High-resolution three-dimensional-pQCT images can be an adequate basis for in-vivo microFE analysis of bone

Micro-finite element (microFE) models based on high-resolution images have enabled the calculation of elastic properties of trabecular bone in vitro. Recently, techniques have been developed to image trabecular bone structure in vivo, albeit at a lesser resolution. The present work studies the usefulness of such in-vivo images for microFE analyses, by comparing their microFE results to those of models based on high-resolution micro-CT (microCT) images. Fifteen specimens obtained from human femoral heads were imaged first with a 3D-pQCT scanner at 165 microns resolution and a second time with a microCT scanner at 56 microns resolution. A third set of images with a resolution of 165 microns was created by downscaling the microCT measurements. The microFE models were created directly from these images. Orthotropic elastic properties and the average tissue von Mises stress of the specimens were calculated from six FE-analyses per specimen. The results of the 165 microns models were compared to those of the 56 microns model, which was taken as the reference model. The results calculated from the pQCT-based models, correlated excellent with those calculated from the reference model for both moduli (R2 > 0.95) and for the average tissue von Mises stress (R2 > 0.83). Results calculated from the downscaled micro-CT models correlated even better with those of the reference models (R2 > 0.99 for the moduli and R2 > 0.96 for the average von Mises stress). In the case of the 3D-pQCT based models, however, the slopes of the regression lines were less than one and had to be corrected. The prediction of the Poisson's ratios was less accurate (R2 > 0.45 and R2 > 0.67) for the models based on 3D-pQCT and downscaled microCT images respectively). The fact that the results from the downscaled and original microCT images were nearly identical indicates that the need for a correction in the case of the 3D-pQCT measurements was not due to the voxel size of the images but due to a higher noise level and a lower contrast in these images, in combination with the application of a filtering procedure at 165 micron images. In summary: the results of microFE models based on in-vivo images of the 3D-pQCT can closely resemble those obtained from microFE models based on higher resolution microCT system.     

Estimation of carcass composition and cut composition from computed tomography images of live growing pigs of different genotypes

The aim of the present work was (1) to study the relationship between cross-sectional computed tomography (CT) images obtained in live growing pigs of different genotypes and dissection measurements and (2) to estimate carcass composition and cut composition from CT measurements. Sixty gilts from three genotypes (Duroc×(Landrace×Large White), Pietrain×(Landrace×Large White), and Landrace×Large White) were CT scanned and slaughtered at 30 kg (n=15), 70 kg (n=15), 100 kg (n=12) or 120 kg (n=18). Carcasses were cut and the four main cuts were dissected. The distribution of density volumes on the Hounsfield scale (HU) were obtained from CT images and classified into fat (HU between −149 and −1), muscle (HU between 0 and 140) or bone (HU between 141 and 1400). Moreover, physical measurements were obtained on an image of the loin and an image of the ham. Four different regression approaches were studied to predict carcass and cut composition: linear regression, quadratic regression and allometric equations using volumes as predictors, and linear regression using volumes and physical measurements as predictors. Results show that measurements from whole animal taken in vivo with CT allow accurate estimation of carcass and cut composition. The prediction accuracy varied across genotypes, BW and variable to be predicted. In general, linear models, allometric models and linear models, which included also physical measurements at the loin and the ham, produced the lowest prediction errors.     

Respiratory motion of adrenal gland metastases: Analyses using four-dimensional computed tomography images

PurposeTo evaluate the respiratory motion of adrenal gland metastases in three-dimensional directions using four-dimensional computed tomography (4DCT) images.MethodsFrom January 2013 to May 2016, 12 patients with adrenal gland metastases were included in this study. They all underwent 4DCT scans to assess respiratory motion of adrenal gland metastases in free breathing state. The 4DCT images were sorted into 10 image series according to the respiratory phase from the end inspiration to the end expiration, and then transferred to FocalSim workstation. All gross tumor volumes (GTVs) of adrenal gland metastases were drawn by a single physician and confirmed by a second. Relative coordinates of adrenal gland metastases were automatically generated to calculate adrenal gland metastases motion in different axial directions.ResultsThe average respiratory motion of adrenal gland metastases in left-right (LR), cranial-caudal (CC), anterior-posterior (AP), 3-dimensional (3D) vector directions was 3.4 ± 2.2 mm, 9.5 ± 5.5 mm, 3.8 ± 2.0 mm and 11.3 ± 5.3 mm, respectively. The ratios were 58.6% ± 11.4% and 63.2% ± 12.5% when the volumes of GTV_In0% and GTV _In100% were compared with volume of IGTV_10phase. The volume ratio of IGTV_10phase to GTV_3D was 1.73 ± 0.48.ConclusionsAdrenal gland metastasis is a respiration-induced moving target, and an internal target volume boundary should be provided when designing the treatment plan. The CC motion of adrenal gland metastasis is predominant and >5 mm, thus motion management strategies are recommended for patients undergoing external radiotherapy for adrenal gland metastasis.     

