Three-dimensional Imaging and Scanning: Current and Future Applications for Pathology

PubMed Central

Farahani, Navid; Braun, Alex; Jutt, Dylan; Huffman, Todd; Reder, Nick; Liu, Zheng; Yagi, Yukako; Pantanowitz, Liron

2017-01-01

Imaging is vital for the assessment of physiologic and phenotypic details. In the past, biomedical imaging was heavily reliant on analog, low-throughput methods, which would produce two-dimensional images. However, newer, digital, and high-throughput three-dimensional (3D) imaging methods, which rely on computer vision and computer graphics, are transforming the way biomedical professionals practice. 3D imaging has been useful in diagnostic, prognostic, and therapeutic decision-making for the medical and biomedical professions. Herein, we summarize current imaging methods that enable optimal 3D histopathologic reconstruction: Scanning, 3D scanning, and whole slide imaging. Briefly mentioned are emerging platforms, which combine robotics, sectioning, and imaging in their pursuit to digitize and automate the entire microscopy workflow. Finally, both current and emerging 3D imaging methods are discussed in relation to current and future applications within the context of pathology. PMID:28966836

Lunar UV-visible-IR mapping interferometric spectrometer

NASA Technical Reports Server (NTRS)

Smith, W. Hayden; Haskin, L.; Korotev, R.; Arvidson, R.; Mckinnon, W.; Hapke, B.; Larson, S.; Lucey, P.

1992-01-01

Ultraviolet-visible-infrared mapping digital array scanned interferometers for lunar compositional surveys was developed. The research has defined a no-moving-parts, low-weight and low-power, high-throughput, and electronically adaptable digital array scanned interferometer that achieves measurement objectives encompassing and improving upon all the requirements defined by the LEXSWIG for lunar mineralogical investigation. In addition, LUMIS provides a new, important, ultraviolet spectral mapping, high-spatial-resolution line scan camera, and multispectral camera capabilities. An instrument configuration optimized for spectral mapping and imaging of the lunar surface and provide spectral results in support of the instrument design are described.

Toward reliable and repeatable automated STEM-EDS metrology with high throughput

NASA Astrophysics Data System (ADS)

Zhong, Zhenxin; Donald, Jason; Dutrow, Gavin; Roller, Justin; Ugurlu, Ozan; Verheijen, Martin; Bidiuk, Oleksii

2018-03-01

New materials and designs in complex 3D architectures in logic and memory devices have raised complexity in S/TEM metrology. In this paper, we report about a newly developed, automated, scanning transmission electron microscopy (STEM) based, energy dispersive X-ray spectroscopy (STEM-EDS) metrology method that addresses these challenges. Different methodologies toward repeatable and efficient, automated STEM-EDS metrology with high throughput are presented: we introduce the best known auto-EDS acquisition and quantification methods for robust and reliable metrology and present how electron exposure dose impacts the EDS metrology reproducibility, either due to poor signalto-noise ratio (SNR) at low dose or due to sample modifications at high dose conditions. Finally, we discuss the limitations of the STEM-EDS metrology technique and propose strategies to optimize the process both in terms of throughput and metrology reliability.

The impact of the condenser on cytogenetic image quality in digital microscope system.

PubMed

Ren, Liqiang; Li, Zheng; Li, Yuhua; Zheng, Bin; Li, Shibo; Chen, Xiaodong; Liu, Hong

2013-01-01

Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved. This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system. Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted. The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%-70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning. Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice.

Optimisation Issues of High Throughput Medical Data and Video Streaming Traffic in 3G Wireless Environments.

PubMed

Istepanian, R S H; Philip, N

2005-01-01

In this paper we describe some of the optimisation issues relevant to the requirements of high throughput of medical data and video streaming traffic in 3G wireless environments. In particular we present a challenging 3G mobile health care application that requires a demanding 3G medical data throughput. We also describe the 3G QoS requirement of mObile Tele-Echography ultra-Light rObot system (OTELO that is designed to provide seamless 3G connectivity for real-time ultrasound medical video streams and diagnosis from a remote site (robotic and patient station) manipulated by an expert side (specialists) that is controlling the robotic scanning operation and presenting a real-time feedback diagnosis using 3G wireless communication links.

MODIS Aqua Optical Throughput Degradation Impact on Relative Spectral Response and Calibration on Ocean Color Products

NASA Technical Reports Server (NTRS)

Lee, Shihyan; Meister, Gerhard

2017-01-01

Since Moderate Resolution Imaging Spectroradiometer Aqua's launch in 2002, the radiometric system gains of the reflective solar bands have been degrading, indicating changes in the systems optical throughput. To estimate the optical throughput degradation, the electronic gain changes were estimated and removed from the measured system gain. The derived optical throughput degradation shows a rate that is much faster in the shorter wavelengths than the longer wavelengths. The wavelength-dependent optical throughput degradation modulated the relative spectral response (RSR) of the bands. In addition, the optical degradation is also scan angle-dependent due to large changes in response versus the scan angle over time. We estimated the modulated RSR as a function of time and scan angles and its impacts on sensor radiometric calibration for the ocean science. Our results show that the calibration bias could be up to 1.8 % for band 8 (412 nm) due to its larger out-of-band response. For the other ocean bands, the calibration biases are much smaller with magnitudes at least one order smaller.

High throughput optical lithography by scanning a massive array of bowtie aperture antennas at near-field

PubMed Central

Wen, X.; Datta, A.; Traverso, L. M.; Pan, L.; Xu, X.; Moon, E. E.

2015-01-01

Optical lithography, the enabling process for defining features, has been widely used in semiconductor industry and many other nanotechnology applications. Advances of nanotechnology require developments of high-throughput optical lithography capabilities to overcome the optical diffraction limit and meet the ever-decreasing device dimensions. We report our recent experimental advancements to scale up diffraction unlimited optical lithography in a massive scale using the near field nanolithography capabilities of bowtie apertures. A record number of near-field optical elements, an array of 1,024 bowtie antenna apertures, are simultaneously employed to generate a large number of patterns by carefully controlling their working distances over the entire array using an optical gap metrology system. Our experimental results reiterated the ability of using massively-parallel near-field devices to achieve high-throughput optical nanolithography, which can be promising for many important nanotechnology applications such as computation, data storage, communication, and energy. PMID:26525906

A review of snapshot multidimensional optical imaging: measuring photon tags in parallel

PubMed Central

Gao, Liang; Wang, Lihong V.

2015-01-01

Multidimensional optical imaging has seen remarkable growth in the past decade. Rather than measuring only the two-dimensional spatial distribution of light, as in conventional photography, multidimensional optical imaging captures light in up to nine dimensions, providing unprecedented information about incident photons’ spatial coordinates, emittance angles, wavelength, time, and polarization. Multidimensional optical imaging can be accomplished either by scanning or parallel acquisition. Compared with scanning-based imagers, parallel acquisition—also dubbed snapshot imaging—has a prominent advantage in maximizing optical throughput, particularly when measuring a datacube of high dimensions. Here, we first categorize snapshot multidimensional imagers based on their acquisition and image reconstruction strategies, then highlight the snapshot advantage in the context of optical throughput, and finally we discuss their state-of-the-art implementations and applications. PMID:27134340

A green fluorescent protein-based assay for high-throughput ligand-binding studies of a mycobacterial biotin protein ligase.

PubMed

Bond, Thomas E H; Sorenson, Alanna E; Schaeffer, Patrick M

2017-12-01

Biotin protein ligase (BirA) has been identified as an emerging drug target in Mycobacterium tuberculosis due to its essential metabolic role. Indeed, it is the only enzyme capable of covalently attaching biotin onto the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase. Despite recent interest in this protein, there is still a gap in cost-effective high-throughput screening assays for rapid identification of mycobacterial BirA-targeting inhibitors. We present for the first time the cloning, expression, purification of mycobacterial GFP-tagged BirA and its application for the development of a high-throughput assay building on the principle of differential scanning fluorimetry of GFP-tagged proteins. The data obtained in this study reveal how biotin and ATP significantly increase the thermal stability (ΔT m =+16.5°C) of M. tuberculosis BirA and lead to formation of a high affinity holoenzyme complex (K obs =7.7nM). The new findings and mycobacterial BirA high-throughput assay presented in this work could provide an efficient platform for future anti-tubercular drug discovery campaigns. Copyright © 2017 Elsevier GmbH. All rights reserved.

Ultra-barcoding in cacao (Theobroma spp.; malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

USDA-ARS?s Scientific Manuscript database

High-throughput next-generation sequencing was used to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an indivi...

High-throughput microfluidic line scan imaging for cytological characterization

NASA Astrophysics Data System (ADS)

Hutcheson, Joshua A.; Powless, Amy J.; Majid, Aneeka A.; Claycomb, Adair; Fritsch, Ingrid; Balachandran, Kartik; Muldoon, Timothy J.

2015-03-01

Imaging cells in a microfluidic chamber with an area scan camera is difficult due to motion blur and data loss during frame readout causing discontinuity of data acquisition as cells move at relatively high speeds through the chamber. We have developed a method to continuously acquire high-resolution images of cells in motion through a microfluidics chamber using a high-speed line scan camera. The sensor acquires images in a line-by-line fashion in order to continuously image moving objects without motion blur. The optical setup comprises an epi-illuminated microscope with a 40X oil immersion, 1.4 NA objective and a 150 mm tube lens focused on a microfluidic channel. Samples containing suspended cells fluorescently stained with 0.01% (w/v) proflavine in saline are introduced into the microfluidics chamber via a syringe pump; illumination is provided by a blue LED (455 nm). Images were taken of samples at the focal plane using an ELiiXA+ 8k/4k monochrome line-scan camera at a line rate of up to 40 kHz. The system's line rate and fluid velocity are tightly controlled to reduce image distortion and are validated using fluorescent microspheres. Image acquisition was controlled via MATLAB's Image Acquisition toolbox. Data sets comprise discrete images of every detectable cell which may be subsequently mined for morphological statistics and definable features by a custom texture analysis algorithm. This high-throughput screening method, comparable to cell counting by flow cytometry, provided efficient examination including counting, classification, and differentiation of saliva, blood, and cultured human cancer cells.

The Impact of the Condenser on Cytogenetic Image Quality in Digital Microscope System

PubMed Central

Ren, Liqiang; Li, Zheng; Li, Yuhua; Zheng, Bin; Li, Shibo; Chen, Xiaodong; Liu, Hong

2013-01-01

Background: Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved. OBJECTIVE: This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system. Methods: Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted. Results: The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%–70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning. Conclusions: Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice. PMID:23676284

Dissecting enzyme function with microfluidic-based deep mutational scanning.

PubMed

Romero, Philip A; Tran, Tuan M; Abate, Adam R

2015-06-09

Natural enzymes are incredibly proficient catalysts, but engineering them to have new or improved functions is challenging due to the complexity of how an enzyme's sequence relates to its biochemical properties. Here, we present an ultrahigh-throughput method for mapping enzyme sequence-function relationships that combines droplet microfluidic screening with next-generation DNA sequencing. We apply our method to map the activity of millions of glycosidase sequence variants. Microfluidic-based deep mutational scanning provides a comprehensive and unbiased view of the enzyme function landscape. The mapping displays expected patterns of mutational tolerance and a strong correspondence to sequence variation within the enzyme family, but also reveals previously unreported sites that are crucial for glycosidase function. We modified the screening protocol to include a high-temperature incubation step, and the resulting thermotolerance landscape allowed the discovery of mutations that enhance enzyme thermostability. Droplet microfluidics provides a general platform for enzyme screening that, when combined with DNA-sequencing technologies, enables high-throughput mapping of enzyme sequence space.

High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis.

PubMed

Zheng, Xianlin; Lu, Yiqing; Zhao, Jiangbo; Zhang, Yuhai; Ren, Wei; Liu, Deming; Lu, Jie; Piper, James A; Leif, Robert C; Liu, Xiaogang; Jin, Dayong

2016-01-19

Compared with routine microscopy imaging of a few analytes at a time, rapid scanning through the whole sample area of a microscope slide to locate every single target object offers many advantages in terms of simplicity, speed, throughput, and potential for robust quantitative analysis. Existing techniques that accommodate solid-phase samples incorporating individual micrometer-sized targets generally rely on digital microscopy and image analysis, with intrinsically low throughput and reliability. Here, we report an advanced on-the-fly stage scanning method to achieve high-precision target location across the whole slide. By integrating X- and Y-axis linear encoders to a motorized stage as the virtual "grids" that provide real-time positional references, we demonstrate an orthogonal scanning automated microscopy (OSAM) technique which can search a coverslip area of 50 × 24 mm(2) in just 5.3 min and locate individual 15 μm lanthanide luminescent microspheres with standard deviations of 1.38 and 1.75 μm in X and Y directions. Alongside implementation of an autofocus unit that compensates the tilt of a slide in the Z-axis in real time, we increase the luminescence detection efficiency by 35% with an improved coefficient of variation. We demonstrate the capability of advanced OSAM for robust quantification of luminescence intensities and lifetimes for a variety of micrometer-scale luminescent targets, specifically single down-shifting and upconversion microspheres, crystalline microplates, and color-barcoded microrods, as well as quantitative suspension array assays of biotinylated-DNA functionalized upconversion nanoparticles.

Ion beam lithography system

DOEpatents

Leung, Ka-Ngo

2005-08-02

A maskless plasma-formed ion beam lithography tool provides for patterning of sub-50 nm features on large area flat or curved substrate surfaces. The system is very compact and does not require an accelerator column and electrostatic beam scanning components. The patterns are formed by switching beamlets on or off from a two electrode blanking system with the substrate being scanned mechanically in one dimension. This arrangement can provide a maskless nano-beam lithography tool for economic and high throughput processing.

Hard-tip, soft-spring lithography.

PubMed

Shim, Wooyoung; Braunschweig, Adam B; Liao, Xing; Chai, Jinan; Lim, Jong Kuk; Zheng, Gengfeng; Mirkin, Chad A

2011-01-27

Nanofabrication strategies are becoming increasingly expensive and equipment-intensive, and consequently less accessible to researchers. As an alternative, scanning probe lithography has become a popular means of preparing nanoscale structures, in part owing to its relatively low cost and high resolution, and a registration accuracy that exceeds most existing technologies. However, increasing the throughput of cantilever-based scanning probe systems while maintaining their resolution and registration advantages has from the outset been a significant challenge. Even with impressive recent advances in cantilever array design, such arrays tend to be highly specialized for a given application, expensive, and often difficult to implement. It is therefore difficult to imagine commercially viable production methods based on scanning probe systems that rely on conventional cantilevers. Here we describe a low-cost and scalable cantilever-free tip-based nanopatterning method that uses an array of hard silicon tips mounted onto an elastomeric backing. This method-which we term hard-tip, soft-spring lithography-overcomes the throughput problems of cantilever-based scanning probe systems and the resolution limits imposed by the use of elastomeric stamps and tips: it is capable of delivering materials or energy to a surface to create arbitrary patterns of features with sub-50-nm resolution over centimetre-scale areas. We argue that hard-tip, soft-spring lithography is a versatile nanolithography strategy that should be widely adopted by academic and industrial researchers for rapid prototyping applications.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels.

PubMed

Sevenler, Derin; Daaboul, George G; Ekiz Kanik, Fulya; Ünlü, Neşe Lortlar; Ünlü, M Selim

2018-05-21

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

High-throughput ultraviolet photoacoustic microscopy with multifocal excitation

NASA Astrophysics Data System (ADS)

Imai, Toru; Shi, Junhui; Wong, Terence T. W.; Li, Lei; Zhu, Liren; Wang, Lihong V.

2018-03-01

Ultraviolet photoacoustic microscopy (UV-PAM) is a promising intraoperative tool for surgical margin assessment (SMA), one that can provide label-free histology-like images with high resolution. In this study, using a microlens array and a one-dimensional (1-D) array ultrasonic transducer, we developed a high-throughput multifocal UV-PAM (MF-UV-PAM). Our new system achieved a 1.6 ± 0.2 μm lateral resolution and produced images 40 times faster than the previously developed point-by-point scanning UV-PAM. MF-UV-PAM provided a readily comprehensible photoacoustic image of a mouse brain slice with specific absorption contrast in ˜16 min, highlighting cell nuclei. Individual cell nuclei could be clearly resolved, showing its practical potential for intraoperative SMA.

High Throughput Differential Scanning Fluorimetry (DSF) Formulation Screening with Complementary Dyes to Assess Protein Unfolding and Aggregation in Presence of Surfactants.

PubMed

McClure, Sean M; Ahl, Patrick L; Blue, Jeffrey T

2018-03-05

The purpose was to evaluate DSF for high throughput screening of protein thermal stability (unfolding/ aggregation) across a wide range of formulations. Particular focus was exploring PROTEOSTAT® - a commercially available fluorescent rotor dye - for detection of aggregation in surfactant containing formulations. Commonly used hydrophobic dyes (e.g. SYPRO™ Orange) interact with surfactants, complicating DSF measurements. CRM197 formulations were prepared and analyzed in standard 96-well plate rT-PCR system, using SYPRO™ Orange and PROTEOSTAT® dyes. Orthogonal techniques (DLS and IPF) are employed to confirm unfolding/aggregation in selected formulations. Selected formulations are subjected to non-thermal stresses (stirring and shaking) in plate based format to characterize aggregation with PROTEOSTAT®. Agreement is observed between SYPRO™ Orange (unfolding) and PROTEOSTAT® (aggregation) DSF melt temperatures across wide range of non-surfactant formulations. PROTEOSTAT® can clearly detect temperature induced aggregation in low concentration (0.2 mg/mL) CRM197 formulations containing surfactant. PROTEOSTAT® can be used to explore aggregation due to non-thermal stresses in plate based format amenable to high throughput screening. DSF measurements with complementary extrinsic dyes (PROTEOSTAT®, SYPRO™ Orange) are suitable for high throughput screening of antigen thermal stability, across a wide range of relevant formulation conditions - including surfactants -with standard, plate based rT-PCR instrumentation.

Cotton phenotyping with lidar from a track-mounted platform

NASA Astrophysics Data System (ADS)

French, Andrew N.; Gore, Michael A.; Thompson, Alison

2016-05-01

High-Throughput Phenotyping (HTP) is a discipline for rapidly identifying plant architectural and physiological responses to environmental factors such as heat and water stress. Experiments conducted since 2010 at Maricopa, Arizona with a three-fold sensor group, including thermal infrared radiometers, active visible/near infrared reflectance sensors, and acoustic plant height sensors, have shown the validity of HTP with a tractor-based system. However, results from these experiments also show that accuracy of plant phenotyping is limited by the system's inability to discriminate plant components and their local environmental conditions. This limitation may be overcome with plant imaging and laser scanning which can help map details in plant architecture and sunlit/shaded leaves. To test the capability for mapping cotton plants with a laser system, a track-mounted platform was deployed in 2015 over a full canopy and defoliated cotton crop consisting of a scanning LIDAR driven by Arduinocontrolled stepper motors. Using custom Python and Tkinter code, the platform moved autonomously along a pipe-track at 0.1 m/s while collecting LIDAR scans at 25 Hz (0.1667 deg. beam). These tests showed that an autonomous LIDAR platform can reduce HTP logistical problems and provide the capability to accurately map cotton plants and cotton bolls. A prototype track-mounted platform was developed to test the use of LIDAR scanning for High- Throughput Phenotyping (HTP). The platform was deployed in 2015 at Maricopa, Arizona over a senescent cotton crop. Using custom Python and Tkinter code, the platform moved autonomously along a pipe-track at <1 m/s while collecting LIDAR scans at 25 Hz (0.1667 deg. beam). Scanning data mapped the canopy heights and widths, and detected cotton bolls.

Microfluidic-SANS: insitu molecular insight into complex fluid processing and high throughput characterisation

NASA Astrophysics Data System (ADS)

Lopez, Carlos; Watanabe, Takaichi; Cabral, Joao; Graham, Peter; Porcar, Lionel; Martel, Anne

2014-03-01

The coupling of microfluidics and small angle neutron scattering (SANS) is successfully demonstrated for the first time. We have developed novel microdevices with suitably low SANS background and high pressure compatibility for the investigation of flow-induced phenomena and high throughput phase mapping of complex fluids. We successfully obtained scattering profiles from 50 micron channels, in 10s - 100s second acquisition times. The microfluidic geometry enables the variation of both flow type and magnitude, beyond traditional rheo-SANS setups, and is exceptionally well-suited for complex fluids due to the commensurability of relevant time and lengthscales. We demonstrate our approach by studying model flow responsive systems, including surfactant/co-surfactant/water mixtures, with well-known equilibrium phase behaviour,: sodium dodecyl sulfate (SDS)/octanol/brine, cetyltrimethyl ammonium chloride (C16TAC)/pentanol/water and a model microemulsion system (C10E4 /decane/ D20), as well as polyelectrolyte solutions. Finally, using an online micromixer we are able to implement a high throughput approach, scanning in excess of 10 scattering profiles/min for a continuous aqueous surfactant dilution over two decades in concentration.

A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

PubMed

Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

2016-10-17

In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.

In-field High Throughput Phenotyping and Cotton Plant Growth Analysis Using LiDAR.

PubMed

Sun, Shangpeng; Li, Changying; Paterson, Andrew H; Jiang, Yu; Xu, Rui; Robertson, Jon S; Snider, John L; Chee, Peng W

2018-01-01

Plant breeding programs and a wide range of plant science applications would greatly benefit from the development of in-field high throughput phenotyping technologies. In this study, a terrestrial LiDAR-based high throughput phenotyping system was developed. A 2D LiDAR was applied to scan plants from overhead in the field, and an RTK-GPS was used to provide spatial coordinates. Precise 3D models of scanned plants were reconstructed based on the LiDAR and RTK-GPS data. The ground plane of the 3D model was separated by RANSAC algorithm and a Euclidean clustering algorithm was applied to remove noise generated by weeds. After that, clean 3D surface models of cotton plants were obtained, from which three plot-level morphologic traits including canopy height, projected canopy area, and plant volume were derived. Canopy height ranging from 85th percentile to the maximum height were computed based on the histogram of the z coordinate for all measured points; projected canopy area was derived by projecting all points on a ground plane; and a Trapezoidal rule based algorithm was proposed to estimate plant volume. Results of validation experiments showed good agreement between LiDAR measurements and manual measurements for maximum canopy height, projected canopy area, and plant volume, with R 2 -values of 0.97, 0.97, and 0.98, respectively. The developed system was used to scan the whole field repeatedly over the period from 43 to 109 days after planting. Growth trends and growth rate curves for all three derived morphologic traits were established over the monitoring period for each cultivar. Overall, four different cultivars showed similar growth trends and growth rate patterns. Each cultivar continued to grow until ~88 days after planting, and from then on varied little. However, the actual values were cultivar specific. Correlation analysis between morphologic traits and final yield was conducted over the monitoring period. When considering each cultivar individually, the three traits showed the best correlations with final yield during the period between around 67 and 109 days after planting, with maximum R 2 -values of up to 0.84, 0.88, and 0.85, respectively. The developed system demonstrated relatively high throughput data collection and analysis.

High-throughput machining using high average power ultrashort pulse lasers and ultrafast polygon scanner

NASA Astrophysics Data System (ADS)

Schille, Joerg; Schneider, Lutz; Streek, André; Kloetzer, Sascha; Loeschner, Udo

2016-03-01

In this paper, high-throughput ultrashort pulse laser machining is investigated on various industrial grade metals (Aluminium, Copper, Stainless steel) and Al2O3 ceramic at unprecedented processing speeds. This is achieved by using a high pulse repetition frequency picosecond laser with maximum average output power of 270 W in conjunction with a unique, in-house developed two-axis polygon scanner. Initially, different concepts of polygon scanners are engineered and tested to find out the optimal architecture for ultrafast and precision laser beam scanning. Remarkable 1,000 m/s scan speed is achieved on the substrate, and thanks to the resulting low pulse overlap, thermal accumulation and plasma absorption effects are avoided at up to 20 MHz pulse repetition frequencies. In order to identify optimum processing conditions for efficient high-average power laser machining, the depths of cavities produced under varied parameter settings are analyzed and, from the results obtained, the characteristic removal values are specified. The maximum removal rate is achieved as high as 27.8 mm3/min for Aluminium, 21.4 mm3/min for Copper, 15.3 mm3/min for Stainless steel and 129.1 mm3/min for Al2O3 when full available laser power is irradiated at optimum pulse repetition frequency.

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buda, I. G.; Lane, C.; Barbiellini, B.

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

DOE PAGES

Buda, I. G.; Lane, C.; Barbiellini, B.; ...

2017-03-23

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Subnuclear foci quantification using high-throughput 3D image cytometry

NASA Astrophysics Data System (ADS)

Wadduwage, Dushan N.; Parrish, Marcus; Choi, Heejin; Engelward, Bevin P.; Matsudaira, Paul; So, Peter T. C.

2015-07-01

Ionising radiation causes various types of DNA damages including double strand breaks (DSBs). DSBs are often recognized by DNA repair protein ATM which forms gamma-H2AX foci at the site of the DSBs that can be visualized using immunohistochemistry. However most of such experiments are of low throughput in terms of imaging and image analysis techniques. Most of the studies still use manual counting or classification. Hence they are limited to counting a low number of foci per cell (5 foci per nucleus) as the quantification process is extremely labour intensive. Therefore we have developed a high throughput instrumentation and computational pipeline specialized for gamma-H2AX foci quantification. A population of cells with highly clustered foci inside nuclei were imaged, in 3D with submicron resolution, using an in-house developed high throughput image cytometer. Imaging speeds as high as 800 cells/second in 3D were achieved by using HiLo wide-field depth resolved imaging and a remote z-scanning technique. Then the number of foci per cell nucleus were quantified using a 3D extended maxima transform based algorithm. Our results suggests that while most of the other 2D imaging and manual quantification studies can count only up to about 5 foci per nucleus our method is capable of counting more than 100. Moreover we show that 3D analysis is significantly superior compared to the 2D techniques.

High throughput on-chip analysis of high-energy charged particle tracks using lensfree imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Wei; Shabbir, Faizan; Gong, Chao

2015-04-13

We demonstrate a high-throughput charged particle analysis platform, which is based on lensfree on-chip microscopy for rapid ion track analysis using allyl diglycol carbonate, i.e., CR-39 plastic polymer as the sensing medium. By adopting a wide-area opto-electronic image sensor together with a source-shifting based pixel super-resolution technique, a large CR-39 sample volume (i.e., 4 cm × 4 cm × 0.1 cm) can be imaged in less than 1 min using a compact lensfree on-chip microscope, which detects partially coherent in-line holograms of the ion tracks recorded within the CR-39 detector. After the image capture, using highly parallelized reconstruction and ion track analysis algorithms running on graphics processingmore » units, we reconstruct and analyze the entire volume of a CR-39 detector within ∼1.5 min. This significant reduction in the entire imaging and ion track analysis time not only increases our throughput but also allows us to perform time-resolved analysis of the etching process to monitor and optimize the growth of ion tracks during etching. This computational lensfree imaging platform can provide a much higher throughput and more cost-effective alternative to traditional lens-based scanning optical microscopes for ion track analysis using CR-39 and other passive high energy particle detectors.« less

Temperature-programmed technique accompanied with high-throughput methodology for rapidly searching the optimal operating temperature of MOX gas sensors.

PubMed

Zhang, Guozhu; Xie, Changsheng; Zhang, Shunping; Zhao, Jianwei; Lei, Tao; Zeng, Dawen

2014-09-08

A combinatorial high-throughput temperature-programmed method to obtain the optimal operating temperature (OOT) of gas sensor materials is demonstrated here for the first time. A material library consisting of SnO2, ZnO, WO3, and In2O3 sensor films was fabricated by screen printing. Temperature-dependent conductivity curves were obtained by scanning this gas sensor library from 300 to 700 K in different atmospheres (dry air, formaldehyde, carbon monoxide, nitrogen dioxide, toluene and ammonia), giving the OOT of each sensor formulation as a function of the carrier and analyte gases. A comparative study of the temperature-programmed method and a conventional method showed good agreement in measured OOT.

Micro-differential scanning calorimeter for liquid biological samples

DOE PAGES

Wang, Shuyu; Yu, Shifeng; Siedler, Michael S.; ...

2016-10-20

Here, we developed an ultrasensitive micro-DSC (differential scanning calorimeter) for liquid protein sample characterization. Our design integrated vanadium oxide thermistors and flexible polymer substrates with microfluidics chambers to achieve a high sensitivity (6 V/W), low thermal conductivity (0.7 mW/K), high power resolutions (40 nW), and well-defined liquid volume (1 μl) calorimeter sensor in a compact and cost-effective way. Furthermore, we demonstrated the performance of the sensor with lysozyme unfolding. The measured transition temperature and enthalpy change were in accordance with the previous literature data. This micro-DSC could potentially raise the prospect of high-throughput biochemical measurement by parallel operation with miniaturizedmore » sample consumption.« less

Lateral Temperature-Gradient Method for High-Throughput Characterization of Material Processing by Millisecond Laser Annealing.

PubMed

Bell, Robert T; Jacobs, Alan G; Sorg, Victoria C; Jung, Byungki; Hill, Megan O; Treml, Benjamin E; Thompson, Michael O

2016-09-12

A high-throughput method for characterizing the temperature dependence of material properties following microsecond to millisecond thermal annealing, exploiting the temperature gradients created by a lateral gradient laser spike anneal (lgLSA), is presented. Laser scans generate spatial thermal gradients of up to 5 °C/μm with peak temperatures ranging from ambient to in excess of 1400 °C, limited only by laser power and materials thermal limits. Discrete spatial property measurements across the temperature gradient are then equivalent to independent measurements after varying temperature anneals. Accurate temperature calibrations, essential to quantitative analysis, are critical and methods for both peak temperature and spatial/temporal temperature profile characterization are presented. These include absolute temperature calibrations based on melting and thermal decomposition, and time-resolved profiles measured using platinum thermistors. A variety of spatially resolved measurement probes, ranging from point-like continuous profiling to large area sampling, are discussed. Examples from annealing of III-V semiconductors, CdSe quantum dots, low-κ dielectrics, and block copolymers are included to demonstrate the flexibility, high throughput, and precision of this technique.

Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection.

PubMed

Yang, Jijin; Ferranti, David C; Stern, Lewis A; Sanford, Colin A; Huang, Jason; Ren, Zheng; Qin, Lu-Chang; Hall, Adam R

2011-07-15

We report the formation of solid-state nanopores using a scanning helium ion microscope. The fabrication process offers the advantage of high sample throughput along with fine control over nanopore dimensions, producing single pores with diameters below 4 nm. Electronic noise associated with ion transport through the resultant pores is found to be comparable with levels measured on devices made with the established technique of transmission electron microscope milling. We demonstrate the utility of our nanopores for biomolecular analysis by measuring the passage of double-strand DNA.

High throughput laser processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harley, Gabriel; Pass, Thomas; Cousins, Peter John

A solar cell is formed using a solar cell ablation system. The ablation system includes a single laser source and several laser scanners. The laser scanners include a master laser scanner, with the rest of the laser scanners being slaved to the master laser scanner. A laser beam from the laser source is split into several laser beams, with the laser beams being scanned onto corresponding wafers using the laser scanners in accordance with one or more patterns. The laser beams may be scanned on the wafers using the same or different power levels of the laser source.

Galvanometer scanning technology for laser additive manufacturing

NASA Astrophysics Data System (ADS)

Luo, Xi; Li, Jin; Lucas, Mark

2017-02-01

A galvanometer laser beam scanning system is an essential element in many laser additive manufacturing (LAM) technologies including Stereolithography (SLA), Selective Laser Sintering (SLS) and Selective Laser Melting (SLM). Understanding the laser beam scanning techniques and recent innovations in this field will greatly benefit the 3D laser printing system integration and technology advance. One of the challenges to achieve high quality 3D printed parts is due to the non-uniform laser power density delivered on the materials caused by the acceleration and deceleration movements of the galvanometer at ends of the hatching and outlining patterns. One way to solve this problem is to modulate the laser power as the function of the scanning speed during the acceleration or deceleration periods. Another strategy is to maintain the constant scanning speed while accurately coordinating the laser on and off operation throughout the job. In this paper, we demonstrate the high speed, high accuracy and low drift digital scanning technology that incorporates both techniques to achieve uniform laser density with minimal additional process development. With the constant scanning speed method, the scanner not only delivers high quality and uniform results, but also a throughput increase of 23% on a typical LAM job, compared to that of the conventional control method that requires galvanometer acceleration and deceleration movements.

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

PubMed Central

Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

2000-01-01

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month. PMID:11076861

Time-Gated Orthogonal Scanning Automated Microscopy (OSAM) for High-speed Cell Detection and Analysis

NASA Astrophysics Data System (ADS)

Lu, Yiqing; Xi, Peng; Piper, James A.; Huo, Yujing; Jin, Dayong

2012-11-01

We report a new development of orthogonal scanning automated microscopy (OSAM) incorporating time-gated detection to locate rare-event organisms regardless of autofluorescent background. The necessity of using long-lifetime (hundreds of microseconds) luminescent biolabels for time-gated detection implies long integration (dwell) time, resulting in slow scan speed. However, here we achieve high scan speed using a new 2-step orthogonal scanning strategy to realise on-the-fly time-gated detection and precise location of 1-μm lanthanide-doped microspheres with signal-to-background ratio of 8.9. This enables analysis of a 15 mm × 15 mm slide area in only 3.3 minutes. We demonstrate that detection of only a few hundred photoelectrons within 100 μs is sufficient to distinguish a target event in a prototype system using ultraviolet LED excitation. Cytometric analysis of lanthanide labelled Giardia cysts achieved a signal-to-background ratio of two orders of magnitude. Results suggest that time-gated OSAM represents a new opportunity for high-throughput background-free biosensing applications.

Quantifying collagen orientation in breast tissue biopsies using SLIM (Conference Presentation)

NASA Astrophysics Data System (ADS)

Majeed, Hassaan; Okoro, Chukwuemeka; Balla, Andre; Toussaint, Kimani C.; Popescu, Gabriel

2017-02-01

Breast cancer is a major public health problem worldwide, being the most common type of cancer among women according to the World Health Organization (WHO). The WHO has further stressed the importance of an early determination of the disease course through prognostic markers. Recent studies have shown that the alignment of collagen fibers in tumor adjacent stroma correlate with poorer health outcomes in patients. Such studies have typically been carried out using Second-Harmonic Generation (SHG) microscopy. SHG images are very useful for quantifying collagen fiber orientation due their specificity to non-centrosymmetric structures in tissue, leading to high contrast in collagen rich areas. However, the imaging throughput in SHG microscopy is limited by its point scanning geometry. In this work, we show that SLIM, a wide-field high-throughput QPI technique, can be used to obtain the same information on collagen fiber orientation as is obtainable through SHG microscopy. We imaged a tissue microarray containing both benign and malignant cores using both SHG microscopy and SLIM. The cellular (non-collagenous) structures in the SLIM images were next segmented out using an algorithm developed in-house. Using the previously published Fourier Transform Second Harmonic Generation (FT-SHG) tool, the fiber orientations in SHG and segmented SLIM images were then quantified. The resulting histograms of fiber orientation angles showed that both SHG and SLIM generate similar measurements of collagen fiber orientation. The SLIM modality, however, can generate these results at much higher throughput due to its wide-field, whole-slide scanning capabilities.

High-throughput accurate-wavelength lens-based visible spectrometer.

PubMed

Bell, Ronald E; Scotti, Filippo

2010-10-01

A scanning visible spectrometer has been prototyped to complement fixed-wavelength transmission grating spectrometers for charge exchange recombination spectroscopy. Fast f/1.8 200 mm commercial lenses are used with a large 2160 mm(-1) grating for high throughput. A stepping-motor controlled sine drive positions the grating, which is mounted on a precision rotary table. A high-resolution optical encoder on the grating stage allows the grating angle to be measured with an absolute accuracy of 0.075 arc  sec, corresponding to a wavelength error ≤0.005 Å. At this precision, changes in grating groove density due to thermal expansion and variations in the refractive index of air are important. An automated calibration procedure determines all the relevant spectrometer parameters to high accuracy. Changes in bulk grating temperature, atmospheric temperature, and pressure are monitored between the time of calibration and the time of measurement to ensure a persistent wavelength calibration.

High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

PubMed

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

2017-11-03

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

High Resolution Melting (HRM) for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

PubMed Central

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz

2017-01-01

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup. PMID:29099791

The MAMMOTH project

NASA Technical Reports Server (NTRS)

Gerchar, Tim

1994-01-01

On the surface MAMMOTH is a high performance 5.25-inch half-high 8mm helical scan tape drive that records a native 20 Gigabytes of data on Advanced Metal Evaporated media at a sustained throughput of 3 Megabyte per second over a high speed SCSI interface, that is scheduled for production in the second half of 1995. But it's much more than that. Inside its custom designed sheet metal enclosure lies one of the greatest technical achievements of its kind. Exabyte's strategic direction is to increase throughput and capacity while continuing to improve drive, data and media reliability to its products. MAMMOTH adheres to that direction and the description of its technical advances is described in this paper. MAMMOTH can be broken down into four main functional assemblies: high-performance integrated digital electronics, high-reliability tape transport mechanism, high-performance scanner, and advanced metal evaporated media. All this technology is packaged into a standard 5.25-inch half-high form factor that dissipates only 15 watts.

High-throughput machining using a high-average power ultrashort pulse laser and high-speed polygon scanner

NASA Astrophysics Data System (ADS)

Schille, Joerg; Schneider, Lutz; Streek, André; Kloetzer, Sascha; Loeschner, Udo

2016-09-01

High-throughput ultrashort pulse laser machining is investigated on various industrial grade metals (aluminum, copper, and stainless steel) and Al2O3 ceramic at unprecedented processing speeds. This is achieved by using a high-average power picosecond laser in conjunction with a unique, in-house developed polygon mirror-based biaxial scanning system. Therefore, different concepts of polygon scanners are engineered and tested to find the best architecture for high-speed and precision laser beam scanning. In order to identify the optimum conditions for efficient processing when using high-average laser powers, the depths of cavities made in the samples by varying the processing parameter settings are analyzed and, from the results obtained, the characteristic removal values are specified. For overlapping pulses of optimum fluence, the removal rate is as high as 27.8 mm3/min for aluminum, 21.4 mm3/min for copper, 15.3 mm3/min for stainless steel, and 129.1 mm3/min for Al2O3, when a laser beam of 187 W average laser powers irradiates. On stainless steel, it is demonstrated that the removal rate increases to 23.3 mm3/min when the laser beam is very fast moving. This is thanks to the low pulse overlap as achieved with 800 m/s beam deflection speed; thus, laser beam shielding can be avoided even when irradiating high-repetitive 20-MHz pulses.

Quantitative detection of benzoyl peroxide in wheat flour by line-scan macro-scale Raman chemical imaging

USDA-ARS?s Scientific Manuscript database

A high-throughput Raman chemical imaging method was developed for direct inspection of benzoyl peroxide (BPO) mixed in wheat flour. A 5 W 785 nm line laser (240 mm long and 1 mm wide) was used as a Raman excitation source in a push-broom Raman imaging system. Hyperspectral Raman images were collecte...

Automated imaging of cellular spheroids with selective plane illumination microscopy on a chip (Conference Presentation)

NASA Astrophysics Data System (ADS)

Paiè, Petra; Bassi, Andrea; Bragheri, Francesca; Osellame, Roberto

2017-02-01

Selective plane illumination microscopy (SPIM) is an optical sectioning technique that allows imaging of biological samples at high spatio-temporal resolution. Standard SPIM devices require dedicated set-ups, complex sample preparation and accurate system alignment, thus limiting the automation of the technique, its accessibility and throughput. We present a millimeter-scaled optofluidic device that incorporates selective plane illumination and fully automatic sample delivery and scanning. To this end an integrated cylindrical lens and a three-dimensional fluidic network were fabricated by femtosecond laser micromachining into a single glass chip. This device can upgrade any standard fluorescence microscope to a SPIM system. We used SPIM on a CHIP to automatically scan biological samples under a conventional microscope, without the need of any motorized stage: tissue spheroids expressing fluorescent proteins were flowed in the microchannel at constant speed and their sections were acquired while passing through the light sheet. We demonstrate high-throughput imaging of the entire sample volume (with a rate of 30 samples/min), segmentation and quantification in thick (100-300 μm diameter) cellular spheroids. This optofluidic device gives access to SPIM analyses to non-expert end-users, opening the way to automatic and fast screening of a high number of samples at subcellular resolution.

Multicapillary SDS-gel electrophoresis for the analysis of fluorescently labeled mAb preparations: a high throughput quality control process for the production of QuantiPlasma and PlasmaScan mAb libraries.

PubMed

Székely, Andrea; Szekrényes, Akos; Kerékgyártó, Márta; Balogh, Attila; Kádas, János; Lázár, József; Guttman, András; Kurucz, István; Takács, László

2014-08-01

Molecular heterogeneity of mAb preparations is the result of various co- and post-translational modifications and to contaminants related to the production process. Changes in molecular composition results in alterations of functional performance, therefore quality control and validation of therapeutic or diagnostic protein products is essential. A special case is the consistent production of mAb libraries (QuantiPlasma™ and PlasmaScan™) for proteome profiling, quality control of which represents a challenge because of high number of mAbs (>1000). Here, we devise a generally applicable multicapillary SDS-gel electrophoresis process for the analysis of fluorescently labeled mAb preparations for the high throughput quality control of mAbs of the QuantiPlasma™ and PlasmaScan™ libraries. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High throughput solar cell ablation system

DOEpatents

Harley, Gabriel; Pass, Thomas; Cousins, Peter John; Viatella, John

2014-10-14

A solar cell is formed using a solar cell ablation system. The ablation system includes a single laser source and several laser scanners. The laser scanners include a master laser scanner, with the rest of the laser scanners being slaved to the master laser scanner. A laser beam from the laser source is split into several laser beams, with the laser beams being scanned onto corresponding wafers using the laser scanners in accordance with one or more patterns. The laser beams may be scanned on the wafers using the same or different power levels of the laser source.

High throughput solar cell ablation system

DOEpatents

Harley, Gabriel; Pass, Thomas; Cousins, Peter John; Viatella, John

2012-09-11

A solar cell is formed using a solar cell ablation system. The ablation system includes a single laser source and several laser scanners. The laser scanners include a master laser scanner, with the rest of the laser scanners being slaved to the master laser scanner. A laser beam from the laser source is split into several laser beams, with the laser beams being scanned onto corresponding wafers using the laser scanners in accordance with one or more patterns. The laser beams may be scanned on the wafers using the same or different power levels of the laser source.

Multiple-mouse MRI with multiple arrays of receive coils.

PubMed

Ramirez, Marc S; Esparza-Coss, Emilio; Bankson, James A

2010-03-01

Compared to traditional single-animal imaging methods, multiple-mouse MRI has been shown to dramatically improve imaging throughput and reduce the potentially prohibitive cost for instrument access. To date, up to a single radiofrequency coil has been dedicated to each animal being simultaneously scanned, thus limiting the sensitivity, flexibility, and ultimate throughput. The purpose of this study was to investigate the feasibility of multiple-mouse MRI with a phased-array coil dedicated to each animal. A dual-mouse imaging system, consisting of a pair of two-element phased-array coils, was developed and used to achieve acceleration factors greater than the number of animals scanned at once. By simultaneously scanning two mice with a retrospectively gated cardiac cine MRI sequence, a 3-fold acceleration was achieved with signal-to-noise ratio in the heart that is equivalent to that achieved with an unaccelerated scan using a commercial mouse birdcage coil. (c) 2010 Wiley-Liss, Inc.

Towards high-throughput automated targeted femtosecond laser-based transfection of adherent cells

NASA Astrophysics Data System (ADS)

Antkowiak, Maciej; Torres-Mapa, Maria Leilani; Gunn-Moore, Frank; Dholakia, Kishan

2011-03-01

Femtosecond laser induced cell membrane poration has proven to be an attractive alternative to the classical methods of drug and gene delivery. It is a selective, sterile, non-contact technique that offers a highly localized operation, low toxicity and consistent performance. However, its broader application still requires the development of robust, high-throughput and user-friendly systems. We present a system capable of unassisted enhanced targeted optoinjection and phototransfection of adherent mammalian cells with a femtosecond laser. We demonstrate the advantages of a dynamic diffractive optical element, namely a spatial light modulator (SLM) for precise three dimensional positioning of the beam. It enables the implementation of a "point-and-shoot" system in which using the software interface a user simply points at the cell and a predefined sequence of precisely positioned doses can be applied. We show that irradiation in three axial positions alleviates the problem of exact beam positioning on the cell membrane and doubles the number of viably optoinjected cells when compared with a single dose. The presented system enables untargeted raster scan irradiation which provides transfection of adherent cells at the throughput of 1 cell per second.

An enzyme-mediated protein-fragment complementation assay for substrate screening of sortase A.

PubMed

Li, Ning; Yu, Zheng; Ji, Qun; Sun, Jingying; Liu, Xiao; Du, Mingjuan; Zhang, Wei

2017-04-29

Enzyme-mediated protein conjugation has gained great attention recently due to the remarkable site-selectivity and mild reaction condition affected by the nature of enzyme. Among all sorts of enzymes reported, sortase A from Staphylococcus aureus (SaSrtA) is the most popular enzyme due to its selectivity and well-demonstrated applications. Position scanning has been widely applied to understand enzyme substrate specificity, but the low throughput of chemical synthesis of peptide substrates and analytical methods (HPLC, LC-ESI-MS) have been the major hurdle to fully decode enzyme substrate profile. We have developed a simple high-throughput substrate profiling method to reveal novel substrates of SaSrtA 7M, a widely used hyperactive peptide ligase, by modified protein-fragment complementation assay (PCA). A small library targeting the LPATG motif recognized by SaSrtA 7M was generated and screened against proteins carrying N-terminal glycine. Using this method, we have confirmed all currently known substrates of the enzyme, and moreover identified some previously unknown substrates with varying activities. The method provides an easy, fast and highly-sensitive way to determine substrate profile of a peptide ligase in a high-throughput manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Accurate virus quantitation using a Scanning Transmission Electron Microscopy (STEM) detector in a scanning electron microscope.

PubMed

Blancett, Candace D; Fetterer, David P; Koistinen, Keith A; Morazzani, Elaine M; Monninger, Mitchell K; Piper, Ashley E; Kuehl, Kathleen A; Kearney, Brian J; Norris, Sarah L; Rossi, Cynthia A; Glass, Pamela J; Sun, Mei G

2017-10-01

A method for accurate quantitation of virus particles has long been sought, but a perfect method still eludes the scientific community. Electron Microscopy (EM) quantitation is a valuable technique because it provides direct morphology information and counts of all viral particles, whether or not they are infectious. In the past, EM negative stain quantitation methods have been cited as inaccurate, non-reproducible, and with detection limits that were too high to be useful. To improve accuracy and reproducibility, we have developed a method termed Scanning Transmission Electron Microscopy - Virus Quantitation (STEM-VQ), which simplifies sample preparation and uses a high throughput STEM detector in a Scanning Electron Microscope (SEM) coupled with commercially available software. In this paper, we demonstrate STEM-VQ with an alphavirus stock preparation to present the method's accuracy and reproducibility, including a comparison of STEM-VQ to viral plaque assay and the ViroCyt Virus Counter. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Massively Parallel Rogue Cell Detection Using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High-Throughput Flow

DTIC Science & Technology

2012-08-01

techniques and STEAM imager. It couples the high-speed capability of the STEAM imager and differential phase contrast imaging of DIC / Nomarski microscopy...On 10 TPE chips, we obtained 9 homogenous and strong bonds, the failed bond being due to operator error and presence of air bubbles in the TPE...instruments, structural dynamics, and microelectromechanical systems (MEMS) via laser-scanning surface vibrometry , and observation of biomechanical motility

Quantitative secondary electron imaging for work function extraction at atomic level and layer identification of graphene

PubMed Central

Zhou, Yangbo; Fox, Daniel S; Maguire, Pierce; O’Connell, Robert; Masters, Robert; Rodenburg, Cornelia; Wu, Hanchun; Dapor, Maurizio; Chen, Ying; Zhang, Hongzhou

2016-01-01

Two-dimensional (2D) materials usually have a layer-dependent work function, which require fast and accurate detection for the evaluation of their device performance. A detection technique with high throughput and high spatial resolution has not yet been explored. Using a scanning electron microscope, we have developed and implemented a quantitative analytical technique which allows effective extraction of the work function of graphene. This technique uses the secondary electron contrast and has nanometre-resolved layer information. The measurement of few-layer graphene flakes shows the variation of work function between graphene layers with a precision of less than 10 meV. It is expected that this technique will prove extremely useful for researchers in a broad range of fields due to its revolutionary throughput and accuracy. PMID:26878907

Clinical and laboratory applications of slide-based cytometry with the LSC, SFM, and the iCYTE imaging cytometer instruments

NASA Astrophysics Data System (ADS)

Bocsi, Jozsef; Luther, Ed; Mittag, Anja; Jensen, Ingo; Sack, Ulrich; Lenz, Dominik; Trezl, Lajos; Varga, Viktor S.; Molnar, Beea; Tarnok, Attila

2004-06-01

Background: Slide based cytometry (SBC) is a technology for the rapid stoichiometric analysis of cells fixed to surfaces. Its applications are highly versatile and ranges from the clinics to high throughput drug discovery. SBC is realized in different instruments such as the Laser Scanning Cytometer (LSC) and Scanning Fluorescent Microscope (SFM) and the novel inverted microscope based iCyte image cytometer (Compucyte Corp.). Methods: Fluorochrome labeled specimens were immobilized on microscopic slides. They were placed on a conventional fluorescence microscope and analyzed by photomultiplayers or digital camera. Data comparable to flow cytometry were generated. In addition, each individual event could be visualized. Applications: The major advantage of instruments is the combination of two features: a) the minimal sample volume needed, and b) the connection of fluorescence data and morphological information. Rare cells were detected, frequency of apoptosis by myricetin formaldehyde and H2O2 mixtures was determined;. Conclusion: LSC, SFM and the novel iCyte have a wide spectrum of applicability in SBC and can be introduced as a standard technology for multiple settings. In addition, the iCyte and SFM instrument is suited for high throughput screening by automation and may be in future adapted to telepathology due to their high quality images. (This study was supported by the IZKF-Leipzig, Germany and T 034245 OTKA, Hungary)

Noninvasive High-Throughput Single-Cell Analysis of HIV Protease Activity Using Ratiometric Flow Cytometry

PubMed Central

Gaber, Rok; Majerle, Andreja; Jerala, Roman; Benčina, Mojca

2013-01-01

To effectively fight against the human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET)-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity. PMID:24287545

Native denaturation differential scanning fluorimetry: Determining the effect of urea using a quantitative real-time thermocycler.

PubMed

Childers, Christine L; Green, Stuart R; Dawson, Neal J; Storey, Kenneth B

2016-09-01

The effect of protein stability on kinetic function is monitored with many techniques that often require large amounts of expensive substrates and specialized equipment not universally available. We present differential scanning fluorimetry (DSF), a simple high-throughput assay performed in real-time thermocyclers, as a technique for analysis of protein unfolding. Furthermore, we demonstrate a correlation between the half-maximal rate of protein unfolding (Knd), and protein unfolding by urea (I50). This demonstrates that DSF methods can determine the structural stability of an enzyme's active site and can compare the relative structural stability of homologous enzymes with a high degree of sequence similarity. Copyright © 2016 Elsevier Inc. All rights reserved.

Miniaturized high throughput detection system for capillary array electrophoresis on chip with integrated light emitting diode array as addressed ring-shaped light source.

PubMed

Ren, Kangning; Liang, Qionglin; Mu, Xuan; Luo, Guoan; Wang, Yiming

2009-03-07

A novel miniaturized, portable fluorescence detection system for capillary array electrophoresis (CAE) on a microfluidic chip was developed, consisting of a scanning light-emitting diode (LED) light source and a single point photoelectric sensor. Without charge coupled detector (CCD), lens, fibers and moving parts, the system was extremely simplified. Pulsed driving of the LED significantly increased the sensitivity, and greatly reduced the power consumption and photobleaching effect. The highly integrated system was robust and easy to use. All the advantages realized the concept of a portable micro-total analysis system (micro-TAS), which could work on a single universal serial bus (USB) port. Compared with traditional CAE detecting systems, the current system could scan the radial capillary array with high scanning rate. An 8-channel CAE of fluorescein isothiocyanate (FITC) labeled arginine (Arg) on chip was demonstrated with this system, resulting in a limit of detection (LOD) of 640 amol.

Optima MDxt: A high throughput 335 keV mid-dose implanter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisner, Edward; David, Jonathan; Justesen, Perry

2012-11-06

The continuing demand for both energy purity and implant angle control along with high wafer throughput drove the development of the Axcelis Optima MDxt mid-dose ion implanter. The system utilizes electrostatic scanning, an electrostatic parallelizing lens and an electrostatic energy filter to produce energetically pure beams with high angular integrity. Based on field proven components, the Optima MDxt beamline architecture offers the high beam currents possible with singly charged species including arsenic at energies up to 335 keV as well as large currents from multiply charged species at energies extending over 1 MeV. Conversely, the excellent energy filtering capability allowsmore » high currents at low beam energies, since it is safe to utilize large deceleration ratios. This beamline is coupled with the >500 WPH capable endstation technology used on the Axcelis Optima XEx high energy ion implanter. The endstation includes in-situ angle measurements of the beam in order to maintain excellent beam-to-wafer implant angle control in both the horizontal and vertical directions. The Optima platform control system provides new generation dose control system that assures excellent dosimetry and charge control. This paper will describe the features and technologies that allow the Optima MDxt to provide superior process performance at the highest wafer throughput, and will provide examples of the process performance achievable.« less

High throughput secondary electron imaging of organic residues on a graphene surface

NASA Astrophysics Data System (ADS)

Zhou, Yangbo; O'Connell, Robert; Maguire, Pierce; Zhang, Hongzhou

2014-11-01

Surface organic residues inhibit the extraordinary electronic properties of graphene, hindering the development of graphene electronics. However, fundamental understanding of the residue morphology is still absent due to a lack of high-throughput and high-resolution surface characterization methods. Here, we demonstrate that secondary electron (SE) imaging in the scanning electron microscope (SEM) and helium ion microscope (HIM) can provide sub-nanometer information of a graphene surface and reveal the morphology of surface contaminants. Nanoscale polymethyl methacrylate (PMMA) residues are visible in the SE imaging, but their contrast, i.e. the apparent lateral dimension, varies with the imaging conditions. We have demonstrated a quantitative approach to readily obtain the physical size of the surface features regardless of the contrast variation. The fidelity of SE imaging is ultimately determined by the probe size of the primary beam. HIM is thus evaluated to be a superior SE imaging technique in terms of surface sensitivity and image fidelity. A highly efficient method to reveal the residues on a graphene surface has therefore been established.

Design of an electron projection system with slider lenses and multiple beams

NASA Astrophysics Data System (ADS)

Moonen, Daniel; Leunissen, Peter L. H. A.; de Jager, Patrick W.; Kruit, Pieter; Bleeker, Arno J.; Van der Mast, Karel D.

2002-07-01

The commercial applicability of electron beam projection lithography systems may be limited at high resolution because of low throughput. The main limitations to the throughput are: (i) Beam current. The Coulomb interaction between electrons result in an image blue. Therefore less beam current can be allowed at higher resolution, impacting the illuminate time of the wafer. (ii) Exposure field size. Early attempts to improve throughput with 'full chip' electron beam projection systems failed, because the system suffered from large off-axis aberrations of the electron optics, which severely restricted the useful field size. This has impact on the overhead time. A new type of projection optics will be proposed in this paper to overcome both limits. A slider lens is proposed that allows an effective field that is much larger than schemes proposed by SCALPEL and PREVAIL. The full width of the die can be exposed without mechanical scanning by sliding the beam through the slit-like bore of the lens. Locally, at the beam position, a 'round'-lens field is created with a combination of a rectangular magnetic field and quadruples that are positioned inside the lens. A die can now be exposed during a single mechanical scan as in state-of-the-art light optical tools. The total beam current can be improved without impact on the Coulomb interaction blur by combining several beams in a single lithography system if these beams do not interfere with each other. Several optical layouts have been proposed that combined up to 5 beams in a projection system consisting of a doublet of slider lenses. This type of projection optics has a potential throughput of 50 WPH at 45 nm with a resist sensitivity of 6 (mu) C/cm2.

