GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures

While crucial for force spectroscopists and microbiologists, three-dimensional (3D) particle tracking suffers from either poor precision, complex calibration, or the need of expensive hardware, preventing its massive adoption. We introduce a new technique, based on a simple piece of cardboard inserted in the objective focal plane, that enables simple 3D tracking of dilute microparticles while offering subnanometer frame-to-frame precision in all directions. Its linearity alleviates calibration procedures, while the interferometric pattern enhances precision. We illustrate its utility in single-molecule force spectroscopy and single-algae motility analysis. As with any technique based on back focal plane engineering, it may be directly embedded in a commercial objective, providing a means to convert any preexisting optical setup in a 3D tracking system. Thanks to its precision, its simplicity, and its versatility, we envision that the technique has the potential to enhance the spreading of high-precision and high-throughput 3D tracking.

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A deductive database system PACADE for the three dimensional structure of protein

10.1109/hicss.1991.183938 ◽

2002 ◽

Author(s):

S. Kuhara ◽

K. Satou ◽

E. Furuichi ◽

T. Takagi ◽

H. Takehara ◽

...

Keyword(s):

Three Dimensional ◽

Database System ◽

Deductive Database ◽

Dimensional Structure ◽

Three Dimensional Structure

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Photoluminescence measurements of carbon quantum dots within three-dimensional hydrogel matrices using a high throughput 96 well plate method

MethodsX ◽

10.1016/j.mex.2019.02.014 ◽

2019 ◽

Vol 6 ◽

pp. 437-441

Author(s):

Adam Truskewycz ◽

Sabrina Beker ◽

Andrew S. Ball ◽

Ivan Cole

Keyword(s):

Quantum Dots ◽

High Throughput ◽

Three Dimensional ◽

Carbon Quantum Dots ◽

Plate Method

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High-Throughput Electron Diffraction Reveals a Hidden Novel Metal-Organic Framework for Electrocatalysis

10.26434/chemrxiv.13725817.v2 ◽

2021 ◽

Author(s):

Meng Ge ◽

Yanzhi Wang ◽

Francesco Carraro ◽

Weibin Liang ◽

Morteza Roostaeinia ◽

...

Keyword(s):

Electron Diffraction ◽

High Throughput ◽

Metal Organic Framework ◽

Three Dimensional ◽

Reduction Reaction ◽

New Materials ◽

X Ray Diffraction ◽

Zeolitic Imidazolate Framework ◽

Wide Range ◽

Metal Organic

Metal-organic frameworks (MOFs) are known for their versatile combination of inorganic building units and organic linkers, which offers immense opportunities in a wide range of applications. However, many MOFs are typically synthesized as multiphasic polycrystalline powders, which are challenging for studies by X-ray diffraction. Therefore, developing new structural characterization techniques is highly desired in order to accelerate discoveries of new materials. Here, we report a high-throughput approach for structural analysis of MOF nano- and sub-microcrystals by three-dimensional electron diffraction (3DED). A new zeolitic-imidazolate framework (ZIF), denoted ZIF-EC1<a>, </a>was first discovered in a trace amount during the study of a known ZIF-CO3-1 material by 3DED. The structures of both ZIFs were solved and refined using 3DED data. ZIF-EC1 has a dense 3D framework structure, which is built by linking mono- and bi-nuclear Zn clusters and 2-methylimidazolates (mIm-). With a composition of Zn3(mIm)5(OH), ZIF-EC1 exhibits high N and Zn densities. We show that the N-doped carbon material derived from ZIF-EC1 is a promising electrocatalysis for oxygen reduction reaction (ORR). The discovery of this new MOF and its conversion to an efficient electrocatalyst highlights the power of 3DED in developing new materials and their applications.

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Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1609569114 ◽

2016 ◽

Vol 113 (52) ◽

pp. 14915-14920 ◽

Cited By ~ 21

Author(s):

Yih Yang Chen ◽

Pamuditha N. Silva ◽

Abdullah Muhammad Syed ◽

Shrey Sindhwani ◽

Jonathan V. Rocheleau ◽

...

