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Energy-aware scheduling with reconstruction and frequency equalization on heterogeneous systems

Yong-xing LIU,Ken-li LI,Zhuo TANG,Ke-qin LI

《信息与电子工程前沿（英文）》 2015年 第16卷 第7期   页码 519-531 doi: 10.1631/FITEE.1400399

摘要： With the increasing energy consumption of computing systems and the growing advocacy for green computing, energy efficiency has become one of the critical challenges in high-performance heterogeneous computing systems. Energy consumption can be reduced by not only hardware design but also software design. In this paper, we propose an energy-aware scheduling algorithm with equalized frequency, called EASEF, for parallel applications on heterogeneous computing systems. The EASEF approach aims to minimize the finish time and overall energy consumption. First, EASEF extracts the set of paths from an application. Then, it reconstructs the application based on the extracted set of paths to achieve a reasonable schedule. Finally, it adopts a progressive way to equalize the frequency of tasks to reduce the total energy consumption of systems. Randomly generated applications and two real-world applications are examined in our experiments. Experimental results show that the EASEF algorithm outperforms two existing algorithms in terms of makespan and energy consumption.

关键词： Directed acyclic graph     Dynamic voltage scaling     Energy aware     Heterogeneous systems     Task scheduling    

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Advances in the study of directed evolution for cellulases

Hailong LIN, Weiguang LI, Changhong GUO, Sihang QU, Nanqi REN

《环境科学与工程前沿（英文）》 2011年 第5卷 第4期   页码 519-525 doi: 10.1007/s11783-011-0326-2

摘要： If cellulose can be effectively hydrolyzed into glucose by cellulase, the production costs of hydrogen, ethanol or other chemicals from cellulosic materials will be greatly decreased, and economically viable production of biohydrogen and bioethanol will become feasible. Cellulose is degraded into glucoses by multi-component enzyme systems. Nowadays cellulases are widely used in brewing, food, bioenergy, fodder, textiles, paper, pharmaceuticals, environmental protection and other industries. However, existing cellulases have several problems that limit their wider applications, including the low turnover number for solid cellulosic materials, and low stability in adapting to various application conditions. For example, high temperature, low pH, and so on. Application of directed evolution technology may be one of the most effective ways for improving the characteristics of cellulases. This paper presents a brief review of the cellulose hydrolysis mechanism by cellulase, advances in cellulases (endoglucanase and -glucosidase) improvement by directed evolution for several characteristics (for instance, thermal stability, pH adaptability and enzyme activity), limitations of directed evolution for cellulases, and the outlook for directed evolution for cellulase.

关键词： biohydrogen     bioethanol     cellulase     cellulose     directed evolution    

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Unnormalized and normalized forms of gefura measures in directed and undirected networks

Raf GUNS,Ronald ROUSSEAU

《信息与电子工程前沿（英文）》 2015年 第16卷 第4期   页码 311-320 doi: 10.1631/FITEE.1400425

摘要： In some networks nodes belong to predefined groups (e.g., authors belong to institutions). Common network centrality measures do not take this structure into account. Gefura measures are designed as indicators of a node’s brokerage role between such groups. They are defined as variants of betweenness centrality and consider to what extent a node belongs to shortest paths between nodes from different groups. In this article we make the following new contributions to their study: (1) We systematically study unnormalized gefura measures and show that, next to the ‘structural’ normalization that has hitherto been applied, a ‘basic’ normalization procedure is possible. While the former normalizes at the level of groups, the latter normalizes at the level of nodes. (2) Treating undirected networks as equivalent to symmetric directed networks, we expand the definition of gefura measures to the directed case. (3) It is shown how Brandes’ algorithm for betweenness centrality can be adjusted to cover these cases.

关键词： Networks subdivided in groups     Partitions     Gefura measures     Q-measures     Brokerage role     Directed and undirected networks     Brandes’     algorithm    

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Classifying multiclass relationships between ASes using graph convolutional network

《工程管理前沿（英文）》   页码 653-667 doi: 10.1007/s42524-022-0217-1

摘要： Precisely understanding the business relationships between autonomous systems (ASes) is essential for studying the Internet structure. To date, many inference algorithms, which mainly focus on peer-to-peer (P2P) and provider-to-customer (P2C) binary classification, have been proposed to classify the AS relationships and have achieved excellent results. However, business-based sibling relationships and structure-based exchange relationships have become an increasingly nonnegligible part of the Internet market in recent years. Existing algorithms are often difficult to infer due to the high similarity of these relationships to P2P or P2C relationships. In this study, we focus on multiclassification of AS relationship for the first time. We first summarize the differences between AS relationships under the structural and attribute features, and the reasons why multiclass relationships are difficult to be inferred. We then introduce new features and propose a graph convolutional network (GCN) framework, AS-GCN, to solve this multiclassification problem under complex scenes. The proposed framework considers the global network structure and local link features concurrently. Experiments on real Internet topological data validate the effectiveness of our method, that is, AS-GCN. The proposed method achieves comparable results on the binary classification task and outperforms a series of baselines on the more difficult multiclassification task, with an overall metrics above 95%.

关键词： autonomous system     multiclass relationship     graph convolutional network     classification algorithm     Internet topology    

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Controllability analysis of second-ordermulti-agent systemswith directed andweighted interconnection

Di GUO,Rong-hao ZHENG,Zhi-yun LIN,Gang-feng YAN

《信息与电子工程前沿（英文）》 2015年 第16卷 第10期   页码 838-847 doi: 10.1631/FITEE.1500069

摘要： This article investigates the controllability problem of multi-agent systems. Each agent is assumed to be governed by a second-order consensus control law corresponding to a directed and weighted graph. Two types of topology are considered. The first is concerned with directed trees, which represent the class of topology with minimum information exchange among all controllable topologies. A very simple necessary and sufficient condition regarding the weighting scheme is obtained for the controllability of double integrator multi-agent systems in this scenario. The second is concerned with a more general graph that can be reduced to a directed tree by contracting a cluster of nodes to a component. A similar necessary and sufficient condition is derived. Finally, several illustrative examples are provided to demonstrate the theoretical analysis results.

关键词： Multi-agent systems     Controllability     Directed tree    

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Ionic strength directed self-assembled polyelectrolyte single-bilayer membrane for low-pressure nanofiltration

《化学科学与工程前沿（英文）》 2022年 第16卷 第5期   页码 699-708 doi: 10.1007/s11705-021-2093-3

摘要： Layer-by-layer assembly is a versatile technique for fabricating nanofiltration membranes, where multiple layers of polyelectrolytes are usually required to achieve reasonable separation performance. In this work, an ionic strength directed self-assembly procedure is described for the preparation of nanofiltration membranes consisting of only a single bilayer of poly(diallyldimethylammoniumchloride) and poly(sodium-4-styrenesulfoate). The influence of background ionic strength as well as membrane substrate properties on the formation of single-bilayer membranes are systematically evaluated. Such a simplified polyelectrolyte deposition procedure results in membranes having outstanding separation performance with permeating flux of 14.2 ± 1.5 L∙m–2∙h–1∙bar–1 and Na2SO4 rejection of 97.1% ± 0.8% under a low applied pressure of 1 bar. These results surpass the ones for conventional multilayered polyelectrolyte membranes. This work encompasses an investigation of ionic strength induced coiling of the polyelectrolyte chains and emphasizes the interplay between-polyelectrolyte chain configuration and substrate pore profile. It thus introduces a new concept on the control of membrane fabrication process toward high performance nanofiltration.

关键词： layer-by-layer self-assembly     single bilayer     nanofiltration membrane     desalination    

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Liver-directed treatment is associated with improved survival and increased response to immune checkpoint

《医学前沿（英文）》   页码 878-888 doi: 10.1007/s11684-023-0993-y

摘要： Metastases of uveal melanoma (UM) spread predominantly to the liver. Due to low response rates to systemic therapies, liver-directed therapies (LDT) are commonly used for tumor control. The impact of LDT on the response to systemic treatment is unknown. A total of 182 patients with metastatic UM treated with immune checkpoint blockade (ICB) were included in this analysis. Patients were recruited from prospective skin cancer centers and the German national skin cancer registry (ADOReg) of the German Dermatologic Cooperative Oncology Group (DeCOG). Two cohorts were compared: patients with LDT (cohort A, n = 78) versus those without LDT (cohort B, n = 104). Data were analyzed for response to treatment, progression-free survival (PFS), and overall survival (OS). The median OS was significantly longer in cohort A than in cohort B (20.1 vs. 13.8 months; P = 0.0016) and a trend towards improved PFS was observed for cohort A (3.0 vs. 2.5 months; P = 0.054). The objective response rate to any ICB (16.7% vs. 3.8%, P = 0.0073) and combined ICB (14.1% vs. 4.5%, P = 0.017) was more favorable in cohort A. Our data suggest that the combination of LDT with ICB may be associated with a survival benefit and higher treatment response to ICB in patients with metastatic UM.

关键词： uveal melanoma     liver-directed therapy     immune checkpoint blockade     SIRT     anti-PD-1     anti-CTLA-4    

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Clinical outcomes of ATP-tumor chemosensitivity assay directed chemotherapy in hepatocellular carcinoma

RAO Rongsheng, CHEN Wenxue, ZHOU Xinwen, ZHOU Zheng, LI Xiaojun, ZENG Zhiping

《医学前沿（英文）》 2007年 第1卷 第2期   页码 157-160 doi: 10.1007/s11684-007-0029-z

摘要： This study aims to investigate the clinical response of ATP tumor chemosensitivity assay (ATP-TCA) directed chemotherapy regimens delivered via hepatic artery infusion in 104 cases of primary liver carcinoma (PLC). Tumor tissue was obtained via laparotomy and cultivated in vitro. This tissue was put through the assay to determine chemosensitivity. A single drug regimen of either 5-FU, MMC and ADM and a combination drug regimen were used. The treatment assigned was dependent on the result of the ATP-TCA. In the control group, 30 cases of diagnosed PLC were given the conventional three-combination drug. The two groups were evaluated after three courses of chemotherapy. The results are as follows. The overall response rate of sensitivity test ranged from 36% to 44% in the single drug therapy groups and 81% in the combination drug group. The clinical overall response rate was 75% in the treatment group and 56% in control group. The treatment group had better results than the control group as survival period over six months was 80% and over one year 44%. In the control group, survival period over six months was 60% and 30% over one year. In short, ATP-TCA directed chemotherapy shows better results for terminal stages of PLC in that you can decrease the dose of drugs thereby reducing the side-effects with possible improvements in therapeutic effects.
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大规模图计算系统综述 Review

Ning LIU, Dong-sheng LI, Yi-ming ZHANG, Xiong-lve LI

《信息与电子工程前沿（英文）》 2020年 第21卷 第3期   页码 384-404 doi: 10.1631/FITEE.1900127

摘要： 图是描述实体之间关系的一种重要数据结构。现实世界中许多应用领域非常依赖图数据。然而，由于图计算应用与传统应用的显著差异，利用通用平台处理图计算应用是低效的，这极大推动了专用图计算系统的研究。本综述系统地对图算法和图计算应用进行分类，将现有图计算系统划分为通用和专用系统，并详细总结。深入分析图计算系统的实现技术，包括编程模型、分区策略、通信模型、执行模型和容错机制。最后，分析图计算领域最新进展，并提出有待进一步研究的4个问题。

关键词： 图算法；图计算应用；图计算系统    

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Site-directed mutagenesis of long QT syndrome KCNQ1 gene

LI Wei, WANG Bin, XU Qiumei, KE Qinmei, YANG Junguo, DU Rong, TIAN Li, WANG Qing

《医学前沿（英文）》 2008年 第2卷 第1期   页码 100-104 doi: 10.1007/s11684-008-0018-x

摘要： To construct a polymerase chain reaction (PCR) site-directed mutagenesis of the long QT syndrome KCNQ1 gene , two sets of primers were designed according to the sequence of KCNQ1 cDNA and a mismatch was introduced into primers. Mutagenesis was performed in a two-step PCR. The amplified fragments from the third PCR which contained the mutation site were sub-cloned into the T-vector pCR2.1. Then, the fragments containing the mutation site was obtained from pCR2.1 using restriction enzymes digestion and inserted into the same restriction site of pIRES-EGFP-KCNQ1. The sequencing analysis shows that the mutation site was correct. Mutation from A to G in site 983 of KCNQ1 cDNA was found. Using the Effectene transfection reagent, pIRES-EGFP-KCNQ1 (G983A) was transfected into HEK cells successfully. These results may shed light on further functional study of KCNQ1 gene.

关键词： restriction     digestion     syndrome     sequence     site-directed mutagenesis    

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oocyst directed assembly of gold nanoparticles and graphene oxide

Sona Jain, Zhicheng Huang, Brent R. Dixon, Syed Sattar, Juewen Liu

《化学科学与工程前沿（英文）》 2019年 第13卷 第3期   页码 608-615 doi: 10.1007/s11705-019-1813-4

摘要： Understanding the interactions between inorganic nanomaterials and biological species is an important topic for surface and environmental chemistry. In this work, we systematically studied the oocysts of as a model protozoan parasite and its interaction with gold nanoparticles (AuNPs) and graphene oxide (GO). The as-prepared citrate-capped AuNPs adsorb strongly on the oocysts leading to a vivid color change. The adsorption of the AuNPs was confirmed by transmission electron microscopy. Heat treatment fully inhibited the color change, indicating a large change of surface chemistry of the oocysts that can be probed by the AuNPs. Adding proteases such as trypsin and proteinase K partially inhibited the color change. DNA-capped AuNPs, on the other hand, could not be adsorbed by the oocysts. GO was found to wrap around the oocysts forming a conformal shell reflecting the shape of the oocysts. Both citrate-capped AuNPs and GO compromised the membrane integrity of the oocysts as indicated by the propidium iodide staining experiment, and they may be potentially used for inactivating the oocysts. This is the first example of using nanomaterials to probe the surface of the oocysts, and it suggests the possibility of using such organisms to template the assembly of nanomaterials.

关键词： nanomaterials     toxicology     water     biosensors    

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Optimized human factor IX expression cassettes for hepatic-directed gene therapy of hemophilia B

null

《医学前沿（英文）》 2015年 第9卷 第1期   页码 90-99 doi: 10.1007/s11684-015-0390-2

摘要：

Gene therapy provides a potential cure for hemophilia B, and significant progress has been achieved in liver-directed gene transfer mediated by adeno-associated viral vectors. Recent clinical trials involving the use of a self-complementary adeno-associated virus serotype 8-human codon-optimized factor IX (AAV8-hFIXco) vector demonstrated encouraging efficacy with hFIX expression stabilized at 1% to 6% of normal level in patients, but safety concerns related to high vector doses are still present. Thus, further improvement of AAV vectors and hFIX expression cassette may positively contribute to the ultimate success of hemophilia B gene therapy. In this study, to obtain a higher expression level of hFIX that potentiates the coagulant capacity of recipients, human FIX expression vector was optimized by upgrading the codon adaption index and adjusting the GC content, inserting a Kozak sequence (GCCACC), and introducing a gain-of-function mutation, R338L (FIX Padua). The efficiency of the published and the presently constructed cassettes was compared through in vivo screening. In addition, the regulatory elements that control the FIX gene expression in these cassettes were screened for liver-specific effectiveness. Among all the constructed cassettes, scAAV-Pre-hFIXco-SIH-R338L, which was the construct under the control of the prothrombin enhancer and prealbumin promoter, resulted in the highest level of coagulant activity, and the expression levels of two constructed cassettes (scAAV-Chi-hFIXco-SIH-R338L and scAAV-Pre-hFIXco-SIH-R338L) were also higher than that of the published cassette (scAAV-LP1-hFIXco-SJ). In summary, our strategies led to a substantial increase in hFIX expression at the protein level or a remarkably elevated coagulant activity. Thus, these reconstructs of hFIX with AAV vector may potentially contribute to the creation of an efficacious gene therapy of hemophilia B.

关键词： factor IX     hemophilia B     liver-specific regulatory elements     hydrodynamic gene transfer    

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Detecting large-scale underwater cracks based on remote operated vehicle and graph convolutional neural

Wenxuan CAO; Junjie LI

《结构与土木工程前沿（英文）》 2022年 第16卷 第11期   页码 1378-1396 doi: 10.1007/s11709-022-0855-8

摘要： It is of great significance to quickly detect underwater cracks as they can seriously threaten the safety of underwater structures. Research to date has mainly focused on the detection of above-water-level cracks and hasn’t considered the large scale cracks. In this paper, a large-scale underwater crack examination method is proposed based on image stitching and segmentation. In addition, a purpose of this paper is to design a new convolution method to segment underwater images. An improved As-Projective-As-Possible (APAP) algorithm was designed to extract and stitch keyframes from videos. The graph convolutional neural network (GCN) was used to segment the stitched image. The GCN’s m-IOU is 24.02% higher than Fully convolutional networks (FCN), proving that GCN has great potential of application in image segmentation and underwater image processing. The result shows that the improved APAP algorithm and GCN can adapt to complex underwater environments and perform well in different study areas.

关键词： underwater cracks     remote operated vehicle     image stitching     image segmentation     graph convolutional neural network    

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Distributed coordination inmulti-agent systems: a graph Laplacian perspective

Zhi-min HAN,Zhi-yun LIN,Min-yue FU,Zhi-yong CHEN

《信息与电子工程前沿（英文）》 2015年 第16卷 第6期   页码 429-448 doi: 10.1631/FITEE.1500118

摘要： This paper reviews some main results and progress in distributed multi-agent coordination from a graph Laplacian perspective. Distributed multi-agent coordination has been a very active subject studied extensively by the systems and control community in last decades, including distributed consensus, formation control, sensor localization, distributed optimization, etc. The aim of this paper is to provide both a comprehensive survey of existing literature in distributed multi-agent coordination and a new perspective in terms of graph Laplacian to categorize the fundamental mechanisms for distributed coordination. For different types of graph Laplacians, we summarize their inherent coordination features and specific research issues. This paper also highlights several promising research directions along with some open problems that are deemed important for future study.