Critical power can be estimated from nonexhaustive tests based on rating of perceived exertion responses

The purpose of this study was to evaluate a novel procedure, based on the perceived exertion threshold (PET) concept, involving non-exhaustive tests (PET14-17) to estimate critical power (CP), as well as to examine the reproducibility of these indices. Twenty young men performed 2 trials (Trial 1 and Trial 2) of 4 exhaustive predictive tests to estimate CP, PET, and PET14-17. The slope coefficients of the regression lines corresponding to the ratings of perceived exertion (RPE) versus time relationship (y axis) obtained during the predictive tests were plotted against the power outputs (x axis) to estimate PET. PET was calculated as the intersection point of the regression line in the power axis. The 14-17 RPE range of each predictive test was modeled using the same mathematical procedures used to estimate PET14-17. CP was derived from the power-time hyperbolic equation. Analysis of variance revealed no significant differences among CP (189-194 W), PET (190-191 W) and PET14-17, (191-195 W). The correlations between CP and PET (r = 0.87), CP and PET14-17 (r = 0.89), and PET and PET14-17 (r = 0.88) were all strong. Additionally, the bias +/- limits of agreement when plotting CP and PET was -2.16 +/- 31.60 W, and -5.70 +/- 31.21 W when comparing CP and PET14-17. Relatively high reproducibility levels of CP (ICC = 0.96), PET (ICC = 0.85) and PET14-17 (ICC = 0.83) were recorded in the test-retest fashion. It can be concluded that the PET14-17 can be utilized with relatively high accuracy and reproducibility to estimate CP without causing exhaustion in the subjects.     

The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment

The optimal gapped local alignment score of two random sequences follows a Gumbel distribution. The Gumbel distribution has two parameters, the scale parameter λ and the pre-factor k. Presently, the basic local alignment search tool (BLAST) programs (BLASTP (BLAST for proteins), PSI-BLAST, etc.) use all time-consuming computer simulations to determine the Gumbel parameters. Because the simulations must be done offline, BLAST users are restricted in their choice of alignment scoring schemes. The ultimate aim of this paper is to speed the simulations, to determine the Gumbel parameters online, and to remove the corresponding restrictions on BLAST users. Simulations for the scale parameter λ can be as much as five times faster, if they use global instead of local alignment [R. Bundschuh (2002) J. Comput. Biol., 9, 243–260]. Unfortunately, the acceleration does not extend in determining the Gumbel pre-factor k, because k has no known mathematical relationship to global alignment. This paper relates k to global alignment and exploits the relationship to show that for the BLASTP defaults, 10000 realizations with sequences of average length 140 suffice to estimate both Gumbel parameters λ and k within the errors required (λ, 0.8%; k, 10%). For the BLASTP defaults, simulations for both Gumbel parameters now take less than 30 s on a 2.8 GHz Pentium 4 processor.     

Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images

Aims

A commonly accepted challenge when visualising plant roots in X-ray micro Computed Tomography (μCT) images is the similar X-ray attenuation of plant roots and soil phases. Soil moisture content remains a recognised, yet currently uncharacterised source of segmentation error. This work sought to quantify the effect of soil moisture content on the ability to segment roots from soil in μCT images.

Methods

Rice (Oryza sativa) plants grown in contrasting soils (loamy sand and clay loam) were μCT scanned daily for nine days whilst drying from saturation. Root volumes were segmented from μCT images and compared with volumes derived by root washing.

Results

At saturation the overlapping attenuation values of root material, water-filled soil pores and soil organic matter significantly hindered segmentation. However, in dry soil (ca. six days of drying post-saturation) the air-filled pores increased image noise adjacent to roots and impeded accurate visualisation of root material. The root volume was most accurately segmented at field capacity.

Conclusions

Root volumes can be accurately segmented from μCT images of undisturbed soil without compromising the growth requirements of the plant providing soil moisture content is kept at field capacity. We propose all future studies in this area should consider the error associated with scanning at different soil moisture contents.     

Ages of giant panda can be accurately predicted using facial images and machine learning

To forecast giant panda (Ailuropoda melanoleuca) population dynamics in the wild, it is crucial to comprehend their age distribution. Traditional methods for estimating the age of panda are costly, time-consuming, and inaccurate. Additionally, these methods only forecast an age group rather than a real age, and lack a uniform standard. However, advances in deep learning and computer vision have given rise to fresh approaches to this problem. Classification models can be improved by using ordinal regression, which uses ordinal correlations across ages to reduce the non-stationary nature of aging tasks. In this study, we collected 8002 images from 272 pandas in various environments, whose ages ranged from 0 to 38. We applied a five-fold subject-exclusive (SE) protocol to train seven Convolutional Neural Networks (CNN) based on ordinal regression. Experiments were conducted on the Panda Age Dataset (PAD Full) and the Lite Panda Age Dataset (PAD Lite). The results were very encouraging and achieved a Mean Absolute Error (MAE) of 2.51 and 2.41, respectively. Our findings demonstrate that this new tool can noninvasively predict the age of giant pandas in captivity and the wild. Continued development of computer vision technology will drive progress in ecology and conservation.     

Insect cell density in bioreactor cultures can be estimated from on-line measurements of optical density

Total cell density in growing insect cell suspension cultures was accurately estimated from both off-line and on-line measurements of optical density (OD). The latter measurements were done with an in-situ autoclavable OD sensor. The ability to continuously monitor cell density in insect cell cultures may be useful for the development of a large-scale process for recombinant protein production using baculovirus expression vectors.     

The regulatory C proteins from different restriction-modification systems can cross-complement.

The BamHI restriction-modification system contains a third gene, bamHIC, which positively regulates bamHIR. Similar small genes from other systems were tested in vivo for their ability to cross-complement. C.BamHI protein was identified, purified, and used to raise polyclonal antibodies. Attempts to detect other C proteins in cell extracts by cross-reactivity with C.BamHI antibodies proved unsuccessful.     

The potency of acyclovir can be markedly different in different cell types

Acyclovir is an acyclic guanine analog with a considerable activity against herpes simplex viruses. We studied the antiherpetic activity of acyclovir in macrophages and fibroblast cell lines. Utilising a plaque reduction assay we found that acyclovir potently inhibited the HSV-1 replication in macrophages (EC50) = 0.0025 microM) compared to Vero (EC50 = 8.5 microM) and MRC-5 (EC50 = 3.3 microM) cells. The cytotoxicity of acyclovir was not detected at concentrations < or = 20 microM, thus the selective index in macrophages was >8000. This marked difference in antiherpetic activity between macrophages and fibroblasts was not observed with Foscarnet and PMEA. We suggest that this potent antiviral effect of acyclovir is mainly due to a proficient phosphorylation of the drug and/or a favourable dGTP/acyclovir triphosphate ratio in macrophage cells.     

Evaluation of four-dimensional cone beam computed tomography ventilation images acquired with two different linear accelerators at various gantry speeds using a deformable lung phantom

We evaluated four-dimensional cone beam computed tomography (4D-CBCT) ventilation images (VI_CBCT) acquired with two different linear accelerator systems at various gantry speeds using a deformable lung phantom.The 4D-CT and 4D-CBCT scans were performed using a computed tomography (CT) scanner, an X-ray volume imaging system (Elekta XVI) mounted in Versa HD, and an On-Board Imager (OBI) system mounted in TrueBeam. Intensity-based deformable image registration (DIR) was performed between peak-exhale and peak-inhale images. VI_CBCT- and 4D-CT-based ventilation images (VI_CT) were derived by DIR using two metrics: one based on the Jacobian determinant and one on changes in the Hounsfield unit (HU). Three different DIR regularization values (λ) were used for VI_CBCT. Correlations between the VI_CBCT and VI_CT values were evaluated using voxel-wise Spearman’s rank correlation coefficient (r).In case of both metrics, the Jacobian-based VI_CBCT with a gantry speed of 0.6 deg/sec in Versa HD showed the highest correlation for all the gantry speeds (e.g., λ = 0.05 and r = 0.68). Thus, the r value of the Jacobian-based VI_CBCT was greater or equal to that of the HU-based VI_CBCT. In addition, the ventilation accuracy of VI_CBCT increased at low gantry speeds.Thus, the image quality of VI_CBCT was affected by the change in gantry speed in both the imaging systems. Additionally, DIR regularization considerably influenced VI_CBCT in both the imaging systems. Our results have the potential to assist in designing CBCT protocols, incorporating VI_CBCT imaging into the functional avoidance planning process.     