Hyperchromatic laser scanning cytometry

NASA Astrophysics Data System (ADS)

Tárnok, Attila; Mittag, Anja

2007-02-01

In the emerging fields of high-content and high-throughput single cell analysis for Systems Biology and Cytomics multi- and polychromatic analysis of biological specimens has become increasingly important. Combining different technologies and staining methods polychromatic analysis (i.e. using 8 or more fluorescent colors at a time) can be pushed forward to measure anything stainable in a cell, an approach termed hyperchromatic cytometry. For cytometric cell analysis microscope based Slide Based Cytometry (SBC) technologies are ideal as, unlike flow cytometry, they are non-consumptive, i.e. the analyzed sample is fixed on the slide. Based on the feature of relocation identical cells can be subsequently reanalyzed. In this manner data on the single cell level after manipulation steps can be collected. In this overview various components for hyperchromatic cytometry are demonstrated for a SBC instrument, the Laser Scanning Cytometer (Compucyte Corp., Cambridge, MA): 1) polychromatic cytometry, 2) iterative restaining (using the same fluorochrome for restaining and subsequent reanalysis), 3) differential photobleaching (differentiating fluorochromes by their different photostability), 4) photoactivation (activating fluorescent nanoparticles or photocaged dyes), and 5) photodestruction (destruction of FRET dyes). With the intelligent combination of several of these techniques hyperchromatic cytometry allows to quantify and analyze virtually all components of relevance on the identical cell. The combination of high-throughput and high-content SBC analysis with high-resolution confocal imaging allows clear verification of phenotypically distinct subpopulations of cells with structural information. The information gained per specimen is only limited by the number of available antibodies and by sterical hindrance.

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

DOE PAGES

Ozturk, Hande; Yan, Hanfei; He, Yan; ...

2018-05-09

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozturk, Hande; Yan, Hanfei; He, Yan

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

Centimeter-scale MEMS scanning mirrors for high power laser application

NASA Astrophysics Data System (ADS)

Senger, F.; Hofmann, U.; v. Wantoch, T.; Mallas, C.; Janes, J.; Benecke, W.; Herwig, Patrick; Gawlitza, P.; Ortega-Delgado, M.; Grune, C.; Hannweber, J.; Wetzig, A.

2015-02-01

A higher achievable scan speed and the capability to integrate two scan axes in a very compact device are fundamental advantages of MEMS scanning mirrors over conventional galvanometric scanners. There is a growing demand for biaxial high speed scanning systems complementing the rapid progress of high power lasers for enabling the development of new high throughput manufacturing processes. This paper presents concept, design, fabrication and test of biaxial large aperture MEMS scanning mirrors (LAMM) with aperture sizes up to 20 mm for use in high-power laser applications. To keep static and dynamic deformation of the mirror acceptably low all MEMS mirrors exhibit full substrate thickness of 725 μm. The LAMM-scanners are being vacuum packaged on wafer-level based on a stack of 4 wafers. Scanners with aperture sizes up to 12 mm are designed as a 4-DOF-oscillator with amplitude magnification applying electrostatic actuation for driving a motor-frame. As an example a 7-mm-scanner is presented that achieves an optical scan angle of 32 degrees at 3.2 kHz. LAMM-scanners with apertures sizes of 20 mm are designed as passive high-Q-resonators to be externally excited by low-cost electromagnetic or piezoelectric drives. Multi-layer dielectric coatings with a reflectivity higher than 99.9 % have enabled to apply cw-laser power loads of more than 600 W without damaging the MEMS mirror. Finally, a new excitation concept for resonant scanners is presented providing advantageous shaping of intensity profiles of projected laser patterns without modulating the laser. This is of interest in lighting applications such as automotive laser headlights.

Software/hardware optimization for attenuation-based microtomography using SR at PETRA III (Conference Presentation)

NASA Astrophysics Data System (ADS)

Beckmann, Felix

2016-10-01

The Helmholtz-Zentrum Geesthacht, Germany, is operating the user experiments for microtomography at the beamlines P05 and P07 using synchrotron radiation produced in the storage ring PETRA III at DESY, Hamburg, Germany. In recent years the software pipeline, sample changing hardware for performing high throughput experiments were developed. In this talk the current status of the beamlines will be given. Furthermore, optimisation and automatisation of scanning techniques, will be presented. These are required to scan samples which are larger than the field of view defined by the X-ray beam. The integration into an optimized reconstruction pipeline will be shown.

High-throughput measurement of rice tillers using a conveyor equipped with x-ray computed tomography

NASA Astrophysics Data System (ADS)

Yang, Wanneng; Xu, Xiaochun; Duan, Lingfeng; Luo, Qingming; Chen, Shangbin; Zeng, Shaoqun; Liu, Qian

2011-02-01

Tillering is one of the most important agronomic traits because the number of shoots per plant determines panicle number, a key component of grain yield. The conventional method of counting tillers is still manual. Under the condition of mass measurement, the accuracy and efficiency could be gradually degraded along with fatigue of experienced staff. Thus, manual measurement, including counting and recording, is not only time consuming but also lack objectivity. To automate this process, we developed a high-throughput facility, dubbed high-throughput system for measuring automatically rice tillers (H-SMART), for measuring rice tillers based on a conventional x-ray computed tomography (CT) system and industrial conveyor. Each pot-grown rice plant was delivered into the CT system for scanning via the conveyor equipment. A filtered back-projection algorithm was used to reconstruct the transverse section image of the rice culms. The number of tillers was then automatically extracted by image segmentation. To evaluate the accuracy of this system, three batches of rice at different growth stages (tillering, heading, or filling) were tested, yielding absolute mean absolute errors of 0.22, 0.36, and 0.36, respectively. Subsequently, the complete machine was used under industry conditions to estimate its efficiency, which was 4320 pots per continuous 24 h workday. Thus, the H-SMART could determine the number of tillers of pot-grown rice plants, providing three advantages over the manual tillering method: absence of human disturbance, automation, and high throughput. This facility expands the application of agricultural photonics in plant phenomics.

High-throughput measurement of rice tillers using a conveyor equipped with x-ray computed tomography.

PubMed

Yang, Wanneng; Xu, Xiaochun; Duan, Lingfeng; Luo, Qingming; Chen, Shangbin; Zeng, Shaoqun; Liu, Qian

2011-02-01

Tillering is one of the most important agronomic traits because the number of shoots per plant determines panicle number, a key component of grain yield. The conventional method of counting tillers is still manual. Under the condition of mass measurement, the accuracy and efficiency could be gradually degraded along with fatigue of experienced staff. Thus, manual measurement, including counting and recording, is not only time consuming but also lack objectivity. To automate this process, we developed a high-throughput facility, dubbed high-throughput system for measuring automatically rice tillers (H-SMART), for measuring rice tillers based on a conventional x-ray computed tomography (CT) system and industrial conveyor. Each pot-grown rice plant was delivered into the CT system for scanning via the conveyor equipment. A filtered back-projection algorithm was used to reconstruct the transverse section image of the rice culms. The number of tillers was then automatically extracted by image segmentation. To evaluate the accuracy of this system, three batches of rice at different growth stages (tillering, heading, or filling) were tested, yielding absolute mean absolute errors of 0.22, 0.36, and 0.36, respectively. Subsequently, the complete machine was used under industry conditions to estimate its efficiency, which was 4320 pots per continuous 24 h workday. Thus, the H-SMART could determine the number of tillers of pot-grown rice plants, providing three advantages over the manual tillering method: absence of human disturbance, automation, and high throughput. This facility expands the application of agricultural photonics in plant phenomics.

Lung nodule detection from CT scans using 3D convolutional neural networks without candidate selection

NASA Astrophysics Data System (ADS)

Jenuwine, Natalia M.; Mahesh, Sunny N.; Furst, Jacob D.; Raicu, Daniela S.

2018-02-01

Early detection of lung nodules from CT scans is key to improving lung cancer treatment, but poses a significant challenge for radiologists due to the high throughput required of them. Computer-Aided Detection (CADe) systems aim to automatically detect these nodules with computer algorithms, thus improving diagnosis. These systems typically use a candidate selection step, which identifies all objects that resemble nodules, followed by a machine learning classifier which separates true nodules from false positives. We create a CADe system that uses a 3D convolutional neural network (CNN) to detect nodules in CT scans without a candidate selection step. Using data from the LIDC database, we train a 3D CNN to analyze subvolumes from anywhere within a CT scan and output the probability that each subvolume contains a nodule. Once trained, we apply our CNN to detect nodules from entire scans, by systematically dividing the scan into overlapping subvolumes which we input into the CNN to obtain the corresponding probabilities. By enabling our network to process an entire scan, we expect to streamline the detection process while maintaining its effectiveness. Our results imply that with continued training using an iterative training scheme, the one-step approach has the potential to be highly effective.

Wavelength-Scanning SPR Imaging Sensors Based on an Acousto-Optic Tunable Filter and a White Light Laser

PubMed Central

Zeng, Youjun; Wang, Lei; Wu, Shu-Yuen; He, Jianan; Qu, Junle; Li, Xuejin; Ho, Ho-Pui; Gu, Dayong; Gao, Bruce Zhi; Shao, Yonghong

2017-01-01

A fast surface plasmon resonance (SPR) imaging biosensor system based on wavelength interrogation using an acousto-optic tunable filter (AOTF) and a white light laser is presented. The system combines the merits of a wide-dynamic detection range and high sensitivity offered by the spectral approach with multiplexed high-throughput data collection and a two-dimensional (2D) biosensor array. The key feature is the use of AOTF to realize wavelength scan from a white laser source and thus to achieve fast tracking of the SPR dip movement caused by target molecules binding to the sensor surface. Experimental results show that the system is capable of completing a SPR dip measurement within 0.35 s. To the best of our knowledge, this is the fastest time ever reported in the literature for imaging spectral interrogation. Based on a spectral window with a width of approximately 100 nm, a dynamic detection range and resolution of 4.63 × 10−2 refractive index unit (RIU) and 1.27 × 10−6 RIU achieved in a 2D-array sensor is reported here. The spectral SPR imaging sensor scheme has the capability of performing fast high-throughput detection of biomolecular interactions from 2D sensor arrays. The design has no mechanical moving parts, thus making the scheme completely solid-state. PMID:28067766

Protein and Antibody Engineering by Phage Display

PubMed Central

Frei, J.C.; Lai, J.R.

2017-01-01

Phage display is an in vitro selection technique that allows for the rapid isolation of proteins with desired properties including increased affinity, specificity, stability, and new enzymatic activity. The power of phage display relies on the phenotype-to-genotype linkage of the protein of interest displayed on the phage surface with the encoding DNA packaged within the phage particle, which allows for selective enrichment of library pools and high-throughput screening of resulting clones. As an in vitro method, the conditions of the binding selection can be tightly controlled. Due to the high-throughput nature, rapidity, and ease of use, phage display is an excellent technological platform for engineering antibody or proteins with enhanced properties. Here, we describe methods for synthesis, selection, and screening of phage libraries with particular emphasis on designing humanizing antibody libraries and combinatorial scanning mutagenesis libraries. We conclude with a brief section on troubleshooting for all stages of the phage display process. PMID:27586328

Characterization of Pleurotus ostreatus Biofilms by Using the Calgary Biofilm Device

PubMed Central

Pesciaroli, Lorena; Petruccioli, Maurizio; Fedi, Stefano; Firrincieli, Andrea; Federici, Federico

2013-01-01

The adequacy of the Calgary biofilm device, often referred to as the MBEC system, as a high-throughput approach to the production and subsequent characterization of Pleurotus ostreatus biofilms was assessed. The hydroxyapatite-coating of pegs was necessary to enable biofilm attachment, and the standardization of vegetative inocula ensured a uniform distribution of P. ostreatus biofilms, which is necessary for high-throughput evaluations of several antimicrobials and exposure conditions. Scanning electron microscopy showed surface-associated growth, the occurrence of a complex aggregated growth organized in multilayers or hyphal bundles, and the encasement of hyphae within an extracellular matrix (ECM), the extent of which increased with time. Chemical analyses showed that biofilms differed from free-floating cultures for their higher contents of total sugars (TS) and ECM, with the latter being mainly composed of TS and, to a lesser extent, protein. Confocal laser scanning microscopy analysis of 4-day-old biofilms showed the presence of interspersed interstitial voids and water channels in the mycelial network, the density and compactness of which increased after a 7-day incubation, with the novel occurrence of ECM aggregates with an α-glucan moiety. In 4- and 7-day-old biofilms, tolerance to cadmium was increased by factors of 3.2 and 11.1, respectively, compared to coeval free-floating counterparts. PMID:23892744

Characterization of Pleurotus ostreatus biofilms by using the calgary biofilm device.

PubMed

Pesciaroli, Lorena; Petruccioli, Maurizio; Fedi, Stefano; Firrincieli, Andrea; Federici, Federico; D'Annibale, Alessandro

2013-10-01

The adequacy of the Calgary biofilm device, often referred to as the MBEC system, as a high-throughput approach to the production and subsequent characterization of Pleurotus ostreatus biofilms was assessed. The hydroxyapatite-coating of pegs was necessary to enable biofilm attachment, and the standardization of vegetative inocula ensured a uniform distribution of P. ostreatus biofilms, which is necessary for high-throughput evaluations of several antimicrobials and exposure conditions. Scanning electron microscopy showed surface-associated growth, the occurrence of a complex aggregated growth organized in multilayers or hyphal bundles, and the encasement of hyphae within an extracellular matrix (ECM), the extent of which increased with time. Chemical analyses showed that biofilms differed from free-floating cultures for their higher contents of total sugars (TS) and ECM, with the latter being mainly composed of TS and, to a lesser extent, protein. Confocal laser scanning microscopy analysis of 4-day-old biofilms showed the presence of interspersed interstitial voids and water channels in the mycelial network, the density and compactness of which increased after a 7-day incubation, with the novel occurrence of ECM aggregates with an α-glucan moiety. In 4- and 7-day-old biofilms, tolerance to cadmium was increased by factors of 3.2 and 11.1, respectively, compared to coeval free-floating counterparts.

High-Throughput Biophysical Analysis and Data Visualization of Conformational Stability of an IgG1 Monoclonal Antibody (mAb) After Deglycosylation

PubMed Central

Alsenaidy, Mohammad A.; Kim, Jae Hyun; Majumdar, Ranajoy; Weis, David D.; Joshi, Sangeeta B.; Tolbert, Thomas J.; Middaugh, C. Russell; Volkin, David B.

2013-01-01

The structural integrity and conformational stability of an IgG1 monoclonal antibody (mAb), after partial and complete enzymatic removal of the N-linked Fc glycan, was compared to the untreated mAb over a wide range of temperature (10° to 90°C) and solution pH (3 to 8) using circular dichroism, fluorescence spectroscopy, and static light scattering combined with data visualization employing empirical phase diagrams (EPDs). Subtle to larger stability differences between the different glycoforms were observed. Improved detection of physical stability differences was then demonstrated over narrower pH range (4.0-6.0) using smaller temperature increments, especially when combined with an alternative data visualization method (radar plots). Differential scanning calorimetry and differential scanning fluorimetry were then utilized and also showed an improved ability to detect differences in mAb glycoform physical stability. Based on these results, a two-step methodology was used in which mAb glycoform conformational stability is first screened with a wide variety of instruments and environmental stresses, followed by a second evaluation with optimally sensitive experimental conditions, analytical techniques and data visualization methods. With this approach, high-throughput biophysical analysis to assess relatively subtle conformational stability differences in protein glycoforms is demonstrated. PMID:24114789

High-speed ultrafast laser machining with tertiary beam positioning (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yang, Chuan; Zhang, Haibin

2017-03-01

For an industrial laser application, high process throughput and low average cost of ownership are critical to commercial success. Benefiting from high peak power, nonlinear absorption and small-achievable spot size, ultrafast lasers offer advantages of minimal heat affected zone, great taper and sidewall quality, and small via capability that exceeds the limits of their predecessors in via drilling for electronic packaging. In the past decade, ultrafast lasers have both grown in power and reduced in cost. For example, recently, disk and fiber technology have both shown stable operation in the 50W to 200W range, mostly at high repetition rate (beyond 500 kHz) that helps avoid detrimental nonlinear effects. However, to effectively and efficiently scale the throughput with the fast-growing power capability of the ultrafast lasers while keeping the beneficial laser-material interactions is very challenging, mainly because of the bottleneck imposed by the inertia-related acceleration limit and servo gain bandwidth when only stages and galvanometers are being used. On the other side, inertia-free scanning solutions like acoustic optics and electronic optical deflectors have small scan field, and therefore not suitable for large-panel processing. Our recent system developments combine stages, galvanometers, and AODs into a coordinated tertiary architecture for high bandwidth and meanwhile large field beam positioning. Synchronized three-level movements allow extremely fast local speed and continuous motion over the whole stage travel range. We present the via drilling results from such ultrafast system with up to 3MHz pulse to pulse random access, enabling high quality low cost ultrafast machining with emerging high average power laser sources.

Correlating Oxygen Evolution Catalysts Activity and Electronic Structure by a High-Throughput Investigation of Ni1-y-zFeyCrzOx

PubMed Central

Schwanke, Christoph; Stein, Helge Sören; Xi, Lifei; Sliozberg, Kirill; Schuhmann, Wolfgang; Ludwig, Alfred; Lange, Kathrin M.

2017-01-01

High-throughput characterization by soft X-ray absorption spectroscopy (XAS) and electrochemical characterization is used to establish a correlation between electronic structure and catalytic activity of oxygen evolution reaction (OER) catalysts. As a model system a quasi-ternary materials library of Ni1-y-zFeyCrzOx was synthesized by combinatorial reactive magnetron sputtering, characterized by XAS, and an automated scanning droplet cell. The presence of Cr was found to increase the OER activity in the investigated compositional range. The electronic structure of NiII and CrIII remains unchanged over the investigated composition spread. At the Fe L-edge a linear combination of two spectra was observed. These spectra were assigned to FeIII in Oh symmetry and FeIII in Td symmetry. The ratio of FeIII Oh to FeIII Td increases with the amount of Cr and a correlation between the presence of the FeIII Oh and a high OER activity is found. PMID:28287134

Correlating Oxygen Evolution Catalysts Activity and Electronic Structure by a High-Throughput Investigation of Ni1-y-zFeyCrzOx

NASA Astrophysics Data System (ADS)

Schwanke, Christoph; Stein, Helge Sören; Xi, Lifei; Sliozberg, Kirill; Schuhmann, Wolfgang; Ludwig, Alfred; Lange, Kathrin M.

2017-03-01

High-throughput characterization by soft X-ray absorption spectroscopy (XAS) and electrochemical characterization is used to establish a correlation between electronic structure and catalytic activity of oxygen evolution reaction (OER) catalysts. As a model system a quasi-ternary materials library of Ni1-y-zFeyCrzOx was synthesized by combinatorial reactive magnetron sputtering, characterized by XAS, and an automated scanning droplet cell. The presence of Cr was found to increase the OER activity in the investigated compositional range. The electronic structure of NiII and CrIII remains unchanged over the investigated composition spread. At the Fe L-edge a linear combination of two spectra was observed. These spectra were assigned to FeIII in Oh symmetry and FeIII in Td symmetry. The ratio of FeIII Oh to FeIII Td increases with the amount of Cr and a correlation between the presence of the FeIII Oh and a high OER activity is found.

Improved spatial resolution of luminescence images acquired with a silicon line scanning camera

NASA Astrophysics Data System (ADS)

Teal, Anthony; Mitchell, Bernhard; Juhl, Mattias K.

2018-04-01

Luminescence imaging is currently being used to provide spatially resolved defect in high volume silicon solar cell production. One option to obtain the high throughput required for on the fly detection is the use a silicon line scan cameras. However, when using a silicon based camera, the spatial resolution is reduced as a result of the weakly absorbed light scattering within the camera's chip. This paper address this issue by applying deconvolution from a measured point spread function. This paper extends the methods for determining the point spread function of a silicon area camera to a line scan camera with charge transfer. The improvement in resolution is quantified in the Fourier domain and in spatial domain on an image of a multicrystalline silicon brick. It is found that light spreading beyond the active sensor area is significant in line scan sensors, but can be corrected for through normalization of the point spread function. The application of this method improves the raw data, allowing effective detection of the spatial resolution of defects in manufacturing.

High-throughput characterization of stresses in thin film materials libraries using Si cantilever array wafers and digital holographic microscopy.

PubMed

Lai, Y W; Hamann, S; Ehmann, M; Ludwig, A

2011-06-01

We report the development of an advanced high-throughput stress characterization method for thin film materials libraries sputter-deposited on micro-machined cantilever arrays consisting of around 1500 cantilevers on 4-inch silicon-on-insulator wafers. A low-cost custom-designed digital holographic microscope (DHM) is employed to simultaneously monitor the thin film thickness, the surface topography and the curvature of each of the cantilevers before and after deposition. The variation in stress state across the thin film materials library is then calculated by Stoney's equation based on the obtained radii of curvature of the cantilevers and film thicknesses. DHM with nanometer-scale out-of-plane resolution allows stress measurements in a wide range, at least from several MPa to several GPa. By using an automatic x-y translation stage, the local stresses within a 4-inch materials library are mapped with high accuracy within 10 min. The speed of measurement is greatly improved compared with the prior laser scanning approach that needs more than an hour of measuring time. A high-throughput stress measurement of an as-deposited Fe-Pd-W materials library was evaluated for demonstration. The fast characterization method is expected to accelerate the development of (functional) thin films, e.g., (magnetic) shape memory materials, whose functionality is greatly stress dependent. © 2011 American Institute of Physics

Corrugated metal-coated tapered tip for scanning near-field optical microscope.

PubMed

Antosiewicz, Tomasz J; Szoplik, Tomasz

2007-08-20

This paper addresses an important issue of light throughput of a metal-coated tapered tip for scanning near-field microscope (SNOM). Corrugations of the interface between the fiber core and metal coating in the form of parallel grooves of different profiles etched in the core considerably increase the energy throughput. In 2D FDTD simulations in the Cartesian coordinates we calculate near-field light emitted from such tips. For a certain wavelength range total intensity of forward emission from the corrugated tip is 10 times stronger than that from a classical tapered tip. When realized in practice the idea of corrugated tip may lead up to twice better resolution of SNOM.

Remote sensing of Earth's atmosphere and surface using a digital array scanned interferometer: A new type of imaging spectrometer

NASA Technical Reports Server (NTRS)

Hammer, Philip D.; Valero, Francisco P. J.; Peterson, David L.; Smith, William Hayden

1991-01-01

The capabilities of the digital array scanned interferometer (DASI) class of instruments for measuring terrestrial radiation fields over the visible to mid-infrared are evaluated. DASI's are capable of high throughput, sensitivity and spectral resolution and have the potential for field-of-view spatial discrimination (an imaging spectrometer). The simplicity of design and operation of DASI's make them particularly suitable for field and airborne platform based remote sensing. The long term objective is to produce a versatile field instrument which may be applied toward a variety of atmospheric and surface studies. The operation of DASI and its advantages over other spectrometers are discussed.

Near-field microscopy with a microfabricated solid immersion lens

NASA Astrophysics Data System (ADS)

Fletcher, Daniel Alden

2001-07-01

Diffraction of focused light prevents optical microscopes from resolving features in air smaller than half the wavelength, λ Spatial resolution can be improved by passing light through a sub-wavelength metal aperture scanned close to a sample, but aperture-based probes suffer from low optical throughput, typically below 10-4. An alternate and more efficient technique is solid immersion microscopy in which light is focused through a high refractive index Solid Immersion Lens (SIL). This work describes the fabrication, modeling, and use of a microfabricated SIL to obtain spatial resolution better than the diffraction limit in air with high optical throughput for infrared applications. SILs on the order of 10 μm in diameter are fabricated from single-crystal silicon and integrated onto silicon cantilevers with tips for scanning. We measure a focused spot size of λ/5 with optical throughput better than 10-1 at a wavelength of λ = 9.3 μm. Spatial resolution is improved to λ/10 with metal apertures fabricated directly on the tip of the silicon SIL. Microlenses have reduced spherical aberration and better transparency than large lenses but cannot be made arbitrarily small and still focus. We model the advantages and limitations of focusing in lenses close to the wavelength in diameter using an extension of Mie theory. We also investigate a new contrast mechanism unique to microlenses resulting from the decrease in field-of-view with lens diameter. This technique is shown to achieve λ/4 spatial resolution. We explore applications of the microfabricated silicon SIL for high spatial resolution thermal microscopy and biological spectroscopy. Thermal radiation is collected through the SIL from a heated surface with spatial resolution four times better than that of a diffraction- limited infrared microscope. Using a Fourier-transform infrared spectrometer, we observe absorption peaks in bacteria cells positioned at the focus of the silicon SIL.

Multi-level scanning method for defect inspection

DOEpatents

Bokor, Jeffrey; Jeong, Seongtae

2002-01-01

A method for performing scanned defect inspection of a collection of contiguous areas using a specified false-alarm-rate and capture-rate within an inspection system that has characteristic seek times between inspection locations. The multi-stage method involves setting an increased false-alarm-rate for a first stage of scanning, wherein subsequent stages of scanning inspect only the detected areas of probable defects at lowered values for the false-alarm-rate. For scanning inspection operations wherein the seek time and area uncertainty is favorable, the method can substantially increase inspection throughput.

Massively Parallel Rogue Cell Detection using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High Throughput Flow

DTIC Science & Technology

2013-06-01

couples  the  high-­‐speed  capability  of  the   STEAM  imager  and  differential  phase... air  bubbles  in  the  TPE  mix.  Moreover,  TPE  chips  were  also  successfully  sealed  to  other  substrates...dynamics,  and  microelectromechanical  systems  (MEMS)  via  laser-­‐scanning  surface   vibrometry ,  and   observation

High-speed two-dimensional laser scanner based on Bragg gratings stored in photothermorefractive glass.

PubMed

Yaqoob, Zahid; Arain, Muzammil A; Riza, Nabeel A

2003-09-10

A high-speed free-space wavelength-multiplexed optical scanner with high-speed wavelength selection coupled with narrowband volume Bragg gratings stored in photothermorefractive (PTR) glass is reported. The proposed scanner with no moving parts has a modular design with a wide angular scan range, accurate beam pointing, low scanner insertion loss, and two-dimensional beam scan capabilities. We present a complete analysis and design procedure for storing multiple tilted Bragg-grating structures in a single PTR glass volume (for normal incidence) in an optimal fashion. Because the scanner design is modular, many PTR glass volumes (each having multiple tilted Bragg-grating structures) can be stacked together, providing an efficient throughput with operations in both the visible and the infrared (IR) regions. A proof-of-concept experimental study is conducted with four Bragg gratings in independent PTR glass plates, and both visible and IR region scanner operations are demonstrated.

Invited review article: high-speed flexure-guided nanopositioning: mechanical design and control issues.

PubMed

Yong, Y K; Moheimani, S O R; Kenton, B J; Leang, K K

2012-12-01

Recent interest in high-speed scanning probe microscopy for high-throughput applications including video-rate atomic force microscopy and probe-based nanofabrication has sparked attention on the development of high-bandwidth flexure-guided nanopositioning systems (nanopositioners). Such nanopositioners are designed to move samples with sub-nanometer resolution with positioning bandwidth in the kilohertz range. State-of-the-art designs incorporate uniquely designed flexure mechanisms driven by compact and stiff piezoelectric actuators. This paper surveys key advances in mechanical design and control of dynamic effects and nonlinearities, in the context of high-speed nanopositioning. Future challenges and research topics are also discussed.

Application of a high-throughput relative chemical stability assay to screen therapeutic protein formulations by assessment of conformational stability and correlation to aggregation propensity.

PubMed

Rizzo, Joseph M; Shi, Shuai; Li, Yunsong; Semple, Andrew; Esposito, Jessica J; Yu, Shenjiang; Richardson, Daisy; Antochshuk, Valentyn; Shameem, Mohammed

2015-05-01

In this study, an automated high-throughput relative chemical stability (RCS) assay was developed in which various therapeutic proteins were assessed to determine stability based on the resistance to denaturation post introduction to a chaotrope titration. Detection mechanisms of both intrinsic fluorescence and near UV circular dichroism (near-UV CD) are demonstrated. Assay robustness was investigated by comparing multiple independent assays and achieving r(2) values >0.95 for curve overlays. The complete reversibility of the assay was demonstrated by intrinsic fluorescence, near-UV CD, and biologic potency. To highlight the method utility, we compared the RCS assay with differential scanning calorimetry and dynamic scanning fluorimetry methodologies. Utilizing C1/2 values obtained from the RCS assay, formulation rank-ordering of 12 different mAb formulations was performed. The prediction of long-term stability on protein aggregation is obtained by demonstrating a good correlation with an r(2) of 0.83 between RCS and empirical aggregation propensity data. RCS promises to be an extremely useful tool to aid in candidate formulation development efforts based on the complete reversibility of the method to allow for multiple assessments without protein loss and the strong correlation between the C1/2 data obtained and accelerated stability under stressed conditions. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Quantification of telomere length by FISH and laser scanning cytometry

NASA Astrophysics Data System (ADS)

Mahoney, John E.; Sahin, Ergun; Jaskelioff, Mariela; Chin, Lynda; DePinho, Ronald A.; Protopopov, Alexei I.

2008-02-01

Telomeres play a critical role in the maintenance of chromosomal stability. Telomere erosion, coupled with loss of DNA damage checkpoint function, results in genomic instability that promotes the development of cancer. The critical role of telomere dynamics in cancer has motivated the development of technologies designed to monitor telomere reserves in a highly quantitative and high-throughput manner in humans and model organisms. To this end, we have adapted and modified two established technologies, telomere-FISH and laser scanning cytometry. Specifically, we have produced a number of enhancements to the iCys LSC (CompuCyte) package including software updates, use of 60X dry objectives, and increased spatial resolution by 0.2 um size of stage steps. In addition, the 633 nm HeNe laser was replaced with a 532 nm green diode laser to better match the viewing options. Utilization of telomere-deficient mouse cells with short dysfunctional telomeres and matched telomerase reconstituted cultures demonstrated significantly higher mean integral specific fluorescence values for mTR transfectants relative to empty vector controls: 4.485M vs. 1.362M (p<0.0001). Histograms of average telomere intensities for individual cells were obtained and demonstrated intercellular heterogeneity in telomere lengths. The validation of the approach derives from a strong correlation between iCys LSC values and Southern blotting. This validated method greatly increases our experimental throughput and objectivity.

Study on the SPR responses of various DNA probe concentrations by parallel scan spectral SPR imaging

NASA Astrophysics Data System (ADS)

Ma, Suihua; Liu, Le; Lu, Weiping; Zhang, Yaou; He, Yonghong; Guo, Jihua

2008-12-01

SPR sensors have become a high sensitive and label free method for characterizing and quantifying chemical and biochemical interactions. However, the relations between the SPR refractive index response and the property (such as concentrations) of biochemical probes are still lacking. In this paper, an experimental study on the SPR responses of varies concentrations of Legionella pneumophila mip DNA probes is presented. We developed a novel two-dimensional SPR sensing technique-parallel scan spectral SPR imaging-to detect an array of mip gene probes. This technique offers quantitative refractive index information with a high sensing throughput. By detecting mip DNA probes with different concentrations, we obtained the relations between the SPR refractive index response and the concentrations of mip DNA probes. These results are valuable for design and developing SPR based mip gene biochips.

High throughput proteomic analysis of the secretome in an explant model of articular cartilage inflammation

PubMed Central

Clutterbuck, Abigail L.; Smith, Julia R.; Allaway, David; Harris, Pat; Liddell, Susan; Mobasheri, Ali

2011-01-01

This study employed a targeted high-throughput proteomic approach to identify the major proteins present in the secretome of articular cartilage. Explants from equine metacarpophalangeal joints were incubated alone or with interleukin-1beta (IL-1β, 10 ng/ml), with or without carprofen, a non-steroidal anti-inflammatory drug, for six days. After tryptic digestion of culture medium supernatants, resulting peptides were separated by HPLC and detected in a Bruker amaZon ion trap instrument. The five most abundant peptides in each MS scan were fragmented and the fragmentation patterns compared to mammalian entries in the Swiss-Prot database, using the Mascot search engine. Tryptic peptides originating from aggrecan core protein, cartilage oligomeric matrix protein (COMP), fibronectin, fibromodulin, thrombospondin-1 (TSP-1), clusterin (CLU), cartilage intermediate layer protein-1 (CILP-1), chondroadherin (CHAD) and matrix metalloproteinases MMP-1 and MMP-3 were detected. Quantitative western blotting confirmed the presence of CILP-1, CLU, MMP-1, MMP-3 and TSP-1. Treatment with IL-1β increased MMP-1, MMP-3 and TSP-1 and decreased the CLU precursor but did not affect CILP-1 and CLU levels. Many of the proteins identified have well-established extracellular matrix functions and are involved in early repair/stress responses in cartilage. This high throughput approach may be used to study the changes that occur in the early stages of osteoarthritis. PMID:21354348

Performance Assessment of the Digital Array Scanned Interferometer (DASI) Concept

NASA Technical Reports Server (NTRS)

Katzberg, Stephen J.; Statham, Richard B.

1996-01-01

Interferometers are known to have higher throughput than grating spectrometers for the same resolvance. The digital array scanned interferometer (DASI) has been proposed as an instrument that can capitalize on the superior throughput of the interferometer and, simultaneously, be adapted to imaging. The DASI is not the first implementation of the dual purpose concept, but it is one that has made several claims of major performance superiority, and it has been developed into a complete instrument. This paper reviews the DASI concept, summarizes its claims, and gives an assessment of how well the claims are justified. It is shown that the claims of signal-to-noise ratio superiority and operational simplicity are realized only modestly, if at all.

Protein and Antibody Engineering by Phage Display.

PubMed

Frei, J C; Lai, J R

2016-01-01

Phage display is an in vitro selection technique that allows for the rapid isolation of proteins with desired properties including increased affinity, specificity, stability, and new enzymatic activity. The power of phage display relies on the phenotype-to-genotype linkage of the protein of interest displayed on the phage surface with the encoding DNA packaged within the phage particle, which allows for selective enrichment of library pools and high-throughput screening of resulting clones. As an in vitro method, the conditions of the binding selection can be tightly controlled. Due to the high-throughput nature, rapidity, and ease of use, phage display is an excellent technological platform for engineering antibody or proteins with enhanced properties. Here, we describe methods for synthesis, selection, and screening of phage libraries with particular emphasis on designing humanizing antibody libraries and combinatorial scanning mutagenesis libraries. We conclude with a brief section on troubleshooting for all stages of the phage display process. © 2016 Elsevier Inc. All rights reserved.

Introducing Discrete Frequency Infrared Technology for High-Throughput Biofluid Screening

NASA Astrophysics Data System (ADS)

Hughes, Caryn; Clemens, Graeme; Bird, Benjamin; Dawson, Timothy; Ashton, Katherine M.; Jenkinson, Michael D.; Brodbelt, Andrew; Weida, Miles; Fotheringham, Edeline; Barre, Matthew; Rowlette, Jeremy; Baker, Matthew J.

2016-02-01

Accurate early diagnosis is critical to patient survival, management and quality of life. Biofluids are key to early diagnosis due to their ease of collection and intimate involvement in human function. Large-scale mid-IR imaging of dried fluid deposits offers a high-throughput molecular analysis paradigm for the biomedical laboratory. The exciting advent of tuneable quantum cascade lasers allows for the collection of discrete frequency infrared data enabling clinically relevant timescales. By scanning targeted frequencies spectral quality, reproducibility and diagnostic potential can be maintained while significantly reducing acquisition time and processing requirements, sampling 16 serum spots with 0.6, 5.1 and 15% relative standard deviation (RSD) for 199, 14 and 9 discrete frequencies respectively. We use this reproducible methodology to show proof of concept rapid diagnostics; 40 unique dried liquid biopsies from brain, breast, lung and skin cancer patients were classified in 2.4 cumulative seconds against 10 non-cancer controls with accuracies of up to 90%.

A power compensated differential scanning calorimeter for protein stability characterization

DOE PAGES

Wang, Shuyu; Yu, Shifeng; Siedler, Michael; ...

2017-10-07

This study presented a power compensated MEMS differential scanning calorimeter (DSC) for protein stability characterization. In this microfabricated sensor, PDMS (Polydimethylsiloxane) and polyimide were used to construct the adiabatic chamber (1 μL) and temperature sensitive vanadium oxide was used as the thermistor material. A power compensation system was implemented to maintain the sample and reference at the same temperature. The resolution study and step response characterization indicated the high sensitivity (6 V/W) and low noise level (60 μk) of the device. The test with IgG1 antibody (mAb1) samples showed clear phase transitions and the data was confirmed to be reasonablemore » by comparing it with the results of commercial DSC’s test. Finally, this device used ~1uL sample amount and could complete the scanning process in 4 min, significantly increasing the throughput of the bimolecular thermodynamics study like drug formulation process.« less

A Parallel Spectroscopic Method for Examining Dynamic Phenomena on the Millisecond Time Scale

PubMed Central

Snively, Christopher M.; Chase, D. Bruce; Rabolt, John F.

2009-01-01

An infrared spectroscopic technique based on planar array infrared (PAIR) spectroscopy has been developed that allows the acquisition of spectra from multiple samples simultaneously. Using this technique, it is possible to acquire spectra over a spectral range of 950–1900cm−1 with a temporal resolution of 2.2ms. The performance of this system was demonstrated by determining the shear-induced orientational response of several low molecular weight liquid crystals. Five different liquid crystals were examined in combination with five different alignment layers, and both primary and secondary screens were demonstrated. Implementation of this high throughput PAIR technique resulted in a reduction in acquisition time as compared to both step-scan and ultra-rapid-scanning FTIR spectroscopy. PMID:19239197

Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

NASA Astrophysics Data System (ADS)

Bae, Euiwon; Patsekin, Valery; Rajwa, Bartek; Bhunia, Arun K.; Holdman, Cheryl; Davisson, V. Jo; Hirleman, E. Daniel; Robinson, J. Paul

2012-04-01

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.

FBI Fingerprint Image Capture System High-Speed-Front-End throughput modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rathke, P.M.

1993-09-01

The Federal Bureau of Investigation (FBI) has undertaken a major modernization effort called the Integrated Automated Fingerprint Identification System (IAFISS). This system will provide centralized identification services using automated fingerprint, subject descriptor, mugshot, and document processing. A high-speed Fingerprint Image Capture System (FICS) is under development as part of the IAFIS program. The FICS will capture digital and microfilm images of FBI fingerprint cards for input into a central database. One FICS design supports two front-end scanning subsystems, known as the High-Speed-Front-End (HSFE) and Low-Speed-Front-End, to supply image data to a common data processing subsystem. The production rate of themore » HSFE is critical to meeting the FBI`s fingerprint card processing schedule. A model of the HSFE has been developed to help identify the issues driving the production rate, assist in the development of component specifications, and guide the evolution of an operations plan. A description of the model development is given, the assumptions are presented, and some HSFE throughput analysis is performed.« less

Computational efficient segmentation of cell nuclei in 2D and 3D fluorescent micrographs

NASA Astrophysics Data System (ADS)

De Vylder, Jonas; Philips, Wilfried

2011-02-01

This paper proposes a new segmentation technique developed for the segmentation of cell nuclei in both 2D and 3D fluorescent micrographs. The proposed method can deal with both blurred edges as with touching nuclei. Using a dual scan line algorithm its both memory as computational efficient, making it interesting for the analysis of images coming from high throughput systems or the analysis of 3D microscopic images. Experiments show good results, i.e. recall of over 0.98.

Identification and Characterization of Genomic Amplifications in Ovarian Serous Carcinoma

DTIC Science & Technology

2006-01-01

Wang (2005) Exploring cancer genome using innovative technologies. Curr Opin Oncol, 17:33-38. • G Singer, R Stohr, L Cope, R Dehari, A Hartmann, D -F...tions/plate × 6 plates/ d ). This high-throughput platform permits a systemic scan of cancer genome at the nucleo- tide level in a short time [35]. This...Carter D , Foellmer HG, et al.: Neu proto-oncogene amplification and expression in ovarian adenocarcinoma cell lines. Am J Pathol 1992, 140:23–31. 12

Coherent imaging at the diffraction limit

PubMed Central

Thibault, Pierre; Guizar-Sicairos, Manuel; Menzel, Andreas

2014-01-01

X-ray ptychography, a scanning coherent diffractive imaging technique, holds promise for imaging with dose-limited resolution and sensitivity. If the foreseen increase of coherent flux by orders of magnitude can be matched by additional technological and analytical advances, ptychography may approach imaging speeds familiar from full-field methods while retaining its inherently quantitative nature and metrological versatility. Beyond promises of high throughput, spectroscopic applications in three dimensions become feasible, as do measurements of sample dynamics through time-resolved imaging or careful characterization of decoherence effects. PMID:25177990

Coherent imaging at the diffraction limit.

PubMed

Thibault, Pierre; Guizar-Sicairos, Manuel; Menzel, Andreas

2014-09-01

X-ray ptychography, a scanning coherent diffractive imaging technique, holds promise for imaging with dose-limited resolution and sensitivity. If the foreseen increase of coherent flux by orders of magnitude can be matched by additional technological and analytical advances, ptychography may approach imaging speeds familiar from full-field methods while retaining its inherently quantitative nature and metrological versatility. Beyond promises of high throughput, spectroscopic applications in three dimensions become feasible, as do measurements of sample dynamics through time-resolved imaging or careful characterization of decoherence effects.

Fast Infrared Chemical Imaging with a Quantum Cascade Laser

PubMed Central

2015-01-01

Infrared (IR) spectroscopic imaging systems are a powerful tool for visualizing molecular microstructure of a sample without the need for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging spectrometers, the current established technology, can record broadband spectral data efficiently but requires scanning the entire spectrum with a low throughput source. The advent of high-intensity, broadly tunable quantum cascade lasers (QCL) has now accelerated IR imaging but results in a fundamentally different type of instrument and approach, namely, discrete frequency IR (DF-IR) spectral imaging. While the higher intensity of the source provides a higher signal per channel, the absence of spectral multiplexing also provides new opportunities and challenges. Here, we couple a rapidly tunable QCL with a high performance microscope equipped with a cooled focal plane array (FPA) detector. Our optical system is conceptualized to provide optimal performance based on recent theory and design rules for high-definition (HD) IR imaging. Multiple QCL units are multiplexed together to provide spectral coverage across the fingerprint region (776.9 to 1904.4 cm–1) in our DF-IR microscope capable of broad spectral coverage, wide-field detection, and diffraction-limited spectral imaging. We demonstrate that the spectral and spatial fidelity of this system is at least as good as the best FT-IR imaging systems. Our configuration provides a speedup for equivalent spectral signal-to-noise ratio (SNR) compared to the best spectral quality from a high-performance linear array system that has 10-fold larger pixels. Compared to the fastest available HD FT-IR imaging system, we demonstrate scanning of large tissue microarrays (TMA) in 3-orders of magnitude smaller time per essential spectral frequency. These advances offer new opportunities for high throughput IR chemical imaging, especially for the measurement of cells and tissues. PMID:25474546

Fast infrared chemical imaging with a quantum cascade laser.

PubMed

Yeh, Kevin; Kenkel, Seth; Liu, Jui-Nung; Bhargava, Rohit

2015-01-06

Infrared (IR) spectroscopic imaging systems are a powerful tool for visualizing molecular microstructure of a sample without the need for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging spectrometers, the current established technology, can record broadband spectral data efficiently but requires scanning the entire spectrum with a low throughput source. The advent of high-intensity, broadly tunable quantum cascade lasers (QCL) has now accelerated IR imaging but results in a fundamentally different type of instrument and approach, namely, discrete frequency IR (DF-IR) spectral imaging. While the higher intensity of the source provides a higher signal per channel, the absence of spectral multiplexing also provides new opportunities and challenges. Here, we couple a rapidly tunable QCL with a high performance microscope equipped with a cooled focal plane array (FPA) detector. Our optical system is conceptualized to provide optimal performance based on recent theory and design rules for high-definition (HD) IR imaging. Multiple QCL units are multiplexed together to provide spectral coverage across the fingerprint region (776.9 to 1904.4 cm(-1)) in our DF-IR microscope capable of broad spectral coverage, wide-field detection, and diffraction-limited spectral imaging. We demonstrate that the spectral and spatial fidelity of this system is at least as good as the best FT-IR imaging systems. Our configuration provides a speedup for equivalent spectral signal-to-noise ratio (SNR) compared to the best spectral quality from a high-performance linear array system that has 10-fold larger pixels. Compared to the fastest available HD FT-IR imaging system, we demonstrate scanning of large tissue microarrays (TMA) in 3-orders of magnitude smaller time per essential spectral frequency. These advances offer new opportunities for high throughput IR chemical imaging, especially for the measurement of cells and tissues.

Ultrafast Microfluidic Cellular Imaging by Optical Time-Stretch.

PubMed

Lau, Andy K S; Wong, Terence T W; Shum, Ho Cheung; Wong, Kenneth K Y; Tsia, Kevin K

2016-01-01

There is an unmet need in biomedicine for measuring a multitude of parameters of individual cells (i.e., high content) in a large population efficiently (i.e., high throughput). This is particularly driven by the emerging interest in bringing Big-Data analysis into this arena, encompassing pathology, drug discovery, rare cancer cell detection, emulsion microdroplet assays, to name a few. This momentum is particularly evident in recent advancements in flow cytometry. They include scaling of the number of measurable colors from the labeled cells and incorporation of imaging capability to access the morphological information of the cells. However, an unspoken predicament appears in the current technologies: higher content comes at the expense of lower throughput, and vice versa. For example, accessing additional spatial information of individual cells, imaging flow cytometers only achieve an imaging throughput ~1000 cells/s, orders of magnitude slower than the non-imaging flow cytometers. In this chapter, we introduce an entirely new imaging platform, namely optical time-stretch microscopy, for ultrahigh speed and high contrast label-free single-cell (in a ultrafast microfluidic flow up to 10 m/s) imaging and analysis with an ultra-fast imaging line-scan rate as high as tens of MHz. Based on this technique, not only morphological information of the individual cells can be obtained in an ultrafast manner, quantitative evaluation of cellular information (e.g., cell volume, mass, refractive index, stiffness, membrane tension) at nanometer scale based on the optical phase is also possible. The technology can also be integrated with conventional fluorescence measurements widely adopted in the non-imaging flow cytometers. Therefore, these two combinatorial and complementary measurement capabilities in long run is an attractive platform for addressing the pressing need for expanding the "parameter space" in high-throughput single-cell analysis. This chapter provides the general guidelines of constructing the optical system for time stretch imaging, fabrication and design of the microfluidic chip for ultrafast fluidic flow, as well as the image acquisition and processing.

2 MeV linear accelerator for industrial applications

NASA Astrophysics Data System (ADS)

Smith, Richard R.; Farrell, Sherman R.

1997-02-01

RPC Industries has developed a high average power scanned electron beam linac system for medium energy industrial processing, such as in-line sterilization. The parameters are: electron energy 2 MeV; average beam current 5.0 mA; and scanned width 0.5 meters. The control system features data logging and a Man-Machine Interface system. The accelerator is vertically mounted, the system height above the floor is 3.4 m, and the footprint is 0.9×1.2 meter2. The typical processing cell inside dimensions are 3.0 m by 3.5 m by 4.2 m high with concrete side walls 0.5 m thick above ground level. The equal exit depth dose is 0.73 gm cm-2. Additional topics that will be reported are: throughput, measurements of dose vs depth, dose uniformity across the web, and beam power by calorimeter and magnetic deflection of the beam.

Electron beam throughput from raster to imaging

NASA Astrophysics Data System (ADS)

Zywno, Marek

2016-12-01

Two architectures of electron beam tools are presented: single beam MEBES Exara designed and built by Etec Systems for mask writing, and the Reflected E-Beam Lithography tool (REBL), designed and built by KLA-Tencor under a DARPA Agreement No. HR0011-07-9-0007. Both tools have implemented technologies not used before to achieve their goals. The MEBES X, renamed Exara for marketing purposes, used an air bearing stage running in vacuum to achieve smooth continuous scanning. The REBL used 2 dimensional imaging to distribute charge to a 4k pixel swath to achieve writing times on the order of 1 wafer per hour, scalable to throughput approaching optical projection tools. Three stage architectures were designed for continuous scanning of wafers: linear maglev, rotary maglev, and dual linear maglev.

Interleaved EPI based fMRI improved by multiplexed sensitivity encoding (MUSE) and simultaneous multi-band imaging.

PubMed

Chang, Hing-Chiu; Gaur, Pooja; Chou, Ying-hui; Chu, Mei-Lan; Chen, Nan-kuei

2014-01-01

Functional magnetic resonance imaging (fMRI) is a non-invasive and powerful imaging tool for detecting brain activities. The majority of fMRI studies are performed with single-shot echo-planar imaging (EPI) due to its high temporal resolution. Recent studies have demonstrated that, by increasing the spatial-resolution of fMRI, previously unidentified neuronal networks can be measured. However, it is challenging to improve the spatial resolution of conventional single-shot EPI based fMRI. Although multi-shot interleaved EPI is superior to single-shot EPI in terms of the improved spatial-resolution, reduced geometric distortions, and sharper point spread function (PSF), interleaved EPI based fMRI has two main limitations: 1) the imaging throughput is lower in interleaved EPI; 2) the magnitude and phase signal variations among EPI segments (due to physiological noise, subject motion, and B0 drift) are translated to significant in-plane aliasing artifact across the field of view (FOV). Here we report a method that integrates multiple approaches to address the technical limitations of interleaved EPI-based fMRI. Firstly, the multiplexed sensitivity-encoding (MUSE) post-processing algorithm is used to suppress in-plane aliasing artifacts resulting from time-domain signal instabilities during dynamic scans. Secondly, a simultaneous multi-band interleaved EPI pulse sequence, with a controlled aliasing scheme incorporated, is implemented to increase the imaging throughput. Thirdly, the MUSE algorithm is then generalized to accommodate fMRI data obtained with our multi-band interleaved EPI pulse sequence, suppressing both in-plane and through-plane aliasing artifacts. The blood-oxygenation-level-dependent (BOLD) signal detectability and the scan throughput can be significantly improved for interleaved EPI-based fMRI. Our human fMRI data obtained from 3 Tesla systems demonstrate the effectiveness of the developed methods. It is expected that future fMRI studies requiring high spatial-resolvability and fidelity will largely benefit from the reported techniques.

Empirical Bayes scan statistics for detecting clusters of disease risk variants in genetic studies.

PubMed

McCallum, Kenneth J; Ionita-Laza, Iuliana

2015-12-01

Recent developments of high-throughput genomic technologies offer an unprecedented detailed view of the genetic variation in various human populations, and promise to lead to significant progress in understanding the genetic basis of complex diseases. Despite this tremendous advance in data generation, it remains very challenging to analyze and interpret these data due to their sparse and high-dimensional nature. Here, we propose novel applications and new developments of empirical Bayes scan statistics to identify genomic regions significantly enriched with disease risk variants. We show that the proposed empirical Bayes methodology can be substantially more powerful than existing scan statistics methods especially so in the presence of many non-disease risk variants, and in situations when there is a mixture of risk and protective variants. Furthermore, the empirical Bayes approach has greater flexibility to accommodate covariates such as functional prediction scores and additional biomarkers. As proof-of-concept we apply the proposed methods to a whole-exome sequencing study for autism spectrum disorders and identify several promising candidate genes. © 2015, The International Biometric Society.

Artifact mitigation of ptychography integrated with on-the-fly scanning probe microscopy

DOE PAGES

Huang, Xiaojing; Yan, Hanfei; Ge, Mingyuan; ...

2017-07-11

In this paper, we report our experiences with conducting ptychography simultaneously with the X-ray fluorescence measurement using the on-the-fly mode for efficient multi-modality imaging. We demonstrate that the periodic artifact inherent to the raster scan pattern can be mitigated using a sufficiently fine scan step size to provide an overlap ratio of >70%. This allows us to obtain transmitted phase contrast images with enhanced spatial resolution from ptychography while maintaining the fluorescence imaging with continuous-motion scans on pixelated grids. Lastly, this capability will greatly improve the competence and throughput of scanning probe X-ray microscopy.

Lens-free computational imaging of capillary morphogenesis within three-dimensional substrates

NASA Astrophysics Data System (ADS)

Weidling, John; Isikman, Serhan O.; Greenbaum, Alon; Ozcan, Aydogan; Botvinick, Elliot

2012-12-01

Endothelial cells cultured in three-dimensional (3-D) extracellular matrices spontaneously form microvessels in response to soluble and matrix-bound factors. Such cultures are common for the study of angiogenesis and may find widespread use in drug discovery. Vascular networks are imaged over weeks to measure the distribution of vessel morphogenic parameters. Measurements require micron-scale spatial resolution, which for light microscopy comes at the cost of limited field-of-view (FOV) and shallow depth-of-focus (DOF). Small FOVs and DOFs necessitate lateral and axial mechanical scanning, thus limiting imaging throughput. We present a lens-free holographic on-chip microscopy technique to rapidly image microvessels within a Petri dish over a large volume without any mechanical scanning. This on-chip method uses partially coherent illumination and a CMOS sensor to record in-line holographic images of the sample. For digital reconstruction of the measured holograms, we implement a multiheight phase recovery method to obtain phase images of capillary morphogenesis over a large FOV (24 mm2) with ˜1.5 μm spatial resolution. On average, measured capillary length in our method was within approximately 2% of lengths measured using a 10× microscope objective. These results suggest lens-free on-chip imaging is a useful toolset for high-throughput monitoring and quantitative analysis of microvascular 3-D networks.

Simple technique for high-throughput marking of distinguishable micro-areas for microscopy.

PubMed

Henrichs, Leonard F; Chen, L I; Bell, Andrew J

2016-04-01

Today's (nano)-functional materials, usually exhibiting complex physical properties require local investigation with different microscopy techniques covering different physical aspects such as dipolar and magnetic structure. However, often these must be employed on the very same sample position to be able to truly correlate those different information and corresponding properties. This can be very challenging if not impossible especially when samples lack prominent features for orientation. Here, we present a simple but effective method to mark hundreds of approximately 15×15 μm sample areas at one time by using a commercial transmission electron microscopy grid as shadow mask in combination with thin-film deposition. Areas can be easily distinguished when using a reference or finder grid structure as shadow mask. We show that the method is suitable to combine many techniques such as light microscopy, scanning probe microscopy and scanning electron microscopy. Furthermore, we find that best results are achieved when depositing aluminium on a flat sample surface using electron-beam evaporation which ensures good line-of-sight deposition. This inexpensive high-throughput method has several advantageous over other marking techniques such as focused ion-beam processing especially when batch processing or marking of many areas is required. Nevertheless, the technique could be particularly valuable, when used in junction with, for example focused ion-beam sectioning to obtain a thin lamellar of a particular pre-selected area. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Plasmonic Imaging of Electrochemical Reactions of Single Nanoparticles.

PubMed

Fang, Yimin; Wang, Hui; Yu, Hui; Liu, Xianwei; Wang, Wei; Chen, Hong-Yuan; Tao, N J

2016-11-15

Electrochemical reactions are involved in many natural phenomena, and are responsible for various applications, including energy conversion and storage, material processing and protection, and chemical detection and analysis. An electrochemical reaction is accompanied by electron transfer between a chemical species and an electrode. For this reason, it has been studied by measuring current, charge, or related electrical quantities. This approach has led to the development of various electrochemical methods, which have played an essential role in the understanding and applications of electrochemistry. While powerful, most of the traditional methods lack spatial and temporal resolutions desired for studying heterogeneous electrochemical reactions on electrode surfaces and in nanoscale materials. To overcome the limitations, scanning probe microscopes have been invented to map local electrochemical reactions with nanometer resolution. Examples include the scanning electrochemical microscope and scanning electrochemical cell microscope, which directly image local electrochemical reaction current using a scanning electrode or pipet. The use of a scanning probe in these microscopes provides high spatial resolution, but at the expense of temporal resolution and throughput. This Account discusses an alternative approach to study electrochemical reactions. Instead of measuring electron transfer electrically, it detects the accompanying changes in the reactant and product concentrations on the electrode surface optically via surface plasmon resonance (SPR). SPR is highly surface sensitive, and it provides quantitative information on the surface concentrations of reactants and products vs time and electrode potential, from which local reaction kinetics can be analyzed and quantified. The plasmonic approach allows imaging of local electrochemical reactions with high temporal resolution and sensitivity, making it attractive for studying electrochemical reactions in biological systems and nanoscale materials with high throughput. The plasmonic approach has two imaging modes: electrochemical current imaging and interfacial impedance imaging. The former images local electrochemical current associated with electrochemical reactions (faradic current), and the latter maps local interfacial impedance, including nonfaradic contributions (e.g., double layer charging). The plasmonic imaging technique can perform voltammetry (cyclic or square wave) in an analogous manner to the traditional electrochemical methods. It can also be integrated with bright field, dark field, and fluorescence imaging capabilities in one optical setup to provide additional capabilities. To date the plasmonic imaging technique has found various applications, including mapping of heterogeneous surface reactions, analysis of trace substances, detection of catalytic reactions, and measurement of graphene quantum capacitance. The plasmonic and other emerging optical imaging techniques (e.g., dark field and fluorescence microscopy), together with the scanning probe-based electrochemical imaging and single nanoparticle analysis techniques, provide new capabilities for one to study single nanoparticle electrochemistry with unprecedented spatial and temporal resolutions. In this Account, we focus on imaging of electrochemical reactions at single nanoparticles.

