Semantic Human Mesh Reconstruction with Textures

The field of 3D detailed human mesh reconstruction has made significant progress in recent years. However, current methods still face challenges when used in industrial applications due to unstable results, low-quality meshes, and a lack of UV unwrapping and skinning weights. In this paper, we present SHERT, a novel pipeline that can reconstruct semantic human meshes with textures and high-precision details. SHERT applies semantic- and normal-based sampling between the detailed surface (e.g. mesh and SDF) and the corresponding SMPL-X model to obtain a partially sampled semantic mesh and then generates the complete semantic mesh by our specifically designed self-supervised completion and refinement networks. Using the complete semantic mesh as a basis, we employ a texture diffusion model to create human textures that are driven by both images and texts. Our reconstructed meshes have stable UV unwrapping, high-quality triangle meshes, and consistent semantic information. The given SMPL-X model provides semantic information and shape priors, allowing SHERT to perform well even with incorrect and incomplete inputs. The semantic information also makes it easy to substitute and animate different body parts such as the face, body, and hands. Quantitative and qualitative experiments demonstrate that SHERT is capable of producing high-fidelity and robust semantic meshes that outperform state-of-the-art methods.Comment: Accepted to CVPR 2024. Project page: https://zhanxy.xyz/projects/shert

Research on incentive mechanisms for anti-heterogeneous federated learning based on reputation and contribution

An optimization algorithm for federated learning, equipped with an incentive mechanism, is introduced to tackle the challenges of excessive iterations, prolonged training durations, and suboptimal efficiency encountered during model training within the federated learning framework. Initially, the algorithm establishes reputation values that are tied to both time and model loss metrics. This foundation enables the creation of incentive mechanisms aimed at rewarding honest nodes while penalizing malicious ones. Subsequently, a bidirectional selection mechanism anchored in blockchain technology is developed, allowing smart contracts to enroll nodes with high reputations in training sessions, thus filtering out malicious clients and enhancing local training efficiency. Furthermore, the integration of the Earth Mover's Distance (EMD) mechanism serves to lessen the impact of non-IID (non-Independent and Identically Distributed) data on the global model, leading to a reduction in the frequency of model training cycles and an improvement in model accuracy. Experimental results confirm that this approach maintains high model accuracy in non-IID data settings, outperforming traditional federated learning algorithms

RES-Scanner:a software package for genome-wide identification of RNA-editing sites

BACKGROUND: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. RESULTS: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. RES-Scanner allows the use of both raw HTS reads and pre-aligned reads in BAM format as inputs. When inputs are HTS reads, RES-Scanner can invoke the BWA mapper to align reads to the reference genome automatically. To rigorously identify potential false positives resulting from genetic variants, we have equipped RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-seq data. These models are applicable to samples from either single individuals or a pool of multiple individuals if the ploidy information is known. In addition, RES-Scanner implements statistical tests to distinguish genuine RNA-editing sites from sequencing errors, and provides a series of sophisticated filtering options to remove false positives resulting from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available. CONCLUSION: RES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-seq and DNA-seq data. The package is freely available. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13742-016-0143-4) contains supplementary material, which is available to authorized users

Polymeric Immunoglobulin Receptor Mediates Immune Excretion of Mucosal IgM–Antigen Complexes Across Intestinal Epithelium in Flounder (Paralichthys olivaceus)