Viral glycoproteins at different stages of intracellular transport can be distinguished using monoclonal antibodies

Monoclonal antibodies were raised against Semliki Forest virus (SFV) and all were found to recognize the E2 spike glycoprotein. The hybridomas were screened by immunofluorescence microscopy of infected cells to look for antibodies recognizing E2 at different stages of intracellular transport and two (9AB4 and 9AD6) were chosen for further study. Immunocytochemical studies at the light and electron microscopic levels were used to show that 9AB4 recognized E2 at all stages of its transport from the rough endoplasmic reticulum (ER), where it was synthesized, to the cell surface via the smooth ER and Golgi complex. In contrast, 9AD6 only recognized E2 once it had left the ER and entered the stacks of flattened Golgi cisternae. Binding of 9AD6 to E2 did not appear to be the result of the changes in oligosaccharide structure that occur in the Golgi complex and the precise modification detected by 9AD6 remains to be elucidated. A later modification, the cleavage of precursor E2 (p62) to give mature E2, was used to show that 9AD6 bound the latter more tightly than the former, whereas 9AB4 bound both with equal affinity. These results show that monoclonal antibodies might be useful when searching for new modifications to proteins undergoing intracellular transport.     

Comparative evaluation of scapular and humeral coordinate systems based on biomedical images of the glenohumeral joint

Bio-imaging techniques represent a powerful tool for shoulder joint biomechanical analysis. However, the restricted field of view may prevent the acquisition of complete scapula and humerus bone models and hence limiting the applicability of standardized anatomical coordinate system (ACS) definitions. The aim of this study was to propose ACS definitions for both scapula and humerus which can be implemented when limited portions of the relevant bones are available. Magnetic resonance (MR) images of twenty right humeri and scapulae were acquired. The proposed ACSs were assessed in terms of (1) sensitivity to bone morphological variation, (2) intra – and inter – operator repeatability and (3) consistency with the anatomical cardinal directions. A comparison with alternative ACS definitions was also performed. Overall, our ACS scapular proposal and that presented in Kedgley and Dunning (2010) were found to be the least sensitive to the morphometric variability (mean angular absolute deviation lower than 8.3 deg) and they were characterized by a high intra – and inter – operator repeatability (mean angular absolute deviation lower than 1.5 deg). The humeral ACS proposal showed a morphometric variability similar to Amadi et al. (2009b) (mean angular absolute deviation lower than 8.3 deg) but a higher reproducibility. The scapular and humeral ACS mean angular deviation from the reference anatomical cardinal directions were smaller than 15 deg and 8.6 deg, respectively. The proposed scapular and humeral ACS definitions are therefore suitable to be applied when a limited portion of the glenohumeral joint is available as it may occur in standard shoulder clinical exams.     

Improvement of image quality for pancreatic cancer using deep learning-generated virtual monochromatic images: Comparison with single-energy computed tomography

PurposeTo construct a deep convolutional neural network that generates virtual monochromatic images (VMIs) from single-energy computed tomography (SECT) images for improved pancreatic cancer imaging quality.Materials and methodsFifty patients with pancreatic cancer underwent a dual-energy CT simulation and VMIs at 77 and 60 keV were reconstructed. A 2D deep densely connected convolutional neural network was modeled to learn the relationship between the VMIs at 77 (input) and 60 keV (ground-truth). Subsequently, VMIs were generated for 20 patients from SECT images using the trained deep learning model.ResultsThe contrast-to-noise ratio was significantly improved (p < 0.001) in the generated VMIs (4.1 ± 1.8) compared to the SECT images (2.8 ± 1.1). The mean overall image quality (4.1 ± 0.6) and tumor enhancement (3.6 ± 0.6) in the generated VMIs assessed on a five-point scale were significantly higher (p < 0.001) than that in the SECT images (3.2 ± 0.4 and 2.8 ± 0.4 for overall image quality and tumor enhancement, respectively).ConclusionsThe quality of the SECT image was significantly improved both objectively and subjectively using the proposed deep learning model for pancreatic tumors in radiotherapy.     

The inhibitory effect of serum on cell attachment can be prevented by cobalt-protoporphyrin IX

The rate of attachment of chick embryo fibroblasts (CEF) incubated for 1 h at pH 6 in the absence of serum, was equal to about 90% with 2% of spreading cells. The addition of 1% horse serum (HS) decreased to about 30% the rate of attached cells but increased to about 30% the proportion of spreading cells. We found that 3 microM cobalt-protoporphyrin IX (CoPP) added for 3 min before the addition of 1% HS increased both the rate of cell attachment (about 60%) and the proportion of cell spreading (about 50%).     

Transposition of target information from the magnetic resonance and computed tomography scan images to conventional X-ray stereotactic space

A technique to apply reconstructed X-ray computed tomography (CT) and magnetic resonance imaging (MRI) for target determination in stereotactic Bragg peak proton beam therapy of intracranial lesions was developed. Twenty-one benign intracranial tumors and vascular abnormalities were managed using this technique. Clinical features of these lesions, as well as targeting problems associated with the MRI and CT image interpretation, are presented.