Transcriptomics-based analysis of genes related to lead stress and their expression in the roots of Pogonatherum crinitum

Revealing plants’ tolerance and transport genes to heavy metal stress play an important role in exploring the potential of phytoremediation. Taking the heavy metal lead (Pb) hyperaccumulator plant Pogonatherum crinitum (Thunb.) Kunth as the research object, a hydroponic simulation stress experiment was set up to determine the physiological indicators such as antioxidant enzymes and non-enzymatic antioxidants in the roots of P. crinitum under different Pb concentrations (0, 300, 500, 1000, 2000 mg·L-1). RNA-Seq was performed, the Unigenes obtained by transcriptome sequencing were enriched and annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the differential expression genes (DEGs) of root were screened and verified by quantitative real-time polymerase chain reaction (qRT-PCR). The results are as follows: with the increase of Pb concentration, superoxide dismutase (SOD), catalase (CAT), and ascorbic acid (AsA) content increased. Peroxidase (POD), malondialdehyde (MDA), and ascorbic acid–glutathione (AsA-GSH) cycles showed low promotion with high inhibition. A total of 38.21 Gb of bases were obtained by transcriptome sequencing, and the base quality of each sample reached Q20 and Q30, accounting for 90%, making the sequencing results reliable. Combined with transcriptome sequencing, functional annotation, and qRT-PCR validation results, 17 root Pb-tolerant genes of P. crinitum were screened out, which were related to antioxidation, transportation, and transcription functions. Moreover, qRT-PCR verification results under different Pb stress concentrations were consistent with the transcriptome sequencing results and changes in physiological indicators. In brief, the root of P. crinitum can adapt to the Pb stress environment by up-regulating the expression of related genes to regulate the physiological characteristics

U-rank: Utility-oriented Learning to Rank with Implicit Feedback

Learning to rank with implicit feedback is one of the most important tasks in many real-world information systems where the objective is some specific utility, e.g., clicks and revenue. However, we point out that existing methods based on probabilistic ranking principle do not necessarily achieve the highest utility. To this end, we propose a novel ranking framework called U-rank that directly optimizes the expected utility of the ranking list. With a position-aware deep click-through rate prediction model, we address the attention bias considering both query-level and item-level features. Due to the item-specific attention bias modeling, the optimization for expected utility corresponds to a maximum weight matching on the item-position bipartite graph. We base the optimization of this objective in an efficient Lambdaloss framework, which is supported by both theoretical and empirical analysis. We conduct extensive experiments for both web search and recommender systems over three benchmark datasets and two proprietary datasets, where the performance gain of U-rank over state-of-the-arts is demonstrated. Moreover, our proposed U-rank has been deployed on a large-scale commercial recommender and a large improvement over the production baseline has been observed in an online A/B testing

Regulation of non-classical immune parameters in immune thrombocytopenic purpura mice by a spleen-invigorating, qi-replenishing and blood-containing formula

AbstractObjectiveThis study investigated the regulatory effect of non-classical immune parameters on immune thrombocytopenic purpura (ITP) mice by a spleen-invigorating, qi-replenishing and blood-containing formula (SQBF).MethodA total of 80 BALB/c mice were randomly divided into four equal groups (20 mice each): control group, model group, prednisone group and spleen-invigorating, qi-replenishing and blood-containing (SQBF) group. Mice in the model group, prednisone group, and SQBF group were administered anti-platelet serum to induce ITP. The dynamic variations of platelet counts in ITP mice were measured with an automatic blood analyzer before modeling and 48 h, and 8, 12 and 15 days following APS injection. Levels of β-endorphin (β-EP), vasoactive intestinal peptide (VIP) and salivary IgA (SIgA) were detected by enzyme-linked immunosorbent assay (ELISA) on 15th day of experiment.ResultsSQBF enhanced peripheral blood platelet counts in ITP mice similar to that of prednisone, and both groups showed a statistically significant response compared with the model group (P < .01). The SQBF significantly decreased β-EP levels compared with the model and prednisone intervention groups (P < .05), significantly increased the levels of VIP and SIgA in ITP mice compared with the model group (P < .05) and had significant protective effects on the thymus of ITP mice compared with the model group (P < .01).ConclusionsThe SQBF had a similar effect to prednisone with regards to enhancing peripheral blood platelet counts in ITP mice. Furthermore, it decreased β-EP levels and increased VIP and SIgA, and protected the thymus. This shows that, on base of the brain-gut axis functions, some non-classical immune vascular active factors or neurotransmitters are also involved in immune responses, and also have relationship with the onset of ITP and bleeding and/or hemostasis. It needs further study to determine whether a change in these active factors is related to immediate hemostasis

