Two new characteristic parameters for runoff computation

A method capable of estimating the hydrograph from a prescribed storm for a practical mild slope upstream catchment is proposed. This method makes use of two new characteristic parameters, andS, in conjunction with the kinematic wave equation to compute lateral inflows of the main stream of the catchment. The depth profile of overland flow at any instant within the catchment and hydrograph at any location can be easily found. Lag times for individual lateral inflows are then considered and are linearly combined to obtain the hydrograph at the outlet of the catchment or depth profile of the main stream at any instant. The validity of the excess rainfall-surface runoff linear relationship in this study has also been verified with Tatsunokuchiyama catchment, and it shows good results for this computed runoff.     

一种基于UML状态图的规约变异测试方法

规约变异测试从软件功能的角度,对规约进行分析,从而揭示规约中存在的问题。本文提出一种基于UML状态图的变异测试方法,针对每种变异算子,分析其是否会引入冲突,进而有效避免不合理的变异操作;分析了每种变异算子产生等价变异体的条件,能够在生成变异体的同时检测并移除等价变异体,进而减少其对测试过程的影响;给出了杀掉每种变异体所需满足的条件,可在此基础上产生杀掉特定变异体所需的测试用例,从而提高测试用例集的质量。在此基础上,根据变异算子的实际功能,整合了功能相同的算子,减少了变异算子的数量,从而进一步降低了变异测试的开销。实验结果表明,本方法能够较好地提高测试用例的质量,进而提升测试的效率。     

Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength

Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R₁/R₂ side-groups as phenyls or R₁–phenyl/R₂–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved K_s, IC₅₀ and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the strongest binder (K_s and IC₅₀ of 0.007 and 0.090 µM, respectively). 3h was the fourth structurally simpler inhibitor superior to ritonavir, which further demonstrates the power of our approach.     

The GAUGAA Motif Is Responsible for the Binding between circSMARCA5 and SRSF1 and Related Downstream Effects on Glioblastoma Multiforme Cell Migration and Angiogenic Potential

Circular RNAs (circRNAs) are a large class of RNAs with regulatory functions within cells. We recently showed that circSMARCA5 is a tumor suppressor in glioblastoma multiforme (GBM) and acts as a decoy for Serine and Arginine Rich Splicing Factor 1 (SRSF1) through six predicted binding sites (BSs). Here we characterized RNA motifs functionally involved in the interaction between circSMARCA5 and SRSF1. Three different circSMARCA5 molecules (Mut1, Mut2, Mut3), each mutated in two predicted SRSF1 BSs at once, were obtained through PCR-based replacement of wild-type (WT) BS sequences and cloned in three independent pcDNA3 vectors. Mut1 significantly decreased its capability to interact with SRSF1 as compared to WT, based on the RNA immunoprecipitation assay. In silico analysis through the “Find Individual Motif Occurrences” (FIMO) algorithm showed GAUGAA as an experimentally validated SRSF1 binding motif significantly overrepresented within both predicted SRSF1 BSs mutated in Mut1 (q-value = 0.0011). U87MG and CAS-1, transfected with Mut1, significantly increased their migration with respect to controls transfected with WT, as revealed by the cell exclusion zone assay. Immortalized human brain microvascular endothelial cells (IM-HBMEC) exposed to conditioned medium (CM) harvested from U87MG and CAS-1 transfected with Mut1 significantly sprouted more than those treated with CM harvested from U87MG and CAS-1 transfected with WT, as shown by the tube formation assay. qRT-PCR showed that the intracellular pro- to anti-angiogenic Vascular Endothelial Growth Factor A (VEGFA) mRNA isoform ratio and the amount of total VEGFA mRNA secreted in CM significantly increased in Mut1-transfected CAS-1 as compared to controls transfected with WT. Our data suggest that GAUGAA is the RNA motif responsible for the interaction between circSMARCA5 and SRSF1 as well as for the circSMARCA5-mediated control of GBM cell migration and angiogenic potential.     

The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway.     

降水和植被变化对龙川江径流量的影响

基于龙川江大峡谷进出口水文控制站楚雄站和小黄瓜园站的长系列水文资料和流域森林盖度变化资料,结合小波分析方法,对降水、植被与径流量变化间相互关系以及径流量各时间尺度准周期变化的本质和形成机制进行了研究。结果表明:研究区降水量序列存在2 a、4 a和14.5 a左右的主周期,径流量序列具有2 a、4 a、6 a和22 a左右的主周期;其中径流量低频振荡所反映的是总径流中来自于壤中水径流和存在于裂隙中的地下水径流的准周期变化,而高频振荡反映的是总径流中来自于地面径流的准周期变化;径流量的年内变化和年际高频振荡主要是由降水量变化所引起的,而径流量序列6 a和22 a的主周期是由土壤和裂隙对降水量序列4 a和14.5 a的主周期滞后放大作用所形成的,径流量序列4 a的主周期是由干热河谷特殊自然地理环境所形成的;径流量与降水量间相互关系在1969年左右发生了突变     

支持向量机及其在径流预测中的应用

给出了支持向量机方法(SVM)的思路、特点及关键之处,探讨了SVM在径流预测中的可能性,并与基于遗传算法的门限回归模型(TR) 进行了对比分析。径流预测实例分析表明,在拟合阶段,SVM模型要好于TR模型;在预留检验阶段,SVM模型与TR模型接近。同时SVM模型适合于小样本情况且能达到全局最优。SVM模型用于径流预测是可行的、优越的。     

西江流域压咸风险调度及其时空传递规律研究

枯水期珠江河口咸潮情势日益加重,径流不确定加剧了压咸风险,严重威胁沿线的供水安全。本文基于概率密度分布描述径流不确定性,构建了单源风险调度基本框架。以西江流域五座水库为研究对象,量化了预报误差与压咸风险的响应关系;揭示了压咸风险的时空传递规律;将压咸风险划分为3个等级;确定出各级风险越级传递的临界阈值。研究表明：随预报误差的增大,压咸风险提前且持续天数增加、风险率增大;压咸风险呈逐时段累积和从上游向下游、从支流向干流的时空传递规律;当预报误差超过±16%、±21%时,压咸风险从轻险越级至中险、中险越级至重险。研究成果对于西江流域压咸风险的调控和粤港澳大湾区的供水安全具有重要的应用价值。     

BRAF Gene and Melanoma: Back to the Future

As widely acknowledged, 40–50% of all melanoma patients harbour an activating BRAF mutation (mostly BRAF V600E). The identification of the RAS–RAF–MEK–ERK (MAP kinase) signalling pathway and its targeting has represented a valuable milestone for the advanced and, more recently, for the completely resected stage III and IV melanoma therapy management. However, despite progress in BRAF-mutant melanoma treatment, the two different approaches approved so far for metastatic disease, immunotherapy and BRAF+MEK inhibitors, allow a 5-year survival of no more than 60%, and most patients relapse during treatment due to acquired mechanisms of resistance. Deep insight into BRAF gene biology is fundamental to describe the acquired resistance mechanisms (primary and secondary) and to understand the molecular pathways that are now being investigated in preclinical and clinical studies with the aim of improving outcomes in BRAF-mutant patients.     

Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies

Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody–antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics.