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Combinatorial pooled sequencing： experiment design and decoding

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Frontiers of Electrical and Electronic Engineering in China 2016年第1期4卷 36-46页

作者： Chang-chang Cao Xiao Sun State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering Southeast University Nanjing210096 China

Owing to rapid advances in the next-generation sequencing technology, the cost of DNA sequencing has been reduced by over several orders of magnitude. However, genomic sequencing of individuals at the population scale is still restricted to a few model species due to the huge challenge of constructing libraries for thousands of samples. Meanwhile, pooled sequencing provides a cost-effective alternative to sequencing individuals separately, which could vastly reduce the time and cost for DNA library preparation. Technological improvements, together with the broad range of biological research questions that require large sample sizes, mean that pooled sequencing will continue to complement the sequencing of individual genomes and become increasingly important in the foreseeable future. However, simply mixing samples together for sequencing makes it impossible to identify reads that belongs to each sample. Barcoding technology could help to solve this problem, nonetheless, currently, barcoding every sample is costly especially for large-scale samples. An alternative to barcoding is combinatorial pooled sequencing which employs pooling pattern rather than short DNA barcodes to encode each sample. In combinatorial pooled sequencing, samples are mixed into few pools according to a carefully designed pooling strategy which allows the sequencing data to be decoded to identify the reads that belongs to the sample that are unique or rare in the population. In this review, we mainly survey the experiment design and decoding procedure for the combinatorial pooled sequencing applied in rare variant and rare haplotype carriers screening, complex genome assembling and single individual haplotyping.

关键词： combinatorial pooled sequencing experiment design decoding

Research on the Infuence of Multiple Parameters on the Responses of a B-type Subway Train

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Chinese Journal of Mechanical Engineering 2022年第4期35卷 313-330页

作者： Yanwen Liu Bing Yang Shoune Xiao Tao Zhu Guangwu Yang Ruixian Xiu State Key Laboratory of Traction Power Southwest Jiaotong UniversityChengdu 610031China Basic R&D Department National Railway Passenger Car Engineering Research CenterChangchun Railway Vehicles Co.LtdChangchun 130113China College of Engineering Changchun Normal UniversityChangchun 130032China

To obtain improved comprehensive crashworthiness criteria for a B-type subway train,the infuence laws of the vehicle design collision weight M and empty stroke D on the train’s collision responses were investigated,and multiobjective optimization and decision-making were performed to minimize TS(total compression displacement along the moving train)and TAMA(the overall mean acceleration along the moving train).Firstly,a one-dimensional train collision dynamics model was established and verifed by comparing with the results of the fnite element ***,based on the dynamics model,the infuence laws of M and D on the collision responses,such as the energy-absorbing devices’displacements and absorbed energy,vehicles’velocity and acceleration,TS,TAMA and the coupling correlation efect were ***,surrogate models for TS and TAMA were developed using the optimal Latin hypercube method(OLHD)and response surface method(RSM),and multi-objective optimization was conducted using the particle swarm optimization algorithm method(MPOSO).Finally,the entropy method was used to obtain the weight coefcients for TS and TAMA,and multi-objective decision-making was *** results indicate that D and M signifcantly afect the compression displacements and energy absorption of the frst three collision interfaces,but have limited impact on the last three collision *** velocity versus time curves of vehicle M1 and M2 are shifted and parallel with diferent ***,the velocity versus time curves of all the vehicles are shifted but gradually divergent with diferent *** maximum collision instantaneous accelerations of the vehicles are directly determined by M,but are only slightly afected by *** the coupling efect,all concerned collision responses are strongly correlated with M;however,the responses are weakly correlated with D except for the compression displacement at the M2-M3 collision interface and the maximum collision instantaneous acceleration

关键词： Train collision response Multi-body dynamics model experiment design Surrogate model Multiobjective optimization Entropy method Multi-objective decision-making

Input signal design to estimate interwell connectivities in mature fields from the capacitance-resistance model

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Petroleum Science 2014年第4期11卷 563-568页

