GRID: Scene-Graph-based Instruction-driven Robotic Task Planning

Recent works have shown that Large Language Models (LLMs) can promote grounding instructions to robotic task planning. Despite the progress, most existing works focused on utilizing raw images to help LLMs understand environmental information, which not only limits the observation scope but also typically requires massive multimodal data collection and large-scale models. In this paper, we propose a novel approach called Graph-based Robotic Instruction Decomposer (GRID), leverages scene graph instead of image to perceive global scene information and continuously plans subtask in each stage for a given instruction. Our method encodes object attributes and relationships in graphs through an LLM and Graph Attention Networks, integrating instruction features to predict subtasks consisting of pre-defined robot actions and target objects in the scene graph. This strategy enables robots to acquire semantic knowledge widely observed in the environment from the scene graph. To train and evaluate GRID, we build a dataset construction pipeline to generate synthetic datasets in graph-based robotic task planning. Experiments have shown that our method outperforms GPT-4 by over 25.4% in subtask accuracy and 43.6% in task accuracy. Experiments conducted on datasets of unseen scenes and scenes with different numbers of objects showed that the task accuracy of GRID declined by at most 3.8%, which demonstrates its good cross-scene generalization ability. We validate our method in both physical simulation and the real world

The ClpP protease homologue is required for the transmission traits and cell division of the pathogen Legionella pneumophila

<p>Abstract</p> <p>Background</p> <p><it>Legionella pneumophila</it>, the intracellular bacterial pathogen that causes Legionnaires' disease, exhibit characteristic transmission traits such as elevated stress tolerance, shortened length and virulence during the transition from the replication phase to the transmission phase. ClpP, the catalytic core of the Clp proteolytic complex, is widely involved in many cellular processes via the regulation of intracellular protein quality.</p> <p>Results</p> <p>In this study, we showed that ClpP was required for optimal growth of <it>L. pneumophila </it>at high temperatures and under several other stress conditions. We also observed that cells devoid of <it>clpP </it>exhibited cell elongation, incomplete cell division and compromised colony formation. Furthermore, we found that the <it>clpP</it>-deleted mutant was more resistant to sodium stress and failed to proliferate in the amoebae host <it>Acanthamoeba castellanii</it>.</p> <p>Conclusions</p> <p>The data present in this study illustrate that the ClpP protease homologue plays an important role in the expression of transmission traits and cell division of <it>L. pneumophila</it>, and further suggest a putative role of ClpP in virulence regulation.</p

Human cytomegalovirus IE1 downregulates Hes1 in neural progenitor cells as a potential E3 ubiquitin ligase

This work was supported by: National Natural Science Foundation of China http://www.nsfc.gov.cn/; #81620108021: Fetal Brain Maldevelopment Caused by Sox2 Downregulation during Congenital Cytomegalovirus Infection; #31600145: The mechanism of HCMV-IE1 regulating Hes1 expression and rhythm in neural progenitor cells; #81571355: Construction of Murine Cytomegalovirus Derived viral tools for Specific Glia Tracing; #81271850: The regulation mechanism of HCMV infection on Notch signaling pathway in NPCs; and Sino-Africa Joint Research Center, Chinese Academy of Sciences http://www.sinafrica.cas.cn/; #SAJC201605: Geographical distribution and genetic variation of pathogens in Africa. This work is tightly linked to or is an important component of the above list projects, and is financially supported by all the fundings.Congenital human cytomegalovirus (HCMV) infection is the leading cause of neurological disabilities in children worldwide, but the mechanisms underlying these disorders are far from well-defined. HCMV infection has been shown to dysregulate the Notch signaling pathway in human neural progenitor cells (NPCs). As an important downstream effector of Notch signaling, the transcriptional regulator Hairy and Enhancer of Split 1 (Hes1) is essential for governing NPC fate and fetal brain development. In the present study, we report that HCMV infection downregulates Hes1 protein levels in infected NPCs. The HCMV 72-kDa immediate-early 1 protein (IE1) is involved in Hes1 degradation by assembling a ubiquitination complex and promoting Hes1 ubiquitination as a potential E3 ubiquitin ligase, followed by proteasomal degradation of Hes1. Sp100A, an important component of PML nuclear bodies, is identified to be another target of IE1-mediated ubiquitination. A C-terminal acidic region in IE1, spanning amino acids 451 to 475, is required for IE1/Hes1 physical interaction and IE1-mediated Hes1 ubiquitination, but is dispensable for IE1/Sp100A interaction and ubiquitination. Our study suggests a novel mechanism linking downregulation of Hes1 protein to neurodevelopmental disorders caused by HCMV infection. Our findings also complement the current knowledge of herpesviruses by identifying IE1 as the first potential HCMV-encoded E3 ubiquitin ligase.Publisher PDFPeer reviewe

Lentiviral Transgenic MicroRNA-Based shRNA Suppressed Mouse Cytochromosome P450 3A (CYP3A) Expression in a Dose-Dependent and Inheritable Manner

Cytochomosome P450 enzymes (CYP) are heme-containing monooxygenases responsible for oxidative metabolism of many exogenous and endogenous compounds including drugs. The species difference of CYP limits the extent to which data obtained from animals can be translated to humans in pharmacodynamics or pharmacokinetics studies. Transgenic expression of human CYP in animals lacking or with largely reduced endogenous CYP counterparts is recognized as an ideal strategy to correct CYP species difference. CYP3A is the most abundant CYP subfamily both in human and mammals. In this study, we designed a microRNA-based shRNA (miR-shRNA) simultaneously targeting four members of mouse CYP3A subfamily (CYP3A11, CYP3A16, CYP3A41 and CYP3A44), and transgenic mice expressing the designed miR-shRNA were generated by lentiviral transgenesis. Results showed that the CYP3A expression level in transgenic mice was markedly reduced compared to that in wild type or unrelated miR-shRNA transgenic mice, and was inversely correlated to the miR-shRNA expression level. The CYP3A expression levels in transgenic offspring of different generations were also remarkably lower compared to those of controls, and moreover the inhibition rate of CYP3A expression remained comparable over generations. The ratio of the targeted CYP3A transcriptional levels was comparable between knockdown and control mice of the same gender as detected by RT-PCR DGGE analysis. These data suggested that transgenic miR-shRNA suppressed CYP3A expression in a dose-dependent and inheritable manner, and transcriptional levels of the targeted CYP3As were suppressed to a similar extent. The observed knockdown efficacy was further confirmed by enzymatic activity analysis, and data showed that CYP3A activities in transgenic mice were markedly reduced compared to those in wild-type or unrelated miR-shRNA transgenic controls (1.11±0.71 vs 5.85±1.74, 5.9±2.4; P<0.01). This work laid down a foundation to further knock down the remaining murine CYP3As or CYPs of other subfamilies, and a basis to generate CYP knockdown animals of other species

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family