registration performance of our method on benchmark datasets., Comment: Accepted by ICCV-2021

Point cloud registration is a fundamental problem in 3D computer vision. In this paper, we cast point cloud registration into a planning problem in reinforcement learning, which can seek the transformation between the source and target point clouds through trial and error. By modeling the point cloud registration process as a Markov decision process (MDP), we develop a latent dynamic model of point clouds, consisting of a transformation network and evaluation network. The transformation network aims to predict the new transformed feature of the point cloud after performing a rigid transformation (i.e., action) on it while the evaluation network aims to predict the alignment precision between the transformed source point cloud and target point cloud as the reward signal. Once the dynamic model of the point cloud is trained, we employ the cross-entropy method (CEM) to iteratively update the planning policy by maximizing the rewards in the point cloud registration process. Thus, the optimal policy, i.e., the transformation between the source and target point clouds, can be obtained via gradually narrowing the search space of the transformation. Experimental results on ModelNet40 and 7Scene benchmark datasets demonstrate that our method can yield good registration performance in an unsupervised manner., Comment: Accepted by IJCAI-2021

Double Q-learning is a popular reinforcement learning algorithm in Markov decision process (MDP) problems. Clipped Double Q-learning, as an effective variant of Double Q-learning, employs the clipped double estimator to approximate the maximum expected action value. Due to the underestimation bias of the clipped double estimator, performance of clipped Double Q-learning may be degraded in some stochastic environments. In this paper, in order to reduce the underestimation bias, we propose an action candidate based clipped double estimator for Double Q-learning. Specifically, we first select a set of elite action candidates with the high action values from one set of estimators. Then, among these candidates, we choose the highest valued action from the other set of estimators. Finally, we use the maximum value in the second set of estimators to clip the action value of the chosen action in the first set of estimators and the clipped value is used for approximating the maximum expected action value. Theoretically, the underestimation bias in our clipped Double Q-learning decays monotonically as the number of the action candidates decreases. Moreover, the number of action candidates controls the trade-off between the overestimation and underestimation biases. In addition, we also extend our clipped Double Q-learning to continuous action tasks via approximating the elite continuous action candidates. We empirically verify that our algorithm can more accurately estimate the maximum expected action value on some toy environments and yield good performance on several benchmark problems., Comment: Accepted by AAAI2021

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

BACKGROUND: Tribolium castaneum is a species of Coleoptera, the largest and most diverse order of all eukaryotes. Components of the innate immune system are hardly known in this insect, which is in a key phylogenetic position to inform us about genetic innovations accompanying the evolution of holometabolous insects. We have annotated immunity-related genes and compared them with homologous molecules from other species. RESULTS: Around 300 candidate defense proteins are identified based on sequence similarity to homologs known to participate in immune responses. In most cases, paralog counts are lower than those of Drosophila melanogaster or Anopheles gambiae but are substantially higher than Apis mellifera. The genome contains probable orthologs for nearly all members of the Toll, IMD, and JAK/STAT pathways. While total numbers of the clip-domain serine proteinases are approximately equal in the fly (29), mosquito (32) and beetle (30), lineage-specific expansion of the family is discovered in all three species. Sixteen of the thirty-one serpin genes form a large cluster in a 50 kb region resulted from extensive gene duplications. Among the nine Toll-like proteins, four are orthologous to Drosophila Toll. The presence of scavenger receptors and other related proteins indicates a role of cellular responses in the entire system. The structures of some antimicrobial peptides drastically differ from those in other orders of insects. CONCLUSIONS: A framework of information on Tribolium immunity is established, which may serve as a stepping stone for future genetic analyses of defense responses in a nondrosophiline genetic model insect.

Heat exchangers have been used extensively and play an important role in the capital cost, energy efficiency and physical size of refrigeration and air conditioning systems. In this dissertation, a simulation and optimization tool to improve effectiveness and efficiency in design, rating, and analysis of air to refrigerant heat exchangers including conventional finned tube coils and emerging microchannel heat exchangers, Coil Designer, is developed and investigated using a general-purpose modeling concept and user-friendly interface. It is applicable to design of condensers, evaporators, and heating and cooling coils under any operating conditions. A network viewpoint was adopted to establish the general-purpose model and allow for analysis of arbitrary tube circuitry and mal-distribution of fluid flow inside the tubes. Comprehensive evaluation of solutions to the highly nonlinear system of equations in the local thermal/hydraulic performance within the tube network was conducted and a new solution method to successively approximate the physics of heat and fluid flow was developed to enhance the solution convergence capability. A segment-by-segment approach within each tube was implemented, to account for two-dimensional non-uniformity of air distribution across the exchanger, and heterogeneous refrigerant flow patterns through a tube. A further sub-dividable-segment model was created in order to address the significant change of properties and heat transfer coefficients in the single-phase and two-phase regime when a segment experiences flow regime change. The effectiveness-NTU method for cross-flow configuration was used also for combined heat and mass transfer problem under dehumidification, by defining equivalent thermal resistance and heat capacity. Object-oriented programming techniques were applied in developing Coil Designer to facilitate flexible and customizable design platform and building graphic user-friendly interface. Coupled heat exchangers with mult