作者： Gustavo A.Moreno Larry W.Lake YPF-Tecnología Baradero S/N (1925) EnsenadaBuenos AiresArgentina YPF Macacha Guemes 515CABAArgentina CPARM University of Texas at AustinAustinTXUSA

Interwell connectivities are fundamental parameters required to manage waterfloods in oil reservoirs. Data-driven models, such as the capacitance-resistance model （CRM）, are fast tools to estimate these parameters from time-correlations of input （injection rates） and output （production rates） signals. Noise and structure of the input time-series impose limits on the information that can be extracted from a given data-set. This work uses the CRM to study general prescriptions for the design of input signals that enhance the information content of injection/production data in the estimation of well-to-well interactions. Numerical schemes and general features of the optimal input signal strategy are derived for this problem.

关键词： Intervell connectivity capacitance-resistance model mature field experiment design

Development and comparison of aerial photograph aided visualization pipelines for LiDAR datasets

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International Journal of Digital Earth 2015年第8期8卷 656-677页

作者： Suddhasheel Ghosh Bharat Lohani Department of Civil Engineering MGM’s Jawaharlal Nehru Engineering CollegeAurangabadIndia Department of Civil Engineering Indian Institute of Technology KanpurKanpurIndia

Light Detection and Ranging(LiDAR)technology generates dense and precise threedimensional datasets in the form of point *** methods of mapping with airborne LiDAR datasets deal with the process of classification or feature specific *** processes have been observed to be time-consuming and unfit to handle in scenarios where topographic information is required in a small amount of *** there is a requirement of developing methods which process the data and reconstruct the scene in a small amount of *** paper presents several pipelines for visualizing LiDAR datasets without going through classification and compares them using statistical methods to rank these processes in the order of depth and feature *** make the comparison more meaningful,a manually classified and computer-aided design(CAD)reconstructed dataset is also included in the list of compared *** show that a heuristic-based method,previously developed by the authors perform almost equivalent to the manually classified and reconstructed dataset,for the purposes of *** paper makes some distinct contributions as:(1)gives a heuristics-based visualization pipeline for LiDAR datasets,and(2)presents an experimental design supported by statistical analysis to compare different pipelines.

关键词： LiDAR mining feature extraction visualization experiment design nonparametric statistics

Fracture mechanism and separation conditions of pineapple fruit-stem and calibration of physical characteristic parameters

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International Journal of Agricultural and Biological Engineering 2023年第5期16卷 248-259页

作者： Mutong Li Lin He Dandan Yue Binbin Wang Junlue Li Key Laboratory of Modern Agricultural Intelligent Equipment in South China Ministry of Agriculture and Rural Affairs of ChinaGuangdong Institute of Modern Agricultural EquipmentGuangzhou 510630China Guangdong Hongke Agricultural Machinery Research and Development Co. LtdGuangzhou 510555China

At present,the research on the physical composition and properties of pineapple plants is scarce,and the uncertainty of fruit picking method is the key bottleneck factor hindering the research and development of pineapple harvesting *** on the statistics of survey data from many places,this paper analyzes the fruit-stem fracture mechanism and the theoretical conditions for optimal separation through structural modeling,mechanical behavior analysis and function *** this basis,the“pineapple plant fixation bench”and“fruit-stem bending separation torque test equipment”were developed,and large-size,small-size tests and random optimization tests were carried out *** test results showed that the larger of the stem-stalk fixation distance,the more torque and fracture starting angle required for fruit fracture would increase,and the change range was small when the stem-stalk fixation distance was within 50 mm,and the probability of brittle fracture and complete separation was very *** the space between the fracture section and the fruit-stem connecting point is about 5mm,the range of bending moment value required for the fruit-stem fracture is 1.88 to 2.77 N·m,the range of fracture starting angle is 12.2°to 18.1°,and the angular travel range during the separation process is 82.9°to 87.5°.When the stem-stalk fixation distance is about 15 mm,it is the best fruit-stem separation condition and the breaking torque measured in the verification test is about 2.76 N·*** fracture starting angle is about 13.8°,the maximum prediction error is 13.1%,and the elastic modulus near the fruit-stem joint ranges from 16.1 to 23.9 *** conclusion can provide an important design basis for the research and development of pineapple field picking robot and harvesting equipment.

