基于网络药理学和分子对接探讨左金丸治疗肝癌的作用机制

目的：运用网络药理学和分子对接方法探讨左金丸治疗肝癌的作用机制。方法：从TCMSP和BATMAN-TCM数据库获取左金丸的化合物及其相应靶点,检索GeneCards、OMIM和TTD 3个数据库获得肝癌的相关靶基因,取两者靶基因交集得到左金丸治疗肝癌的预测靶基因;运用Cytoscape 3.7.1软件构建左金丸-化合物-靶点-肝癌和PPI网络图;运用R软件对预测靶基因进行GO和KEGG富集分析;最后运用分子对接技术对关键化合物和靶点进行验证。结果：共获取左金丸35个化合物及173个相应靶点,左金丸与肝癌的共同靶点有103个。PPI结果表明AKT1、MAPK1、TP53、JUN和RELA可能为左金丸治疗肝癌的关键靶点。富集分析示左金丸可能通过乙型肝炎、卡波西肉瘤相关疱疹病毒感染、人巨细胞病毒感染、丙型肝炎、MAPK信号通路、肝癌等信号通路抗肝癌。分子对接结果示槲皮素和黄连素均能与AKT1和MAPK1稳定结合。结论：本研究初步揭示了左金丸通过多成分、多靶点、多通路治疗肝癌的作用机制,为后续左金丸治疗肝癌提供理论参考。     

The information system of the French Peatland Observation Service: Service National d'Observation Tourbières – A valuable tool to assess the impact of global changes on the hydrology and biogeochemistry of temperate peatlands through long term monitoring

Mitigating and adapting to global changes requires a better understanding of the response of the Biosphere to these environmental variations. Human disturbances and their effects act in the long term (decades to centuries) and consequently, a similar time frame is needed to fully understand the hydrological and biogeochemical functioning of a natural system. To this end, the ‘Centre National de la Recherche Scientifique’ (CNRS) promotes and certifies long-term monitoring tools called national observation services or ‘Service National d'Observation’ (SNO) in a large range of hydrological and biogeochemical systems (e.g., cryosphere, catchments, aquifers). The SNO investigating peatlands, the SNO ‘Tourbières’, was certified in 2011 ( https://www.sno-tourbieres.cnrs.fr/ ). Peatlands are mostly found in the high latitudes of the northern hemisphere and French peatlands are located in the southern part of this area. Thus, they are located in environmental conditions that will occur in northern peatlands in coming decades or centuries and can be considered as sentinels. The SNO Tourbières is composed of four peatlands: La Guette (lowland central France), Landemarais (lowland oceanic western France), Frasne (upland continental eastern France) and Bernadouze (upland southern France). Thirty target variables are monitored to study the hydrological and biogeochemical functioning of the sites. They are grouped into four datasets: hydrology, fluvial export of organic matter, greenhouse gas fluxes and meteorology/soil physics. The data from all sites follow a common processing chain from the sensors to the public repository. The raw data are stored on an FTP server. After operator or automatic processing, data are stored in a database, from which a web application extracts the data to make them available ( https://data-snot.cnrs.fr/data-access/ ). Each year at least, an archive of each dataset is stored in Zenodo, with a digital object identifier (DOI) attribution ( https://zenodo.org/communities/sno_tourbieres_data/ ).     

Describing alpine lake influence on stream network temperatures: A statistical modelling approach

Systematic variations in atmospheric heat exchange, surface residence time, and groundwater influx across montane stream networks commonly produce an increasing stream temperature trend with decreasing elevation. However, complex stream temperature profiles that differ from this common longitudinal trend also exist, suggesting that stream temperatures may be influenced by complex interactions among hydrologic and atmospheric processes. Lakes within stream networks form one potential source of temperature profile complexity due to the spatially variable contribution of lake-sourced water to stream flow. We investigated temperature profile complexity in a multi-season stream temperature dataset collected across a montane stream network containing many alpine lakes. This investigation was performed by making comparisons between multiple statistical models that used different combinations of stream and lake characteristics to represent specific hypotheses for the controls on stream temperature. The compared models included a set of models which used a topographically derived estimate of the hydrologic influence of lakes to separate and quantify the effects of stream elevation and lake source-water contributions to longitudinal stream temperature patterns. This source-water mixing model provided a parsimonious explanation for complex stream-network temperature patterns in the summer and autumn, and this approach may be further applicable to other systems where stream temperatures are influenced by multiple water sources. Simpler models that discounted lake effects were more optimal during the winter and spring, suggesting that complex patterns in stream temperature profiles may emerge and subside temporally, across seasons, in response to diversity of water temperatures from different sources.     

MARC: a robust method for multiple-aspect trajectory classification via space,time, and semantic embeddings

ABSTRACT

The increasing popularity of Location-Based Social Networks (LBSNs) and the semantic enrichment of mobility data in several contexts in the last years has led to the generation of large volumes of trajectory data. In contrast to GPS-based trajectories, LBSN and context-aware trajectories are more complex data, having several semantic textual dimensions besides space and time, which may reveal interesting mobility patterns. For instance, people may visit different places or perform different activities depending on the weather conditions. These new semantically rich data, known as multiple-aspect trajectories, pose new challenges in trajectory classification, which is the problem that we address in this paper. Existing methods for trajectory classification cannot deal with the complexity of heterogeneous data dimensions or the sequential aspect that characterizes movement. In this paper we propose MARC, an approach based on attribute embedding and Recurrent Neural Networks (RNNs) for classifying multiple-aspect trajectories, that tackles all trajectory properties: space, time, semantics, and sequence. We highlight that MARC exhibits good performance especially when trajectories are described by several textual/categorical attributes. Experiments performed over four publicly available datasets considering the Trajectory-User Linking (TUL) problem show that MARC outperformed all competitors, with respect to accuracy, precision, recall, and F1-score.     

Pedestrian network generation based on crowdsourced tracking data

ABSTRACT

Pedestrian networks play an important role in various applications, such as pedestrian navigation services and mobility modeling. This paper presents a novel method to extract pedestrian networks from crowdsourced tracking data based on a two-layer framework. This framework includes a walking pattern classification layer and a pedestrian network generation layer. In the first layer, we propose a multi-scale fractal dimension (MFD) algorithm in order to recognize the two different types of walking patterns: walking with a clear destination (WCD) or walking without a clear destination (WOCD). In the second layer, we generate the pedestrian network by combining the pedestrian regions and pedestrian paths. The pedestrian regions are extracted based on a modified connected component analysis (CCA) algorithm from the WOCD traces. We generate the pedestrian paths using a kernel density estimation (KDE)-based point clustering algorithm from the WCD traces. The pedestrian network generation results using two actual crowdsourced datasets show that the proposed method has good performance in both geometrical correctness and topological correctness.     

Dynamic,discontinuous stream networks: hydrologically driven variations in active drainage density,flowing channels and stream order

Despite decades of research on the ecological consequences of stream network expansion, contraction and fragmentation, surprisingly little is known about the hydrological mechanisms that shape these processes. Here, we present field surveys of the active drainage networks of four California headwater streams (4–27 km²) spanning diverse topographic, geologic and climatic settings. We show that these stream networks dynamically expand, contract, disconnect and reconnect across all the sites we studied. Stream networks at all four sites contract and disconnect during seasonal flow recessions, with their total active network length, and thus their active drainage densities, decreasing by factors of two to three across the range of flows captured in our field surveys. The total flowing lengths of the active stream networks are approximate power‐law functions of unit discharge, with scaling exponents averaging 0.27 ± 0.04 (range: 0.18–0.40). The number of points where surface flow originates obey similar power‐law relationships, as do the lengths and origination points of flowing networks that are continuously connected to the outlet, with scaling exponents averaging 0.36–0.48. Even stream order shifts seasonally by up to two Strahler orders in our study catchments. Broadly, similar stream length scaling has been observed in catchments spanning widely varying geologic, topographic and climatic settings and spanning more than two orders of magnitude in size, suggesting that network extension/contraction is a general phenomenon that may have a general explanation. Points of emergence or disappearance of surface flow represent the balance between subsurface transmissivity in the hyporheic zone and the delivery of water from upstream. Thus the dynamics of stream network expansion and contraction, and connection and disconnection, may offer important clues to the spatial structure of the hyporheic zone, and to patterns and processes of runoff generation. Copyright © 2014 John Wiley & Sons, Ltd.     

历史名人轨迹的空间可视化与分析

历史名人的行为轨迹反映了当时的历史文化背景,通过历史名人行为轨迹的空间化和可视化,可以对历史社会状态进行探索和分析。对历史名人的社交关系网络进行可视化研究,有利于剖析当时的政治背景与人物关系。目前,基于GIS的空间人文社会科学深层次分析方法和工具还很少,根据地理位置对历史人物的社交网络进行分时段的研究也很少。本文以玄奘和欧阳修为例,探索了基于WebGIS的历史人物轨迹空间可视化分析方法,基于核密度估计与标准差椭圆的空间分析方法,分析历史名人轨迹点的空间分布特征,统计迁徙指数、首都距、家乡距、成长地距以分析基于距离的轨迹点移动特点;分时段构建了历史名人的空间社交网络,并结合历史背景、名人事迹、名人作品和空间化结果进行了综合分析。分析结果表明： ① 历史名人的迁移轨迹与当时的历史人口迁移趋势基本是一致的,受社会变动影响较大;② 历史名人在事业上升期有更大的社交网络圈,而在人生没落阶段社交网络圈减小。本文对历史名人轨迹的空间可视化与分析方法进行了探索,可以为空间人文社会科学相关领域的分析研究提供参考。     

Inference of in situ stress from thermoporoelastic borehole breakouts based on artificial neural network

The determination of in situ stresses is very important in petroleum engineering. Hydraulic fracturing is a widely accepted technique for the determination of in situ stresses nowadays. Unfortunately, the hydraulic fracturing test is time-consuming and expensive. Taking advantage of the shape of borehole breakouts measured from widely available caliper and image logs to determine in situ stress in petroleum engineering is highly attractive. By finite element modeling of borehole breakouts considering thermoporoelasticity, the authors simulate the process of borehole breakouts in terms of initiation, development, and stabilization under Mogi-Coulomb criterion and end up with the shape of borehole breakouts. Artificial neural network provides such a tool to establish the relationship between in situ stress and shape of borehole breakouts, which can be used to determine in situ stress based on different shape of borehole breakouts by inverse analysis. In this paper, two steps are taken to determine in situ stress by inverse analysis. First, sets of finite element modeling provide sets of data on in situ stress and borehole breakout measures considering the influence of drilling fluid temperature and pore pressure, which will be used to train an artificial neural network that can eventually represent the relationship between the in situ stress and borehole breakout measures. Second, for a given measure of borehole breakouts in a certain drilling fluid temperature, the trained artificial neural network will be used to predict the corresponding in situ stress. Results of numerical experiments show that the inverse analysis based on finite element modeling of borehole breakouts and artificial neural network is a promising method to determine in situ stress.     

Impacts of small cascaded hydropower plants on river discharge in a basin in Southern China

The run‐off volume altered by the construction of hydropower plants affects ecohydrological processes in catchments. Although the impacts of large hydropower plants have been well documented in the literature, few studies have been conducted on the impacts of small cascaded hydropower plants (SCHPs). To evaluate the impacts of SCHPs on river flow, we chose a representative basin affected by hydropower projects and, to a lesser degree, by other human activities, that is, the Qiuxiang River basin in Southern China. The observed river discharge and climate data during the period of 1958–2016 were investigated. The datasets were divided into a low‐impact period and a high‐impact period based on the number of SCHPs and the capacities of the reservoirs. The daily river discharge alteration was assessed by applying the Indicators of Hydrologic Alteration. To separate the impact of the SCHPs on the local river discharge from that of climate‐related precipitation, the back‐propagation neural network was used to simulate the monthly average river discharge process. An abnormal result was found: Unlike large reservoirs in large watersheds, the SCHPs regulated the flows during the flood season but were not able to mitigate the droughts during the dry season due to their limited storage and the commonly occurring inappropriate interregulations of the SCHPs. The SCHPs also reduced the annual average river discharge in the research basin. The contribution of the SCHPs to the river discharge changes was 85.37%, much higher than the contributions of climate change (13.43%) and other human activities (1.20%). The results demonstrated that the impacts of the SCHPs were different from those of large dams and reservoirs that regulate floods and relieve droughts. It is necessary to raise the awareness of the impacts of these river barriers.