scholarly journals PROTALIGN: A 3-DIMENSIONAL PROTEIN ALIGNMENT ASSESSMENT TOOL

1998 ◽  
Author(s):  
DOANNA MEADS ◽  
MARC D. HANSEN ◽  
ALEX PANG
Keyword(s):  
Assessment Tool ◽  
Protein Alignment ◽  
3 Dimensional

scholarly journals Using computerized assessment in simulated colonoscopy: a validation study

2020 ◽  
Vol 08 (06) ◽  
pp. E783-E791
Author(s):  
Andreas Slot Vilmann ◽  
Christian Lachenmeier ◽  
Morten Bo Søndergaard Svendsen ◽  
Bo Søndergaard ◽  
Yoon Soo Park ◽  
...  
Keyword(s):  
Assessment Tool ◽  
Assessment Tools ◽  
Continuous Assessment ◽  
Computerized Assessment ◽  
3 Dimensional ◽  
Phantom Model ◽  
Significant Difference ◽  
Simulation Based ◽  
Travel Length ◽  
Colon Data

Abstract Background and study aims Patient safety during a colonoscopy highly depends on endoscopist competence. Endoscopic societies have been calling for an objective and regular assessment of the endoscopists, but existing assessment tools are time-consuming and prone to bias. We aimed to develop and gather evidence of validity for a computerized assessment tool delivering automatic and unbiased assessment of colonoscopy based on 3 dimensional coordinates from the colonoscope. Methods Twenty-four participants were recruited and divided into two groups based on experience: 12 experienced and 12 novices. Participants performed twice on a physical phantom model with a standardized alpha loop in the sigmoid colon. Data was gathered directly from the Olympus ScopeGuide system providing XYZ-coordinates along the length of the colonoscope. Five different motor skill measures were developed based on the data, named: Travel Length, Tip Progression, Chase Efficiency, Shaft movement without tip progression, and Looping. Results The experinced had a lower travel length (P < 0.001), tip progression (P < 0.001), chase efficiency (P = 0.001) and looping (P = 0.006), and a higher shaft movement without tip progression (P < 0.001) reaching the cecum compared with the novices. A composite score was developed based on the five measurements to create a combined score of progression, the 3D-Colonoscopy-Progression-Score (3D-CoPS). The 3D-CoPS revealed a significant difference between groups (experienced: 0.495 (SD 0.303) and novices –0.454 (SD 0.707), P < 0.001). Conclusion This study presents a novel, real-time computerized assessment tool for colonoscopy, and strong evidence of validity was gathered in a simulation-based setting. The system shows promising opportunities for automatic, unbiased and continuous assessment of colonoscopy performance.

scholarly journals 3-Dimensional Printing in Rehabilitation: Feasibility of Printing an Upper Extremity Gross Motor Function Assessment Tool

2020 ◽  
Author(s):  
Naaz Kapadia ◽  
Mathew Myers ◽  
Kristin Musselman ◽  
Rosalie Wang ◽  
Aaron Yurkewich ◽  
...  
Keyword(s):  
Upper Extremity ◽  
Outcome Measures ◽  
Motor Function ◽  
Assessment Tool ◽  
Hand Function ◽  
Primary Objective ◽  
Rater Reliability ◽  
3 Dimensional ◽  
3D Printed ◽  
Dimensional Printing

