Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV)

Ranaviruses are emerging pathogens that have led to global impact and public concern. As a rarely endangered species and the largest amphibian in the world, the Chinese giant salamander, Andrias davidianus, has recently undergone outbreaks of epidemic diseases with high mortality. In this study, we isolated and identified a novel ranavirus from the Chinese giant salamanders that exhibited systemic hemorrhage and swelling syndrome with high death rate in China during May 2011 to August 2012. The isolate, designated Andrias davidianus ranavirus (ADRV), not only could induce cytopathic effects in different fish cell lines and yield high viral titers, but also caused severely hemorrhagic lesions and resulted in 100% mortality in experimental infections of salamanders. The complete genome of ADRV was sequenced and compared with other sequenced amphibian ranaviruses. Gene content and phylogenetic analyses revealed that ADRV should belong to an amphibian subgroup in genus Ranavirus, and is more closely related to frog ranaviruses than to other salamander ranaviruses. Homologous gene comparisons show that ADRV contains 99%, 97%, 94%, 93% and 85% homologues in RGV, FV3, CMTV, TFV and ATV genomes respectively. In addition, several variable major genes, such as duplicate US22 family-like genes, viral eukaryotic translation initiation factor 2 alpha gene and novel 75L gene with both motifs of nuclear localization signal (NLS) and nuclear export signal (NES), were predicted to contribute to pathogen virulence and host susceptibility. These findings confirm the etiologic role of ADRV in epidemic diseases of Chinese giant salamanders, and broaden our understanding of evolutionary emergence of ranaviruses

Experimental study on biaxial dynamical compressive test and PFC2D numerical simulation of artificial rock sample with single joint

Dynamic biaxial compression tests and Particle Flow Code numerical simulations of the cement mortar specimens with a single joint were carried out to study the mechanical properties and crack evolution of artificial rock samples with a single joint. The effects of lateral stress 2, loading rate V , the dip angle β (between the vertical loading direction and the joint) on the biaxial compressive strength b, and the evolution lawof crackwere investigated. Test results showed that; (1) when both the dip angle β and the loading rate V remained unchanged, the biaxial compressive strength b increased with the increase in the lateral stress 2, while 2 had no obvious effect on the crack evolution law; (2) when both the dip angle β and the lateral stress 2 were kept unchanged, the loading rate V had an insignificant effect on the biaxial compressive strength b and the crack evolution law; (3) when both the lateral stress 2 and the loading rate V were constant, the biaxial compressive strength b decreased first and then increased with the increase in the dip angle β ; however, the dip angle β did not significantly affect the crack evolution law. The conclusions obtained in this paper are presented for the first time

Paragraph-to-Image Generation with Information-Enriched Diffusion Model

Text-to-image (T2I) models have recently experienced rapid development, achieving astonishing performance in terms of fidelity and textual alignment capabilities. However, given a long paragraph (up to 512 words), these generation models still struggle to achieve strong alignment and are unable to generate images depicting complex scenes. In this paper, we introduce an information-enriched diffusion model for paragraph-to-image generation task, termed ParaDiffusion, which delves into the transference of the extensive semantic comprehension capabilities of large language models to the task of image generation. At its core is using a large language model (e.g., Llama V2) to encode long-form text, followed by fine-tuning with LORA to alignthe text-image feature spaces in the generation task. To facilitate the training of long-text semantic alignment, we also curated a high-quality paragraph-image pair dataset, namely ParaImage. This dataset contains a small amount of high-quality, meticulously annotated data, and a large-scale synthetic dataset with long text descriptions being generated using a vision-language model. Experiments demonstrate that ParaDiffusion outperforms state-of-the-art models (SD XL, DeepFloyd IF) on ViLG-300 and ParaPrompts, achieving up to 15% and 45% human voting rate improvements for visual appeal and text faithfulness, respectively. The code and dataset will be released to foster community research on long-text alignment.Comment: The project website is at: https://weijiawu.github.io/ParaDiffusionPage/. Code: https://github.com/weijiawu/ParaDiffusio

Natrium Benzoate Alleviates Neuronal Apoptosis via the DJ-1-Related Anti-oxidative Stress Pathway Involving Akt Phosphorylation in a Rat Model of Traumatic Spinal Cord Injury

This study aimed to explore the neuroprotective effects and mechanisms of natrium benzoate (NaB) and DJ-1 in attenuating reactive oxygen species (ROS)-induced neuronal apoptosis in traumatic spinal cord injury (t-SCI) in rats. T-SCI was induced by clip compression. The protein expression and neuronal apoptosis was evaluated by Western blotting, double immunofluorescence staining and transmission electron microscope (TEM). ROS level, spinal cord water content (SCWC) and Evans blue (EB) extravasation was also examined. Locomotor function was evaluated by Basso, Beattie, and Bresnahan (BBB) and inclined plane test (IPT) scores. We found that DJ-1 is expressed in spinal cord neurons and increased after t-SCI. At 24 h post-injury, the levels of DJ-1, p-Akt, SOD2, ROS, p-p38 MAPK/p38 MAPK ratio, and CC-3 increased, while the Bcl-2/Bax ratio decreased. NaB upregulated DJ-1, p-Akt, and SOD2, decreased ROS, p-p38 MAPK/p38 MAPK ratio, and CC-3, and increased the Bcl-2/Bax ratio, which were reversed by DJ-1 siRNA. The proportion of CC-3- and TUNEL-positive neurons also increased after t-SCI and was reduced by NaB. These effects were reversed by MK2206. Moreover, the level of oxDJ-1 increased after t-SCI, which was decreased by DJ-1 siRNA, NaB or the combination of them. NaB also reduced mitochondrial vacuolization, SCWC and EB extravasation, and improved locomotor function assessed by the BBB and IPT scores. In conclusion, NaB increased DJ-1, and thus reduced ROS and ROS-induced neuronal apoptosis by promoting Akt phosphorylation in t-SCI rats. NaB shows potential as a therapeutic agent for t-SCI, with DJ-1 as its main target

KwaiYiiMath: Technical Report

Recent advancements in large language models (LLMs) have demonstrated remarkable abilities in handling a variety of natural language processing (NLP) downstream tasks, even on mathematical tasks requiring multi-step reasoning. In this report, we introduce the KwaiYiiMath which enhances the mathematical reasoning abilities of KwaiYiiBase1, by applying Supervised Fine-Tuning (SFT) and Reinforced Learning from Human Feedback (RLHF), including on both English and Chinese mathematical tasks. Meanwhile, we also constructed a small-scale Chinese primary school mathematics test set (named KMath), consisting of 188 examples to evaluate the correctness of the problem-solving process generated by the models. Empirical studies demonstrate that KwaiYiiMath can achieve state-of-the-art (SOTA) performance on GSM8k, CMath, and KMath compared with the similar size models, respectively.Comment: technical report. arXiv admin note: text overlap with arXiv:2306.16636 by other author

Universal phase transitions of B1 structured stoichiometric transition-metal carbides

The high-pressure phase transitions of B1-structured stoichiometric transition metal carbides (TMCs, TM=Ti, Zr, Hf, V, Nb, and Ta) were systematically investigated using ab initio calculations. These carbides underwent universal phase transitions along two novel phase-transition routes, namely, B1\rightarrowdistorted TlI (TlI')\rightarrowTlI and/or B1\rightarrowdistorted TiB (TiB')\rightarrowTiB, when subjected to pressures. The two routes can coexist possibly because of the tiny enthalpy differences between the new phases under corresponding pressures. Four new phases result from atomic slips of the B1-structured parent phases under pressure. After completely releasing the pressure, taking TiC as a representative of TMCs, only its new TlI'-type phase is mechanically and dynamically stable, and may be recovered.Comment: [email protected]

Hyaluronic acid ameliorates intervertebral disc degeneration via promoting mitophagy activation

Activation of mitophagy was considered to be a potential therapeutic strategy for intervertebral disc degeneration (IDD). There was evidence suggesting that hyaluronic acid (HA) can protect mitochondria from oxidative stress in chondrocytes, but its protective effects and mechanism in nucleus pulposus cells (NPCs) remain unclear. This study aimed to confirm the effect of HA promoting mitophagy and protecting mitochondria function in NPCs, and explore its underlying mechanism. NPCs were treated with high molecular weight HA, tert-butyl hydroperoxide (TBHP) and Cyclosporin A (CsA). Mitophagy, mitochondrial function, apoptosis, senescence and extracellular matrix (ECM) degradation were measured. Then, NPCs were transfected with C1QBP siRNA, mitophagy and mitochondrial function were tested. The therapeutic effects of HA on IDD by promoting mitophagy were assessed in bovine intervertebral disc organ culture model. The results showed that TBHP induced oxidative stress, mitochondrial dysfunction, NPCs apoptosis, senescence and ECM degradation. Treated by HA, mitophagy was activated, concomitantly, mitochondrial dysfunction, apoptosis, senescence and ECM degradation were ameliorated. Mitophagy inhibition by CsA partially eliminated the protective effects of HA against oxidative stress. After transfected with C1QBP siRNA to reduce the expression of C1QBP in NPCs, the effect of HA promoting mitophagy was inhibited and the protective effect of HA against oxidative stress was weaken. Additionally, HA alleviated NPCs apoptosis and ECM degradation in bovine intervertebral disc organ culture model. These findings suggest that HA can protect mitochondrial function through activation of mitophagy in NPCs and ameliorate IDD. Furthermore, C1QBP is involved in HA promoting mitophagy and protecting NPCs from oxidative stress. Taken together, our results provide substantial evidence for the clinical applications of HA in the prevention and treatment of IDD

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies

Molecular characterization and clinical relevance of metabolic expression subtypes in human cancers.

Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1—master regulators of carbohydrate metabolic subtypes-modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility

Dietary supplementation with inulin improves burn-induced skeletal muscle atrophy by regulating gut microbiota disorders

Abstract Inulin, as a prebiotic, could modulate the gut microbiota. Burn injury leads to gut microbiota disorders and skeletal muscle catabolism. Therefore, whether inulin can improve burn-induced muscle atrophy by regulating microbiota disorders remains unknown. This study aimed to clarify that inulin intake alleviates gut microbiota disorders and skeletal muscle atrophy in burned rats. Rats were divided into the sham group, burn group, prebiotic inulin intervention group, and pseudo-aseptic validation group. A 30% total body surface area (TBSA) third-degree burn wound on dorsal skin was evaluated in all groups except the sham group. Animals in the intervention group received 7 g/L inulin. Animals in the validation group received antibiotic cocktail and inulin treatment. In our study inulin intervention could significantly alleviate the burn-induced skeletal muscle mass decrease and skeletal myoblast cell apoptosis. Inulin intake increased the abundances of Firmicutes and Actinobacteria but decreased the abundance of Proteobacteria. The biosynthesis of amino acids was the most meaningful metabolic pathway distinguishing the inulin intervention group from the burn group, and further mechanistic studies have shown that inulin can promote the phosphorylation of the myogenesis-related proteins PI3K, AKT and P70S6K and activate PI3K/AKT signaling for protein synthesis. In conclusion, inulin alleviated burn induced muscle atrophy through PI3K/AKT signaling and regulated gut microbiota dysbiosis