Rigorous quantitative elemental microanalysis by scanning electron microscopy/energy dispersive x-ray spectrometry (SEM/EDS) with spectrum processing by NIST DTSA-II

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2014-09-01

Quantitative electron-excited x-ray microanalysis by scanning electron microscopy/silicon drift detector energy dispersive x-ray spectrometry (SEM/SDD-EDS) is capable of achieving high accuracy and high precision equivalent to that of the high spectral resolution wavelength dispersive x-ray spectrometer even when severe peak interference occurs. The throughput of the SDD-EDS enables high count spectra to be measured that are stable in calibration and resolution (peak shape) across the full deadtime range. With this high spectral stability, multiple linear least squares peak fitting is successful for separating overlapping peaks and spectral background. Careful specimen preparation is necessary to remove topography on unknowns and standards. The standards-based matrix correction procedure embedded in the NIST DTSA-II software engine returns quantitative results supported by a complete error budget, including estimates of the uncertainties from measurement statistics and from the physical basis of the matrix corrections. NIST DTSA-II is available free for Java-platforms at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

CA resist with high sensitivity and sub-100-nm resolution for advanced mask making

NASA Astrophysics Data System (ADS)

Huang, Wu-Song; Kwong, Ranee W.; Hartley, John G.; Moreau, Wayne M.; Angelopoulos, Marie; Magg, Christopher; Lawliss, Mark

2000-07-01

Recently, there is significant interest in using CA resist for electron beam (E-beam) applications including mask making, direct write, and projection printing. CA resists provide superior lithographic performance in comparison to traditional non-CA E-beam resist in particular high contrast, resolution, and sensitivity. However, most of the commercially available CA resist have the concern of airborne base contaminants and sensitivity to PAB and/or PEB temperatures. In this presentation, we will discuss a new improved ketal resists system referred to as KRS-XE which exhibits excellent lithography, is robust toward airborne base, compatible with 0.263N TMAH aqueous developer and exhibits excellent lithography, is robust toward airborne base, compatible with 0.263N TMAH aqueous developer and exhibits a large PAB/PEB latitude. With the combination of a high performance mask making E-beam exposure tool, high kV shaped beam system EL4+ and the KRS-XE resist, we have printed 75nm lines/space feature with excellent profile control at a dose of 13(mu) C/cm2 at 75kV. The shaped beam vector scan system used here provides a unique property in resolving small features in lithography and throughput. Overhead in EL4+$ limits the systems ability to fully exploit the sensitivity of the new resist for throughput. The EL5 system has sufficiently low overhead that it is projected to print a 4X, 16G DRAM mask with OPC in under 3 hours with the CA resist. We will discuss the throughput advantages of the next generation EL5 system over the existing EL4+.

Two-Dimensional Optoelectronic Graphene Nanoprobes for Neural Nerwork

NASA Astrophysics Data System (ADS)

Hong, Tu; Kitko, Kristina; Wang, Rui; Zhang, Qi; Xu, Yaqiong

2014-03-01

Brain is the most complex network created by nature, with billions of neurons connected by trillions of synapses through sophisticated wiring patterns and countless modulatory mechanisms. Current methods to study the neuronal process, either by electrophysiology or optical imaging, have significant limitations on throughput and sensitivity. Here, we use graphene, a monolayer of carbon atoms, as a two-dimensional nanoprobe for neural network. Scanning photocurrent measurement is applied to detect the local integration of electrical and chemical signals in mammalian neurons. Such interface between nanoscale electronic device and biological system provides not only ultra-high sensitivity, but also sub-millisecond temporal resolution, owing to the high carrier mobility of graphene.

Upgrading a high-throughput spectrometer for high-frequency (<400 kHz) measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishizawa, T., E-mail: nishizawa@wisc.edu; Nornberg, M. D.; Den Hartog, D. J.

2016-11-15

The upgraded spectrometer used for charge exchange recombination spectroscopy on the Madison Symmetric Torus resolves emission fluctuations up to 400 kHz. The transimpedance amplifier’s cutoff frequency was increased based upon simulations comparing the change in the measured photon counts for time-dynamic signals. We modeled each signal-processing stage of the diagnostic and scanned the filtering frequency to quantify the uncertainty in the photon counting rate. This modeling showed that uncertainties can be calculated based on assuming each amplification stage is a Poisson process and by calibrating the photon counting rate with a DC light source to address additional variation.

Upgrading a high-throughput spectrometer for high-frequency (<400 kHz) measurements

NASA Astrophysics Data System (ADS)

Nishizawa, T.; Nornberg, M. D.; Den Hartog, D. J.; Craig, D.

2016-11-01

The upgraded spectrometer used for charge exchange recombination spectroscopy on the Madison Symmetric Torus resolves emission fluctuations up to 400 kHz. The transimpedance amplifier's cutoff frequency was increased based upon simulations comparing the change in the measured photon counts for time-dynamic signals. We modeled each signal-processing stage of the diagnostic and scanned the filtering frequency to quantify the uncertainty in the photon counting rate. This modeling showed that uncertainties can be calculated based on assuming each amplification stage is a Poisson process and by calibrating the photon counting rate with a DC light source to address additional variation.

TeraSCREEN: multi-frequency multi-mode Terahertz screening for border checks

NASA Astrophysics Data System (ADS)

Alexander, Naomi E.; Alderman, Byron; Allona, Fernando; Frijlink, Peter; Gonzalo, Ramón; Hägelen, Manfred; Ibáñez, Asier; Krozer, Viktor; Langford, Marian L.; Limiti, Ernesto; Platt, Duncan; Schikora, Marek; Wang, Hui; Weber, Marc Andree

2014-06-01

The challenge for any security screening system is to identify potentially harmful objects such as weapons and explosives concealed under clothing. Classical border and security checkpoints are no longer capable of fulfilling the demands of today's ever growing security requirements, especially with respect to the high throughput generally required which entails a high detection rate of threat material and a low false alarm rate. TeraSCREEN proposes to develop an innovative concept of multi-frequency multi-mode Terahertz and millimeter-wave detection with new automatic detection and classification functionalities. The system developed will demonstrate, at a live control point, the safe automatic detection and classification of objects concealed under clothing, whilst respecting privacy and increasing current throughput rates. This innovative screening system will combine multi-frequency, multi-mode images taken by passive and active subsystems which will scan the subjects and obtain complementary spatial and spectral information, thus allowing for automatic threat recognition. The TeraSCREEN project, which will run from 2013 to 2016, has received funding from the European Union's Seventh Framework Programme under the Security Call. This paper will describe the project objectives and approach.

Ultrafast dark-field surface inspection with hybrid-dispersion laser scanning

NASA Astrophysics Data System (ADS)

Yazaki, Akio; Kim, Chanju; Chan, Jacky; Mahjoubfar, Ata; Goda, Keisuke; Watanabe, Masahiro; Jalali, Bahram

2014-06-01

High-speed surface inspection plays an important role in industrial manufacturing, safety monitoring, and quality control. It is desirable to go beyond the speed limitation of current technologies for reducing manufacturing costs and opening a new window onto a class of applications that require high-throughput sensing. Here, we report a high-speed dark-field surface inspector for detection of micrometer-sized surface defects that can travel at a record high speed as high as a few kilometers per second. This method is based on a modified time-stretch microscope that illuminates temporally and spatially dispersed laser pulses on the surface of a fast-moving object and detects scattered light from defects on the surface with a sensitive photodetector in a dark-field configuration. The inspector's ability to perform ultrafast dark-field surface inspection enables real-time identification of difficult-to-detect features on weakly reflecting surfaces and hence renders the method much more practical than in the previously demonstrated bright-field configuration. Consequently, our inspector provides nearly 1000 times higher scanning speed than conventional inspectors. To show our method's broad utility, we demonstrate real-time inspection of the surface of various objects (a non-reflective black film, transparent flexible film, and reflective hard disk) for detection of 10 μm or smaller defects on a moving target at 20 m/s within a scan width of 25 mm at a scan rate of 90.9 MHz. Our method holds promise for improving the cost and performance of organic light-emitting diode displays for next-generation smart phones, lithium-ion batteries for green electronics, and high-efficiency solar cells.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

2016-06-13

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

PubMed

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons.

PubMed

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3-4 and 8-9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

PubMed Central

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M.; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X.; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner. PMID:26052271

Reflective optical imaging system

DOEpatents

Shafer, David R.

2000-01-01

An optical system compatible with short wavelength (extreme ultraviolet) radiation comprising four reflective elements for projecting a mask image onto a substrate. The four optical elements are characterized in order from object to image as convex, concave, convex and concave mirrors. The optical system is particularly suited for step and scan lithography methods. The invention increases the slit dimensions associated with ringfield scanning optics, improves wafer throughput and allows higher semiconductor device density.

Reflective optical imaging method and circuit

DOEpatents

Shafer, David R.

2001-01-01

An optical system compatible with short wavelength (extreme ultraviolet) radiation comprising four reflective elements for projecting a mask image onto a substrate. The four optical elements are characterized in order from object to image as convex, concave, convex and concave mirrors. The optical system is particularly suited for step and scan lithography methods. The invention increases the slit dimensions associated with ringfield scanning optics, improves wafer throughput and allows higher semiconductor device density.

Gold Nanoparticle Mediated Laser Transfection for Efficient siRNA Mediated Gene Knock Down

PubMed Central

Heinemann, Dag; Schomaker, Markus; Kalies, Stefan; Schieck, Maximilian; Carlson, Regina; Escobar, Hugo Murua; Ripken, Tammo; Meyer, Heiko; Heisterkamp, Alexander

2013-01-01

Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types. PMID:23536802

Scanning fluorescence detector for high-throughput DNA genotyping

NASA Astrophysics Data System (ADS)

Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

1996-04-01

A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA samples X polymorphic markers) at a total cost of

Development of critical dimension measurement scanning electron microscope for ULSI (S-8000 series)

NASA Astrophysics Data System (ADS)

Ezumi, Makoto; Otaka, Tadashi; Mori, Hiroyoshi; Todokoro, Hideo; Ose, Yoichi

1996-05-01

The semiconductor industry is moving from half-micron to quarter-micron design rules. To support this evolution, Hitachi has developed a new critical dimension measurement scanning electron microscope (CD-SEM), the model S-8800 series, for quality control of quarter- micron process lines. The new CD-SEM provides detailed examination of process conditions with 5 nm resolution and 5 nm repeatability (3 sigma) at accelerating voltage 800 V using secondary electron imaging. In addition, a newly developed load-lock system has a capability of achieving a high sample throughput of 20 wafers/hour (5 point measurements per wafer) under continuous operation. To support user friendliness, the system incorporates a graphical user interface (GUI), an automated pattern recognition system which helps locating measurement points, both manual and semi-automated operation, and user-programmable operating parameters.

Development of a Whole Slide Imaging System on Smartphones and Evaluation With Frozen Section Samples

PubMed Central

Jiang, Liren

2017-01-01

Background The aim was to develop scalable Whole Slide Imaging (sWSI), a WSI system based on mainstream smartphones coupled with regular optical microscopes. This ultra-low-cost solution should offer diagnostic-ready imaging quality on par with standalone scanners, supporting both oil and dry objective lenses of different magnifications, and reasonably high throughput. These performance metrics should be evaluated by expert pathologists and match those of high-end scanners. Objective The aim was to develop scalable Whole Slide Imaging (sWSI), a whole slide imaging system based on smartphones coupled with optical microscopes. This ultra-low-cost solution should offer diagnostic-ready imaging quality on par with standalone scanners, supporting both oil and dry object lens of different magnification. All performance metrics should be evaluated by expert pathologists and match those of high-end scanners. Methods In the sWSI design, the digitization process is split asynchronously between light-weight clients on smartphones and powerful cloud servers. The client apps automatically capture FoVs at up to 12-megapixel resolution and process them in real-time to track the operation of users, then give instant feedback of guidance. The servers first restitch each pair of FoVs, then automatically correct the unknown nonlinear distortion introduced by the lens of the smartphone on the fly, based on pair-wise stitching, before finally combining all FoVs into one gigapixel VS for each scan. These VSs can be viewed using Internet browsers anywhere. In the evaluation experiment, 100 frozen section slides from patients randomly selected among in-patients of the participating hospital were scanned by both a high-end Leica scanner and sWSI. All VSs were examined by senior pathologists whose diagnoses were compared against those made using optical microscopy as ground truth to evaluate the image quality. Results The sWSI system is developed for both Android and iPhone smartphones and is currently being offered to the public. The image quality is reliable and throughput is approximately 1 FoV per second, yielding a 15-by-15 mm slide under 20X object lens in approximately 30-35 minutes, with little training required for the operator. The expected cost for setup is approximately US $100 and scanning each slide costs between US $1 and $10, making sWSI highly cost-effective for infrequent or low-throughput usage. In the clinical evaluation of sample-wise diagnostic reliability, average accuracy scores achieved by sWSI-scan-based diagnoses were as follows: 0.78 for breast, 0.88 for uterine corpus, 0.68 for thyroid, and 0.50 for lung samples. The respective low-sensitivity rates were 0.05, 0.05, 0.13, and 0.25 while the respective low-specificity rates were 0.18, 0.08, 0.20, and 0.25. The participating pathologists agreed that the overall quality of sWSI was generally on par with that produced by high-end scanners, and did not affect diagnosis in most cases. Pathologists confirmed that sWSI is reliable enough for standard diagnoses of most tissue categories, while it can be used for quick screening of difficult cases. Conclusions As an ultra-low-cost alternative to whole slide scanners, diagnosis-ready VS quality and robustness for commercial usage is achieved in the sWSI solution. Operated on main-stream smartphones installed on normal optical microscopes, sWSI readily offers affordable and reliable WSI to resource-limited or infrequent clinical users. PMID:28916508

Simultaneous multimodal ophthalmic imaging using swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography

PubMed Central

Malone, Joseph D.; El-Haddad, Mohamed T.; Bozic, Ivan; Tye, Logan A.; Majeau, Lucas; Godbout, Nicolas; Rollins, Andrew M.; Boudoux, Caroline; Joos, Karen M.; Patel, Shriji N.; Tao, Yuankai K.

2016-01-01

Scanning laser ophthalmoscopy (SLO) benefits diagnostic imaging and therapeutic guidance by allowing for high-speed en face imaging of retinal structures. When combined with optical coherence tomography (OCT), SLO enables real-time aiming and retinal tracking and provides complementary information for post-acquisition volumetric co-registration, bulk motion compensation, and averaging. However, multimodality SLO-OCT systems generally require dedicated light sources, scanners, relay optics, detectors, and additional digitization and synchronization electronics, which increase system complexity. Here, we present a multimodal ophthalmic imaging system using swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography (SS-SESLO-OCT) for in vivo human retinal imaging. SESLO reduces the complexity of en face imaging systems by multiplexing spatial positions as a function of wavelength. SESLO image quality benefited from single-mode illumination and multimode collection through a prototype double-clad fiber coupler, which optimized scattered light throughput and reduce speckle contrast while maintaining lateral resolution. Using a shared 1060 nm swept-source, shared scanner and imaging optics, and a shared dual-channel high-speed digitizer, we acquired inherently co-registered en face retinal images and OCT cross-sections simultaneously at 200 frames-per-second. PMID:28101411

Parallelized multi–graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy

PubMed Central

Tankam, Patrice; Santhanam, Anand P.; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P.

2014-01-01

Abstract. Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing. PMID:24695868

Parallelized multi-graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy.

PubMed

Tankam, Patrice; Santhanam, Anand P; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P

2014-07-01

Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing.

Line-edge quality optimization of electron beam resist for high-throughput character projection exposure utilizing atomic force microscope analysis

NASA Astrophysics Data System (ADS)

Ikeno, Rimon; Mita, Yoshio; Asada, Kunihiro

2017-04-01

High-throughput electron-beam lithography (EBL) by character projection (CP) and variable-shaped beam (VSB) methods is a promising technique for low-to-medium volume device fabrication with regularly arranged layouts, such as standard-cell logics and memory arrays. However, non-VLSI applications like MEMS and MOEMS may not fully utilize the benefits of CP method due to their wide variety of layout figures including curved and oblique edges. In addition, the stepwise shapes that appear on such irregular edges by VSB exposure often result in intolerable edge roughness, which may degrade performances of the fabricated devices. In our former study, we proposed a general EBL methodology for such applications utilizing a combination of CP and VSB methods, and demonstrated its capabilities in electron beam (EB) shot reduction and edge-quality improvement by using a leading-edge EB exposure tool, ADVANTEST F7000S-VD02, and high-resolution Hydrogen Silsesquioxane resist. Both scanning electron microscope and atomic force microscope observations were used to analyze quality of the resist edge profiles to determine the influence of the control parameters used in the exposure-data preparation process. In this study, we carried out detailed analysis of the captured edge profiles utilizing Fourier analysis, and successfully distinguish the systematic undulation by the exposed CP character profiles from random roughness components. Such capability of precise edge-roughness analysis is useful to our EBL methodology to maintain both the line-edge quality and the exposure throughput by optimizing the control parameters in the layout data conversion.

High-throughput label-free detection of aggregate platelets with optofluidic time-stretch microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jiang, Yiyue; Lei, Cheng; Yasumoto, Atsushi; Ito, Takuro; Guo, Baoshan; Kobayashi, Hirofumi; Ozeki, Yasuyuki; Yatomi, Yutaka; Goda, Keisuke

2017-02-01

According to WHO, approximately 10 million new cases of thrombotic disorders are diagnosed worldwide every year. In the U.S. and Europe, their related diseases kill more people than those from AIDS, prostate cancer, breast cancer and motor vehicle accidents combined. Although thrombotic disorders, especially arterial ones, mainly result from enhanced platelet aggregability in the vascular system, visual detection of platelet aggregates in vivo is not employed in clinical settings. Here we present a high-throughput label-free platelet aggregate detection method, aiming at the diagnosis and monitoring of thrombotic disorders in clinical settings. With optofluidic time-stretch microscopy with a spatial resolution of 780 nm and an ultrahigh linear scanning rate of 75 MHz, it is capable of detecting aggregated platelets in lysed blood which flows through a hydrodynamic-focusing microfluidic device at a high throughput of 10,000 particles/s. With digital image processing and statistical analysis, we are able to distinguish them from single platelets and other blood cells via morphological features. The detection results are compared with results of fluorescence-based detection (which is slow and inaccurate, but established). Our results indicate that the method holds promise for real-time, low-cost, label-free, and minimally invasive detection of platelet aggregates, which is potentially applicable to detection of platelet aggregates in vivo and to the diagnosis and monitoring of thrombotic disorders in clinical settings. This technique, if introduced clinically, may provide important clinical information in addition to that obtained by conventional techniques for thrombotic disorder diagnosis, including ex vivo platelet aggregation tests.

High throughput film dosimetry in homogeneous and heterogeneous media for a small animal irradiator

PubMed Central

Wack, L.; Ngwa, W.; Tryggestad, E.; Tsiamas, P.; Berbeco, R.; Ng, S.K.; Hesser, J.

2013-01-01

Purpose We have established a high-throughput Gafchromic film dosimetry protocol for narrow kilo-voltage beams in homogeneous and heterogeneous media for small-animal radiotherapy applications. The kV beam characterization is based on extensive Gafchromic film dosimetry data acquired in homogeneous and heterogeneous media. An empirical model is used for parameterization of depth and off-axis dependence of measured data. Methods We have modified previously published methods of film dosimetry to suit the specific tasks of the study. Unlike film protocols used in previous studies, our protocol employs simultaneous multichannel scanning and analysis of up to nine Gafchromic films per scan. A scanner and background correction were implemented to improve accuracy of the measurements. Measurements were taken in homogeneous and inhomogeneous phantoms at 220 kVp and a field size of 5 × 5 mm2. The results were compared against Monte Carlo simulations. Results Dose differences caused by variations in background signal were effectively removed by the corrections applied. Measurements in homogeneous phantoms were used to empirically characterize beam data in homogeneous and heterogeneous media. Film measurements in inhomogeneous phantoms and their empirical parameterization differed by about 2%–3%. The model differed from MC by about 1% (water, lung) to 7% (bone). Good agreement was found for measured and modelled off-axis ratios. Conclusions EBT2 films are a valuable tool for characterization of narrow kV beams, though care must be taken to eliminate disturbances caused by varying background signals. The usefulness of the empirical beam model in interpretation and parameterization of film data was demonstrated. PMID:23510532

Towards machine learned quality control: A benchmark for sharpness quantification in digital pathology.

PubMed

Campanella, Gabriele; Rajanna, Arjun R; Corsale, Lorraine; Schüffler, Peter J; Yagi, Yukako; Fuchs, Thomas J

2018-04-01

Pathology is on the verge of a profound change from an analog and qualitative to a digital and quantitative discipline. This change is mostly driven by the high-throughput scanning of microscope slides in modern pathology departments, reaching tens of thousands of digital slides per month. The resulting vast digital archives form the basis of clinical use in digital pathology and allow large scale machine learning in computational pathology. One of the most crucial bottlenecks of high-throughput scanning is quality control (QC). Currently, digital slides are screened manually to detected out-of-focus regions, to compensate for the limitations of scanner software. We present a solution to this problem by introducing a benchmark dataset for blur detection, an in-depth comparison of state-of-the art sharpness descriptors and their prediction performance within a random forest framework. Furthermore, we show that convolution neural networks, like residual networks, can be used to train blur detectors from scratch. We thoroughly evaluate the accuracy of feature based and deep learning based approaches for sharpness classification (99.74% accuracy) and regression (MSE 0.004) and additionally compare them to domain experts in a comprehensive human perception study. Our pipeline outputs spacial heatmaps enabling to quantify and localize blurred areas on a slide. Finally, we tested the proposed framework in the clinical setting and demonstrate superior performance over the state-of-the-art QC pipeline comprising commercial software and human expert inspection by reducing the error rate from 17% to 4.7%. Copyright © 2017. Published by Elsevier Ltd.

High-speed spectral nanocytology for early cancer screening

PubMed Central

Subramanian, Hariharan; Maneval, Charles D.; White, Craig A.; Levenson, Richard M.; Backman, Vadim

2013-01-01

Abstract. High-throughput partial wave spectroscopy (HTPWS) is introduced as a high-speed spectral nanocytology technique that utilizes the field effect of carcinogenesis to perform minimally invasive cancer screening on at-risk populations. HTPWS uses fully automated hardware and an acousto-optic tunable filter to scan slides at low magnification, to select cells, and to rapidly acquire spectra at each spatial pixel in a cell between 450 and 700 nm, completing measurements of 30 cells in 40 min. Statistical quantitative analysis on the size and density of intracellular nanostructures extracted from the spectra at each pixel in a cell yields the diagnostic biomarker, disorder strength (Ld). Linear correlation between Ld and the length scale of nanostructures was measured in phantoms with R2=0.93. Diagnostic sensitivity was demonstrated by measuring significantly higher Ld from a human colon cancer cell line (HT29 control vector) than a less aggressive variant (epidermal growth factor receptor knockdown). Clinical diagnostic performance for lung cancer screening was tested on 23 patients, yielding a significant difference in Ld between smokers and cancer patients, p=0.02 and effect size=1.00. The high-throughput performance, nanoscale sensitivity, and diagnostic sensitivity make HTPWS a potentially clinically relevant modality for risk stratification of the large populations at risk of developing cancer. PMID:24193949

Interleaved diffusion-weighted EPI improved by adaptive partial-Fourier and multi-band multiplexed sensitivity-encoding reconstruction

PubMed Central

Chang, Hing-Chiu; Guhaniyogi, Shayan; Chen, Nan-kuei

2014-01-01

Purpose We report a series of techniques to reliably eliminate artifacts in interleaved echo-planar imaging (EPI) based diffusion weighted imaging (DWI). Methods First, we integrate the previously reported multiplexed sensitivity encoding (MUSE) algorithm with a new adaptive Homodyne partial-Fourier reconstruction algorithm, so that images reconstructed from interleaved partial-Fourier DWI data are free from artifacts even in the presence of either a) motion-induced k-space energy peak displacement, or b) susceptibility field gradient induced fast phase changes. Second, we generalize the previously reported single-band MUSE framework to multi-band MUSE, so that both through-plane and in-plane aliasing artifacts in multi-band multi-shot interleaved DWI data can be effectively eliminated. Results The new adaptive Homodyne-MUSE reconstruction algorithm reliably produces high-quality and high-resolution DWI, eliminating residual artifacts in images reconstructed with previously reported methods. Furthermore, the generalized MUSE algorithm is compatible with multi-band and high-throughput DWI. Conclusion The integration of the multi-band and adaptive Homodyne-MUSE algorithms significantly improves the spatial-resolution, image quality, and scan throughput of interleaved DWI. We expect that the reported reconstruction framework will play an important role in enabling high-resolution DWI for both neuroscience research and clinical uses. PMID:24925000

Vision-based Nano Robotic System for High-throughput Non-embedded Cell Cutting

NASA Astrophysics Data System (ADS)

Shang, Wanfeng; Lu, Haojian; Wan, Wenfeng; Fukuda, Toshio; Shen, Yajing

2016-03-01

Cell cutting is a significant task in biology study, but the highly productive non-embedded cell cutting is still a big challenge for current techniques. This paper proposes a vision-based nano robotic system and then realizes automatic non-embedded cell cutting with this system. First, the nano robotic system is developed and integrated with a nanoknife inside an environmental scanning electron microscopy (ESEM). Then, the positions of the nanoknife and the single cell are recognized, and the distance between them is calculated dynamically based on image processing. To guarantee the positioning accuracy and the working efficiency, we propose a distance-regulated speed adapting strategy, in which the moving speed is adjusted intelligently based on the distance between the nanoknife and the target cell. The results indicate that the automatic non-embedded cutting is able to be achieved within 1-2 mins with low invasion benefiting from the high precise nanorobot system and the sharp edge of nanoknife. This research paves a way for the high-throughput cell cutting at cell’s natural condition, which is expected to make significant impact on the biology studies, especially for the in-situ analysis at cellular and subcellular scale, such as cell interaction investigation, neural signal transduction and low invasive cell surgery.

High-throughput, high-resolution X-ray phase contrast tomographic microscopy for visualisation of soft tissue

NASA Astrophysics Data System (ADS)

McDonald, S. A.; Marone, F.; Hintermüller, C.; Bensadoun, J.-C.; Aebischer, P.; Stampanoni, M.

2009-09-01

The use of conventional absorption based X-ray microtomography can become limited for samples showing only very weak absorption contrast. However, a wide range of samples studied in biology and materials science can produce significant phase shifts of the X-ray beam, and thus the use of the phase signal can provide substantially increased contrast and therefore new and otherwise inaccessible information. The application of two approaches for high-throughput, high-resolution X-ray phase contrast tomography, both available on the TOMCAT beamline of the SLS, is illustrated. Differential Phase Contrast (DPC) imaging uses a grating interferometer and a phase-stepping technique. It has been integrated into the beamline environment on TOMCAT in terms of the fast acquisition and reconstruction of data and the availability to scan samples within an aqueous environment. The second phase contrast approach is a modified transfer of intensity approach that can yield the 3D distribution of the phase (refractive index) of a weakly absorbing object from a single tomographic dataset. These methods are being used for the evaluation of cell integrity in 3D, with the specific aim of following and analyzing progressive cell degeneration to increase knowledge of the mechanistic events of neurodegenerative disorders such as Parkinson's disease.

CA resist with high sensitivity and sub-100-nm resolution for advanced mask and device making

NASA Astrophysics Data System (ADS)

Kwong, Ranee W.; Huang, Wu-Song; Hartley, John G.; Moreau, Wayne M.; Robinson, Christopher F.; Angelopoulos, Marie; Magg, Christopher; Lawliss, Mark

2000-07-01

Recently, there is significant interest in using CA resists for electron beam (E-Beam) applications including mask making, direct write, and projection printing. CA resists provide superior lithographic performance in comparison to traditional non CA E-beam resists in particular high contrast, resolution, and sensitivity. However, most of the commercially available CA resists have the concern of airborne base contaminants and sensitivity to PAB and/or PEB temperatures. In this presentation, we will discuss a new improved ketal resist system referred to as KRS-XE which exhibits excellent lithography, is robust toward airborne base, compatible with 0.263 N TMAH aqueous developer and exhibits a large PAB/PEB latitude. With the combination of a high performance mask making E-beam exposure tool, high kV (75 kV) shaped beam system EL4+ and the KRS-XE resist, we have printed 75 nm lines/space features with excellent profile control at a dose of 13 (mu) C/cm2 at 75 kV. The shaped beam vector scan system used here provides an unique property in resolving small features in lithography and throughput. Overhead in EL4+ limits the systems ability to fully exploit the sensitivity of the new resist for throughput. The EL5 system, currently in the build phase, has sufficiently low overhead that it is projected to print a 4X, 16G, DRAM mask with OPC in under 3 hours with the CA resist. We will discuss the throughput advantages of the next generation EL5 system over the existing EL4+. In addition we will show the resolution of KRS-XE down to 70 nm using the PREVAIL projection printing system.

Automating PACS quality control with the Vanderbilt image processing enterprise resource

NASA Astrophysics Data System (ADS)

Esparza, Michael L.; Welch, E. Brian; Landman, Bennett A.

2012-02-01

Precise image acquisition is an integral part of modern patient care and medical imaging research. Periodic quality control using standardized protocols and phantoms ensures that scanners are operating according to specifications, yet such procedures do not ensure that individual datasets are free from corruption; for example due to patient motion, transient interference, or physiological variability. If unacceptable artifacts are noticed during scanning, a technologist can repeat a procedure. Yet, substantial delays may be incurred if a problematic scan is not noticed until a radiologist reads the scans or an automated algorithm fails. Given scores of slices in typical three-dimensional scans and widevariety of potential use cases, a technologist cannot practically be expected inspect all images. In large-scale research, automated pipeline systems have had great success in achieving high throughput. However, clinical and institutional workflows are largely based on DICOM and PACS technologies; these systems are not readily compatible with research systems due to security and privacy restrictions. Hence, quantitative quality control has been relegated to individual investigators and too often neglected. Herein, we propose a scalable system, the Vanderbilt Image Processing Enterprise Resource (VIPER) to integrate modular quality control and image analysis routines with a standard PACS configuration. This server unifies image processing routines across an institutional level and provides a simple interface so that investigators can collaborate to deploy new analysis technologies. VIPER integrates with high performance computing environments has successfully analyzed all standard scans from our institutional research center over the course of the last 18 months.

Strategic and Operational Plan for Integrating Transcriptomics ...

EPA Pesticide Factsheets

Plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT; the details are in the attached slide presentation presentation on plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT, given at the OECD meeting on June 23, 2016

High-Throughput Experimental Approach Capabilities | Materials Science |

Science.gov Websites

NREL High-Throughput Experimental Approach Capabilities High-Throughput Experimental Approach by yellow and is for materials in the upper right sector. NREL's high-throughput experimental ,Te) and oxysulfide sputtering Combi-5: Nitrides and oxynitride sputtering We also have several non

Using Power Spectrum Analysis to Evaluate 18O-Water Labeling Data Acquired from Low Resolution Mass Spectrometers

PubMed Central

Sadygov, Rovshan G.; Zhao, Yingxin; Haidacher, Sigmund J.; Starkey, Jonathan M.; Tilton, Ronald G.; Denner, Larry

2010-01-01

We describe a method for ratio estimations in 18O-water labeling experiments acquired from low resolution isotopically resolved data. The method is implemented in a software package specifically designed for use in experiments making use of zoom-scan mode data acquisition. Zoom-scan mode data allows commonly used ion trap mass spectrometers to attain isotopic resolution, which make them amenable to use in labeling schemes such as 18O-water labeling, but algorithms and software developed for high resolution instruments may not be appropriate for the lower resolution data acquired in zoom-scan mode. The use of power spectrum analysis is proposed as a general approach which may be uniquely suited to these data types. The software implementation uses power spectrum to remove high-frequency noise, and band-filter contributions from co-eluting species of differing charge states. From the elemental composition of a peptide sequence we generate theoretical isotope envelopes of heavy-light peptide pairs in five different ratios; these theoretical envelopes are correlated with the filtered experimental zoom scans. To automate peptide quantification in high-throughput experiments, we have implemented our approach in a computer program, MassXplorer. We demonstrate the application of MassXplorer to two model mixtures of known proteins, and to a complex mixture of mouse kidney cortical extract. Comparison with another algorithm for ratio estimations demonstrates the increased precision and automation of MassXplorer. PMID:20568695

High-throughput physical mapping of chromosomes using automated in situ hybridization.

PubMed

George, Phillip; Sharakhova, Maria V; Sharakhov, Igor V

2012-06-28

Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila, allows the user to visualize more details on chromosomes than the regular squashing technique. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

Actinic inspection of EUV reticles with arbitrary pattern design

NASA Astrophysics Data System (ADS)

Mochi, Iacopo; Helfenstein, Patrick; Rajeev, Rajendran; Fernandez, Sara; Kazazis, Dimitrios; Yoshitake, Shusuke; Ekinci, Yasin

2017-10-01

The re ective-mode EUV mask scanning lensless imaging microscope (RESCAN) is being developed to provide actinic mask inspection capabilities for defects and patterns with high resolution and high throughput, for 7 nm node and beyond. Here we, will report on our progress and present the results on programmed defect detection on random, logic-like patterns. The defects we investigated range from 200 nm to 50 nm size on the mask. We demonstrated the ability of RESCAN to detect these defects in die-to-die and die-to-database mode with a high signal to noise ratio. We also describe future plans for the upgrades to increase the resolution, the sensitivity, and the inspection speed of the demo tool.

TH-CD-209-12: Spatial Mapping of Scanned Proton Biologic Effect Using the High-Throughput Technique, Continued

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerr, M; Bronk, L; Guan, F

Purpose: To investigate the biologic effects of scanned protons by evenly sampling dose-averaged LET (LETd) values. Methods: Our previous high-throughput clonogenic study demonstrated a distinct relationship between RBE and LETd. However, our initial experimental design resulted in over-sampling the low LETd values in the plateau region of the Bragg curve while under-sampling in the region proximal to the Bragg peak as well as the high LETd values in the distal edge of the Bragg curve. To further examine the relationship between RBE and LETd, we refined the experimental design to more evenly sample proton LETd values from 1 to 20more » keV/µm by optimizing the thicknesses of the irradiation jig steps. We used the clonogenic survival as the biological endpoint for the H460 lung cancer cell line cultured in 96-well plates (12 columns by 8 rows). In the irradiation, the 8 wells in each column received a uniform dose-LETd pair. The dose-LETd pairs of the 12 different columns were sampled along the Bragg curve of 81.4 MeV scanned protons. Five peak dose levels from 1.5 Gy to 7.5 Gy were delivered with an increment of 1.5 Gy in the preliminary test. Two 96-well plates were irradiated simultaneously to decrease the statistical uncertainties. Results: In the proximal region, for LETd = 5 keV/µm and 8 keV/µm, we did not observe any distinct differential biologic effects between the survival curves. At the Bragg peak (LETd = 9.5 keV/µm) and in the distal edge, irradiation with increasing LET values resulted in decreasing cell survival. Conclusion: The survival curves from the new experimental design support our previous findings that below 10 keV/µm, the LET effect in cell kill is obscured, but above 10 keV/µm, the biologic effects increase with LETd. Funding Support: U19 CA021239-35 and R21 CA187484-01.« less

Immobilization of human papillomavirus DNA probe for surface plasmon resonance imaging

NASA Astrophysics Data System (ADS)

Chong, Xinyuan; Ji, Yanhong; Ma, Suihua; Liu, Le; Liu, Zhiyi; Li, Yao; He, Yonghong; Guo, Jihua

2009-08-01

Human papillomavirus (HPV) is a kind of double-stranded DNA virus whose subspecies have diversity. Near 40 kinds of subspecies can invade reproductive organ and cause some high risk disease, such as cervical carcinoma. In order to detect the type of the subspecies of the HPV DNA, we used the parallel scan spectral surface plasmon resonance (SPR) imaging technique, which is a novel type of two- dimensional bio-sensing method based on surface plasmon resonance and is proposed in our previous work, to study the immobilization of the HPV DNA probes on the gold film. In the experiment, four kinds of the subspecies of the HPV DNA (HPV16, HPV18, HPV31, HPV58) probes are fixed on one gold film, and incubate in the constant temperature condition to get a HPV DNA probe microarray. We use the parallel scan spectral SPR imaging system to detect the reflective indices of the HPV DNA subspecies probes. The benefits of this new approach are high sensitive, label-free, strong specificity and high through-put.

Fluorescence lifetime microscopy with a time- and space-resolved single-photon counting detector

PubMed Central

Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky, P.; Pinaud, F. F.; Millaud, J.E.; Weiss, S.

2017-01-01

We have recently developed a wide-field photon-counting detector (the H33D detector) having high-temporal and high-spatial resolutions and capable of recording up to 500,000 photons per sec. Its temporal performance has been previously characterized using solutions of fluorescent materials with different lifetimes, and its spatial resolution using sub-diffraction objects (beads and quantum dots). Here we show its application to fluorescence lifetime imaging of live cells and compare its performance to a scanning confocal TCSPC approach. With the expected improvements in photocathode sensitivity and increase in detector throughput, this technology appears as a promising alternative to the current lifetime imaging solutions. PMID:29449756

Three-dimensional nanoscale imaging by plasmonic Brownian microscopy

NASA Astrophysics Data System (ADS)

Labno, Anna; Gladden, Christopher; Kim, Jeongmin; Lu, Dylan; Yin, Xiaobo; Wang, Yuan; Liu, Zhaowei; Zhang, Xiang

2017-12-01

Three-dimensional (3D) imaging at the nanoscale is a key to understanding of nanomaterials and complex systems. While scanning probe microscopy (SPM) has been the workhorse of nanoscale metrology, its slow scanning speed by a single probe tip can limit the application of SPM to wide-field imaging of 3D complex nanostructures. Both electron microscopy and optical tomography allow 3D imaging, but are limited to the use in vacuum environment due to electron scattering and to optical resolution in micron scales, respectively. Here we demonstrate plasmonic Brownian microscopy (PBM) as a way to improve the imaging speed of SPM. Unlike photonic force microscopy where a single trapped particle is used for a serial scanning, PBM utilizes a massive number of plasmonic nanoparticles (NPs) under Brownian diffusion in solution to scan in parallel around the unlabeled sample object. The motion of NPs under an evanescent field is three-dimensionally localized to reconstruct the super-resolution topology of 3D dielectric objects. Our method allows high throughput imaging of complex 3D structures over a large field of view, even with internal structures such as cavities that cannot be accessed by conventional mechanical tips in SPM.

StarScan: a web server for scanning small RNA targets from degradome sequencing data.

PubMed

Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2015-07-01

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-wide scans for loci under selection in humans

PubMed Central

2005-01-01

Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection. PMID:16004726

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Shuyu; Yu, Shifeng; Siedler, Michael

This study presented a power compensated MEMS differential scanning calorimeter (DSC) for protein stability characterization. In this microfabricated sensor, PDMS (Polydimethylsiloxane) and polyimide were used to construct the adiabatic chamber (1 μL) and temperature sensitive vanadium oxide was used as the thermistor material. A power compensation system was implemented to maintain the sample and reference at the same temperature. The resolution study and step response characterization indicated the high sensitivity (6 V/W) and low noise level (60 μk) of the device. The test with IgG1 antibody (mAb1) samples showed clear phase transitions and the data was confirmed to be reasonablemore » by comparing it with the results of commercial DSC’s test. Finally, this device used ~1uL sample amount and could complete the scanning process in 4 min, significantly increasing the throughput of the bimolecular thermodynamics study like drug formulation process.« less

Non-linear optical flow cytometry using a scanned, Bessel beam light-sheet.

PubMed

Collier, Bradley B; Awasthi, Samir; Lieu, Deborah K; Chan, James W

2015-05-29

Modern flow cytometry instruments have become vital tools for high-throughput analysis of single cells. However, as issues with the cellular labeling techniques often used in flow cytometry have become more of a concern, the development of label-free modalities for cellular analysis is increasingly desired. Non-linear optical phenomena (NLO) are of growing interest for label-free analysis because of the ability to measure the intrinsic optical response of biomolecules found in cells. We demonstrate that a light-sheet consisting of a scanned Bessel beam is an optimal excitation geometry for efficiently generating NLO signals in a microfluidic environment. The balance of photon density and cross-sectional area provided by the light-sheet allowed significantly larger two-photon fluorescence intensities to be measured in a model polystyrene microparticle system compared to measurements made using other excitation focal geometries, including a relaxed Gaussian excitation beam often used in conventional flow cytometers.

Spatially sculpted laser scissors for study of DNA damage and repair

NASA Astrophysics Data System (ADS)

Stephens, Jared; Mohanty, Samarendra K.; Genc, Suzanne; Kong, Xiangduo; Yokomori, Kyoko; Berns, Michael W.

2009-09-01

We present a simple and efficient method for controlled linear induction of DNA damage in live cells. By passing a pulsed laser beam through a cylindrical lens prior to expansion, an elongated elliptical beam profile is created with the ability to expose controlled linear patterns while keeping the beam and the sample stationary. The length and orientation of the beam at the sample plane were reliably controlled by an adjustable aperture and rotation of the cylindrical lens, respectively. Localized immunostaining by the DNA double strand break (DSB) markers phosphorylated H2AX (γH2AX) and Nbs1 in the nuclei of HeLa cells exposed to the ``line scissors'' was shown via confocal imaging. The line scissors method proved more efficient than the scanning mirror and scanning stage methods at induction of DNA DSB damage with the added benefit of having a greater potential for high throughput applications.

Magnetic high throughput screening system for the development of nano-sized molecularly imprinted polymers for controlled delivery of curcumin.

PubMed

Piletska, Elena V; Abd, Bashar H; Krakowiak, Agata S; Parmar, Anitha; Pink, Demi L; Wall, Katie S; Wharton, Luke; Moczko, Ewa; Whitcombe, Michael J; Karim, Kal; Piletsky, Sergey A

2015-05-07

Curcumin is a versatile anti-inflammatory and anti-cancer agent known for its low bioavailability, which could be improved by developing materials capable of binding and releasing drug in a controlled fashion. The present study describes the preparation of magnetic nano-sized Molecularly Imprinted Polymers (nanoMIPs) for the controlled delivery of curcumin and their high throughput characterisation using microtitre plates modified with magnetic inserts. NanoMIPs were synthesised using functional monomers chosen with the aid of molecular modelling. The rate of release of curcumin from five polymers was studied under aqueous conditions and was found to correlate well with the binding energies obtained computationally. The presence of specific monomers was shown to be significant in ensuring effective binding of curcumin and to the rate of release obtained. Characterisation of the polymer particles was carried out using dynamic light scattering (DLS) technique and scanning electron microscopy (SEM) in order to establish the relationship between irradiation time and particle size. The protocols optimised during this study could be used as a blueprint for the development of nanoMIPs capable of the controlled release of potentially any compound of interest.

Microarrays for the evaluation of cell-biomaterial surface interactions

NASA Astrophysics Data System (ADS)

Thissen, H.; Johnson, G.; McFarland, G.; Verbiest, B. C. H.; Gengenbach, T.; Voelcker, N. H.

2007-01-01

The evaluation of cell-material surface interactions is important for the design of novel biomaterials which are used in a variety of biomedical applications. While traditional in vitro test methods have routinely used samples of relatively large size, microarrays representing different biomaterials offer many advantages, including high throughput and reduced sample handling. Here, we describe the simultaneous cell-based testing of matrices of polymeric biomaterials, arrayed on glass slides with a low cell-attachment background coating. Arrays were constructed using a microarray robot at 6 fold redundancy with solid pins having a diameter of 375 μm. Printed solutions contained at least one monomer, an initiator and a bifunctional crosslinker. After subsequent UV polymerisation, the arrays were washed and characterised by X-ray photoelectron spectroscopy. Cell culture experiments were carried out over 24 hours using HeLa cells. After labelling with CellTracker ® Green for the final hour of incubation and subsequent fixation, the arrays were scanned. In addition, individual spots were also viewed by fluorescence microscopy. The evaluation of cell-surface interactions in high-throughput assays as demonstrated here is a key enabling technology for the effective development of future biomaterials.

Ultra-high frequency ultrasound biomicroscopy and high throughput cardiovascular phenotyping in a large scale mouse mutagenesis screen

NASA Astrophysics Data System (ADS)

Liu, Xiaoqin; Francis, Richard; Tobita, Kimimasa; Kim, Andy; Leatherbury, Linda; Lo, Cecilia W.

2013-02-01

Ultrasound biomicroscopy (UBM) is ideally suited for phenotyping fetal mice for congenital heart disease (CHD), as imaging can be carried out noninvasively to provide both hemodynamic and structural information essential for CHD diagnosis. Using the UBM (Vevo 2100; 40Hz) in conjunction with the clinical ultrasound system (Acuson Sequioa C512; 15Hz), we developed a two-step screening protocol to scan thousands fetuses derived from ENU mutagenized pedigrees. A wide spectrum of CHD was detected by the UBM, which were subsequently confirmed with follow-up necropsy and histopathology examination with episcopic fluorescence image capture. CHD observed included outflow anomalies, left/right heart obstructive lesions, septal/valvular defects and cardiac situs anomalies. Meanwhile, various extracardiac defects were found, such as polydactyly, craniofacial defects, exencephaly, omphalocele-cleft palate, most of which were associated with cardiac defects. Our analyses showed the UBM was better at assessing cardiac structure and blood flow profiles, while conventional ultrasound allowed higher throughput low-resolution screening. Our study showed the integration of conventional clinical ultrasound imaging with the UBM for fetal mouse cardiovascular phenotyping can maximize the detection and recovery of CHD mutants.

Automated Analysis of Barley Organs Using 3D Laser Scanning: An Approach for High Throughput Phenotyping

PubMed Central

Paulus, Stefan; Dupuis, Jan; Riedel, Sebastian; Kuhlmann, Heiner

2014-01-01

Due to the rise of laser scanning the 3D geometry of plant architecture is easy to acquire. Nevertheless, an automated interpretation and, finally, the segmentation into functional groups are still difficult to achieve. Two barley plants were scanned in a time course, and the organs were separated by applying a histogram-based classification algorithm. The leaf organs were represented by meshing algorithms, while the stem organs were parameterized by a least-squares cylinder approximation. We introduced surface feature histograms with an accuracy of 96% for the separation of the barley organs, leaf and stem. This enables growth monitoring in a time course for barley plants. Its reliability was demonstrated by a comparison with manually fitted parameters with a correlation R2 = 0.99 for the leaf area and R2 = 0.98 for the cumulated stem height. A proof of concept has been given for its applicability for the detection of water stress in barley, where the extension growth of an irrigated and a non-irrigated plant has been monitored. PMID:25029283

Cytotoxicity Test Based on Human Cells Labeled with Fluorescent Proteins: Fluorimetry, Photography, and Scanning for High-Throughput Assay.

PubMed

Kalinina, Marina A; Skvortsov, Dmitry A; Rubtsova, Maria P; Komarova, Ekaterina S; Dontsova, Olga A

2018-06-01

High- and medium-throughput assays are now routine methods for drug screening and toxicology investigations on mammalian cells. However, a simple and cost-effective analysis of cytotoxicity that can be carried out with commonly used laboratory equipment is still required. The developed cytotoxicity assays are based on human cell lines stably expressing eGFP, tdTomato, mCherry, or Katushka2S fluorescent proteins. Red fluorescent proteins exhibit a higher signal-to-noise ratio, due to less interference by medium autofluorescence, in comparison to green fluorescent protein. Measurements have been performed on a fluorescence scanner, a plate fluorimeter, and a camera photodocumentation system. For a 96-well plate assay, the sensitivity per well and the measurement duration were 250 cells and 15 min for the scanner, 500 cells and 2 min for the plate fluorimeter, and 1000 cells and less than 1 min for the camera detection. These sensitivities are similar to commonly used MTT (tetrazolium dye) assays. The used scanner and the camera had not been previously applied for cytotoxicity evaluation. An image processing scheme for the high-resolution scanner is proposed that significantly diminishes the number of control wells, even for a library containing fluorescent substances. The suggested cytotoxicity assay has been verified by measurements of the cytotoxicity of several well-known cytotoxic drugs and further applied to test a set of novel bacteriotoxic compounds in a medium-throughput format. The fluorescent signal of living cells is detected without disturbing them and adding any reagents, thus allowing to investigate time-dependent cytotoxicity effects on the same sample of cells. A fast, simple and cost-effective assay is suggested for cytotoxicity evaluation based on mammalian cells expressing fluorescent proteins and commonly used laboratory equipment.

3D imaging of optically cleared tissue using a simplified CLARITY method and on-chip microscopy

PubMed Central

Zhang, Yibo; Shin, Yoonjung; Sung, Kevin; Yang, Sam; Chen, Harrison; Wang, Hongda; Teng, Da; Rivenson, Yair; Kulkarni, Rajan P.; Ozcan, Aydogan

2017-01-01

High-throughput sectioning and optical imaging of tissue samples using traditional immunohistochemical techniques can be costly and inaccessible in resource-limited areas. We demonstrate three-dimensional (3D) imaging and phenotyping in optically transparent tissue using lens-free holographic on-chip microscopy as a low-cost, simple, and high-throughput alternative to conventional approaches. The tissue sample is passively cleared using a simplified CLARITY method and stained using 3,3′-diaminobenzidine to target cells of interest, enabling bright-field optical imaging and 3D sectioning of thick samples. The lens-free computational microscope uses pixel super-resolution and multi-height phase recovery algorithms to digitally refocus throughout the cleared tissue and obtain a 3D stack of complex-valued images of the sample, containing both phase and amplitude information. We optimized the tissue-clearing and imaging system by finding the optimal illumination wavelength, tissue thickness, sample preparation parameters, and the number of heights of the lens-free image acquisition and implemented a sparsity-based denoising algorithm to maximize the imaging volume and minimize the amount of the acquired data while also preserving the contrast-to-noise ratio of the reconstructed images. As a proof of concept, we achieved 3D imaging of neurons in a 200-μm-thick cleared mouse brain tissue over a wide field of view of 20.5 mm2. The lens-free microscope also achieved more than an order-of-magnitude reduction in raw data compared to a conventional scanning optical microscope imaging the same sample volume. Being low cost, simple, high-throughput, and data-efficient, we believe that this CLARITY-enabled computational tissue imaging technique could find numerous applications in biomedical diagnosis and research in low-resource settings. PMID:28819645

A high-throughput microfluidic dental plaque biofilm system to visualize and quantify the effect of antimicrobials

PubMed Central

Nance, William C.; Dowd, Scot E.; Samarian, Derek; Chludzinski, Jeffrey; Delli, Joseph; Battista, John; Rickard, Alexander H.

2013-01-01

Objectives Few model systems are amenable to developing multi-species biofilms in parallel under environmentally germane conditions. This is a problem when evaluating the potential real-world effectiveness of antimicrobials in the laboratory. One such antimicrobial is cetylpyridinium chloride (CPC), which is used in numerous over-the-counter oral healthcare products. The aim of this work was to develop a high-throughput microfluidic system that is combined with a confocal laser scanning microscope (CLSM) to quantitatively evaluate the effectiveness of CPC against oral multi-species biofilms grown in human saliva. Methods Twenty-four-channel BioFlux microfluidic plates were inoculated with pooled human saliva and fed filter-sterilized saliva for 20 h at 37°C. The bacterial diversity of the biofilms was evaluated by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). The antimicrobial/anti-biofilm effect of CPC (0.5%–0.001% w/v) was examined using Live/Dead stain, CLSM and 3D imaging software. Results The analysis of biofilms by bTEFAP demonstrated that they contained genera typically found in human dental plaque. These included Aggregatibacter, Fusobacterium, Neisseria, Porphyromonas, Streptococcus and Veillonella. Using Live/Dead stain, clear gradations in killing were observed when the biofilms were treated with CPC between 0.5% and 0.001% w/v. At 0.5% (w/v) CPC, 90% of the total signal was from dead/damaged cells. Below this concentration range, less killing was observed. In the 0.5%–0.05% (w/v) range CPC penetration/killing was greatest and biofilm thickness was significantly reduced. Conclusions This work demonstrates the utility of a high-throughput microfluidic–CLSM system to grow multi-species oral biofilms, which are compositionally similar to naturally occurring biofilms, to assess the effectiveness of antimicrobials. PMID:23800904

Application of High-Throughput Seebeck Microprobe Measurements on Thermoelectric Half-Heusler Thin Film Combinatorial Material Libraries.

PubMed

Ziolkowski, Pawel; Wambach, Matthias; Ludwig, Alfred; Mueller, Eckhard

2018-01-08

In view of the variety and complexity of thermoelectric (TE) material systems, combinatorial approaches to materials development come to the fore for identifying new promising compounds. The success of this approach is related to the availability and reliability of high-throughput characterization methods for identifying interrelations between materials structures and properties within the composition spread libraries. A meaningful characterization starts with determination of the Seebeck coefficient as a major feature of TE materials. Its measurement, and hence the accuracy and detectability of promising material compositions, may be strongly affected by thermal and electrical measurement conditions. This work illustrates the interrelated effects of the substrate material, the layer thickness, and spatial property distributions of thin film composition spread libraries, which are studied experimentally by local thermopower scans by means of the Potential and Seebeck Microprobe (PSM). The study is complemented by numerical evaluation. Material libraries of the half-Heusler compound system Ti-Ni-Sn were deposited on selected substrates (Si, AlN, Al 2 O 3 ) by magnetron sputtering. Assuming homogeneous properties of a film, significant decrease of the detected thermopower S m can be expected on substrates with higher thermal conductivity, yielding an underestimation of materials thermopower between 15% and 50%, according to FEM (finite element methods) simulations. Thermally poor conducting substrates provide a better accuracy with thermopower underestimates lower than 8%, but suffer from a lower spatial resolution. According to FEM simulations, local scanning of sharp thermopower peaks on lowly conductive substrates is linked to an additional deviation of the measured thermopower of up to 70% compared to homogeneous films, which is 66% higher than for corresponding cases on substrates with higher thermal conductivity of this study.

High-resolution, high-throughput imaging with a multibeam scanning electron microscope

PubMed Central

EBERLE, AL; MIKULA, S; SCHALEK, R; LICHTMAN, J; TATE, ML KNOTHE; ZEIDLER, D

2015-01-01

Electron–electron interactions and detector bandwidth limit the maximal imaging speed of single-beam scanning electron microscopes. We use multiple electron beams in a single column and detect secondary electrons in parallel to increase the imaging speed by close to two orders of magnitude and demonstrate imaging for a variety of samples ranging from biological brain tissue to semiconductor wafers. Lay Description The composition of our world and our bodies on the very small scale has always fascinated people, making them search for ways to make this visible to the human eye. Where light microscopes reach their resolution limit at a certain magnification, electron microscopes can go beyond. But their capability of visualizing extremely small features comes at the cost of a very small field of view. Some of the questions researchers seek to answer today deal with the ultrafine structure of brains, bones or computer chips. Capturing these objects with electron microscopes takes a lot of time – maybe even exceeding the time span of a human being – or new tools that do the job much faster. A new type of scanning electron microscope scans with 61 electron beams in parallel, acquiring 61 adjacent images of the sample at the same time a conventional scanning electron microscope captures one of these images. In principle, the multibeam scanning electron microscope’s field of view is 61 times larger and therefore coverage of the sample surface can be accomplished in less time. This enables researchers to think about large-scale projects, for example in the rather new field of connectomics. A very good introduction to imaging a brain at nanometre resolution can be found within course material from Harvard University on http://www.mcb80x.org/# as featured media entitled ‘connectomics’. PMID:25627873

High Throughput PBTK: Open-Source Data and Tools for ...