Polymeric immunoglobulin receptor (pIgR) is one important player of mucosal defenses, but very little is known on pIgR-mediated immune excretion of the antigens that penetrate mucosal surface in fish. Previously, we cloned the pIgR of flounder (Paralichthys olivaceus) and developed anti-pIgR antibody. In this study, the flounders were immunized intraperitoneally with the chicken ovalbumin (OVA) and the control protein bovine serum albumin (BSA) to elicit mucosal IgM antibody and pIgR response, and then challenged with OVA via caudal vein injection after the immunized OVA was absent from fish body at the fourth week after immunization. After OVA challenge, strong OVA-positive fluorescence signals were observed in lamina propria (LP) submucosa and epithelial cells of the hindgut at 30 min, increased proceeding toward the distal portion of intestinal folds, reached a peak at 2–3 h, and then weakened and disappeared at 12 h, indicating that the OVA rapidly diffused from bloodstream into LP submucosa and excreted across intestinal epithelium. Whereas in BSA-immunized and OVA-challenged control fish, the OVA was detected in LP submucosa but not in intestinal epithelium due to the lack of OVA-specific antibody. Accordingly, in intestinal epithelium, the transepithelial transport of OVA was confirmed by immunogold electron microscopy, and co-localization of OVA, IgM, and pIgR was illuminated by multiple-label immunofluorescence confocal microscopy and analyzed using Image J software. Furthermore, in gut mucus but not in serum, an ~800-kDa protein band showed IgM-positive, OVA-positive, and pIgR-positive simultaneously, and the OVA, together with IgM and secretory component (SC) of pIgR, could be immunoprecipitated by anti-OVA antibody, demonstrating the existence of SC–polymeric IgM–OVA complexes. All these results collectively revealed that the pIgR could transport mucosal IgM–OVA complexes from LP across intestinal epithelium into gut mucus via the transcytosis in flounder. These new findings provided direct evidences for pIgR-mediated immune excretion of IgM–antigen complexes, and better understanding the role of pIgR in mucosal immunity in teleost fish

Efficient wide-bandgap perovskite solar cells with open-circuit voltage deficit below 0.4 V via hole-selective interface engineering

Wide-bandgap mixed-halide perovskite solar cells (WBG-PSCs) are promising top cells for efficient tandem photovoltaics to achieve high power conversion efficiency (PCE) at low cost. However, the open-circuit voltage (VOC) of WBG-PSCs is still unsatisfactory as the VOC-deficit is generally larger than 0.45 V. Herein, we report a buried interface engineering strategy that substantially improves the VOC of WBG-PSCs by inserting amphophilic molecular hole-selective materials featuring with a cyanovinyl phosphonic acid (CPA) anchoring group between the perovskite and substrate. The assembly and redistribution of CPA-based amphiphilic molecules at the perovskite-substrate buried interface not only promotes the growth of a low-defect crystalline perovskite thin film, but also suppresses the photo-induced halide phase separation. The energy level alignment between wide-bandgap perovskite and the hole-selective layer is further improved by modulating the substituents on the triphenylamine donor moiety (methoxyls for MPA-CPA, methyls for MePA-CPA, and bare TPA-CPA). Using a 1.68 eV bandgap perovskite, the MePA-CPA-based devices achieved an unprecedentedly high VOC of 1.29 V and PCE of 22.3% under standard AM 1.5 sunlight. The VOC-deficit (&lt;0.40 V) is the lowest value reported for WBG-PSCs. This work not only provides an effective approach to decreasing the VOC-deficit of WBG-PSCs, but also confirms the importance of energy level alignment at the charge-selective layers in PSCs.</p

Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum

The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis-related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light-dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates

Predicting Microsatellite Instability Status in Colorectal Cancer Based on Triphasic Enhanced Computed Tomography Radiomics Signatures: A Multicenter Study

BackgroundThis study aimed to develop and validate a computed tomography (CT)-based radiomics model to predict microsatellite instability (MSI) status in colorectal cancer patients and to identify the radiomics signature with the most robust and high performance from one of the three phases of triphasic enhanced CT.MethodsIn total, 502 colorectal cancer patients with preoperative contrast-enhanced CT images and available MSI status (441 in the training cohort and 61 in the external validation cohort) were enrolled from two centers in our retrospective study. Radiomics features of the entire primary tumor were extracted from arterial-, delayed-, and venous-phase CT images. The least absolute shrinkage and selection operator method was used to retain the features closely associated with MSI status. Radiomics, clinical, and combined Clinical Radiomics models were built to predict MSI status. Model performance was evaluated by receiver operating characteristic curve analysis.ResultsThirty-two radiomics features showed significant correlation with MSI status. Delayed-phase models showed superior predictive performance compared to arterial- or venous-phase models. Additionally, age, location, and carcinoembryonic antigen were considered useful predictors of MSI status. The Clinical Radiomics nomogram that incorporated both clinical risk factors and radiomics parameters showed excellent performance, with an AUC, accuracy, and sensitivity of 0.898, 0.837, and 0.821 in the training cohort and 0.964, 0.918, and 1.000 in the validation cohort, respectively.ConclusionsThe proposed CT-based radiomics signature has excellent performance in predicting MSI status and could potentially guide individualized therapy