Abstract Background: Use of standardized and scientifically sound outcome measures is highly encouraged in clinical practice and research. Researchers have identified that with the development of newer rehabilitation therapies we need technology-supported upper extremity outcome measures that are easily accessible and can measure change consistently and reliably. 3‐dimensional printing (3D-printing) has recently seen a meteoric rise in interest within medicine including the field of Physical Medicine and Rehabilitation. The primary objective of the current study was to evaluate the feasibility of designing and constructing a 3D printed version of the Toronto Rehabilitation Institute-Hand Function Test (TRI-HFT). The secondary objective was to assess the preliminary psychometrics of the 3D TRI-HFT in individuals with stroke. Results: 3D design files were created using the measurements of the original TRI-HFT objects. The 3D printed objects were then compared to the original test objects to ensure that the original dimensions were preserved. All objects were successfully printed except the sponge and paper which required some modification. The error margin for weight of the objects was within 10% for the rest of the objects. Nine participants underwent the following assessments: the Chedoke Arm and Hand Activity Inventory (CAHAI), Fugl Meyer Assessment-Hand (FMA-Hand), Chedoke McMaster stages of recovery of the arm (CMSA-Arm) and Chedoke McMaster stages of recovery of the hand (CMSA-Hand) and the 3D TRI-HFT for assessment of psychometric properties of the test. The video recorded assessment of the 3D TRI-HFT was reviewed by two assessors for reliability testing. Construct validity was assessed by comparing the scores on 3D TRI-HFT with the scores on CAHAI, CMSA-Arm, CMSA-Hand and FMA-Hand. The 3D TRI-HFT had high inter-rater reliability (ICC of 0.99; P < 0.000), high intra-rater reliability (ICC of 0.99; P < 0.000) and moderate to strong correlation with the CMSA-Arm, CMSA-Hand and FMA-Hand scores. Conclusions: The TRI-HFT could be successfully 3D printed and initial testing indicates that the test is a reliable and valid measure of upper extremity motor function in individuals with stroke.

scholarly journals 3-Dimensional printing in rehabilitation: feasibility of printing an upper extremity gross motor function assessment tool

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Naaz Kapadia ◽  
Mathew Myers ◽  
Kristin Musselman ◽  
Rosalie H. Wang ◽  
Aaron Yurkewich ◽  
...  
Keyword(s):  
Upper Extremity ◽  
Outcome Measures ◽  
Motor Function ◽  
Assessment Tool ◽  
Gross Motor ◽  
3 Dimensional ◽  
Gross Motor Function ◽  
3D Printed ◽  
Dimensional Printing ◽  
Function Assessment

Abstract Background Use of standardized and scientifically sound outcome measures is encouraged in clinical practice and research. With the development of newer rehabilitation therapies, we need technology-supported upper extremity outcome measures that are easily accessible, reliable and valid. 3‐Dimensional printing (3D-printing) has recently seen a meteoric rise in interest within medicine including the field of Physical Medicine and Rehabilitation. The primary objective of this study was to evaluate the feasibility of designing and constructing a 3D printed version of the Toronto Rehabilitation Institute-Hand Function Test (TRI-HFT). The TRI-HFT is an upper extremity gross motor function assessment tool that measures function at the intersection of the International Classification of Function’s body structure and function, and activity domain. The secondary objective was to assess the preliminary psychometrics of this test in individuals with stroke. Results 3D design files were created using the measurements of the original TRI-HFT objects. The 3D printed objects were then compared to the original test objects to ensure that the original dimensions were preserved. All objects were successfully printed except the sponge and paper which required some modification. The error margin for weight of the objects was within 10% of the original TRI-HFT for the rest of the objects. Nine participants underwent the following assessments: the Chedoke Arm and Hand Activity Inventory (CAHAI), Fugl Meyer Assessment-Hand (FMA-Hand), Chedoke McMaster stages of recovery of the arm (CMSA-Arm) and Chedoke McMaster stages of recovery of the hand (CMSA-Hand) and the 3D TRI-HFT for assessment of psychometric properties of the test. The video recorded assessment of the 3D TRI-HFT was used for reliability testing. Construct validity was assessed by comparing the scores on 3D TRI-HFT with the scores on CAHAI, CMSA-Arm, CMSA-Hand and FMA-Hand. The 3D TRI-HFT had high inter-rater reliability (Intra-Class Correlation Co-efficient (ICC) of 0.99; P < 0.000), high intra-rater reliability (ICC of 0.99; P < 0.000) and moderate-to-strong correlation with the CMSA-Arm, CMSA-Hand and FMA-Hand scores. Conclusions The TRI-HFT could be successfully 3D printed and initial testing indicates that the test is a reliable and valid measure of upper extremity motor function in individuals with stroke.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

Structural preservation and absolute contrast of catalase crystal sections prepared with tannic acid