关键词： Multi-agent systems     Distributed coordination     Graph Laplacian    

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Efficacy of intelligent diagnosis with a dynamic uncertain causality graph model for rare disorders of

Dongping Ning, Zhan Zhang, Kun Qiu, Lin Lu, Qin Zhang, Yan Zhu, Renzhi Wang

《医学前沿（英文）》 2020年 第14卷 第4期   页码 498-505 doi: 10.1007/s11684-020-0791-8

摘要： Disorders of sex development (DSD) are a group of rare complex clinical syndromes with multiple etiologies. Distinguishing the various causes of DSD is quite difficult in clinical practice, even for senior general physicians because of the similar and atypical clinical manifestations of these conditions. In addition, DSD are difficult to diagnose because most primary doctors receive insufficient training for DSD. Delayed diagnoses and misdiagnoses are common for patients with DSD and lead to poor treatment and prognoses. On the basis of the principles and algorithms of dynamic uncertain causality graph (DUCG), a diagnosis model for DSD was jointly constructed by experts on DSD and engineers of artificial intelligence. “Chaining” inference algorithm and weighted logic operation mechanism were applied to guarantee the accuracy and efficiency of diagnostic reasoning under incomplete situations and uncertain information. Verification was performed using 153 selected clinical cases involving nine common DSD-related diseases and three causes other than DSD as the differential diagnosis. The model had an accuracy of 94.1%, which was significantly higher than that of interns and third-year residents. In conclusion, the DUCG model has broad application prospects as a computer-aided diagnostic tool for DSD-related diseases.

关键词： disorders of sex development (DSD)     intelligent diagnosis     dynamic uncertain causality graph    

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标题 作者 时间 类型 操作

Energy-aware scheduling with reconstruction and frequency equalization on heterogeneous systems

Yong-xing LIU,Ken-li LI,Zhuo TANG,Ke-qin LI

期刊论文

Advances in the study of directed evolution for cellulases

Hailong LIN, Weiguang LI, Changhong GUO, Sihang QU, Nanqi REN

期刊论文

Unnormalized and normalized forms of gefura measures in directed and undirected networks

Raf GUNS,Ronald ROUSSEAU

期刊论文

Classifying multiclass relationships between ASes using graph convolutional network

期刊论文

Controllability analysis of second-ordermulti-agent systemswith directed andweighted interconnection

Di GUO,Rong-hao ZHENG,Zhi-yun LIN,Gang-feng YAN

期刊论文

Ionic strength directed self-assembled polyelectrolyte single-bilayer membrane for low-pressure nanofiltration

期刊论文

Liver-directed treatment is associated with improved survival and increased response to immune checkpoint

期刊论文

Clinical outcomes of ATP-tumor chemosensitivity assay directed chemotherapy in hepatocellular carcinoma

RAO Rongsheng, CHEN Wenxue, ZHOU Xinwen, ZHOU Zheng, LI Xiaojun, ZENG Zhiping

期刊论文

大规模图计算系统综述

Ning LIU, Dong-sheng LI, Yi-ming ZHANG, Xiong-lve LI

期刊论文

Site-directed mutagenesis of long QT syndrome KCNQ1 gene

LI Wei, WANG Bin, XU Qiumei, KE Qinmei, YANG Junguo, DU Rong, TIAN Li, WANG Qing

期刊论文

oocyst directed assembly of gold nanoparticles and graphene oxide

Sona Jain, Zhicheng Huang, Brent R. Dixon, Syed Sattar, Juewen Liu

期刊论文

Optimized human factor IX expression cassettes for hepatic-directed gene therapy of hemophilia B

null

期刊论文

Detecting large-scale underwater cracks based on remote operated vehicle and graph convolutional neural

Wenxuan CAO; Junjie LI

期刊论文

Distributed coordination inmulti-agent systems: a graph Laplacian perspective

Zhi-min HAN,Zhi-yun LIN,Min-yue FU,Zhi-yong CHEN

期刊论文

Efficacy of intelligent diagnosis with a dynamic uncertain causality graph model for rare disorders of

Dongping Ning, Zhan Zhang, Kun Qiu, Lin Lu, Qin Zhang, Yan Zhu, Renzhi Wang

期刊论文