High resolution PET, SPECT and projection imaging in small animals

Positron emission tomography, single photon emission computed tomography and planar projection imaging of radioactive tracers have long been in use for detecting and diagnosing disease in human subjects. More recently, advanced versions of these same technologies have begun to be used across the breadth of modern biomedical research to study non-invasively small laboratory animals in a myriad of experimental settings. In this report, we describe some of the new instruments and techniques that make these measurements possible and illustrate, with a few examples, the potential power of these methods in modern biomedical researchPublicad

PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks

Background How can we obtain fast and high-quality clusters in genome scale bio-networks? Graph clustering is a powerful tool applied on bio-networks to solve various biological problems such as protein complexes detection, disease module detection, and gene function prediction. Especially, MCL (Markov Clustering) has been spotlighted due to its superior performance on bio-networks. MCL, however, is skewed towards finding a large number of very small clusters (size 1-3) and fails to detect many larger clusters (size 10+). To resolve this fragmentation problem, MLR-MCL (Multi-level Regularized MCL) has been developed. MLR-MCL still suffers from the fragmentation and, in cases, unrealistically large clusters are generated. Results In this paper, we propose PS-MCL (Parallel Shotgun Coarsened MCL), a parallel graph clustering method outperforming MLR-MCL in terms of running time and cluster quality. PS-MCL adopts an efficient coarsening scheme, called SC (Shotgun Coarsening), to improve graph coarsening in MLR-MCL. SC allows merging multiple nodes at a time, which leads to improvement in quality, time and space usage. Also, PS-MCL parallelizes main operations used in MLR-MCL which includes matrix multiplication. Conclusions Experiments show that PS-MCL dramatically alleviates the fragmentation problem, and outperforms MLR-MCL in quality and running time. We also show that the running time of PS-MCL is effectively reduced with parallelization.Publication of this article has been funded by National Research Foundation of Korea grant funded by the Korea government (NRF-2018R1A5A1060031, NRF-2018R1A1A3A0407953) and by Korea Institute of Science and Technology Information (K-18-L03-C02)

PET, CT, and MR image registration of the rat brain and skull

Spatially registered positron emission tomography (PET), computed tomography (CT), and magnetic resonance (MR) images of the same small animal offer potential advantages over PET alone: CT images should allow accurate, nearly noise-free correction of the PET image data for attenuation; the CT or MR images should permit more certain identification of structures evident in the PET images; and CT images provide a priori anatomical information that may be of use with resolution-improving image-reconstruction algorithms that model the PET imaging process. However, image registration algorithms effective in human studies have not been characterized in the small-animal setting. Accordingly, the authors evaluated the ability of the automated image registration (AIR) and mutual information (MI) algorithms to register PET images of the rat skull and brain to CT or MR images of the same animal. External fiducial marks visible in all three modalities were used to estimate residual errors after registration. The AIR algorithm registered PET bone-to-CT bone images with a maximum error of less than 1.0 mm, The registration errors for PET brain-to-CT brain images, however, were greater, and considerable user intervention was required prior to registration. The AIR algorithm either failed or required excessive user intervention to register PET and MR brain images. In contrast, the MI algorithm yielded smaller registration errors in all scenarios with little user intervention. The MI algorithm thus appears to be a more robust method for registering PET, CT, and MR images of the rat headPublicad

Performance of a Distributed Simultaneous Strain and Temperature Sensor Based on a Fabry-Perot Laser Diode and a Dual-Stage FBG Optical Demultiplexer

A simultaneous strain and temperature measurement method using a Fabry-Perot laser diode (FP-LD) and a dual-stage fiber Bragg grating (FBG) optical demultiplexer was applied to a distributed sensor system based on Brillouin optical time domain reflectometry (BOTDR). By using a Kalman filter, we improved the performance of the FP-LD based OTDR, and decreased the noise using the dual-stage FBG optical demultiplexer. Applying the two developed components to the BOTDR system and using a temperature compensating algorithm, we successfully demonstrated the simultaneous measurement of strain and temperature distributions under various experimental conditions. The observed errors in the temperature and strain measured using the developed sensing system were 0.6 °C and 50 με, and the spatial resolution was 1 m, respectively

Scintillator identification and performance characteristics of LSO and GSO PSPMTdetector modules combined through common X and Y resistive dividers

Combining signal channels from detector arrays can reduce complexity and minimize cost but, potentially, at the expense of other performance parameters. We evaluated a method that reduces the number of signals by combining the anode outputs of three position-sensitive photomultiplier tubes (PSPMTs) through a common X resistive charge divider and three individual Y resistive charge dividers. Field flood images at 511 keV of two LSO modules combined with a single GSO module were compared to images obtained when the modules were illuminated separately. At moderate count rates only a small reduction in position detection accuracy was observed in the combined tubes. Event mis-positioning was minimal for total count rates < 300,000 cps. At higher rates, pulse pileup degraded accuracy. Delayed charge integration, a method for identifying scintillators by differences in their light decay times, allowed the LSO and GSO arrays to be distinguished from one another and also reduced the effect of pulse pileup. Thus, combining PSPMTs anodes through common X and common Y rcsistivc dividers may be useful in reducing signal number from PSPMT deteclor modules while maintaining good event localization and scintillator identification accuracy at reasonable event rates.Publicad

