Surface functionalization for self-referencing surface plasmon resonance (SPR) biosensors by multi-step self-assembly

Recently, a novel SPR sensor with on-chip referencing has been realized. In this sensor, one-half of the gold sensing surface is covered with a high refractive index overlayer of tantalum pentoxide (Ta₂O₅). When polychromatic beam illuminates the sensing surface, surface plasmon resonance in the areas with and without the overlayer occur at different wavelengths. Therefore, the reflected light exhibits two dips associated with SPRs in those two areas. When functionalized properly, one of the areas can be used as a specific sensing channel for detection of specific bio-interactions and the other can act as a reference channel for compensation for background refractive index fluctuations. In this paper we present a new functionalization approach for these mixed architecture chips. The gold side of the chip is functionalized with a mixed self-assembled monolayer of polyethylene oxide (PEO) and biotin terminated (BAT) thiols whereas the Ta₂O₅ side is coated with PEO terminated silanes. The PEO terminated thiols and silanes serve as a protein resistant background, while the biotin terminated thiols are used to bind streptavidin, which in turn immobilizes biotinylated antibodies. Hence, the gold side of the chip is used for the binding and detection of target analytes and the Ta₂O₅ side functions as a reference channel that monitors bulk refractive index changes and temperature drift. We have studied human chorionic gonadotropin (hCG) as a model system, currently detecting down to 5 ng/ml. In addition, we demonstrate the power of the on-chip reference channel for compensating for refractive index changes and eliminating false alarms.     

Portable bead-based fluorescence detection system for multiplex nucleic acid testing: a case study with Bacillus anthracis

This paper describes the design, functioning and use of a portable detection platform for multiplex nucleic acid testing. The system features a bead-supported DNA hybridization assay performed inside a microfluidic cartridge. Polystyrene particles modified with DNA capture probes are confined in the detection area and exposed to a solution of fluorescently labeled target DNA strands. The cartridge, fabricated from inexpensive thermoplastic polymers, allows for conducting up to eight assays in parallel. The detection instrument is equipped with a pneumatic module and a manifold lid serving as an interface to mediate fluid displacement on the cartridge. The fluorescence signal deriving from each assay is recorded by a semi-confocal fluorescence reader embedded in the detection platform. The compact design of the instrument and its level of integration make it possible to obtain an analytical result in less than 15 min, while only few manual steps need to be performed in between. A proof-of-concept demonstration involving Cy3-labeled, PCR-amplified genomic DNA confirms the ability to detect Bacillus anthracis in a multiplexed single-assay format using lef and capC genes. Limits of quantification are on the order of 1 × 10⁹ copies/μL for lef targets.     

Development of an SH-SAW sensor for the detection of DNA hybridization

We have developed SH (shear horizontal) surface acoustic wave (SAW) sensors for the detection of DNA (deoxyribonucleic acid) hybridization on the gold-coated delay line of transverse SAW devices. DNA hybridization experiments were performed with 15-mer oligonucleotides (probe and complementary target DNA). The sensor consists of twin SAW delay line oscillators (sensing channel and reference channel) operating at 100 MHz fabricated on 36° rotated Y-cut X-propagation LiTaO₃ piezoelectric single crystals. The relative change in the frequency of the two oscillators was monitored to detect hybridization between the target DNA and probe DNA immobilized on the delay line of the SAW sensor. The measurement results showed a good response of the sensor to the mass loading effects of the DNA hybridization with a sensitivity level up to 1.55 ng/ml/Hz.     

Characterization of DNA hybridization kinetics in a microfluidic flow channel

In this investigation we report on the influence of volumetric flow rate, flow velocity, complementary DNA concentration, height of a microfluidic flow channel and time on DNA hybridization kinetics. A syringe pump was used to drive Cy3-labeled target DNA through a polydimethylsiloxane (PDMS) microfluidic flow channel to hybridize with immobilized DNA from the West Nile Virus. We demonstrate that a reduction of channel height, while keeping a fixed volumetric flow rate or a fixed flow velocity, enhances mass transport of target DNA to the capture probes. Compared to a passive hybridization, the DNA hybridization in the microfluidic flow channel generates higher fluorescence intensities for lower concentration of target DNA during the same fixed period of time. Within a fixed 2 min time period the fastest DNA hybridization at a 50 pM concentration of target DNA is achieved with a continuous flow of target DNA at the highest flow rate and the lowest channel height.     