EPA Pesticide Factsheets

Presentation on High Throughput PBTK at the PBK Modelling in Risk Assessment meeting in Ispra, Italy Presentation on High Throughput PBTK at the PBK Modelling in Risk Assessment meeting in Ispra, Italy

Raman microspectrometer combined with scattering microscopy and lensless imaging for bacteria identification

NASA Astrophysics Data System (ADS)

Strola, S. A.; Schultz, E.; Allier, C. P.; DesRoches, B.; Lemmonier, J.; Dinten, J.-M.

2013-03-01

In this paper, we report on a compact prototype capable both of lensfree imaging, Raman spectrometry and scattering microscopy from bacteria samples. This instrument allows high-throughput real-time characterization without the need of markers, making it potentially suitable to field label-free biomedical and environmental applications. Samples are illuminated from above with a focused-collimated 532nm laser beam and can be x-y-z scanned. The bacteria detection is based on emerging lensfree imaging technology able to localize cells of interest over a large field-of-view of 24mm2. Raman signal and scattered light are then collected by separate measurement arms simultaneously. In the first arm the emission light is fed by a fiber into a prototype spectrometer, developed by Tornado Spectral System based on Tornado's High Throughput Virtual Slit (HTVS) novel technology. The enhanced light throughput in the spectral region of interest (500-1800 cm-1) reduces Raman acquisition time down to few seconds, thus facilitating experimental protocols and avoiding the bacteria deterioration induced by laser thermal heating. Scattered light impinging in the second arm is collected onto a charge-coupled-device. The reconstructed image allows studying the single bacteria diffraction pattern and their specific structural features. The characterization and identification of different bacteria have been performed to validate and optimize the acquisition system and the component setup. The results obtained demonstrate the benefits of these three techniques combination by providing the precise bacteria localization, their chemical composition and a morphology description. The procedure for a rapid identification of particular pathogen bacteria in a sample is illustrated.

Lensless on-chip imaging of cells provides a new tool for high-throughput cell-biology and medical diagnostics.

PubMed

Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan

2009-12-14

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as approximately 18 cm(2). Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of approximately 5 mm without the need for refocusing which corresponds to up to approximately 9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments.

Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics

PubMed Central

Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan

2009-01-01

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as ~18 cm2. Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of ~5 mm without the need for refocusing which corresponds to up to ~9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments. PMID:20010542

Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Khan, Sajida; Chatterjee, Anushree; Nagpal, Prashant

2017-03-01

Nanoelectronic DNA sequencing can provide an important alternative to sequencing-by-synthesis by reducing sample preparation time, cost, and complexity as a high-throughput next-generation technique with accurate single-molecule identification. However, sample noise and signature overlap continue to prevent high-resolution and accurate sequencing results. Probing the molecular orbitals of chemically distinct DNA nucleobases offers a path for facile sequence identification, but molecular entropy (from nucleotide conformations) makes such identification difficult when relying only on the energies of lowest-unoccupied and highest-occupied molecular orbitals (LUMO and HOMO). Here, nine biophysical parameters are developed to better characterize molecular orbitals of individual nucleobases, intended for single-molecule DNA sequencing using quantum tunneling of charges. For this analysis, theoretical models for quantum tunneling are combined with transition voltage spectroscopy to obtain measurable parameters unique to the molecule within an electronic junction. Scanning tunneling spectroscopy is then used to measure these nine biophysical parameters for DNA nucleotides, and a modified machine learning algorithm identified nucleobases. The new parameters significantly improve base calling over merely using LUMO and HOMO frontier orbital energies. Furthermore, high accuracies for identifying DNA nucleobases were observed at different pH conditions. These results have significant implications for developing a robust and accurate high-throughput nanoelectronic DNA sequencing technique. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A scalable diffraction-based scanning 3D colour video display as demonstrated by using tiled gratings and a vertical diffuser.

PubMed

Jia, Jia; Chen, Jhensi; Yao, Jun; Chu, Daping

2017-03-17

A high quality 3D display requires a high amount of optical information throughput, which needs an appropriate mechanism to distribute information in space uniformly and efficiently. This study proposes a front-viewing system which is capable of managing the required amount of information efficiently from a high bandwidth source and projecting 3D images with a decent size and a large viewing angle at video rate in full colour. It employs variable gratings to support a high bandwidth distribution. This concept is scalable and the system can be made compact in size. A horizontal parallax only (HPO) proof-of-concept system is demonstrated by projecting holographic images from a digital micro mirror device (DMD) through rotational tiled gratings before they are realised on a vertical diffuser for front-viewing.

Application of ToxCast High-Throughput Screening and ...

EPA Pesticide Factsheets

Slide presentation at the SETAC annual meeting on High-Throughput Screening and Modeling Approaches to Identify Steroidogenesis Distruptors Slide presentation at the SETAC annual meeting on High-Throughput Screening and Modeling Approaches to Identify Steroidogenssis Distruptors

Fast analysis of triterpenoids in Ganoderma lucidum spores by ultra-performance liquid chromatography coupled with triple quadrupole mass spectrometry.

PubMed

Yan, Zhou; Xia, Bing; Qiu, Ming Hua; Li Sheng, Ding; Xu, Hong Xi

2013-11-01

A rapid and reliable method was established for simultaneous determination of main triterpenoids in Ganoderma lucidum spores using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-TQ-MS). The established method was validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to determine the contents of 10 main triterpenoids in different batches of G. lucidum spores. The analysis results showed that moderate levels of triterpenoids were found in G. lucidum spores. In addition, a MS full scan with a daughter ion scan experiment was performed to identify the potential derivatives of triterpenoids present in G. lucidum spores. As a result, a total of 22 triterpenoids from different G. lucidum spores were unequivocally or tentatively identified via comparisons with authentic standards and literatures. This method provides both qualitative and quantitative results without the need for repetitive UPLC-MS analyses, thereby increasing efficiency and productivity, making it suitable for high-throughput applications. Copyright © 2013 John Wiley & Sons, Ltd.

Applying deep learning technology to automatically identify metaphase chromosomes using scanning microscopic images: an initial investigation

NASA Astrophysics Data System (ADS)

Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin

2016-03-01

Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.

The high throughput biomedicine unit at the institute for molecular medicine Finland: high throughput screening meets precision medicine.

PubMed

Pietiainen, Vilja; Saarela, Jani; von Schantz, Carina; Turunen, Laura; Ostling, Paivi; Wennerberg, Krister

2014-05-01

The High Throughput Biomedicine (HTB) unit at the Institute for Molecular Medicine Finland FIMM was established in 2010 to serve as a national and international academic screening unit providing access to state of the art instrumentation for chemical and RNAi-based high throughput screening. The initial focus of the unit was multiwell plate based chemical screening and high content microarray-based siRNA screening. However, over the first four years of operation, the unit has moved to a more flexible service platform where both chemical and siRNA screening is performed at different scales primarily in multiwell plate-based assays with a wide range of readout possibilities with a focus on ultraminiaturization to allow for affordable screening for the academic users. In addition to high throughput screening, the equipment of the unit is also used to support miniaturized, multiplexed and high throughput applications for other types of research such as genomics, sequencing and biobanking operations. Importantly, with the translational research goals at FIMM, an increasing part of the operations at the HTB unit is being focused on high throughput systems biological platforms for functional profiling of patient cells in personalized and precision medicine projects.

High Throughput Screening For Hazard and Risk of Environmental Contaminants

EPA Science Inventory

High throughput toxicity testing provides detailed mechanistic information on the concentration response of environmental contaminants in numerous potential toxicity pathways. High throughput screening (HTS) has several key advantages: (1) expense orders of magnitude less than an...

Laser scanning cytometry for automation of the micronucleus assay

PubMed Central

Darzynkiewicz, Zbigniew; Smolewski, Piotr; Holden, Elena; Luther, Ed; Henriksen, Mel; François, Maxime; Leifert, Wayne; Fenech, Michael

2011-01-01

Laser scanning cytometry (LSC) provides a novel approach for automated scoring of micronuclei (MN) in different types of mammalian cells, serving as a biomarker of genotoxicity and mutagenicity. In this review, we discuss the advances to date in measuring MN in cell lines, buccal cells and erythrocytes, describe the advantages and outline potential challenges of this distinctive approach of analysis of nuclear anomalies. The use of multiple laser wavelengths in LSC and the high dynamic range of fluorescence and absorption detection allow simultaneous measurement of multiple cellular and nuclear features such as cytoplasmic area, nuclear area, DNA content and density of nuclei and MN, protein content and density of cytoplasm as well as other features using molecular probes. This high-content analysis approach allows the cells of interest to be identified (e.g. binucleated cells in cytokinesis-blocked cultures) and MN scored specifically in them. MN assays in cell lines (e.g. the CHO cell MN assay) using LSC are increasingly used in routine toxicology screening. More high-content MN assays and the expansion of MN analysis by LSC to other models (i.e. exfoliated cells, dermal cell models, etc.) hold great promise for robust and exciting developments in MN assay automation as a high-content high-throughput analysis procedure. PMID:21164197

High Throughput Transcriptomics: From screening to pathways

EPA Science Inventory

The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...

A high brightness probe of polymer nanoparticles for biological imaging

NASA Astrophysics Data System (ADS)

Zhou, Sirong; Zhu, Jiarong; Li, Yaping; Feng, Liheng

2018-03-01

Conjugated polymer nanoparticles (CPNs) with high brightness in long wavelength region were prepared by the nano-precipitation method. Based on fluorescence resonance energy transfer (FRET) mechanism, the high brightness property of the CPNs was realized by four different emission polymers. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) displayed that the CPNs possessed a spherical structure and an average diameter of 75 nm. Analysis assays showed that the CPNs had excellent biocompatibility, good photostability and low cytotoxicity. The CPNs were bio-modified with a cell penetrating peptide (Tat, a targeted element) through covalent link. Based on the entire wave fluorescence emission, the functionalized CPNs1-4 can meet multichannel and high throughput assays in cell and organ imaging. The contribution of the work lies in not only providing a new way to obtain a high brightness imaging probe in long wavelength region, but also using targeted cell and organ imaging.

Quantitative description on structure-property relationships of Li-ion battery materials for high-throughput computations

NASA Astrophysics Data System (ADS)

Wang, Youwei; Zhang, Wenqing; Chen, Lidong; Shi, Siqi; Liu, Jianjun

2017-12-01

Li-ion batteries are a key technology for addressing the global challenge of clean renewable energy and environment pollution. Their contemporary applications, for portable electronic devices, electric vehicles, and large-scale power grids, stimulate the development of high-performance battery materials with high energy density, high power, good safety, and long lifetime. High-throughput calculations provide a practical strategy to discover new battery materials and optimize currently known material performances. Most cathode materials screened by the previous high-throughput calculations cannot meet the requirement of practical applications because only capacity, voltage and volume change of bulk were considered. It is important to include more structure-property relationships, such as point defects, surface and interface, doping and metal-mixture and nanosize effects, in high-throughput calculations. In this review, we established quantitative description of structure-property relationships in Li-ion battery materials by the intrinsic bulk parameters, which can be applied in future high-throughput calculations to screen Li-ion battery materials. Based on these parameterized structure-property relationships, a possible high-throughput computational screening flow path is proposed to obtain high-performance battery materials.

Quantitative description on structure-property relationships of Li-ion battery materials for high-throughput computations.

PubMed

Wang, Youwei; Zhang, Wenqing; Chen, Lidong; Shi, Siqi; Liu, Jianjun

2017-01-01

Li-ion batteries are a key technology for addressing the global challenge of clean renewable energy and environment pollution. Their contemporary applications, for portable electronic devices, electric vehicles, and large-scale power grids, stimulate the development of high-performance battery materials with high energy density, high power, good safety, and long lifetime. High-throughput calculations provide a practical strategy to discover new battery materials and optimize currently known material performances. Most cathode materials screened by the previous high-throughput calculations cannot meet the requirement of practical applications because only capacity, voltage and volume change of bulk were considered. It is important to include more structure-property relationships, such as point defects, surface and interface, doping and metal-mixture and nanosize effects, in high-throughput calculations. In this review, we established quantitative description of structure-property relationships in Li-ion battery materials by the intrinsic bulk parameters, which can be applied in future high-throughput calculations to screen Li-ion battery materials. Based on these parameterized structure-property relationships, a possible high-throughput computational screening flow path is proposed to obtain high-performance battery materials.

High Throughput Experimental Materials Database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakutayev, Andriy; Perkins, John; Schwarting, Marcus

The mission of the High Throughput Experimental Materials Database (HTEM DB) is to enable discovery of new materials with useful properties by releasing large amounts of high-quality experimental data to public. The HTEM DB contains information about materials obtained from high-throughput experiments at the National Renewable Energy Laboratory (NREL).

Development of high-productivity, strong cation-exchange adsorbers for protein capture by graft polymerization from membranes with different pore sizes

PubMed Central

Chenette, Heather C.S.; Robinson, Julie R.; Hobley, Eboni; Husson, Scott M.

2012-01-01

This paper describes the surface modification of macroporous membranes using ATRP (atom transfer radical polymerization) to create cation-exchange adsorbers with high protein binding capacity at high product throughput. The work is motivated by the need for a more economical and rapid capture step in downstream processing of protein therapeutics. Membranes with three reported nominal pore sizes (0.2, 0.45, 1.0 μm) were modified with poly(3-sulfopropyl methacrylate, potassium salt) tentacles, to create a high density of protein binding sites. A special formulation was used in which the monomer was protected by a crown ether to enable surface-initiated ATRP of this cationic polyelectrolyte. Success with modification was supported by chemical analysis using Fourier-transform infrared spectroscopy and indirectly by measurement of pure water flux as a function of polymerization time. Uniformity of modification within the membranes was visualized with confocal laser scanning microscopy. Static and dynamic binding capacities were measured using lysozyme protein to allow comparisons with reported performance data for commercial cation-exchange materials. Dynamic binding capacities were measured for flow rates ranging from 13 to 109 column volumes (CV)/min. Results show that this unique ATRP formulation can be used to fabricate cation-exchange membrane adsorbers with dynamic binding capacities as high as 70 mg/mL at a throughput of 100 CV/min and unprecedented productivity of 300 mg/mL/min. PMID:23175597

20180311 - High Throughput Transcriptomics: From screening to pathways (SOT 2018)

EPA Science Inventory

The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...

Evaluation of Sequencing Approaches for High-Throughput Transcriptomics - (BOSC)

EPA Science Inventory

Whole-genome in vitro transcriptomics has shown the capability to identify mechanisms of action and estimates of potency for chemical-mediated effects in a toxicological framework, but with limited throughput and high cost. The generation of high-throughput global gene expression...

Reflective optical imaging systems with balanced distortion

DOEpatents

Hudyma, Russell M.

2001-01-01

Optical systems compatible with extreme ultraviolet radiation comprising four reflective elements for projecting a mask image onto a substrate are described. The four optical elements comprise, in order from object to image, convex, concave, convex and concave mirrors. The optical systems are particularly suited for step and scan lithography methods. The invention enables the use of larger slit dimensions associated with ring field scanning optics, improves wafer throughput, and allows higher semiconductor device density. The inventive optical systems are characterized by reduced dynamic distortion because the static distortion is balanced across the slit width.

High Throughput Determination of Critical Human Dosing Parameters (SOT)

EPA Science Inventory

High throughput toxicokinetics (HTTK) is a rapid approach that uses in vitro data to estimate TK for hundreds of environmental chemicals. Reverse dosimetry (i.e., reverse toxicokinetics or RTK) based on HTTK data converts high throughput in vitro toxicity screening (HTS) data int...

High Throughput Determinations of Critical Dosing Parameters (IVIVE workshop)

EPA Science Inventory

High throughput toxicokinetics (HTTK) is an approach that allows for rapid estimations of TK for hundreds of environmental chemicals. HTTK-based reverse dosimetry (i.e, reverse toxicokinetics or RTK) is used in order to convert high throughput in vitro toxicity screening (HTS) da...

Optimization of high-throughput nanomaterial developmental toxicity testing in zebrafish embryos

EPA Science Inventory

Nanomaterial (NM) developmental toxicities are largely unknown. With an extensive variety of NMs available, high-throughput screening methods may be of value for initial characterization of potential hazard. We optimized a zebrafish embryo test as an in vivo high-throughput assay...

Fluorescence lifetime imaging system with nm-resolution and single-molecule sensitivity

NASA Astrophysics Data System (ADS)

Wahl, Michael; Rahn, Hans-Juergen; Ortmann, Uwe; Erdmann, Rainer; Boehmer, Martin; Enderlein, Joerg

2002-03-01

Fluorescence lifetime measurement of organic fluorophores is a powerful tool for distinguishing molecules of interest from background or other species. This is of interest in sensitive analysis and Single Molecule Detection (SMD). A demand in many applications is to provide 2-D imaging together with lifetime information. The method of choice is then Time-Correlated Single Photon Counting (TCSPC). We have devloped a compact system on a single PC board that can perform TCSPC at high throughput, while synchronously driving a piezo scanner holding the immobilized sample. The system allows count rates up to 3 MHz and a resolution down to 30 ps. An overall Instrument Response Function down to 300ps is achieved with inexpensive detectors and diode lasers. The board is designed for the PCI bus, permitting high throughput without loss of counts. It is reconfigurable to operate in different modes. The Time-Tagged Time-Resolved (TTTR) mode permits the recording of all photon events with a real-time tag allowing data analysis with unlimited flexibility. We use the Time-Tag clock for an external piezo scanner that moves the sample. As the clock source is common for scanning and tagging, the individual photons can be matched to pixels. Demonstrating the capablities of the system we studied single molecule solutions. Lifetime imaging can be performed at high resolution with as few as 100 photons per pixel.

Exploring the diversity of Listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype.

PubMed

Guilbaud, Morgan; Piveteau, Pascal; Desvaux, Mickaël; Brisse, Sylvain; Briandet, Romain

2015-03-01

Listeria monocytogenes is involved in food-borne illness with a high mortality rate. The persistence of the pathogen along the food chain can be associated with its ability to form biofilms on inert surfaces. While most of the phenotypes associated with biofilms are related to their spatial organization, most published data comparing biofilm formation by L. monocytogenes isolates are based on the quantitative crystal violet assay, which does not give access to structural information. Using a high-throughput confocal-imaging approach, the aim of this work was to decipher the structural diversity of biofilms formed by 96 L. monocytogenes strains isolated from various environments. Prior to large-scale analysis, an experimental design was created to improve L. monocytogenes biofilm formation in microscopic-grade microplates, with special emphasis on the growth medium composition. Microscopic analysis of biofilms formed under the selected conditions by the 96 isolates revealed only weak correlation between the genetic lineages of the isolates and the structural properties of the biofilms. However, a gradient in their geometric descriptors (biovolume, mean thickness, and roughness), ranging from flat multilayers to complex honeycomb-like structures, was shown. The dominant honeycomb-like morphotype was characterized by hollow voids hosting free-swimming cells and localized pockets containing mixtures of dead cells and extracellular DNA (eDNA). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Extensive scanning of the calpain-3 gene broadens the spectrum of LGMD2A phenotypes.

PubMed

Piluso, G; Politano, L; Aurino, S; Fanin, M; Ricci, E; Ventriglia, V M; Belsito, A; Totaro, A; Saccone, V; Topaloglu, H; Nascimbeni, A C; Fulizio, L; Broccolini, A; Canki-Klain, N; Comi, L I; Nigro, G; Angelini, C; Nigro, V

2005-09-01

The limb girdle muscular dystrophies (LGMD) are a heterogeneous group of Mendelian disorders highlighted by weakness of the pelvic and shoulder girdle muscles. Seventeen autosomal loci have been so far identified and genetic tests are mandatory to distinguish among the forms. Mutations at the calpain 3 locus (CAPN3) cause LGMD type 2A. To obtain unbiased information on the consequences of CAPN3 mutations. 530 subjects with different grades of symptoms and 300 controls. High throughput denaturing HPLC analysis of DNA pools. 141 LGMD2A cases were identified, carrying 82 different CAPN3 mutations (45 novel), along with 18 novel polymorphisms/variants. Females had a more favourable course than males. In 94% of the more severely affected patient group, the defect was also discovered in the second allele. This proves the sensitivity of the approach. CAPN3 mutations were found in 35.1% of classical LGMD phenotypes. Mutations were also found in 18.4% of atypical patients and in 12.6% of subjects with high serum creatine kinase levels. A non-invasive and cost-effective strategy, based on the high throughput denaturing HPLC analysis of DNA pools, was used to obtain unbiased information on the consequences of CAPN3 mutations in the largest genetic study ever undertaken. This broadens the spectrum of LGMD2A phenotypes and sets the carrier frequency at 1:103.

A scalable diffraction-based scanning 3D colour video display as demonstrated by using tiled gratings and a vertical diffuser

PubMed Central

Jia, Jia; Chen, Jhensi; Yao, Jun; Chu, Daping

2017-01-01

A high quality 3D display requires a high amount of optical information throughput, which needs an appropriate mechanism to distribute information in space uniformly and efficiently. This study proposes a front-viewing system which is capable of managing the required amount of information efficiently from a high bandwidth source and projecting 3D images with a decent size and a large viewing angle at video rate in full colour. It employs variable gratings to support a high bandwidth distribution. This concept is scalable and the system can be made compact in size. A horizontal parallax only (HPO) proof-of-concept system is demonstrated by projecting holographic images from a digital micro mirror device (DMD) through rotational tiled gratings before they are realised on a vertical diffuser for front-viewing. PMID:28304371

Development of a Whole Slide Imaging System on Smartphones and Evaluation With Frozen Section Samples.

PubMed

Yu, Hong; Gao, Feng; Jiang, Liren; Ma, Shuoxin

2017-09-15

The aim was to develop scalable Whole Slide Imaging (sWSI), a WSI system based on mainstream smartphones coupled with regular optical microscopes. This ultra-low-cost solution should offer diagnostic-ready imaging quality on par with standalone scanners, supporting both oil and dry objective lenses of different magnifications, and reasonably high throughput. These performance metrics should be evaluated by expert pathologists and match those of high-end scanners. The aim was to develop scalable Whole Slide Imaging (sWSI), a whole slide imaging system based on smartphones coupled with optical microscopes. This ultra-low-cost solution should offer diagnostic-ready imaging quality on par with standalone scanners, supporting both oil and dry object lens of different magnification. All performance metrics should be evaluated by expert pathologists and match those of high-end scanners. In the sWSI design, the digitization process is split asynchronously between light-weight clients on smartphones and powerful cloud servers. The client apps automatically capture FoVs at up to 12-megapixel resolution and process them in real-time to track the operation of users, then give instant feedback of guidance. The servers first restitch each pair of FoVs, then automatically correct the unknown nonlinear distortion introduced by the lens of the smartphone on the fly, based on pair-wise stitching, before finally combining all FoVs into one gigapixel VS for each scan. These VSs can be viewed using Internet browsers anywhere. In the evaluation experiment, 100 frozen section slides from patients randomly selected among in-patients of the participating hospital were scanned by both a high-end Leica scanner and sWSI. All VSs were examined by senior pathologists whose diagnoses were compared against those made using optical microscopy as ground truth to evaluate the image quality. The sWSI system is developed for both Android and iPhone smartphones and is currently being offered to the public. The image quality is reliable and throughput is approximately 1 FoV per second, yielding a 15-by-15 mm slide under 20X object lens in approximately 30-35 minutes, with little training required for the operator. The expected cost for setup is approximately US $100 and scanning each slide costs between US $1 and $10, making sWSI highly cost-effective for infrequent or low-throughput usage. In the clinical evaluation of sample-wise diagnostic reliability, average accuracy scores achieved by sWSI-scan-based diagnoses were as follows: 0.78 for breast, 0.88 for uterine corpus, 0.68 for thyroid, and 0.50 for lung samples. The respective low-sensitivity rates were 0.05, 0.05, 0.13, and 0.25 while the respective low-specificity rates were 0.18, 0.08, 0.20, and 0.25. The participating pathologists agreed that the overall quality of sWSI was generally on par with that produced by high-end scanners, and did not affect diagnosis in most cases. Pathologists confirmed that sWSI is reliable enough for standard diagnoses of most tissue categories, while it can be used for quick screening of difficult cases. As an ultra-low-cost alternative to whole slide scanners, diagnosis-ready VS quality and robustness for commercial usage is achieved in the sWSI solution. Operated on main-stream smartphones installed on normal optical microscopes, sWSI readily offers affordable and reliable WSI to resource-limited or infrequent clinical users. ©Hong Yu, Feng Gao, Liren Jiang, Shuoxin Ma. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 15.09.2017.

Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high-throughput, efficient cell sorting

DOE PAGES

Jung, Seung-Yong; Notton, Timothy; Fong, Erika; ...

2015-01-07

Particle sorting using acoustofluidics has enormous potential but widespread adoption has been limited by complex device designs and low throughput. Here, we report high-throughput separation of particles and T lymphocytes (600 μL min -1) by altering the net sonic velocity to reposition acoustic pressure nodes in a simple two-channel device. Finally, the approach is generalizable to other microfluidic platforms for rapid, high-throughput analysis.

Quantitative description on structure–property relationships of Li-ion battery materials for high-throughput computations

PubMed Central

Wang, Youwei; Zhang, Wenqing; Chen, Lidong; Shi, Siqi; Liu, Jianjun

2017-01-01

Abstract Li-ion batteries are a key technology for addressing the global challenge of clean renewable energy and environment pollution. Their contemporary applications, for portable electronic devices, electric vehicles, and large-scale power grids, stimulate the development of high-performance battery materials with high energy density, high power, good safety, and long lifetime. High-throughput calculations provide a practical strategy to discover new battery materials and optimize currently known material performances. Most cathode materials screened by the previous high-throughput calculations cannot meet the requirement of practical applications because only capacity, voltage and volume change of bulk were considered. It is important to include more structure–property relationships, such as point defects, surface and interface, doping and metal-mixture and nanosize effects, in high-throughput calculations. In this review, we established quantitative description of structure–property relationships in Li-ion battery materials by the intrinsic bulk parameters, which can be applied in future high-throughput calculations to screen Li-ion battery materials. Based on these parameterized structure–property relationships, a possible high-throughput computational screening flow path is proposed to obtain high-performance battery materials. PMID:28458737

High-throughput screening (HTS) and modeling of the retinoid ...

EPA Pesticide Factsheets

Presentation at the Retinoids Review 2nd workshop in Brussels, Belgium on the application of high throughput screening and model to the retinoid system Presentation at the Retinoids Review 2nd workshop in Brussels, Belgium on the application of high throughput screening and model to the retinoid system

Evaluating High Throughput Toxicokinetics and Toxicodynamics for IVIVE (WC10)

EPA Science Inventory

High-throughput screening (HTS) generates in vitro data for characterizing potential chemical hazard. TK models are needed to allow in vitro to in vivo extrapolation (IVIVE) to real world situations. The U.S. EPA has created a public tool (R package “httk” for high throughput tox...

High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes

USDA-ARS?s Scientific Manuscript database

High-throughput SNP genotyping provides a rapid way of developing resourceful set of markers for delineating the genetic architecture and for effective species discrimination. In the presented research, we demonstrate a set of 192 SNPs for effective genotyping in sugar beet using high-throughput mar...

Alginate Immobilization of Metabolic Enzymes (AIME) for High-Throughput Screening Assays (SOT)

EPA Science Inventory

Alginate Immobilization of Metabolic Enzymes (AIME) for High-Throughput Screening Assays DE DeGroot, RS Thomas, and SO SimmonsNational Center for Computational Toxicology, US EPA, Research Triangle Park, NC USAThe EPA’s ToxCast program utilizes a wide variety of high-throughput s...

A quantitative literature-curated gold standard for kinase-substrate pairs

PubMed Central

2011-01-01

We describe the Yeast Kinase Interaction Database (KID, http://www.moseslab.csb.utoronto.ca/KID/), which contains high- and low-throughput data relevant to phosphorylation events. KID includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments. By quantitatively integrating these data, we identified 517 high-confidence kinase-substrate pairs that we consider a gold standard. We show that this gold standard can be used to assess published high-throughput datasets, suggesting that it will enable similar rigorous assessments in the future. PMID:21492431

High-Throughput Industrial Coatings Research at The Dow Chemical Company.

PubMed

Kuo, Tzu-Chi; Malvadkar, Niranjan A; Drumright, Ray; Cesaretti, Richard; Bishop, Matthew T

2016-09-12

At The Dow Chemical Company, high-throughput research is an active area for developing new industrial coatings products. Using the principles of automation (i.e., using robotic instruments), parallel processing (i.e., prepare, process, and evaluate samples in parallel), and miniaturization (i.e., reduce sample size), high-throughput tools for synthesizing, formulating, and applying coating compositions have been developed at Dow. In addition, high-throughput workflows for measuring various coating properties, such as cure speed, hardness development, scratch resistance, impact toughness, resin compatibility, pot-life, surface defects, among others have also been developed in-house. These workflows correlate well with the traditional coatings tests, but they do not necessarily mimic those tests. The use of such high-throughput workflows in combination with smart experimental designs allows accelerated discovery and commercialization.

Outlook for Development of High-throughput Cryopreservation for Small-bodied Biomedical Model Fishes★

PubMed Central

Tiersch, Terrence R.; Yang, Huiping; Hu, E.

2011-01-01

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach. PMID:21440666

Mapping quantum yield for (Fe-Zn-Sn-Ti)Ox photoabsorbers using a high throughput photoelectrochemical screening system.

PubMed

Xiang, Chengxiang; Haber, Joel; Marcin, Martin; Mitrovic, Slobodan; Jin, Jian; Gregoire, John M

2014-03-10

Combinatorial synthesis and screening of light absorbers are critical to material discoveries for photovoltaic and photoelectrochemical applications. One of the most effective ways to evaluate the energy-conversion properties of a semiconducting light absorber is to form an asymmetric junction and investigate the photogeneration, transport and recombination processes at the semiconductor interface. This standard photoelectrochemical measurement is readily made on a semiconductor sample with a back-side metallic contact (working electrode) and front-side solution contact. In a typical combinatorial material library, each sample shares a common back contact, requiring novel instrumentation to provide spatially resolved and thus sample-resolved measurements. We developed a multiplexing counter electrode with a thin layer assembly, in which a rectifying semiconductor/liquid junction was formed and the short-circuit photocurrent was measured under chopped illumination for each sample in a material library. The multiplexing counter electrode assembly demonstrated a photocurrent sensitivity of sub-10 μA cm(-2) with an external quantum yield sensitivity of 0.5% for each semiconductor sample under a monochromatic ultraviolet illumination source. The combination of cell architecture and multiplexing allows high-throughput modes of operation, including both fast-serial and parallel measurements. To demonstrate the performance of the instrument, the external quantum yields of 1819 different compositions from a pseudoquaternary metal oxide library, (Fe-Zn-Sn-Ti)Ox, at 385 nm were collected in scanning serial mode with a throughput of as fast as 1 s per sample. Preliminary screening results identified a promising ternary composition region centered at Fe0.894Sn0.103Ti0.0034Ox, with an external quantum yield of 6.7% at 385 nm.

Applications of pathology-assisted image analysis of immunohistochemistry-based biomarkers in oncology.

PubMed

Shinde, V; Burke, K E; Chakravarty, A; Fleming, M; McDonald, A A; Berger, A; Ecsedy, J; Blakemore, S J; Tirrell, S M; Bowman, D

2014-01-01

Immunohistochemistry-based biomarkers are commonly used to understand target inhibition in key cancer pathways in preclinical models and clinical studies. Automated slide-scanning and advanced high-throughput image analysis software technologies have evolved into a routine methodology for quantitative analysis of immunohistochemistry-based biomarkers. Alongside the traditional pathology H-score based on physical slides, the pathology world is welcoming digital pathology and advanced quantitative image analysis, which have enabled tissue- and cellular-level analysis. An automated workflow was implemented that includes automated staining, slide-scanning, and image analysis methodologies to explore biomarkers involved in 2 cancer targets: Aurora A and NEDD8-activating enzyme (NAE). The 2 workflows highlight the evolution of our immunohistochemistry laboratory and the different needs and requirements of each biological assay. Skin biopsies obtained from MLN8237 (Aurora A inhibitor) phase 1 clinical trials were evaluated for mitotic and apoptotic index, while mitotic index and defects in chromosome alignment and spindles were assessed in tumor biopsies to demonstrate Aurora A inhibition. Additionally, in both preclinical xenograft models and an acute myeloid leukemia phase 1 trial of the NAE inhibitor MLN4924, development of a novel image algorithm enabled measurement of downstream pathway modulation upon NAE inhibition. In the highlighted studies, developing a biomarker strategy based on automated image analysis solutions enabled project teams to confirm target and pathway inhibition and understand downstream outcomes of target inhibition with increased throughput and quantitative accuracy. These case studies demonstrate a strategy that combines a pathologist's expertise with automated image analysis to support oncology drug discovery and development programs.

Ultra-high-speed variable focus optics for novel applications in advanced imaging

NASA Astrophysics Data System (ADS)

Kang, S.; Dotsenko, E.; Amrhein, D.; Theriault, C.; Arnold, C. B.

2018-02-01

With the advancement of ultra-fast manufacturing technologies, high speed imaging with high 3D resolution has become increasingly important. Here we show the use of an ultra-high-speed variable focus optical element, the TAG Lens, to enable new ways to acquire 3D information from an object. The TAG Lens uses sound to adjust the index of refraction profile in a liquid and thereby can achieve focal scanning rates greater than 100 kHz. When combined with a high-speed pulsed LED and a high-speed camera, we can exploit this phenomenon to achieve high-resolution imaging through large depths. By combining the image acquisition with digital image processing, we can extract relevant parameters such as tilt and angle information from objects in the image. Due to the high speeds at which images can be collected and processed, we believe this technique can be used as an efficient method of industrial inspection and metrology for high throughput applications.

High-throughput measurements of biochemical responses using the plate::vision multimode 96 minilens array reader.

PubMed

Huang, Kuo-Sen; Mark, David; Gandenberger, Frank Ulrich

2006-01-01

The plate::vision is a high-throughput multimode reader capable of reading absorbance, fluorescence, fluorescence polarization, time-resolved fluorescence, and luminescence. Its performance has been shown to be quite comparable with other readers. When the reader is integrated into the plate::explorer, an ultrahigh-throughput screening system with event-driven software and parallel plate-handling devices, it becomes possible to run complicated assays with kinetic readouts in high-density microtiter plate formats for high-throughput screening. For the past 5 years, we have used the plate::vision and the plate::explorer to run screens and have generated more than 30 million data points. Their throughput, performance, and robustness have speeded up our drug discovery process greatly.

Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

PubMed

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

2011-01-17

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

Detection of Somatic Mutations by High-Resolution DNA Melting (HRM) Analysis in Multiple Cancers

PubMed Central

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S.; Garcia-Closas, Montserrat; Sherman, Mark E.; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P.; Khan, Javed; Chanock, Stephen

2011-01-01

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples. PMID:21264207

The high throughput virtual slit enables compact, inexpensive Raman spectral imagers

NASA Astrophysics Data System (ADS)

Gooding, Edward; Deutsch, Erik R.; Huehnerhoff, Joseph; Hajian, Arsen R.

2018-02-01

Raman spectral imaging is increasingly becoming the tool of choice for field-based applications such as threat, narcotics and hazmat detection; air, soil and water quality monitoring; and material ID. Conventional fiber-coupled point source Raman spectrometers effectively interrogate a small sample area and identify bulk samples via spectral library matching. However, these devices are very slow at mapping over macroscopic areas. In addition, the spatial averaging performed by instruments that collect binned spectra, particularly when used in combination with orbital raster scanning, tends to dilute the spectra of trace particles in a mixture. Our design, employing free space line illumination combined with area imaging, reveals both the spectral and spatial content of heterogeneous mixtures. This approach is well suited to applications such as detecting explosives and narcotics trace particle detection in fingerprints. The patented High Throughput Virtual Slit1 is an innovative optical design that enables compact, inexpensive handheld Raman spectral imagers. HTVS-based instruments achieve significantly higher spectral resolution than can be obtained with conventional designs of the same size. Alternatively, they can be used to build instruments with comparable resolution to large spectrometers, but substantially smaller size, weight and unit cost, all while maintaining high sensitivity. When used in combination with laser line imaging, this design eliminates sample photobleaching and unwanted photochemistry while greatly enhancing mapping speed, all with high selectivity and sensitivity. We will present spectral image data and discuss applications that are made possible by low cost HTVS-enabled instruments.

Solution-Phase Photochemical Nanopatterning Enabled by High-Refractive-Index Beam Pen Arrays.

PubMed

Xie, Zhuang; Gordiichuk, Pavlo; Lin, Qing-Yuan; Meckes, Brian; Chen, Peng-Cheng; Sun, Lin; Du, Jingshan S; Zhu, Jinghan; Liu, Yuan; Dravid, Vinayak P; Mirkin, Chad A

2017-08-22

A high-throughput, solution-based, scanning-probe photochemical nanopatterning approach, which does not require the use of probes with subwavelength apertures, is reported. Specifically, pyramid arrays made from high-refractive-index polymeric materials were constructed and studied as patterning tools in a conventional liquid-phase beam pen lithography experiment. Two versions of the arrays were explored with either metal-coated or metal-free tips. Importantly, light can be channeled through both types of tips and the appropriate solution phase (e.g., H 2 O or CH 3 OH) and focused on subwavelength regions of a substrate to effect a photoreaction in solution that results in localized patterning of a self-assembled monolayer (SAM)-coated Au thin film substrate. Arrays with as many as 4500 pyramid-shaped probes were used to simultaneously initiate thousands of localized free-radical photoreactions (decomposition of a lithium acylphosphinate photoinitiator in an aqueous solution) that result in oxidative removal of the SAM. The technique is attractive since it allows one to rapidly generate features less than 200 nm in diameter, and the metal-free tips afford more than 10-fold higher intensity than the tips with nanoapertures over a micrometer propagation length. In principle, this mask-free method can be utilized as a versatile tool for performing a wide variety of photochemistries across multiple scales that may be important in high-throughput combinatorial screening applications related to chemistry, biology, and materials science.

TCP Throughput Profiles Using Measurements over Dedicated Connections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Nageswara S.; Liu, Qiang; Sen, Satyabrata

Wide-area data transfers in high-performance computing infrastructures are increasingly being carried over dynamically provisioned dedicated network connections that provide high capacities with no competing traffic. We present extensive TCP throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs). Contrary to the general expectation, they show significant statistical and temporal variations, in addition to the overall dependencies on the congestion control mechanism, buffer size, and the number of parallel streams. We analyze several throughput profiles that have highly desirable concave regions wherein the throughput decreases slowly with RTTs, inmore » stark contrast to the convex profiles predicted by various TCP analytical models. We present a generic throughput model that abstracts the ramp-up and sustainment phases of TCP flows, which provides insights into qualitative trends observed in measurements across TCP variants: (i) slow-start followed by well-sustained throughput leads to concave regions; (ii) large buffers and multiple parallel streams expand the concave regions in addition to improving the throughput; and (iii) stable throughput dynamics, indicated by a smoother Poincare map and smaller Lyapunov exponents, lead to wider concave regions. These measurements and analytical results together enable us to select a TCP variant and its parameters for a given connection to achieve high throughput with statistical guarantees.« less

Enhancing high throughput toxicology - development of putative adverse outcome pathways linking US EPA ToxCast screening targets to relevant apical hazards.

EPA Science Inventory

High throughput toxicology programs, such as ToxCast and Tox21, have provided biological effects data for thousands of chemicals at multiple concentrations. Compared to traditional, whole-organism approaches, high throughput assays are rapid and cost-effective, yet they generall...

Evaluation of High-Throughput Chemical Exposure Models via Analysis of Matched Environmental and Biological Media Measurements

EPA Science Inventory

The U.S. EPA, under its ExpoCast program, is developing high-throughput near-field modeling methods to estimate human chemical exposure and to provide real-world context to high-throughput screening (HTS) hazard data. These novel modeling methods include reverse methods to infer ...

The development of a general purpose ARM-based processing unit for the ATLAS TileCal sROD

NASA Astrophysics Data System (ADS)

Cox, M. A.; Reed, R.; Mellado, B.

2015-01-01

After Phase-II upgrades in 2022, the data output from the LHC ATLAS Tile Calorimeter will increase significantly. ARM processors are common in mobile devices due to their low cost, low energy consumption and high performance. It is proposed that a cost-effective, high data throughput Processing Unit (PU) can be developed by using several consumer ARM processors in a cluster configuration to allow aggregated processing performance and data throughput while maintaining minimal software design difficulty for the end-user. This PU could be used for a variety of high-level functions on the high-throughput raw data such as spectral analysis and histograms to detect possible issues in the detector at a low level. High-throughput I/O interfaces are not typical in consumer ARM System on Chips but high data throughput capabilities are feasible via the novel use of PCI-Express as the I/O interface to the ARM processors. An overview of the PU is given and the results for performance and throughput testing of four different ARM Cortex System on Chips are presented.

[Current applications of high-throughput DNA sequencing technology in antibody drug research].

PubMed

Yu, Xin; Liu, Qi-Gang; Wang, Ming-Rong

2012-03-01

Since the publication of a high-throughput DNA sequencing technology based on PCR reaction was carried out in oil emulsions in 2005, high-throughput DNA sequencing platforms have been evolved to a robust technology in sequencing genomes and diverse DNA libraries. Antibody libraries with vast numbers of members currently serve as a foundation of discovering novel antibody drugs, and high-throughput DNA sequencing technology makes it possible to rapidly identify functional antibody variants with desired properties. Herein we present a review of current applications of high-throughput DNA sequencing technology in the analysis of antibody library diversity, sequencing of CDR3 regions, identification of potent antibodies based on sequence frequency, discovery of functional genes, and combination with various display technologies, so as to provide an alternative approach of discovery and development of antibody drugs.

Passive 350 GHz Video Imaging Systems for Security Applications

NASA Astrophysics Data System (ADS)

Heinz, E.; May, T.; Born, D.; Zieger, G.; Anders, S.; Zakosarenko, V.; Meyer, H.-G.; Schäffel, C.

2015-10-01

Passive submillimeter-wave imaging is a concept that has been in the focus of interest as a promising technology for personal security screening for a number of years. In contradiction to established portal-based millimeter-wave scanning techniques, it allows for scanning people from a distance in real time with high throughput and without a distinct inspection procedure. This opens up new possibilities for scanning, which directly address an urgent security need of modern societies: protecting crowds and critical infrastructure from the growing threat of individual terror attacks. Considering the low radiometric contrast of indoor scenes in the submillimeter range, this objective calls for an extremely high detector sensitivity that can only be achieved using cooled detectors. Our approach to this task is a series of passive standoff video cameras for the 350 GHz band that represent an evolving concept and a continuous development since 2007. Arrays of superconducting transition-edge sensors (TES), operated at temperatures below 1 K, are used as radiation detectors. By this means, background limited performance (BLIP) mode is achieved, providing the maximum possible signal to noise ratio. At video rates, this leads to a temperature resolution well below 1 K. The imaging system is completed by reflector optics based on free-form mirrors. For object distances of 5-25 m, a field of view up to 2 m height and a diffraction-limited spatial resolution in the order of 1-2 cm is provided. Opto-mechanical scanning systems are part of the optical setup and capable of frame rates of up to 25 frames per second.

Bulk combinatorial synthesis and high throughput characterization for rapid assessment of magnetic materials: Application of laser engineered net shaping (LENS)

DOE PAGES

Geng, J.; Nlebedim, I. C.; Besser, M. F.; ...

2016-04-15

A bulk combinatorial approach for synthesizing alloy libraries using laser engineered net shaping (LENS; i.e., 3D printing) was utilized to rapidly assess material systems for magnetic applications. The LENS system feeds powders in different ratios into a melt pool created by a laser to synthesize samples with bulk (millimeters) dimensions. By analyzing these libraries with autosampler differential scanning calorimeter/thermal gravimetric analysis and vibrating sample magnetometry, we are able to rapidly characterize the thermodynamic and magnetic properties of the libraries. Furthermore, the Fe-Co binary alloy was used as a model system and the results were compared with data in the literature.

Compartmental genomics in living cells revealed by single-cell nanobiopsy.

PubMed

Actis, Paolo; Maalouf, Michelle M; Kim, Hyunsung John; Lohith, Akshar; Vilozny, Boaz; Seger, R Adam; Pourmand, Nader

2014-01-28

The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Here, we developed a single-cell nanobiopsy platform based on scanning ion conductance microscopy (SICM) for continuous sampling of intracellular content from individual cells. The nanobiopsy platform uses electrowetting within a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. We demonstrate the subcellular resolution of the nanobiopsy platform by isolating small subpopulations of mitochondria from single living cells, and quantify mutant mitochondrial genomes in those single cells with high throughput sequencing technology. These findings may provide the foundation for dynamic subcellular genomic analysis.

Application of polarization in high speed, high contrast inspection

NASA Astrophysics Data System (ADS)

Novak, Matthew J.

2017-08-01

Industrial optical inspection often requires high speed and high throughput of materials. Engineers use a variety of techniques to handle these inspection needs. Some examples include line scan cameras, high speed multi-spectral and laser-based systems. High-volume manufacturing presents different challenges for inspection engineers. For example, manufacturers produce some components in quantities of millions per month, per week or even per day. Quality control of so many parts requires creativity to achieve the measurement needs. At times, traditional vision systems lack the contrast to provide the data required. In this paper, we show how dynamic polarization imaging captures high contrast images. These images are useful for engineers to perform inspection tasks in some cases where optical contrast is low. We will cover basic theory of polarization. We show how to exploit polarization as a contrast enhancement technique. We also show results of modeling for a polarization inspection application. Specifically, we explore polarization techniques for inspection of adhesives on glass.

Lessons from high-throughput protein crystallization screening: 10 years of practical experience

PubMed Central

JR, Luft; EH, Snell; GT, DeTitta

2011-01-01

Introduction X-ray crystallography provides the majority of our structural biological knowledge at a molecular level and in terms of pharmaceutical design is a valuable tool to accelerate discovery. It is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. It is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomics. Areas covered The authors describe their experiences in high-throughput crystallization screening in the context of structural genomics and the general biomedical community. They focus on the lessons learnt from the operation of a high-throughput crystallization screening laboratory, which to date has screened over 12,500 biological macromolecules. They also describe the approaches taken to maximize the success while minimizing the effort. Through this, the authors hope that the reader will gain an insight into the efficient design of a laboratory and protocols to accomplish high-throughput crystallization on a single-, multiuser-laboratory or industrial scale. Expert Opinion High-throughput crystallization screening is readily available but, despite the power of the crystallographic technique, getting crystals is still not a solved problem. High-throughput approaches can help when used skillfully; however, they still require human input in the detailed analysis and interpretation of results to be more successful. PMID:22646073

High-throughput screening based on label-free detection of small molecule microarrays

NASA Astrophysics Data System (ADS)

Zhu, Chenggang; Fei, Yiyan; Zhu, Xiangdong

2017-02-01

Based on small-molecule microarrays (SMMs) and oblique-incidence reflectivity difference (OI-RD) scanner, we have developed a novel high-throughput drug preliminary screening platform based on label-free monitoring of direct interactions between target proteins and immobilized small molecules. The screening platform is especially attractive for screening compounds against targets of unknown function and/or structure that are not compatible with functional assay development. In this screening platform, OI-RD scanner serves as a label-free detection instrument which is able to monitor about 15,000 biomolecular interactions in a single experiment without the need to label any biomolecule. Besides, SMMs serves as a novel format for high-throughput screening by immobilization of tens of thousands of different compounds on a single phenyl-isocyanate functionalized glass slide. Based on the high-throughput screening platform, we sequentially screened five target proteins (purified target proteins or cell lysate containing target protein) in high-throughput and label-free mode. We found hits for respective target protein and the inhibition effects for some hits were confirmed by following functional assays. Compared to traditional high-throughput screening assay, the novel high-throughput screening platform has many advantages, including minimal sample consumption, minimal distortion of interactions through label-free detection, multi-target screening analysis, which has a great potential to be a complementary screening platform in the field of drug discovery.

High-throughput analysis of yeast replicative aging using a microfluidic system

PubMed Central

Jo, Myeong Chan; Liu, Wei; Gu, Liang; Dang, Weiwei; Qin, Lidong

2015-01-01

Saccharomyces cerevisiae has been an important model for studying the molecular mechanisms of aging in eukaryotic cells. However, the laborious and low-throughput methods of current yeast replicative lifespan assays limit their usefulness as a broad genetic screening platform for research on aging. We address this limitation by developing an efficient, high-throughput microfluidic single-cell analysis chip in combination with high-resolution time-lapse microscopy. This innovative design enables, to our knowledge for the first time, the determination of the yeast replicative lifespan in a high-throughput manner. Morphological and phenotypical changes during aging can also be monitored automatically with a much higher throughput than previous microfluidic designs. We demonstrate highly efficient trapping and retention of mother cells, determination of the replicative lifespan, and tracking of yeast cells throughout their entire lifespan. Using the high-resolution and large-scale data generated from the high-throughput yeast aging analysis (HYAA) chips, we investigated particular longevity-related changes in cell morphology and characteristics, including critical cell size, terminal morphology, and protein subcellular localization. In addition, because of the significantly improved retention rate of yeast mother cell, the HYAA-Chip was capable of demonstrating replicative lifespan extension by calorie restriction. PMID:26170317

Reflective optical imaging system with balanced distortion

DOEpatents

Chapman, Henry N.; Hudyma, Russell M.; Shafer, David R.; Sweeney, Donald W.

1999-01-01

An optical system compatible with short wavelength (extreme ultraviolet) An optical system compatible with short wavelength (extreme ultraviolet) radiation comprising four reflective elements for projecting a mask image onto a substrate. The four optical elements comprise, in order from object to image, convex, concave, convex and concave mirrors. The optical system is particularly suited for step and scan lithography methods. The invention enables the use of larger slit dimensions associated with ring field scanning optics, improves wafer throughput and allows higher semiconductor device density. The inventive optical system is characterized by reduced dynamic distortion because the static distortion is balanced across the slit width.

Resolution modeling of dispersive imaging spectrometers

NASA Astrophysics Data System (ADS)

Silny, John F.

2017-08-01

This paper presents best practices for modeling the resolution of dispersive imaging spectrometers. The differences between sampling, width, and resolution are discussed. It is proposed that the spectral imaging community adopt a standard definition for resolution as the full-width at half maximum of the total line spread function. Resolution should be computed for each of the spectral, cross-scan spatial, and along-scan spatial/temporal dimensions separately. A physical optics resolution model is presented that incorporates the effects of slit diffraction and partial coherence, the result of which is a narrower slit image width and reduced radiometric throughput.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yulaev, Alexander; Guo, Hongxuan; Strelcov, Evgheni

Atomic-scale thickness, molecular impermeability, low atomic number, and mechanical strength make graphene an ideal electron-transparent membrane for material characterization in liquids and gases with scanning electron microscopy and spectroscopy. Here in this paper, we present a novel sample platform made of an array of thousands of identical isolated graphene-capped microchannels with high aspect ratio. A combination of a global wide field of view with high resolution local imaging of the array allows for high throughput in situ studies as well as for combinatorial screening of solutions, liquid interfaces, and immersed samples. We demonstrate the capabilities of this platform by studyingmore » a pure water sample in comparison with alkali halide solutions, a model electrochemical plating process, and beam-induced crystal growth in liquid electrolyte. Spectroscopic characterization of liquid interfaces and immersed objects with Auger and X-ray fluorescence analysis through the graphene membrane are also demonstrated.« less

Graphene Microcapsule Arrays for Combinatorial Electron Microscopy and Spectroscopy in Liquids

DOE PAGES

Yulaev, Alexander; Guo, Hongxuan; Strelcov, Evgheni; ...

2017-04-27

Atomic-scale thickness, molecular impermeability, low atomic number, and mechanical strength make graphene an ideal electron-transparent membrane for material characterization in liquids and gases with scanning electron microscopy and spectroscopy. Here in this paper, we present a novel sample platform made of an array of thousands of identical isolated graphene-capped microchannels with high aspect ratio. A combination of a global wide field of view with high resolution local imaging of the array allows for high throughput in situ studies as well as for combinatorial screening of solutions, liquid interfaces, and immersed samples. We demonstrate the capabilities of this platform by studyingmore » a pure water sample in comparison with alkali halide solutions, a model electrochemical plating process, and beam-induced crystal growth in liquid electrolyte. Spectroscopic characterization of liquid interfaces and immersed objects with Auger and X-ray fluorescence analysis through the graphene membrane are also demonstrated.« less

Measuring molecular biomarkers in epidemiologic studies: laboratory techniques and biospecimen considerations.

PubMed

Erickson, Heidi S

2012-09-28

The future of personalized medicine depends on the ability to efficiently and rapidly elucidate a reliable set of disease-specific molecular biomarkers. High-throughput molecular biomarker analysis methods have been developed to identify disease risk, diagnostic, prognostic, and therapeutic targets in human clinical samples. Currently, high throughput screening allows us to analyze thousands of markers from one sample or one marker from thousands of samples and will eventually allow us to analyze thousands of markers from thousands of samples. Unfortunately, the inherent nature of current high throughput methodologies, clinical specimens, and cost of analysis is often prohibitive for extensive high throughput biomarker analysis. This review summarizes the current state of high throughput biomarker screening of clinical specimens applicable to genetic epidemiology and longitudinal population-based studies with a focus on considerations related to biospecimens, laboratory techniques, and sample pooling. Copyright © 2012 John Wiley & Sons, Ltd.

Synthesis of nanoparticles in a flame aerosol reactor with independent and strict control of their size, crystal phase and morphology

NASA Astrophysics Data System (ADS)

Jiang, Jingkun; Chen, Da-Ren; Biswas, Pratim

2007-07-01

A flame aerosol reactor (FLAR) was developed to synthesize nanoparticles with desired properties (crystal phase and size) that could be independently controlled. The methodology was demonstrated for TiO2 nanoparticles, and this is the first time that large sets of samples with the same size but different crystal phases (six different ratios of anatase to rutile in this work) were synthesized. The degree of TiO2 nanoparticle agglomeration was determined by comparing the primary particle size distribution measured by scanning electron microscopy (SEM) to the mobility-based particle size distribution measured by online scanning mobility particle spectrometry (SMPS). By controlling the flame aerosol reactor conditions, both spherical unagglomerated particles and highly agglomerated particles were produced. To produce monodisperse nanoparticles, a high throughput multi-stage differential mobility analyser (MDMA) was used in series with the flame aerosol reactor. Nearly monodisperse nanoparticles (geometric standard deviation less than 1.05) could be collected in sufficient mass quantities (of the order of 10 mg) in reasonable time (1 h) that could be used in other studies such as determination of functionality or biological effects as a function of size.

Ultra-short pulse laser micro patterning with highest throughput by utilization of a novel multi-beam processing head

NASA Astrophysics Data System (ADS)

Homburg, Oliver; Jarczynski, Manfred; Mitra, Thomas; Brüning, Stephan

2017-02-01

In the last decade much improvement has been achieved for ultra-short pulse lasers with high repetition rates. This laser technology has vastly matured so that it entered a manifold of industrial applications recently compared to mainly scientific use in the past. Compared to ns-pulse ablation ultra-short pulses in the ps- or even fs regime lead to still colder ablation and further reduced heat-affected zones. This is crucial for micro patterning when structure sizes are getting smaller and requirements are getting stronger at the same time. An additional advantage of ultra-fast processing is its applicability to a large variety of materials, e.g. metals and several high bandgap materials like glass and ceramics. One challenge for ultra-fast micro machining is throughput. The operational capacity of these processes can be maximized by increasing the scan rate or the number of beams - parallel processing. This contribution focuses on process parallelism of ultra-short pulsed lasers with high repetition rate and individually addressable acousto-optical beam modulation. The core of the multi-beam generation is a smooth diffractive beam splitter component with high uniform spots and negligible loss, and a prismatic array compressor to match beam size and pitch. The optical design and the practical realization of an 8 beam processing head in combination with a high average power single mode ultra-short pulsed laser source are presented as well as the currently on-going and promising laboratory research and micro machining results. Finally, an outlook of scaling the processing head to several tens of beams is given.

Optical detection of metastatic cancer cells using a scanned laser pico-projection system

NASA Astrophysics Data System (ADS)

Huang, Chih-Ling; Chiu, Wen-Tai; Lo, Yu-Lung; Chuang, Chin-Ho; Chen, Yu-Bin; Chang, Shu-Jing; Ke, Tung-Ting; Cheng, Hung-Chi; Wu, Hua-Lin

2015-03-01

Metastasis is responsible for 90% of all cancer-related deaths in humans. As a result, reliable techniques for detecting metastatic cells are urgently required. Although various techniques have been proposed for metastasis detection, they are generally capable of detecting metastatic cells only once migration has already occurred. Accordingly, the present study proposes an optical method for physical characterization of metastatic cancer cells using a scanned laser pico-projection system (SLPP). The validity of the proposed method is demonstrated using five pairs of cancer cell lines and two pairs of non-cancer cell lines treated by IPTG induction in order to mimic normal cells with an overexpression of oncogene. The results show that for all of the considered cell lines, the SLPP speckle contrast of the high-metastatic cells is significantly higher than that of the low-metastatic cells. As a result, the speckle contrast measurement provides a reliable means of distinguishing quantitatively between low- and high-metastatic cells of the same origin. Compared to existing metastasis detection methods, the proposed SLPP approach has many advantages, including a higher throughput, a lower cost, a larger sample size and a more reliable diagnostic performance. As a result, it provides a highly promising solution for physical characterization of metastatic cancer cells in vitro.

40 CFR Table 9 to Subpart Eeee of... - Continuous Compliance With Operating Limits-High Throughput Transfer Racks

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Continuous Compliance With Operating Limits-High Throughput Transfer Racks 9 Table 9 to Subpart EEEE of Part 63 Protection of Environment...—Continuous Compliance With Operating Limits—High Throughput Transfer Racks As stated in §§ 63.2378(a) and (b...

Accelerating the design of solar thermal fuel materials through high throughput simulations.

PubMed

Liu, Yun; Grossman, Jeffrey C

2014-12-10

Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.

Multiple-animal MR imaging using a 3T clinical scanner and multi-channel coil for volumetric analysis in a mouse tumor model.

PubMed

Mitsuda, Minoru; Yamaguchi, Masayuki; Furuta, Toshihiro; Nabetani, Akira; Hirayama, Akira; Nozaki, Atsushi; Niitsu, Mamoru; Fujii, Hirofumi

2011-01-01

Multiple small-animal magnetic resonance (MR) imaging to measure tumor volume may increase the throughput of preclinical cancer research assessing tumor response to novel therapies. We used a clinical scanner and multi-channel coil to evaluate the usefulness of this imaging to assess experimental tumor volume in mice. We performed a phantom study to assess 2-dimensional (2D) geometric distortion using 9-cm spherical and 32-cell (8×4 one-cm(2) grids) phantoms using a 3-tesla clinical MR scanner and dedicated multi-channel coil composed of 16 5-cm circular coils. Employing the multi-channel coil, we simultaneously scanned 6 or 8 mice bearing sarcoma 180 tumors. We estimated tumor volume from the sum of the product of tumor area and slice thickness on 2D spin-echo images (repetition time/echo time, 3500/16 ms; in-plane resolution, 0.195×0.195×1 mm(3)). After MR acquisition, we excised and weighed tumors, calculated reference tumor volumes from actual tumor weight assuming a density of 1.05 g/cm(3), and assessed the correlation between the estimated and reference volumes using Pearson's test. Two-dimensional geometric distortion was acceptable below 5% in the 9-cm spherical phantom and in every cell in the 32-cell phantom. We scanned up to 8 mice simultaneously using the multi-channel coil and found 11 tumors larger than 0.1 g in 12 mice. Tumor volumes were 1.04±0.73 estimated by MR imaging and 1.04±0.80 cm(3) by reference volume (average±standard deviation) and highly correlated (correlation coefficient, 0.995; P<0.01, Pearson's test). Use of multiple small-animal MR imaging employing a clinical scanner and multi-channel coil enabled accurate assessment of experimental tumor volume in a large number of mice and may facilitate high throughput monitoring of tumor response to therapy in preclinical research.

The combination of gas-phase fluorophore technology and automation to enable high-throughput analysis of plant respiration.

PubMed

Scafaro, Andrew P; Negrini, A Clarissa A; O'Leary, Brendan; Rashid, F Azzahra Ahmad; Hayes, Lucy; Fan, Yuzhen; Zhang, You; Chochois, Vincent; Badger, Murray R; Millar, A Harvey; Atkin, Owen K

2017-01-01

Mitochondrial respiration in the dark ( R dark ) is a critical plant physiological process, and hence a reliable, efficient and high-throughput method of measuring variation in rates of R dark is essential for agronomic and ecological studies. However, currently methods used to measure R dark in plant tissues are typically low throughput. We assessed a high-throughput automated fluorophore system of detecting multiple O 2 consumption rates. The fluorophore technique was compared with O 2 -electrodes, infrared gas analysers (IRGA), and membrane inlet mass spectrometry, to determine accuracy and speed of detecting respiratory fluxes. The high-throughput fluorophore system provided stable measurements of R dark in detached leaf and root tissues over many hours. High-throughput potential was evident in that the fluorophore system was 10 to 26-fold faster per sample measurement than other conventional methods. The versatility of the technique was evident in its enabling: (1) rapid screening of R dark in 138 genotypes of wheat; and, (2) quantification of rarely-assessed whole-plant R dark through dissection and simultaneous measurements of above- and below-ground organs. Variation in absolute R dark was observed between techniques, likely due to variation in sample conditions (i.e. liquid vs. gas-phase, open vs. closed systems), indicating that comparisons between studies using different measuring apparatus may not be feasible. However, the high-throughput protocol we present provided similar values of R dark to the most commonly used IRGA instrument currently employed by plant scientists. Together with the greater than tenfold increase in sample processing speed, we conclude that the high-throughput protocol enables reliable, stable and reproducible measurements of R dark on multiple samples simultaneously, irrespective of plant or tissue type.

Simultaneous Measurements of Auto-Immune and Infectious Disease Specific Antibodies Using a High Throughput Multiplexing Tool

PubMed Central

Asati, Atul; Kachurina, Olga; Kachurin, Anatoly

2012-01-01

Considering importance of ganglioside antibodies as biomarkers in various immune-mediated neuropathies and neurological disorders, we developed a high throughput multiplexing tool for the assessment of gangliosides-specific antibodies based on Biolpex/Luminex platform. In this report, we demonstrate that the ganglioside high throughput multiplexing tool is robust, highly specific and demonstrating ∼100-fold higher concentration sensitivity for IgG detection than ELISA. In addition to the ganglioside-coated array, the high throughput multiplexing tool contains beads coated with influenza hemagglutinins derived from H1N1 A/Brisbane/59/07 and H1N1 A/California/07/09 strains. Influenza beads provided an added advantage of simultaneous detection of ganglioside- and influenza-specific antibodies, a capacity important for the assay of both infectious antigen-specific and autoimmune antibodies following vaccination or disease. Taken together, these results support the potential adoption of the ganglioside high throughput multiplexing tool for measuring ganglioside antibodies in various neuropathic and neurological disorders. PMID:22952605

High-throughput sample adaptive offset hardware architecture for high-efficiency video coding

NASA Astrophysics Data System (ADS)

Zhou, Wei; Yan, Chang; Zhang, Jingzhi; Zhou, Xin

2018-03-01

A high-throughput hardware architecture for a sample adaptive offset (SAO) filter in the high-efficiency video coding video coding standard is presented. First, an implementation-friendly and simplified bitrate estimation method of rate-distortion cost calculation is proposed to reduce the computational complexity in the mode decision of SAO. Then, a high-throughput VLSI architecture for SAO is presented based on the proposed bitrate estimation method. Furthermore, multiparallel VLSI architecture for in-loop filters, which integrates both deblocking filter and SAO filter, is proposed. Six parallel strategies are applied in the proposed in-loop filters architecture to improve the system throughput and filtering speed. Experimental results show that the proposed in-loop filters architecture can achieve up to 48% higher throughput in comparison with prior work. The proposed architecture can reach a high-operating clock frequency of 297 MHz with TSMC 65-nm library and meet the real-time requirement of the in-loop filters for 8 K × 4 K video format at 132 fps.

Micro-computed tomography imaging and analysis in developmental biology and toxicology.

PubMed

Wise, L David; Winkelmann, Christopher T; Dogdas, Belma; Bagchi, Ansuman

2013-06-01

Micro-computed tomography (micro-CT) is a high resolution imaging technique that has expanded and strengthened in use since it was last reviewed in this journal in 2004. The technology has expanded to include more detailed analysis of bone, as well as soft tissues, by use of various contrast agents. It is increasingly applied to questions in developmental biology and developmental toxicology. Relatively high-throughput protocols now provide a powerful and efficient means to evaluate embryos and fetuses subjected to genetic manipulations or chemical exposures. This review provides an overview of the technology, including scanning, reconstruction, visualization, segmentation, and analysis of micro-CT generated images. This is followed by a review of more recent applications of the technology in some common laboratory species that highlight the diverse issues that can be addressed. Copyright © 2013 Wiley Periodicals, Inc.

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

Extensive scanning of the calpain-3 gene broadens the spectrum of LGMD2A phenotypes

PubMed Central

Piluso, G; Politano, L; Aurino, S; Fanin, M; Ricci, E; Ventriglia, V; Belsito, A; Totaro, A; Saccone, V; Topaloglu, H; Nascimbeni, A; Fulizio, L; Broccolini, A; Canki-Klain, N; Comi, L; Nigro, G; Angelini, C; Nigro, V

2005-01-01

Background: The limb girdle muscular dystrophies (LGMD) are a heterogeneous group of Mendelian disorders highlighted by weakness of the pelvic and shoulder girdle muscles. Seventeen autosomal loci have been so far identified and genetic tests are mandatory to distinguish among the forms. Mutations at the calpain 3 locus (CAPN3) cause LGMD type 2A. Objective: To obtain unbiased information on the consequences of CAPN3 mutations. Patients: 530 subjects with different grades of symptoms and 300 controls. Methods: High throughput denaturing HPLC analysis of DNA pools. Results: 141 LGMD2A cases were identified, carrying 82 different CAPN3 mutations (45 novel), along with 18 novel polymorphisms/variants. Females had a more favourable course than males. In 94% of the more severely affected patient group, the defect was also discovered in the second allele. This proves the sensitivity of the approach. CAPN3 mutations were found in 35.1% of classical LGMD phenotypes. Mutations were also found in 18.4% of atypical patients and in 12.6% of subjects with high serum creatine kinase levels. Conclusions: A non-invasive and cost–effective strategy, based on the high throughput denaturing HPLC analysis of DNA pools, was used to obtain unbiased information on the consequences of CAPN3 mutations in the largest genetic study ever undertaken. This broadens the spectrum of LGMD2A phenotypes and sets the carrier frequency at 1:103. PMID:16141003

Development of a detachable high speed miniature scanning probe microscope for large area substrates inspection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadeghian, Hamed, E-mail: hamed.sadeghianmarnani@tno.nl, E-mail: h.sadeghianmarnani@tudelft.nl; Department of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628 CD Delft; Herfst, Rodolf

We have developed a high speed, miniature scanning probe microscope (MSPM) integrated with a Positioning Unit (PU) for accurately positioning the MSPM on a large substrate. This combination enables simultaneous, parallel operation of many units on a large sample for high throughput measurements. The size of the MSPM is 19 × 45 × 70 mm{sup 3}. It contains a one-dimensional flexure stage with counter-balanced actuation for vertical scanning with a bandwidth of 50 kHz and a z-travel range of more than 2 μm. This stage is mechanically decoupled from the rest of the MSPM by suspending it on specific dynamicallymore » determined points. The motion of the probe, which is mounted on top of the flexure stage is measured by a very compact optical beam deflection (OBD). Thermal noise spectrum measurements of short cantilevers show a bandwidth of 2 MHz and a noise of less than 15 fm/Hz{sup 1/2}. A fast approach and engagement of the probe to the substrate surface have been achieved by integrating a small stepper actuator and direct monitoring of the cantilever response to the approaching surface. The PU has the same width as the MSPM, 45 mm and can position the MSPM to a pre-chosen position within an area of 275×30 mm{sup 2} to within 100 nm accuracy within a few seconds. During scanning, the MSPM is detached from the PU which is essential to eliminate mechanical vibration and drift from the relatively low-resonance frequency and low-stiffness structure of the PU. Although the specific implementation of the MSPM we describe here has been developed as an atomic force microscope, the general architecture is applicable to any form of SPM. This high speed MSPM is now being used in a parallel SPM architecture for inspection and metrology of large samples such as semiconductor wafers and masks.« less

High-resolution melting (HRM) assay for the detection of recurrent BRCA1/BRCA2 germline mutations in Tunisian breast/ovarian cancer families.

PubMed

Riahi, Aouatef; Kharrat, Maher; Lariani, Imen; Chaabouni-Bouhamed, Habiba

2014-12-01

Germline deleterious mutations in the BRCA1/BRCA2 genes are associated with an increased risk for the development of breast and ovarian cancer. Given the large size of these genes the detection of such mutations represents a considerable technical challenge. Therefore, the development of cost-effective and rapid methods to identify these mutations became a necessity. High resolution melting analysis (HRM) is a rapid and efficient technique extensively employed as high-throughput mutation scanning method. The purpose of our study was to assess the specificity and sensitivity of HRM for BRCA1 and BRCA2 genes scanning. As a first step we estimate the ability of HRM for detection mutations in a set of 21 heterozygous samples harboring 8 different known BRCA1/BRCA2 variations, all samples had been preliminarily investigated by direct sequencing, and then we performed a blinded analysis by HRM in a set of 68 further sporadic samples of unknown genotype. All tested heterozygous BRCA1/BRCA2 variants were easily identified. However the HRM assay revealed further alteration that we initially had not searched (one unclassified variant). Furthermore, sequencing confirmed all the HRM detected mutations in the set of unknown samples, including homozygous changes, indicating that in this cohort, with the optimized assays, the mutations detections sensitivity and specificity were 100 %. HRM is a simple, rapid and efficient scanning method for known and unknown BRCA1/BRCA2 germline mutations. Consequently the method will allow for the economical screening of recurrent mutations in Tunisian population.

Evaluating the effects of buffer conditions and extremolytes on thermostability of granulocyte colony-stimulating factor using high-throughput screening combined with design of experiments.

PubMed

Ablinger, Elisabeth; Hellweger, Monika; Leitgeb, Stefan; Zimmer, Andreas

2012-10-15

In this study, we combined a high-throughput screening method, differential scanning fluorimetry (DSF), with design of experiments (DoE) methodology to evaluate the effects of several formulation components on the thermostability of granulocyte colony stimulating factor (G-CSF). First we performed a primary buffer screening where we tested thermal stability of G-CSF in different buffers, pH values and buffer concentrations. The significance of each factor and the two-way interactions between them were studied by multivariable regression analysis. pH was identified as most critical factor regarding thermal stability. The most stabilizing buffer, sodium glutamate, and sodium acetate were determined for further investigations. Second we tested the effect of 6 naturally occurring extremolytes (trehalose, sucrose, ectoine, hydroxyectoine, sorbitol, mannitol) on the thermal stability of G-CSF, using a central composite circumscribed design. At low pH (3.8) and low buffer concentration (5 mM) all extremolytes led to a significant increase in thermal stability except the addition of ectoine which resulted in a strong destabilization of G-CSF. Increasing pH and buffer concentration led to an increase in thermal stability with all investigated extremolytes. The described systematic approach allowed to create a ranking of stabilizing extremolytes at different buffer conditions. Copyright © 2012. Published by Elsevier B.V.

Detection of co-eluted peptides using database search methods

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y; Kwok, Siwei; Wu, Wells W; Wang, Guanghui; Shen, Rong-Fong; Yu, Yi-Kuo

2008-01-01

Background Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. Results We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. Open peer review Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section. PMID:18597684

Coupling unbiased mutagenesis to high-throughput DNA sequencing uncovers functional domains in the Ndc80 kinetochore protein of Saccharomyces cerevisiae.

PubMed

Tien, Jerry F; Fong, Kimberly K; Umbreit, Neil T; Payen, Celia; Zelter, Alex; Asbury, Charles L; Dunham, Maitreya J; Davis, Trisha N

2013-09-01

During mitosis, kinetochores physically link chromosomes to the dynamic ends of spindle microtubules. This linkage depends on the Ndc80 complex, a conserved and essential microtubule-binding component of the kinetochore. As a member of the complex, the Ndc80 protein forms microtubule attachments through a calponin homology domain. Ndc80 is also required for recruiting other components to the kinetochore and responding to mitotic regulatory signals. While the calponin homology domain has been the focus of biochemical and structural characterization, the function of the remainder of Ndc80 is poorly understood. Here, we utilized a new approach that couples high-throughput sequencing to a saturating linker-scanning mutagenesis screen in Saccharomyces cerevisiae. We identified domains in previously uncharacterized regions of Ndc80 that are essential for its function in vivo. We show that a helical hairpin adjacent to the calponin homology domain influences microtubule binding by the complex. Furthermore, a mutation in this hairpin abolishes the ability of the Dam1 complex to strengthen microtubule attachments made by the Ndc80 complex. Finally, we defined a C-terminal segment of Ndc80 required for tetramerization of the Ndc80 complex in vivo. This unbiased mutagenesis approach can be generally applied to genes in S. cerevisiae to identify functional properties and domains.

Application of DNA Chip Scanning Technology for Automatic Detection of Chlamydia trachomatis and Chlamydia pneumoniae Inclusions

PubMed Central

Bogdanov, Anita; Endrész, Valeria; Urbán, Szabolcs; Lantos, Ildikó; Deák, Judit; Burián, Katalin; Önder, Kamil; Ayaydin, Ferhan; Balázs, Péter

2014-01-01

Chlamydiae are obligate intracellular bacteria that propagate in the inclusion, a specific niche inside the host cell. The standard method for counting chlamydiae is immunofluorescent staining and manual counting of chlamydial inclusions. High- or medium-throughput estimation of the reduction in chlamydial inclusions should be the basis of testing antichlamydial compounds and other drugs that positively or negatively influence chlamydial growth, yet low-throughput manual counting is the common approach. To overcome the time-consuming and subjective manual counting, we developed an automatic inclusion-counting system based on a commercially available DNA chip scanner. Fluorescently labeled inclusions are detected by the scanner, and the image is processed by ChlamyCount, a custom plug-in of the ImageJ software environment. ChlamyCount was able to measure the inclusion counts over a 1-log-unit dynamic range with a high correlation to the theoretical counts. ChlamyCount was capable of accurately determining the MICs of the novel antimicrobial compound PCC00213 and the already known antichlamydial antibiotics moxifloxacin and tetracycline. ChlamyCount was also able to measure the chlamydial growth-altering effect of drugs that influence host-bacterium interaction, such as gamma interferon, DEAE-dextran, and cycloheximide. ChlamyCount is an easily adaptable system for testing antichlamydial antimicrobials and other compounds that influence Chlamydia-host interactions. PMID:24189259

Neural network control of focal position during time-lapse microscopy of cells.

PubMed

Wei, Ling; Roberts, Elijah

2018-05-09

Live-cell microscopy is quickly becoming an indispensable technique for studying the dynamics of cellular processes. Maintaining the specimen in focus during image acquisition is crucial for high-throughput applications, especially for long experiments or when a large sample is being continuously scanned. Automated focus control methods are often expensive, imperfect, or ill-adapted to a specific application and are a bottleneck for widespread adoption of high-throughput, live-cell imaging. Here, we demonstrate a neural network approach for automatically maintaining focus during bright-field microscopy. Z-stacks of yeast cells growing in a microfluidic device were collected and used to train a convolutional neural network to classify images according to their z-position. We studied the effect on prediction accuracy of the various hyperparameters of the neural network, including downsampling, batch size, and z-bin resolution. The network was able to predict the z-position of an image with ±1 μm accuracy, outperforming human annotators. Finally, we used our neural network to control microscope focus in real-time during a 24 hour growth experiment. The method robustly maintained the correct focal position compensating for 40 μm of focal drift and was insensitive to changes in the field of view. About ~100 annotated z-stacks were required to train the network making our method quite practical for custom autofocus applications.

Isolation of Exosome-Like Nanoparticles and Analysis of MicroRNAs Derived from Coconut Water Based on Small RNA High-Throughput Sequencing.

PubMed

Zhao, Zhehao; Yu, Siran; Li, Min; Gui, Xin; Li, Ping

2018-03-21

In this study, the presence of microRNAs in coconut water was identified by real-time polymerase chain reaction (PCR) based on the results of high-throughput small RNA sequencing. In addition, the differences in microRNA content between immature and mature coconut water were compared. A total of 47 known microRNAs belonging to 25 families and 14 new microRNAs were identified in coconut endosperm. Through analysis using a target gene prediction software, potential microRNA target genes were identified in the human genome. Real-time PCR showed that the level of most microRNAs was higher in mature coconut water than in immature coconut water. Then, exosome-like nanoparticles were isolated from coconut water. After ultracentrifugation, some particle structures were seen in coconut water samples using 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate fluorescence staining. Subsequent scanning electron microscopy observation and dynamic light scattering analysis also revealed some exosome-like nanoparticles in coconut water, and the mean diameters of the particles detected by the two methods were 13.16 and 59.72 nm, respectively. In conclusion, there are extracellular microRNAs in coconut water, and their levels are higher in mature coconut water than in immature coconut water. Some exosome-like nanoparticles were isolated from coconut water, and the diameter of these particles was smaller than that of animal-derived exosomes.

High throughput light absorber discovery, Part 1: An algorithm for automated tauc analysis

DOE PAGES

Suram, Santosh K.; Newhouse, Paul F.; Gregoire, John M.

2016-09-23

High-throughput experimentation provides efficient mapping of composition-property relationships, and its implementation for the discovery of optical materials enables advancements in solar energy and other technologies. In a high throughput pipeline, automated data processing algorithms are often required to match experimental throughput, and we present an automated Tauc analysis algorithm for estimating band gap energies from optical spectroscopy data. The algorithm mimics the judgment of an expert scientist, which is demonstrated through its application to a variety of high throughput spectroscopy data, including the identification of indirect or direct band gaps in Fe 2O 3, Cu 2V 2O 7, and BiVOmore » 4. Here, the applicability of the algorithm to estimate a range of band gap energies for various materials is demonstrated by a comparison of direct-allowed band gaps estimated by expert scientists and by automated algorithm for 60 optical spectra.« less

Ultra-High Throughput Synthesis of Nanoparticles with Homogeneous Size Distribution Using a Coaxial Turbulent Jet Mixer

PubMed Central

2015-01-01

High-throughput production of nanoparticles (NPs) with controlled quality is critical for their clinical translation into effective nanomedicines for diagnostics and therapeutics. Here we report a simple and versatile coaxial turbulent jet mixer that can synthesize a variety of NPs at high throughput up to 3 kg/d, while maintaining the advantages of homogeneity, reproducibility, and tunability that are normally accessible only in specialized microscale mixing devices. The device fabrication does not require specialized machining and is easy to operate. As one example, we show reproducible, high-throughput formulation of siRNA-polyelectrolyte polyplex NPs that exhibit effective gene knockdown but exhibit significant dependence on batch size when formulated using conventional methods. The coaxial turbulent jet mixer can accelerate the development of nanomedicines by providing a robust and versatile platform for preparation of NPs at throughputs suitable for in vivo studies, clinical trials, and industrial-scale production. PMID:24824296

A GPU-Parallelized Eigen-Based Clutter Filter Framework for Ultrasound Color Flow Imaging.

PubMed

Chee, Adrian J Y; Yiu, Billy Y S; Yu, Alfred C H

2017-01-01

Eigen-filters with attenuation response adapted to clutter statistics in color flow imaging (CFI) have shown improved flow detection sensitivity in the presence of tissue motion. Nevertheless, its practical adoption in clinical use is not straightforward due to the high computational cost for solving eigendecompositions. Here, we provide a pedagogical description of how a real-time computing framework for eigen-based clutter filtering can be developed through a single-instruction, multiple data (SIMD) computing approach that can be implemented on a graphical processing unit (GPU). Emphasis is placed on the single-ensemble-based eigen-filtering approach (Hankel singular value decomposition), since it is algorithmically compatible with GPU-based SIMD computing. The key algebraic principles and the corresponding SIMD algorithm are explained, and annotations on how such algorithm can be rationally implemented on the GPU are presented. Real-time efficacy of our framework was experimentally investigated on a single GPU device (GTX Titan X), and the computing throughput for varying scan depths and slow-time ensemble lengths was studied. Using our eigen-processing framework, real-time video-range throughput (24 frames/s) can be attained for CFI frames with full view in azimuth direction (128 scanlines), up to a scan depth of 5 cm ( λ pixel axial spacing) for slow-time ensemble length of 16 samples. The corresponding CFI image frames, with respect to the ones derived from non-adaptive polynomial regression clutter filtering, yielded enhanced flow detection sensitivity in vivo, as demonstrated in a carotid imaging case example. These findings indicate that the GPU-enabled eigen-based clutter filtering can improve CFI flow detection performance in real time.

Characterization of matrix effects in developing rugged high-throughput LC-MS/MS methods for bioanalysis.

PubMed

Li, Fumin; Wang, Jun; Jenkins, Rand

2016-05-01

There is an ever-increasing demand for high-throughput LC-MS/MS bioanalytical assays to support drug discovery and development. Matrix effects of sofosbuvir (protonated) and paclitaxel (sodiated) were thoroughly evaluated using high-throughput chromatography (defined as having a run time ≤1 min) under 14 elution conditions with extracts from protein precipitation, liquid-liquid extraction and solid-phase extraction. A slight separation, in terms of retention time, between underlying matrix components and sofosbuvir/paclitaxel can greatly alleviate matrix effects. High-throughput chromatography, with proper optimization, can provide rapid and effective chromatographic separation under 1 min to alleviate matrix effects and enhance assay ruggedness for regulated bioanalysis.

A compact sub-Kelvin ultrahigh vacuum scanning tunneling microscope with high energy resolution and high stability.

PubMed

Zhang, L; Miyamachi, T; Tomanić, T; Dehm, R; Wulfhekel, W

2011-10-01

We designed a scanning tunneling microscope working at sub-Kelvin temperatures in ultrahigh vacuum (UHV) in order to study the magnetic properties on the nanoscale. An entirely homebuilt three-stage cryostat is used to cool down the microscope head. The first stage is cooled with liquid nitrogen, the second stage with liquid (4)He. The third stage uses a closed-cycle Joule-Thomson refrigerator of a cooling power of 1 mW. A base temperature of 930 mK at the microscope head was achieved using expansion of (4)He, which can be reduced to ≈400 mK when using (3)He. The cryostat has a low liquid helium consumption of only 38 ml/h and standing times of up to 280 h. The fast cooling down of the samples (3 h) guarantees high sample throughput. Test experiments with a superconducting tip show a high energy resolution of 0.3 meV when performing scanning tunneling spectroscopy. The vertical stability of the tunnel junction is well below 1 pm (peak to peak) and the electric noise floor of tunneling current is about 6fA/√Hz. Atomic resolution with a tunneling current of 1 pA and 1 mV was achieved on Au(111). The lateral drift of the microscope at stable temperature is below 20 pm/h. A superconducting spilt-coil magnet allows to apply an out-of-plane magnetic field of up to 3 T at the sample surface. The flux vortices of a Nb(110) sample were clearly resolved in a map of differential conductance at 1.1 K and a magnetic field of 0.21 T. The setup is designed for in situ preparation of tip and samples under UHV condition.

Broad screening of illicit ingredients in cosmetics using ultra-high-performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry with customized accurate-mass database and mass spectral library.

PubMed

Meng, Xianshuang; Bai, Hua; Guo, Teng; Niu, Zengyuan; Ma, Qiang

2017-12-15

Comprehensive identification and quantitation of 100 multi-class regulated ingredients in cosmetics was achieved using ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid quadrupole-Orbitrap high-resolution mass spectrometry (Q-Orbitrap HRMS). A simple, efficient, and inexpensive sample pretreatment protocol was developed using ultrasound-assisted extraction (UAE), followed by dispersive solid-phase extraction (dSPE). The cosmetic samples were analyzed by UHPLC-Q-Orbitrap HRMS under synchronous full-scan MS and data-dependent MS/MS (full-scan MS 1 /dd-MS 2 ) acquisition mode. The mass resolution was set to 70,000 FWHM (full width at half maximum) for full-scan MS 1 and 17,500 FWHM for dd-MS 2 stage with the experimentally measured mass deviations of less than 2ppm (parts per million) for quasi-molecular ions and 5ppm for characteristic fragment ions for each individual analyte. An accurate-mass database and a mass spectral library were built in house for searching the 100 target compounds. Broad screening was conducted by comparing the experimentally measured exact mass of precursor and fragment ions, retention time, isotopic pattern, and ionic ratio with the accurate-mass database and by matching the acquired MS/MS spectra against the mass spectral library. The developed methodology was evaluated and validated in terms of limits of detection (LODs), limits of quantitation (LOQs), linearity, stability, accuracy, and matrix effect. The UHPLC-Q-Orbitrap HRMS approach was applied for the analysis of 100 target illicit ingredients in 123 genuine cosmetic samples, and exhibited great potential for high-throughput, sensitive, and reliable screening of multi-class illicit compounds in cosmetics. Copyright © 2017 Elsevier B.V. All rights reserved.

Screening of Carotenoids in Tomato Fruits by Using Liquid Chromatography with Diode Array-Linear Ion Trap Mass Spectrometry Detection.

PubMed

Gentili, Alessandra; Caretti, Fulvia; Ventura, Salvatore; Pérez-Fernández, Virginia; Venditti, Alessandro; Curini, Roberta

2015-08-26

This paper presents an analytical strategy for a large-scale screening of carotenoids in tomato fruits by exploiting the potentialities of the triple quadrupole-linear ion trap hybrid mass spectrometer (QqQLIT). The method involves separation on C30 reversed-phase column and identification by means of diode array detection (DAD) and atmospheric pressure chemical ionization-mass spectrometry (APCI-MS). The authentic standards of six model compounds were used to optimize the separative conditions and to predict the chromatographic behavior of untargeted carotenoids. An information dependent acquisition (IDA) was performed with (i) enhanced-mass scan (EMS) as the survey scan, (ii) enhanced-resolution (ER) scan to obtain the exact mass of the precursor ions (16-35 ppm), and (iii) enhanced product ion (EPI) scan as dependent scan to obtain structural information. LC-DAD-multiple reaction monitoring (MRM) chromatograms were also acquired for the identification of targeted carotenoids occurring at low concentrations; for the first time, the relative abundance between the MRM transitions (ion ratio) was used as an extra tool for the MS distinction of structural isomers and the related families of geometrical isomers. The whole analytical strategy was high-throughput, because a great number of experimental data could be acquired with few analytical steps, and cost-effective, because only few standards were used; when applied to characterize some tomato varieties ('Tangerine', 'Pachino', 'Datterino', and 'Camone') and passata of 'San Marzano' tomatoes, our method succeeded in identifying up to 44 carotenoids in the 'Tangerine'" variety.

High throughput system for magnetic manipulation of cells, polymers, and biomaterials

PubMed Central

Spero, Richard Chasen; Vicci, Leandra; Cribb, Jeremy; Bober, David; Swaminathan, Vinay; O’Brien, E. Timothy; Rogers, Stephen L.; Superfine, R.

2008-01-01

In the past decade, high throughput screening (HTS) has changed the way biochemical assays are performed, but manipulation and mechanical measurement of micro- and nanoscale systems have not benefited from this trend. Techniques using microbeads (particles ∼0.1–10 μm) show promise for enabling high throughput mechanical measurements of microscopic systems. We demonstrate instrumentation to magnetically drive microbeads in a biocompatible, multiwell magnetic force system. It is based on commercial HTS standards and is scalable to 96 wells. Cells can be cultured in this magnetic high throughput system (MHTS). The MHTS can apply independently controlled forces to 16 specimen wells. Force calibrations demonstrate forces in excess of 1 nN, predicted force saturation as a function of pole material, and powerlaw dependence of F∼r−2.7±0.1. We employ this system to measure the stiffness of SR2+ Drosophila cells. MHTS technology is a key step toward a high throughput screening system for micro- and nanoscale biophysical experiments. PMID:19044357

Carbohydrate Microarray Technology Applied to High-Throughput Mapping of Plant Cell Wall Glycans Using Comprehensive Microarray Polymer Profiling (CoMPP).

PubMed

Kračun, Stjepan Krešimir; Fangel, Jonatan Ulrik; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Vidal-Melgosa, Silvia; Willats, William George Tycho

2017-01-01

Cell walls are an important feature of plant cells and a major component of the plant glycome. They have both structural and physiological functions and are critical for plant growth and development. The diversity and complexity of these structures demand advanced high-throughput techniques to answer questions about their structure, functions and roles in both fundamental and applied scientific fields. Microarray technology provides both the high-throughput and the feasibility aspects required to meet that demand. In this chapter, some of the most recent microarray-based techniques relating to plant cell walls are described together with an overview of related contemporary techniques applied to carbohydrate microarrays and their general potential in glycoscience. A detailed experimental procedure for high-throughput mapping of plant cell wall glycans using the comprehensive microarray polymer profiling (CoMPP) technique is included in the chapter and provides a good example of both the robust and high-throughput nature of microarrays as well as their applicability to plant glycomics.

Identification of functional modules using network topology and high-throughput data.

PubMed

Ulitsky, Igor; Shamir, Ron

2007-01-26

With the advent of systems biology, biological knowledge is often represented today by networks. These include regulatory and metabolic networks, protein-protein interaction networks, and many others. At the same time, high-throughput genomics and proteomics techniques generate very large data sets, which require sophisticated computational analysis. Usually, separate and different analysis methodologies are applied to each of the two data types. An integrated investigation of network and high-throughput information together can improve the quality of the analysis by accounting simultaneously for topological network properties alongside intrinsic features of the high-throughput data. We describe a novel algorithmic framework for this challenge. We first transform the high-throughput data into similarity values, (e.g., by computing pairwise similarity of gene expression patterns from microarray data). Then, given a network of genes or proteins and similarity values between some of them, we seek connected sub-networks (or modules) that manifest high similarity. We develop algorithms for this problem and evaluate their performance on the osmotic shock response network in S. cerevisiae and on the human cell cycle network. We demonstrate that focused, biologically meaningful and relevant functional modules are obtained. In comparison with extant algorithms, our approach has higher sensitivity and higher specificity. We have demonstrated that our method can accurately identify functional modules. Hence, it carries the promise to be highly useful in analysis of high throughput data.

High-Throughput Computation and the Applicability of Monte Carlo Integration in Fatigue Load Estimation of Floating Offshore Wind Turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graf, Peter A.; Stewart, Gordon; Lackner, Matthew

Long-term fatigue loads for floating offshore wind turbines are hard to estimate because they require the evaluation of the integral of a highly nonlinear function over a wide variety of wind and wave conditions. Current design standards involve scanning over a uniform rectangular grid of metocean inputs (e.g., wind speed and direction and wave height and period), which becomes intractable in high dimensions as the number of required evaluations grows exponentially with dimension. Monte Carlo integration offers a potentially efficient alternative because it has theoretical convergence proportional to the inverse of the square root of the number of samples, whichmore » is independent of dimension. In this paper, we first report on the integration of the aeroelastic code FAST into NREL's systems engineering tool, WISDEM, and the development of a high-throughput pipeline capable of sampling from arbitrary distributions, running FAST on a large scale, and postprocessing the results into estimates of fatigue loads. Second, we use this tool to run a variety of studies aimed at comparing grid-based and Monte Carlo-based approaches with calculating long-term fatigue loads. We observe that for more than a few dimensions, the Monte Carlo approach can represent a large improvement in computational efficiency, but that as nonlinearity increases, the effectiveness of Monte Carlo is correspondingly reduced. The present work sets the stage for future research focusing on using advanced statistical methods for analysis of wind turbine fatigue as well as extreme loads.« less

Screening of 485 Pesticide Residues in Fruits and Vegetables by Liquid Chromatography-Quadrupole-Time-of-Flight Mass Spectrometry Based on TOF Accurate Mass Database and QTOF Spectrum Library.

PubMed

Pang, Guo-Fang; Fan, Chun-Lin; Chang, Qiao-Ying; Li, Jian-Xun; Kang, Jian; Lu, Mei-Ling

2018-03-22

This paper uses the LC-quadrupole-time-of-flight MS technique to evaluate the behavioral characteristics of MSof 485 pesticides under different conditions and has developed an accurate mass database and spectra library. A high-throughput screening and confirmation method has been developed for the 485 pesticides in fruits and vegetables. Through the optimization of parameters such as accurate mass number, time of retention window, ionization forms, etc., the method has improved the accuracy of pesticide screening, thus avoiding the occurrence of false-positive and false-negative results. The method features a full scan of fragments, with 80% of pesticide qualitative points over 10, which helps increase pesticide qualitative accuracy. The abundant differences of fragment categories help realize the effective separation and qualitative identification of isomer pesticides. Four different fruits and vegetables-apples, grapes, celery, and tomatoes-were chosen to evaluate the efficiency of the method at three fortification levels of 5, 10, and 20 μg/kg, and satisfactory results were obtained. With this method, a national survey of pesticide residues was conducted between 2012 and 2015 for 12 551 samples of 146 different fruits and vegetables collected from 638 sampling points in 284 counties across 31 provincial capitals/cities directly under the central government, which provided scientific data backup for ensuring pesticide residue safety of the fruits and vegetables consumed daily by the public. Meanwhile, the big data statistical analysis of the new technique also further proves it to be of high speed, high throughput, high accuracy, high reliability, and high informatization.

Microfluidic device for a rapid immobilization of zebrafish larvae in environmental scanning electron microscopy.

PubMed

Akagi, Jin; Zhu, Feng; Skommer, Joanna; Hall, Chris J; Crosier, Philip S; Cialkowski, Michal; Wlodkowic, Donald

2015-03-01

Small vertebrate model organisms have recently gained popularity as attractive experimental models that enhance our understanding of human tissue and organ development. Despite a large body of evidence using optical spectroscopy for the characterization of small model organism on chip-based devices, no attempts have been so far made to interface microfabricated technologies with environmental scanning electron microscopy (ESEM). Conventional scanning electron microscopy requires high vacuum environments and biological samples must be, therefore, submitted to many preparative procedures to dehydrate, fix, and subsequently stain the sample with gold-palladium deposition. This process is inherently low-throughput and can introduce many analytical artifacts. This work describes a proof-of-concept microfluidic chip-based system for immobilizing zebrafish larvae for ESEM imaging that is performed in a gaseous atmosphere, under low vacuum mode and without any need for sample staining protocols. The microfabricated technology provides a user-friendly and simple interface to perform ESEM imaging on zebrafish larvae. Presented lab-on-a-chip device was fabricated using a high-speed infrared laser micromachining in a biocompatible poly(methyl methacrylate) thermoplastic. It consisted of a reservoir with multiple semispherical microwells designed to hold the yolk of dechorionated zebrafish larvae. Immobilization of the larvae was achieved by a gentle suction generated during blotting of the medium. Trapping region allowed for multiple specimens to be conveniently positioned on the chip-based device within few minutes for ESEM imaging. © 2014 International Society for Advancement of Cytometry.

Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering.

PubMed

Groen, Nathalie; Guvendiren, Murat; Rabitz, Herschel; Welsh, William J; Kohn, Joachim; de Boer, Jan

2016-04-01

The research paradigm in biomaterials science and engineering is evolving from using low-throughput and iterative experimental designs towards high-throughput experimental designs for materials optimization and the evaluation of materials properties. Computational science plays an important role in this transition. With the emergence of the omics approach in the biomaterials field, referred to as materiomics, high-throughput approaches hold the promise of tackling the complexity of materials and understanding correlations between material properties and their effects on complex biological systems. The intrinsic complexity of biological systems is an important factor that is often oversimplified when characterizing biological responses to materials and establishing property-activity relationships. Indeed, in vitro tests designed to predict in vivo performance of a given biomaterial are largely lacking as we are not able to capture the biological complexity of whole tissues in an in vitro model. In this opinion paper, we explain how we reached our opinion that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. In this opinion paper, we postulate that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. Copyright © 2016. Published by Elsevier Ltd.

A high-throughput AO/PI-based cell concentration and viability detection method using the Celigo image cytometry.

PubMed

Chan, Leo Li-Ying; Smith, Tim; Kumph, Kendra A; Kuksin, Dmitry; Kessel, Sarah; Déry, Olivier; Cribbes, Scott; Lai, Ning; Qiu, Jean

2016-10-01

To ensure cell-based assays are performed properly, both cell concentration and viability have to be determined so that the data can be normalized to generate meaningful and comparable results. Cell-based assays performed in immuno-oncology, toxicology, or bioprocessing research often require measuring of multiple samples and conditions, thus the current automated cell counter that uses single disposable counting slides is not practical for high-throughput screening assays. In the recent years, a plate-based image cytometry system has been developed for high-throughput biomolecular screening assays. In this work, we demonstrate a high-throughput AO/PI-based cell concentration and viability method using the Celigo image cytometer. First, we validate the method by comparing directly to Cellometer automated cell counter. Next, cell concentration dynamic range, viability dynamic range, and consistency are determined. The high-throughput AO/PI method described here allows for 96-well to 384-well plate samples to be analyzed in less than 7 min, which greatly reduces the time required for the single sample-based automated cell counter. In addition, this method can improve the efficiency for high-throughput screening assays, where multiple cell counts and viability measurements are needed prior to performing assays such as flow cytometry, ELISA, or simply plating cells for cell culture.

Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy

PubMed Central

Actis, Paolo; Maalouf, Michelle; Kim, Hyunsung John; Lohith, Akshar; Vilozny, Boaz; Seger, R. Adam; Pourmand, Nader

2014-01-01

The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Here, we developed a single-cell nanobiopsy platform based on scanning ion conductance microscopy (SICM) for continuous sampling of intracellular content from individual cells. The nanobiopsy platform uses electrowetting within a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. We demonstrate the subcellular resolution of the nanobiopsy platform by isolating small subpopulations of mitochondria from single living cells, and quantify mutant mitochondrial genomes in those single cells with high throughput sequencing technology. These findings may provide the foundation for dynamic subcellular genomic analysis. PMID:24279711

Characterization of the NEXT Hollow Cathode Inserts After Long-Duration Testing

NASA Technical Reports Server (NTRS)

Mackey, J.; Shastry, R.; Soulas, G.

2017-01-01

Hollow dispenser cathode inserts are a critical element of electric propulsion systems, and should therefore be well understood during long term operation to ensure reliable system performance. This work destructively investigated cathode inserts from the NEXT long-duration test which demonstrated 51,184 hours of high-voltage operation, 918 kg of propellant throughput, and 35.5 MN-s of total impulse. The characterization methods used include scanning electron microscopy with energy dispersive spectroscopy and X-ray diffraction. Microscopy analysis has been performed on fractured surfaces, emission surfaces, and metallographically polished cross-sections of post-test inserts and unused inserts. Impregnate distribution, etch region thickness, impregnate chemical content, emission surface topography, and emission surface phase identification are the primary factors investigated.

Advances in gallium arsenide monolithic microwave integrated-circuit technology for space communications systems

NASA Technical Reports Server (NTRS)

Bhasin, K. B.; Connolly, D. J.

1986-01-01

Future communications satellites are likely to use gallium arsenide (GaAs) monolithic microwave integrated-circuit (MMIC) technology in most, if not all, communications payload subsystems. Multiple-scanning-beam antenna systems are expected to use GaAs MMIC's to increase functional capability, to reduce volume, weight, and cost, and to greatly improve system reliability. RF and IF matrix switch technology based on GaAs MMIC's is also being developed for these reasons. MMIC technology, including gigabit-rate GaAs digital integrated circuits, offers substantial advantages in power consumption and weight over silicon technologies for high-throughput, on-board baseband processor systems. In this paper, current developments in GaAs MMIC technology are described, and the status and prospects of the technology are assessed.

A zero-error operational video data compression system

NASA Technical Reports Server (NTRS)

Kutz, R. L.

1973-01-01

A data compression system has been operating since February 1972, using ATS spin-scan cloud cover data. With the launch of ITOS 3 in October 1972, this data compression system has become the only source of near-realtime very high resolution radiometer image data at the data processing facility. The VHRR image data are compressed and transmitted over a 50 kilobit per second wideband ground link. The goal of the data compression experiment was to send data quantized to six bits at twice the rate possible when no compression is used, while maintaining zero error between the transmitted and reconstructed data. All objectives of the data compression experiment were met, and thus a capability of doubling the data throughput of the system has been achieved.

Accelerating the Design of Solar Thermal Fuel Materials through High Throughput Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Y; Grossman, JC

2014-12-01

Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastablemore » structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.« less

40 CFR Table 3 to Subpart Eeee of... - Operating Limits-High Throughput Transfer Racks

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Operating Limits-High Throughput Transfer Racks 3 Table 3 to Subpart EEEE of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION... Throughput Transfer Racks As stated in § 63.2346(e), you must comply with the operating limits for existing...

Compound Transfer by Acoustic Droplet Ejection Promotes Quality and Efficiency in Ultra-High-Throughput Screening Campaigns.

PubMed

Dawes, Timothy D; Turincio, Rebecca; Jones, Steven W; Rodriguez, Richard A; Gadiagellan, Dhireshan; Thana, Peter; Clark, Kevin R; Gustafson, Amy E; Orren, Linda; Liimatta, Marya; Gross, Daniel P; Maurer, Till; Beresini, Maureen H

2016-02-01

Acoustic droplet ejection (ADE) as a means of transferring library compounds has had a dramatic impact on the way in which high-throughput screening campaigns are conducted in many laboratories. Two Labcyte Echo ADE liquid handlers form the core of the compound transfer operation in our 1536-well based ultra-high-throughput screening (uHTS) system. Use of these instruments has promoted flexibility in compound formatting in addition to minimizing waste and eliminating compound carryover. We describe the use of ADE for the generation of assay-ready plates for primary screening as well as for follow-up dose-response evaluations. Custom software has enabled us to harness the information generated by the ADE instrumentation. Compound transfer via ADE also contributes to the screening process outside of the uHTS system. A second fully automated ADE-based system has been used to augment the capacity of the uHTS system as well as to permit efficient use of previously picked compound aliquots for secondary assay evaluations. Essential to the utility of ADE in the high-throughput screening process is the high quality of the resulting data. Examples of data generated at various stages of high-throughput screening campaigns are provided. Advantages and disadvantages of the use of ADE in high-throughput screening are discussed. © 2015 Society for Laboratory Automation and Screening.

An Automated High-Throughput System to Fractionate Plant Natural Products for Drug Discovery

PubMed Central

Tu, Ying; Jeffries, Cynthia; Ruan, Hong; Nelson, Cynthia; Smithson, David; Shelat, Anang A.; Brown, Kristin M.; Li, Xing-Cong; Hester, John P.; Smillie, Troy; Khan, Ikhlas A.; Walker, Larry; Guy, Kip; Yan, Bing

2010-01-01

The development of an automated, high-throughput fractionation procedure to prepare and analyze natural product libraries for drug discovery screening is described. Natural products obtained from plant materials worldwide were extracted and first prefractionated on polyamide solid-phase extraction cartridges to remove polyphenols, followed by high-throughput automated fractionation, drying, weighing, and reformatting for screening and storage. The analysis of fractions with UPLC coupled with MS, PDA and ELSD detectors provides information that facilitates characterization of compounds in active fractions. Screening of a portion of fractions yielded multiple assay-specific hits in several high-throughput cellular screening assays. This procedure modernizes the traditional natural product fractionation paradigm by seamlessly integrating automation, informatics, and multimodal analytical interrogation capabilities. PMID:20232897

High-throughput Raman chemical imaging for evaluating food safety and quality

NASA Astrophysics Data System (ADS)

Qin, Jianwei; Chao, Kuanglin; Kim, Moon S.

2014-05-01

A line-scan hyperspectral system was developed to enable Raman chemical imaging for large sample areas. A custom-designed 785 nm line-laser based on a scanning mirror serves as an excitation source. A 45° dichroic beamsplitter reflects the laser light to form a 24 cm x 1 mm excitation line normally incident on the sample surface. Raman signals along the laser line are collected by a detection module consisting of a dispersive imaging spectrograph and a CCD camera. A hypercube is accumulated line by line as a motorized table moves the samples transversely through the laser line. The system covers a Raman shift range of -648.7-2889.0 cm-1 and a 23 cm wide area. An example application, for authenticating milk powder, was presented to demonstrate the system performance. In four minutes, the system acquired a 512x110x1024 hypercube (56,320 spectra) from four 47-mm-diameter Petri dishes containing four powder samples. Chemical images were created for detecting two adulterants (melamine and dicyandiamide) that had been mixed into the milk powder.

Multiplexed phase-space imaging for 3D fluorescence microscopy.

PubMed

Liu, Hsiou-Yuan; Zhong, Jingshan; Waller, Laura

2017-06-26

Optical phase-space functions describe spatial and angular information simultaneously; examples of optical phase-space functions include light fields in ray optics and Wigner functions in wave optics. Measurement of phase-space enables digital refocusing, aberration removal and 3D reconstruction. High-resolution capture of 4D phase-space datasets is, however, challenging. Previous scanning approaches are slow, light inefficient and do not achieve diffraction-limited resolution. Here, we propose a multiplexed method that solves these problems. We use a spatial light modulator (SLM) in the pupil plane of a microscope in order to sequentially pattern multiplexed coded apertures while capturing images in real space. Then, we reconstruct the 3D fluorescence distribution of our sample by solving an inverse problem via regularized least squares with a proximal accelerated gradient descent solver. We experimentally reconstruct a 101 Megavoxel 3D volume (1010×510×500µm with NA 0.4), demonstrating improved acquisition time, light throughput and resolution compared to scanning aperture methods. Our flexible patterning scheme further allows sparsity in the sample to be exploited for reduced data capture.

Complete Prevention of Dendrite Formation in Zn Metal Anodes by Means of Pulsed Charging Protocols.

PubMed

Garcia, Grecia; Ventosa, Edgar; Schuhmann, Wolfgang

2017-06-07

Zn metal as anode in rechargeable batteries, such as Zn/air or Zn/Ni, suffers from poor cyclability. The formation of Zn dendrites upon cycling is the key limiting step. We report a systematic study of the influence of pulsed electroplating protocols on the formation of Zn dendrites and in turn on strategies to completely prevent Zn dendrite formation. Because of the large number of variables in electroplating protocols, a scanning droplet cell technique was adapted as a high-throughput methodology in which a descriptor of the surface roughness can be in situ derived by means of electrochemical impedance spectroscopy. Upon optimizing the electroplating protocol by controlling nucleation, zincate ion depletion, and zincate ion diffusion, scanning electron microscopy and atomic force microscopy confirmed the growth of uniform and homogenous Zn deposits with a complete prevention of dendrite growth. The implementation of pulsed electroplating as the charging protocol for commercially available Ni-Zn batteries leads to substantially prolonged cyclability demonstrating the benefits of pulsed charging in Zn metal-based batteries.

Portable concealed weapon detection using millimeter-wave FMCW radar imaging

NASA Astrophysics Data System (ADS)

Johnson, Michael A.; Chang, Yu-Wen

2001-02-01

Unobtrusive detection of concealed weapons on persons or in abandoned bags would provide law enforcement a powerful tool to focus resources and increase traffic throughput in high- risk situations. We have developed a fast image scanning 94 GHz radar system that is suitable for portable operation and remote viewing of radar data. This system includes a novel fast image-scanning antenna that allows for the acquisition of medium resolution 3D millimeter wave images of stationary targets with frame times on order of one second. The 3D radar data allows for potential isolation of concealed weapons from body and environmental clutter such as nearby furniture or other people. The radar is an active system so image quality is not affected indoors, emitted power is however very low so there are no health concerns for operator or targets. The low power operation is still sufficient to penetrate heavy clothing or material. Small system size allows for easy transport and rapid deployment of the system as well as an easy migration path to future hand held systems.

High-throughput measurements of the optical redox ratio using a commercial microplate reader.

PubMed

Cannon, Taylor M; Shah, Amy T; Walsh, Alex J; Skala, Melissa C

2015-01-01

There is a need for accurate, high-throughput, functional measures to gauge the efficacy of potential drugs in living cells. As an early marker of drug response in cells, cellular metabolism provides an attractive platform for high-throughput drug testing. Optical techniques can noninvasively monitor NADH and FAD, two autofluorescent metabolic coenzymes. The autofluorescent redox ratio, defined as the autofluorescence intensity of NADH divided by that of FAD, quantifies relative rates of cellular glycolysis and oxidative phosphorylation. However, current microscopy methods for redox ratio quantification are time-intensive and low-throughput, limiting their practicality in drug screening. Alternatively, high-throughput commercial microplate readers quickly measure fluorescence intensities for hundreds of wells. This study found that a commercial microplate reader can differentiate the receptor status of breast cancer cell lines (p < 0.05) based on redox ratio measurements without extrinsic contrast agents. Furthermore, microplate reader redox ratio measurements resolve response (p < 0.05) and lack of response (p > 0.05) in cell lines that are responsive and nonresponsive, respectively, to the breast cancer drug trastuzumab. These studies indicate that the microplate readers can be used to measure the redox ratio in a high-throughput manner and are sensitive enough to detect differences in cellular metabolism that are consistent with microscopy results.

High-speed atomic force microscopy and peak force tapping control

NASA Astrophysics Data System (ADS)

Hu, Shuiqing; Mininni, Lars; Hu, Yan; Erina, Natalia; Kindt, Johannes; Su, Chanmin

2012-03-01

ITRS Roadmap requires defect size measurement below 10 nanometers and challenging classifications for both blank and patterned wafers and masks. Atomic force microscope (AFM) is capable of providing metrology measurement in 3D at sub-nanometer accuracy but has long suffered from drawbacks in throughput and limitation of slow topography imaging without chemical information. This presentation focus on two disruptive technology developments, namely high speed AFM and quantitative nanomechanical mapping, which enables high throughput measurement with capability of identifying components through concurrent physical property imaging. The high speed AFM technology has allowed the imaging speed increase by 10-100 times without loss of the data quality. Such improvement enables the speed of defect review on a wafer to increase from a few defects per hour to nearly 100 defects an hour, approaching the requirements of ITRS Roadmap. Another technology development, Peak Force Tapping, substantially simplified the close loop system response, leading to self-optimization of most challenging samples groups to generate expert quality data. More importantly, AFM also simultaneously provides a series of mechanical property maps with a nanometer spatial resolution during defect review. These nanomechanical maps (including elastic modulus, hardness, and surface adhesion) provide complementary information for elemental analysis, differentiate defect materials by their physical properties, and assist defect classification beyond topographic measurements. This paper will explain the key enabling technologies, namely high speed tip-scanning AFM using innovative flexure design and control algorithm. Another critical element is AFM control using Peak Force Tapping, in which the instantaneous tip-sample interaction force is measured and used to derive a full suite of physical properties at each imaging pixel. We will provide examples of defect review data on different wafers and media disks. The similar AFM-based defect review capacity was also applied to EUV masks.

Measuring multielectron beam imaging fidelity with a signal-to-noise ratio analysis

NASA Astrophysics Data System (ADS)

Mukhtar, Maseeh; Bunday, Benjamin D.; Quoi, Kathy; Malloy, Matt; Thiel, Brad

2016-07-01

Java Monte Carlo Simulator for Secondary Electrons (JMONSEL) simulations are used to generate expected imaging responses of chosen test cases of patterns and defects with the ability to vary parameters for beam energy, spot size, pixel size, and/or defect material and form factor. The patterns are representative of the design rules for an aggressively scaled FinFET-type design. With these simulated images and resulting shot noise, a signal-to-noise framework is developed, which relates to defect detection probabilities. Additionally, with this infrastructure, the effect of detection chain noise and frequency-dependent system response can be made, allowing for targeting of best recipe parameters for multielectron beam inspection validation experiments. Ultimately, these results should lead to insights into how such parameters will impact tool design, including necessary doses for defect detection and estimations of scanning speeds for achieving high throughput for high-volume manufacturing.

NIR hyperspectral compressive imager based on a modified Fabry–Perot resonator

NASA Astrophysics Data System (ADS)

Oiknine, Yaniv; August, Isaac; Blumberg, Dan G.; Stern, Adrian

2018-04-01

The acquisition of hyperspectral (HS) image datacubes with available 2D sensor arrays involves a time consuming scanning process. In the last decade, several compressive sensing (CS) techniques were proposed to reduce the HS acquisition time. In this paper, we present a method for near-infrared (NIR) HS imaging which relies on our rapid CS resonator spectroscopy technique. Within the framework of CS, and by using a modified Fabry–Perot resonator, a sequence of spectrally modulated images is used to recover NIR HS datacubes. Owing to the innovative CS design, we demonstrate the ability to reconstruct NIR HS images with hundreds of spectral bands from an order of magnitude fewer measurements, i.e. with a compression ratio of about 10:1. This high compression ratio, together with the high optical throughput of the system, facilitates fast acquisition of large HS datacubes.

A high-throughput in vitro ring assay for vasoactivity using magnetic 3D bioprinting

PubMed Central

Tseng, Hubert; Gage, Jacob A.; Haisler, William L.; Neeley, Shane K.; Shen, Tsaiwei; Hebel, Chris; Barthlow, Herbert G.; Wagoner, Matthew; Souza, Glauco R.

2016-01-01

Vasoactive liabilities are typically assayed using wire myography, which is limited by its high cost and low throughput. To meet the demand for higher throughput in vitro alternatives, this study introduces a magnetic 3D bioprinting-based vasoactivity assay. The principle behind this assay is the magnetic printing of vascular smooth muscle cells into 3D rings that functionally represent blood vessel segments, whose contraction can be altered by vasodilators and vasoconstrictors. A cost-effective imaging modality employing a mobile device is used to capture contraction with high throughput. The goal of this study was to validate ring contraction as a measure of vasoactivity, using a small panel of known vasoactive drugs. In vitro responses of the rings matched outcomes predicted by in vivo pharmacology, and were supported by immunohistochemistry. Altogether, this ring assay robustly models vasoactivity, which could meet the need for higher throughput in vitro alternatives. PMID:27477945

An image analysis toolbox for high-throughput C. elegans assays

PubMed Central

Wählby, Carolina; Kamentsky, Lee; Liu, Zihan H.; Riklin-Raviv, Tammy; Conery, Annie L.; O’Rourke, Eyleen J.; Sokolnicki, Katherine L.; Visvikis, Orane; Ljosa, Vebjorn; Irazoqui, Javier E.; Golland, Polina; Ruvkun, Gary; Ausubel, Frederick M.; Carpenter, Anne E.

2012-01-01

We present a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems. This WormToolbox is available via the open-source CellProfiler project and enables objective scoring of whole-animal high-throughput image-based assays of C. elegans for the study of diverse biological pathways relevant to human disease. PMID:22522656

High-throughput, image-based screening of pooled genetic variant libraries

PubMed Central

Emanuel, George; Moffitt, Jeffrey R.; Zhuang, Xiaowei

2018-01-01

Image-based, high-throughput screening of genetic perturbations will advance both biology and biotechnology. We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in numerous individual cells. We achieve genotyping by introducing barcoded genetic variants into cells and using massively multiplexed FISH to measure the barcodes. We demonstrated this method by screening mutants of the fluorescent protein YFAST, yielding brighter and more photostable YFAST variants. PMID:29083401

Experimental Design for Combinatorial and High Throughput Materials Development

NASA Astrophysics Data System (ADS)

Cawse, James N.

2002-12-01

In the past decade, combinatorial and high throughput experimental methods have revolutionized the pharmaceutical industry, allowing researchers to conduct more experiments in a week than was previously possible in a year. Now high throughput experimentation is rapidly spreading from its origins in the pharmaceutical world to larger industrial research establishments such as GE and DuPont, and even to smaller companies and universities. Consequently, researchers need to know the kinds of problems, desired outcomes, and appropriate patterns for these new strategies. Editor James Cawse's far-reaching study identifies and applies, with specific examples, these important new principles and techniques. Experimental Design for Combinatorial and High Throughput Materials Development progresses from methods that are now standard, such as gradient arrays, to mathematical developments that are breaking new ground. The former will be particularly useful to researchers entering the field, while the latter should inspire and challenge advanced practitioners. The book's contents are contributed by leading researchers in their respective fields. Chapters include: -High Throughput Synthetic Approaches for the Investigation of Inorganic Phase Space -Combinatorial Mapping of Polymer Blends Phase Behavior -Split-Plot Designs -Artificial Neural Networks in Catalyst Development -The Monte Carlo Approach to Library Design and Redesign This book also contains over 200 useful charts and drawings. Industrial chemists, chemical engineers, materials scientists, and physicists working in combinatorial and high throughput chemistry will find James Cawse's study to be an invaluable resource.

Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing

PubMed Central

Chandran, Anandhakumar; Syed, Junetha; Taylor, Rhys D.; Kashiwazaki, Gengo; Sato, Shinsuke; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

2016-01-01

Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2 showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing. PMID:27098039

Development of rapid and sensitive high throughput pharmacologic assays for marine phycotoxins.

PubMed

Van Dolah, F M; Finley, E L; Haynes, B L; Doucette, G J; Moeller, P D; Ramsdell, J S

1994-01-01

The lack of rapid, high throughput assays is a major obstacle to many aspects of research on marine phycotoxins. Here we describe the application of microplate scintillation technology to develop high throughput assays for several classes of marine phycotoxin based on their differential pharmacologic actions. High throughput "drug discovery" format microplate receptor binding assays developed for brevetoxins/ciguatoxins and for domoic acid are described. Analysis for brevetoxins/ciguatoxins is carried out by binding competition with [3H] PbTx-3 for site 5 on the voltage dependent sodium channel in rat brain synaptosomes. Analysis of domoic acid is based on binding competition with [3H] kainic acid for the kainate/quisqualate glutamate receptor using frog brain synaptosomes. In addition, a high throughput microplate 45Ca flux assay for determination of maitotoxins is described. These microplate assays can be completed within 3 hours, have sensitivities of less than 1 ng, and can analyze dozens of samples simultaneously. The assays have been demonstrated to be useful for assessing algal toxicity and for assay-guided purification of toxins, and are applicable to the detection of biotoxins in seafood.

Fast and accurate: high-speed metrological large-range AFM for surface and nanometrology

NASA Astrophysics Data System (ADS)

Dai, Gaoliang; Koenders, Ludger; Fluegge, Jens; Hemmleb, Matthias

2018-05-01

Low measurement speed remains a major shortcoming of the scanning probe microscopic technique. It not only leads to a low measurement throughput, but a significant measurement drift over the long measurement time needed (up to hours or even days). To overcome this challenge, PTB, the national metrology institute of Germany, has developed a high-speed metrological large-range atomic force microscope (HS Met. LR-AFM) capable of measuring speeds up to 1 mm s‑1. This paper has introduced the design concept in detail. After modelling scanning probe microscopic measurements, our results suggest that the signal spectrum of the surface to be measured is the spatial spectrum of the surface scaled by the scanning speed. The higher the scanning speed , the broader the spectrum to be measured. To realise an accurate HS Met. LR-AFM, our solution is to combine different stages/sensors synchronously in measurements, which provide a much larger spectrum area for high-speed measurement capability. Two application examples have been demonstrated. The first is a new concept called reference areal surface metrology. Using the developed HS Met. LR-AFM, surfaces are measured accurately and traceably at a speed of 500 µm s‑1 and the results are applied as a reference 3D data map of the surfaces. By correlating the reference 3D data sets and 3D data sets of tools under calibration, which are measured at the same surface, it has the potential to comprehensively characterise the tools, for instance, the spectrum properties of the tools. The investigation results of two commercial confocal microscopes are demonstrated, indicating very promising results. The second example is the calibration of a kind of 3D nano standard, which has spatially distributed landmarks, i.e. special unique features defined by 3D-coordinates. Experimental investigations confirmed that the calibration accuracy is maintained at a measurement speed of 100 µm s‑1, which improves the calibration efficiency by a factor of 10.

High-Throughput/High-Content Screening Assays with Engineered Nanomaterials in ToxCast

EPA Science Inventory

High-throughput and high-content screens are attractive approaches for prioritizing nanomaterial hazards and informing targeted testing due to the impracticality of using traditional toxicological testing on the large numbers and varieties of nanomaterials. The ToxCast program a...

High-throughput protein concentration and buffer exchange: comparison of ultrafiltration and ammonium sulfate precipitation.

PubMed

Moore, Priscilla A; Kery, Vladimir

2009-01-01

High-throughput protein purification is a complex, multi-step process. There are several technical challenges in the course of this process that are not experienced when purifying a single protein. Among the most challenging are the high-throughput protein concentration and buffer exchange, which are not only labor-intensive but can also result in significant losses of purified proteins. We describe two methods of high-throughput protein concentration and buffer exchange: one using ammonium sulfate precipitation and one using micro-concentrating devices based on membrane ultrafiltration. We evaluated the efficiency of both methods on a set of 18 randomly selected purified proteins from Shewanella oneidensis. While both methods provide similar yield and efficiency, the ammonium sulfate precipitation is much less labor intensive and time consuming than the ultrafiltration.

Narcotics detection using piezoelectric ringing

NASA Astrophysics Data System (ADS)

Rayner, Timothy J.; Magnuson, Erik E.; West, Rebecca; Lyndquist, R.

1997-02-01

Piezo-electric ringing (PER) has been demonstrated to be an effective means of scanning cargo for the presence of hidden narcotics. The PER signal is characteristic of certain types of crystallized material, such as cocaine hydrochloride. However, the PER signal cannot be used to conclusively identify all types of narcotic material, as the signal is not unique. For the purposes of cargo scanning, the PER technique is therefore most effective when used in combination with quadrupole resonance analysis (QRA). PER shares the same methodology as QRA technology, and can therefore be very easily and inexpensively integrated into existing QRA detectors. PER can be used as a pre-scanning technique before the QRA scan is applied and, because the PER scan is of a very short duration, can effectively offset some of the throughput limitations of standard QRA narcotics detectors. Following is a discussion of a PER detector developed by Quantum Manetics under contract to United States Customs. Design philosophy and performance are discussed, supported by results from recent tests conducted by the U.S. Drug Enforcement Agency and U.S. Customs.

Label-free cell-cycle analysis by high-throughput quantitative phase time-stretch imaging flow cytometry

NASA Astrophysics Data System (ADS)

Mok, Aaron T. Y.; Lee, Kelvin C. M.; Wong, Kenneth K. Y.; Tsia, Kevin K.

2018-02-01

Biophysical properties of cells could complement and correlate biochemical markers to characterize a multitude of cellular states. Changes in cell size, dry mass and subcellular morphology, for instance, are relevant to cell-cycle progression which is prevalently evaluated by DNA-targeted fluorescence measurements. Quantitative-phase microscopy (QPM) is among the effective biophysical phenotyping tools that can quantify cell sizes and sub-cellular dry mass density distribution of single cells at high spatial resolution. However, limited camera frame rate and thus imaging throughput makes QPM incompatible with high-throughput flow cytometry - a gold standard in multiparametric cell-based assay. Here we present a high-throughput approach for label-free analysis of cell cycle based on quantitative-phase time-stretch imaging flow cytometry at a throughput of > 10,000 cells/s. Our time-stretch QPM system enables sub-cellular resolution even at high speed, allowing us to extract a multitude (at least 24) of single-cell biophysical phenotypes (from both amplitude and phase images). Those phenotypes can be combined to track cell-cycle progression based on a t-distributed stochastic neighbor embedding (t-SNE) algorithm. Using multivariate analysis of variance (MANOVA) discriminant analysis, cell-cycle phases can also be predicted label-free with high accuracy at >90% in G1 and G2 phase, and >80% in S phase. We anticipate that high throughput label-free cell cycle characterization could open new approaches for large-scale single-cell analysis, bringing new mechanistic insights into complex biological processes including diseases pathogenesis.

Increased Throughput and Sensitivity of Synchrotron-Based Characterization for Photovoltaic Materials

DOE PAGES

Morishige, Ashley E.; Laine, Hannu S.; Looney, Erin E.; ...

2017-04-03

Optimizing photovoltaic (PV) devices requires characterization and optimization across several length scales, from centimeters to nanometers. Synchrotron-based micro-X-ray fluorescence spectromicroscopy (μ-XRF) is a valuable link in the PV-related material and device characterization suite. μ-XRF maps of elemental distributions in PV materials have high spatial resolution and excellent sensitivity and can be measured on absorber materials and full devices. Recently, we implemented on-the-fly data collection (flyscan) at Beamline 2-ID-D at the Advanced Photon Source at Argonne National Laboratory, eliminating a 300 ms per-pixel overhead time. This faster scanning enables high-sensitivity (~10 14 atoms/cm 2), large-area (10 000s of μm 2), high-spatialmore » resolution (<;200 nm scale) maps to be completed within a practical scanning time. We specifically show that when characterizing detrimental trace metal precipitate distributions in multicrystalline silicon wafers for PV, flyscans can increase the productivity of μ-XRF by an order of magnitude. Additionally, flyscan μ-XRF mapping enables relatively large-area correlative microscopy. As an example, we map the transition metal distribution in a 50 μm-diameter laser-fired contact of a silicon solar cell before and after lasing. As a result, while we focus on μ-XRF of mc-Si wafers for PV, our results apply broadly to synchrotron-based mapping of PV absorbers and devices.« less

Campanile Near-Field Probes Fabricated by Nanoimprint Lithography on the Facet of an Optical Fiber

DOE PAGES

Calafiore, Giuseppe; Koshelev, Alexander; Darlington, Thomas P.; ...

2017-05-10

One of the major challenges to the widespread adoption of plasmonic and nano-optical devices in real-life applications is the difficulty to mass-fabricate nano-optical antennas in parallel and reproducible fashion, and the capability to precisely place nanoantennas into devices with nanometer-scale precision. In this study, we present a solution to this challenge using the state-of-the-art ultraviolet nanoimprint lithography (UV-NIL) to fabricate functional optical transformers onto the core of an optical fiber in a single step, mimicking the 'campanile' near-field probes. Imprinted probes were fabricated using a custom-built imprinter tool with co-axial alignment capability with sub < 100 nm position accuracy, followedmore » by a metallization step. Scanning electron micrographs confirm high imprint fidelity and precision with a thin residual layer to facilitate efficient optical coupling between the fiber and the imprinted optical transformer. The imprinted optical transformer probe was used in an actual NSOM measurement performing hyperspectral photoluminescence mapping of standard fluorescent beads. The calibration scans confirmed that imprinted probes enable sub-diffraction limited imaging with a spatial resolution consistent with the gap size. This novel nano-fabrication approach promises a low-cost, high-throughput, and reproducible manufacturing of advanced nano-optical devices.« less

Campanile Near-Field Probes Fabricated by Nanoimprint Lithography on the Facet of an Optical Fiber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calafiore, Giuseppe; Koshelev, Alexander; Darlington, Thomas P.

One of the major challenges to the widespread adoption of plasmonic and nano-optical devices in real-life applications is the difficulty to mass-fabricate nano-optical antennas in parallel and reproducible fashion, and the capability to precisely place nanoantennas into devices with nanometer-scale precision. In this study, we present a solution to this challenge using the state-of-the-art ultraviolet nanoimprint lithography (UV-NIL) to fabricate functional optical transformers onto the core of an optical fiber in a single step, mimicking the 'campanile' near-field probes. Imprinted probes were fabricated using a custom-built imprinter tool with co-axial alignment capability with sub < 100 nm position accuracy, followedmore » by a metallization step. Scanning electron micrographs confirm high imprint fidelity and precision with a thin residual layer to facilitate efficient optical coupling between the fiber and the imprinted optical transformer. The imprinted optical transformer probe was used in an actual NSOM measurement performing hyperspectral photoluminescence mapping of standard fluorescent beads. The calibration scans confirmed that imprinted probes enable sub-diffraction limited imaging with a spatial resolution consistent with the gap size. This novel nano-fabrication approach promises a low-cost, high-throughput, and reproducible manufacturing of advanced nano-optical devices.« less

The Atmospheric Scanning Electron Microscope with open sample space observes dynamic phenomena in liquid or gas.

PubMed

Suga, Mitsuo; Nishiyama, Hidetoshi; Konyuba, Yuji; Iwamatsu, Shinnosuke; Watanabe, Yoshiyuki; Yoshiura, Chie; Ueda, Takumi; Sato, Chikara

2011-12-01

Although conventional electron microscopy (EM) requires samples to be in vacuum, most chemical and physical reactions occur in liquid or gas. The Atmospheric Scanning Electron Microscope (ASEM) can observe dynamic phenomena in liquid or gas under atmospheric pressure in real time. An electron-permeable window made of pressure-resistant 100 nm-thick silicon nitride (SiN) film, set into the bottom of the open ASEM sample dish, allows an electron beam to be projected from underneath the sample. A detector positioned below captures backscattered electrons. Using the ASEM, we observed the radiation-induced self-organization process of particles, as well as phenomena accompanying volume change, including evaporation-induced crystallization. Using the electrochemical ASEM dish, we observed tree-like electrochemical depositions on the cathode. In silver nitrate solution, we observed silver depositions near the cathode forming incidental internal voids. The heated ASEM dish allowed observation of patterns of contrast in melting and solidifying solder. Finally, to demonstrate its applicability for monitoring and control of industrial processes, silver paste and solder paste were examined at high throughput. High resolution, imaging speed, flexibility, adaptability, and ease of use facilitate the observation of previously difficult-to-image phenomena, and make the ASEM applicable to various fields. Copyright © 2011 Elsevier B.V. All rights reserved.

Electrodeposition and Screening of Photoelectrochemical Activity in Conjugated Polymers Using Scanning Electrochemical Cell Microscopy.

PubMed

Aaronson, Barak D B; Garoz-Ruiz, Jesus; Byers, Joshua C; Colina, Alvaro; Unwin, Patrick R

2015-11-24

A number of renewable energy systems require an understanding and correlation of material properties and photoelectrochemical activity on the micro to nanoscale. Among these, conducting polymer electrodes continue to be important materials. In this contribution, an ultrasensitive scanning electrochemical cell microscopy (SECCM) platform is used to electrodeposit microscale thin films of poly(3-hexylthiophene) (P3HT) on an optically transparent gold electrode and to correlate the morphology (film thickness and structural order) with photoactivity. The electrochemical growth of P3HT begins with a thin ordered film up to 10 nm thick, after which a second more disordered film is deposited, as revealed by micro-Raman spectroscopy. A decrease in photoactivity for the thicker films, measured in situ immediately following film deposition, is attributed to an increase in bulk film disorder that limits charge transport. Higher resolution ex situ SECCM phototransient measurements, using a smaller diameter probe, show local variations in photoactivity within a given deposit. Even after aging, thinner, more ordered regions within a deposit exhibit sustained enhanced photocurrent densities compared to areas where the film is thicker and more disordered. The platform opens up new possibilities for high-throughput combinatorial correlation studies, by allowing materials fabrication and high spatial resolution probing of processes in photoelectrochemical materials.

Specimen preparation, imaging, and analysis protocols for knife-edge scanning microscopy.

PubMed

Choe, Yoonsuck; Mayerich, David; Kwon, Jaerock; Miller, Daniel E; Sung, Chul; Chung, Ji Ryang; Huffman, Todd; Keyser, John; Abbott, Louise C

2011-12-09

Major advances in high-throughput, high-resolution, 3D microscopy techniques have enabled the acquisition of large volumes of neuroanatomical data at submicrometer resolution. One of the first such instruments producing whole-brain-scale data is the Knife-Edge Scanning Microscope (KESM), developed and hosted in the authors' lab. KESM has been used to section and image whole mouse brains at submicrometer resolution, revealing the intricate details of the neuronal networks (Golgi), vascular networks (India ink), and cell body distribution (Nissl). The use of KESM is not restricted to the mouse nor the brain. We have successfully imaged the octopus brain, mouse lung, and rat brain. We are currently working on whole zebra fish embryos. Data like these can greatly contribute to connectomics research; to microcirculation and hemodynamic research; and to stereology research by providing an exact ground-truth. In this article, we will describe the pipeline, including specimen preparation (fixing, staining, and embedding), KESM configuration and setup, sectioning and imaging with the KESM, image processing, data preparation, and data visualization and analysis. The emphasis will be on specimen preparation and visualization/analysis of obtained KESM data. We expect the detailed protocol presented in this article to help broaden the access to KESM and increase its utilization.

Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy.

PubMed

Yang, Darren; Wong, Wesley P

2018-01-01

We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

High throughput single cell counting in droplet-based microfluidics.

PubMed

Lu, Heng; Caen, Ouriel; Vrignon, Jeremy; Zonta, Eleonora; El Harrak, Zakaria; Nizard, Philippe; Baret, Jean-Christophe; Taly, Valérie

2017-05-02

Droplet-based microfluidics is extensively and increasingly used for high-throughput single-cell studies. However, the accuracy of the cell counting method directly impacts the robustness of such studies. We describe here a simple and precise method to accurately count a large number of adherent and non-adherent human cells as well as bacteria. Our microfluidic hemocytometer provides statistically relevant data on large populations of cells at a high-throughput, used to characterize cell encapsulation and cell viability during incubation in droplets.

High-Throughput Sequencing of Germline and Tumor From Men with Early-Onset Metastatic Prostate Cancer

DTIC Science & Technology

2016-12-01

AWARD NUMBER: W81XWH-13-1-0371 TITLE: High-Throughput Sequencing of Germline and Tumor From Men with Early- Onset Metastatic Prostate Cancer...DATES COVERED 30 Sep 2013 - 29 Sep 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER High-Throughput Sequencing of Germline and Tumor From Men with...presenting with metastatic prostate cancer at a young age (before age 60 years). Whole exome sequencing identified a panel of germline variants that have

Conical scan impact study. Volume 1: General central data processing facility. [multispectral band scanner design alternatives for earth resources data

NASA Technical Reports Server (NTRS)

Ebert, D. H.; Eppes, T. A.; Thomas, D. J.

1973-01-01

The impact of a conical scan versus a linear scan multispectral scanner (MSS) instrument was studied in terms of: (1) design modifications required in framing and continuous image recording devices; and (2) changes in configurations of an all-digital precision image processor. A baseline system was defined to provide the framework for comparison, and included pertinent spacecraft parameters, a conical MSS, a linear MSS, an image recording system, and an all-digital precision processor. Lateral offset pointing of the sensors over a range of plus or minus 20 deg was considered. The study addressed the conical scan impact on geometric, radiometric, and aperture correction of MSS data in terms of hardware and software considerations, system complexity, quality of corrections, throughput, and cost of implementation. It was concluded that: (1) if the MSS data are to be only film recorded, then there is only a nomial concial scan impact on the ground data processing system; and (2) if digital data are to be provided to users on computer compatible tapes in rectilinear format, then there is a significant conical scan impact on the ground data processing system.

Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

NASA Astrophysics Data System (ADS)

Esposito, Alessandro

2006-05-01

This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These techniques have the capability to quantitatively probe the biochemical environment of fluorophores. An automated microscope capable of unsupervised operation has been developed that enables the investigation of molecular and cellular properties at high throughput levels and the analysis of cellular heterogeneity. State-of-the-art Förster Resonance Energy Transfer imaging, Fluorescence Lifetime Imaging Microscopy, Confocal Laser Scanning Microscopy and the newly developed tools have been combined with cellular and molecular biology techniques for the investigation of protein-protein interactions, oligomerization and post-translational modifications of α-Synuclein and Tau, two proteins involved in Parkinson’s and Alzheimer’s disease, respectively. The high inter-disciplinarity of this project required the merging of the expertise of both the Molecular Biophysics Group at the Debye Institute - Utrecht University and the Cell Biophysics Group at the European Neuroscience Institute - Gαttingen University. This project was conducted also with the support and the collaboration of the Center for the Molecular Physiology of the Brain (Göttingen), particularly with the groups associated with the Molecular Quantitative Microscopy and Parkinson’s Disease and Aggregopathies areas. This work demonstrates that molecular and cellular quantitative microscopy can be used in combination with high-throughput screening as a powerful tool for the investigation of the molecular mechanisms of complex biological phenomena like those occurring in neurodegenerative diseases.

High throughput web inspection system using time-stretch real-time imaging

NASA Astrophysics Data System (ADS)

Kim, Chanju

Photonic time-stretch is a novel technology that enables capturing of fast, rare and non-repetitive events. Therefore, it operates in real-time with ability to record over long period of time while having fine temporal resolution. The powerful property of photonic time-stretch has already been employed in various fields of application such as analog-to-digital conversion, spectroscopy, laser scanner and microscopy. Further expanding the scope, we fully exploit the time-stretch technology to demonstrate a high throughput web inspection system. Web inspection, namely surface inspection is a nondestructive evaluation method which is crucial for semiconductor wafer and thin film production. We successfully report a dark-field web inspection system with line scan speed of 90.9 MHz which is up to 1000 times faster than conventional inspection instruments. The manufacturing of high quality semiconductor wafer and thin film may directly benefit from this technology as it can easily locate defects with area of less than 10 microm x 10 microm where it allows maximum web flow speed of 1.8 km/s. The thesis provides an overview of our web inspection technique, followed by description of the photonic time-stretch technique which is the keystone in our system. A detailed explanation of each component is covered to provide quantitative understanding of the system. Finally, imaging results from a hard-disk sample and flexible films are presented along with performance analysis of the system. This project was the first application of time-stretch to industrial inspection, and was conducted under financial support and with close involvement by Hitachi, Ltd.

The path of least resistance: is there a better route?

PubMed

Loree, Ann; Maihack, Marcia; Powell, Marge

2003-01-01

In May 2000, the radiology department at Stanford University Medical Center embarked on a five-year journey toward complete digitization. While the end goal was known, there was much less certainty about the steps involved along the way. Stanford worked with a team from GE Medical Systems to implement Six Sigma process improvement methodologies and related change management techniques. The methodical and evidence-based framework of Six Sigma significantly organized the process of "going digital" by breaking it into manageable projects with clear objectives. Stanford identified five key areas where improvement could be made: MR outpatient throughput, CT inpatient throughput, CT outpatient throughput, report turnaround time, and Lucile Packard Children's Hospital CR/Ortho throughput and digitization. The CT project is presented in this article. Although labor intensive, collecting radiology data manually is often the best way to obtain the level of detail required, unless there is a robust RIS in place with solid data integrity. To gather the necessary information without unduly impacting staff and workflow at Stanford, the consultants working onsite handled the actual observation and recording of data. Some of the changes introduced through Six Sigma may appear, at least on the surface, to be common sense. It is only by presenting clear evidence in terms of data, however, that the improvements can actually be implemented and accepted. By converting all appointments to 30 minutes and expanding hours of operation, Stanford was able to boost diagnostic imaging productivity, volume and revenue. With the ability to scan over lunch breaks and rest periods, potential appointment capacity increased by 140 CT scans per month. Overall, the CT project increased potential for outpatient appointment capacity by nearly 75% and projected over $1.5 million in additional annual gross revenue. The complex process of moving toward a digital radiology department at Stanford demonstrates that healthcare cannot be healed by technology alone. The ability to optimize patient services revolves around a combination of leading edge technology, dedicated and well-trained staff, and careful examination of processes and productivity.

Novel Infiltration Diagnostics based on Laser-line Scanning and Infrared Temperature Field Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xinwei

This project targets the building energy efficiency problems induced by building infiltration/leaks. The current infiltration inspection techniques often require extensive visual inspection and/or whole building pressure test. These current techniques cannot meet more than three of the below five criteria of ideal infiltration diagnostics: 1. location and extent diagnostics, 2. building-level application, 3. least surface preparation, 4. weather-proof, and 5. non-disruption to building occupants. These techniques are either too expensive or time consuming, and often lack accuracy and repeatability. They are hardly applicable to facades/facades section. The goal of the project was to develop a novel infiltration diagnostics technology basedmore » on laser line-scanning and simultaneous infrared temperature imaging. A laboratory scale experimental setup was designed to mimic a model house of well-defined pressure difference below or above the outside pressure. Algorithms and Matlab-based programs had been developed for recognition of the hole location in infrared images. Our experiment based on laser wavelengths of 450 and 1550 nm and laser beam diameters of 4-25 mm showed that the location of the holes could be identified using laser heating; the diagnostic approach however could not readily distinguish between infiltration and non-infiltration points. To significantly improve the scanning throughput and recognition accuracy, a second approach was explored, developed, and extensively tested. It incorporates a liquid spray on the surface to induce extra phase change cooling effect. In this spray method, we termed it as PECIT (Phase-change Enhanced Cooling Infrared Thermography), phase-change enhanced cooling was used, which significantly amplifies the effect of air flow (infiltration and exfiltration). This heat transfer method worked extremely well to identify infiltration and exfiltration locations with high accuracy and increased throughput. The PECIT technique was systematically developed and tested for through holes with diameters 1 mm to 2 mm, and diagonal lines of 0.5 mm width at different camera-wall distances of 46 cm to 200 cm, under different pressure differences from 5 Pa to 20 Pa, and under different wind conditions. The PECIT technique had either met or exceeded the goals proposed in the project. For exfiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa (proposed one: 50 Pa with stretch goal of 15 Pa). For infiltration, we achieved >90% accuracy under a much lower pressure difference of 10 Pa (proposed one: 50 Pa with stretch goal of 15Pa). For exfiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa. For infiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa. The PECIT technique can reach a throughput of 120 m2/h, which is 4 times the proposed goal for the laser line-scanning and simultaneous infrared temperature imaging approach. For commercialization and market penetration, we had meetings with two companies for feedback collection and further improvement for practical use. Also, we have interacted with Office of Intellectual Property and Technology Transfer of Iowa State University for idea disclosure and patent application.« less

Performance-scalable volumetric data classification for online industrial inspection

NASA Astrophysics Data System (ADS)

Abraham, Aby J.; Sadki, Mustapha; Lea, R. M.

2002-03-01

Non-intrusive inspection and non-destructive testing of manufactured objects with complex internal structures typically requires the enhancement, analysis and visualization of high-resolution volumetric data. Given the increasing availability of fast 3D scanning technology (e.g. cone-beam CT), enabling on-line detection and accurate discrimination of components or sub-structures, the inherent complexity of classification algorithms inevitably leads to throughput bottlenecks. Indeed, whereas typical inspection throughput requirements range from 1 to 1000 volumes per hour, depending on density and resolution, current computational capability is one to two orders-of-magnitude less. Accordingly, speeding up classification algorithms requires both reduction of algorithm complexity and acceleration of computer performance. A shape-based classification algorithm, offering algorithm complexity reduction, by using ellipses as generic descriptors of solids-of-revolution, and supporting performance-scalability, by exploiting the inherent parallelism of volumetric data, is presented. A two-stage variant of the classical Hough transform is used for ellipse detection and correlation of the detected ellipses facilitates position-, scale- and orientation-invariant component classification. Performance-scalability is achieved cost-effectively by accelerating a PC host with one or more COTS (Commercial-Off-The-Shelf) PCI multiprocessor cards. Experimental results are reported to demonstrate the feasibility and cost-effectiveness of the data-parallel classification algorithm for on-line industrial inspection applications.

High-throughput sequencing methods to study neuronal RNA-protein interactions.

PubMed

Ule, Jernej

2009-12-01

UV-cross-linking and RNase protection, combined with high-throughput sequencing, have provided global maps of RNA sites bound by individual proteins or ribosomes. Using a stringent purification protocol, UV-CLIP (UV-cross-linking and immunoprecipitation) was able to identify intronic and exonic sites bound by splicing regulators in mouse brain tissue. Ribosome profiling has been used to quantify ribosome density on budding yeast mRNAs under different environmental conditions. Post-transcriptional regulation in neurons requires high spatial and temporal precision, as is evident from the role of localized translational control in synaptic plasticity. It remains to be seen if the high-throughput methods can be applied quantitatively to study the dynamics of RNP (ribonucleoprotein) remodelling in specific neuronal populations during the neurodegenerative process. It is certain, however, that applications of new biochemical techniques followed by high-throughput sequencing will continue to provide important insights into the mechanisms of neuronal post-transcriptional regulation.

Evaluation of Compatibility of ToxCast High-Throughput/High-Content Screening Assays with Engineered Nanomaterials

EPA Science Inventory

High-throughput and high-content screens are attractive approaches for prioritizing nanomaterial hazards and informing targeted testing due to the impracticality of using traditional toxicological testing on the large numbers and varieties of nanomaterials. The ToxCast program a...

X-ray Raman spectroscopic study of benzene at high pressure.

PubMed

Pravica, Michael; Grubor-Urosevic, Ognjen; Hu, Michael; Chow, Paul; Yulga, Brian; Liermann, Peter

2007-10-11

We have used X-ray Raman spectroscopy (XRS) to study benzene up to approximately 20 GPa in a diamond anvil cell at ambient temperature. The experiments were performed at the High-Pressure Collaborative Access Team's 16 ID-D undulator beamline at the Advanced Photon Source. Scanned monochromatic X-rays near 10 keV were used to probe the carbon X-ray edge near 284 eV via inelastic scattering. The diamond cell axis was oriented perpendicular to the X-ray beam axis to prevent carbon signal contamination from the diamonds. Beryllium gaskets confined the sample because of their high transmission throughput in this geometry. Spectral alterations with pressure indicate bonding changes that occur with pressure because of phase changes (liquid: phase I, II, III, and III') and possibly due to changes in the hybridization of the bonds. Changes in the XRS spectra were especially evident in the data taken when the sample was in phase III', which may be related to a rate process observed in earlier shock wave studies.

AutoTag and AutoSnap: Standardized, semi-automatic capture of regions of interest from whole slide images

PubMed Central

Marien, Koen M.; Andries, Luc; De Schepper, Stefanie; Kockx, Mark M.; De Meyer, Guido R.Y.

2015-01-01

Tumor angiogenesis is measured by counting microvessels in tissue sections at high power magnification as a potential prognostic or predictive biomarker. Until now, regions of interest1 (ROIs) were selected by manual operations within a tumor by using a systematic uniform random sampling2 (SURS) approach. Although SURS is the most reliable sampling method, it implies a high workload. However, SURS can be semi-automated and in this way contribute to the development of a validated quantification method for microvessel counting in the clinical setting. Here, we report a method to use semi-automated SURS for microvessel counting: • Whole slide imaging with Pannoramic SCAN (3DHISTECH) • Computer-assisted sampling in Pannoramic Viewer (3DHISTECH) extended by two self-written AutoHotkey applications (AutoTag and AutoSnap) • The use of digital grids in Photoshop® and Bridge® (Adobe Systems) This rapid procedure allows traceability essential for high throughput protein analysis of immunohistochemically stained tissue. PMID:26150998

Helium Ion Beam Microscopy for Copper Grain Identification in BEOL Structures

NASA Astrophysics Data System (ADS)

van den Boom, Ruud J. J.; Parvaneh, Hamed; Voci, Dave; Huynh, Chuong; Stern, Lewis; Dunn, Kathleen A.; Lifshin, Eric

2009-09-01

Grain size determination in advanced metallization structures requires a technique with resolution ˜2 nm, with a high signal-to-noise ratio and high orientation-dependant contrast for unambiguous identification of grain boundaries. Ideally, such a technique would also be capable of high-throughput and rapid time-to-knowledge. The Helium Ion Microscope (HIM) offers one possibility for achieving these aims in a single platform. This article compares the performance of the HIM with Focused Ion Beam, Scanning Electron and Transmission Electron Microscopes, in terms of achievable image resolution and contrast, using plan-view and cross-sectional imaging of electroplated samples. Although the HIM is capable of sub-nanometer beam diameter, the low signal-to-noise ratio in the images necessitates signal averaging, which degrades the measured image resolution to 6-8 nm. Strategies for improving S/N are discussed in light of the trade-off between beam current and probe size, accelerating voltage, and dwell time.

Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics

DOE PAGES

Xu, Yi-Fan; Lu, Wenyun; Rabinowitz, Joshua D.

2015-01-15

Liquid chromatography–mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. Furthermore, when analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, andmore » hexose-phosphates generate triose-phosphates. We also evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Finally and accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.« less

Optical critical dimension metrology for directed self-assembly assisted contact hole shrink

NASA Astrophysics Data System (ADS)

Dixit, Dhairya; Green, Avery; Hosler, Erik R.; Kamineni, Vimal; Preil, Moshe E.; Keller, Nick; Race, Joseph; Chun, Jun Sung; O'Sullivan, Michael; Khare, Prasanna; Montgomery, Warren; Diebold, Alain C.

2016-01-01

Directed self-assembly (DSA) is a potential patterning solution for future generations of integrated circuits. Its main advantages are high pattern resolution (˜10 nm), high throughput, no requirement of high-resolution mask, and compatibility with standard fab-equipment and processes. The application of Mueller matrix (MM) spectroscopic ellipsometry-based scatterometry to optically characterize DSA patterned contact hole structures fabricated with phase-separated polystyrene-b-polymethylmethacrylate (PS-b-PMMA) is described. A regression-based approach is used to calculate the guide critical dimension (CD), DSA CD, height of the PS column, thicknesses of underlying layers, and contact edge roughness of the post PMMA etch DSA contact hole sample. Scanning electron microscopy and imaging analysis is conducted as a comparative metric for scatterometry. In addition, optical model-based simulations are used to investigate MM elements' sensitivity to various DSA-based contact hole structures, predict sensitivity to dimensional changes, and its limits to characterize DSA-induced defects, such as hole placement inaccuracy, missing vias, and profile inaccuracy of the PMMA cylinder.

SwellGel: an affinity chromatography technology for high-capacity and high-throughput purification of recombinant-tagged proteins.

PubMed

Draveling, C; Ren, L; Haney, P; Zeisse, D; Qoronfleh, M W

2001-07-01

The revolution in genomics and proteomics is having a profound impact on drug discovery. Today's protein scientist demands a faster, easier, more reliable way to purify proteins. A high capacity, high-throughput new technology has been developed in Perbio Sciences for affinity protein purification. This technology utilizes selected chromatography media that are dehydrated to form uniform aggregates. The SwellGel aggregates will instantly rehydrate upon addition of the protein sample, allowing purification and direct performance of multiple assays in a variety of formats. SwellGel technology has greater stability and is easier to handle than standard wet chromatography resins. The microplate format of this technology provides high-capacity, high-throughput features, recovering milligram quantities of protein suitable for high-throughput screening or biophysical/structural studies. Data will be presented applying SwellGel technology to recombinant 6x His-tagged protein and glutathione-S-transferase (GST) fusion protein purification. Copyright 2001 Academic Press.

Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model

NASA Astrophysics Data System (ADS)

Mondal, Sudip; Hegarty, Evan; Martin, Chris; Gökçe, Sertan Kutal; Ghorashian, Navid; Ben-Yakar, Adela

2016-10-01

Next generation drug screening could benefit greatly from in vivo studies, using small animal models such as Caenorhabditis elegans for hit identification and lead optimization. Current in vivo assays can operate either at low throughput with high resolution or with low resolution at high throughput. To enable both high-throughput and high-resolution imaging of C. elegans, we developed an automated microfluidic platform. This platform can image 15 z-stacks of ~4,000 C. elegans from 96 different populations using a large-scale chip with a micron resolution in 16 min. Using this platform, we screened ~100,000 animals of the poly-glutamine aggregation model on 25 chips. We tested the efficacy of ~1,000 FDA-approved drugs in improving the aggregation phenotype of the model and identified four confirmed hits. This robust platform now enables high-content screening of various C. elegans disease models at the speed and cost of in vitro cell-based assays.

Synthetic aperture tomographic phase microscopy for 3D imaging of live cells in translational motion

PubMed Central

Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Badizadegan, Kamran; Dasari, Ramachandra R.; Feld, Michael S.

2009-01-01

We present a technique for 3D imaging of live cells in translational motion without need of axial scanning of objective lens. A set of transmitted electric field images of cells at successive points of transverse translation is taken with a focused beam illumination. Based on Hyugens’ principle, angular plane waves are synthesized from E-field images of a focused beam. For a set of synthesized angular plane waves, we apply a filtered back-projection algorithm and obtain 3D maps of refractive index of live cells. This technique, which we refer to as synthetic aperture tomographic phase microscopy, can potentially be combined with flow cytometry or microfluidic devices, and will enable high throughput acquisition of quantitative refractive index data from large numbers of cells. PMID:18825263

Particle sizer and DNA sequencer

DOEpatents

Olivares, Jose A.; Stark, Peter C.

2005-09-13

An electrophoretic device separates and detects particles such as DNA fragments, proteins, and the like. The device has a capillary which is coated with a coating with a low refractive index such as Teflon.RTM. AF. A sample of particles is fluorescently labeled and injected into the capillary. The capillary is filled with an electrolyte buffer solution. An electrical field is applied across the capillary causing the particles to migrate from a first end of the capillary to a second end of the capillary. A detector light beam is then scanned along the length of the capillary to detect the location of the separated particles. The device is amenable to a high throughput system by providing additional capillaries. The device can also be used to determine the actual size of the particles and for DNA sequencing.

A Method for Identifying Small-Molecule Aggregators Using Photonic Crystal Biosensor Microplates

PubMed Central

Chan, Leo L.; Lidstone, Erich A.; Finch, Kristin E.; Heeres, James T.; Hergenrother, Paul J.; Cunningham, Brian T.

2010-01-01

Small molecules identified through high-throughput screens are an essential element in pharmaceutical discovery programs. It is now recognized that a substantial fraction of small molecules exhibit aggregating behavior leading to false positive results in many screening assays, typically due to nonspecific attachment to target proteins. Therefore, the ability to efficiently identify compounds within a screening library that aggregate can streamline the screening process by eliminating unsuitable molecules from further consideration. In this work, we show that photonic crystal (PC) optical biosensor microplate technology can be used to identify and quantify small-molecule aggregation. A group of aggregators and nonaggregators were tested using the PC technology, and measurements were compared with those gathered by three alternative methods: dynamic light scattering (DLS), an α-chymotrypsin colorimetric assay, and scanning electron microscopy (SEM). The PC biosensor measurements of aggregation were confirmed by visual observation using SEM, and were in general agreement with the α-chymotrypsin assay. DLS measurements, in contrast, demonstrated inconsistent readings for many compounds that are found to form aggregates in shapes, very different from the classical spherical particles assumed in DLS modeling. As a label-free detection method, the PC biosensor aggregation assay is simple to implement and provides a quantitative direct measurement of the mass density of material adsorbed to the transducer surface, whereas the microplate-based sensor format enables compatibility with high-throughput automated liquid-handling methods used in pharmaceutical screening. PMID:20930952

Identifying initiation and elongation inhibitors of dengue virus RNA polymerase in a high-throughput lead-finding campaign.

PubMed

Smith, Thomas M; Lim, Siew Pheng; Yue, Kimberley; Busby, Scott A; Arora, Rishi; Seh, Cheah Chen; Wright, S Kirk; Nutiu, Razvan; Niyomrattanakit, Pornwaratt; Wan, Kah Fei; Beer, David; Shi, Pei-Yong; Benson, Timothy E

2015-01-01

Dengue virus (DENV) is the most significant mosquito-borne viral pathogen in the world and is the cause of dengue fever. The DENV RNA-dependent RNA polymerase (RdRp) is conserved among the four viral serotypes and is an attractive target for antiviral drug development. During initiation of viral RNA synthesis, the polymerase switches from a "closed" to "open" conformation to accommodate the viral RNA template. Inhibitors that lock the "closed" or block the "open" conformation would prevent viral RNA synthesis. Herein, we describe a screening campaign that employed two biochemical assays to identify inhibitors of RdRp initiation and elongation. Using a DENV subgenomic RNA template that promotes RdRp de novo initiation, the first assay measures cytosine nucleotide analogue (Atto-CTP) incorporation. Liberated Atto fluorophore allows for quantification of RdRp activity via fluorescence. The second assay uses the same RNA template but is label free and directly detects RdRp-mediated liberation of pyrophosphates of native ribonucleotides via liquid chromatography-mass spectrometry. The ability of inhibitors to bind and stabilize a "closed" conformation of the DENV RdRp was further assessed in a differential scanning fluorimetry assay. Last, active compounds were evaluated in a renilla luciferase-based DENV replicon cell-based assay to monitor cellular efficacy. All assays described herein are medium to high throughput, are robust and reproducible, and allow identification of inhibitors of the open and closed forms of DENV RNA polymerase. © 2014 Society for Laboratory Automation and Screening.

Volume determination of irregularly-shaped quasi-spherical nanoparticles.

PubMed

Attota, Ravi Kiran; Liu, Eileen Cherry

2016-11-01

Nanoparticles (NPs) are widely used in diverse application areas, such as medicine, engineering, and cosmetics. The size (or volume) of NPs is one of the most important parameters for their successful application. It is relatively straightforward to determine the volume of regular NPs such as spheres and cubes from a one-dimensional or two-dimensional measurement. However, due to the three-dimensional nature of NPs, it is challenging to determine the proper physical size of many types of regularly and irregularly-shaped quasi-spherical NPs at high-throughput using a single tool. Here, we present a relatively simple method that determines a better volume estimate of NPs by combining measurements from their top-down projection areas and peak heights using two tools. The proposed method is significantly faster and more economical than the electron tomography method. We demonstrate the improved accuracy of the combined method over scanning electron microscopy (SEM) or atomic force microscopy (AFM) alone by using modeling, simulations, and measurements. This study also exposes the existence of inherent measurement biases for both SEM and AFM, which usually produce larger measured diameters with SEM than with AFM. However, in some cases SEM measured diameters appear to have less error compared to AFM measured diameters, especially for widely used IS-NPs such as of gold, and silver. The method provides a much needed, proper high-throughput volumetric measurement method useful for many applications. Graphical Abstract The combined method for volume determination of irregularly-shaped quasi-spherical nanoparticles.

ToxCast Dashboard

EPA Pesticide Factsheets

The ToxCast Dashboard helps users examine high-throughput assay data to inform chemical safety decisions. To date, it has data on over 9,000 chemicals and information from more than 1,000 high-throughput assay endpoint components.

RapidTox Dashboard

EPA Pesticide Factsheets

The ToxCast Dashboard helps users examine high-throughput assay data to inform chemical safety decisions. To date, it has data on over 9,000 chemicals and information from more than 1,000 high-throughput assay endpoint components.

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

PubMed Central

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

Self-leveling 2D DPN probe arrays

NASA Astrophysics Data System (ADS)

Haaheim, Jason R.; Val, Vadim; Solheim, Ed; Bussan, John; Fragala, J.; Nelson, Mike

2010-02-01

Dip Pen Nanolithography® (DPN®) is a direct write scanning probe-based technique which operates under ambient conditions, making it suitable to deposit a wide range of biological and inorganic materials. Precision nanoscale deposition is a fundamental requirement to advance nanoscale technology in commercial applications, and tailoring chemical composition and surface structure on the sub-100 nm scale benefits researchers in areas ranging from cell adhesion to cell-signaling and biomimetic membranes. These capabilities naturally suggest a "Desktop Nanofab" concept - a turnkey system that allows a non-expert user to rapidly create high resolution, scalable nanostructures drawing upon well-characterized ink and substrate pairings. In turn, this system is fundamentally supported by a portfolio of MEMS devices tailored for microfluidic ink delivery, directed placement of nanoscale materials, and cm2 tip arrays for high-throughput nanofabrication. Massively parallel two-dimensional nanopatterning is now commercially available via NanoInk's 2D nano PrintArray™, making DPN a high-throughput (>3×107 μm2 per hour), flexible and versatile method for precision nanoscale pattern formation. However, cm2 arrays of nanoscopic tips introduce the nontrivial problem of getting them all evenly touching the surface to ensure homogeneous deposition; this requires extremely precise leveling of the array. Herein, we describe how we have made the process simple by way of a selfleveling gimbal attachment, coupled with semi-automated software leveling routines which bring the cm^2 chip to within 0.002 degrees of co-planarity. This excellent co-planarity yields highly homogeneous features across a square centimeter, with <6% feature size standard deviation. We have engineered the devices to be easy to use, wire-free, and fully integrated with both of our patterning tools: the DPN 5000, and the NLP 2000.

Development of a non-contact diagnostic tool for high power lasers

NASA Astrophysics Data System (ADS)

Simmons, Jed A.; Guttman, Jeffrey L.; McCauley, John

2016-03-01

High power lasers in excess of 1 kW generate enough Rayleigh scatter, even in the NIR, to be detected by silicon based sensor arrays. A lens and camera system in an off-axis position can therefore be used as a non-contact diagnostic tool for high power lasers. Despite the simplicity of the concept, technical challenges have been encountered in the development of an instrument referred to as BeamWatch. These technical challenges include reducing background radiation, achieving high signal to noise ratio, reducing saturation events caused by particulates crossing the beam, correcting images to achieve accurate beam width measurements, creating algorithms for the removal of non-uniformities, and creating two simultaneous views of the beam from orthogonal directions. Background radiation in the image was reduced by the proper positioning of the back plane and the placement of absorbing materials on the internal surfaces of BeamWatch. Maximizing signal to noise ratio, important to the real-time monitoring of focus position, was aided by increasing lens throughput. The number of particulates crossing the beam path was reduced by creating a positive pressure inside BeamWatch. Algorithms in the software removed non-uniformities in the data prior to generating waist width, divergence, BPP, and M2 results. A dual axis version of BeamWatch was developed by the use of mirrors. By its nature BeamWatch produced results similar to scanning slit measurements. Scanning slit data was therefore taken and compared favorably with BeamWatch results.

Nanoparticle light scattering on interferometric surfaces

NASA Astrophysics Data System (ADS)

Hayrapetyan, K.; Arif, K. M.; Savran, C. A.; Nolte, D. D.

2011-03-01

We present a model based on Mie Surface Double Interaction (MSDI) to explore bead-based detection mechanisms using imaging and scanning. The application goal of this work is to explore the trade-offs between the sensitivity and throughput among various detection methods. Experimentally we use thermal oxide on silicon to establish and control surface interferometric conditions. Surface-captured gold beads are detected using Molecular Interferometric Imaging (MI2) and Spinning-Disc Interferometry (SDI).

A high-quality annotated transcriptome of swine peripheral blood

USDA-ARS?s Scientific Manuscript database

Background: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes an...

Secretory glands and microvascular systems imaged in aqueous solution by atmospheric scanning electron microscopy (ASEM).

PubMed

Yamazawa, Toshiko; Nakamura, Naotoshi; Sato, Mari; Sato, Chikara

2016-12-01

Exocrine glands, e.g., salivary and pancreatic glands, play an important role in digestive enzyme secretion, while endocrine glands, e.g., pancreatic islets, secrete hormones that regulate blood glucose levels. The dysfunction of these secretory organs immediately leads to various diseases, such as diabetes or Sjögren's syndrome, by poorly understood mechanisms. Gland-related diseases have been studied by optical microscopy (OM), and at higher resolution by transmission electron microscopy (TEM) of Epon embedded samples, which necessitates hydrophobic sample pretreatment. Here, we report the direct observation of tissue in aqueous solution by atmospheric scanning electron microscopy (ASEM). Salivary glands, lacrimal glands, and pancreas were fixed, sectioned into slabs, stained with phosphotungstic acid (PTA), and inspected in radical scavenger d-glucose solution from below by an inverted scanning electron microscopy (SEM), guided by optical microscopy from above to target the tissue substructures. A 2- to 3-µm specimen thickness was visualized by the SEM. In secretory cells, cytoplasmic vesicles and other organelles were clearly imaged at high resolution, and the former could be classified according to the degree of PTA staining. In islets of Langerhans, the microvascular system used as an outlet by the secretory cells was also clearly observed. Microvascular system is also critically involved in the onset of diabetic complications and was clearly visible in subcutaneous tissue imaged by ASEM. The results suggest the use of in-solution ASEM for histology and to study vesicle secretion systems. Further, the high-throughput of ASEM makes it a potential tool for the diagnosis of exocrine and endocrine-related diseases. © 2016 Wiley Periodicals, Inc.

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

PubMed Central

Bacik, John-Paul; Wrenbeck, Emily E.; Michalczyk, Ryszard; Whitehead, Timothy A.

2017-01-01

Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes. We assayed a TEM-1 beta-lactamase variant and levoglucosan kinase (LGK) using yeast surface display (YSD) screening and a twin-arginine translocation pathway selection. We then compared these scans with published experimental fitness landscapes. Results from the YSD screen could explain 37% of the variance in the fitness landscapes for one enzyme. Five percent to 10% of all single missense mutations improve solubility, matching theoretical predictions of global protein stability. For a given solubility-enhancing mutation, the probability that it would retain wild-type fitness was correlated with evolutionary conservation and distance to active site, and anticorrelated with contact number. Hybrid classification models were developed that could predict solubility-enhancing mutations that maintain wild-type fitness with an accuracy of 90%. The downside of using such classification models is the removal of rare mutations that improve both fitness and solubility. To reveal the biophysical basis of enhanced protein solubility and function, we determined the crystallographic structure of one such LGK mutant. Beyond fundamental insights into trade-offs between stability and activity, these results have potential biotechnological applications. PMID:28196882

WE-EF-BRA-05: Experimental Design for High-Throughput In-Vitro RBE Measurements Using Protons, Helium and Carbon Ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, F; Titt, U; Patel, D

2015-06-15

Purpose: To design and validate experimental setups for investigation of dose and LET effects in cell kill for protons, helium and carbon ions, in high throughput and high accuracy cell experiments. Methods: Using the Geant4 Monte Carlo toolkit, we designed 3 custom range compensators to simultaneously expose cancer cells to different doses and LETs from selected portions of pristine ion beams from the entrance to points just beyond the Bragg peak. To minimize the spread of LET, we utilized mono-energetic uniformly scanned beams at the HIT facility with support from the DKFZ. Using different entrance doses and LETs, a matrixmore » of cell survival data was acquired leading to a specific RBE matrix. We utilized the standard clonogenic assay for H460 and H1437 lung-cancer cell lines grown in 96-well plates. Using these plates, the data could be acquired in a small number of exposures. The ion specific compensators were located in a horizontal beam, designed to hold two 96-wells plates (12 columns by 8 rows) at an angle of 30o with respect to the beam direction. Results: Using about 20 hours of beam time, a total of about 11,000 wells containing cancer cells could be irradiated. The H460 and H1437 cell lines exhibited a significant dependence on LET when they were exposed to comparable doses. The results were similar for each of the investigated ion species, and indicate the need to incorporate RBE into the ion therapy planning process. Conclusion: The experimental design developed is a viable approach to rapidly acquire large amounts of accurate in-vitro RBE data. We plan to further improve the design to achieve higher accuracy and throughput, thereby facilitating the irradiation of multiple cell types. The results are indicative of the possibility to develop a new degree of freedom (variable RBE) for future clinical ion therapy optimization. Work supported by the Sister Institute Network Fund (SINF), University of Texas MD Anderson Cancer Center.« less

Multiplex and high-throughput DNA detection using surface plasmon mediated fluorescence

NASA Astrophysics Data System (ADS)

Mei, Zhong

The overall objective of this research project was to develop a user-friendly and sensitive biosensor for nucleic acid aptamers with multiplexing and high-throughput capability. The sensing was based on the fluorescence signals emitted by the fluorophores coupling with plamonic nanoparticle (gold nanorod) deposited on a patterned substrate. Gold nanorods (GNRs) were synthesized using a binary mixture of hexadecyltrimethylammonium bromide (CTAB) and sodium oleate (NaOL) in seed mediated growth method. Polytetrafluoroethylene (PTFE) printed glass slides were selectively coated with a gold thin-film to define hydrophilic areas for GNR deposition. Due to the wettablity contrast, GNR solution dropped on the slide was induced to assemble exclusively in the hydrophilic spots. By controlling temperature and humidity of the evaporation process, vertically-standing GNR arrays were achieved on the pattered slide. Fluorescence was conjugated to GNR surface via DNA double strand with tunable length. Theoretical simulation predicted a flat layer ( 30 nm thick) of uniform "hot spots" presented on the GNR tips, which could modify the nearby fluorescence. Experimentally, the vertical GNR arrays yielded metallic enhanced fluorescence (MEF) effect, which was dependent on the spectrum overlap and GNR-fluorophore distance. Specifically, the maximum enhancement of Quasar 670 and Alexa 750 was observed when it was coupled with GNR664 (plasmonic wavelength 664 nm) and GNR778 respectively at a distance of 16 nm, while the carboxyfluorescein (FAM) was at maximal intensity when attached to gold nanosphere520. This offers an opportunity for multiplexed DNA sensing. Based on this, we developed a novel GNR mediated fluorescence biosensor for DNA detection. Fluorescence labeled haipin-DNA probes were introduced to designated spots of GNR array with the matching LSPR wavelengths on the substrate. The fluorescence was quenched originally because of Forster resonance energy transfer (FRET) effect. Upon hybridization with their complimentary target DNAs, hairpin structures were opened and the fluorescence enhancement from each GNR sensing spot was measured by fluorescence scanning. We demonstrated multiple DNA sequences were simultaneously detected at a picomolar level with high-throughput capability using the ordered GNR array biochip.

Industrializing electrophysiology: HT automated patch clamp on SyncroPatch® 96 using instant frozen cells.

PubMed

Polonchuk, Liudmila

2014-01-01

Patch-clamping is a powerful technique for investigating the ion channel function and regulation. However, its low throughput hampered profiling of large compound series in early drug development. Fortunately, automation has revolutionized the area of experimental electrophysiology over the past decade. Whereas the first automated patch-clamp instruments using the planar patch-clamp technology demonstrated rather a moderate throughput, few second-generation automated platforms recently launched by various companies have significantly increased ability to form a high number of high-resistance seals. Among them is SyncroPatch(®) 96 (Nanion Technologies GmbH, Munich, Germany), a fully automated giga-seal patch-clamp system with the highest throughput on the market. By recording from up to 96 cells simultaneously, the SyncroPatch(®) 96 allows to substantially increase throughput without compromising data quality. This chapter describes features of the innovative automated electrophysiology system and protocols used for a successful transfer of the established hERG assay to this high-throughput automated platform.

HIGH THROUGHPUT ASSESSMENTS OF CONVENTIONAL AND ALTERNATIVE COMPOUNDS

EPA Science Inventory

High throughput approaches for quantifying chemical hazard, exposure, and sustainability have the potential to dramatically impact the pace and nature of risk assessments. Integrated evaluation strategies developed at the US EPA incorporate inherency,bioactivity,bioavailability, ...

Capillary array scanner for time-resolved detection and identification of fluorescently labelled DNA fragments.

PubMed

Neumann, M; Herten, D P; Dietrich, A; Wolfrum, J; Sauer, M

2000-02-25

The first capillary array scanner for time-resolved fluorescence detection in parallel capillary electrophoresis based on semiconductor technology is described. The system consists essentially of a confocal fluorescence microscope and a x,y-microscope scanning stage. Fluorescence of the labelled probe molecules was excited using a short-pulse diode laser emitting at 640 nm with a repetition rate of 50 MHz. Using a single filter system the fluorescence decays of different labels were detected by an avalanche photodiode in combination with a PC plug-in card for time-correlated single-photon counting (TCSPC). The time-resolved fluorescence signals were analyzed and identified by a maximum likelihood estimator (MLE). The x,y-microscope scanning stage allows for discontinuous, bidirectional scanning of up to 16 capillaries in an array, resulting in longer fluorescence collection times per capillary compared to scanners working in a continuous mode. Synchronization of the alignment and measurement process were developed to allow for data acquisition without overhead. Detection limits in the subzeptomol range for different dye molecules separated in parallel capillaries have been achieved. In addition, we report on parallel time-resolved detection and separation of more than 400 bases of single base extension DNA fragments in capillary array electrophoresis. Using only semiconductor technology the presented technique represents a low-cost alternative for high throughput DNA sequencing in parallel capillaries.

GiNA, an efficient and high-throughput software for horticultural phenotyping

USDA-ARS?s Scientific Manuscript database

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed,...

High-throughput quantification of hydroxyproline for determination of collagen.

PubMed

Hofman, Kathleen; Hall, Bronwyn; Cleaver, Helen; Marshall, Susan

2011-10-15

An accurate and high-throughput assay for collagen is essential for collagen research and development of collagen products. Hydroxyproline is routinely assayed to provide a measurement for collagen quantification. The time required for sample preparation using acid hydrolysis and neutralization prior to assay is what limits the current method for determining hydroxyproline. This work describes the conditions of alkali hydrolysis that, when combined with the colorimetric assay defined by Woessner, provide a high-throughput, accurate method for the measurement of hydroxyproline. Copyright © 2011 Elsevier Inc. All rights reserved.

High-Throughput Method for Strontium Isotope Analysis by Multi-Collector-Inductively Coupled Plasma-Mass Spectrometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Andrew J.; Capo, Rosemary C.; Stewart, Brian W.

2016-09-22

This technical report presents the details of the Sr column configuration and the high-throughput Sr separation protocol. Data showing the performance of the method as well as the best practices for optimizing Sr isotope analysis by MC-ICP-MS is presented. Lastly, this report offers tools for data handling and data reduction of Sr isotope results from the Thermo Scientific Neptune software to assist in data quality assurance, which help avoid issues of data glut associated with high sample throughput rapid analysis.

High-Throughput Method for Strontium Isotope Analysis by Multi-Collector-Inductively Coupled Plasma-Mass Spectrometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hakala, Jacqueline Alexandra

2016-11-22

This technical report presents the details of the Sr column configuration and the high-throughput Sr separation protocol. Data showing the performance of the method as well as the best practices for optimizing Sr isotope analysis by MC-ICP-MS is presented. Lastly, this report offers tools for data handling and data reduction of Sr isotope results from the Thermo Scientific Neptune software to assist in data quality assurance, which help avoid issues of data glut associated with high sample throughput rapid analysis.

A Memory Efficient Network Encryption Scheme

NASA Astrophysics Data System (ADS)

El-Fotouh, Mohamed Abo; Diepold, Klaus

In this paper, we studied the two widely used encryption schemes in network applications. Shortcomings have been found in both schemes, as these schemes consume either more memory to gain high throughput or low memory with low throughput. The need has aroused for a scheme that has low memory requirements and in the same time possesses high speed, as the number of the internet users increases each day. We used the SSM model [1], to construct an encryption scheme based on the AES. The proposed scheme possesses high throughput together with low memory requirements.

HTP-NLP: A New NLP System for High Throughput Phenotyping.

PubMed

Schlegel, Daniel R; Crowner, Chris; Lehoullier, Frank; Elkin, Peter L

2017-01-01

Secondary use of clinical data for research requires a method to quickly process the data so that researchers can quickly extract cohorts. We present two advances in the High Throughput Phenotyping NLP system which support the aim of truly high throughput processing of clinical data, inspired by a characterization of the linguistic properties of such data. Semantic indexing to store and generalize partially-processed results and the use of compositional expressions for ungrammatical text are discussed, along with a set of initial timing results for the system.

Combined Effect of Random Transmit Power Control and Inter-Path Interference Cancellation on DS-CDMA Packet Mobile Communications

NASA Astrophysics Data System (ADS)

Kudoh, Eisuke; Ito, Haruki; Wang, Zhisen; Adachi, Fumiyuki

In mobile communication systems, high speed packet data services are demanded. In the high speed data transmission, throughput degrades severely due to severe inter-path interference (IPI). Recently, we proposed a random transmit power control (TPC) to increase the uplink throughput of DS-CDMA packet mobile communications. In this paper, we apply IPI cancellation in addition to the random TPC. We derive the numerical expression of the received signal-to-interference plus noise power ratio (SINR) and introduce IPI cancellation factor. We also derive the numerical expression of system throughput when IPI is cancelled ideally to compare with the Monte Carlo numerically evaluated system throughput. Then we evaluate, by Monte-Carlo numerical computation method, the combined effect of random TPC and IPI cancellation on the uplink throughput of DS-CDMA packet mobile communications.

Enhanced capture rate for haze defects in production wafer inspection

NASA Astrophysics Data System (ADS)

Auerbach, Ditza; Shulman, Adi; Rozentsvige, Moshe

2010-03-01

Photomask degradation via haze defect formation is an increasing troublesome yield problem in the semiconductor fab. Wafer inspection is often utilized to detect haze defects due to the fact that it can be a bi-product of process control wafer inspection; furthermore, the detection of the haze on the wafer is effectively enhanced due to the multitude of distinct fields being scanned. In this paper, we demonstrate a novel application for enhancing the wafer inspection tool's sensitivity to haze defects even further. In particular, we present results of bright field wafer inspection using the on several photo layers suffering from haze defects. One way in which the enhanced sensitivity can be achieved in inspection tools is by using a double scan of the wafer: one regular scan with the normal recipe and another high sensitivity scan from which only the repeater defects are extracted (the non-repeater defects consist largely of noise which is difficult to filter). Our solution essentially combines the double scan into a single high sensitivity scan whose processing is carried out along two parallel routes (see Fig. 1). Along one route, potential defects follow the standard recipe thresholds to produce a defect map at the nominal sensitivity. Along the alternate route, potential defects are used to extract only field repeater defects which are identified using an optimal repeater algorithm that eliminates "false repeaters". At the end of the scan, the two defect maps are merged into one with optical scan images available for all the merged defects. It is important to note, that there is no throughput hit; in addition, the repeater sensitivity is increased relative to a double scan, due to a novel runtime algorithm implementation whose memory requirements are minimized, thus enabling to search a much larger number of potential defects for repeaters. We evaluated the new application on photo wafers which consisted of both random and haze defects. The evaluation procedure involved scanning with three different recipe types: Standard Inspection: Nominal recipe with a low false alarm rate was used to scan the wafer and repeaters were extracted from the final defect map. Haze Monitoring Application: Recipe sensitivity was enhanced and run on a single field column from which on repeating defects were extracted. Enhanced Repeater Extractor: Defect processing included the two parallel routes: a nominal recipe for the random defects and the new high sensitive repeater extractor algorithm. The results showed that the new application (recipe #3) had the highest capture rate on haze defects and detected new repeater defects not found in the first two recipes. In addition, the recipe was much simpler to setup since repeaters are filtered separately from random defects. We expect that in the future, with the advent of mask-less lithography and EUV lithography, the monitoring of field and die repeating defects on the wafer will become a necessity for process control in the semiconductor fab.

Evaluating Rapid Models for High-Throughput Exposure Forecasting (SOT)

EPA Science Inventory

High throughput exposure screening models can provide quantitative predictions for thousands of chemicals; however these predictions must be systematically evaluated for predictive ability. Without the capability to make quantitative, albeit uncertain, forecasts of exposure, the ...

Solar fuels photoanode materials discovery by integrating high-throughput theory and experiment

DOE PAGES

Yan, Qimin; Yu, Jie; Suram, Santosh K.; ...

2017-03-06

The limited number of known low-band-gap photoelectrocatalytic materials poses a significant challenge for the generation of chemical fuels from sunlight. Here, using high-throughput ab initio theory with experiments in an integrated workflow, we find eight ternary vanadate oxide photoanodes in the target band-gap range (1.2-2.8 eV). Detailed analysis of these vanadate compounds reveals the key role of VO 4 structural motifs and electronic band-edge character in efficient photoanodes, initiating a genome for such materials and paving the way for a broadly applicable high-throughput-discovery and materials-by-design feedback loop. Considerably expanding the number of known photoelectrocatalysts for water oxidation, our study establishesmore » ternary metal vanadates as a prolific class of photoanodematerials for generation of chemical fuels from sunlight and demonstrates our high-throughput theory-experiment pipeline as a prolific approach to materials discovery.« less

Microfluidics for cell-based high throughput screening platforms - A review.

PubMed

Du, Guansheng; Fang, Qun; den Toonder, Jaap M J

2016-01-15

In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery. Copyright © 2015 Elsevier B.V. All rights reserved.

Solar fuels photoanode materials discovery by integrating high-throughput theory and experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Qimin; Yu, Jie; Suram, Santosh K.

The limited number of known low-band-gap photoelectrocatalytic materials poses a significant challenge for the generation of chemical fuels from sunlight. Here, using high-throughput ab initio theory with experiments in an integrated workflow, we find eight ternary vanadate oxide photoanodes in the target band-gap range (1.2-2.8 eV). Detailed analysis of these vanadate compounds reveals the key role of VO 4 structural motifs and electronic band-edge character in efficient photoanodes, initiating a genome for such materials and paving the way for a broadly applicable high-throughput-discovery and materials-by-design feedback loop. Considerably expanding the number of known photoelectrocatalysts for water oxidation, our study establishesmore » ternary metal vanadates as a prolific class of photoanodematerials for generation of chemical fuels from sunlight and demonstrates our high-throughput theory-experiment pipeline as a prolific approach to materials discovery.« less

Fulfilling the promise of the materials genome initiative with high-throughput experimental methodologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, Martin L.; Choi, C. L.; Hattrick-Simpers, J. R.

The Materials Genome Initiative, a national effort to introduce new materials into the market faster and at lower cost, has made significant progress in computational simulation and modeling of materials. To build on this progress, a large amount of experimental data for validating these models, and informing more sophisticated ones, will be required. High-throughput experimentation generates large volumes of experimental data using combinatorial materials synthesis and rapid measurement techniques, making it an ideal experimental complement to bring the Materials Genome Initiative vision to fruition. This paper reviews the state-of-the-art results, opportunities, and challenges in high-throughput experimentation for materials design. Asmore » a result, a major conclusion is that an effort to deploy a federated network of high-throughput experimental (synthesis and characterization) tools, which are integrated with a modern materials data infrastructure, is needed.« less

Development and Validation of an Automated High-Throughput System for Zebrafish In Vivo Screenings

PubMed Central

Virto, Juan M.; Holgado, Olaia; Diez, Maria; Izpisua Belmonte, Juan Carlos; Callol-Massot, Carles

2012-01-01

The zebrafish is a vertebrate model compatible with the paradigms of drug discovery. The small size and transparency of zebrafish embryos make them amenable for the automation necessary in high-throughput screenings. We have developed an automated high-throughput platform for in vivo chemical screenings on zebrafish embryos that includes automated methods for embryo dispensation, compound delivery, incubation, imaging and analysis of the results. At present, two different assays to detect cardiotoxic compounds and angiogenesis inhibitors can be automatically run in the platform, showing the versatility of the system. A validation of these two assays with known positive and negative compounds, as well as a screening for the detection of unknown anti-angiogenic compounds, have been successfully carried out in the system developed. We present a totally automated platform that allows for high-throughput screenings in a vertebrate organism. PMID:22615792

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

PubMed Central

Lutsik, Pavlo; Feuerbach, Lars; Arand, Julia; Lengauer, Thomas; Walter, Jörn; Bock, Christoph

2011-01-01

Bisulfite sequencing is a widely used method for measuring DNA methylation in eukaryotic genomes. The assay provides single-base pair resolution and, given sufficient sequencing depth, its quantitative accuracy is excellent. High-throughput sequencing of bisulfite-converted DNA can be applied either genome wide or targeted to a defined set of genomic loci (e.g. using locus-specific PCR primers or DNA capture probes). Here, we describe BiQ Analyzer HT (http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/), a user-friendly software tool that supports locus-specific analysis and visualization of high-throughput bisulfite sequencing data. The software facilitates the shift from time-consuming clonal bisulfite sequencing to the more quantitative and cost-efficient use of high-throughput sequencing for studying locus-specific DNA methylation patterns. In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data. PMID:21565797

A Self-Reporting Photocatalyst for Online Fluorescence Monitoring of High Throughput RAFT Polymerization.

PubMed

Yeow, Jonathan; Joshi, Sanket; Chapman, Robert; Boyer, Cyrille Andre Jean Marie

2018-04-25

Translating controlled/living radical polymerization (CLRP) from batch to the high throughput production of polymer libraries presents several challenges in terms of both polymer synthesis and characterization. Although recently there have been significant advances in the field of low volume, high throughput CLRP, techniques able to simultaneously monitor multiple polymerizations in an "online" manner have not yet been developed. Here, we report our discovery that 5,10,15,20-tetraphenyl-21H,23H-porphine zinc (ZnTPP) is a self-reporting photocatalyst that can mediate PET-RAFT polymerization as well as report on monomer conversion via changes in its fluorescence properties. This enables the use of a microplate reader to conduct high throughput "online" monitoring of PET-RAFT polymerizations performed directly in 384-well, low volume microtiter plates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fulfilling the promise of the materials genome initiative with high-throughput experimental methodologies

DOE PAGES

Green, Martin L.; Choi, C. L.; Hattrick-Simpers, J. R.; ...

2017-03-28

The Materials Genome Initiative, a national effort to introduce new materials into the market faster and at lower cost, has made significant progress in computational simulation and modeling of materials. To build on this progress, a large amount of experimental data for validating these models, and informing more sophisticated ones, will be required. High-throughput experimentation generates large volumes of experimental data using combinatorial materials synthesis and rapid measurement techniques, making it an ideal experimental complement to bring the Materials Genome Initiative vision to fruition. This paper reviews the state-of-the-art results, opportunities, and challenges in high-throughput experimentation for materials design. Asmore » a result, a major conclusion is that an effort to deploy a federated network of high-throughput experimental (synthesis and characterization) tools, which are integrated with a modern materials data infrastructure, is needed.« less

High Throughput Genotoxicity Profiling of the US EPA ToxCast Chemical Library

EPA Science Inventory

A key aim of the ToxCast project is to investigate modern molecular and genetic high content and high throughput screening (HTS) assays, along with various computational tools to supplement and perhaps replace traditional assays for evaluating chemical toxicity. Genotoxicity is a...

Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering☆

PubMed Central

Rabitz, Herschel; Welsh, William J.; Kohn, Joachim; de Boer, Jan

2016-01-01

The research paradigm in biomaterials science and engineering is evolving from using low-throughput and iterative experimental designs towards high-throughput experimental designs for materials optimization and the evaluation of materials properties. Computational science plays an important role in this transition. With the emergence of the omics approach in the biomaterials field, referred to as materiomics, high-throughput approaches hold the promise of tackling the complexity of materials and understanding correlations between material properties and their effects on complex biological systems. The intrinsic complexity of biological systems is an important factor that is often oversimplified when characterizing biological responses to materials and establishing property-activity relationships. Indeed, in vitro tests designed to predict in vivo performance of a given biomaterial are largely lacking as we are not able to capture the biological complexity of whole tissues in an in vitro model. In this opinion paper, we explain how we reached our opinion that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. PMID:26876875

A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens

PubMed Central

Besaratinia, Ahmad; Li, Haiqing; Yoon, Jae-In; Zheng, Albert; Gao, Hanlin; Tommasi, Stella

2012-01-01

Many carcinogens leave a unique mutational fingerprint in the human genome. These mutational fingerprints manifest as specific types of mutations often clustering at certain genomic loci in tumor genomes from carcinogen-exposed individuals. To develop a high-throughput method for detecting the mutational fingerprint of carcinogens, we have devised a cost-, time- and labor-effective strategy, in which the widely used transgenic Big Blue® mouse mutation detection assay is made compatible with the Roche/454 Genome Sequencer FLX Titanium next-generation sequencing technology. As proof of principle, we have used this novel method to establish the mutational fingerprints of three prominent carcinogens with varying mutagenic potencies, including sunlight ultraviolet radiation, 4-aminobiphenyl and secondhand smoke that are known to be strong, moderate and weak mutagens, respectively. For verification purposes, we have compared the mutational fingerprints of these carcinogens obtained by our newly developed method with those obtained by parallel analyses using the conventional low-throughput approach, that is, standard mutation detection assay followed by direct DNA sequencing using a capillary DNA sequencer. We demonstrate that this high-throughput next-generation sequencing-based method is highly specific and sensitive to detect the mutational fingerprints of the tested carcinogens. The method is reproducible, and its accuracy is comparable with that of the currently available low-throughput method. In conclusion, this novel method has the potential to move the field of carcinogenesis forward by allowing high-throughput analysis of mutations induced by endogenous and/or exogenous genotoxic agents. PMID:22735701

A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens.

PubMed

Besaratinia, Ahmad; Li, Haiqing; Yoon, Jae-In; Zheng, Albert; Gao, Hanlin; Tommasi, Stella

2012-08-01

Many carcinogens leave a unique mutational fingerprint in the human genome. These mutational fingerprints manifest as specific types of mutations often clustering at certain genomic loci in tumor genomes from carcinogen-exposed individuals. To develop a high-throughput method for detecting the mutational fingerprint of carcinogens, we have devised a cost-, time- and labor-effective strategy, in which the widely used transgenic Big Blue mouse mutation detection assay is made compatible with the Roche/454 Genome Sequencer FLX Titanium next-generation sequencing technology. As proof of principle, we have used this novel method to establish the mutational fingerprints of three prominent carcinogens with varying mutagenic potencies, including sunlight ultraviolet radiation, 4-aminobiphenyl and secondhand smoke that are known to be strong, moderate and weak mutagens, respectively. For verification purposes, we have compared the mutational fingerprints of these carcinogens obtained by our newly developed method with those obtained by parallel analyses using the conventional low-throughput approach, that is, standard mutation detection assay followed by direct DNA sequencing using a capillary DNA sequencer. We demonstrate that this high-throughput next-generation sequencing-based method is highly specific and sensitive to detect the mutational fingerprints of the tested carcinogens. The method is reproducible, and its accuracy is comparable with that of the currently available low-throughput method. In conclusion, this novel method has the potential to move the field of carcinogenesis forward by allowing high-throughput analysis of mutations induced by endogenous and/or exogenous genotoxic agents.

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility.

PubMed

Yennawar, Neela H; Fecko, Julia A; Showalter, Scott A; Bevilacqua, Philip C

2016-01-01

Many labs have conventional calorimeters where denaturation and binding experiments are setup and run one at a time. While these systems are highly informative to biopolymer folding and ligand interaction, they require considerable manual intervention for cleaning and setup. As such, the throughput for such setups is limited typically to a few runs a day. With a large number of experimental parameters to explore including different buffers, macromolecule concentrations, temperatures, ligands, mutants, controls, replicates, and instrument tests, the need for high-throughput automated calorimeters is on the rise. Lower sample volume requirements and reduced user intervention time compared to the manual instruments have improved turnover of calorimetry experiments in a high-throughput format where 25 or more runs can be conducted per day. The cost and efforts to maintain high-throughput equipment typically demands that these instruments be housed in a multiuser core facility. We describe here the steps taken to successfully start and run an automated biological calorimetry facility at Pennsylvania State University. Scientists from various departments at Penn State including Chemistry, Biochemistry and Molecular Biology, Bioengineering, Biology, Food Science, and Chemical Engineering are benefiting from this core facility. Samples studied include proteins, nucleic acids, sugars, lipids, synthetic polymers, small molecules, natural products, and virus capsids. This facility has led to higher throughput of data, which has been leveraged into grant support, attracting new faculty hire and has led to some exciting publications. © 2016 Elsevier Inc. All rights reserved.

Expedient Caution: Approximating Exposure and Dosimetry to Understand Chemical Risk (OSU EMT Research Day keynote presentation)

EPA Science Inventory

I describe research on high throughput exposure and toxicokinetics. These tools provide context for data generated by high throughput toxicity screening to allow risk-based prioritization of thousands of chemicals.

MIPHENO: Data normalization for high throughput metabolic analysis.

EPA Science Inventory

High throughput methodologies such as microarrays, mass spectrometry and plate-based small molecule screens are increasingly used to facilitate discoveries from gene function to drug candidate identification. These large-scale experiments are typically carried out over the course...

High-Throughput Pharmacokinetics for Environmental Chemicals (SOT)

EPA Science Inventory

High throughput screening (HTS) promises to allow prioritization of thousands of environmental chemicals with little or no in vivo information. For bioactivity identified by HTS, toxicokinetic (TK) models are essential to predict exposure thresholds below which no significant bio...

High Throughput Computing Impact on Meta Genomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Gore, Brooklin

2018-02-01

This presentation includes a brief background on High Throughput Computing, correlating gene transcription factors, optical mapping, genotype to phenotype mapping via QTL analysis, and current work on next gen sequencing.

Establishment of integrated protocols for automated high throughput kinetic chlorophyll fluorescence analyses.

PubMed

Tschiersch, Henning; Junker, Astrid; Meyer, Rhonda C; Altmann, Thomas

2017-01-01

Automated plant phenotyping has been established as a powerful new tool in studying plant growth, development and response to various types of biotic or abiotic stressors. Respective facilities mainly apply non-invasive imaging based methods, which enable the continuous quantification of the dynamics of plant growth and physiology during developmental progression. However, especially for plants of larger size, integrative, automated and high throughput measurements of complex physiological parameters such as photosystem II efficiency determined through kinetic chlorophyll fluorescence analysis remain a challenge. We present the technical installations and the establishment of experimental procedures that allow the integrated high throughput imaging of all commonly determined PSII parameters for small and large plants using kinetic chlorophyll fluorescence imaging systems (FluorCam, PSI) integrated into automated phenotyping facilities (Scanalyzer, LemnaTec). Besides determination of the maximum PSII efficiency, we focused on implementation of high throughput amenable protocols recording PSII operating efficiency (Φ PSII ). Using the presented setup, this parameter is shown to be reproducibly measured in differently sized plants despite the corresponding variation in distance between plants and light source that caused small differences in incident light intensity. Values of Φ PSII obtained with the automated chlorophyll fluorescence imaging setup correlated very well with conventionally determined data using a spot-measuring chlorophyll fluorometer. The established high throughput operating protocols enable the screening of up to 1080 small and 184 large plants per hour, respectively. The application of the implemented high throughput protocols is demonstrated in screening experiments performed with large Arabidopsis and maize populations assessing natural variation in PSII efficiency. The incorporation of imaging systems suitable for kinetic chlorophyll fluorescence analysis leads to a substantial extension of the feature spectrum to be assessed in the presented high throughput automated plant phenotyping platforms, thus enabling the simultaneous assessment of plant architectural and biomass-related traits and their relations to physiological features such as PSII operating efficiency. The implemented high throughput protocols are applicable to a broad spectrum of model and crop plants of different sizes (up to 1.80 m height) and architectures. The deeper understanding of the relation of plant architecture, biomass formation and photosynthetic efficiency has a great potential with respect to crop and yield improvement strategies.

Identifying drought adaptive traits in upland cotton using a proximal sensing cart for high-throughput phenotyping

USDA-ARS?s Scientific Manuscript database

Field-based high-throughput phenotyping is an emerging approach to characterize difficult, time-sensitive plant traits in relevant growing conditions. Proximal sensing carts have been developed as an alternative platform to more costly high-clearance tractors for phenotyping dynamic traits in the fi...

High-throughput profiling and analysis of plant responses over time to abiotic stress

USDA-ARS?s Scientific Manuscript database

Energy sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass, annual crop prized for abiotic stress tolerance. Measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. High throughput phenotyping within controlled environments has been proposed as a po...

ToxCast Workflow: High-throughput screening assay data processing, analysis and management (SOT)

EPA Science Inventory

US EPA’s ToxCast program is generating data in high-throughput screening (HTS) and high-content screening (HCS) assays for thousands of environmental chemicals, for use in developing predictive toxicity models. Currently the ToxCast screening program includes over 1800 unique c...

A high-throughput multiplex method adapted for GMO detection.

PubMed

Chaouachi, Maher; Chupeau, Gaëlle; Berard, Aurélie; McKhann, Heather; Romaniuk, Marcel; Giancola, Sandra; Laval, Valérie; Bertheau, Yves; Brunel, Dominique

2008-12-24

A high-throughput multiplex assay for the detection of genetically modified organisms (GMO) was developed on the basis of the existing SNPlex method designed for SNP genotyping. This SNPlex assay allows the simultaneous detection of up to 48 short DNA sequences (approximately 70 bp; "signature sequences") from taxa endogenous reference genes, from GMO constructions, screening targets, construct-specific, and event-specific targets, and finally from donor organisms. This assay avoids certain shortcomings of multiplex PCR-based methods already in widespread use for GMO detection. The assay demonstrated high specificity and sensitivity. The results suggest that this assay is reliable, flexible, and cost- and time-effective for high-throughput GMO detection.

RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

PubMed Central

Singh, Guramrit; Ricci, Emiliano P.; Moore, Melissa J.

2013-01-01

Development of high-throughput approaches to map the RNA interaction sites of individual RNA binding proteins (RBPs) transcriptome-wide is rapidly transforming our understanding of post-transcriptional gene regulatory mechanisms. Here we describe a ribonucleoprotein (RNP) footprinting approach we recently developed for identifying occupancy sites of both individual RBPs and multi-subunit RNP complexes. RNA:protein immunoprecipitation in tandem (RIPiT) yields highly specific RNA footprints of cellular RNPs isolated via two sequential purifications; the resulting RNA footprints can then be identified by high-throughput sequencing (Seq). RIPiT-Seq is broadly applicable to all RBPs regardless of their RNA binding mode and thus provides a means to map the RNA binding sites of RBPs with poor inherent ultraviolet (UV) crosslinkability. Further, among current high-throughput approaches, RIPiT has the unique capacity to differentiate binding sites of RNPs with overlapping protein composition. It is therefore particularly suited for studying dynamic RNP assemblages whose composition evolves as gene expression proceeds. PMID:24096052

Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms.

PubMed

Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

2015-01-05

The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.

Development and Validation of A 48-Target Analytical Method for High-throughput Monitoring of Genetically Modified Organisms

PubMed Central

Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

2015-01-01

The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection. PMID:25556930

Sparsity-Based Super Resolution for SEM Images.

PubMed

Tsiper, Shahar; Dicker, Or; Kaizerman, Idan; Zohar, Zeev; Segev, Mordechai; Eldar, Yonina C

2017-09-13

The scanning electron microscope (SEM) is an electron microscope that produces an image of a sample by scanning it with a focused beam of electrons. The electrons interact with the atoms in the sample, which emit secondary electrons that contain information about the surface topography and composition. The sample is scanned by the electron beam point by point, until an image of the surface is formed. Since its invention in 1942, the capabilities of SEMs have become paramount in the discovery and understanding of the nanometer world, and today it is extensively used for both research and in industry. In principle, SEMs can achieve resolution better than one nanometer. However, for many applications, working at subnanometer resolution implies an exceedingly large number of scanning points. For exactly this reason, the SEM diagnostics of microelectronic chips is performed either at high resolution (HR) over a small area or at low resolution (LR) while capturing a larger portion of the chip. Here, we employ sparse coding and dictionary learning to algorithmically enhance low-resolution SEM images of microelectronic chips-up to the level of the HR images acquired by slow SEM scans, while considerably reducing the noise. Our methodology consists of two steps: an offline stage of learning a joint dictionary from a sequence of LR and HR images of the same region in the chip, followed by a fast-online super-resolution step where the resolution of a new LR image is enhanced. We provide several examples with typical chips used in the microelectronics industry, as well as a statistical study on arbitrary images with characteristic structural features. Conceptually, our method works well when the images have similar characteristics, as microelectronics chips do. This work demonstrates that employing sparsity concepts can greatly improve the performance of SEM, thereby considerably increasing the scanning throughput without compromising on analysis quality and resolution.

A high-throughput label-free nanoparticle analyser.

PubMed

Fraikin, Jean-Luc; Teesalu, Tambet; McKenney, Christopher M; Ruoslahti, Erkki; Cleland, Andrew N

2011-05-01

Synthetic nanoparticles and genetically modified viruses are used in a range of applications, but high-throughput analytical tools for the physical characterization of these objects are needed. Here we present a microfluidic analyser that detects individual nanoparticles and characterizes complex, unlabelled nanoparticle suspensions. We demonstrate the detection, concentration analysis and sizing of individual synthetic nanoparticles in a multicomponent mixture with sufficient throughput to analyse 500,000 particles per second. We also report the rapid size and titre analysis of unlabelled bacteriophage T7 in both salt solution and mouse blood plasma, using just ~1 × 10⁻⁶ l of analyte. Unexpectedly, in the native blood plasma we discover a large background of naturally occurring nanoparticles with a power-law size distribution. The high-throughput detection capability, scalable fabrication and simple electronics of this instrument make it well suited for diverse applications.

High Performance Computing Modernization Program Kerberos Throughput Test Report

DTIC Science & Technology

2017-10-26

functionality as Kerberos plugins. The pre -release production kit was used in these tests to compare against the current release kit. YubiKey support...HPCMP Kerberos Throughput Test Report 3 2. THROUGHPUT TESTING 2.1 Testing Components Throughput testing was done to determine the benefits of the pre ...both the current release kit and the pre -release production kit for a total of 378 individual tests in order to note any improvements. Based on work

Metabolomics Approach for Toxicity Screening of Volatile Substances

EPA Science Inventory

In 2007 the National Research Council envisioned the need for inexpensive, high throughput, cell based toxicity testing methods relevant to human health. High Throughput Screening (HTS) in vitro screening approaches have addressed these problems by using robotics. However, the ch...

AOPs & Biomarkers: Bridging High Throughput Screening and Regulatory Decision Making.

EPA Science Inventory

As high throughput screening (HTS) approaches play a larger role in toxicity testing, computational toxicology has emerged as a critical component in interpreting the large volume of data produced. Computational models for this purpose are becoming increasingly more sophisticated...

New High Throughput Methods to Estimate Chemical Exposure

EPA Science Inventory

EPA has made many recent advances in high throughput bioactivity testing. However, concurrent advances in rapid, quantitative prediction of human and ecological exposures have been lacking, despite the clear importance of both measures for a risk-based approach to prioritizing an...

Fully Bayesian Analysis of High-throughput Targeted Metabolomics Assays

EPA Science Inventory

High-throughput metabolomic assays that allow simultaneous targeted screening of hundreds of metabolites have recently become available in kit form. Such assays provide a window into understanding changes to biochemical pathways due to chemical exposure or disease, and are usefu...

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime

NASA Astrophysics Data System (ADS)

Ioanna Skilitsi, Anastasia; Turko, Timothé; Cianfarani, Damien; Barre, Sophie; Uhring, Wilfried; Hassiepen, Ulrich; Léonard, Jérémie

2017-09-01

Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.

High Throughput Determination of Critical Human Dosing ...

EPA Pesticide Factsheets

High throughput toxicokinetics (HTTK) is a rapid approach that uses in vitro data to estimate TK for hundreds of environmental chemicals. Reverse dosimetry (i.e., reverse toxicokinetics or RTK) based on HTTK data converts high throughput in vitro toxicity screening (HTS) data into predicted human equivalent doses that can be linked with biologically relevant exposure scenarios. Thus, HTTK provides essential data for risk prioritization for thousands of chemicals that lack TK data. One critical HTTK parameter that can be measured in vitro is the unbound fraction of a chemical in plasma (Fub). However, for chemicals that bind strongly to plasma, Fub is below the limits of detection (LOD) for high throughput analytical chemistry, and therefore cannot be quantified. A novel method for quantifying Fub was implemented for 85 strategically selected chemicals: measurement of Fub was attempted at 10%, 30%, and 100% of physiological plasma concentrations using rapid equilibrium dialysis assays. Varying plasma concentrations instead of chemical concentrations makes high throughput analytical methodology more likely to be successful. Assays at 100% plasma concentration were unsuccessful for 34 chemicals. For 12 of these 34 chemicals, Fub could be quantified at 10% and/or 30% plasma concentrations; these results imply that the assay failure at 100% plasma concentration was caused by plasma protein binding for these chemicals. Assay failure for the remaining 22 chemicals may

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy.

PubMed

Allan, Kristina J; Mahoney, Douglas J; Baird, Stephen D; Lefebvre, Charles A; Stojdl, David F

2018-04-03

High-throughput genome-wide RNAi (RNA interference) screening technology has been widely used for discovering host factors that impact virus replication. Here we present the application of this technology to uncovering host targets that specifically modulate the replication of Maraba virus, an oncolytic rhabdovirus, and vaccinia virus with the goal of enhancing therapy. While the protocol has been tested for use with oncolytic Maraba virus and oncolytic vaccinia virus, this approach is applicable to other oncolytic viruses and can also be utilized for identifying host targets that modulate virus replication in mammalian cells in general. This protocol describes the development and validation of an assay for high-throughput RNAi screening in mammalian cells, the key considerations and preparation steps important for conducting a primary high-throughput RNAi screen, and a step-by-step guide for conducting a primary high-throughput RNAi screen; in addition, it broadly outlines the methods for conducting secondary screen validation and tertiary validation studies. The benefit of high-throughput RNAi screening is that it allows one to catalogue, in an extensive and unbiased fashion, host factors that modulate any aspect of virus replication for which one can develop an in vitro assay such as infectivity, burst size, and cytotoxicity. It has the power to uncover biotherapeutic targets unforeseen based on current knowledge.

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

PubMed Central

Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Wan, Frank; Sheraden, Paige N.; Broecker, Jana; Ernst, Oliver P.; Gennis, Robert B.

2017-01-01

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å. PMID:28469762

High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots.

PubMed

Liu, Guangbo; Lanham, Clayton; Buchan, J Ross; Kaplan, Matthew E

2017-01-01

Saccharomyces cerevisiae (budding yeast) is a powerful eukaryotic model organism ideally suited to high-throughput genetic analyses, which time and again has yielded insights that further our understanding of cell biology processes conserved in humans. Lithium Acetate (LiAc) transformation of yeast with DNA for the purposes of exogenous protein expression (e.g., plasmids) or genome mutation (e.g., gene mutation, deletion, epitope tagging) is a useful and long established method. However, a reliable and optimized high throughput transformation protocol that runs almost no risk of human error has not been described in the literature. Here, we describe such a method that is broadly transferable to most liquid handling high-throughput robotic platforms, which are now commonplace in academic and industry settings. Using our optimized method, we are able to comfortably transform approximately 1200 individual strains per day, allowing complete transformation of typical genomic yeast libraries within 6 days. In addition, use of our protocol for gene knockout purposes also provides a potentially quicker, easier and more cost-effective approach to generating collections of double mutants than the popular and elegant synthetic genetic array methodology. In summary, our methodology will be of significant use to anyone interested in high throughput molecular and/or genetic analysis of yeast.

High-Throughput Toxicity Testing: New Strategies for ...

EPA Pesticide Factsheets

In recent years, the food industry has made progress in improving safety testing methods focused on microbial contaminants in order to promote food safety. However, food industry toxicologists must also assess the safety of food-relevant chemicals including pesticides, direct additives, and food contact substances. With the rapidly growing use of new food additives, as well as innovation in food contact substance development, an interest in exploring the use of high-throughput chemical safety testing approaches has emerged. Currently, the field of toxicology is undergoing a paradigm shift in how chemical hazards can be evaluated. Since there are tens of thousands of chemicals in use, many of which have little to no hazard information and there are limited resources (namely time and money) for testing these chemicals, it is necessary to prioritize which chemicals require further safety testing to better protect human health. Advances in biochemistry and computational toxicology have paved the way for animal-free (in vitro) high-throughput screening which can characterize chemical interactions with highly specific biological processes. Screening approaches are not novel; in fact, quantitative high-throughput screening (qHTS) methods that incorporate dose-response evaluation have been widely used in the pharmaceutical industry. For toxicological evaluation and prioritization, it is the throughput as well as the cost- and time-efficient nature of qHTS that makes it

Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond

PubMed Central

Arjmandi-Tash, Hadi; Belyaeva, Liubov A.

2016-01-01

Graphene and other two dimensional (2D) materials are currently integrated into nanoscaled devices that may – one day – sequence genomes. The challenge to solve is conceptually straightforward: cut a sheet out of a 2D material and use the edge of the sheet to scan an unfolded biomolecule from head to tail. As the scan proceeds – and because 2D materials are atomically thin – the information provided by the edge might be used to identify different segments – ideally single nucleotides – in the biomolecular strand. So far, the most efficient approach was to drill a nano-sized pore in the sheet and use this pore as a channel to guide and detect individual molecules by measuring the electrochemical ionic current. Nanoscaled gaps between two electrodes in 2D materials recently emerged as powerful alternatives to nanopores. This article reviews the current status and prospects of integrating 2D materials in nanopores, nanogaps and similar devices for single molecule biosensing applications. We discuss the pros and cons, the challenges, and the latest achievements in the field. To achieve high-throughput sequencing with 2D materials, interdisciplinary research is essential. PMID:26612268

Lead discovery for mammalian elongation of long chain fatty acids family 6 using a combination of high-throughput fluorescent-based assay and RapidFire mass spectrometry assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takamiya, Mari; Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kawagishi, Toda-shi, Saitama; Sakurai, Masaaki

A high-throughput RapidFire mass spectrometry assay is described for elongation of very long-chain fatty acids family 6 (Elovl6). Elovl6 is a microsomal enzyme that regulates the elongation of C12-16 saturated and monounsaturated fatty acids. Elovl6 may be a new therapeutic target for fat metabolism disorders such as obesity, type 2 diabetes, and nonalcoholic steatohepatitis. To identify new Elovl6 inhibitors, we developed a high-throughput fluorescence screening assay in 1536-well format. However, a number of false positives caused by fluorescent interference have been identified. To pick up the real active compounds among the primary hits from the fluorescence assay, we developed amore » RapidFire mass spectrometry assay and a conventional radioisotope assay. These assays have the advantage of detecting the main products directly without using fluorescent-labeled substrates. As a result, 276 compounds (30%) of the primary hits (921 compounds) in a fluorescence ultra-high-throughput screening method were identified as common active compounds in these two assays. It is concluded that both methods are very effective to eliminate false positives. Compared with the radioisotope method using an expensive {sup 14}C-labeled substrate, the RapidFire mass spectrometry method using unlabeled substrates is a high-accuracy, high-throughput method. In addition, some of the hit compounds selected from the screening inhibited cellular fatty acid elongation in HEK293 cells expressing Elovl6 transiently. This result suggests that these compounds may be promising lead candidates for therapeutic drugs. Ultra-high-throughput fluorescence screening followed by a RapidFire mass spectrometry assay was a suitable strategy for lead discovery against Elovl6. - Highlights: • A novel assay for elongation of very-long-chain fatty acids 6 (Elovl6) is proposed. • RapidFire mass spectrometry (RF-MS) assay is useful to select real screening hits. • RF-MS assay is proved to be beneficial because of its high-throughput and accuracy. • A combination of fluorescent and RF-MS assays is effective for Elovl6 inhibitors.« less

Multimodal ophthalmic imaging using spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography

NASA Astrophysics Data System (ADS)

El-Haddad, Mohamed T.; Malone, Joseph D.; Li, Jianwei D.; Bozic, Ivan; Arquitola, Amber M.; Joos, Karen M.; Patel, Shriji N.; Tao, Yuankai K.

2017-08-01

Ophthalmic surgery involves manipulation of delicate, layered tissue structures on milli- to micrometer scales. Traditional surgical microscopes provide an inherently two-dimensional view of the surgical field with limited depth perception which precludes accurate depth-resolved visualization of these tissue layers, and limits the development of novel surgical techniques. We demonstrate multimodal swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography (SS-SESLO-OCT) to address current limitations of image-guided ophthalmic microsurgery. SS-SESLO-OCT provides inherently co-registered en face and cross-sectional field-of-views (FOVs) at a line rate of 400 kHz and >2 GPix/s throughput. We show in vivo imaging of the anterior segment and retinal fundus of a healthy volunteer, and preliminary results of multi-volumetric mosaicking for ultrawide-field retinal imaging with 90° FOV. Additionally, a scan-head was rapid-prototyped with a modular architecture which enabled integration of SS-SESLO-OCT with traditional surgical microscope and slit-lamp imaging optics. Ex vivo surgical maneuvers were simulated in cadaveric porcine eyes. The system throughput enabled volumetric acquisition at 10 volumes-per-second (vps) and allowed visualization of surgical dynamics in corneal sweeps, compressions, and dissections, and retinal sweeps, compressions, and elevations. SESLO en face images enabled simple real-time co-registration with the surgical microscope FOV, and OCT cross-sections provided depth-resolved visualization of instrument-tissue interactions. Finally, we demonstrate novel augmented-reality integration with the surgical view using segmentation overlays to aid surgical guidance. SS-SESLO-OCT may benefit clinical diagnostics by enabling aiming, registration, and mosaicking; and intraoperative imaging by allowing for real-time surgical feedback, instrument tracking, and overlays of computationally extracted biomarkers of disease.

Reconfigurable Antennas for High Data Rate Multi-beam Communication Systems

NASA Technical Reports Server (NTRS)

Bernhard, Jennifer T.; Michielssen, Eric

2005-01-01

High-speed (2-100 Mb/sec) wireless data communication - whether land- or satellite-based - faces a major challenge: high error rates caused by interference and unpredictable environments. A planar antenna system that can be reconfigured to respond to changing conditions has the potential to dramatically improve data throughput and system reliability. Moreover, new planar antenna designs that reduce array size, weight, and cost can have a significant impact on terrestrial and satellite communication system performance. This research developed new individually-reconfigurable planar antenna array elements that can be adjusted to provide multiple beams while providing increased scan angles and higher aperture efficiency than traditional diffraction-limited arrays. These new elements are microstrip spiral antennas with specialized tuning mechanisms that provide adjustable radiation patterns. We anticipate that these new elements can be used in both large and small arrays for inter-satellite communication as well as tracking of multiple mobile surface-based units. Our work has developed both theoretical descriptions as well as experimental prototypes of the antennas in both single element and array embodiments. The technical summary of the results of this work is divided into six sections: A. Cavity model for analysis and design of pattern reconfigurable antennas; B. Performance of antenna in array configurations for broadside and endfire operation; C. Performance of antenna in array configurations for beam scanning operation; D. Simulation of antennas in infinite phased arrays; E. Demonstration of antenna with commercially-available RF MEMS switches; F. Design of antenna MEMS switch combinations for direct simultaneous fabrication.

Photometric Repeatability of Scanned Imagery: UVIS

NASA Astrophysics Data System (ADS)

Shanahan, Clare E.; McCullough, Peter; Baggett, Sylvia

2017-08-01

We provide the preliminary results of a study on the photometric repeatability of spatial scans of bright, isolated white dwarf stars with the UVIS channel of the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST). We analyze straight-line scans from the first pair of identical orbits of HST program 14878 to assess if sub 0.1% repeatability can be attained with WFC3/UVIS. This study is motivated by the desire to achieve better signal-to-noise in the UVIS contamination and stability monitor, in which observations of standard stars in staring mode have been taken from the installation of WFC3 in 2009 to the present to assess temporal photometric stability. Higher signal to noise in this program would greatly benefit the sensitivity to detect contamination, and to better characterize the observed small throughput drifts over time. We find excellent repeatability between identical visits of program 14878, with sub 0.1% repeatability achieved in most filters. These! results support the initiative to transition the staring mode UVIS contamination and photometric stability monitor from staring mode images to spatial scans.

Applications of Biophysics in High-Throughput Screening Hit Validation.

PubMed

Genick, Christine Clougherty; Barlier, Danielle; Monna, Dominique; Brunner, Reto; Bé, Céline; Scheufler, Clemens; Ottl, Johannes

2014-06-01

For approximately a decade, biophysical methods have been used to validate positive hits selected from high-throughput screening (HTS) campaigns with the goal to verify binding interactions using label-free assays. By applying label-free readouts, screen artifacts created by compound interference and fluorescence are discovered, enabling further characterization of the hits for their target specificity and selectivity. The use of several biophysical methods to extract this type of high-content information is required to prevent the promotion of false positives to the next level of hit validation and to select the best candidates for further chemical optimization. The typical technologies applied in this arena include dynamic light scattering, turbidometry, resonance waveguide, surface plasmon resonance, differential scanning fluorimetry, mass spectrometry, and others. Each technology can provide different types of information to enable the characterization of the binding interaction. Thus, these technologies can be incorporated in a hit-validation strategy not only according to the profile of chemical matter that is desired by the medicinal chemists, but also in a manner that is in agreement with the target protein's amenability to the screening format. Here, we present the results of screening strategies using biophysics with the objective to evaluate the approaches, discuss the advantages and challenges, and summarize the benefits in reference to lead discovery. In summary, the biophysics screens presented here demonstrated various hit rates from a list of ~2000 preselected, IC50-validated hits from HTS (an IC50 is the inhibitor concentration at which 50% inhibition of activity is observed). There are several lessons learned from these biophysical screens, which will be discussed in this article. © 2014 Society for Laboratory Automation and Screening.

Biofilm Inhibition by Novel Natural Product- and Biocide-Containing Coatings Using High-Throughput Screening.

PubMed

Salta, Maria; Dennington, Simon P; Wharton, Julian A

2018-05-10

The use of natural products (NPs) as possible alternative biocidal compounds for use in antifouling coatings has been the focus of research over the past decades. Despite the importance of this field, the efficacy of a given NP against biofilm (mainly bacteria and diatoms) formation is tested with the NP being in solution, while almost no studies test the effect of an NP once incorporated into a coating system. The development of a novel bioassay to assess the activity of NP-containing and biocide-containing coatings against marine biofilm formation has been achieved using a high-throughput microplate reader and highly sensitive confocal laser scanning microscopy (CLSM), as well as nucleic acid staining. Juglone, an isolated NP that has previously shown efficacy against bacterial attachment, was incorporated into a simple coating matrix. Biofilm formation over 48 h was assessed and compared against coatings containing the NP and the commonly used booster biocide, cuprous oxide. Leaching of the NP from the coating was quantified at two time points, 24 h and 48 h, showing evidence of both juglone and cuprous oxide being released. Results from the microplate reader showed that the NP coatings exhibited antifouling efficacy, significantly inhibiting biofilm formation when compared to the control coatings, while NP coatings and the cuprous oxide coatings performed equally well. CLSM results and COMSTAT analysis on biofilm 3D morphology showed comparable results when the NP coatings were tested against the controls, with higher biofilm biovolume and maximum thickness being found on the controls. This new method proved to be repeatable and insightful and we believe it is applicable in antifouling and other numerous applications where interactions between biofilm formation and surfaces is of interest.

Investigating the Responses of Cronobacter sakazakii to Garlic-Drived Organosulfur Compounds: a Systematic Study of Pathogenic-Bacterium Injury by Use of High-Throughput Whole-Transcriptome Sequencing and Confocal Micro-Raman Spectroscopy

PubMed Central

Feng, Shaolong; Eucker, Tyson P.; Holly, Mayumi K.; Konkel, Michael E.

2014-01-01

We present the results of a study using high-throughput whole-transcriptome sequencing (RNA-seq) and vibrational spectroscopy to characterize and fingerprint pathogenic-bacterium injury under conditions of unfavorable stress. Two garlic-derived organosulfur compounds were found to be highly effective antimicrobial compounds against Cronobacter sakazakii, a leading pathogen associated with invasive infection of infants and causing meningitis, necrotizing entercolitis, and bacteremia. RNA-seq shows changes in gene expression patterns and transcriptomic response, while confocal micro-Raman spectroscopy characterizes macromolecular changes in the bacterial cell resulting from this chemical stress. RNA-seq analyses showed that the bacterial response to ajoene differed from the response to diallyl sulfide. Specifically, ajoene caused downregulation of motility-related genes, while diallyl sulfide treatment caused an increased expression of cell wall synthesis genes. Confocal micro-Raman spectroscopy revealed that the two compounds appear to have the same phase I antimicrobial mechanism of binding to thiol-containing proteins/enzymes in bacterial cells generating a disulfide stretching band but different phase II antimicrobial mechanisms, showing alterations in the secondary structures of proteins in two different ways. Diallyl sulfide primarily altered the α-helix and β-sheet, as reflected in changes in amide I, while ajoene altered the structures containing phenylalanine and tyrosine. Bayesian probability analysis validated the ability of principal component analysis to differentiate treated and control C. sakazakii cells. Scanning electron microscopy confirmed cell injury, showing significant morphological variations in cells following treatments by these two compounds. Findings from this study aid in the development of effective intervention strategies to reduce the risk of C. sakazakii contamination in the food production environment and on food contact surfaces, reducing the risks to susceptible consumers. PMID:24271174

Single-Cell Analysis of [18F]Fluorodeoxyglucose Uptake by Droplet Radiofluidics.

PubMed

Türkcan, Silvan; Nguyen, Julia; Vilalta, Marta; Shen, Bin; Chin, Frederick T; Pratx, Guillem; Abbyad, Paul

2015-07-07

Radiolabels can be used to detect small biomolecules with high sensitivity and specificity without interfering with the biochemical activity of the labeled molecule. For instance, the radiolabeled glucose analogue, [18F]fluorodeoxyglucose (FDG), is routinely used in positron emission tomography (PET) scans for cancer diagnosis, staging, and monitoring. However, despite their widespread usage, conventional radionuclide techniques are unable to measure the variability and modulation of FDG uptake in single cells. We present here a novel microfluidic technique, dubbed droplet radiofluidics, that can measure radiotracer uptake for single cells encapsulated into an array of microdroplets. The advantages of this approach are multiple. First, droplets can be quickly and easily positioned in a predetermined pattern for optimal imaging throughput. Second, droplet encapsulation reduces cell efflux as a confounding factor, because any effluxed radionuclide is trapped in the droplet. Last, multiplexed measurements can be performed using fluorescent labels. In this new approach, intracellular radiotracers are imaged on a conventional fluorescence microscope by capturing individual flashes of visible light that are produced as individual positrons, emitted during radioactive decay, traverse a scintillator plate placed below the cells. This method is used to measure the cell-to-cell heterogeneity in the uptake of tracers such as FDG in cell lines and cultured primary cells. The capacity of the platform to perform multiplexed measurements was demonstrated by measuring differential FDG uptake in single cells subjected to different incubation conditions and expressing different types of glucose transporters. This method opens many new avenues of research in basic cell biology and human disease by capturing the full range of stochastic variations in highly heterogeneous cell populations in a repeatable and high-throughput manner.

High-throughput Screening of ToxCast" Phase I Chemicals in an Embryonic Stem Cell Assay Reveals Potential Disruption of a Critical Developmental Signaling Pathway

EPA Science Inventory

Little is known about the developmental toxicity of the expansive chemical landscape in existence today. Significant efforts are being made to apply novel methods to predict developmental activity of chemicals utilizing high-throughput screening (HTS) and high-content screening (...

Comparison of Human Induced Pluripotent Stem Cell-Derived Neurons and Rat Primary CorticalNeurons as In Vitro Models of Neurite Outgrowth

EPA Science Inventory

High-throughput assays that can quantify chemical-induced changes at the cellular and molecular level have been recommended for use in chemical safety assessment. High-throughput, high content imaging assays for the key cellular events of neurodevelopment have been proposed to ra...

Evaluation of sequencing approaches for high-throughput toxicogenomics (SOT)

EPA Science Inventory

Whole-genome in vitro transcriptomics has shown the capability to identify mechanisms of action and estimates of potency for chemical-mediated effects in a toxicological framework, but with limited throughput and high cost. We present the evaluation of three toxicogenomics platfo...

High Throughput Assays and Exposure Science (ISES annual meeting)

EPA Science Inventory

High throughput screening (HTS) data characterizing chemical-induced biological activity has been generated for thousands of environmentally-relevant chemicals by the US inter-agency Tox21 and the US EPA ToxCast programs. For a limited set of chemicals, bioactive concentrations r...

High Throughput Exposure Estimation Using NHANES Data (SOT)

EPA Science Inventory

In the ExpoCast project, high throughput (HT) exposure models enable rapid screening of large numbers of chemicals for exposure potential. Evaluation of these models requires empirical exposure data and due to the paucity of human metabolism/exposure data such evaluations includ...

Atlanta I-85 HOV-to-HOT conversion : analysis of vehicle and person throughput.

DOT National Transportation Integrated Search

2013-10-01

This report summarizes the vehicle and person throughput analysis for the High Occupancy Vehicle to High Occupancy Toll Lane : conversion in Atlanta, GA, undertaken by the Georgia Institute of Technology research team. The team tracked changes in : o...

EMBRYONIC VASCULAR DISRUPTION ADVERSE OUTCOMES: LINKING HIGH THROUGHPUT SIGNALING SIGNATURES WITH FUNCTIONAL CONSEQUENCES

EPA Science Inventory

Embryonic vascular disruption is an important adverse outcome pathway (AOP) given the knowledge that chemical disruption of early cardiovascular system development leads to broad prenatal defects. High throughput screening (HTS) assays provide potential building blocks for AOP d...

Accounting For Uncertainty in The Application Of High Throughput Datasets

EPA Science Inventory

The use of high throughput screening (HTS) datasets will need to adequately account for uncertainties in the data generation process and propagate these uncertainties through to ultimate use. Uncertainty arises at multiple levels in the construction of predictors using in vitro ...

Advances in High-Throughput Speed, Low-Latency Communication for Embedded Instrumentation (7th Annual SFAF Meeting, 2012)

ScienceCinema

Jordan, Scott

2018-01-24

Scott Jordan on "Advances in high-throughput speed, low-latency communication for embedded instrumentation" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

Inter-Individual Variability in High-Throughput Risk Prioritization of Environmental Chemicals (Sot)

EPA Science Inventory

We incorporate realistic human variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which have...

Inter-individual variability in high-throughput risk prioritization of environmental chemicals (IVIVE)

EPA Science Inventory

We incorporate inter-individual variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which hav...