Affordable method of video recording for ecologists and citizen-science participants

Abstract Observations and video documentation of interactions between animals living in dens, cavities, and other enclosed spaces are difficult, but they play an important role in field biology, ecology, and conservation. For example, bird parents visiting nests and feeding their nestlings may provide crucial information for testing of ecological hypotheses and may easily attract attention of participants of citizen-science ecological and conservation projects. Because of the nest concealment of cavity-nesting birds, their behaviors in the nest can only be studied by using video surveillance. Professional wildlife surveillance systems are extremely expensive. Here, we describe an inexpensive video setup that can be constructed with relatively little effort and is more affordable than any previously described system. We anticipate that the relatively low cost of about 250 USD for a battery-operated system is an important feature for citizen-science type of projects and for applications in heavily populated areas where the potential for theft and vandalism may be high. Based on our experiences, we provide methodological advice on practical aspects of using this system in the field for ecological research on birds. We highlight the low cost, easiness of construction, and potential availability to a large number of observers taking part in wildlife monitoring projects, and we offer technical help to participants of such research projects

Performance characteristic of the NIH atlas small animal PET scanner

[Abstract] AMI International Conference 2003, September 21 - 27, Madrid, Spain: "High Resolution Molecular Imaging: from Basic Science to Clinical Applications"The Advanced Technology Laboratory Animal Scanner (ATLAS) is a small animal positron emission tomography (PET) scanner with depth-of-interaction (DOI) capability designed to image animals the size of mice and rats. We report performance measurements and show animal studies that suggest that ATLAS offers advantages over systems without DOI capabilityPublicad

Numerical study of a freely-falling maple seed

학위논문 (박사)-- 서울대학교 대학원 : 기계항공공학부, 2016. 8. 최해천.Many winged seeds such as those of maples exploit autorotation to decrease the descending velocity and increase the dispersal distance for their conservation of species. They have a simple configuration without neuromuscular control for driving as in animal flight, and even those with damaged wing can still autorotate. It means that autorotating seeds have a mechanically robust design unlike the flapping or rotating-blade mechanism, and thus they fascinate many researchers to develop micro air vehicles (MAVs) equipped with sensors for the reconnaissance, munition, and atmospheric researches. In this study, high-fidelity numerical simulations are conducted for flow around a freely-falling maple seed using an immersed boundary method in a non-inertial reference frame. A three-dimensional seed model is obtained by scanning a maple seed (Acer palmatum). The seed reaches a steady autorotation after a transient period. This transient period depends on the initial position of a seed and is shorter when the wing leading edge or nut or trailing edge of the seed is initially positioned upward. During autorotation, a stable leading-edge vortex is attached on the surface of the rotating seed. Two different approaches are considered to obtain scaling laws describing the relation among the seed weight and geometry, and descending and rotating velocities. The first uses the conservation of mass, linear and angular momentum, and energy. In this approach, a model constant to be determined, called the axial induction factor, is obtained from the result of present simulation. The second approach employs a classical steady wing theory in which the vortical strength is scaled with the circulation around a wing and the lift force is modeled by the time derivative of vortical impulse. Available data from winged seeds are applied to the present scaling laws, showing excellent collapses onto the scaling laws. These theoretical analyses can provide a simple guideline for researchers who seek the evolutionary direction of the morphologies and kinematics on autorotating seeds or who design autorotation-based micro air vehicles.Chapter 1 Introduction 1 1.1 Previous studies on the autorotating seed: experiments 3 1.2 Previous studies on the autorotating seed: theoretical analyses 4 1.3 Objectives 5 Chapter 2 Numerical methods 9 2.1 Reference frames 9 2.2 Navier-Stokes equations for fluid motion 11 2.3 Dynamic equations for the body motion 13 Chapter 3 Freely-falling maple seed in quiescent condition 19 3.1 Experimental validation 20 3.2 Computational details 22 3.3 Kinematic characteristics 23 3.4 Flow characteristics 26 3.5 Sectional drag coefficient 27 3.6 Initial posture of the seed 29 3.7 Freely-falling maple seed in the presence of wind 31 3.8 Summary 32 Chapter 4 Theoretical analysis for autorotating seeds 62 4.1 Scaling law for the drag of autorotating seed 70 4.2 Simple analysis based on the axial momentum theory 63 4.3 Summary 74 Chapter 5 Summary and Concluding Remarks 91 References 94 요약 100Docto