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Rodríguez Outeiral R, Bos P, van der Hulst HJ, Al-Mamgani A, Jasperse B, Simões R, van der Heide UA. Strategies for tackling the class imbalance problem of oropharyngeal primary tumor segmentation on magnetic resonance imaging. Phys Imaging Radiat Oncol 2022; 23:144-149. [PMID: 36035088 PMCID: PMC9405079 DOI: 10.1016/j.phro.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 12/05/2022] Open
Abstract
Loss functions that account for class imbalance may not improve the segmentations. Our two-stage segmentation approach can outperform the 3D U-Net. A fully-automatic two-stage approach can perform comparably to a semi-automatic approach.
Background and purpose Contouring oropharyngeal primary tumors in radiotherapy is currently done manually which is time-consuming. Autocontouring techniques based on deep learning methods are a desirable alternative, but these methods can render suboptimal results when the structure to segment is considerably smaller than the rest of the image. The purpose of this work was to investigate different strategies to tackle the class imbalance problem in this tumor site. Materials and methods A cohort of 230 oropharyngeal cancer patients treated between 2010 and 2018 was retrospectively collected. The following magnetic resonance imaging (MRI) sequences were available: T1-weighted, T2-weighted, 3D T1-weighted after gadolinium injection. Two strategies to tackle the class imbalance problem were studied: training with different loss functions (namely: Dice loss, Generalized Dice loss, Focal Tversky loss and Unified Focal loss) and implementing a two-stage approach (i.e. splitting the task in detection and segmentation). Segmentation performance was measured with Sørensen–Dice coefficient (Dice), 95th Hausdorff distance (HD) and Mean Surface Distance (MSD). Results The network trained with the Generalized Dice Loss yielded a median Dice of 0.54, median 95th HD of 10.6 mm and median MSD of 2.4 mm but no significant differences were observed among the different loss functions (p-value > 0.7). The two-stage approach resulted in a median Dice of 0.64, median HD of 8.7 mm and median MSD of 2.1 mm, significantly outperforming the end-to-end 3D U-Net (p-value < 0.05). Conclusion No significant differences were observed when training with different loss functions. The two-stage approach outperformed the end-to-end 3D U-Net.
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Simões R, Jayaprakash KT. OncoFlash - Research Updates in a Flash! (June 2022). Clin Oncol (R Coll Radiol) 2022; 34:351-352. [PMID: 35512928 DOI: 10.1016/j.clon.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Loggetto S, Veríssimo M, Darrigo-Junior L, Simões R, Bernardo W, Braga J. Guidelines on sickle cell disease: secondary stroke prevention in children and adolescents. Associação Brasileira de Hematologia, Hemoterapia e Terapia Celular guidelines project: Associação Médica Brasileira - 2022. Hematol Transfus Cell Ther 2022; 44:246-255. [PMID: 35305940 PMCID: PMC9123578 DOI: 10.1016/j.htct.2022.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 11/02/2022] Open
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Simões R, Miranda I, Pereira H. Cutin extraction and composition determined under differing depolymerisation conditions in cork oak leaves. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:127-135. [PMID: 34155712 DOI: 10.1002/pca.3075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Cutin is a biopolyester involved in waterproofing aerial plant organs, including leaves. Cutin quantification and compositional profiling require depolymerisation, namely by methanolysis, but specific protocols are not available. OBJECTIVES Investigate how different methanolysis conditions regarding catalyst concentration effect cutin depolymerisation and monomer release, to better define protocols for cutin content determination and composition profiling. MATERIAL AND METHODS Cork oak (Quercus suber) dewaxed leaves were reacted with five sodium methoxide (NaOMe) concentrations. Extracts were analysed: glycerol by high-performance liquid chromatography (HPLC) and long-chain lipids by gas chromatography-mass spectrometry (GC-MS). RESULTS Cutin was completely removed by 3% NaOMe (8.4% of dewaxed leaves), while mild 0.1% and 0.01% NaOMe methanolysis only depolymerised 14% of total cutin. Reactivity of cutin ester bonds is not homogeneous and glyceridic ester bonds are more easily cleaved, releasing the existing glycerol already under the mildest conditions (0.53% with 0.01% NaOMe and 0.41% with 3% NaOMe). The composition of cutin extracts varies with depolymerisation extent, with easier release of alkanoic acids and alkanols, respectively, 34.9% and 8.8% of total monomers at 0.1% NaOMe, while ω-hydroxyacids (49.3% of total monomers) and α,ω-diacids (9.0% of the monomers) are solubilised under more intensive reactive conditions. CONCLUSION Cutin of Quercus suber leaves is confirmed as a glyceridic polyester of ω-hydroxyacids and alkanoic acids, with minor content of α,ω-diacids, and including coumarate moieties. The protocol for the determination of cutin content and compositional profiling was established regarding catalyst concentration. The molar composition of cutin suggests a macromolecular assembly based on glycerol linked to lipid oligomeric chains with moderate cross-linking.
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Taghavi M, Staal FCR, Simões R, Hong EK, Lambregts DMJ, van der Heide UA, Beets-Tan RGH, Maas M. CT radiomics models are unable to predict new liver metastasis after successful thermal ablation of colorectal liver metastases. Acta Radiol 2021; 64:5-12. [PMID: 34918955 DOI: 10.1177/02841851211060437] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Patients with colorectal liver metastases (CRLM) who undergo thermal ablation are at risk of developing new CRLM after ablation. Identification of these patients might enable individualized treatment. PURPOSE To investigate whether an existing machine-learning model with radiomics features based on pre-ablation computed tomography (CT) images of patients with colorectal cancer can predict development of new CRLM. MATERIAL AND METHODS In total, 94 patients with CRLM who were treated with thermal ablation were analyzed. Radiomics features were extracted from the healthy liver parenchyma of CT images in the portal venous phase, before thermal ablation. First, a previously developed radiomics model (Original model) was applied to the entire cohort to predict new CRLM after 6 and 24 months of follow-up. Next, new machine-learning models were developed (Radiomics, Clinical, and Combined), based on radiomics features, clinical features, or a combination of both. RESULTS The external validation of the Original model reached an area under the curve (AUC) of 0.57 (95% confidence interval [CI]=0.56-0.58) and 0.52 (95% CI=0.51-0.53) for 6 and 24 months of follow-up. The new predictive radiomics models yielded a higher performance at 6 months compared to 24 months. For the prediction of CRLM at 6 months, the Combined model had slightly better performance (AUC=0.60; 95% CI=0.59-0.61) compared to the Radiomics and Clinical models (AUC=0.55-0.57), while all three models had a low performance for the prediction at 24 months (AUC=0.52-0.53). CONCLUSION Both the Original and newly developed radiomics models were unable to predict new CLRM based on healthy liver parenchyma in patients who will undergo ablation for CRLM.
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Salazar SB, Valez N, Sotti-Novais D, Simões R, Souza JA, Faustino MJ, Mendonça C, Lopes MM, Rodrigues V, Mira NP. Unveiling azole resistance mechanisms in Candida glabrata clinical isolates encoding wild-type or gain-of-function CgPdr1 alleles. Access Microbiol 2021. [DOI: 10.1099/acmi.cc2021.po0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The relevance of C. glabrata as a human pathogen is linked with its poor susceptibility to azoles as well as its extreme genomic plasticity that allows the rapid acquisition of resistance. Extensive characterization of azole-resistant C. glabrata strains unveiled the central role of the transcriptional regulator CgPdr1 in the resistance phenotype, with many strains encoding hyperactive (or gain-of-function; GOF) CgPdr1 alleles. Large scale profiling of a collection of clinical C. glabrata isolates recovered in hospitals of the Lisbon area, in Portugal, led to the identification of 11 strains exhibiting resistance to fluconazole and voriconazole, while 2 were only resistant to fluconazole. Among these strains, 10 were found to encode alleles of the CgPDR1 gene harbouring multiple non-synonymous SNPs that were not found in the alleles encoded by susceptible strains, including K274Q, I392M and I803T not previously described as GOF mutations. The isolates encoding these alleles were found to over-express several CgPdr1 target genes including the azole efflux pump CgCDR1 sustaining the idea that these represent new gain-of-function CgPdr1 alleles. Only one of the identified azole-resistant strains was found to encode a CgPDR1 allele fully identical to the one encoded by susceptible strains. To better understand the resistance phenotype of this strain, its transcriptome was compared with the one of a susceptible strain and of strains encoding CgPdr1 GOF alleles. The results of this comparative transcriptomic analysis will be discussed shedding light into the different azole-resistance mechanisms evolved by C. glabrata, including those independent of CgPdr1 GOF strains.
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Gonçalves A, Oliveira J, Simões R, Canas N, Vale J. Hemiparkinsonism Secondary to Giant Aneurysm. Neurology 2021; 98:325-326. [PMID: 34873016 DOI: 10.1212/wnl.0000000000013150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Forster M, Mendes R, Guerrero Urbano T, Evans M, Lei M, Spanswick V, Miles E, Simões R, Wheeler G, Forsyth S, White L. 866P ORCA-2: A phase I study of olaparib in addition to cisplatin-based concurrent chemoradiotherapy for patients with high risk locally advanced (LA) squamous cell carcinoma of the head and neck (HNSCC). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Gonzalez P, Mans A, Schaake E, Nowee M, van der Heide U, Simões R. PD-0927 MRI-based deep learning auto-contouring for organs-at-risk in gynecological brachytherapy. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07206-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Nowee ME, van Pelt VWJ, Walraven I, Simões R, Liskamp CP, Lambregts DMJ, Heijmink S, Schaake E, van der Heide UA, Janssen TM. The impact of image acquisition time on registration, delineation and image quality for magnetic resonance guided radiotherapy of prostate cancer patients. PHYSICS & IMAGING IN RADIATION ONCOLOGY 2021; 19:85-89. [PMID: 34355071 PMCID: PMC8325094 DOI: 10.1016/j.phro.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/03/2021] [Accepted: 07/01/2021] [Indexed: 12/22/2022]
Abstract
Background and Purpose Magnetic resonance (MR) guided radiotherapy utilizes MR images for (online) plan adaptation and image guidance. The aim of this study was to investigate the impact of variation in MR acquisition time and scan resolution on image quality, interobserver variation in contouring and interobserver variation in registration. Materials and Methods Nine patients with prostate cancer were included. Four T2-weighted 3D turbo spin echo (T2w 3D TSE) sequences were acquired with different acquisition times and resolutions. Two radiologists assessed image quality, conspicuity of the capsule, peripheral zone and central gland architecture and motion artefacts on a 5 point scale. Images were delineated by two radiation oncologists and interobserver variation was assessed by the 95% Hausdorff distance. Seven observers registered the MR images on the planning CT. Registrations were compared on systematic offset and interobserver variation. Results Acquisition times ranged between 1.3 and 6.3 min. Overall image quality and capsule definition were significantly worse for the MR sequence with an acquisition time of 1.3 min compared to the other sequences. Median 95% Hausdorff distance showed no significant differences in interobserver variation of contouring. Systematic offset and interobserver variation in registration were small (<1 mm) and of no clinical significance. Conclusions Our results can be used to effectively shorten overall fraction time for online adaptive MR guided radiotherapy by optimising the imaging sequence used for registration. From the sequences studied, a sequence of 3.1 min with anisotropic voxels of 1.2 × 1.2 × 2.4 mm3 provided the shortest acquisition time without compromising image quality.
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Rodríguez Outeiral R, Bos P, Al-Mamgani A, Jasperse B, Simões R, van der Heide UA. Oropharyngeal primary tumor segmentation for radiotherapy planning on magnetic resonance imaging using deep learning. PHYSICS & IMAGING IN RADIATION ONCOLOGY 2021; 19:39-44. [PMID: 34307917 PMCID: PMC8295848 DOI: 10.1016/j.phro.2021.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/31/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022]
Abstract
Reducing the context around the tumor results in better segmentations with CNNs. Combining multiple MRI sequences as input can be beneficial to segmentation networks. A semi-automatic approach is fast and can potentially improve the accuracy of segmentations.
Background and purpose Segmentation of oropharyngeal squamous cell carcinoma (OPSCC) is needed for radiotherapy planning. We aimed to segment the primary tumor for OPSCC on MRI using convolutional neural networks (CNNs). We investigated the effect of multiple MRI sequences as input and we proposed a semi-automatic approach for tumor segmentation that is expected to save time in the clinic. Materials and methods We included 171 OPSCC patients retrospectively from 2010 until 2015. For all patients the following MRI sequences were available: T1-weighted, T2-weighted and 3D T1-weighted after gadolinium injection. We trained a 3D UNet using the entire images and images with reduced context, considering only information within clipboxes around the tumor. We compared the performance using different combinations of MRI sequences as input. Finally, a semi-automatic approach by two human observers defining clipboxes around the tumor was tested. Segmentation performance was measured with Sørensen–Dice coefficient (Dice), 95th Hausdorff distance (HD) and Mean Surface Distance (MSD). Results The 3D UNet trained with full context and all sequences as input yielded a median Dice of 0.55, HD of 8.7 mm and MSD of 2.7 mm. Combining all MRI sequences was better than using single sequences. The semi-automatic approach with all sequences as input yielded significantly better performance (p < 0.001): a median Dice of 0.74, HD of 4.6 mm and MSD of 1.2 mm. Conclusion Reducing the amount of context around the tumor and combining multiple MRI sequences improved the segmentation performance. A semi-automatic approach was accurate and clinically feasible.
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Severiano E Sousa C, Fabbri M, Godinho C, Simões R, Chendo I, Coelho M, Martins IP, Ferreira JJ. Clinical Diagnostic Criteria Have a High Impact on the Frequency of Dementia in Late-Stage Parkinson's Disease. Front Neurol 2021; 12:652424. [PMID: 34093399 PMCID: PMC8172803 DOI: 10.3389/fneur.2021.652424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Cognitive impairment is a potential late feature of Parkinson's disease (PD). However, studies in patients with late-stage PD are lacking due to the particular characteristics of this population. Objectives: To evaluate the frequency of dementia in late-stage PD patients and to assess the impact of using different diagnostic criteria. Methods: We conducted a cross-sectional study to estimate the frequency of dementia in late-stage PD patients using the International Parkinson and Movement Disorders Society (MDS) (Level II) clinical diagnostic criteria as the primary outcome. We also applied other diagnostic criteria [MDS (Level I), DSM-IV, and DSM-5 criteria] to determine their applicability and impact on dementia frequency. Results: 93 participants with a mean age of 75.8 years (SD 6.8) and 16.5 years (SD 7.5) of disease duration were included. 64.3% were classified as demented using the International Parkinson and Movement Disorders Society (MDS) (Level II) clinical diagnostic criteria. We observed a high discrepancy on the frequency of dementia depending on the criteria applied [6.2% with MDS (Level I), 58.8% with DSM-IV, and 72.0% with DSM-5 criteria]. Conclusions: We found a frequency of dementia below what was observed in similar populations. The particular characteristics of our sample may have contributed as protective factors for late-stage dementia. Dementia frequency varied depending on the criteria used mainly due to the presence of major depression.
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Papaconstadopoulos P, González P, Carbaat C, Simões R, Beemster H, Koetsveld F, Remeijer P, Janssen T. An anomaly detector as a clinical decision support system for parotid gland delineations. Phys Med Biol 2021; 66. [PMID: 33906177 DOI: 10.1088/1361-6560/abfbf5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/27/2021] [Indexed: 11/11/2022]
Abstract
Purpose. Auto-contouring (AC) is rapidly becoming standard practice for OAR contouring. However, in clinical practice, clinicians still need to manually check and correct contours. Anomaly detection systems (ADS) can aid the clinical decision process by suggesting which structures require corrections or not, greatly enhancing the value of AC. The purpose of this work is to develop and evaluate a decision support system for detecting anomalies in the case of parotid gland delineations. METHODS Head and neck parotid gland delineations (1037 right, 1038 left), were retrieved from the Netherlands Cancer Institute (NKI) database. Morphological and image-based features were extracted from each patient's CT and structure set. An isolation forest model was initially trained on 70% of the data, of which 10% had synthetically generated anomalies and validated on the remaining 30% of clinical data. The ADS was tested on an independent set of 250 patients (Normal: 174, Anomalies: 76) and on a clinical autocontouring software. RESULTS Applied to the validation set, the ADS system resulted in area under the curve (AUC) values of 0.93 and 0.94 for the parotid left and right respectively. Image features appeared more important than morphological, but using all features resulted marginally in the best model. Applied to the test set the ADS system reached an accuracy level of 0.83 and 0.81 for the parotid left and right respectively. The ADS was particularly sensitive to uniform expansions/contractions, misplacements, extra/missing slices and anisotropic over-contouring. CONCLUSION Anomaly detection can serve as a powerful contour quality assurance tool, especially for cases of organ misplacement and over-contouring.
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Simões R, Pimentel C, Ferreira-Dias S, Miranda I, Pereira H. Phytochemical characterization of phloem in maritime pine and stone pine in three sites in Portugal. Heliyon 2021; 7:e06718. [PMID: 33898836 PMCID: PMC8055561 DOI: 10.1016/j.heliyon.2021.e06718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
This study analyzes the content and chemical profile of extractives present in the young phloem of mature trees of maritime pine (Pinus pinaster) and stone pine (P. pinea) in three sites in Portugal located in different climatic environments. The cross-sites average of extractives was similar in both pines with 38.5% in P. pinea and 37.7% in P. pinaster phloem. The hydrophilic fraction represented 82% and 70% of P. pinea and P. pinaster total extractives respectively, with large contents of phenolic compounds, flavonoids and tannins, and showed very high oxygen scavenging and reducing ability. Lipophilic extractives were present in higher proportion in P. pinaster phloem than in P. pinea phloem, and showed a large content of resin acids, with the predominance of abietic acid in P. pinaster, and dehydroabietic acid in P. pinea phloems, and of alkanoic acids. P. pinaster and P. pinea have specific defences related to phloem production of resin and phenolic compounds with the ratio phenolic-to-oleoresin compounds higher for P. pinea (4.7 vs 2.3 for P. pinaster) and constant in the three sites. The phytochemical content and composition of the young phloem of P. pinaster and P. pinea showed site differences highlighting the relationship between environment and metabolic production.
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van Pelt V, Gerrets S, Simões R, Elkhuizen P, Janssen T. Evaluation of delineating the target volume by radiation therapists in breast cancer patients. Tech Innov Patient Support Radiat Oncol 2021; 17:78-81. [PMID: 34007911 PMCID: PMC8110937 DOI: 10.1016/j.tipsro.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/12/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
Aim Breast radiotherapy accounts for a significant workload in radiotherapy departments. In 2015 it became clinical practice at the Netherlands Cancer Institute for radiation therapists (RTTs) to delineate the clinical target volume of the breast tissue (CTVbreast) and in 2017 axilla level I-II (CTVln12) according to a delineation atlas. All RTTs were trained and got individual feedback. The aim of this retrospective study was to investigate the variation between the CTVbreast with or without CTVln12 delineated by a trained group of radiation therapists and the clinical adjusted delineations by the radiation oncologist/physician assistant (RO/PA), in a large group of patients treated between January 2017 and June 2020. Materials and Methods 1012 computer tomography based delineations of CTVbreast and 146 of CTVln12 were collected from January 2017-June 2020. The RTT and RO/PA delineations were compared using the Dice coefficient and the 95th percentile Hausdorff Distance (95%HD). Statistical significance of the differences was tested using a Mann-Whitney test. Results Differences in CTVbreast delineations were small. A median Dice score of 1.00 for all years, where 83% of the patients had a Dice score > 0.99. For CTVln12 the magnitude of edits made by RO/PAs decreased over time, with the Dice increasing from a median of 0.87 in 2017 to 0.90 in 2020 (p = 0.031). The 95%HD decreased from a median of 0.93 cm in 2017 to 0.61 cm in 2020 (p = 0.051). Conclusions This retrospective study shows that trained dedicated RTTs are capable in delivering the same quality delineations as RO/PAs. The low variability supports the increasing role of RTTs in the contouring process, likely making it more time efficient.
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Taghavi M, Trebeschi S, Simões R, Meek DB, Beckers RCJ, Lambregts DMJ, Verhoef C, Houwers JB, van der Heide UA, Beets-Tan RGH, Maas M. Machine learning-based analysis of CT radiomics model for prediction of colorectal metachronous liver metastases. Abdom Radiol (NY) 2021; 46:249-256. [PMID: 32583138 DOI: 10.1007/s00261-020-02624-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Early identification of patients at risk of developing colorectal liver metastases can help personalizing treatment and improve oncological outcome. The aim of this study was to investigate in patients with colorectal cancer (CRC) whether a machine learning-based radiomics model can predict the occurrence of metachronous metastases. METHODS In this multicentre study, the primary staging portal venous phase CT of 91 CRC patients were retrospectively analysed. Two groups were assessed: patients without liver metastases at primary staging, or during follow-up of ≥ 24 months (n = 67) and patients without liver metastases at primary staging but developed metachronous liver metastases < 24 months after primary staging (n = 24). After liver parenchyma segmentation, 1767 radiomics features were extracted for each patient. Three predictive models were constructed based on (1) radiomics features, (2) clinical features and (3) a combination of clinical and radiomics features. Stability of features across hospitals was assessed by the Kruskal-Wallis test and inter-correlated features were removed if their correlation coefficient was higher than 0.9. Bayesian-optimized random forest with wrapper feature selection was used for prediction models. RESULTS The three predictive models that included radiomics features, clinical features and a combination of radiomics with clinical features resulted in an AUC in the validation cohort of 86% (95%CI 85-87%), 71% (95%CI 69-72%) and 86% (95% CI 85-87%), respectively. CONCLUSION A machine learning-based radiomics analysis of routine clinical CT imaging at primary staging can provide valuable biomarkers to identify patients at high risk for developing colorectal liver metastases.
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Simões R, Miranda I, Pereira H. Chemical composition of leaf cutin in six Quercus suber provenances. PHYTOCHEMISTRY 2021; 181:112570. [PMID: 33166753 DOI: 10.1016/j.phytochem.2020.112570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
The cutin content and composition of cork oak (Quercus suber) leaves was determined in six provenances with different seed geographical origin spreading across the species natural distribution. The cutin layer on the leaf surface was on average 518 μg/cm2 of leaf area and represented 6.7% of the leaf dry weight, with no significant differences among provenances. Cutin depolymerisation was carried out by transesterification on whole leaves. The cutin composition of cork oak leaves is presented here for the first time. It is essentially composed of long-chain aliphatic ω-hydroxy fatty acids (44.4% of the total monomers), mostly with mid-chain hydroxyl and epoxy groups, fatty acids (20.7%), and a smaller proportion of α,ω-dicarboxylic acids (6.5%). The predominant compounds are 10,16-dihydroxy hexadecanoic acid (17.7-25.2%) and 9,10,18-trihydroxyoctadecanoic acid (15.6-18.0%). Alkanols represent 2.8% and aromatic compounds 12.8%, mainly coumarates. Isolation of cuticles from Q. suber leaves was performed using an enzymatic separation procedure and the fragments were analysed. Cuticle isolation is difficult and direct depolymerisation applied to whole leaves proved a suitable method to study cutin monomeric composition, which did not differ substantially to that of the isolated cuticles. No differences between provenances were found regarding cutin content and composition, thereby ruling out a significant genetic determination of these traits, but rather a highly adaptive phenotypic plasticity of cork oak. Although overall similar in their chemical nature, cutin and suberin in cork oak differ in the proportion of the major chemical families, i.e. ω-hydroxy acids, α,ω-diacids, and fatty acids.
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Simões R, Rodrigues A, Ferreira-Dias S, Miranda I, Pereira H. Chemical Composition of Cuticular Waxes and Pigments and Morphology of Leaves of Quercus suber Trees of Different Provenance. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091165. [PMID: 32916803 PMCID: PMC7570358 DOI: 10.3390/plants9091165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
The chemical composition of cuticular waxes and pigments and the morphological features of cork oak (Quercus suber) leaves were determined for six samples with seeds of different geographical origins covering the natural distribution of the species. The leaves of all samples exhibited a hard texture and oval shape with a dark green colour on the hairless adaxial surface, while the abaxial surface was lighter, with numerous stomata and densely covered with trichomes in the form of stellate multicellular hairs. The results suggest an adaptive role of leaf features among samples of different provenance and the potential role of such variability in dealing with varying temperatures and rainfall regimes through local adaptation and phenotypic plasticity, as was seen in the trial site, since no significant differences in leaf traits among the various specimens were found, for example, specific leaf area 55.6-67.8 cm2/g, leaf size 4.6-6.8 cm2 and photosynthetic pigment (total chlorophyll, 31.8-40.4 µg/cm2). The leaves showed a substantial cuticular wax layer (154.3-235.1 µg/cm2) composed predominantly of triterpenes and aliphatic compounds (61-72% and 17-23% of the identified compounds, respectively) that contributed to forming a nearly impermeable membrane that helps the plant cope with drought conditions. These characteristics are related to the species and did not differ among trees of different seed origin. The major identified compound was lupeol, indicating that cork oak leaves may be considered as a potential source of this bioactive compound.
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Pinto J, Almeida P, Ribeiro F, Simões R. Cardiopulmonary Resuscitation Induced Consciousness A Case Report in an Elderly Patient. Eur J Case Rep Intern Med 2020; 7:001409. [PMID: 32133313 PMCID: PMC7050970 DOI: 10.12890/2020_001409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 11/05/2022] Open
Abstract
Cardiopulmonary resuscitation-induced consciousness is a rarely described and often misunderstood phenomenon, although it can be encountered. High quality cardiopulmonary resuscitation (CPR) may lead a patient to recover consciousness while in cardiac arrest. The authors present the case of an 89-year-old male patient who received CPR after a cardiac arrest. Spontaneous movements during CPR were noted and prompted several CPR interruptions. These movements immediately stopped during chest compression pauses. Physical restraint was used in order to be able to continue with the CPR algorithm, but sedation may be the best approach. Guidelines on how to identify and manage these cases need to be developed. LEARNING POINTS Although rare, cardiopulmonary resuscitation-induced consciousness is a phenomenon that physicians should be aware of, given the implications it may have during resuscitation manoeuvres.Cardiopulmonary resuscitation-induced consciousness can readily be recognised by the presence during cardiac arrest of spontaneous and purposeful patient movements that immediately cease after stopping chest compressions.The use of sedative and analgesic drugs such as ketamine may be the best choice to manage cardiopulmonary resuscitation-induced consciousness, as an alternative to physical restraint.