关键词： pineapple harvesting fracture mechanism of fruit and stem separation conditions experiment design reverse calibration

Multi-Objective Structural Optimization of Wind Turbine Tower Using Nondominated Sorting Genetic Algorithm

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Journal of Beijing Institute of Technology 2020年第3期29卷 417-424页

作者： Yuqiao Zheng Lu Zhang Fugang Dong Bo Dong School of Mechanical and Electronic Engineering Lanzhou University of TechnologyLanzhou 730050China

A multi-objective optimization process for wind turbine steel towers is described in present *** objective functions are tower top deformation and *** tower's height,radius and thickness are considered as design *** mathematical relationships between objective functions and variables were predicted by adopting a response surface methodology(RSM).Furthermore,the multi-objective non-dominated sorting genetic algorithm-II(NSGA-II)is adopted to optimize the tower structure to achieve accurate results with the minimum top deformation and total mass.A case study on a 2MW wind turbine tower optimization is given,which computes the desired tower structure *** results are compared with the original tower:a reduction of tower top deformation reduction by about 16.5%and a reduction of a mass by about 1.5%could be achieved for such an optimization process.

关键词： wind turbine tower statics analysis experiment design multi-objective optimization

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design of Calibration experiments for Identification of Manipulator Elastostatic Parameters

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Journal of Mechanics Engineering and Automation 2012年第9期2卷 531-542页

作者： Alexandr Klimchik Anatol Pashkevichl Yier Wu Stephane Caro Benoit Furet Ecole des mines de Nantes Nantes 44300 France Research Institute of Communications and Cybernetics of Nantes (1RCCyN) Nantes 44300 France National Centre for Scientific Research (CNRS) Paris 75016 France Department of Mechanical Engineering and Manufacturing University of Nantes Carquefou 44475 France

The paper is devoted to the elastostatic calibration of industrial robots, which is used for precise machining of large-dimensional parts made of composite materials. In this technological process, the interaction between the robot and the workpiece causes essential elastic deflections of the manipulator components that should be compensated by the robot controller using relevant elastostatic model of this mechanism. To estimate parameters of this model, an advanced calibration technique is applied that is based on the non-linear experiment design theory, which is adopted for this particular application. In contrast to previous works, it is proposed a concept of the user-defined test-pose, which is used to evaluate the calibration experiments quality. In the frame of this concept, the related optimization problem is defined and numerical routines are developed, which allow generating optimal set of manipulator configurations and corresponding forces/torques for a given number of the calibration experiments. Some specific kinematic constraints are also taken into account, which insure feasibility of calibration experiments for the obtained configurations and allow avoiding collision between the robotic manipulator and the measurement equipment. The efficiency of the developed technique is illustrated by an application example that deals with elastostatic calibration of the serial manipulator used for robot-based machining.

关键词： Industrial robot elastostatic calibration experiment design industry-oriented performance measure test-pose basedapproach.

Reform of Paleontology experiment Teaching for Geology Majors

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Journal of Educational Theory and Management 2021年第1期5卷 56-59页

作者： Jianpeng Chu School of Resources and Environmental Engineering Shandong University of TechnologyZiboShandong255049China

Due to the development of science and technology and the transformation of society’s demand for talents of geology majors,many changes have taken place in the arrangement of teaching hours and teaching content of paleontology experiment *** paleontology experiment teaching of geology majors has problems such as unreasonable experiment design,no independent experiment arrangement,single teaching method,absence of experiment contents,*** article believes that the reform should be made in the following aspects:setting up independent experiment teaching arrangement,improvement of experiment teaching design,continuing to improve the laboratory hardware and software construction,reform of teaching methods.

关键词： experiment teaching Paleontology experiment design Teaching reform

Research on Methods of MDB Test

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Research on Methods of MDB Test