FaSTrack: a Modular Framework for Real-Time Motion Planning and Guaranteed Safe Tracking

Real-time, guaranteed safe trajectory planning is vital for navigation in unknown environments. However, real-time navigation algorithms typically sacrifice robustness for computation speed. Alternatively, provably safe trajectory planning tends to be too computationally intensive for real-time replanning. We propose FaSTrack, Fast and Safe Tracking, a framework that achieves both real-time replanning and guaranteed safety. In this framework, real-time computation is achieved by allowing any trajectory planner to use a simplified \textit{planning model} of the system. The plan is tracked by the system, represented by a more realistic, higher-dimensional \textit{tracking model}. We precompute the tracking error bound (TEB) due to mismatch between the two models and due to external disturbances. We also obtain the corresponding tracking controller used to stay within the TEB. The precomputation does not require prior knowledge of the environment. We demonstrate FaSTrack using Hamilton-Jacobi reachability for precomputation and three different real-time trajectory planners with three different tracking-planning model pairs.Comment: Published in the IEEE Transactions on Automatic Contro

Is the NH4+-induced growth inhibition caused by the NH4+ form of the nitrogen source or by soil acidification?

Soil acidification often occurs when the concentration of ammonium (NH4+) in soil rises, such as that observed in farmland. Both soil acidification and excess NH4+ have serious adverse effects on crop growth and food production. However, we still do not know which of these two inhibitors has a greater impact on the growth of crops, and the degree of their inhibitory effect on crop growth have not been accurately evaluated. 31 wheat cultivars originating in various areas of China were planted under 5 mM sole NH4+ (ammonium nitrogen, AN) or nitrate nitrogen in combined with two pH levels resembling acidified conditions (5.0 and 6.5). The results showed that the shoots and roots biomass were severely reduced by AN in both and these reduction effects were strengthened by a low medium pH. The concentration of free NH4+ and amino acids, the glutamine synthetase activity were significantly higher, but the total soluble sugar content was reduced under NH4+ conditions, and the glutamine synthetase activity was reduced by a low medium pH. Cultivar variance was responsible for the largest proportion of the total variance in plant dry weight, leaf area, nodal root number, total root length and root volume; the nitrogen (N) form explains most of the variation in N and C metabolism; the effects of pH were the greatest for plant height and root average diameter. So, soil acidification and excess NH4+ would cause different degrees of inhibition effects on different plant tissues. The findings are expected to be useful for applying effective strategies for reducing NH4+ stress in the field

Unraveling the transcriptome-based network of tfh cells in primary sjogren syndrome: insights from a systems biology approach

BackgroundPrimary Sjogren Syndrome (pSS) is an autoimmune disease characterized by immune cell infiltration. While the presence of follicular T helper (Tfh) cells in the glandular microenvironment has been observed, their biological functions and clinical significance remain poorly understood.MethodsWe enrolled a total of 106 patients with pSS and 46 patients without pSS for this study. Clinical data and labial salivary gland (LSG) biopsies were collected from all participants. Histological staining was performed to assess the distribution of Tfh cells and B cells. Transcriptome analysis using RNA-sequencing (RNA-seq) was conducted on 56 patients with pSS and 26 patients without pSS to uncover the underlying molecular mechanisms of Tfh cells. To categorize patients, we employed the single-sample gene set enrichment analysis (ssGSEA) algorithm, dividing them into low- and high-Tfh groups. We then utilized gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and deconvolution tools to explore functional and immune infiltration differences between the low- and high-Tfh groups.ResultsPatients with pSS had a higher positive rate of the antinuclear antibody (ANA), anti-Ro52, anti-SSA, anti-SSB and hypergammaglobulinaemia and higher levels of serum IgG compared to the non-pSS. Histopathologic analyses revealed the presence of Tfh cells (CD4+CXCR5+ICOS+) in germinal centers (GC) within the labial glands of pSS patients. GSEA, WGCNA, and correlation analysis indicated that the high-Tfh group was associated with an immune response related to virus-mediated IFN response and metabolic processes, primarily characterized by hypoxia, elevated glycolysis, and oxidative phosphorylation levels. In pSS, most immune cell types exhibited significantly higher infiltration levels in the high-Tfh group compared to the low-Tfh group. Additionally, patients in the Tfh-high group demonstrated a higher positive rate of the ANA, rheumatoid factor (RF), and hypergammaglobulinaemia, as well as higher serum IgG levels.ConclusionOur study suggests that Tfh cells may play a crucial role in the pathogenesis of pSS and could serve as potential therapeutic targets in pSS patients

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

Abstract Background Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China. Results Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata. Conclusion Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata