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A Survey of Bitmap Index Compression Algorithms for Big Data

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Tsinghua Science and Technology 2015年第1期20卷 100-115页

作者： Zhen Chen Yuhao Wen Junwei Cao Wenxun Zheng jiahui chang Yinjun Wu Ge Ma Mourad Hakmaoui Guodong Peng the Research Institute of Information Technology Tsinghua University Tsinghua National Laboratory for Information Science and Technology (TNList) Tsinghua University Department of Electronic Engineering Tsinghua University Department of Physics Tsinghua University Department of Aerospace Engineering Tsinghua University Department of Automation Tsinghua University Department of Computer Science and Technology Tsinghua University Department of Mechanical Engineering Tsinghua University

With the growing popularity of Internet applications and the widespread use of mobile Internet, Internet traffic has maintained rapid growth over the past two decades. Internet Traffic Archival Systems（ITAS） for packets or flow records have become more and more widely used in network monitoring, network troubleshooting, and user behavior and experience analysis. Among the three key technologies in ITAS, we focus on bitmap index compression algorithm and give a detailed survey in this paper. The current state-of-the-art bitmap index encoding schemes include： BBC, WAH, PLWAH, EWAH, PWAH, CONCISE, COMPAX, VLC, DF-WAH, and VAL-WAH. Based on differences in segmentation, chunking, merge compress, and Near Identical（NI） features, we provide a thorough categorization of the state-of-the-art bitmap index compression algorithms. We also propose some new bitmap index encoding algorithms, such as SECOMPAX, ICX, MASC, and PLWAH＋, and present the state diagrams for their encoding algorithms. We then evaluate their CPU and GPU implementations with a real Internet trace from CAIDA. Finally, we summarize and discuss the future direction of bitmap index compression algorithms. Beyond the application in network security and network forensic, bitmap index compression with faster bitwise-logical operations and reduced search space is widely used in analysis in genome data, geographical information system, graph databases, image retrieval, Internet of things, etc. It is expected that bitmap index compression will thrive and be prosperous again in Big Data era since 1980s.

关键词： Internet traffic big data traffic archival network security bitmap index bitmap compression algorithm

Using MsfNet to Predict the ISUP Grade of Renal Clear Cell Carcinoma in Digital Pathology Images

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Computers, Materials & Continua 2024年第1期78卷 393-410页

作者： Kun Yang Shilong chang Yucheng Wang Minghui Wang jiahui Yang Shuang Liu Kun Liu Linyan Xue College of Quality and Technical Supervision Hebei UniversityBaoding071002China National and Local Joint Engineering Research Center of Metrology Instrument and System Hebei UniversityBaoding071002China Hebei Technology Innovation Center for Lightweight of New Energy Vehicle Power System Hebei UniversityBaoding071002China

Clear cell renal cell carcinoma(ccRCC)represents the most frequent form of renal cell carcinoma(RCC),and accurate International Society of Urological Pathology(ISUP)grading is crucial for prognosis and treatment *** study presents a new deep network called Multi-scale Fusion Network(MsfNet),which aims to enhance the automatic ISUP grade of ccRCC with digital histopathology pathology *** MsfNet overcomes the limitations of traditional ResNet50 by multi-scale information fusion and dynamic allocation of channel *** model was trained and tested using 90 Hematoxylin and Eosin(H&E)stained whole slide images(WSIs),which were all cropped into 320×320-pixel patches at 40×*** achieved a micro-averaged area under the curve(AUC)of 0.9807,a macro-averaged AUC of 0.9778 on the test *** Gradient-weighted Class Activation Mapping(Grad-CAM)visually demonstrated MsfNet’s ability to distinguish and highlight abnormal areas more effectively than *** t-Distributed Stochastic Neighbor Embedding(t-SNE)plot indicates our model can efficiently extract critical features from images,reducing the impact of noise and redundant *** results suggest that MsfNet offers an accurate ISUP grade of ccRCC in digital images,emphasizing the potential of AI-assisted histopathological systems in clinical practice.