1983 ◽  
Vol 41 ◽  
pp. 448-449
Author(s):  
C.W. Akey ◽  
M. Szalay ◽  
S.J. Edelstein
Keyword(s):  
Tannic Acid ◽  
Beef Heart ◽  
X Rays ◽  
Screw Axis ◽  
General Applicability ◽  
Thin Sections ◽  
Beef Liver ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Structural Preservation

Three methods of obtaining 20 Å resolution in sectioned protein crystals have recently been described. They include tannic acid fixation, low temperature embedding and grid sectioning. To be useful for 3-dimensional reconstruction thin sections must possess suitable resolution, structural fidelity and a known contrast. Tannic acid fixation appears to satisfy the above criteria based on studies of crystals of Pseudomonas cytochrome oxidase, orthorhombic beef liver catalase and beef heart F1-ATPase. In order to develop methods with general applicability, we have concentrated our efforts on a trigonal modification of catalase which routinely demonstrated a resolution of 40 Å. The catalase system is particularly useful since a comparison with the structure recently solved with x-rays will permit evaluation of the accuracy of 3-D reconstructions of sectioned crystals.Initially, we re-evaluated the packing of trigonal catalase crystals studied by Longley. Images of the (001) plane are of particular interest since they give a projection down the 31-screw axis in space group P3121. Images obtained by the method of Longley or by tannic acid fixation are negatively contrasted since control experiments with orthorhombic catalase plates yield negatively stained specimens with conditions used for the larger trigonal crystals.

Deviations from Ideal Decagonal Symmetry in Electron Diffraction Patterns of the “Decagonal” Phase in the Al-Co-Cu Alloy System

1991 ◽  
Vol 49 ◽  
pp. 914-915
Author(s):  
Atul S. Ramani ◽  
Earle R. Ryba ◽  
Paul R. Howell
Keyword(s):  
Electron Microscope ◽  
Alloy System ◽  
Nominal Composition ◽  
Dimensional Lattice ◽  
3 Dimensional ◽  
Decagonal Phase ◽  
Cu Alloy ◽  
Transmission Electron ◽  
Lattice Periodicity ◽  
Diffraction Patterns

The “decagonal” phase in the Al-Co-Cu system of nominal composition Al65CO15Cu20 first discovered by He et al. is especially suitable as a topic of investigation since it has been claimed that it is thermodynamically stable and is reported to be periodic in the dimension perpendicular to the plane of quasiperiodic 10-fold symmetry. It can thus be expected that it is an important link between fully periodic and fully quasiperiodic phases. In the present paper, we report important findings of our transmission electron microscope (TEM) study that concern deviations from ideal decagonal symmetry of selected area diffraction patterns (SADPs) obtained from several “decagonal” phase crystals and also observation of a lattice of main reflections on the 10-fold and 2-fold SADPs that implies complete 3-dimensional lattice periodicity and the fundamentally incommensurate nature of the “decagonal” phase. We also present diffraction evidence for a new transition phase that can be classified as being one-dimensionally quasiperiodic if the lattice of main reflections is ignored.

A Novel Reconstitution Method for Inducing the Formation of Regular 2-Dimensional Arrays of Membrane Proteins and Lipids

1988 ◽  
Vol 46 ◽  
pp. 152-153 ◽  
Author(s):  
A. Engel ◽  
A. Holzenburg ◽  
K. Stauffer ◽  
J. Rosenbusch ◽  
U. Aebi
Keyword(s):  
Membrane Proteins ◽  
Flow Rate ◽  
Lipid Membranes ◽  
Functional Characterization ◽  
Dimensional Structure ◽  
Electron Crystallography ◽  
Peltier Element ◽  
Protein Ratio ◽  
Precise Control ◽  
3 Dimensional

Reconstitution of solubilized and purified membrane proteins in the presence of phospholipids into vesicles allows their functions to be studied by simple bulk measurements (e.g. diffusion of differently sized solutes) or by conductance measurements after transformation into planar membranes. On the other hand, reconstitution into regular protein-lipid arrays, usually forming at a specific lipid-to-protein ratio, provides the basis for determining the 3-dimensional structure of membrane proteins employing the tools of electron crystallography.To refine reconstitution conditions for reproducibly inducing formation of large and highly ordered protein-lipid membranes that are suitable for both electron crystallography and patch clamping experiments aimed at their functional characterization, we built a flow-dialysis device that allows precise control of temperature and flow-rate (Fig. 1). The flow rate is generated by a peristaltic pump and can be adjusted from 1 to 500 ml/h. The dialysis buffer is brought to a preselected temperature during its travel through a meandering path before it enters the dialysis reservoir. A Z-80 based computer controls a Peltier element allowing the temperature profile to be programmed as function of time.

