Skeena: Efficient and Consistent Cross-Engine Transactions

Database systems are becoming increasingly multi-engine. In particular, a main-memory database engine may coexist with a traditional storage-centric engine in a system to support various applications. It is desirable to allow applications to access data in both engines using cross-engine transactions. But existing systems are either only designed for single-engine accesses, or impose many restrictions by limiting cross-engine transactions to certain isolation levels and table operations. The result is inadequate cross-engine support in terms of correctness, performance and programmability. This paper describes Skeena, a holistic approach to cross-engine transactions. We propose a lightweight snapshot tracking structure and an atomic commit protocol to efficiently ensure correctness and support various isolation levels. Evaluation results show that Skeena maintains high performance for single-engine transactions and enables cross-engine transactions which can improve throughput by up to 30x by judiciously placing tables in different engines.Comment: To appear at SIGMOD 202

Sulfur Isotopic Analysis and Sulfur Source Study of Phosphorite-associated Sulfate from the Ediacaran Doushantuo Formation in Guizhou Province

BACKGROUND： Phosphate deposit of the Ediacaran Doushantuo Formation in Guizhou province is a typical representative of the global phosphorite formation event in the late Neoproterozoic, which is closely related to climate change and evolution of life. However, the current research on the deposition of phosphorus deposits is limited to the mechanism of phosphorus formation and the source of phosphorus, and research on the phosphorus formation process of this deposit and its correlation with the paleo-ocean environment of the same period by isotopic geochemical indicators is relatively weak. OBJECTIVES： In order to determine the sulfur source of phosphorite-associated sulfate. METHODS: Based on the field section observation and the study of petrological characteristics under the microscope, elemental analyzer-isotope ratio mass spectrometry (EA-IRMS) was used to measure the sulfur isotopic composition of phosphorite-associated sulfate from the Ediacaran Doushantuo Formation. RESULTS: The sulfur isotopic composition of phosphorite-associated sulfate ranged from 32.7‰ to 36.9‰ (n=32, mean=34.1‰), which was 11‰ lower than that of the seawater of the same period, indicating that the phosphorite-associated sulfate was not all from the surface seawater. CONCLUSIONS: The idealized early ocean (>520Ma) chemical zoning model indicates that there is a relatively 34S-depleted H2S zone in the seawater at the same time. Combined with the understanding that the source of phosphorus in the phosphorite is closely related to the upwelling, it can be considered that the sulfur isotopic composition of phosphorite-associated sulfate of the Doushantuo Formation represents the mixed signal of surface seawater and upwelling

Extracellular matrix-derived peptide stimulates the generation of endocrine progenitors and islet organoids from iPSCs

Induced pluripotent stem cells (iPSCs) have enormous potential in producing human tissues endlessly. We previously reported that type V collagen (COL5), a pancreatic extracellular matrix protein, promotes islet development and maturation from iPSCs. In this study, we identified a bioactive peptide domain of COL5, WWASKS, through bioinformatic analysis of decellularized pancreatic ECM (dpECM)-derived collagens. RNA-sequencing suggests that WWASKS induces the formation of pancreatic endocrine progenitors while suppressing the development of other types of organs. The expressions of hypoxic genes were significantly downregulated in the endocrine progenitors formed under peptide stimulation. Furthermore, we unveiled an enhancement of iPSC-derived islets’ (i-islets) glucose sensitivity under peptide stimulation. These i-islets secrete insulin in a glucose responsive manner. They were comprised of α, β, δ, and γ cells and were assembled into a tissue architecture similar to that of human islets. Mechanistically, the peptide is able to activate the canonical Wnt signaling pathway, permitting the translocation of β-catenin from the cytoplasm to the nucleus for pancreatic progenitor development. Collectively, for the first time, we demonstrated that an ECM-derived peptide dictates iPSC fate toward the generation of endocrine progenitors and subsequent islet organoids

Domain Adaptation for Sensor-Based Human Activity Recognition with a Graph Convolutional Network

Sensor-based human activity recognition (HAR) plays a fundamental role in various mobile application scenarios, but the model performance of HAR heavily relies on the richness of the dataset and the completeness of data annotation. To address the shortage of comprehensive activity types in collected datasets, we adopt the domain adaptation technique with a graph neural network-based approach by incorporating an adaptive learning mechanism to enhance the action recognition model’s generalization ability, especially when faced with limited sample sizes. To evaluate the effectiveness of our proposed approach, we conducted experiments using three well-known datasets: MHealth, PAMAP2, and TNDA. The experimental results demonstrate the efficacy of our approach in sensor-based HAR tasks, achieving impressive average accuracies of 98.88%, 98.58%, and 97.78% based on the respective datasets. Furthermore, we conducted transfer learning experiments to address the domain adaptation problem. These experiments revealed that our proposed model exhibits exceptional transferability and distinguishing ability, even in scenarios with limited available samples. Thus, our approach offers a practical and viable solution for sensor-based HAR tasks

Anaerobic Ammonium Oxidation in Acidic Red Soils

Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 106 to 1.81 × 109 and 4.81 × 106 to 4.54 × 108 copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a 15N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g−1 h−1, contributing 16.67–53.27% to N2 production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China

Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3

Abstract Background Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. Results Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47–69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography–mass spectrometry (LC–MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. Conclusions Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization

Effectiveness of enteral feeding protocol on clinical outcomes in critically ill patients: A before and after study.

Enteral nutrition (EN) feeding protocol was proposed to have positive impact on critically ill patients. However, current studies showed conflicting results. The present study aimed to investigate whether enteral feeding protocol was able to improve clinical outcomes in critically ill patients.A before (stage 1) and after (stage 2) interventional study was performed in 10 tertiary care hospitals. All patients expected to stay in the intensive care unit (ICU) for over three days were potentially eligible. Clinical outcomes such as 28-day mortality, ICU length of stay, duration of mechanical ventilation (MV), and nosocomial infection were compared between the two stages.A total of 410 patients were enrolled during the study period, including 236 in stage 1 and 174 in stage 2. EN feeding protocol was able to increase the proportion of EN in day 2 (41.8±22.3 vs. 50.0±28.3%; p = 0.006) and day 6 (70.3±25.2 vs. 77.6±25.8%; p = 0.006). EN percentages tended to be higher in stage 1 than that in stage 2 on other days, but statistical significance was not reached. There was no difference in 28-day mortality between stage 1 and 2 (0.14 vs. 0.14; p = 0.984). Implementation of EN feeding protocol marginally reduced ICU length of stay (19.44±18.48 vs. 16.29±16.19 days; p = 0.077). There was no difference in the duration of MV between stage a and stage 2 (14.24±14.49 vs. 14.51±17.55 days; p = 0.877).The study found that the EN feeding protocol was able to increase the proportion of EN feeding, but failed to reduce 28-day mortality, incidence of nosocomial infection or duration of MV