Brain PET imaging optimization with time of flight and point spread function modelling

PurposeTo assess the influence of reconstruction algorithms and parameters on the PET image quality of brain phantoms in order to optimize reconstruction for clinical PET brain studies in a new generation PET/CT.MethodsThe 3D Hoffman phantom that simulates ¹⁸F-fluorodeoxyglucose (FDG) distribution was imaged in a Siemens Biograph mCT TrueV PET/CT with Time of Flight (TOF) and Point Spread Function (PSF) modelling. Contrast-to-Noise Ratio (CNR), contrast and noise were studied for different reconstruction models: OSEM, OSEM + TOF, OSEM + PSF and OSEM + PSF + TOF.The 2D multi-compartment Hoffman phantom was filled to simulate 4 different tracers' spatial distribution: FDG, ¹¹C-flumazenil (FMZ), ¹¹C-Methionine (MET) and 6-¹⁸F-fluoro-l-dopa (FDOPA). The best algorithm for each tracer was selected by visual inspection. The maximization of CNR determined the optimal parameters for each reconstruction.ResultsIn the 3D Hoffman phantom, both noise and contrast increased with increasing number of iterations and decreased with increasing FWHM. OSEM + PSF + TOF reconstruction was generally superior to other reconstruction models. Visual analysis of the 2D Hoffman brain phantom suggested that OSEM + PSF + TOF is the optimum algorithm for tracers with focal uptake, such as MET or FDOPA, and OSEM + TOF for tracers with diffuse cortical uptake (i.e. FDG and FMZ). Optimization of CNR demonstrated that OSEM + TOF reconstruction must be performed with 2 iterations and a filter FWHM of 3 mm, and OSEM + PSF + TOF reconstruction with 4 iterations and 1 mm FWHM filter.ConclusionsOptimization of reconstruction algorithm and parameters has been performed to take particular advantage of the last generation PET scanner, recommending specific settings for different brain PET radiotracers.     

Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control

This protocol outlines a procedure for collecting and analyzing point spread functions (PSFs). It describes how to prepare fluorescent microsphere samples, set up a confocal microscope to properly collect 3D confocal image data of the microspheres and perform PSF measurements. The analysis of the PSF is used to determine the resolution of the microscope and to identify any problems with the quality of the microscope's images. The PSF geometry is used as an indicator to identify problems with the objective lens, confocal laser scanning components and other relay optics. Identification of possible causes of PSF abnormalities and solutions to improve microscope performance are provided. The microsphere sample preparation requires 2-3 h plus an overnight drying period. The microscope setup requires 2 h (1 h for laser warm up), whereas collecting and analyzing the PSF images require an additional 2-3 h.     

基于多指标的中国淡水拟除虫菊酯水质基准

在US EPA水质基准制定指南框架基础上,利用从ECOTOX和CNKI数据库获取的3种拟除虫菊酯农药对中国淡水水生生物的急性毒性数据和生物标记物毒性数据,得出了基于多指标的中国淡水水体中溴氰菊酯、氯氰菊酯和氰戊菊酯的基准最大浓度(criteria maximum concentration,CMC)和基准连续浓度(criteria continuous concentration,CCC),分别为:7.5和0.9,110和19,21和3.5 ng·L-1。引入SOD、CAT、Ach E、MDA、G-SH、DNA/RNA含量等生物标记物指标,可以从多角度、多层次、多水平反映污染物的生态毒性效应,提出的基准值可以更加精准地预测污染物的生态风险。本研究可为水质基准推导方法的完善及拟除虫菊酯农药的水生生态风险控制提供参考。     

Derivation of radiation quality average parameters in neutron-gamma radiation fields with the high-pressure ionization chamber: theory and practice

The established radiation quality parameters in mixed neutron-gamma radiation fields may be measured by applying the initial (columnar) recombination of ions in tissue-equivalent (TE) high-pressure ionization chambers (recombination chambers). The mean quality factor can be determined to within 10-15% for mixed fields with neutrons ranging from thermal to 10 MeV, and the dose mean LET of the proton component can be determined to within 10-15% if the gamma-ray absorbed dose fraction is known. These average parameters are derived by measuring the ratio of the ionization currents collected at two high-field strengths and constant gas pressure applied to the ionization chamber. By utilizing approximate correlations between physical parameters in the neutron energy region from thermal to 10 MeV, the dose mean LET of the heavy ion component, the overall dose mean LET, and the microdosimetric parameter y0,D of the mixed field can also be derived. Experimental verification of the method is presented for various neutron-gamma radiation spectra in air and in water by comparison to theoretical calculations and results from low-pressure proportional counter measurements. Good agreement is shown. The TE high-pressure ionization chamber appears to have wide potential for use as a dose-equivalent meter in radiation protection or as a beam characterization device in radiobiology.     

Recent advances in point spread function engineering and related computational microscopy approaches: from one viewpoint

This personal hybrid review piece, written in light of my recipience of the UIPAB 2020 young investigator award, contains a mixture of my scientific biography and work so far. This paper is not intended to be a comprehensive review, but only to highlight my contributions to computation-related aspects of super-resolution microscopy, as well as their origins and future directions.     

Modelling the effect of heterogeneity of shedding on the within herd Coxiella burnetii spread and identification of key parameters by sensitivity analysis

Coxiella burnetii is the bacterium responsible for Q fever, a worldwide zoonosis. Ruminants, especially cattle, are recognized as the most important source of human infections. Although a great heterogeneity between shedder cows has been described, no previous studies have determined which features such as shedding route and duration or the quantity of bacteria shed have the strongest impact on the environmental contamination and thus on the zoonotic risk. Our objective was to identify key parameters whose variation highly influences C. burnetii spread within a dairy cattle herd, especially those related to the heterogeneity of shedding.To compare the impact of epidemiological parameters on different dynamical aspects of C. burnetii infection, we performed a sensitivity analysis on an original stochastic model describing the bacterium spread and representing the individual variability of the shedding duration, routes and intensity as well as herd demography. This sensitivity analysis consisted of a principal component analysis followed by an ANOVA. Our findings show that the most influential parameters are the probability distribution governing the levels of shedding, especially in vaginal mucus and faeces, the characteristics of the bacterium in the environment (i.e. its survival and the fraction of bacteria shed reaching the environment), and some physiological parameters related to the intermittency of shedding (transition probability from a non-shedding infected state to a shedding state) or to the transition from one type of shedder to another one (transition probability from a seronegative shedding state to a seropositive shedding state).Our study is crucial for the understanding of the dynamics of C. burnetii infection and optimization of control measures. Indeed, as control measures should impact the parameters influencing the bacterium spread most, our model can now be used to assess the effectiveness of different control strategies of Q fever within dairy cattle herds.     

The use of biotin-streptavidin systems for enhancing the parameters of immunometric analysis

The possibility of improving analytical parameters of the immunometric assay with the use of biotinylated antibodies and biotin-streptavidin complexes in comparison with the commonly known approach of direct antibody modification with 125I has been studied. Experiments have been carried out with the use of low-affinity antibodies (Kass approximately 10(9) M-1) to ferritin. The signal-to-noise ratio in the immunometric increases 2.3 times when streptavidin labeled with horse-radish peroxidase is used and 4.3 times when the preformed streptavidin + biotin-peroxidase complex is used in comparison with assay systems based on 125I-labeled antibodies. The improvement of assay parameters of immunochemical systems by means of biotin-streptavidin complexes has been found to permit the use of low-affinity antibodies as assay reagents, thus ensuring analytical parameters attaining or close to those of immunoradiometric assay systems based on high-affinity 125I-labeled antibodies (Kass approximately 10(10) M-1). As shown in this study, the following factors ensure the signal enhancement in biotin-streptoavidin systems: (a) the biotin modification of several lysin residues per IgG molecule, the optimum extent of modification being 3-4 residues per molecule; (b) mild procedure for biotinylation. In contrast to oxidative iodination, the modification of NH2 groups with biotin esters does not significantly affect their antigen-binding properties.     

The use of population parameters in the analysis of germination of lettuce seed

Probit analysis was used to determine the parameters of the germinating population of lettuce seed. Seeds were induced to germinate under different conditions and it was shown that with light induced germination the germinating populations were the same. However, when gibberellic acid (GA₃) was the inductive agent then the germinating populations were not the same being concentration dependent. – This type of analysis offers a rigorous comparison of different inductive treatments.     

Natural Mediterranean photoperiod does not affect the main parameters of boar-semen quality analysis

Photoperiod is an important factor in the modulation of male reproduction in mammals. In boars, however, it is a controversial factor. The main aim of this work is to determine the precise effect of the natural, Mediterranean photoperiod on boar-semen quality. To do this, boars were housekept in strictly controlled temperature and humidity conditions, whereas light periods were also strictly adjusted to obtain a light-cycle in the farm. The work was performed over a period of one year, thus allowing for the determination of the putative yearly oscillations of boar-semen quality. Variations of the natural Mediterranean photoperiod do not induce substantial changes in overall semen-quality parameters like the percentages of viability, morphological abnormalities and total motility, the response to the osmotic resistance test and sperm motion characteristics. Only the motile-sperm subpopulation structure was significantly (P<0.05) changed depending on the variations of the natural photoperiod. Furthermore, the boar-semen ability for storage at 15-17 degrees C in a commercial extender was not modified by photoperiod changes. Our results indicate that the natural Mediterranean photoperiod does not induce strong changes in boar-semen characteristics, probably due to boar sperm having a strong capability of adaptation to the light variations of this photoperiod.     

Determination of the parameters of self-association by direct fitting of the omega function

Nonlinear regression is used to fit the omega function vs. protein concentration curves (first described by B.K. Milthorpe, P.D. Jeffrey and L.W. Nichol, Biophys. Chem. 3 (1975) 169) obtained from sedimentation equilibrium experiments on self-associating macromolecules. Nonlinear regression allows the direct fit of these curves with discrete or indefinite self-association reaction models in order to obtain values for the equilibrium constants and second virial coefficient. The method is independent of the choice of reference concentration and avoids the original method of extrapolating an omega function curve to zero concentration and then using the extrapolated value to construct a monomer activity curve used for analysis. This extrapolation can become very difficult for mild to strong self-associations where incorrectly extrapolated values lead to systematic error in the monomer activity curves. The method is applied to results from a mild, indefinite self-association, exemplified by the self-association of human spectrin, and to computer-simulated data of weak, mild and strong, indefinite self-associations.     

Quantitative rat liver function test by galactose single point method

The purpose of this study was to investigate the galactose single point (GSP) method, a residual liver function test recently recommended by the US Food and Drug Administration, which can be a useful tool for rat liver function measurement. Rats were treated either with carbon tetrachloride (CCl(4)) alone (1 mL/kg, intraperitoneally [i.p.]) for one day or with isoniazid (INH) alone (150 mg/kg, i.p.) or (in order to ameliorate the effects of INH) with a combination of INH and bis-p-nitrophenyl phosphate (BNPP) (25 mg/kg, i.p.) for 21 days. Hepatotoxicity was assayed by plasma aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activities and scores of histological activity index-necroinflammation (HAI-NI) of the respective liver specimens. The GSP method in rats was defined by the galactose blood level after 60 min. Significant differences in GSP values were observed between controls and the CCl(4)-treated rats. After 21 days of treatment, no significant changes in AST and ALT values were observed among the control, INH and INH-BNPP groups. There were significant differences in average GSP values for controls (P < 0.001) and INH-BNPP (P < 0.001) compared with INH alone. Highly significant correlations (P < 0.001) were obtained between GSP and scores of HAI-NI for all the groups. GSP was concluded to be a more sensitive biomarker of INH-induced hepatotoxicity than AST or ALT in the rats. The GSP method has been proved to be a simple and useful tool for the quantitative determination of liver function in rats, which can possibly be extended to other animals.     

