Machine learning predictive performance evaluation of conventional and fuzzy radiomics in clinical cancer imaging cohorts

BACKGROUND

Hybrid imaging became an instrumental part of medical imaging, particularly cancer imaging processes in clinical routine. To date, several radiomic and machine learning studies investigated the feasibility of in vivo tumor characterization with variable outcomes. This study aims to investigate the effect of recently proposed fuzzy radiomics and compare its predictive performance to conventional radiomics in cancer imaging cohorts. In addition, lesion vs. lesion+surrounding fuzzy and conventional radiomic analysis was conducted.

METHODS

Previously published 11C Methionine (MET) positron emission tomography (PET) glioma, 18F-FDG PET/computed tomography (CT) lung, and 68GA-PSMA-11 PET/magneto-resonance imaging (MRI) prostate cancer retrospective cohorts were included in the analysis to predict their respective clinical endpoints. Four delineation methods including manually defined reference binary (Ref-B), its smoothed, fuzzified version (Ref-F), as well as extended binary (Ext-B) and its fuzzified version (Ext-F) were incorporated to extract imaging biomarker standardization initiative (IBSI)-conform radiomic features from each cohort. Machine learning for the four delineation approaches was performed utilizing a Monte Carlo cross-validation scheme to estimate the predictive performance of the four delineation methods.

RESULTS

Reference fuzzy (Ref-F) delineation outperformed its binary delineation (Ref-B) counterpart in all cohorts within a volume range of 938-354987 mm³ with relative cross-validation area under the receiver operator characteristics curve (AUC) of  +4.7-10.4. Compared to Ref-B, the highest AUC performance difference was observed by the Ref-F delineation in the glioma cohort (Ref-F: 0.74 vs. Ref-B: 0.70) and in the prostate cohort by Ref-F and Ext-F (Ref-F: 0.84, Ext-F: 0.86 vs. Ref-B: 0.80). In addition, fuzzy radiomics decreased feature redundancy by approx. 20%.

CONCLUSIONS

Fuzzy radiomics has the potential to increase predictive performance particularly in small lesion sizes compared to conventional binary radiomics in PET. We hypothesize that this effect is due to the ability of fuzzy radiomics to model partial volume effects and delineation uncertainties at small lesion boundaries. In addition, we consider that the lower redundancy of fuzzy radiomic features supports the identification of imaging biomarkers in future studies. Future studies shall consider systematically analyzing lesions and their surroundings with fuzzy and binary radiomics.

Supervised machine learning enables non-invasive lesion characterization in primary prostate cancer with [68Ga]Ga-PSMA-11 PET/MRI

PURPOSE

Risk classification of primary prostate cancer in clinical routine is mainly based on prostate-specific antigen (PSA) levels, Gleason scores from biopsy samples, and tumor-nodes-metastasis (TNM) staging. This study aimed to investigate the diagnostic performance of positron emission tomography/magnetic resonance imaging (PET/MRI) in vivo models for predicting low-vs-high lesion risk (LH) as well as biochemical recurrence (BCR) and overall patient risk (OPR) with machine learning.

METHODS

Fifty-two patients who underwent multi-parametric dual-tracer [18F]FMC and [68Ga]Ga-PSMA-11 PET/MRI as well as radical prostatectomy between 2014 and 2015 were included as part of a single-center pilot to a randomized prospective trial (NCT02659527). Radiomics in combination with ensemble machine learning was applied including the [68Ga]Ga-PSMA-11 PET, the apparent diffusion coefficient, and the transverse relaxation time-weighted MRI scans of each patient to establish a low-vs-high risk lesion prediction model (MLH). Furthermore, MBCR and MOPR predictive model schemes were built by combining MLH, PSA, and clinical stage values of patients. Performance evaluation of the established models was performed with 1000-fold Monte Carlo (MC) cross-validation. Results were additionally compared to conventional [68Ga]Ga-PSMA-11 standardized uptake value (SUV) analyses.

RESULTS

The area under the receiver operator characteristic curve (AUC) of the MLH model (0.86) was higher than the AUC of the [68Ga]Ga-PSMA-11 SUVmax analysis (0.80). MC cross-validation revealed 89% and 91% accuracies with 0.90 and 0.94 AUCs for the MBCR and MOPR models respectively, while standard routine analysis based on PSA, biopsy Gleason score, and TNM staging resulted in 69% and 70% accuracies to predict BCR and OPR respectively.

CONCLUSION

Our results demonstrate the potential to enhance risk classification in primary prostate cancer patients built on PET/MRI radiomics and machine learning without biopsy sampling.

The impact of management practices to prevent and control mycotoxins in the European food supply chain: MyToolBox project results

The presence of mycotoxins in cereals has led to large economic losses in Europe. In the course of the European project MyToolBox, prevention and control measures to reduce mycotoxin contamination in cereals were developed. This study aimed to estimate the impact of these prevention and control measures on both the reduction in crop losses and the increased volume of crops suitable for food and/or feed. It focused on the following measures: the use of fungicides during wheat cultivation, the use of resistant maize cultivars and/or biocontrol during maize cultivation, the use of real time sensors in storage silos, the use of innovative milling strategies during the pasta making process, and the employment of degrading enzymes during the process of bioethanol and Dried Distillers Grains with Solubles (DDGS) production. The impact assessment was based on the annual volume of cereals produced, the annual levels of mycotoxin contamination, and experimental data on the prevention and control measures collected in the course of the MyToolBox project. Results are expressed in terms of reduced volumes of cereals lost, or as additional volumes of cereals available for food meeting the current European legal limits. Results showed that a reduction in crop losses as well as an increase in the volume of crops suitable as food and/or feed is feasible with each proposed prevention or control measure along the supply chain. The impact was the largest in areas and in years with the highest mycotoxin contamination levels but would have less impact in years with low mycotoxin levels. In further research, the impact assessment may be validated using future data from more years and European sites. Decision makers in the food and feed supply chain can use this impact assessment to decide on the relevant prevention and control strategies to apply.

Production of plant protection agents in medium containing waste glycerol by Streptomyces hygroscopicus: Bioprocess analysis

The surplus of waste glycerol, by-product of the biodiesel production process, is available at the global market. Some species of the genera Streptomyces have the ability to assimilate glycerol and convert it into valuable metabolic products. In the present study, the ability of Streptomyces hygroscopicus to assimilate waste glycerol and convert it into metabolic compounds with antifungal activity against four phytopathogenic fungi obtained from apple fruit samples expressing rot symptoms, was investigated. Production of antifungal metabolites by S. hygroscopicus was carried out in 3 l stirred tank bioreactor through 7 days. Fermentation was carried out at 27 °C with aeration rate of 1.5 vvm and agitation rate of 100 r.p.m. The aim of this work was to analyse bioprocess parameters and to determine at which stage of bioprocess the production of antifungal metabolites occurs. Activity of the cultivation liquid on two isolates of Alternaria alternata and two isolates of Fusarium avenaceum were determined every 12 h using in vitro well diffusion method. It was found that the maximum production of antifungal metabolites occurred at 108 hour of cultivation. Formed inhibition zones have shown that the produced antifungal metabolites have high efficacy on tested phytopathogenic fungi (inhibition zone diameter higher than 35 mm for all test organisms).

Matrix metalloproteinases MMP-1, MMP-2, and MMP-13 are overexpressed in primary nodular melanoma

BACKGROUND

The spread and invasion of malignant melanoma cells involve degradation and reorganization of the extracellular matrix by the activation of several matrix metalloproteinases (MMPs). This study analyzed the expression of MMP-1, MMP-2, and MMP-13 proteins in primary nodular melanoma (NM) and dysplastic nevi (DN) as a significant risk factor for melanoma development. The secondary goal was to analyze the correlation of MMPs protein expression in NM with tumor invasion, BRAF V600 mutation status, and overall survival.

METHODS

Immunohistochemistry for MMP-1, MMP-2, and MMP-13 was performed on nodular melanoma (n = 52) and dysplastic nevi (n = 28) on tissue microarray (TMA). BRAF V600 mutation analysis on NM samples was performed by the Sanger sequencing method.

RESULTS

A high level of MMPs expression in NM samples (>30%) compared with DN (<8%) was statistically significant (P < 0.001). BRAF V600 mutations were detected in 15 of 39 (38.5%) NM samples. This study revealed an interesting finding that MMP-1 and MMP-13 protein expression in the BRAF V600 mutated melanomas were significantly lower than in the BRAF V600 wild type (P < 0.05).

CONCLUSION

Cox analysis revealed that Clark categories, Breslow thickness, and MMP-1 high protein expression are predictive factors for shorter overall survival (P < 0.05).

PROTECTION OF SWEET CORN FROM OSTRINIA NUBILALIS HBN. AND HELICOVERPA ARMIGERA HBN

O. nubilalis and H. armigera regularly occur and cause significant damages in corn crops in Serbia, particularly under global warming conditions. Several measures are applied against these pests (crop rotation, tolerant and resistant hybrids, monitoring, forecast, chemical measures). Larvae damage stem, panicle and ear, which favour development of saprophytes and secondary infections by mycotoxin producing, pathogenic fungi. The aim of the paper was to test the efficacy of the insecticides azadirachtin and indoxacarb in sweet corn protection against the mentioned pests. The trials were conducted in 2014 at two localities (Becej B. and PoIjanice P.) on sweet corn, hybrid Enterprise according to standard OEPP methods (PP1/13; 1/152; 1/135). Products on the basis of azadirachtin (10 g a.i./I of product) at a rate of 0.4 and 0.5% and indoxacarb (150 g a.i./I of product) at a rate of 0.25 I/ha, were applied. Treatments were conducted on the 5th of August with tractor sprayers (high clearance). The plot size was 5000 m². Three assessments were made. The first one prior to treatment, on 25 randomly selected plants per replicate, and the number of O. nubilalis and H. armigera egg masses and larvae on silk was registered. In the second assessment (18th of August), on 20 randomly selected plants per replicate, the number of damaged plants and the number of vital larvae was registered. In the third assessment, immediately before harvest (28th of August, i.e. 12th of September) on 20 randomly selected plants per replicate, the number of plants broken below ear (fallen on the ground), damaged ears and vital larvae, was determined. Results are presented as means, efficacy (E%) according to Abbott and significance of differences by LSD test (5%). At B locality egg masses of O. nubilalis were registered on ear silk on 13-19% of plants and larvae on 3-7%, and larvae of H. armigera on 2-4%. At P locality egg masses of O. nubilalis were present on 34-40.8% of plants. After 13 days from treatment, at B locality the percentage of damaged plants was 3.8-7.5% and at a significantly lower level compared to control where 40.0% of damaged plants was recorded. Vital larvae of O. nubilalis were present on 1.3-31% of plants, depending on the insecticide and application rate, and in the control on 41.3%. At P locality the percentage of damaged plants per treatment ranged from 20 to 46.3% depending on insecticide and application rate, and in the control 63.8%, and the presence of vital larvae of O. nubilalis on 16.3-21.3% of plants, and in the control on 53.5%. Immediately before harvest, at B locality azadirachtin efficacy, depending on application rate and counted parameters, was 88.5-92.5%; 66.7-72.9% and 69.1-75.2%. Efficacy of indoxacarb in general was 75-100%. At P locality, efficacy of azadirachtin depending on application rate and counted parameters, was 77.8-88.9%; 66.5-83.3% and 44.1-74.6%, while efficacy of this insecticide in general amounted 91.5-100%.

EGFR expression is linked to osteopontin and Nf-κB signaling in clear cell renal cell carcinoma

AIM AND BACKGROUND

Epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase involved in many important aspects of cell biology that are related to tumorigenesis. There are opposite evidences of the role of EGFR in renal cancer and the outcome of EGFR-targeted therapies, suggesting the complexity of EGFR signaling pathways. In vitro, osteopontin (OPN) and nuclear factor kappa B (NF-κB) are thought to be involved in specific ligand-independent EGFR activation that could have a role in resistance to EGFR mAb therapy. Aim of this study was to analyze the relationship between EGFR and OPN at the protein and mRNA level, as well as their relation to NF-κB in clear cell renal cell carcinoma (CCRCC).