HIGH-THROUGHPUT IDENTIFICATION OF CATALYTIC REDOX-ACTIVE CYSTEINE RESIDUES

EPA Science Inventory

Cysteine (Cys) residues often play critical roles in proteins; however, identification of their specific functions has been limited to case-by-case experimental approaches. We developed a procedure for high-throughput identification of catalytic redox-active Cys in proteins by se...

Development of a thyroperoxidase inhibition assay for high-throughput screening

EPA Science Inventory

High-throughput screening (HTPS) assays to detect inhibitors of thyroperoxidase (TPO), the enzymatic catalyst for thyroid hormone (TH) synthesis, are not currently available. Herein we describe the development of a HTPS TPO inhibition assay. Rat thyroid microsomes and a fluores...

High-throughput screening, predictive modeling and computational embryology - Abstract

EPA Science Inventory

High-throughput screening (HTS) studies are providing a rich source of data that can be applied to chemical profiling to address sensitivity and specificity of molecular targets, biological pathways, cellular and developmental processes. EPA’s ToxCast project is testing 960 uniq...

Evaluating and Refining High Throughput Tools for Toxicokinetics

EPA Science Inventory

This poster summarizes efforts of the Chemical Safety for Sustainability's Rapid Exposure and Dosimetry (RED) team to facilitate the development and refinement of toxicokinetics (TK) tools to be used in conjunction with the high throughput toxicity testing data generated as a par...

Picking Cell Lines for High-Throughput Transcriptomic Toxicity Screening (SOT)

EPA Science Inventory

High throughput, whole genome transcriptomic profiling is a promising approach to comprehensively evaluate chemicals for potential biological effects. To be useful for in vitro toxicity screening, gene expression must be quantified in a set of representative cell types that captu...

20180312 - Uncertainty and Variability in High-Throughput Toxicokinetics for Risk Prioritization (SOT)

EPA Science Inventory

Streamlined approaches that use in vitro experimental data to predict chemical toxicokinetics (TK) are increasingly being used to perform risk-based prioritization based upon dosimetric adjustment of high-throughput screening (HTS) data across thousands of chemicals. However, ass...

A rapid enzymatic assay for high-throughput screening of adenosine-producing strains

PubMed Central

Dong, Huina; Zu, Xin; Zheng, Ping; Zhang, Dawei

2015-01-01

Adenosine is a major local regulator of tissue function and industrially useful as precursor for the production of medicinal nucleoside substances. High-throughput screening of adenosine overproducers is important for industrial microorganism breeding. An enzymatic assay of adenosine was developed by combined adenosine deaminase (ADA) with indophenol method. The ADA catalyzes the cleavage of adenosine to inosine and NH3, the latter can be accurately determined by indophenol method. The assay system was optimized to deliver a good performance and could tolerate the addition of inorganic salts and many nutrition components to the assay mixtures. Adenosine could be accurately determined by this assay using 96-well microplates. Spike and recovery tests showed that this assay can accurately and reproducibly determine increases in adenosine in fermentation broth without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. This assay was also applied to high-throughput screening for high adenosine-producing strains. The high selectivity and accuracy of the ADA assay provides rapid and high-throughput analysis of adenosine in large numbers of samples. PMID:25580842

The cyber threat landscape: Challenges and future research directions

NASA Astrophysics Data System (ADS)

Gil, Santiago; Kott, Alexander; Barabási, Albert-László

2014-07-01

While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security.

A genetic epidemiology approach to cyber-security.

PubMed

Gil, Santiago; Kott, Alexander; Barabási, Albert-László

2014-07-16

While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security.

A genetic epidemiology approach to cyber-security

PubMed Central

Gil, Santiago; Kott, Alexander; Barabási, Albert-László

2014-01-01

While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security. PMID:25028059

Optical properties of acute kidney injury measured by quantitative phase imaging

PubMed Central

Ban, Sungbea; Min, Eunjung; Baek, Songyee; Kwon, Hyug Moo; Popescu, Gabriel

2018-01-01

The diagnosis of acute kidney disease (AKI) has been examined mainly by histology, immunohistochemistry and western blot. Though these approaches are widely accepted in the field, it has an inherent limitation due to the lack of high-throughput and quantitative information. For a better understanding of prognosis in AKI, we present a new approach using quantitative phase imaging combined with a wide-field scanning platform. Through the phase-delay information from the tissue, we were able to predict a stage of AKI based on various optical properties such as light scattering coefficient and anisotropy. These optical parameters quantify the deterioration process of the AKI model of tissue. Our device would be a very useful tool when it is required to deliver fast feedback of tissue pathology or when diseases are related to mechanical properties such as fibrosis. PMID:29541494

Nanopipette Apparatus for Manipulating Cells

NASA Technical Reports Server (NTRS)

Vilozny, Boaz (Inventor); Seger, R. Adam (Inventor); Actis, Paolo (Inventor); Pourmand, Nader (Inventor)

2017-01-01

Disclosed herein are methods and systems for controlled ejection of desired material onto surfaces including in single cells using nanopipettes, as well as ejection onto and into cells. Some embodiments are directed to a method and system comprising nanopipettes combined with an xyz controller for depositing a user defined pattern on an arbitrary substrate for the purpose of controlled cell adhesion and growth. Alternate embodiments are directed to a method and system comprising nanopipettes combined with an xyz controller and electronic control of a voltage differential in a bore of the nanopipette electroosmotically injecting material into a cell in a high-throughput manner and with minimal damage to the cell. Yet other embodiments are directed to method and system comprising functionalized nanopipettes combined with scanning ion conductance microscopy for studying molecular interactions and detection of biomolecules inside a single living cell.

High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets.

PubMed

Madanecki, Piotr; Bałut, Magdalena; Buckley, Patrick G; Ochocka, J Renata; Bartoszewski, Rafał; Crossman, David K; Messiaen, Ludwine M; Piotrowski, Arkadiusz

2018-01-01

High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp).

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets

PubMed Central

Bałut, Magdalena; Buckley, Patrick G.; Ochocka, J. Renata; Bartoszewski, Rafał; Crossman, David K.; Messiaen, Ludwine M.; Piotrowski, Arkadiusz

2018-01-01

High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp). PMID:29432475

Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

PubMed Central

Chung, Ji Ryang; Sung, Chul; Mayerich, David; Kwon, Jaerock; Miller, Daniel E.; Huffman, Todd; Keyser, John; Abbott, Louise C.; Choe, Yoonsuck

2011-01-01

Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions. PMID:22275895

Lung cancer screening beyond low-dose computed tomography: the role of novel biomarkers.

PubMed

Hasan, Naveed; Kumar, Rohit; Kavuru, Mani S

2014-10-01

Lung cancer is the most common and lethal malignancy in the world. The landmark National lung screening trial (NLST) showed a 20% relative reduction in mortality in high-risk individuals with screening low-dose computed tomography. However, the poor specificity and low prevalence of lung cancer in the NLST provide major limitations to its widespread use. Furthermore, a lung nodule on CT scan requires a nuanced and individualized approach towards management. In this regard, advances in high through-put technology (molecular diagnostics, multi-gene chips, proteomics, and bronchoscopic techniques) have led to discovery of lung cancer biomarkers that have shown potential to complement the current screening standards. Early detection of lung cancer can be achieved by analysis of biomarkers from tissue samples within the respiratory tract such as sputum, saliva, nasal/bronchial airway epithelial cells and exhaled breath condensate or through peripheral biofluids such as blood, serum and urine. Autofluorescence bronchoscopy has been employed in research setting to identify pre-invasive lesions not identified on CT scan. Although these modalities are not yet commercially available in clinic setting, they will be available in the near future and clinicians who care for patients with lung cancer should be aware. In this review, we present up-to-date state of biomarker development, discuss their clinical relevance and predict their future role in lung cancer management.

Widely-targeted quantitative lipidomics methodology by supercritical fluid chromatography coupled with fast-scanning triple quadrupole mass spectrometry.

PubMed

Takeda, Hiroaki; Izumi, Yoshihiro; Takahashi, Masatomo; Paxton, Thanai; Tamura, Shohei; Koike, Tomonari; Yu, Ying; Kato, Noriko; Nagase, Katsutoshi; Shiomi, Masashi; Bamba, Takeshi

2018-05-03

Lipidomics, the mass spectrometry-based comprehensive analysis of lipids, has attracted attention as an analytical approach to provide novel insight into lipid metabolism and to search for biomarkers. However, an ideal method for both comprehensive and quantitative analysis of lipids has not been fully developed. Herein, we have proposed a practical methodology for widely-targeted quantitative lipidome analysis using supercritical fluid chromatography fast-scanning triple-quadrupole mass spectrometry (SFC/QqQMS) and theoretically calculated a comprehensive lipid multiple reaction monitoring (MRM) library. Lipid classes can be separated by SFC with a normal phase diethylamine-bonded silica column with high-resolution, high-throughput, and good repeatability. Structural isomers of phospholipids can be monitored by mass spectrometric separation with fatty acyl-based MRM transitions. SFC/QqQMS analysis with an internal standard-dilution method offers quantitative information for both lipid class and individual lipid molecular species in the same lipid class. Additionally, data acquired using this method has advantages including reduction of misidentification and acceleration of data analysis. Using the SFC/QqQMS system, alteration of plasma lipid levels in myocardial infarction-prone rabbits to the supplementation of eicosapentaenoic acid was first observed. Our developed SFC/QqQMS method represents a potentially useful tool for in-depth studies focused on complex lipid metabolism and biomarker discovery. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Temporal and spatial resolution required for imaging myocardial function

NASA Astrophysics Data System (ADS)

Eusemann, Christian D.; Robb, Richard A.

2004-05-01

4-D functional analysis of myocardial mechanics is an area of significant interest and research in cardiology and vascular/interventional radiology. Current multidimensional analysis is limited by insufficient temporal resolution of x-ray and magnetic resonance based techniques, but recent improvements in system design holds hope for faster and higher resolution scans to improve images of moving structures allowing more accurate functional studies, such as in the heart. This paper provides a basis for the requisite temporal and spatial resolution for useful imaging during individual segments of the cardiac cycle. Multiple sample rates during systole and diastole are compared to determine an adequate sample frequency to reduce regional myocardial tracking errors. Concurrently, out-of-plane resolution has to be sufficiently high to minimize partial volume effect. Temporal resolution and out-of-plane spatial resolution are related factors that must be considered together. The data used for this study is a DSR dynamic volume image dataset with high temporal and spatial resolution using implanted fiducial markers to track myocardial motion. The results of this study suggest a reduced exposure and scan time for x-ray and magnetic resonance imaging methods, since a lower sample rate during systole is sufficient, whereas the period of rapid filling during diastole requires higher sampling. This could potentially reduce the cost of these procedures and allow higher patient throughput.

A comparison of high-throughput techniques for assaying circadian rhythms in plants.

PubMed

Tindall, Andrew J; Waller, Jade; Greenwood, Mark; Gould, Peter D; Hartwell, James; Hall, Anthony

2015-01-01

Over the last two decades, the development of high-throughput techniques has enabled us to probe the plant circadian clock, a key coordinator of vital biological processes, in ways previously impossible. With the circadian clock increasingly implicated in key fitness and signalling pathways, this has opened up new avenues for understanding plant development and signalling. Our tool-kit has been constantly improving through continual development and novel techniques that increase throughput, reduce costs and allow higher resolution on the cellular and subcellular levels. With circadian assays becoming more accessible and relevant than ever to researchers, in this paper we offer a review of the techniques currently available before considering the horizons in circadian investigation at ever higher throughputs and resolutions.

Turning tumor-promoting copper into an anti-cancer weapon via high-throughput chemistry.

PubMed

Wang, F; Jiao, P; Qi, M; Frezza, M; Dou, Q P; Yan, B

2010-01-01

Copper is an essential element for multiple biological processes. Its concentration is elevated to a very high level in cancer tissues for promoting cancer development through processes such as angiogenesis. Organic chelators of copper can passively reduce cellular copper and serve the role as inhibitors of angiogenesis. However, they can also actively attack cellular targets such as proteasome, which plays a critical role in cancer development and survival. The discovery of such molecules initially relied on a step by step synthesis followed by biological assays. Today high-throughput chemistry and high-throughput screening have significantly expedited the copper-binding molecules discovery to turn "cancer-promoting" copper into anti-cancer agents.

HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis.

PubMed

Camilo, Cesar M; Lima, Gustavo M A; Maluf, Fernando V; Guido, Rafael V C; Polikarpov, Igor

2016-01-01

Following burgeoning genomic and transcriptomic sequencing data, biochemical and molecular biology groups worldwide are implementing high-throughput cloning and mutagenesis facilities in order to obtain a large number of soluble proteins for structural and functional characterization. Since manual primer design can be a time-consuming and error-generating step, particularly when working with hundreds of targets, the automation of primer design process becomes highly desirable. HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.

A high performance hardware implementation image encryption with AES algorithm

NASA Astrophysics Data System (ADS)

Farmani, Ali; Jafari, Mohamad; Miremadi, Seyed Sohrab

2011-06-01

This paper describes implementation of a high-speed encryption algorithm with high throughput for encrypting the image. Therefore, we select a highly secured symmetric key encryption algorithm AES(Advanced Encryption Standard), in order to increase the speed and throughput using pipeline technique in four stages, control unit based on logic gates, optimal design of multiplier blocks in mixcolumn phase and simultaneous production keys and rounds. Such procedure makes AES suitable for fast image encryption. Implementation of a 128-bit AES on FPGA of Altra company has been done and the results are as follow: throughput, 6 Gbps in 471MHz. The time of encrypting in tested image with 32*32 size is 1.15ms.

High-throughput continuous hydrothermal synthesis of nanomaterials (part II): unveiling the as-prepared CexZryYzO2-δ phase diagram.

PubMed

Quesada-Cabrera, Raul; Weng, Xiaole; Hyett, Geoff; Clark, Robin J H; Wang, Xue Z; Darr, Jawwad A

2013-09-09

High-throughput continuous hydrothermal flow synthesis was used to manufacture 66 unique nanostructured oxide samples in the Ce-Zr-Y-O system. This synthesis approach resulted in a significant increase in throughput compared to that of conventional batch or continuous hydrothermal synthesis methods. The as-prepared library samples were placed into a wellplate for both automated high-throughput powder X-ray diffraction and Raman spectroscopy data collection, which allowed comprehensive structural characterization and phase mapping. The data suggested that a continuous cubic-like phase field connects all three Ce-Zr-O, Ce-Y-O, and Y-Zr-O binary systems together with a smooth and steady transition between the structures of neighboring compositions. The continuous hydrothermal process led to as-prepared crystallite sizes in the range of 2-7 nm (as determined by using the Scherrer equation).

State of the Art High-Throughput Approaches to Genotoxicity: Flow Micronucleus, Ames II, GreenScreen and Comet

EPA Pesticide Factsheets

State of the Art High-Throughput Approaches to Genotoxicity: Flow Micronucleus, Ames II, GreenScreen and Comet (Presented by Dr. Marilyn J. Aardema, Chief Scientific Advisor, Toxicology, Dr. Leon Stankowski, et. al. (6/28/2012)

Fun with High Throughput Toxicokinetics (CalEPA webinar)

EPA Science Inventory

Thousands of chemicals have been profiled by high-throughput screening (HTS) programs such as ToxCast and Tox21. These chemicals are tested in part because there are limited or no data on hazard, exposure, or toxicokinetics (TK). TK models aid in predicting tissue concentrations ...

Incorporating Human Dosimetry and Exposure into High-Throughput In Vitro Toxicity Screening

EPA Science Inventory

Many chemicals in commerce today have undergone limited or no safety testing. To reduce the number of untested chemicals and prioritize limited testing resources, several governmental programs are using high-throughput in vitro screens for assessing chemical effects across multip...

Environmental Impact on Vascular Development Predicted by High Throughput Screening

EPA Science Inventory

Understanding health risks to embryonic development from exposure to environmental chemicals is a significant challenge given the diverse chemical landscape and paucity of data for most of these compounds. High throughput screening (HTS) in EPA’s ToxCastTM project provides vast d...

High-Throughput Dietary Exposure Predictions for Chemical Migrants from Food Packaging Materials

EPA Science Inventory

United States Environmental Protection Agency researchers have developed a Stochastic Human Exposure and Dose Simulation High -Throughput (SHEDS-HT) model for use in prioritization of chemicals under the ExpoCast program. In this research, new methods were implemented in SHEDS-HT...

AOPs and Biomarkers: Bridging High Throughput Screening and Regulatory Decision Making

EPA Science Inventory

As high throughput screening (HTS) plays a larger role in toxicity testing, camputational toxicology has emerged as a critical component in interpreting the large volume of data produced. Computational models designed to quantify potential adverse effects based on HTS data will b...

Human variability in high-throughput risk prioritization of environmental chemicals (Texas AM U. webinar)

EPA Science Inventory

We incorporate inter-individual variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which hav...

HTTK: R Package for High-Throughput Toxicokinetics

EPA Science Inventory

Thousands of chemicals have been profiled by high-throughput screening programs such as ToxCast and Tox21; these chemicals are tested in part because most of them have limited or no data on hazard, exposure, or toxicokinetics. Toxicokinetic models aid in predicting tissue concent...

tcpl: The ToxCast Pipeline for High-Throughput Screening Data

EPA Science Inventory

Motivation: The large and diverse high-throughput chemical screening efforts carried out by the US EPAToxCast program requires an efficient, transparent, and reproducible data pipeline.Summary: The tcpl R package and its associated MySQL database provide a generalized platform fo...

High-throughput screening, predictive modeling and computational embryology

EPA Science Inventory

High-throughput screening (HTS) studies are providing a rich source of data that can be applied to profile thousands of chemical compounds for biological activity and potential toxicity. EPA’s ToxCast™ project, and the broader Tox21 consortium, in addition to projects worldwide,...

In Vitro Toxicity Screening Technique for Volatile Substances Using Flow-Through System#

EPA Science Inventory

In 2007 the National Research Council envisioned the need for inexpensive, high throughput, cell based toxicity testing methods relevant to human health. High Throughput Screening (HTS) in vitro screening approaches have addressed these problems by using robotics. However the cha...

Integration of Dosimetry, Exposure and High-Throughput Screening Data in Chemical Toxicity Assessment

EPA Science Inventory

High-throughput in vitro toxicity screening can provide an efficient way to identify potential biological targets for chemicals. However, relying on nominal assay concentrations may misrepresent potential in vivo effects of these chemicals due to differences in bioavailability, c...

High-Throughput Toxicokinetics (HTTK) R package (CompTox CoP presentation)

EPA Science Inventory

Toxicokinetics (TK) provides a bridge between HTS and HTE by predicting tissue concentrations due to exposure, but traditional TK methods are resource intensive. Relatively high throughput TK (HTTK) methods have been used by the pharmaceutical industry to determine range of effic...

A review of the theory, methods and recent applications of high-throughput single-cell droplet microfluidics

NASA Astrophysics Data System (ADS)

Lagus, Todd P.; Edd, Jon F.

2013-03-01

Most cell biology experiments are performed in bulk cell suspensions where cell secretions become diluted and mixed in a contiguous sample. Confinement of single cells to small, picoliter-sized droplets within a continuous phase of oil provides chemical isolation of each cell, creating individual microreactors where rare cell qualities are highlighted and otherwise undetectable signals can be concentrated to measurable levels. Recent work in microfluidics has yielded methods for the encapsulation of cells in aqueous droplets and hydrogels at kilohertz rates, creating the potential for millions of parallel single-cell experiments. However, commercial applications of high-throughput microdroplet generation and downstream sensing and actuation methods are still emerging for cells. Using fluorescence-activated cell sorting (FACS) as a benchmark for commercially available high-throughput screening, this focused review discusses the fluid physics of droplet formation, methods for cell encapsulation in liquids and hydrogels, sensors and actuators and notable biological applications of high-throughput single-cell droplet microfluidics.

High-Throughput Cloning and Expression Library Creation for Functional Proteomics

PubMed Central

Festa, Fernanda; Steel, Jason; Bian, Xiaofang; Labaer, Joshua

2013-01-01

The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particular important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single gene experiments, creating the need for fast, flexible and reliable cloning systems. These collections of open reading frame (ORF) clones can be coupled with high-throughput proteomics platforms, such as protein microarrays and cell-based assays, to answer biological questions. In this tutorial we provide the background for DNA cloning, discuss the major high-throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator™ DNA Cloning System) and compare them side-by-side. We also report an example of high-throughput cloning study and its application in functional proteomics. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP12). Details can be found at http://www.proteomicstutorials.org. PMID:23457047

High-Throughput Lectin Microarray-Based Analysis of Live Cell Surface Glycosylation

PubMed Central

Li, Yu; Tao, Sheng-ce; Zhu, Heng; Schneck, Jonathan P.

2011-01-01

Lectins, plant-derived glycan-binding proteins, have long been used to detect glycans on cell surfaces. However, the techniques used to characterize serum or cells have largely been limited to mass spectrometry, blots, flow cytometry, and immunohistochemistry. While these lectin-based approaches are well established and they can discriminate a limited number of sugar isomers by concurrently using a limited number of lectins, they are not amenable for adaptation to a high-throughput platform. Fortunately, given the commercial availability of lectins with a variety of glycan specificities, lectins can be printed on a glass substrate in a microarray format to profile accessible cell-surface glycans. This method is an inviting alternative for analysis of a broad range of glycans in a high-throughput fashion and has been demonstrated to be a feasible method of identifying binding-accessible cell surface glycosylation on living cells. The current unit presents a lectin-based microarray approach for analyzing cell surface glycosylation in a high-throughput fashion. PMID:21400689

Optimization of High-Throughput Sequencing Kinetics for determining enzymatic rate constants of thousands of RNA substrates

PubMed Central

Niland, Courtney N.; Jankowsky, Eckhard; Harris, Michael E.

2016-01-01

Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High Throughput Sequencing Kinetics (HTS-Kin) uses high throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigate the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we find that high-throughput sequencing, and experimental reproducibility contribute their own sources of error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed. PMID:27296633

Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data

PubMed Central

Fujimori, Shigeo; Hirai, Naoya; Ohashi, Hiroyuki; Masuoka, Kazuyo; Nishikimi, Akihiko; Fukui, Yoshinori; Washio, Takanori; Oshikubo, Tomohiro; Yamashita, Tatsuhiro; Miyamoto-Sato, Etsuko

2012-01-01

Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks. PMID:23056904

NCBI GEO: archive for high-throughput functional genomic data.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Edgar, Ron

2009-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Advanced Virus Detection Technologies Interest Group (AVDTIG): Efforts on High Throughput Sequencing (HTS) for Virus Detection.

PubMed

Khan, Arifa S; Vacante, Dominick A; Cassart, Jean-Pol; Ng, Siemon H S; Lambert, Christophe; Charlebois, Robert L; King, Kathryn E

Several nucleic-acid based technologies have recently emerged with capabilities for broad virus detection. One of these, high throughput sequencing, has the potential for novel virus detection because this method does not depend upon prior viral sequence knowledge. However, the use of high throughput sequencing for testing biologicals poses greater challenges as compared to other newly introduced tests due to its technical complexities and big data bioinformatics. Thus, the Advanced Virus Detection Technologies Users Group was formed as a joint effort by regulatory and industry scientists to facilitate discussions and provide a forum for sharing data and experiences using advanced new virus detection technologies, with a focus on high throughput sequencing technologies. The group was initiated as a task force that was coordinated by the Parenteral Drug Association and subsequently became the Advanced Virus Detection Technologies Interest Group to continue efforts for using new technologies for detection of adventitious viruses with broader participation, including international government agencies, academia, and technology service providers. © PDA, Inc. 2016.

The application of the high throughput sequencing technology in the transposable elements.

PubMed

Liu, Zhen; Xu, Jian-hong

2015-09-01

High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

An improved high-throughput lipid extraction method for the analysis of human brain lipids.

PubMed

Abbott, Sarah K; Jenner, Andrew M; Mitchell, Todd W; Brown, Simon H J; Halliday, Glenda M; Garner, Brett

2013-03-01

We have developed a protocol suitable for high-throughput lipidomic analysis of human brain samples. The traditional Folch extraction (using chloroform and glass-glass homogenization) was compared to a high-throughput method combining methyl-tert-butyl ether (MTBE) extraction with mechanical homogenization utilizing ceramic beads. This high-throughput method significantly reduced sample handling time and increased efficiency compared to glass-glass homogenizing. Furthermore, replacing chloroform with MTBE is safer (less carcinogenic/toxic), with lipids dissolving in the upper phase, allowing for easier pipetting and the potential for automation (i.e., robotics). Both methods were applied to the analysis of human occipital cortex. Lipid species (including ceramides, sphingomyelins, choline glycerophospholipids, ethanolamine glycerophospholipids and phosphatidylserines) were analyzed via electrospray ionization mass spectrometry and sterol species were analyzed using gas chromatography mass spectrometry. No differences in lipid species composition were evident when the lipid extraction protocols were compared, indicating that MTBE extraction with mechanical bead homogenization provides an improved method for the lipidomic profiling of human brain tissue.

Graph-based signal integration for high-throughput phenotyping

PubMed Central

2012-01-01

Background Electronic Health Records aggregated in Clinical Data Warehouses (CDWs) promise to revolutionize Comparative Effectiveness Research and suggest new avenues of research. However, the effectiveness of CDWs is diminished by the lack of properly labeled data. We present a novel approach that integrates knowledge from the CDW, the biomedical literature, and the Unified Medical Language System (UMLS) to perform high-throughput phenotyping. In this paper, we automatically construct a graphical knowledge model and then use it to phenotype breast cancer patients. We compare the performance of this approach to using MetaMap when labeling records. Results MetaMap's overall accuracy at identifying breast cancer patients was 51.1% (n=428); recall=85.4%, precision=26.2%, and F1=40.1%. Our unsupervised graph-based high-throughput phenotyping had accuracy of 84.1%; recall=46.3%, precision=61.2%, and F1=52.8%. Conclusions We conclude that our approach is a promising alternative for unsupervised high-throughput phenotyping. PMID:23320851

High-throughput cloning and expression library creation for functional proteomics.

PubMed

Festa, Fernanda; Steel, Jason; Bian, Xiaofang; Labaer, Joshua

2013-05-01

The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particularly important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single-gene experiments, creating the need for fast, flexible, and reliable cloning systems. These collections of ORF clones can be coupled with high-throughput proteomics platforms, such as protein microarrays and cell-based assays, to answer biological questions. In this tutorial, we provide the background for DNA cloning, discuss the major high-throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator(TM) DNA Cloning System) and compare them side-by-side. We also report an example of high-throughput cloning study and its application in functional proteomics. This tutorial is part of the International Proteomics Tutorial Programme (IPTP12). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR library

PubMed Central

Zhu, Shiyou; Li, Wei; Liu, Jingze; Chen, Chen-Hao; Liao, Qi; Xu, Ping; Xu, Han; Xiao, Tengfei; Cao, Zhongzheng; Peng, Jingyu; Yuan, Pengfei; Brown, Myles; Liu, Xiaole Shirley; Wei, Wensheng

2017-01-01

CRISPR/Cas9 screens have been widely adopted to analyse coding gene functions, but high throughput screening of non-coding elements using this method is more challenging, because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. Herein, we report a high throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We individually validated 9 lncRNAs using CRISPR/Cas9-mediated genomic deletion and functional rescue, CRISPR activation or inhibition, and gene expression profiling. Our high-throughput pgRNA genome deletion method should enable rapid identification of functional mammalian non-coding elements. PMID:27798563

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

PubMed Central

Choudhry, Priya

2016-01-01

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays. PMID:26848849

High-throughput determination of structural phase diagram and constituent phases using GRENDEL

NASA Astrophysics Data System (ADS)

Kusne, A. G.; Keller, D.; Anderson, A.; Zaban, A.; Takeuchi, I.

2015-11-01

Advances in high-throughput materials fabrication and characterization techniques have resulted in faster rates of data collection and rapidly growing volumes of experimental data. To convert this mass of information into actionable knowledge of material process-structure-property relationships requires high-throughput data analysis techniques. This work explores the use of the Graph-based endmember extraction and labeling (GRENDEL) algorithm as a high-throughput method for analyzing structural data from combinatorial libraries, specifically, to determine phase diagrams and constituent phases from both x-ray diffraction and Raman spectral data. The GRENDEL algorithm utilizes a set of physical constraints to optimize results and provides a framework by which additional physics-based constraints can be easily incorporated. GRENDEL also permits the integration of database data as shown by the use of critically evaluated data from the Inorganic Crystal Structure Database in the x-ray diffraction data analysis. Also the Sunburst radial tree map is demonstrated as a tool to visualize material structure-property relationships found through graph based analysis.

High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics

NASA Astrophysics Data System (ADS)

Beneyton, Thomas; Wijaya, I. Putu Mahendra; Postros, Prexilia; Najah, Majdi; Leblond, Pascal; Couvent, Angélique; Mayot, Estelle; Griffiths, Andrew D.; Drevelle, Antoine

2016-06-01

Filamentous fungi are an extremely important source of industrial enzymes because of their capacity to secrete large quantities of proteins. Currently, functional screening of fungi is associated with low throughput and high costs, which severely limits the discovery of novel enzymatic activities and better production strains. Here, we describe a nanoliter-range droplet-based microfluidic system specially adapted for the high-throughput sceening (HTS) of large filamentous fungi libraries for secreted enzyme activities. The platform allowed (i) compartmentalization of single spores in ~10 nl droplets, (ii) germination and mycelium growth and (iii) high-throughput sorting of fungi based on enzymatic activity. A 104 clone UV-mutated library of Aspergillus niger was screened based on α-amylase activity in just 90 minutes. Active clones were enriched 196-fold after a single round of microfluidic HTS. The platform is a powerful tool for the development of new production strains with low cost, space and time footprint and should bring enormous benefit for improving the viability of biotechnological processes.

A simple dual online ultra-high pressure liquid chromatography system (sDO-UHPLC) for high throughput proteome analysis.

PubMed

Lee, Hangyeore; Mun, Dong-Gi; Bae, Jingi; Kim, Hokeun; Oh, Se Yeon; Park, Young Soo; Lee, Jae-Hyuk; Lee, Sang-Won

2015-08-21

We report a new and simple design of a fully automated dual-online ultra-high pressure liquid chromatography system. The system employs only two nano-volume switching valves (a two-position four port valve and a two-position ten port valve) that direct solvent flows from two binary nano-pumps for parallel operation of two analytical columns and two solid phase extraction (SPE) columns. Despite the simple design, the sDO-UHPLC offers many advantageous features that include high duty cycle, back flushing sample injection for fast and narrow zone sample injection, online desalting, high separation resolution and high intra/inter-column reproducibility. This system was applied to analyze proteome samples not only in high throughput deep proteome profiling experiments but also in high throughput MRM experiments.

Optimization and high-throughput screening of antimicrobial peptides.

PubMed

Blondelle, Sylvie E; Lohner, Karl

2010-01-01

While a well-established process for lead compound discovery in for-profit companies, high-throughput screening is becoming more popular in basic and applied research settings in academia. The development of combinatorial libraries combined with easy and less expensive access to new technologies have greatly contributed to the implementation of high-throughput screening in academic laboratories. While such techniques were earlier applied to simple assays involving single targets or based on binding affinity, they have now been extended to more complex systems such as whole cell-based assays. In particular, the urgent need for new antimicrobial compounds that would overcome the rapid rise of drug-resistant microorganisms, where multiple target assays or cell-based assays are often required, has forced scientists to focus onto high-throughput technologies. Based on their existence in natural host defense systems and their different mode of action relative to commercial antibiotics, antimicrobial peptides represent a new hope in discovering novel antibiotics against multi-resistant bacteria. The ease of generating peptide libraries in different formats has allowed a rapid adaptation of high-throughput assays to the search for novel antimicrobial peptides. Similarly, the availability nowadays of high-quantity and high-quality antimicrobial peptide data has permitted the development of predictive algorithms to facilitate the optimization process. This review summarizes the various library formats that lead to de novo antimicrobial peptide sequences as well as the latest structural knowledge and optimization processes aimed at improving the peptides selectivity.

Multi-step high-throughput conjugation platform for the development of antibody-drug conjugates.

PubMed

Andris, Sebastian; Wendeler, Michaela; Wang, Xiangyang; Hubbuch, Jürgen

2018-07-20

Antibody-drug conjugates (ADCs) form a rapidly growing class of biopharmaceuticals which attracts a lot of attention throughout the industry due to its high potential for cancer therapy. They combine the specificity of a monoclonal antibody (mAb) and the cell-killing capacity of highly cytotoxic small molecule drugs. Site-specific conjugation approaches involve a multi-step process for covalent linkage of antibody and drug via a linker. Despite the range of parameters that have to be investigated, high-throughput methods are scarcely used so far in ADC development. In this work an automated high-throughput platform for a site-specific multi-step conjugation process on a liquid-handling station is presented by use of a model conjugation system. A high-throughput solid-phase buffer exchange was successfully incorporated for reagent removal by utilization of a batch cation exchange step. To ensure accurate screening of conjugation parameters, an intermediate UV/Vis-based concentration determination was established including feedback to the process. For conjugate characterization, a high-throughput compatible reversed-phase chromatography method with a runtime of 7 min and no sample preparation was developed. Two case studies illustrate the efficient use for mapping the operating space of a conjugation process. Due to the degree of automation and parallelization, the platform is capable of significantly reducing process development efforts and material demands and shorten development timelines for antibody-drug conjugates. Copyright © 2018 Elsevier B.V. All rights reserved.

High-throughput combinatorial chemical bath deposition: The case of doping Cu (In, Ga) Se film with antimony

NASA Astrophysics Data System (ADS)

Yan, Zongkai; Zhang, Xiaokun; Li, Guang; Cui, Yuxing; Jiang, Zhaolian; Liu, Wen; Peng, Zhi; Xiang, Yong

2018-01-01

The conventional methods for designing and preparing thin film based on wet process remain a challenge due to disadvantages such as time-consuming and ineffective, which hinders the development of novel materials. Herein, we present a high-throughput combinatorial technique for continuous thin film preparation relied on chemical bath deposition (CBD). The method is ideally used to prepare high-throughput combinatorial material library with low decomposition temperatures and high water- or oxygen-sensitivity at relatively high-temperature. To check this system, a Cu(In, Ga)Se (CIGS) thin films library doped with 0-19.04 at.% of antimony (Sb) was taken as an example to evaluate the regulation of varying Sb doping concentration on the grain growth, structure, morphology and electrical properties of CIGS thin film systemically. Combined with the Energy Dispersive Spectrometer (EDS), X-ray Photoelectron Spectroscopy (XPS), automated X-ray Diffraction (XRD) for rapid screening and Localized Electrochemical Impedance Spectroscopy (LEIS), it was confirmed that this combinatorial high-throughput system could be used to identify the composition with the optimal grain orientation growth, microstructure and electrical properties systematically, through accurately monitoring the doping content and material composition. According to the characterization results, a Sb2Se3 quasi-liquid phase promoted CIGS film-growth model has been put forward. In addition to CIGS thin film reported here, the combinatorial CBD also could be applied to the high-throughput screening of other sulfide thin film material systems.

Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

PubMed

Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

2017-04-01

Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for the final evaluation. After the second evaluation, the final amplification curves and melting curves have been achieved.

High-throughput multipesticides residue analysis in earthworms by the improvement of purification method: Development and application of magnetic Fe3 O4 -SiO2 nanoparticles based dispersive solid-phase extraction.

PubMed

Sun, Yuhan; Qi, Peipei; Cang, Tao; Wang, Zhiwei; Wang, Xiangyun; Yang, Xuewei; Wang, Lidong; Xu, Xiahong; Wang, Qiang; Wang, Xinquan; Zhao, Changshan

2018-06-01

As a key representative organism, earthworms can directly illustrate the influence of pesticides on environmental organisms in soil ecosystems. The present work aimed to develop a high-throughput multipesticides residue analytical method for earthworms using solid-liquid extraction with acetonitrile as the solvent and magnetic material-based dispersive solid-phase extraction for purification. Magnetic Fe 3 O 4 nanoparticles were modified with a thin silica layer to form Fe 3 O 4 -SiO 2 nanoparticles, which were fully characterized by field-emission scanning electron microscopy, transmission electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffractometry, and vibrating sample magnetometry. The Fe 3 O 4 -SiO 2 nanoparticles were used as the separation media in dispersive solid-phase extraction with primary secondary amine and ZrO 2 as the cleanup adsorbents to eliminate matrix interferences. The amounts of nanoparticles and adsorbents were optimized for the simultaneous determination of 44 pesticides and six metabolites in earthworms by liquid chromatography with tandem mass spectrometry. The method performance was systematically validated with satisfactory results. The limits of quantification were 20 μg/kg for all analytes studied, while the recoveries of the target analytes ranged from 65.1 to 127% with relative standard deviation values lower than 15.0%. The developed method was subsequently utilized to explore the bioaccumulation of bitertanol in earthworms exposed to contaminated soil, verifying its feasibility for real sample analysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomimetic macroporous hydrogel scaffolds in a high-throughput screening format for cell-based assays.

PubMed

Dainiak, Maria B; Savina, Irina N; Musolino, Isabella; Kumar, Ashok; Mattiasson, Bo; Galaev, Igor Yu

2008-01-01

Macroporous hydrogels (MHs) hold great promise as scaffolds in tissue engineering and cell-based assays. In this study, the possibility of combination of three-dimensional (3D) cell culture with a miniaturized screening format was demonstrated on human colon cancer HCT116, human acute myeloid leukemia KG-1 cells, and embryonic fibroblasts cultured on MHs (12.5 mm x 7.1 mm I.D.) in a 96-minicolumn plate format. MHs were prepared by cryogelation technique and functionalized by coating with type I collagen and by copolymerization with agmatine-based mimetic of cell adhesive peptide RGD (abRGDm). Cancer cells formed multicellular aggregates while fibroblasts formed adhesions on abRGDm-containing and collagen-MHs but not on plain MHs, as was demonstrated by scanning electron microscopy. HCT116 and KG-1 cells grown as aggregates were more resistant to the treatment with cis-diaminedichloroplatinum (II) (cisplatin) and cytosine 1-beta-D-arabinofuranoside (Ara-C), respectively, during the first 18-24 h of incubation, than single cells grown on unmodified MH. HCT116 cells grown as 2D cultures in conventional 96-well tissue culture plates were 1.5- to 3.5-fold more sensitive to the treatment with 70 microM cisplatin than cells in 3D cultures in functionalized MHs. Further development of the described experimental system including matching of a specific cell type with appropriate extracellular matrix (ECM) components and 3D cocultures on ECM-modified MHs may provide a realistic in vitro experimental model for high-throughput toxicity tests.

Analysis of mutational spectra by denaturant capillary electrophoresis

PubMed Central

Ekstrøm, Per O.; Khrapko, Konstantin; Li-Sucholeiki, Xiao-Cheng; Hunter, Ian W.; Thilly, William G.

2009-01-01

Numbers and kinds of point mutant within DNA from cells, tissues and human population may be discovered for nearly any 75–250bp DNA sequence. High fidelity DNA amplification incorporating a thermally stable DNA “clamp” is followed by separation by denaturing capillary electrophoresis (DCE). DCE allows for peak collection and verification sequencing. DCE in a mode of cycling temperature, e.g.+/− 5°C, CyDCE, permits high resolution of mutant sequences using computer defined analytes without preliminary optimization experiments. DNA sequencers have been modified to permit higher throughput CyDCE and a massively parallel,~25,000 capillary system, has been designed for pangenomic scans in large human populations. DCE has been used to define quantitative point mutational spectra for study a wide variety of genetic phenomena: errors of DNA polymerases, mutations induced in human cells by chemicals and irradiation, testing of human gene-common disease associations and the discovery of origins of point mutations in human development and carcinogenesis. PMID:18600220

Automated detection system of single nucleotide polymorphisms using two kinds of functional magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Liu, Hongna; Li, Song; Wang, Zhifei; Li, Zhiyang; Deng, Yan; Wang, Hua; Shi, Zhiyang; He, Nongyue

2008-11-01

Single nucleotide polymorphisms (SNPs) comprise the most abundant source of genetic variation in the human genome wide codominant SNPs identification. Therefore, large-scale codominant SNPs identification, especially for those associated with complex diseases, has induced the need for completely high-throughput and automated SNP genotyping method. Herein, we present an automated detection system of SNPs based on two kinds of functional magnetic nanoparticles (MNPs) and dual-color hybridization. The amido-modified MNPs (NH 2-MNPs) modified with APTES were used for DNA extraction from whole blood directly by electrostatic reaction, and followed by PCR, was successfully performed. Furthermore, biotinylated PCR products were captured on the streptavidin-coated MNPs (SA-MNPs) and interrogated by hybridization with a pair of dual-color probes to determine SNP, then the genotype of each sample can be simultaneously identified by scanning the microarray printed with the denatured fluorescent probes. This system provided a rapid, sensitive and highly versatile automated procedure that will greatly facilitate the analysis of different known SNPs in human genome.

Development of a Digital Microarray with Interferometric Reflectance Imaging

NASA Astrophysics Data System (ADS)

Sevenler, Derin

This dissertation describes a new type of molecular assay for nucleic acids and proteins. We call this technique a digital microarray since it is conceptually similar to conventional fluorescence microarrays, yet it performs enumerative ('digital') counting of the number captured molecules. Digital microarrays are approximately 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing (i.e., many different tests on the same sample simultaneously). Digital microarrays use gold nanorods to label the captured target molecules. Each gold nanorod on the array is individually detected based on its light scattering, with an interferometric microscopy technique called SP-IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Digital DNA microarrays may have utility in applications where sequencing is prohibitively expensive or slow. As an example, we describe a digital microarray assay for gene expression markers of bacterial drug resistance.

Snapshot imaging Fraunhofer line discriminator for detection of plant fluorescence

NASA Astrophysics Data System (ADS)

Gupta Roy, S.; Kudenov, M. W.

2015-05-01

Non-invasive quantification of plant health is traditionally accomplished using reflectance based metrics, such as the normalized difference vegetative index (NDVI). However, measuring plant fluorescence (both active and passive) to determine photochemistry of plants has gained importance. Due to better cost efficiency, lower power requirements, and simpler scanning synchronization, detecting passive fluorescence is preferred over active fluorescence. In this paper, we propose a high speed imaging approach for measuring passive plant fluorescence, within the hydrogen alpha Fraunhofer line at ~656 nm, using a Snapshot Imaging Fraunhofer Line Discriminator (SIFOLD). For the first time, the advantage of snapshot imaging for high throughput Fraunhofer Line Discrimination (FLD) is cultivated by our system, which is based on a multiple-image Fourier transform spectrometer and a spatial heterodyne interferometer (SHI). The SHI is a Sagnac interferometer, which is dispersion compensated using blazed diffraction gratings. We present data and techniques for calibrating the SIFOLD to any particular wavelength. This technique can be applied to quantify plant fluorescence at low cost and reduced complexity of data collection.

DIGE Analysis Software and Protein Identification Approaches.

PubMed

Hmmier, Abduladim; Dowling, Paul

2018-01-01

DIGE is a high-resolution two-dimensional gel electrophoresis method, with excellent dynamic range obtained by fluorescent tag labeling of protein samples. Scanned images of DIGE gels show thousands of protein spots, each spot representing a single or a group of protein isoforms. By using commercially available software, each protein spot is defined by an outline, which is digitized and correlated with the quantity of proteins present in each spot. Software packages include DeCyder, SameSpots, and Dymension 3. In addition, proteins of interest can be excised from post-stained gels and identified with conventional mass spectrometry techniques. High-throughput mass spectrometry is performed using sophisticated instrumentation including matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF), MALDI-TOF/TOF, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Tandem MS (MALDI-TOF/TOF or LC-MS/MS), analyzes fragmented peptides, resulting in amino acid sequence information, especially useful when protein spots are low abundant or where a mixture of proteins is present.

Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation.

PubMed

Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

2016-09-16

Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

Mix & match electron beam & scanning probe lithography for high throughput sub-10 nm lithography

NASA Astrophysics Data System (ADS)

Kaestner, Marcus; Hofer, Manuel; Rangelow, Ivo W.

2013-03-01

The prosperous demonstration of a technique able to produce features with single nanometer (SN) resolution could guide the semiconductor industry into the desired beyond CMOS era. In the lithographic community immense efforts are being made to develop extreme ultra-violet lithography (EUVL) and multiple-e-beam direct-write systems as possible successor for next generation lithography (NGL). However, patterning below 20 nm resolution and sub-10 nm overlay alignment accuracy becomes an extremely challenging quest. Herein, the combination of electron beam lithography (EBL) or EUVL with the outstanding capabilities of closed-loop scanning proximal probe nanolithography (SPL) reveals a promising way to improve both patterning resolution and reproducibility in combination with excellent overlay and placement accuracy. In particular, the imaging and lithographic resolution capabilities provided by scanning probe microscopy (SPM) methods touches the atomic level, which expresses the theoretical limit of constructing nanoelectronic devices. Furthermore, the symbiosis between EBL (EUVL) and SPL expands the process window of EBL (EUVL) far beyond state-of-the-art allowing SPL-based pre- and post-patterning of EBL (EUVL) written features at critical dimension level with theoretically nanometer precise pattern overlay alignment. Moreover, we can modify the EBL (EUVL) pattern before as well as after the development step. In this paper we demonstrate proof of concept using the ultra-high resolution molecular glass resist calixarene. Therefor we applied Gaussian E-beam lithography system operating at 10 keV and a home-developed SPL set-up. The introduced Mix and Match lithography strategy enables a powerful use of our SPL set-up especially as post-patterning tool for inspection and repair functions below the sub-10 nm critical dimension level.

Application of an industrial robot to nuclear pharmacy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Viola, J.

1994-12-31

Increased patient throughput and lengthened P.E.T. scan protocols have increased the radiation dose received by P.E.T. technologists. Automated methods of tracer infusion and blood sampling have been introduced to reduce direct contact with the radioisotopes, but significant radiation exposure still exists during the receipt and dispensing of the patient dose. To address this situation the authors have developed an automated robotic system which performs these tasks, thus limiting the physical contact between operator and radioisotope.

First installation of a dual-room IVR-CT system in the emergency room.

PubMed

Wada, Daiki; Nakamori, Yasushi; Kanayama, Shuji; Maruyama, Shuhei; Kawada, Masahiro; Iwamura, Hiromu; Hayakawa, Koichi; Saito, Fukuki; Kuwagata, Yasuyuki

2018-03-05

Computed tomography (CT) embedded in the emergency room has gained importance in the early diagnostic phase of trauma care. In 2011, we implemented a new trauma workflow concept with a sliding CT scanner system with interventional radiology features (IVR-CT) that allows CT examination and emergency therapeutic intervention without relocating the patient, which we call the Hybrid emergency room (Hybrid ER). In the Hybrid ER, all life-saving procedures, CT examination, damage control surgery, and transcatheter arterial embolisation can be performed on the same table. Although the trauma workflow realized in the Hybrid ER may improve mortality in severe trauma, the Hybrid ER can potentially affect the efficacy of other in/outpatient diagnostic workflow because one room is occupied by one severely injured patient undergoing both emergency trauma care and CT scanning for long periods. In July 2017, we implemented a new trauma workflow concept with a dual-room sliding CT scanner system with interventional radiology features (dual-room IVR-CT) to increase patient throughput. When we perform emergency surgery or interventional radiology for a severely injured or ill patient in the Hybrid ER, the sliding CT scanner moves to the adjacent CT suite, and we can perform CT scanning of another in/outpatient. We believe that dual-room IVR-CT can contribute to the improvement of both the survival of severely injured or ill patients and patient throughput.

Rise of the micromachines: microfluidics and the future of cytometry.

PubMed

Wlodkowic, Donald; Darzynkiewicz, Zbigniew

2011-01-01

The past decade has brought many innovations to the field of flow and image-based cytometry. These advancements can be seen in the current miniaturization trends and simplification of analytical components found in the conventional flow cytometers. On the other hand, the maturation of multispectral imaging cytometry in flow imaging and the slide-based laser scanning cytometers offers great hopes for improved data quality and throughput while proving new vistas for the multiparameter, real-time analysis of cells and tissues. Importantly, however, cytometry remains a viable and very dynamic field of modern engineering. Technological milestones and innovations made over the last couple of years are bringing the next generation of cytometers out of centralized core facilities while making it much more affordable and user friendly. In this context, the development of microfluidic, lab-on-a-chip (LOC) technologies is one of the most innovative and cost-effective approaches toward the advancement of cytometry. LOC devices promise new functionalities that can overcome current limitations while at the same time promise greatly reduced costs, increased sensitivity, and ultra high throughputs. We can expect that the current pace in the development of novel microfabricated cytometric systems will open up groundbreaking vistas for the field of cytometry, lead to the renaissance of cytometric techniques and most importantly greatly support the wider availability of these enabling bioanalytical technologies. Copyright © 2011 Elsevier Inc. All rights reserved.

Rise of the Micromachines: Microfluidics and the Future of Cytometry

PubMed Central

Wlodkowic, Donald; Darzynkiewicz, Zbigniew

2011-01-01

The past decade has brought many innovations to the field of flow and image-based cytometry. These advancements can be seen in the current miniaturization trends and simplification of analytical components found in the conventional flow cytometers. On the other hand, the maturation of multispectral imaging cytometry in flow imaging and the slide-based laser scanning cytometers offers great hopes for improved data quality and throughput while proving new vistas for the multiparameter, real-time analysis of cells and tissues. Importantly, however, cytometry remains a viable and very dynamic field of modern engineering. Technological milestones and innovations made over the last couple of years are bringing the next generation of cytometers out of centralized core facilities while making it much more affordable and user friendly. In this context, the development of microfluidic, lab-on-a-chip (LOC) technologies is one of the most innovative and cost-effective approaches toward the advancement of cytometry. LOC devices promise new functionalities that can overcome current limitations while at the same time promise greatly reduced costs, increased sensitivity, and ultra high throughputs. We can expect that the current pace in the development of novel microfabricated cytometric systems will open up groundbreaking vistas for the field of cytometry, lead to the renaissance of cytometric techniques and most importantly greatly support the wider availability of these enabling bioanalytical technologies. PMID:21704837

High-throughput and cost-effective global DNA methylation assay by liquid chromatography-mass spectrometry

PubMed Central

Li, Xingnan; Franke, Adrian A.

2015-01-01

An affordable and fast liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the accurate and precise determination of global DNA methylation levels in peripheral blood. Global DNA methylation extent was expressed as the ratio of methylated 2′-deoxycytidine (5MedC) to 2′-deoxyguanosine (dG), which were obtained after DNA extraction and hydrolysis and determined by positive electrospray LC–ESI-MS/MS. The cost-effective internal standards 15N3-dC and 15N5-dG were incorporated for the accurate quantification of 5MedC and dG, respectively. The desired nucleoside analytes were separated and eluted by LC within 2.5 min on a reverse phase column with a limit of detection of 1.4 femtomole on column for 5MedC. Sample preparation in 96-well format has significantly increased the assay throughput and filtration was found to be a necessary step to assure precision. Precision was performed with repeated analysis of four DNA QC sample over 12 days, with mean intra- and inter-day CVs of 6% and 11%, respectively. Accuracy was evaluated by comparison with a previously reported method showing a mean CV of 4% for 5 subjects analyzed. Furthermore, application of the assay using a benchtop orbitrap LCMS in exact mass full scan mode showed comparable sensitivity to tandem LCMS using multiple reaction monitoring. PMID:21843675

High Throughput Transcriptomics @ USEPA (Toxicology ...

EPA Pesticide Factsheets

The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

Mobile element biology – new possibilities with high-throughput sequencing

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Jorde, Lynn B.

2014-01-01

Mobile elements compose more than half of the human genome, but until recently their large-scale detection was time-consuming and challenging. With the development of new high-throughput sequencing technologies, the complete spectrum of mobile element variation in humans can now be identified and analyzed. Thousands of new mobile element insertions have been discovered, yielding new insights into mobile element biology, evolution, and genomic variation. We review several high-throughput methods, with an emphasis on techniques that specifically target mobile element insertions in humans, and we highlight recent applications of these methods in evolutionary studies and in the analysis of somatic alterations in human cancers. PMID:23312846

Advances in high throughput DNA sequence data compression.

PubMed

Sardaraz, Muhammad; Tahir, Muhammad; Ikram, Ataul Aziz

2016-06-01

Advances in high throughput sequencing technologies and reduction in cost of sequencing have led to exponential growth in high throughput DNA sequence data. This growth has posed challenges such as storage, retrieval, and transmission of sequencing data. Data compression is used to cope with these challenges. Various methods have been developed to compress genomic and sequencing data. In this article, we present a comprehensive review of compression methods for genome and reads compression. Algorithms are categorized as referential or reference free. Experimental results and comparative analysis of various methods for data compression are presented. Finally, key challenges and research directions in DNA sequence data compression are highlighted.

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.

PubMed

Ellingson, Sally R; Dakshanamurthy, Sivanesan; Brown, Milton; Smith, Jeremy C; Baudry, Jerome

2014-04-25

In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.

LOCATE: a mouse protein subcellular localization database

PubMed Central

Fink, J. Lynn; Aturaliya, Rajith N.; Davis, Melissa J.; Zhang, Fasheng; Hanson, Kelly; Teasdale, Melvena S.; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Teasdale, Rohan D.

2006-01-01

We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing >1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for ∼40% of the mouse proteome. It is available at . PMID:16381849

An economical and effective high-throughput DNA extraction protocol for molecular marker analysis in honey bees

USDA-ARS?s Scientific Manuscript database

Extraction of DNA from tissue samples can be expensive both in time and monetary resources and can often require handling and disposal of hazardous chemicals. We have developed a high throughput protocol for extracting DNA from honey bees that is of a high enough quality and quantity to enable hundr...

Applications of high throughput (combinatorial) methodologies to electronic, magnetic, optical, and energy-related materials

NASA Astrophysics Data System (ADS)

Green, Martin L.; Takeuchi, Ichiro; Hattrick-Simpers, Jason R.

2013-06-01

High throughput (combinatorial) materials science methodology is a relatively new research paradigm that offers the promise of rapid and efficient materials screening, optimization, and discovery. The paradigm started in the pharmaceutical industry but was rapidly adopted to accelerate materials research in a wide variety of areas. High throughput experiments are characterized by synthesis of a "library" sample that contains the materials variation of interest (typically composition), and rapid and localized measurement schemes that result in massive data sets. Because the data are collected at the same time on the same "library" sample, they can be highly uniform with respect to fixed processing parameters. This article critically reviews the literature pertaining to applications of combinatorial materials science for electronic, magnetic, optical, and energy-related materials. It is expected that high throughput methodologies will facilitate commercialization of novel materials for these critically important applications. Despite the overwhelming evidence presented in this paper that high throughput studies can effectively inform commercial practice, in our perception, it remains an underutilized research and development tool. Part of this perception may be due to the inaccessibility of proprietary industrial research and development practices, but clearly the initial cost and availability of high throughput laboratory equipment plays a role. Combinatorial materials science has traditionally been focused on materials discovery, screening, and optimization to combat the extremely high cost and long development times for new materials and their introduction into commerce. Going forward, combinatorial materials science will also be driven by other needs such as materials substitution and experimental verification of materials properties predicted by modeling and simulation, which have recently received much attention with the advent of the Materials Genome Initiative. Thus, the challenge for combinatorial methodology will be the effective coupling of synthesis, characterization and theory, and the ability to rapidly manage large amounts of data in a variety of formats.

20171015 - Capabilities and Evaluation of the US EPA’s HTTK (High Throughput Toxicokinetics) R package (ISES)

EPA Science Inventory

Toxicokinetics (TK) provides a bridge between toxicity and exposure assessment by predicting tissue concentrations due to exposure, however traditional TK methods are resource intensive. Relatively high throughput TK (HTTK) methods have been used by the pharmaceutical industry to...

High-throughput dietary exposure predictions for chemical migrants from food contact substances for use in chemical prioritization

EPA Science Inventory

Under the ExpoCast program, United States Environmental Protection Agency (EPA) researchers have developed a high-throughput (HT) framework for estimating aggregate exposures to chemicals from multiple pathways to support rapid prioritization of chemicals. Here, we present method...

Environmental surveillance and monitoring. The next frontiers for high-throughput toxicology

EPA Science Inventory

High throughput toxicity testing (HTT) technologies along with the world-wide web are revolutionizing both generation and access to data regarding the bioactivities that chemicals can elicit when they interact with specific proteins, genes, or other targets in the body of an orga...