Structure and Interaction of Protamine by Dark Field Electron Microscopy

1976 ◽  
Vol 34 ◽  
pp. 160-161
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Electron Microscopy ◽  
Dark Field ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Field Electron ◽  
Proposed Model ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Positively Charged

It has been shown for some time that it is possible to obtain images of small unstained proteins, with a resolution of approximately 5Å using dark field electron microscopy (1,2). Applying this technique, we have observed a uniformity in size and shape of the 2-dimensional images of pure specimens of fish protamines (salmon, herring (clupeine, Y-l) and rainbow trout (Salmo irideus)). On the basis of these images, a model for the 3-dimensional structure of the fish protamines has been proposed (2).The known amino acid sequences of fish protamines show stretches of positively charged arginines, separated by regions of neutral amino acids (3). The proposed model for protamine structure (2) consists of an irregular, right-handed helix with the segments of adjacent arginines forming the loops of the coil.

Design and calibration of an IVEM for general 3-dimensional imaging of non-diffracting materials

1992 ◽  
Vol 50 (2) ◽  
pp. 1040-1041
Author(s):  
Neil Rowlands ◽  
Jeff Price ◽  
Michael Kersker ◽  
Seichi Suzuki ◽  
Steve Young ◽  
...  
Keyword(s):  
3D Imaging ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3 Dimensional ◽  
3D Microstructure ◽  
Image Translation ◽  
Digital Correlation ◽  
On Line ◽  
Mechanical Stage ◽  
Projection Angle

Three-dimensional (3D) microstructure visualization on the electron microscope requires that the sample be tilted to different positions to collect a series of projections. This tilting should be performed rapidly for on-line stereo viewing and precisely for off-line tomographic reconstruction. Usually a projection series is collected using mechanical stage tilt alone. The stereo pairs must be viewed off-line and the 60 to 120 tomographic projections must be aligned with fiduciary markers or digital correlation methods. The delay in viewing stereo pairs and the alignment problems in tomographic reconstruction could be eliminated or improved by tilting the beam if such tilt could be accomplished without image translation.A microscope capable of beam tilt with simultaneous image shift to eliminate tilt-induced translation has been investigated for 3D imaging of thick (1 μm) biologic specimens. By tilting the beam above and through the specimen and bringing it back below the specimen, a brightfield image with a projection angle corresponding to the beam tilt angle can be recorded (Fig. 1a).

4-dimensional, high-resolution imaging of living cells

1992 ◽  
Vol 50 (1) ◽  
pp. 416-417
Author(s):  
Shinya Inoué
Keyword(s):  
Light Microscope ◽  
Living Cells ◽  
Live Cells ◽  
Video Tape ◽  
Active Living ◽  
High Resolution Imaging ◽  
3 Dimensional ◽  
Dynamic Architecture ◽  
Resolution Imaging ◽  
Disk Memory

This paper reports progress of our effort to rapidly capture, and display in time-lapsed mode, the 3-dimensional dynamic architecture of active living cells and developing embryos at the highest resolution of the light microscope. Our approach entails: (A) real-time video tape recording of through-focal, ultrathin optical sections of live cells at the highest resolution of the light microscope; (B) repeat of A at time-lapsed intervals; (C) once each time-lapsed interval, an image at home focus is recorded onto Optical Disk Memory Recorder (OMDR); (D) periods of interest are selected using the OMDR and video tape records; (E) selected stacks of optical sections are converted into plane projections representing different view angles (±4 degrees for stereo view, additional angles when revolving stereos are desired); (F) analysis using A - D.

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