Redesign of the GATE PET coincidence sorter

The GATE software platform, based on the Geant4 toolkit for simulating particle interactions with matter, enables simulation of, among other medical imaging and treatment systems, positron emission tomography. However, at least one publication (Moraes et al 2015 Phys. Med . 31 43–8) has reported discrepancies between the expected results and those obtained using GATE simulations, specifically with respect to the coincidence sorter which processes single events detected by the scanner to find coincidence pairs. In particular, the current software appears to overestimate the number of ‘true’ coincidence pairs when in multi-window mode, while the delayed coincidence window, used to estimate the randoms present in the prompt coincidence window, underestimates the randoms. Both effects are particularly evident at high count rates. We have investigated this discrepancy and reproduced the reported problems. We have also rewritten the relevant portion of the GATE cod...

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2cjiEP4
via IFTTT

Non-local total-variation (NLTV) minimization combined with reweighted L1-norm for compressed sensing CT reconstruction

The compressed sensing (CS) technique has been employed to reconstruct CT/CBCT images from fewer projections as it is designed to recover a sparse signal from highly under-sampled measurements. Since the CT image itself cannot be sparse, a variety of transforms were developed to make the image sufficiently sparse. The total-variation (TV) transform with local image gradient in L1-norm was adopted in most cases. This approach, however, which utilizes very local information and penalizes the weight at a constant rate regardless of different degrees of spatial gradient, may not produce qualified reconstructed images from noise-contaminated CT projection data. This work presents a new non-local operator of total-variation (NLTV) to overcome the deficits stated above by utilizing a more global search and non-uniform weight penalization in reconstruction. To further improve the reconstructed results, a reweighted L1-norm that approximates the ideal sparse signal recovery of the L0-nor...

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2bYmrU3
via IFTTT

Motion-aware temporal regularization for improved 4D cone-beam computed tomography

Four-dimensional cone-beam computed tomography (4D-CBCT) of the free-breathing thorax is a valuable tool in image-guided radiation therapy of the thorax and the upper abdomen. It allows the determination of the position of a tumor throughout the breathing cycle, while only its mean position can be extracted from three-dimensional CBCT. The classical approaches are not fully satisfactory: respiration-correlated methods allow one to accurately locate high-contrast structures in any frame, but contain strong streak artifacts unless the acquisition is significantly slowed down. Motion-compensated methods can yield streak-free, but static, reconstructions. This work proposes a 4D-CBCT method that can be seen as a trade-off between respiration-correlated and motion-compensated reconstruction. It builds upon the existing reconstruction using spatial and temporal regularization (ROOSTER) and is called motion-aware ROOSTER (MA-ROOSTER). It performs temporal regularization along curved tr...

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2cjiIOK
via IFTTT

How a young maverick’s grit saved the world’s rarest bird

Carl Jones battled with his scientific elders to save the Mauritius kestrel. His renegade success taught him that mainstream conservation needs a rethink

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2c6G90n
via IFTTT

IJMS, Vol. 17, Pages 1467: Aberrant JAK/STAT Signaling Suppresses TFF1 and TFF2 through Epigenetic Silencing of GATA6 in Gastric Cancer

Aberrant Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling is crucial to the development of gastric cancer. In this study, we examined the role of STAT3 in the expression and methylation of its targets in gastric cancer patients. Results from RNA sequencing identified an inverse correlation between the expression of STAT3 and GATA6 in 23 pairs of gastric cancer patient samples. We discovered that the expression of GATA6 is epigenetically silenced through promoter methylation in gastric cancer cell lines. Interestingly, the inhibition of STAT3 using a novel STAT3 inhibitor restored the expression of GATA6 and its targets, trefoil factors 1 and 2 (TFF1/2). Moreover, disruption of STAT3 binding to GATA6 promoter by small hairpin RNA restored GATA6 expression in AGS cells. A clinically significant correlation was also observed between the expression of GATA6 and TFF1/2 among tissue samples from 60 gastric cancer patients. Finally, bisulfite pyrosequencing revealed GATA6 methylation in 65% (39/60) of the patients, and those with higher GATA6 methylation tended to have shorter overall survival. In conclusion, we demonstrated that aberrant JAK/STAT signaling suppresses TFF1/2 partially through the epigenetic silencing of GATA6. Therapeutic intervention of STAT3 in reversing the epigenetic status of GATA6 could benefit the treatment of gastric cancer and is worthy of further investigation.

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2bZdaNb
via IFTTT

IJMS, Vol. 17, Pages 1469: Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition.

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2c6Bk76
via IFTTT

IJMS, Vol. 17, Pages 1427: MicroRNA-378 Alleviates Cerebral Ischemic Injury by Negatively Regulating Apoptosis Executioner Caspase-3

miRNAs have been linked to many human diseases, including ischemic stroke, and are being pursued as clinical diagnostics and therapeutic targets. Among the aberrantly expressed miRNAs in our previous report using large-scale microarray screening, the downregulation of miR-378 in the peri-infarct region of middle cerebral artery occluded (MCAO) mice can be reversed by hypoxic preconditioning (HPC). In this study, the role of miR-378 in the ischemic injury was further explored. We found that miR-378 levels significantly decreased in N2A cells following oxygen-glucose deprivation (OGD) treatment. Overexpression of miR-378 significantly enhanced cell viability, decreased TUNEL-positive cells and the immunoreactivity of cleaved-caspase-3. Conversely, downregulation of miR-378 aggravated OGD-induced apoptosis and ischemic injury. By using bioinformatic algorithms, we discovered that miR-378 may directly bind to the predicted 3′-untranslated region (UTR) of Caspase-3 gene. The protein level of caspase-3 increased significantly upon OGD treatment, and can be downregulated by pri-miR-378 transfection. The luciferase reporter assay confirmed the binding of miR-378 to the 3′-UTR of Caspase-3 mRNA and repressed its translation. In addition, miR-378 agomir decreased cleaved-caspase-3 ratio, reduced infarct volume and neural cell death induced by MCAO. Furthermore, caspase-3 knockdown could reverse anti-miR-378 mediated neuronal injury. Taken together, our data demonstrated that miR-378 attenuated ischemic injury by negatively regulating the apoptosis executioner, caspase-3, providing a potential therapeutic target for ischemic stroke.

from #AlexandrosSfakianakis via Alexandros G.Sfakianakis on Inoreader http://ift.tt/2bQ8Zjh
via IFTTT