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Simões R, Miles E, Yang H, Le Grange F, Bhat R, Forsyth S, Seddon B. IMRiS phase II study of IMRT in limb sarcomas: Results of the pre-trial QA facility questionnaire and workshop. Radiography (Lond) 2020; 26:71-75. [PMID: 31902458 DOI: 10.1016/j.radi.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Soft tissue sarcomas of the extremities (STSE) are rare malignancies. We report current UK practice for immobilisation of soft tissue sarcoma of STSE, as part of the initial study set-up within the IMRiS trial, a phase II study of intensity modulated radiotherapy (IMRT) in primary bone and soft tissue sarcoma. METHODS A facility questionnaire (FQ) was circulated to 29 IMRiS centres investigating the variation in immobilisation devices, planning techniques, and imaging protocols. A workshop was held to address concerns raised by centres. It focused on STSE immobilisation and patient set-up. Robustness of patient set-up at each centre was evaluated based on the following criteria: evidence of local set-up audit, calculation of margins based on set-up audit results, imaging frequency, and number of patients treated per centre per annum. RESULTS Twenty-seven (93%) questionnaires were returned. 30% (8/27) of responders routinely treated STSE with IMRT. The remaining 70% (19/27) had little or no experience with IMRT for STSE. Vacuum bags were the most frequent immobilisation device (9/27), followed by thermoplastic shells (7/27). Nine centres had audited their local set-up; however, only 4 had calculated margins in response to the results. Ten centres were classified as having high level of robustness. CONCLUSIONS Immobilisation devices and planning techniques for STSE are inconsistent across centres. Robustness of set-up is an important tool to ensure quality of results in a multicentre trial setting with such different levels of experience. The IMRiS trial Quality Assurance programme encourages centres to assess robustness of set-up through local audit and subsequent calculation of treatment margins. IMPLICATIONS FOR PRACTICE This is the first study that used robustness criteria to tailor QA support to individual centres.
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Ferreira V, Simões R, Gonçalves RS, Machado L, Roriz P. The optimal degree of lateral wedge insoles for reducing knee joint load: a systematic review and meta-analysis. Arch Physiother 2019; 9:18. [PMID: 31890292 PMCID: PMC6921534 DOI: 10.1186/s40945-019-0068-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background Lateral wedge insoles are traditionally used to reduce the adduction moment that crosses the knee during walking in people with medial knee osteoarthritis. However, the best degree to reduce knee joint load is not yet well established. Methods Electronic databases were searched from their inception until May 2017. Included studies reported on the immediate biomechanical effects of different degrees of lateral wedge insoles during walking in people with knee osteoarthritis. The main measures of interest relating to the biomechanics were the first and second peak of external knee adduction moment and knee adduction angular impulse. For the comparison of the biomechanical effects of different degrees of insoles, the studies were divided in three subgroups: insoles with a degree higher than 0° and equal to or lower than 5°; insoles higher than 5° and equal to or lower than 9°; and insoles higher than 9°. Eligible studies were pooled using random-effects meta-analysis. Results Fifteen studies with a total of 415 participants met all eligibility criteria and were included in the final review and meta-analysis. The overall effect suggests that lateral wedge insoles resulted in a statistically significant reduction in the first peak (standardized mean difference [SMD] -0.25; 95% confidence interval [CI] -0.36, - 0.13; P < 0.001), second peak (SMD -0.26 [95% CI -0.48, - 0.04]; P = 0.02) and knee adduction angular impulse (SMD -0.17 [95% CI -0.31, - 0.03]; P = 0.02). The test of subgroups found no statistically significant differences. Conclusion Systematic review and meta-analysis suggests that lateral wedge insoles cause an overall slight reduction in the biomechanical parameters. Higher degrees do not show higher reductions than lower degrees. Prior analysis of biomechanical parameters may be a valid option for selecting the optimal angle of wedge that best fits in knee osteoarthritis patients with the lowest possible degree.
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Simões R, Wortel G, Wiersma TG, Janssen TM, van der Heide UA, Remeijer P. Geometrical and dosimetric evaluation of breast target volume auto-contouring. PHYSICS & IMAGING IN RADIATION ONCOLOGY 2019; 12:38-43. [PMID: 33458293 PMCID: PMC7807634 DOI: 10.1016/j.phro.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 11/17/2022]
Abstract
Background and purpose Automatic delineations are often used as a starting point in the radiotherapy contouring workflow, after which they are manually reviewed and adapted. The purpose of this work was to quantify the geometric differences between automatic and manually edited breast clinical target volume (CTV) contours and evaluate the dosimetric impact of such differences. Materials and methods Eighty-seven automatically generated and manually edited contours of the left breast were retrieved from our clinical database. The automatic contours were obtained with a commercial auto-segmentation toolbox. The geometrical comparison was performed both locally and globally using the Dice score and the 95% Hausdorff distance (HD). Two treatment plans were generated for each patient and the obtained dosimetric differences were quantified using dose-volume histogram (DVH) parameters in the lungs, heart and planning target volume (PTV). An inter-observer variability study with four observers was performed on a subset of ten patients. Results A median Dice score of 0.95 and a median 95% HD of 9.7 mm were obtained. Larger breasts were consistently under-contoured. Cranial under-contouring resulted in more than 5% relative decrease in PTV coverage in 15% of the patients while lateroposterior over-contouring increased the lung V20Gy by a maximum of 2%. The inter-observer variability of the PTV coverage was smaller than the difference between PTV coverage achieved by the automatic and the consensus contours. Conclusions Cranial under-contouring resulted in under-treatment, while lateroposterior over-contouring resulted in an increased lung dosage that is clinically irrelevant, showing the need to consider dose distributions to assess the clinical impact of local geometrical differences.