Large Language Models for Software Engineering: A Systematic Literature Review

Large Language Models (LLMs) have significantly impacted numerous domains, notably including Software Engineering (SE). Nevertheless, a well-rounded understanding of the application, effects, and possible limitations of LLMs within SE is still in its early stages. To bridge this gap, our systematic literature review takes a deep dive into the intersection of LLMs and SE, with a particular focus on understanding how LLMs can be exploited in SE to optimize processes and outcomes. Through a comprehensive review approach, we collect and analyze a total of 229 research papers from 2017 to 2023 to answer four key research questions (RQs). In RQ1, we categorize and provide a comparative analysis of different LLMs that have been employed in SE tasks, laying out their distinctive features and uses. For RQ2, we detail the methods involved in data collection, preprocessing, and application in this realm, shedding light on the critical role of robust, well-curated datasets for successful LLM implementation. RQ3 allows us to examine the specific SE tasks where LLMs have shown remarkable success, illuminating their practical contributions to the field. Finally, RQ4 investigates the strategies employed to optimize and evaluate the performance of LLMs in SE, as well as the common techniques related to prompt optimization. Armed with insights drawn from addressing the aforementioned RQs, we sketch a picture of the current state-of-the-art, pinpointing trends, identifying gaps in existing research, and flagging promising areas for future study

Compound Kushen Injection suppresses human breast cancer stem-like cells by down-regulating the canonical Wnt/β-catenin pathway

<p>Abstract</p> <p>Background</p> <p>Cancer stem cells (CSCs) play an important role in cancer initiation, relapse and metastasis. To date, no specific medicine has been found to target CSCs as they are resistant to most conventional therapies and proliferate indefinitely. Compound Kushen Injection (CKI) has been widely used for cancer patients with remarkable therapeutic effects in Chinese clinical settings for many years. This study focused on whether CKI could inhibit MCF-7 SP cells in vitro and in vivo.</p> <p>Methods</p> <p>The analysis of CKI on SP population and the main genes of Wnt signaling pathway were studied first. Then we studied the tumorigenicity of SP cells and the effects of CKI on SP cells in vivo. The mice inoculated with 10,000 SP cells were randomly divided into three groups (6 in each group) and treated with CKI, cisplatin and saline (as a control) respectively for 7 weeks. The tumor formation rates of each group were compared. The main genes and proteins of the Wnt signaling pathway were analyzed by RT-PCR and western blot.</p> <p>Results</p> <p>CKI suppressed the size of SP population (approximately 90%), and down-regulated the main genes of Wnt signaling pathway. We also determined that MCF-7 SP cells were more tumorigenic than non-SP and unsorted cells. The Wnt signaling pathway was up-regulated in tumors derived from SP cells compared with that in tumors from non-SP cells. The tumor formation rate of the CKI Group was 33% (2/6, <it>P </it>< 0.05), and that of Cisplatin Group was 50%(3/6, <it>P </it>< 0.05), whereas that of the Control Group was 100% (6/6).The RT-PCR and western blot results indicated that CKI suppressed tumor growth by down-regulating the Wnt/β-catenin pathway, while cisplatin activated the Wnt/β-catenin pathway and might spare SP cells.</p> <p>Conclusions</p> <p>It suggested that CKI may serve as a novel drug targeting cancer stem-like cells, though further studies are recommended.</p

Impermeable inorganic “walls” sandwiching perovskite layer toward inverted and indoor photovoltaic devices

Interfaces between the perovskite active layer and the charge-transport layers (CTLs) play a critical role in both efficiency and stability of halide-perovskite photovoltaics. One of the major concerns is that surface defects of perovskite could cause detrimental nonradiative recombination and material degradation. In this work, we addressed this challenging problem by inserting ultrathin alkali-fluoride (AF) films between the tri-cation lead-iodide perovskite layer and both CTLs. This bilateral inorganic “walls” strategy makes use of both physical-blocking and chemical-anchoring functionalities of the continuous, uniform and compact AF framework: on the one hand, the uniformly distributed alkali-iodine coordination at the perovskite-AF interfaces effectively suppresses the formation of iodine-vacancy defects at the surfaces, thus reducing the trap-assisted recombination at the perovskite-CTL interfaces and therewith the open-voltage loss; on the other hand, the impermeable AF buffer layers effectively prevent the bidirectional ion migration at the perovskite-CTLs interfaces even under harsh working conditions. As a result, a power-conversion efficiency (PCE) of 22.02% (certified efficiency 20.4%) with low open-voltage deficit (<0.4 V) was achieved for the low-temperature processed inverted planar perovskite solar cells. Exceptional operational stability (500 h, ISOS-L-2) and thermal stability (1000 h, ISOS-D-2) were obtained. Meanwhile, a 35.7% PCE was obtained under dim-light source (1000 lux white LED light) with the optimized device, which is among the best records in perovskite indoor photovoltaics

Genome-wide Mendelian randomization identifies putatively causal gut microbiota for multiple peptic ulcer diseases

ObjectiveThe pathogenesis of peptic ulcer diseases (PUDs) involves multiple factors, and the contribution of gut microbiota to this process remains unclear. While previous studies have associated gut microbiota with peptic ulcers, the precise nature of the relationship, whether causal or influenced by biases, requires further elucidation.DesignThe largest meta-analysis of genome-wide association studies was conducted by the MiBioGen consortium, which provided the summary statistics of gut microbiota for implementation in the Mendelian randomization (MR) analysis. Summary statistics for five types of PUDs were compiled using the FinnGen Consortium R8 release data. Various statistical techniques, including inverse variance weighting (IVW), MR-Egger, weighted median (WM), weighted mode, and simple mode, were employed to assess the causal relationships between gut microbiota and these five PUDs.ResultIn the intestinal microbiome of 119 known genera, we found a total of 14 causal associations with various locations of PUDs and reported the potential pathogenic bacteria of Bilophila et al. Among them, four had causal relationships with esophageal ulcer, one with gastric ulcer, three with gastroduodenal ulcer, four with duodenal ulcer, and two with gastrojejunal ulcer.ConclusionIn this study, the pathogenic bacterial genera in the gut microbiota that promote the occurrence of PUDs were found to be causally related. There are multiple correlations between intestinal flora and PUDs, overlapping PUDs have overlapping associated genera. The variance in ulcer-related bacterial genera across different locations underscores the potential influence of anatomical locations and physiological functions

Different Effects of Total Bilirubin on 90-Day Mortality in Hospitalized Patients With Cirrhosis and Advanced Fibrosis: A Quantitative Analysis

Introduction: Total bilirubin (TB) is a major prognosis predictor representing liver failure in patients with acute on chronic liver failure (ACLF). However, the cutoff value of TB for liver failure and whether the same cutoff could be applied in both cirrhotic and non-cirrhotic patients remain controversial. There is a need to obtain the quantitative correlation between TB and short-term mortality via evidence-based methods, which is critical in establishing solid ACLF diagnostic criteria.Methods: Patients hospitalized with cirrhosis or advanced fibrosis (FIB-4 &gt; 1.45) were studied. TB and other variables were measured at baseline. The primary outcome was 90-day transplantation-free mortality. Multi-variable Cox proportional hazard model was used to present the independent risk of mortality due to TB. Generalized additive model and second derivate (acceleration) were used to plot the “TB-mortality correlation curves.” The mathematical (maximum acceleration) and clinical (adjusted 28-day transplantation-free mortality rate reaching 15%) TB cutoffs for liver failure were both calculated.Results: Among the 3,532 included patients, the number of patients with cirrhosis and advanced fibrosis were 2,592 and 940, respectively, of which cumulative 90-day mortality were 16.6% (430/2592) and 7.4% (70/940), respectively. Any increase of TB was found the independent risk factor of mortality in cirrhotic patients, while only TB &gt;12 mg/dL independently increased the risk of mortality in patients with advanced fibrosis. In cirrhotic patients, the mathematical TB cutoff for liver failure is 14.2 mg/dL, with 23.3% (605/2592) patients exceeding it, corresponding to 13.3 and 25.0% adjusted 28- and 90-day mortality rate, respectively. The clinical TB cutoff for is 18.1 mg/dL, with 18.2% (471/2592) patients exceeding it. In patients with advanced fibrosis, the mathematical TB cutoff is 12.1 mg/dL, 33.1% (311/940) patients exceeding it, corresponding to 2.9 and 8.0% adjusted 28- and 90-day mortality rate, respectively; the clinical TB cutoff was 36.0 mg/dL, 1.3% (12/940) patients above it.Conclusion: This study clearly demonstrated the significantly different impact of TB on 90-day mortality in patients with cirrhosis and advanced fibrosis, proving that liver failure can be determined by TB alone in cirrhosis but not in advanced fibrosis. The proposed TB cutoffs for liver failure provides solid support for the establishment of ACLF diagnostic criteria

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data