MATERIALS AND METHODS

Expression of EGFR, OPN, and p65 NF-κB protein was analyzed using immunohistochemistry and compared mutually in 88 CCRCC samples. Expression of EGFR and OPN mRNAs was analyzed using quantitative Real-time PCR in 22 CCRCC samples and compared mutually and with NF-κB protein expression.

RESULTS

Epidermal growth factor receptor mRNA level was higher in CCRCC samples in comparison with normal renal tissue (p = 0.012) and was associated with high OPN mRNA level, and with NF-κB activation (p < 0.001 and p = 0.045, respectively). Immunohistochemical staining showed the inverse association; high EGFR protein expression was related with low OPN and NF-κB protein expression (p < 0.001 and p = 0.047, respectively).

CONCLUSION

Epidermal growth factor receptor gene is upregulated in CRCC and associated with OPN gene expression and NF-kB signaling. The inverse relation between OPN and EGFR at the protein level could probably reflect dynamic changes that EGFR undergoes following activation.

Osteopontin expression correlates with nuclear factor-κB activation and apoptosis downregulation in clear cell renal cell carcinoma

Osteopontin (OPN) is a phosphoglycoprotein implicated in tumorigenesis and tumor cell metastasis. Apoptosis inhibition is one of the mechanisms that contribute to development and progression of cancer, and might be initiated by OPN interaction with tumor cells. The aim of this study was to analyze the relation between OPN and nuclear factor-kappa B (NF-κB) expression in clear cell renal cell carcinoma (CCRCC), as well as their relation to apoptotic activity of tumor cells. Expression of OPN protein and p65 NF-κB subunit was analyzed immunohistochemically in 87 CCRCC samples, and compared mutually and with apoptotic index. Expression of OPN mRNA was analyzed using quantitative real-time PCR and compared with OPN and NF-κB protein expression in 22 CCRCC samples. Statistical analysis showed an association of p65 NF-κB with OPN mRNA (p=0.015) and protein (p<0.001). Also, we found an inverse relationship of OPN with NF-κB protein expression and apoptotic activity of tumor cells (p=0.006 and p=0.022, respectively). Our results indicate that p65 NF-κB signaling pathway may be involved in OPN-mediated CCRCC progression, partly by protecting tumor cells from apoptosis. Therefore, both molecules can constitute potential targets for therapeutic intervention in CCRCC.

Fulminant primary manifestations of Wegener's granulomatosis might not be pauci-immune

Wegener’s granulomatosis is an ANCA-associated small vessel vasculitis. Because histologically immune complex deposits are frequently lacking, the term pauci-immune has been introduced for this subgroup. We report a patient with fulminant, severe PR3-ANCA-positive Wegener’s granulomatosis and multi-organ involvement (upper respiratory tract, lung, kidneys, skin and general symptoms), who showed pronounced immunoglobulin and complement deposits within the skin biopsy. Our observation supports the hypothesis that immune complex deposits may be under-recognized in early lesions of ANCA-associated Wegener’s granulomatosis.

Hypoxia inducible factor-1alpha correlates with vascular endothelial growth factor A and C indicating worse prognosis in clear cell renal cell carcinoma

BACKGROUND

The role of angiogenesis in the pathogenesis of renal cell carcinoma is well recognized, however, the influence of tumor cells in this activity has not yet been fully clarified. The aim of this study was to analyze the expression of hypoxia inducible factor-1alpha (HIF-1alpha), a regulatory factor of angiogenic switch, in comparison to vascular endothelial growth factor A and C (VEGF-A and VEGF-C), recognized to be involved in blood and lymph vessel neoangiogenesis, with potential association in the prognosis of patients with renal cell carcinoma.

METHODS

Ninety-four patients with diagnosis of clear cell renal cell carcinomas (CCRCC), all clinicopathological characteristics and overall survival were unrolled in this study. Immunohistochemicaly VEGF-A, VEGF-C, HIF-1alpha and Ki67 were detected on tumor cells and the staining was performed on tissue microarrays (TMA). The staining was evaluated as a percentage of cytoplasmic or nuclear positive tumor cells.

