Radiomics and artificial Intelligence for PET imaging analysis

In recent years, processing of the imaging signal derived from CT, MR or positron emission has proven to be able to predict outcome parameters in cancer patients. The processing techniques of the signal constitute the discipline of radiomics. The quantitative analysis of medical images outperform the information that can be obtained through traditional visual analysis. The recognition of neoplasm molecular and genetic characteristics in a non-invasive way, based on routine radiological examinations, potentially allow complete tumor profiling and subsequent treatment customization at practically zero costs. This process is further boosted with the availability of increased computing power and development of artificial intelligence approaches

SPECT-CT fusion: a new diagnostic tool for endocrinology

Wstęp: Wprowadzenie standardu DICOM do wszystkich urządzeń diagnostyki obrazowej umożliwiło fuzję obrazów tomografii emisyjnej pojedynczego fotonu (SPECT, single photon emission computed tomography), tomografii komputerowej (CT, computed tomography), magnetycznego rezonansu jądrowego (MRI, magnetic resonanse imaging) i innych typów danych obrazowania biomedycznego. Fuzję można wykonywanywać w dwojaki sposób, za pomocą dedykowanych skanerów hybrydowych lub przez oprogramowanie niezwiązane z konkretnym urządzeniem. Technologia fuzji posiada niezmierny potencjał w diagnostyce obrazowej do wykrywania licznych stanów, takich jak choroby nowotworowe, choroba Alzheimera oraz inne zaburzenia nerwowe. W ośrodku autorów ponad 2 lata temu stopniowo wprowadzono fuzję SPECT-CT w diagnostyce klinicznej wielu schorzeń endokrynologicznych oraz onkologicznych. Użyto danych obrazowych SPECT oraz CT wykonanych na oddzielnych i niezależnych urządzeniach (dwugłowicowej gamma-kamerze E.Cam-Duet firmy Siemens i szesnastorzędowym tomografie komputerowym Somatom Sensation firmy Siemens). Materiał i metody: Prosty i szybki algorytm o niskiej złożoności obliczeniowej zastosowano do wykonania fuzji kolejnych 81 przypadków. Trzydziestu dwóch pacjentów zakwalifikowano do fuzji SPECT-CT po terapeutycznym leczeniu 131I u chorych po amputacji tarczycy z powodu raka, 12 - po podaniu radioaktywnych analogów somatostatyny, 7 - po terapeutycznym podaniu 131 I MIBG, 6 - po diagnostycznym podaniu MIBG z 131I lub 123I, 3 - po scyntygrafii przytarczyc oraz 2 - po scyntygrafii kości. Najbardziej powszechnym wskazaniem do fuzji była potrzeba scharakteryzowania podejrzanych zmian wykrytych na skanach CT poprzez zachodzące w nich zmiany metaboliczne. Lokalizacja anatomiczna ognisk gromadzenia widzianych na obrazach SPECT oraz ocena efektów terapii radioizotopowej były kolejnymi najczęstszymi przyczynami wskazań. Wyniki: Obserwowane błędy nałożenia wynikały z tak zwanych czynników ludzkich: nieprecyzyjnego wyboru położenia markerów, ruchów oddechowych oraz przemieszczenia markerów między kolejnymi badaniami. Fuzję ponad 74% chorych określono jako "bardzo dobrą" lub "dobrą". Wnioski: Wybór chorych, wyszkolenie personelu (zwłaszcza techników i fizyków) oraz współpraca z radiologiem to najbardziej istotne czynniki, które umożliwiają właściwe zastosowanie oraz interpretację fuzji obrazów SPECT-CT.Introduction: The introduction of the DICOM format in all diagnostic imaging devices allowed coregistering SPECT, CT, MR and other types of biomedical imaging. Fusion can be performed by dedicated hybrid devices or by means of software. The fusion algorithm consists of two steps: coregistration and simultaneous visualization. Our center gradually implemented SPECT-CT fusion in clinical diagnostic work-up of several endocrinologic and oncologic diseases more than 2 years ago. Material and methods: An easy and fast algorithm in terms of computational complexity of image fusion was presented and applied to 81 consecutive cases. Thirty-two patients were scheduled to SPECT-CT fusion after thyroidectomy and 131I treatment for thyroid cancer, twelve after somatostatine receptor scintigraphy, seven after 131I MIBG therapy, six after diagnostic MIBG scintigraphy with 123I or 131I, three after parathyroid scintigraphy and two after bone scan. The most common indication to the fusion was the need of metabolic characterization of suspected lesions detected on CT scan. The anatomic localization of a focal uptake seen on SPECT and the evaluation of the radiometabolic therapy effect folloved. Results: A variance of error level observed was a result of human factor, decision on marker’s placement, respiratory movements and marker’s displacement between acquisitions. However, 74% of patients in our series have fusion results classified as "very good" or "good". Conclusions: The selection of patients, the training of the personel and the cooperation with radiologists are the most important factors for a correct application and interpretation of the SPECT-CT image fusion

Oxygen-enhanced MRI assessment of tumour hypoxia in head and neck cancer is feasible and well tolerated in the clinical setting

Background: Tumour hypoxia is a recognised cause of radiotherapy treatment resistance in head and neck squamous cell carcinoma (HNSCC). Current positron emission tomography-based hypoxia imaging techniques are not routinely available in many centres. We investigated if an alternative technique called oxygen-enhanced magnetic resonance imaging (OE-MRI) could be performed in HNSCC. Methods: A volumetric OE-MRI protocol for dynamic T1 relaxation time mapping was implemented on 1.5-T clinical scanners. Participants were scanned breathing room air and during high-flow oxygen administration. Oxygen-induced changes in T1 times (ΔT1) and R2* rates (ΔR2*) were measured in malignant tissue and healthy organs. Unequal variance t-test was used. Patients were surveyed on their experience of the OE-MRI protocol. Results: Fifteen patients with HNSCC (median age 59years, range 38 to 76) and 10 non-HNSCC subjects (median age 46.5years, range 32 to 62) were scanned; the OE-MRI acquisition took less than 10min and was well tolerated. Fifteen histologically confirmed primary tumours and 41 malignant nodal masses were identified. Median (range) of ΔT1 times and hypoxic fraction estimates for primary tumours were -3.5% (-7.0 to -0.3%) and 30.7% (6.5 to 78.6%) respectively. Radiotherapy-responsive and radiotherapy-resistant primary tumours had mean estimated hypoxic fractions of 36.8% (95% confidence interval [CI] 17.4 to 56.2%) and 59.0% (95% CI 44.6 to 73.3%), respectively (p = 0.111). Conclusions: We present a well-tolerated implementation of dynamic, volumetric OE-MRI of the head and neck region allowing discernment of differing oxygen responses within biopsy-confirmed HNSCC. Trial registration: ClinicalTrials.gov, NCT04724096. Registered on 26 January 2021. Relevance statement: MRI of tumour hypoxia in head and neck cancer using routine clinical equipment is feasible and well tolerated and allows estimates of tumour hypoxic fractions in less than ten minutes. Key points: • Oxygen-enhanced MRI (OE-MRI) can estimate tumour hypoxic fractions in ten-minute scanning. • OE-MRI may be incorporable into routine clinical tumour imaging. • OE-MRI has the potential to predict outcomes after radiotherapy treatment. Graphical Abstract: (Figure presented.

The stilbene and dibenzo[b,f]oxepine derivatives as anticancer compounds

In the present study, the synthesis and cytotoxic effect of six stilbenes and three oxepine derivatives against twocancerous–HeLa and U87, and two normal–EUFA30 and HEK293 cell lines has been reported. The results ofcytotoxic assay andflow cytometry analysis revealed that compounds 9-nitrobenzo[b]naphtho[1,2-f]oxepine(4), (E)-3,3′,4,4′,5,5′-hexamethoxystilbene (6) and 4-hydroxy-2′,4′-dinitrostilbene (8) were the most active andtheir interaction with tubulin (crystal structure from PDB) has been analyzed by computer molecular modeling.Molecular docking of these compounds on colchicine binding site of the tubulin indicates the interaction of (4),(6) and (8) with tubulin. The compound (4) could interact stronger with tubulin, relative to colchicine, however,with no selectivity of action against cancer and normal cells. Conversely, compounds (6) and (8) interact moreweakly with tubulin, relative to colchicine but they act more selectively towards cancerous versus normal celllines. Obtained results proved that the compounds that are the most active against cancerous cells operatethrough tubulin binding

GPU accelerated Monte Carlo scoring of positron emitting isotopes produced during proton therapy for PET verification.

Objective.Verification of delivered proton therapy treatments is essential for reaping the many benefits of the modality, with the most widely proposedin vivoverification technique being the imaging of positron emitting isotopes generated in the patient during treatment using positron emission tomography (PET). The purpose of this work is to reduce the computational resources and time required for simulation of patient activation during proton therapy using the GPU accelerated Monte Carlo code FRED, and to validate the predicted activity against the widely used Monte Carlo code GATE.Approach.We implement a continuous scoring approach for the production of positron emitting isotopes within FRED version 5.59.9. We simulate treatment plans delivered to 95 head and neck patients at Centrum Cyklotronowe Bronowice using this GPU implementation, and verify the accuracy using the Monte Carlo toolkit GATE version 9.0.Main results.We report an average reduction in computational time by a factor of 50 when using a local system with 2 GPUs as opposed to a large compute cluster utilising between 200 to 700 CPU threads, enabling simulation of patient activity within an average of 2.9 min as opposed to 146 min. All simulated plans are in good agreement across the two Monte Carlo codes. The two codes agree within a maximum of 0.95σon a voxel-by-voxel basis for the prediction of 7 different isotopes across 472 simulated fields delivered to 95 patients, with the average deviation over all fields being 6.4 × 10-3σ.Significance.The implementation of activation calculations in the GPU accelerated Monte Carlo code FRED provides fast and reliable simulation of patient activation following proton therapy, allowing for research and development of clinical applications of range verification for this treatment modality using PET to proceed at a rapid pace

Circadian Profile of Salivary Melatonin Secretion in Hypoxic Ischemic Encephalopathy

Purpose. In the present study, the salivary melatonin secretion in the hypoxic ischemic encephalopathy (HIE) children was measured. The logit model was fitted to the data to obtain the salivary dim light melatonin onsets (DLMOs), and the results were compared with the values estimated from the classic threshold method with a linear interpolation and those previously published for the blood measurements. Materials and Methods. 9 patients suffering from HIE aged from 65 to 80 months were included in the study. The melatonin levels were assessed by a radioimmunoassay (RIA). The diurnal melatonin secretion was estimated using a nonlinear least squares method. Student’s t-test and the Mann–Whitney U test were used for the comparisons of the obtained parameters. Results. The circadian profiles of the melatonin secretion for both calculation methods do not differ statistically. The DLMO parameters obtained in the blood and saliva samples in children with hypoxic is chemic encephalopathy were similar

ProTheRaMon : a GATE simulation framework for proton therapy range monitoring using PET imaging

Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user’s needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022)

TreeCmp: Comparison of Trees in Polynomial Time

When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees