Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

<p>Abstract</p> <p>Background</p> <p>It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (<it>LYP9</it>) and its parental cultivars (<it>93-11 </it>and <it>PA64s</it>) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis.</p> <p>Results</p> <p>By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (<it>93-11 and PA64s</it>), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with <it>P</it>-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (<it>P </it>< 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis.</p> <p>Conclusion</p> <p>We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.</p

Effectiveness and safety of co-administration of moxifloxacin with netilmicin in drug-resistant tuberculosis patients, and its impact on inflammatory factors and immune function

Purpose: To study the effectiveness and safety of co-administration of moxifloxacin with netilmicin in drug-resistant tuberculosis (TB) patients, and its impact on levels of inflammatory factors and immune function. Methods: We enrolled 100 patients with drug-resistant TB admitted to People’s Hospital of Rizhao between May 2017 and October 2019. The patients were randomly allocated to control group and study group, with 50 patients per group. The control group received moxifloxacin at a dose of 0.2 g t.i.d. for 6 months and the study group received netilmicin at a dose of 0.1 g t.i.d. plus. The response, incidence of adverse reactions, expression levels of inflammatory factors, immune function, and sputum-negative status after 2, 4 and 6 months of TB treatment were compared. Results: The study group showed markedly higher response than the control group (p &lt; 0.05). Moreover, there were lower incidence of adverse effects in the study group than in the control group (p &lt; 0.05). The expression levels of inflammatory factors were significantly lower in the study group, while the concentrations of CD3+, CD4+, and CD8+ were markedly higher (p &lt; 0.05). After 2, 4 and 6 months of TB treatment, cases of sputum-negative conversion were significantly higher in the study group than in the control group (p &lt; 0.05). Conclusion: Co-administration of moxifloxacin with netilmicin produces much higher effectiveness and safety than moxifloxacin monotherapy, decreases inflammatory factor levels and improves immune function in patients with drug-resistant TB

ModelScope-Agent: Building Your Customizable Agent System with Open-source Large Language Models

Large language models (LLMs) have recently demonstrated remarkable capabilities to comprehend human intentions, engage in reasoning, and design planning-like behavior. To further unleash the power of LLMs to accomplish complex tasks, there is a growing trend to build agent framework that equips LLMs, such as ChatGPT, with tool-use abilities to connect with massive external APIs. In this work, we introduce ModelScope-Agent, a general and customizable agent framework for real-world applications, based on open-source LLMs as controllers. It provides a user-friendly system library, with customizable engine design to support model training on multiple open-source LLMs, while also enabling seamless integration with both model APIs and common APIs in a unified way. To equip the LLMs with tool-use abilities, a comprehensive framework has been proposed spanning over tool-use data collection, tool retrieval, tool registration, memory control, customized model training, and evaluation for practical real-world applications. Finally, we showcase ModelScopeGPT, a real-world intelligent assistant of ModelScope Community based on the ModelScope-Agent framework, which is able to connect open-source LLMs with more than 1000 public AI models and localized community knowledge in ModelScope. The ModelScope-Agent library\footnote{https://github.com/modelscope/modelscope-agent} and online demo\footnote{https://modelscope.cn/studios/damo/ModelScopeGPT/summary} are now publicly available

Characteristics of Micro-Seismic Events Induced by Ground Collapse—A Case Study in the Rongxing Gypsum Mine in Hubei Province, China

Mining activities can damage rock masses and easily induce ground collapse, which seriously threatens safe production in mining areas. Micro-seismic systems can monitor rock mass deformation signals in real time and provide more accurate data for rock mass deformation analysis. Therefore, in this study, the waveform characteristics of micro-seismic events induced by ground collapse in the Rongxing gypsum mine were analyzed; the occurrence of these events was introduced on the basis of Fast Fourier Transform, an established Frequency–Time–Amplitude model, in order to put forward the index of energy proportion of the main band. The results showed the following. (1) The seismic sequence type of ground collapse was foreshock–mainshock–aftershocks. The interval between the foreshock and mainshock was longer than that between the mainshock and aftershocks. (2) The deformation corresponding to the foreshock micro-seismic events was mainly that of a small-scale crack. The deformation corresponding to the micro-seismic events during the mainshock was characterized by the gradual development of small-scale cracks, and the development of large-scale cracks accelerated, accompanied by slight rock collapse. The deformation corresponding to the micro-seismic events during the aftershocks showed that almost no small-scale cracks developed, and the large-scale crack development was intense, and accompanied by numerous rock and soil mass collapses. (3) The observed decreasing frequency distribution and energy dispersion can be used as possible precursors of ground collapse

Effects of Long-term Fertilization on Soil Nitrogen and Phosphorus Activation in Purple Paddy Soil with Different Fertility