Development of an integrated CMOS DNA detection biochip

This paper presents a CMOS DNA detection biochip using an electrical detection method with self-assembly multilayer gold nanoparticles (AuNPs). Each measuring spot of this biochip consists of three major parts; a pair of electrodes with a nanogap, a current amplifier circuit, and a heater with an embedded temperature sensor. The biochip is first fabricated by a TSMC (Taiwan Semiconductor Manufacturing Company Ltd.) 0.35 μm 2P4M standard CMOS process. Then, post-CMOS micromachining etch processes are used to expose the surface of the nanogap to test samples for the establishment of multilayer AuNPs through hybridization between single strand DNAs in the samples. The gap distance between a pair of electrodes is 350 nm. Before taking DNA detection measurements, self-assembly monolayer AuNPs is established on the nanogap surface between two microelectrodes. Multilayer AuNPs can be observed if hybridization between single strand DNAs occurs. An approximately 1000-fold increase in electric current between the multilayer AuNPs over the monolayer AuNPs serves an indication of the presence of target DNA in test samples. After integrating the electrodes with an embedded current amplifier, the electric current of multilayer AuNPs is amplified to the order of mA that can be easily measured by a commercial Volt-Ohm-Milliammeter. The heating system with a heating element and a temperature sensor can be used to distinguish single base-pair mismatch hybridization from complementary hybridization for the establishment of multilayer AuNPs. The lowest detectable concentration of target DNA on this biochip is 0.1 nM.     

基于TD-SCDMA的改进的联合检测算法及仿真

大多数多用户联合检测算法都存在复杂度高,不利于在终端上应用的缺陷.针对TD-SCDMA系统中下行链路多用户联合检测算法MMSE-BLE-SD需要用到的活动码道数,给出了一种改进的检测算法.该算法在信道变化缓慢的情况下可以达到非常理想的性能.另外还提出了一种基于FFT的低复杂度的联合检测算法,可以有效的降低传统算法中矩阵求逆所需要的巨大的运算量.仿真结果表明,算法具有良好的检测性能,大大的降低了系统的复杂度.     

基于“树枝状”信号放大的电化学DNA生物传感器研究

发展了一种基于"树枝状"信号放大的电化学生物传感器用于DNA的检测。该传感器利用两种DNA功能化的纳米金颗粒,通过两次"三明治"杂交,在电极表面形成"树枝"状结构,从而实现DNA的定量检测。首先通过共价交联方法获得巯基DNA1和DNA2修饰的两种纳米金颗粒,其中DNA1和DNA2与目标cDNA部分互补。然后,修饰在金电极上的捕获探针DNA1与目标cDNA分子及巯基DNA2修饰的纳米金颗粒(DNA2-AuNPs)形成第一个"三明治"杂交结构,实现一次放大检测。接着,DNA2-AuNPs又可与cDNA、巯基DNA1修饰的纳米金颗粒(DNA1-AuNPs)形成第二个"三明治"杂交结构,实现二次放大检测。这种"树枝状"放大信号的方法的检测限是0.13pmol/L,相对仅利用纳米金颗粒放大的方法而言,其检测限降低了4倍。并且,该传感器具有较好的识别碱基错配的能力。     

Mimic: An active covert channel that evades regularity-based detection

A covert timing channel is a hidden communication channel based on network timing that an attacker can use to sneak secrets out of a secure system. Active covert channels, in which the attacker uses a program to automatically generate innocuous traffic to use as a medium for embedding the covert channel, are especially problematic, as they allow the attacker to output large amounts of secret data. Further, it is relatively easy to create an active covert channel that outputs traffic with the same delay distribution as legitimate traffic. However, these channels are generally detectable due to their regularity – as they are generate by a computer program, they do not have the variations found in human-generated traffic. In this work, we show how to build a an active covert channel that generates traffic in a purposefully irregular manner. In particular, we propose Mimic, an active covert channel that mimics both the shape and regularity of legitimate traffic to disguise its presence. Mimic includes two modules, a shape modeler and a regularity modeler, for learning about the statistical properties of real traffic and generating traffic with the same properties. The main novelty of Mimic stems from its ability to produce irregular patterns similar to those of legitimate traffic while maintaining the distribution shape. To measure the effectiveness of our mechanism, we run experiments for both detection and throughput over a LAN and over the Internet. Our results show that Mimic can generate channels with a wide range of regularity values, making it undetectable by any known detection technique, without sacrificing channel capacity.     

Detection of specific single-stranded DNA molecules through SiNW surface modulation

This paper demonstrate a silicon nanowire biosensor for the detection of specific ssDNA biomarker detection. The biosensor was fabricated using conventional photolithography coupled with an inductively coupled plasma dry etching process. The detection was performed with a semiconductor parameter analyzer which measured the changes in current and conductance of the nanowire electrodes upon target DNA hybridization. The sensor surface was silanized and directly aminated with (3-aminopropyl)triethoxysilane to create a molecular binding chemistry for bio-functionalization. The resulting Si–O–Si-components were functionalized with receptor ssDNA, which interacted with the targeted ssDNA to create a field across the silicon nanowire and increase the current. Hybridization detection discrimination among various concentration, the device response to the targets shows selectivity for the ssDNA in a linear range from ssDNA concentrations of 100 pM to 150 nM. Linearity of the device to molecular concentration, was confirm linear fit curve for the (0.1–0.5) nM concentration and (0–40) nM concentration.     

纳米颗粒在DNA固定化中的应用进展

介绍了在固体支持物表面固定DNA过程中使用的纳米颗粒的种类、固定方法及其特点。纳米颗粒巨大的比表面积及其与DNA良好的生物相容性可以增加DNA的固定量,改善杂化反应的识别能力,进而提高DNA传感器的检测灵敏度。     

可满足问题的分子信标计算模型(英文)

分子信标（Molecular Beacon）是一种发夹状的荧光探针,它可以特异地和那些与分子信标的环（Loop）互补的核酸靶序列杂交,具有单个碱基错配的检测能力．肽核酸（Peptide Nucleic Acid）是人工合成的核酸（DNA）的类似物．PNA骨架为酰胺键,与DNA补链杂交更稳定,可以阻止聚合酶延伸反应．文中将可满足问题的约束变量编码于分子信标的环部识别区,通过分子信标与使得给定范式为真的变量的PNA补链杂交,再利用PNA链可以阻止聚合酶延伸反应的性质,用限制性内切酶EcoRI降解对应于非解的分子信标,最后通过加热表面使分子信标构形发生变化,产生荧光读解．提出的可满足问题的分子信标计算模型具有可靠性高、无需观察和记录计算的中间结果、读解简单等优点．     

Modeling of coupled momentum, heat and solute transport during DNA hybridization in a microchannel in the presence of electro-osmotic effects and axial pressure gradients

An integrated thermofluidic analysis of DNA hybridization, in the presence of combined electrokinetically and/or pressure-driven microchannel flows, is presented in this work. A comprehensive model is developed that combines bulk and surface transport of momentum, heat and solute with the pertinent hybridization kinetics, in a detailed manner. Results confirm that electrokinetic accumulation of DNA occurs within a few seconds or minutes, as compared to passive hybridization that could sometimes take several hours. Further, it is observed that by increasing the accumulation time, significantly higher concentration of DNA can be achieved at the capture probes. However, this eventually tends to attain a saturation state, due to a lesser probability of successful hybridization on account of a prior accumulation of target DNA molecules on the capture probe strands. While favorable pressure gradients augment DNA hybridization rates that are otherwise established by the electro-osmotic transport, adverse pressure gradients of comparable magnitude may turn out to be much less consequential in retarding the same. Such effects can be of potential significance in the designing of a microfluidic arrangement to achieve the fastest rate of DNA hybridization.     