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Three Dimensional ◽

Microfluidic System ◽

High Throughput Drug Screening ◽

Image Analysis Algorithm ◽

Screening Assays ◽

On Chip ◽

Tissue Models

On-chip imaging of intact three-dimensional tissues within microfluidic devices is fundamentally hindered by intratissue optical scattering, which impedes their use as tissue models for high-throughput screening assays. Here, we engineered a microfluidic system that preserves and converts tissues into optically transparent structures in less than 1 d, which is 20× faster than current passive clearing approaches. Accelerated clearing was achieved because the microfluidic system enhanced the exchange of interstitial fluids by 567-fold, which increased the rate of removal of optically scattering lipid molecules from the cross-linked tissue. Our enhanced clearing process allowed us to fluorescently image and map the segregation and compartmentalization of different cells during the formation of tumor spheroids, and to track the degradation of vasculature over time within extracted murine pancreatic islets in static culture, which may have implications on the efficacy of beta-cell transplantation treatments for type 1 diabetes. We further developed an image analysis algorithm that automates the analysis of the vasculature connectivity, volume, and cellular spatial distribution of the intact tissue. Our technique allows whole tissue analysis in microfluidic systems, and has implications in the development of organ-on-a-chip systems, high-throughput drug screening devices, and in regenerative medicine.

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Integrated and Intelligent Database Systems for Plant Engineering Framework

ASME 1994 8th Annual Database Symposium ◽

10.1115/edm1994-0494 ◽

1994 ◽

Author(s):

N. Narikawa ◽

T. Sato ◽

N. Sasaki

Keyword(s):

Three Dimensional ◽

Database Systems ◽

Database System ◽

Structure Design ◽

Object Oriented Programming ◽

Design Knowledge ◽

Automation System ◽

Functional Requirements ◽

Plant Structure ◽

Cad System

Abstract This paper gives an overview of an integrated and intelligent database system for a plant engineering framework. We have integrated existing two-dimensional (2D) CAD systems, a three-dimensional (3D) CAD system, and a relational database system which stores engineering information such as design conditions, maintenance histories, and inherent properties. By integrating these systems, the infrastructure for concurrent engineering has been realized. As for design knowledge, we treat object-oriented programming as a useful knowledge representation method. We analyze the plant structure and functional requirements of the system, and then represented them by using the hierarchical Class structure. Design knowledge accompanies the Class, so we represent it using Method. As a design automation system, we develop an automated design check system. This is implemented by using the Common Lisp Object System. These systems are the main parts of the plant engineering framework, and are utilized in the practical design. We intend to develop a mechanical/electronic design framework using the same approach.

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High-throughput phenotyping in cotton: a review

Journal of Cotton Research ◽

10.1186/s42397-019-0035-0 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 2

Author(s):

Irish Lorraine B. PABUAYON ◽

Yazhou SUN ◽

Wenxuan GUO ◽

Glen L. RITCHIE

Keyword(s):

High Throughput ◽

Cropping Systems ◽

Three Dimensional ◽

Growth Yield ◽

Analytical Techniques ◽

Phenotypic Traits ◽

Technological Advances ◽

Recent Developments ◽

Potential Applications ◽

High Throughput Phenotyping

Abstract Recent technological advances in cotton (Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis. High-throughput phenotyping (HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth, yield, and adaptation to biotic or abiotic stress. Researchers have conducted extensive experiments on HTP and developed techniques including spectral, fluorescence, thermal, and three-dimensional imaging to measure the morphological, physiological, and pathological resistance traits of cotton. In addition, ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems. This review paper highlights the techniques and recent developments for HTP in cotton, reviews the potential applications according to morphological and physiological traits of cotton, and compares the advantages and limitations of these HTP systems when used in cotton cropping systems. Overall, the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton. However, because of its relative novelty, HTP has some limitations that constrains the ability to take full advantage of what it can offer. These challenges need to be addressed to increase the accuracy and utility of HTP, which can be done by integrating analytical techniques for big data and continuous advances in imaging.

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