Network analysis of global influenza spread

Although vaccines pose the best means of preventing influenza infection, strain selection and optimal implementation remain difficult due to antigenic drift and a lack of understanding global spread. Detecting viral movement by sequence analysis is complicated by skewed geographic and seasonal distributions in viral isolates. We propose a probabilistic method that accounts for sampling bias through spatiotemporal clustering and modeling regional and seasonal transmission as a binomial process. Analysis of H3N2 not only confirmed East-Southeast Asia as a source of new seasonal variants, but also increased the resolution of observed transmission to a country level. H1N1 data revealed similar viral spread from the tropics. Network analysis suggested China and Hong Kong as the origins of new seasonal H3N2 strains and the United States as a region where increased vaccination would maximally disrupt global spread of the virus. These techniques provide a promising methodology for the analysis of any seasonal virus, as well as for the continued surveillance of influenza.     

The use of different statistical methods in epidemiological analysis to assess the seasonality and territorial spread of infectious diseases

To solve the problems connected with the evaluation of the seasonal and territorial distribution of infectious diseases, indications and limitations for the use of the following statistical methods have been worked out: the calculation of the monthly morbidity level, the proportion of cases of infectious diseases falling on the months of seasonal morbidity rises, the proportion of such cases appearing due to the influence of seasonal factors, the total and partial indices, the average monthly rate of increase in seasonal morbidity, the complex evaluation of seasonal morbidity, the evaluation of the nonparallelism of two curves, the determination of the mean quadratic deviations and Shannon's entropy. The algorithms based on these methods lie in the foundation of 11 computer programs, forming the software complex "Epidanalysis" and provided with the service menu permitting an epidemiologist to proceed from the task via indications and limitations to the corresponding program. The programs are intended for different types of computers (IBM PC XT, EC-1640, Robotron 1715).     

Estimating the localization spread function of static single-molecule localization microscopy images

Single-molecule localization microscopy (SMLM) permits the visualization of cellular structures an order of magnitude smaller than the diffraction limit of visible light, and an accurate, objective evaluation of the resolution of an SMLM data set is an essential aspect of the image processing and analysis pipeline. Here, we present a simple method to estimate the localization spread function (LSF) of a static SMLM data set directly from acquired localizations, exploiting the correlated dynamics of individual emitters and properties of the pair autocorrelation function evaluated in both time and space. The method is demonstrated on simulated localizations, DNA origami rulers, and cellular structures labeled by dye-conjugated antibodies, DNA-PAINT, or fluorescent fusion proteins. We show that experimentally obtained images have LSFs that are broader than expected from the localization precision alone, due to additional uncertainty accrued when localizing molecules imaged over time.     

Derivation of biological structure and function: A general theory

A general theory (conceptual basis and formalism) has been developed representing evolution as a random walk in a multidimensional representation space. The biological structures correspond to states in that space, and they are defined in terms of discrete quantized parameters characterizing biomolecular specificity, interactions, barriers to the interactions, and transports through these barriers. The random walk in the representation space is subject to constraints by laws of physics, relative efficiency considerations, and the occupation of certain other states. The walk proceeds from every occupied state to every available state in proportion to their relative probability, evolutionary accessibility as measured in time required. This theory is subsequently applied to analyze nucleic acid molecules and the available barriers to regulate their information processing. This leads to a general conceptual framework for the evolution and theoretical derivation of cell structure, function, regulation, complementarity of cell and virus replicating processes, mechanism of cell differentiations, and loss of cell growth control that leads to carcinogenesis. This theoretical approach is general, it is applicable to all structure and function that arises through evolutionary process.