关键词： Renal cell carcinoma computer-aided diagnosis pathology image deep learning machine learning

Orally administered BZL-s RNA-20 oligonucleotide targeting TLR4 effectively ameliorates acute lung injury in mice

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Science China(Life Sciences) 2023年第7期66卷 1589-1599页

作者： Dandan Zhao Yuhao Qin Jiaqi Liu Kegong Tang Shuaiyao Lu Zirui Liu Yexuan Lin Cong Zhang Fengming Huang jiahui chang chang Li Mingyao Tian Yiming Ma Xiaoyun Li Congzhao Zhou Xiao Li Xiaozhong Peng Ningyi Jin Chengyu Jiang State Key Laboratory of Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical SciencesDepartment of BiochemistryPeking Union Medical CollegeBeijing 100005China Institute of Medical Biology Chinese Academy of Medical SciencesKunming 650031China Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences University of Science and Technology of ChinaHefei 230027China changchun Veterinary Research Institute Chinese Academy of Agricultural SciencesChangchun 130122China

The global COVID-19 pandemic emerged at the end of December *** respiratory distress syndrome(ARDS)and acute lung injury(ALI)are common lethal outcomes of bacterial lipopolysaccharide(LPS),avian influenza virus,and SARS-Co ***-like receptor 4(TLR4)is a key target in the pathological pathway of ARDS and *** studies have reported that herbal small RNAs(s RNAs)are a functional medical ***-s RNA-20(Accession number:B59471456;Family ID:F2201.Q001979.B11)is a potent inhibitor of Toll-like receptor 4(TLR4)and pro-inflammatory ***,BZLs RNA-20 reduces intracellular levels of cytokines induced by lipoteichoic acid(LTA)and polyinosinic-polycytidylic acid(poly(I:C)).We found that BZL-s RNA-20 rescued the viability of cells infected with avian influenza H5N1,SARS-Co V-2,and several of its variants of concern(VOCs).Acute lung injury induced by LPS and SARS-Co V-2 in mice was significantly ameliorated by the oral medical decoctosome mimic(bencaosome;sphinganine(d22:0)+BZL-s RNA-20).Our findings suggest that BZLs RNA-20 could be a pan-anti-ARDS/ALI drug.

关键词： oligonucleotide drug herbal medicine ARDS/ALI SARS-CoV-2

Eugenol targeting CrtM inhibits the biosynthesis of staphyloxanthin in Staphylococcus aureus

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Food Science and Human Wellness 2024年第3期13卷 1368-1377页

作者： Jiang chang Bo Chen Zeqian Du Bowen Zhao jiahui Li Ziyi Li Kannappan Arunachalam Ting Shi Dongqing Wei Chunlei Shi MOST-USDA Joint Research Center for Food Safety School of Agriculture and BiologyState Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghai 200240China School of Life Sciences and Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China

Staphylococcus aureus is a serious foodborne pathogen threatening food safety and public *** the emergence of methicillin-resistant Staphylococcus aureus(MRSA)increased the difficulty of *** *** is a crucial virulence factor of *** staphyloxanthin production could help the host immune system counteract the invading *** *** this study,we first screened for staphyloxanthin inhibitors using a virtual screening *** outcome of the virtual screening method resulted in the identification of eugenol(300μg/mL),which significantly inhibits the staphyloxanthin production in *** ATCC 29213,*** Newman,MRSA ATCC 43300 and MRSA ATCC BAA1717by 84.2%,63.5%,68.1%,and 79.5%,*** outcome of the growth curve assay,field-emission scanning electron,and confocal laser scanning microscopy analyses confirmed that eugenol at the test concentration did not affect the morphology and growth of ***,the survival rate of *** ATCC 29213 and MRSA ATCC 43300 under H_(2)O_(2) pressure decreased to 51.9%and 45.5%in the presence of eugenol,*** quantitative RT-PCR and molecular simulation studies revealed that eugenol targets staphyloxanthin biosynthesis by downregulating the transcription of the crtM gene and inhibiting the activity of the CrtM *** together,we first determined that eugenol was a prominent compound for staphyloxanthin inhibitor to combat *** especially MRSA infections.

关键词： Staphylococcus aureus Staphyloxanthin Eugenol Virtual screening 4 4’-Diapophytoene synthase(CrtM)

靶向TLR4的口服寡核苷酸药物BZL-sRNA-20可有效缓解小鼠急性肺损伤

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中国科学：生命科学 2024年第7期54卷 1279-1291页

作者：赵丹丹秦宇豪刘佳齐汤克功鲁帅尧刘子睿林烨暄张聪黄凤鸣常佳慧李昌田明尧马一鸣李晓芸周丛照李霄彭小忠金宁一蒋澄宇中国医学科学院基础医学研究所&北京协和医学院基础学院生物化学与分子生物学系重大疾病共性机制研究全国重点实验室北京100005 中国医学科学院医学生物学研究所昆明650031 中国农业科学院长春兽医研究所长春130122 中国科学技术大学合肥微尺度物质科学国家研究中心合肥230027

2019年12月底,新型冠状病毒病(coronavirus disease 2019,COVID-19)开始流行.急性呼吸窘迫综合征(acute respiratory distress syndrome,ARDS)和急性肺损伤(acute lung injury,ALI)是由细菌脂多糖(lipopolysaccharide,LPS)、禽流感病毒和新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)等引发的高致死疾病.Toll样受体4(Toll-like receptor 4,TLR4)是ARDS和ALI病理通路中的关键靶点.草药小RNA(small RNA,sRNA)已被报道是草药药效的重要成分之一.本研究发现,半枝莲来源的小核酸BZL-sRNA-20(检索号:B59471456;ID:F2201.Q001979.B11)是TLR4及促炎细胞因子的有效抑制剂,可下调细菌脂磷壁酸(lipoteichoic acid,LTA)和聚肌苷酸-聚胞苷酸(Poly(I:C))引发上升的促炎细胞因子水平,并能挽救禽流感病毒H5N1,SARSCoV-2及其多种变异株感染所致的细胞死亡.此外,口服本草体(bencaosome):(鞘氨醇(d22:0)+BZL-sRNA-20)可缓解LPS与SARS-CoV-2诱导的小鼠急性肺损伤.本研究结果表明,半枝莲来源的BZL-sRNA-20可能是一种广谱治疗ARDS/ALI的寡核苷酸药物.

关键词：寡核苷酸药物中草药 ARDS/ALI SARS-CoV-2

Herbal decoctosome is a novel form of medicine

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Science China(Life Sciences) 2019年第3期62卷 333-348页

作者： Xiaoyun Li Zhu Liang Jianchao Du Zhiqing Wang Song Mei Zhiqing Li Yan Zhao DANDan Zhao Yiming Ma Jun Ye Jiantao Xu Yu Zhao jiahui chang Yuhao Qin Lanlan Yu Chenxuan Wang Chengyu Jiang State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences Department of Biochemistry Peking Union Medical College Institute of Basic Medical Sciences Chinese Academy of Medical Sciences Department of Biophysics and Structural Biology Peking Union Medical College