Pyramid context learning for object detection

Contextual information in complex scenarios is critical for accurate object detection. Existing state-of-the-art detectors have greatly improved detection performance with the use of contexts around objects. However, these detectors consider the local and global contexts separately, which limits the improvement in detection accuracy. In this paper, we propose a pyramid context learning module (PCL) for object detection, which makes full use of the feature context at different levels. Specifically, two operators, named aggregation and distribution, are designed to assemble and synthesize contextual information at different levels. In addition, a channel context learning operator is also used to capture the channel context. PCL is a universal module, so it can be easily integrated into most of the detection frameworks. To evaluate our PCL, we apply it into some popular detectors, e.g., SSD, Faster R-CNN and RetinaNet, and conduct extensive experiments on PASCAL VOC and MS COCO datasets. Experimental results show that PCL can produce competitive performance gains and significantly improve the baselines.

     

Microfluidic DNA hybridization assays

DNA hybridization is one of the most powerful techniques applied in diagnostic assays. Microfluidics provides a promising means to analyse small sample volumes, reduce reagent consumption and cost, shorten processing time as well as develop fast, sensitive and portable diagnostic tools. By coupling with the microfluidic technology, DNA hybridization assay can achieve high sensitivity, enhance hybridization kinetics and decrease the non-specific target-probe binding. The microfluidic-based DNA hybridization technology has a great potential for developing low-cost, rapid, automatic and point-of-care diagnostic devices. In this article, we provide an overview and summarize the recent advances on the merging of microfluidics to DNA hybridization assays. The advantages and disadvantages of various methods are discussed. Potential improvements required for these technologies are proposed as well.     

SDN环境下的DDoS检测与缓解机制

软件定义网络(Software-defined Network,SDN)以可编程的形式定义路由,对传统网络架构进行了一次彻底颠覆。通过采用中心化的拓扑结构,SDN有效实现了对网络基础设施的全局控制。然而这种中心化的拓扑极易受到网络攻击的威胁,如分布式拒绝服务攻击(Distributed Denial of Service,DDoS)。传统的DDoS通过堵塞交换机带宽,消耗控制器计算资源的方式实现拒绝服务。近年来,又有新型的DDoS变种通过攻击控制器与交换机通信的南向通道,攻击交换机流表的方式实现拒绝服务。为了缓解传统DDoS和新型DDoS带来的安全问题,本文提出了一个面向SDN的轻量化DDoS检测防御框架SDDetector(Software Defined Detector)。可以在粗粒度和细粒度两种模式下运行,粗粒度模式通过提取SDN交换机中的统计特征对可疑的攻击行为进行阈值警报;触发警报后,细粒度模式再进行二次特征提取,并利用熵检测算法和SVM检测算法做进一步地攻击判别。研究发现,熵检测算法擅长处理采用源IP伪造技术的DDoS攻击以及针对SDN的新型DDoS攻击;而SVM检测算法擅长处理基于应用层协议的、需要交互的DDoS攻击。SDDetector以近似并行的模式运行两种算法,自动使特征提取速度最快的算法来完成攻击检测,从而大幅降低了系统对攻击的响应时间。经过实验验证发现,在特定场景下,本文提出的模型能够比单一的检测方案少用75%的响应时间。     

Electrical detection of DNA hybridization with multilayer gold nanoparticles between nanogap electrodes

This study presents a DNA detection method via hybridization of a probe oligonucleotide with a target DNA and with a substrate oligonucleotide, which leads to self-assembly of gold nanoparticles and a change in the observed current. In contrast to previously reported methods, the present method can be used to detect a target DNA without a silver enhancement step. The device can be washed with 0.3 M PBS below 50 °C for a few minutes, indicating the stringency of target DNA hybridization. Target DNA concentration of as low as 10 picomolar can be detected by this method. Importantly, identification of single-base-pair mismatch in the target DNA can be accomplished with this nano-gap DNA chip.The authors thank for Shu-Fen, Hos group and her assistant, Mr. Wong for useful discussions. Dr. Ho has also been supported in measuring the electricity properties.     