RESULTS

Variable expression of all three proteins was confirmed. Both angiogenic factors demonstrated perimembranous or diffuse cytoplasmic staining, with diffuse pattern positively associated (p < 0.001). Nuclear HIF-1alpha expression (nHIF-1alpha) showed inverse correlation with diffuse cytoplasmic VEGF-A (p = 0.002) and VEGF-C (p = 0.053), while cytoplasmic HIF-1alpha expression (cHIF-1alpha) showed positive correlation with diffuse staining of both angiogenic factors (p < 0.001; p < 0.001, respectively). In comparison to clinicopathological characteristics, a higher nuclear grade (p = 0.006; p < 0.001, respectively), larger tumor size (p = 0.009; p = 0.015, respectively), higher stage (p = 0.023; p = 0.027, respectively) and shorter survival (p = 0.018; p = 0.024, respectively) were associated with overexpression of cHIF-1alpha and diffuse cytoplasmic VEGF-A expression. In contrary, overexpression of nHIF-1alpha was associated with better diagnostic parameters i.e. lower nuclear grade (p = 0.006), smaller tumor size (p = 0.057), and longer survival (p = 0.005).

CONCLUSION

Overexpression of VEGF-A and cHIF-1alpha in tumor cells highlights a more aggressive subtype of CCRCC that might have some clinical implications. The significance of nHIF-1alpha expression associated with better differentiated tumors should be further elucidated.

Unrecognized dermatophyte infection in ichthyosis vulgaris

A case of unrecognized widespread dermatophyte infection associated with ichthyosis vulgaris and atopy is described. Our patient was a young woman in which the diagnosis of ichthyosis vulgaris and atopic dermatitis blocked the recognition of widespread dermatophyte infection for more than six months. The case showed some clinical peculiarities in terms of both extent of lesions and their clinical appearance.

Comparison of molecular assays for detection and typing of human papillomavirus

OBJECTIVE

The objective of the study was to compare the performance of 3 different extraction instruments in conjunction with 4 different amplification and detection kits for detection and typing of human papillomavirus (HPV) deoxyribonucleic acid (DNA).

STUDY DESIGN

A total of 42 cervical swabs were investigated. HPV DNA was extracted on the 3 different instruments. Each of the extracts was then amplified, and HPV DNA amplification products were detected with 4 different kits.

RESULTS

In 31 samples, HPV DNA was detected by both the Amplicor HPV test and the LINEAR ARRAY HPV genotyping test in conjunction with DNA extraction on the easyMAG instrument. In another 6 samples, only low-risk types were detected with the linear array HPV genotyping test. After extraction on the easyMAG instrument, 32 samples tested positive when the PapilloCheck with the HotStarTaq DNA polymerase was used.

CONCLUSION

Together with extraction on the easyMAG instrument, the Amplicor HPV test, the linear array HPV genotyping test, and the new PapilloCheck with the HotStarTaq DNA polymerase provide comparable results allowing reliable and safe HPV diagnostics in the routine laboratory. Use of alternative assays may lead to an increase of invalid and divergent HPV typing results.

Determination of the hepatitis C virus subtype: comparison of sequencing and reverse hybridization assays

BACKGROUND

Hepatitis C virus (HCV) genotyping and accurate subtyping is becoming increasingly relevant to epidemiological studies, clinical management, pathogenicity, and vaccine development.

METHODS

The TRUGENE HCV 5'NC Genotyping Kit, the new VERSANT HCV Genotype 2.0 Assay (LiPA), and a new laboratory-developed HCV NS5b sequencing assay designed for automated sequencing of the HCV NS5b region were used. Clinical samples and a molecular diagnostics HCV genotyping proficiency program panel were used to determine accuracy and differentiate performance characteristics of the three methods.

RESULTS

All amplified samples from among the members of a HCV genotyping proficiency program panel that contained a single HCV genotype were subtyped correctly using all three HCV genotyping assays. With the TRUGENE HCV 5'NC Genotyping Kit, the HCV subtype was determined in 357 of 441 of routine clinical samples. When the 84 samples with only genotype results were retested with the VERSANT HCV Genotype 2.0 Assay (LiPA), 61 could be further subtyped accurately. With the new laboratory-developed HCV NS5b sequencing assay, all 84 could be subtyped accurately.

CONCLUSIONS

The two new methods show advantages over the routinely used TRUGENE HCV 5'NC Genotyping Kit in terms of genotyping and subtyping accuracy by utilizing part of the HCV core region and NS5b region, respectively.

Prevalence of human papillomavirus among Croatian women attending regular gynecological visit

Human papillomavirus (HPV) infection has been identified as major risk factor for cervical intraepithelial neoplasia (CIN) and invasive cervical cancer. About 40 HPV viral types are commonly found in the genital tract. Most HPV infections resolve spontaneously, while persistent infection with oncogenic types, namely HPV 16 and 18 is necessary for CIN to occur and progress to cancer. Cervical screening is presently based on the Pap smear that is designed to diagnose precancerous lesions and cervical cancer The aim of this study was to investigate the prevalence of HPV DNA and to determine HPV types distribution among 361 women attending regular gynecological visit. There were 205 women (29+/-8 years old) without determined abnormal cervical lesions and 156 women (34+/-15 years old) with abnormal Pap smear; low grade squamous intraepitehelial lesions (LSIL, n=69), high grade squamous intraepithelial lesions (HSIL, n=72) and atypical squamous cells of undetermined significance (ASCUS, n=15). HPV DNA detection and genotyping was performed by Hybrid Capture 2 assay and additionally by consensus and type-specific primers directed PCR. The overall prevalence of high-risk HPV (hrHPV) in women with abnormal Pap smears was 67.9% (106/156), of which in ASCUS 33.4% (5/15), LSIL 62.3% (43/69) and HSIL 80.6% (58/72). In HPV positive specimens, HPV 16 was found as predominant type in 60.4% cases, followed by HPV 31 (8.5%), HPV 33 (6.6%) and HPV 18 (3.7%). In the group of women without obvious cervical changes the overall hrHPV prevalence was 35.6% with HPV 16 found in 43.8% cases, followed by HPV 31 (17.8%), HPV33 (9.5%) and HPV18 (6.8%). In both study groups, women with and without cervical lesions, the prevalence of HPVof indeterminate type was 14.2% and 13.7%, respectively. Our results indicate that cervical intraepithelial lesions are largely associated with HPV type 16, followed by HPV types 31, 33, 18 and HPV of indeterminate type. Although there is a significant difference in hrHPV DNA prevalence among two groups, no significant differences between particular hrHPV types distribution were observed.

Ribavirin Levels and Haemoglobin Decline in Early Virological Responders and Non-Responders to Hepatitis C Virus Combination Therapy

Therapeutic drug monitoring of ribavirin has been claimed to predict virological response and/or haematological side effects in patients with chronic hepatitis C undergoing peginterferon/ribavirin combination treatment. In the present study, steady-state ribavirin levels were retrospectively analyzed in serum samples from patients at week 12 of combination therapy with peginterferon alpha-2a or alpha-2b and ribavirin. Patients were classified as early virological responders on the basis of undetectable HCV-RNA or HCV-RNA drop >or=2 log from baseline at week 12. The mean ribavirin level was not different between early virological responders (2.3 +/- 0.1 microg/ml, n = 45) and early virological non-responders (2.0 +/- 0.2 microg/ml, n = 10). There was no correlation between ribavirin levels at week 12 and early virological response. In patients with early virological response, haemoglobin (Hb) levels were found to be decreased by 18% on average from the basal values; however, in only 2 patients Hb levels declined below 100 g/l. There was a moderate negative correlation between ribavirin levels and Hb levels at week 12 (R = -0.50, p < 0.001); however, ribavirin levels did not correlate with relative or absolute decline in Hb as compared to basal levels or with ribavirin dose per kilogram body weight. In addition, a significant negative correlation between ribavirin levels and glomerular filtration rate was found (R = -0.31, p < 0.05). Based on our results, monitoring of ribavirin serum levels at week 12 of HCV combination therapy does not appear to predict early virological response or reductions in Hb levels. Further research is needed to assess their diagnostic value at other time points of peginterferon/ribavirin combination treatment and/or in patients with renal insufficiency.