Traditionally, herbal medicine is consumed by drinking decoctions produced by boiling herbs with water. The functional components of the decoction are heat stable. Small RNAs(sRNAs) were reported as a new class of functional components in decoctions. However, the mechanisms by which sRNAs survive heat treatment of the decoction and enter cells are *** studies showed that plant-derived exosome-like nanoparticles(ELNs), which we call botanosomes, could deliver therapeutic reagents in vivo. Here, we report that heat-stable decoctosomes(ELNs) from decoctions have more therapeutic effects than the decoctions in vitro and demonstrate therapeutic efficacy in vivo. Furthermore, sRNAs, such as HJT-sRNA-m7 and PGY-sRNA-6, in the decoctosome exhibit potent anti-fibrosis and anti-inflammatory effects, respectively. Decoctosome is comprised of lipids, chemical compounds, proteins, and s RNAs. A medical decoctosome mimic is called bencaosome. A single lipid sphinganine(d22:0) identified in the decoctosome was mixed and heated with the synthesized sRNAs to form the simplest bencaosome. This simple bencaosome structure was identified by critical micelle concentration(cmc) assay that sRNAs coassembled with sphinganine(d22:0) to form the lipid layers of vesicles. The heating process facilitates co-assembly of sRNAs and sphinganine(d22:0) until a steady state is reached. The artificially produced sphinganine-HJT-sRNA-m7 and sphinganinePGY-sRNA-6 bencaosomes could ameliorate bleomycin-induced lung fibrosis and poly(I:C)-induced lung inflammation, respectively, following oral administration in mice. Our study not only demonstrates that the herbal decoctosome may represent a combinatory remedy in precision medicine but also provides an effective oral delivery route for nucleic acid therapy.

关键词： decoctosome bencaosome sphinganine

Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7

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Science China(Life Sciences) 2019年第3期62卷 309-320页

作者： Jianchao Du Zhu Liang Jiantao Xu Yan Zhao Xiaoyun Li Yanli Zhang DANDan Zhao Ruxuan Chen Yang Liu Trupti Joshi jiahui chang Zhiqing Wang Yanxu Zhang Jindong Zhu Qiang Liu Dong Xu Chengyu Jiang State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical SciencesDepartment of Biochemistry Peking Union Medical College Department of Internal Medicine Peking Union Medical College Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Department of Computer Science Informatics Institute and Christopher S.Bond Life Science Center University of Missouri Department of Health Management and Informatics and Office of Medical Research School of Medicine University of Missouri State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy West China Hospital Sichuan University

Pulmonary fibrosis, a progressive chronic disease with a high mortality rate, has limited treatment options. Currently, lung transplantation remains the only effective treatment. Here we report that a small RNA, HJT-sRNA-m7, from a Chinese herbal medicine Hong Jing Tian(HJT, RHODIOHAE CRENULATAE RADIX ET RHIZOMA, Rhodiola crenulata) can effectively reduce the expressions of fibrotic hallmark genes and proteins both in alveolar in vitro and in mouse lung tissues in vivo. We also discovered over one hundred oil-soluble chemicals from HJT decoctions, most of which are found in lipid extracts from other Chinese herbals decoctions, including Pu Gong Ying(PGY, TARAXACI HERBA, Taraxacum mongolicum), Chuan Xin Lian(CXL, changed to "ANDROGRAPHIS HERBA, Andrographis paniculata"), and Jin Yin Hua(JYH, lonicera japonica or Honeysuckle). We identified the active component in these decoctions as two forms of phosphocholines, PC(18:0/18:2) and PC(16:0/18:2). These PCs potentially could form liposomes with small RNAs to enter human alveolar and gastric cells. Our experimental results suggest an unprecendent lipid complex route through which botanic small RNA can enter human *** results provide an innovative treatment strategy for oral delivery of siRNAs as therapeutic medication.

关键词： PC cellular uptake anti-fibrotic HJT sRNA

Stretchable polymer composites with ultrahigh piezoelectric performance

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National Science Review 2023年第8期10卷 203-210页

