Utility of Multi-Parametric Quantitative Magnetic Resonance Imaging for Characterization and Radiotherapy Response Assessment in Soft-Tissue Sarcomas and Correlation With Histopathology.

Purpose: To evaluate repeatability of quantitative multi-parametric MRI in retroperitoneal sarcomas, assess parameter changes with radiotherapy, and correlate pre-operative values with histopathological findings in the surgical specimens. Materials and Methods: Thirty patients with retroperitoneal sarcoma were imaged at baseline, of whom 27 also underwent a second baseline examination for repeatability assessment. 14/30 patients were treated with pre-operative radiotherapy and were imaged again after completing radiotherapy (50.4 Gy in 28 daily fractions, over 5.5 weeks). The following parameter estimates were assessed in the whole tumor volume at baseline and following radiotherapy: apparent diffusion coefficient (ADC), parameters of the intra-voxel incoherent motion model of diffusion-weighted MRI (D, f, D*), transverse relaxation rate, fat fraction, and enhancing fraction after gadolinium-based contrast injection. Correlation was evaluated between pre-operative quantitative parameters and histopathological assessments of cellularity and fat fraction in post-surgical specimens (ClinicalTrials.gov, registration number NCT01902667). Results: Upper and lower 95% limits of agreement were 7.1 and -6.6%, respectively for median ADC at baseline. Median ADC increased significantly post-radiotherapy. Pre-operative ADC and D were negatively correlated with cellularity (r = -0.42, p = 0.01, 95% confidence interval (CI) -0.22 to -0.59 for ADC; r = -0.45, p = 0.005, 95% CI -0.25 to -0.62 for D), and fat fraction from Dixon MRI showed strong correlation with histopathological assessment of fat fraction (r = 0.79, p = 10-7, 95% CI 0.69-0.86). Conclusion: Fat fraction on MRI corresponded to fat content on histology and therefore contributes to lesion characterization. Measurement repeatability was excellent for ADC; this parameter increased significantly post-radiotherapy even in disease categorized as stable by size criteria, and corresponded to cellularity on histology. ADC can be utilized for characterizing and assessing response in heterogeneous retroperitoneal sarcomas

Comparative genomics of prevaccination and modern Bordetella pertussis strains

Contains fulltext : 89571.pdf (publisher's version ) (Open Access)BACKGROUND: Despite vaccination since the 1950s, pertussis has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. The resurgence of pertussis has been associated with the expansion of Bordetella pertussis strains with a novel allele for the pertussis toxin (Ptx) promoter, ptxP3, which have replaced resident ptxP1 strains. Compared to ptxP1 strains, ptxP3 produce more Ptx resulting in increased virulence and immune suppression. To elucidate how B. pertussis has adapted to vaccination, we compared genome sequences of two ptxP3 strains with four strains isolated before and after the introduction vaccination. RESULTS: The distribution of SNPs in regions involved in transcription and translation suggested that changes in gene regulation play an important role in adaptation. No evidence was found for acquisition of novel genes. Modern strains differed significantly from prevaccination strains, both phylogenetically and with respect to particular alleles. The ptxP3 strains were found to have diverged recently from modern ptxP1 strains. Differences between ptxP3 and modern ptxP1 strains included SNPs in a number of pathogenicity-associated genes. Further, both gene inactivation and reactivation was observed in ptxP3 strains relative to modern ptxP1 strains. CONCLUSIONS: Our work suggests that B. pertussis adapted by successive accumulation of SNPs and by gene (in)activation. In particular changes in gene regulation may have played a role in adaptation

Remote detection of invasive alien species

The spread of invasive alien species (IAS) is recognized as the most severe threat to biodiversity outside of climate change and anthropogenic habitat destruction. IAS negatively impact ecosystems, local economies, and residents. They are especially problematic because once established, they give rise to positive feedbacks, increasing the likelihood of further invasions and spread. The integration of remote sensing (RS) to the study of invasion, in addition to contributing to our understanding of invasion processes and impacts to biodiversity, has enabled managers to monitor invasions and predict the spread of IAS, thus supporting biodiversity conservation and management action. This chapter focuses on RS capabilities to detect and monitor invasive plant species across terrestrial, riparian, aquatic, and human-modified ecosystems. All of these environments have unique species assemblages and their own optimal methodology for effective detection and mapping, which we discuss in detail

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

Value of diffusion-weighted imaging for monitoring tissue change during magnetic resonance-guided high-intensity focused ultrasound therapy in bone applications: an ex-vivo study.

BACKGROUND: Magnetic resonance (MR)-guided high-intensity focused ultrasound (HIFU) can palliate metastatic bone pain by periosteal neurolysis. We investigated the value of diffusion-weighted imaging (DWI) for monitoring soft tissue changes adjacent to bone during MR-guided HIFU. We evaluated the repeatability of the apparent diffusion coefficient (ADC) measurement, the temporal evolution of ADC change after sonication, and its relationship with thermal parameters. METHODS: Ex-vivo experiments in lamb legs (n = 8) were performed on a Sonalleve MR-guided HIFU system. Baseline proton resonance frequency shift (PRFS) thermometry evaluated the accuracy of temperature measurements and tissue cooling times after exposure. PRFS acquired during sonication (n = 27) was used to estimate thermal dose volume and temperature. After repeat baseline measurements, DWI was assessed longitudinally and relative ADC changes were derived for heated regions. RESULTS: Baseline PRFS was accurate to 1 °C and showed that tissues regained baseline temperatures within 5 min. Before sonication, coefficient of variation for repeat ADC measurements was 0.8%. After sonication, ADC increased in the muscle adjacent to the exposed periosteum, it was maximal 1-5 min after sonication, and it significantly differed between samples with persistent versus non-persistent ADC changes beyond 20 min. ADC increases at 20 min were stable for 2 h and correlated significantly with thermal parameters (ADC versus applied acoustic energy at 16-20 min: r = 0.77, p < 0.001). A 20% ADC increase resulted in clear macroscopic tissue damage. CONCLUSIONS: Our preliminary results suggest that DWI can detect intra-procedural changes in ex-vivo muscle overlying the periosteum. This could be useful for studying the safety and efficacy of clinical MR-guided HIFU bone treatments

Value of diffusion-weighted imaging for monitoring tissue change during magnetic resonance-guided high-intensity focused ultrasound therapy in bone applications: an ex-vivo study.

Magnetic resonance (MR)-guided high-intensity focused ultrasound (HIFU) can palliate metastatic bone pain by periosteal neurolysis. We investigated the value of diffusion-weighted imaging (DWI) for monitoring soft tissue changes adjacent to bone during MR-guided HIFU. We evaluated the repeatability of the apparent diffusion coefficient (ADC) measurement, the temporal evolution of ADC change after sonication, and its relationship with thermal parameters.Ex-vivo experiments in lamb legs (n = 8) were performed on a Sonalleve MR-guided HIFU system. Baseline proton resonance frequency shift (PRFS) thermometry evaluated the accuracy of temperature measurements and tissue cooling times after exposure. PRFS acquired during sonication (n = 27) was used to estimate thermal dose volume and temperature. After repeat baseline measurements, DWI was assessed longitudinally and relative ADC changes were derived for heated regions.Baseline PRFS was accurate to 1 °C and showed that tissues regained baseline temperatures within 5 min. Before sonication, coefficient of variation for repeat ADC measurements was 0.8%. After sonication, ADC increased in the muscle adjacent to the exposed periosteum, it was maximal 1-5 min after sonication, and it significantly differed between samples with persistent versus non-persistent ADC changes beyond 20 min. ADC increases at 20 min were stable for 2 h and correlated significantly with thermal parameters (ADC versus applied acoustic energy at 16-20 min: r = 0.77, p < 0.001). A 20% ADC increase resulted in clear macroscopic tissue damage.Our preliminary results suggest that DWI can detect intra-procedural changes in ex-vivo muscle overlying the periosteum. This could be useful for studying the safety and efficacy of clinical MR-guided HIFU bone treatments