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Miranda I, Simões R, Medeiros B, Nampoothiri KM, Sukumaran RK, Rajan D, Pereira H, Ferreira-Dias S. Valorization of lignocellulosic residues from the olive oil industry by production of lignin, glucose and functional sugars. BIORESOURCE TECHNOLOGY 2019; 292:121936. [PMID: 31398542 DOI: 10.1016/j.biortech.2019.121936] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Spent olive pomace from the two-phase extraction system of virgin olive oil and olive pomace oil, is a major agro-industrial residue. Present study aimed at the valorization of residual olive pomace and stones (seeds) by hydrothermal treatment and enzymatic hydrolysis of glucans. Both residues contain lignin (31.2% and 42.1%), glucans (13.8% and 15.3%) and xylans (18.9% and 20.3%). After hydrothermal pretreatment (130 °C, 30 min; severity factor log R0 = 2.99), 65% and 75% of hemicelluloses (65% of xylan) were hydrolysed into xylo-oligosaccharides in pomace and stones, respectively. Cellulose and lignin were not substantially affected. Three commercial enzyme preparations, Saczyme Yield, Ultimase BWL 40 and Celluclast 1.5 L, were evaluated for saccharification of pomace or stones at three biomass loads (10, 20 and 30%, w/v). Saczyme and Ultimase were active with high solid loads (30%), reaching 80 and 90% of glucan conversion in pomace, and 40 and 55% in stones, respectively, after 5 h.
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Dinis Fernandes C, Simões R, Ghobadi G, Heijmink SW, Schoots IG, de Jong J, Walraven I, van der Poel HG, van Houdt PJ, Smolic M, Pos FJ, van der Heide UA. Multiparametric MRI Tumor Probability Model for the Detection of Locally Recurrent Prostate Cancer After Radiation Therapy: Pathologic Validation and Comparison With Manual Tumor Delineations. Int J Radiat Oncol Biol Phys 2019; 105:140-148. [DOI: 10.1016/j.ijrobp.2019.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/17/2019] [Accepted: 05/05/2019] [Indexed: 12/12/2022]
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Hamilton TRS, Simões R, Mendes CM, Goissis MD, Nakajima E, Martins EAL, Visintin JA, Assumpção MEOA. Detection of protamine 2 in bovine spermatozoa and testicles. Andrology 2019; 7:373-381. [PMID: 30920782 DOI: 10.1111/andr.12610] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/14/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Sperm DNA integrity is crucial for transmission of genetic information to future generations and DNA damage can occur during chromatin packaging. Chromatin packaging involves the replacement of somatic nucleosomal histones by nuclear proteins called protamines. Protamine 1 (PRM1) is transcribed and translated in spermatids of all mammals; however, protamine 2 (PRM2) is transcribed in low levels in spermatids and it is not yet described in bull mature spermatozoa. OBJECTIVES The aim of this study was to assess gene and protein expression of PRM2 and corroborate gene and protein expression of PRM1 in bull spermatozoa and testis. MATERIALS AND METHODS For this purpose, absolute q-RT-PCR was performed to calculate the number of copies of PRM1 and PRM2 mRNAs in bovine epididymal spermatozoa and testicular tissue. Western blot and mass spectrometry were performed to identify PRM1 and PRM2 in samples of bovine epididymal spermatozoa. Samples of bovine testicular tissue were collected to identify PRM1 and PRM2 by immunohistochemistry. RESULTS We evaluated that the number of PRM1 mRNA copies was about hundred times higher than PRM2 mRNA copies in sperm and testicular samples (p < 0.0001). In addition, we estimated the PRM1: PRM2 ratio based on mRNA number of copies. In spermatozoa, the ratio was 1: 0.014, and in testicle, the ratio was 1: 0.009. We also evaluated the immunolocalization for PRM1 and PRM2 in bovine testis, and both proteins were detected in spermatids. Western blot and mass spectrometry in bovine epididymal spermatozoa confirmed these results. CONCLUSION Our work identifies, for the first time, PRM2 in bovine epididymal spermatozoa and in testis. Further studies are still needed to understand the role of PRM2 on the chromatin of the spermatozoa and to verify how possible changes in PRM2 levels may influence the bull fertility.
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