作者： Tongxiang Tang Zhonghui Shen Jian Wang Shiqi Xu Jiaxi Jiang jiahui chang Mengfan Guo Youjun Fan Yao Xiao Zhihao Dong Houbing Huang Xiaoyan Li Yihui Zhang Danyang Wang Long-Qing Chen Ke Wang Shujun Zhang Ce-Wen Nan Yang Shen State Key Lab of New Ceramics and Fine Processing School of Materials Science and Engineering Tsinghua University State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Center of Smart Materials and Devices Wuhan University of Technology Advanced Research Institute of Multidisciplinary Science Beijing Institute of Technology Applied Mechanics Laboratory Department of Engineering Mechanics Tsinghua University Center for Flexible Electronics Technology Tsinghua University School of Materials Science and Engineering University of New South Wales Department of Materials Science and Engineering The Pennsylvania State University State College Institute for Superconducting and Electronic Materials Australian Institute for Innovative MaterialsUniversity of Wollongong

Flexible piezoelectric materials capable of withstanding large deformation play key roles in flexible electronics. Ferroelectric ceramics with a high piezoelectric coefficient are inherently brittle, whereas polar polymers exhibit a low piezoelectric coefficient. Here we report a highly stretchable/compressible piezoelectric composite composed of ferroelectric ceramic skeleton, elastomer matrix and relaxor ferroelectric-based hybrid at the ceramic/matrix interface as dielectric transition layers, exhibiting a giant piezoelectric coefficient of 250 picometers per volt, high electromechanical coupling factor keff of 65%,ultralow acoustic impedance of 3MRyl and high cyclic stability under 50% compression strain. The superior flexibility and piezoelectric properties are attributed to the electric polarization and mechanical load transfer paths formed by the ceramic skeleton, and dielectric mismatch mitigation between ceramic fillers and elastomer matrix by the dielectric transition layer. The synergistic fusion of ultrahigh piezoelectric properties and superior flexibility in these polymer composites is expected to drive emerging applications in flexible smart electronics.

关键词： polymer composites piezoelectric materials structure design flexible electronics

Spatiotemporal characteristics of seed rain and soil seed bank of artificial Caragana korshinskii Kom. forest in the Tengger Desert, China

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Journal of Arid Land 2024年第4期16卷 550-566页

作者： SHEN Jianxiang WANG Xin WANG Lei WANG jiahui QU Wenjie ZHANG Xue chang Xuanxuan YANG Xinguo CHEN Lin QIN Weichun ZHANG Bo NIU Jinshuai College of Ecological Environment Ningxia UniversityYinchuan 750021China Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwest China Ministry of EducationNingxia UniversityYinchuan 750021China College of Agriculture Ningxia UniversityYinchuan 750021China

Vegetation restoration and reconstruction are effective approaches to desertification control and achieving social and economic sustainability in desert ***,the self-succession ability of native plants during the later periods of vegetation restoration remains ***,this study was conducted to bridge the knowledge gap by investigating the regeneration dynamics of artificial forest under natural *** information of seed rain and soil seed bank was collected and quantified from an artificial Caragana korshinskii *** in the Tengger Desert,*** germination tests were conducted in a laboratory *** analysis of species quantity and diversity in seed rain and soil seed bank was conducted to assess the impact of different durations of sand fixation(60,40,and 20 a)on the progress of vegetation restoration and ecological conditions in artificial *** *** results showed that the top three dominant plant species in seed rain were Echinops gmelinii Turcz.,Eragrostis minor Host.,and Agropyron mongolicum Keng.,and the top three dominant plant species in soil seed bank were ***,Chloris virgata Sw.,and *** restoration period increased,the density of seed rain and soil seed bank increased first and then *** for species richness,as restoration period increased,it gradually increased in seed rain but decreased in soil seed *** was a positive correlation between seed rain density and soil seed bank density among all the three restoration *** species similarity between seed rain or soil seed bank and aboveground vegetation decreased with the extension of restoration *** shape of the seeds,specifically those with external appendages such as spines and crown hair,clearly had an effect on their dispersal,then resulting in lower seed density in soil seed *** addition,precipitation was a crucial factor in promoting rapid germination,also resulting in lower seed density in soi

关键词： ecological restoration soil seed bank seed rain artificial forest vegetation desertification Caragana korshinskii Tengger Desert