【Objective】The study was carried out to reveal the impact of long-term fertilization on the capacities of soil nitrogen (N) and phosphorus (P) activation, and their correlations with pH and soil organic carbon (SOC) in purple paddy soil with different fertility, with a view to providing references for soil fertilization.【Method】Based on a 36-year different fertilization experiment of purple soil, different fertilization treatments including no fertilization (LF), balanced chemical nitrogen (N), phosphorus (P) and potassium (K) fertilizer (MF), and chemical N, P and K fertilizer plus organic fertilizer (HF) were set. Dynamics of soil total and available N and P contents, and nutrient activation rates under different fertility were measured, and relationships between soil pH, SOC and nutrient activation rates were analyzed.【Result】Crop yields under MF and HF were significantly higher than those under LF. The contents of total N and P had no significant changes, available N content efficiently improved, while available P slightly decreased under LF treatment. However, total and available N and P contents significantly increased under MF and HF treatments. There were variation in promotion of N and P content under different fertility paddy soil. For example Under LF, MF, and HF treatments, the annual increase rates of total N contents were 5.5, 14.2, and 17.0 mg/kg, 0.40, 1.05, and 1.32 mg/kg for available N, 0.8, 17.1, and 18.0 mg/kg for total P, and -0.03, 2.05, and 1.85 mg/kg for available P, respectively. Compared with the LF treatment, N activation rates under MF and HF treatments increased from 8.15% to 428.77%. There was no significant linear relationship between N activation rate and pH or SOC. A significant negative correlation was observed between P activation rate and pH, while there was a significant positive linear correlation between P activation rate and SOC. If the annual application amount of N was 240 kg/hm2 and amount of P2O5 was 120 kg/hm2, the purple soil was N-saturated after 13 years and it was P-saturated after 9 years.【Conclusion】In the purple paddy soil regions of Southwest China, balanced fertilization with N, P and K or application of chemical fertilizer with organic fertilizer could promote soil N and P contents and activation rates

Impacts from Waste Oyster Shell on the Durability and Biological Attachment of Recycled Aggregate Porous Concrete for Artificial Reef

Poor biological attachment of artificial reef (AR) prepared by the recycled aggregate limit the application in the area of marine engineering. In this study, the waste oyster shell (WOS) was used as raw materials to prepare the recycled aggregate porous concrete (RAPC), the compressive strength, split tensile strength, chloride penetration resistance, freezing-thawing resistance, low temperature resistance, and the biological attachment were tested, aiming to improve the biological attachment and decrease carbon dioxide emission. The experiment results demonstrate that the use of WOS can decrease the compressive and split tensile strength, but the effect of designed porous structure on the mechanical strength is higher than that of WOS. To ensure the durability of RAPC, the contents of WOS should not exceed 20%. Additionally, the addition of WOS and designed porous structure are beneficial to biological attachment. However, the porous structure of RAPC only improves biological attachment in the short term, and the reverse phenomenon is true in the long term. As the partial replacement of cement with WOS is 40%, the total carbon dioxide emission decreases by about 52%. In conclusion, the use of WOS in the RAPC is an eco-friendly method in the artificial reef (AR) with improved ecological attachment and reduced carbon dioxide emission

Titanium–Porphyrin Metal–Organic Frameworks as Visible-Light-Driven Catalysts for Highly Efficient Sonophotocatalytic Reduction of Cr(VI)

In this work, we synthesized and characterized four titanium–porphyrin metal–organic frameworks (MOFs) [DGIST-1(M), M = Co(II), Fe(III), Zn(II), and H2] and used them as visible-light-driven catalysts for sonophotocatalytic Cr(VI) reduction. DGIST-1(M) exhibited open-framework, broad light absorption stemmed from ligand and sensitive photocurrent responses owing to the integration of one-dimensional Ti-oxo chains and 4-connected conjugated TCPP ligand (TCPP = tetrakis(4-carboxyphenyl)-porphyrin). DGIST-1(M) presented efficient reduction of Cr(VI) to Cr(III) in aqueous solution when used as sonophotocatalytic catalysts. The average reduction rates upon Cr(VI) were 0.920, 0.476, 0.377, and 0.194 mg·L–1·min–1 for DGIST-1(H2), DGIST-1(Zn), DGIST-1(Co), and DGIST-1(Fe), which are 1.15–2.45 times higher than those in photocatalysis. Sonophotocatalytic experiments and electron paramagnetic resonance measurement proved that Ti-oxo chain units and porphyrin ligand in the structures of DGIST-1(M) existed as catalytic active centers for sonophotocatalytic reduction of Cr(VI). Photoluminescence and UV absorption spectra revealed that the unity of photocatalysis and sonochemistry strengthened the migration of photogenerated electrons from DGIST-1(M) to Cr(VI), which improved the activities of catalysts. This study suggested that the association of titanium–porphyrin MOFs and sonophotocatalytic technology is an impactful program for enhancing MOF-based photocatalytic systems