Automatic Channel Detection Using DNN on 2D Seismic Data

Geologists interpret seismic data to understand subsurface properties and subsequently to locate underground hydrocarbon resources. Channels are among the most important geological features interpreters analyze to locate petroleum reservoirs. However, manual channel picking is both time consuming and tedious. Moreover, similar to any other process dependent on human intervention, manual channel picking is error prone and inconsistent. To address these issues, automatic channel detection is both necessary and important for efficient and accurate seismic interpretation. Modern systems make use of real-time image processing techniques for different tasks. Automatic channel detection is a combination of different mathematical methods in digital image processing that can identify streaks within the images called channels that are important to the oil companies. In this paper, we propose an innovative automatic channel detection algorithm based on machine learning techniques. The new algorithm can identify channels in seismic data/images fully automatically and tremendously increases the efficiency and accuracy of the interpretation process. The algorithm uses deep neural network to train the classifier with both the channel and non-channel patches. We provide a field data example to demonstrate the performance of the new algorithm. The training phase gave a maximum accuracy of 84.6% for the classifier and it performed even better in the testing phase, giving a maximum accuracy of 90%.     

The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA

We provide designs for the first autonomousDNA nanomechanical devices that execute cycles of motion without external environmental changes. These DNA devices translate along a circular strand of ssDNA and rotate simultaneously. The designs use various energy sources to fuel the movements, include (i) ATP consumption by DNA ligase in conjunction with restriction enzyme operations, (ii) DNA hybridization energy in trapped states, and (iii) kinetic (heat) energy. We show that each of these energy sources can be used to fuel random bidirectional movements that acquire after n steps an expected translational deviation of O(√n). For the devices using the first two fuel sources, the rate of stepping is accelerated over the rate of random drift due to kinetic (heat) energy. Our first DNA device, which we call walking DNA, achieves random bidirectional motion around a circular ssDNA strand by use of DNA ligase and two restriction enzymes. Our other DNA device, which we call rolling DNA, achieves random bidirectional motion without use of DNA ligase or any restriction enzyme, and instead using hybridization energy. We also describe how to modify the design for the rolling DNA device to include a ``latching mechanism' that fixes the wheels position at specified location along the road, so as to provide for overall unidirectional translational movement. This revised version was published online in June 2006 with corrections to the Cover Date.     

A novel method for label-free detection of ricin using liquid crystals supported on chemically functionalized surfaces

In this paper, we report a simple and novel liquid-crystal based sensor for ricin detection. The method relies on the use of liquid crystals (LCs) 5CB to amplify and report the presence of ricin captured by an affinity ligand. A merit of this approach is that the ricin can be imaged on the chemically functionalized surfaces and transduced into optical signal by using LCs, the optical signal caused by the orientational transition of the LCs could be easily identified with polarized light microscopy. In addition, the sensor exhibited high sensitivity with strong selectivity, experimental results showed that the minimum detection concentration was as low as 10 μg/mL, demonstrating the feasibility of using these devices to detect and positively identify ricin. Furthermore, the success of LC-based sensor reported here does not use complex instrumentations and does not involve any labeling steps.     

Orbiting magnetic microbeads enable rapid microfluidic mixing

We use three-dimensional numerical simulations and experiments to examine microfluidic mixing induced by orbiting magnetic microbeads in a microfluidic channel. We show that orbiting microbeads can lead to rapid fluid mixing in low Reynolds number flow, and identify two distinct mixing mechanisms. Bulk advection of fluid across the channel occurs due to the flow pattern that is developed when the ratio of flow velocity to bead velocity is low, and leads to rapid mixing. At higher velocity ratios, dispersion of small amounts of fluid across the channel occurs and results in increased mixing. We use simulations to investigate the effect of system parameters on the distance required to achieve a desired mixing level. We develop an experimental continuous-flow device and use it to validate our simulations and to demonstrate rapid microfluidic mixing. This device has the flexibility to also be applied to a mixing chamber or to stop-flow applications for rapid and controllable mixing. In addition to rapid mixing, the use of orbiting magnetic microbeads has the added benefit that functionalized microbeads can be used to capture particles from the fluid solution during mixing, and that they can be extracted from the device for analysis, thus serving multiple functionalities in a single device.