Learning to divide and conquer: applying the L* algorithm to automate assume-guarantee reasoning

Assume-guarantee reasoning enables a “divide-and-conquer” approach to the verification of large systems that checks system components separately while using assumptions about each component’s environment. Developing appropriate assumptions used to be a difficult and manual process. Over the past five years, we have developed a framework for performing assume-guarantee verification of systems in an incremental and fully automated fashion. The framework uses an off-the-shelf learning algorithm to compute the assumptions. The assumptions are initially approximate and become more precise by means of counterexamples obtained by model checking components separately. The framework supports different assume-guarantee rules, both symmetric and asymmetric. Moreover, we have recently introduced alphabet refinement, which extends the assumption learning process to also infer assumption alphabets. This refinement technique starts with assumption alphabets that are a subset of the minimal interface between a component and its environment, and adds actions to it as necessary until a given property is shown to hold or to be violated in the system. We have applied the learning framework to a number of case studies that show that compositional verification by learning assumptions can be significantly more scalable than non-compositional verification. J.M. Cobleigh currently employed by The MathWorks, Inc., 3 Apple Hill Drive, Natick, MA 01760, USA.     

Unraveling the Role of Histone Variant CENP-A and Chaperone HJURP Expression in Thymic Epithelial Neoplasms

Background: Recent advances demonstrate the role of chromatin regulators, including histone variants and histone chaperones, in cancer initiation and progression. Methods: Histone H3K4me3, histone variant centromere protein (CENP-A) and histone chaperones Holliday junction recognition protein (HJURP) as well as DAXX expression were examined immunohistochemically in 95 thymic epithelial tumor (TET) specimens. Our results were compared with the expression profile of DAXX, HJURP and CENP-A in gene expression profiling interactive analysis (GEPIA2). Results: The lymphocyte-poor B3- and C-type TETs were more frequently DAXX negative (p = 0.043). B3 and C-Type TETs showed higher cytoplasmic and nuclear CENP-A (p = 0.007 and p = 0.002) and higher cytoplasmic HJURP H-score (p < 0.001). Higher nuclear CENP-A and cytoplasmic HJURP expression was associated with advanced Masaoka–Koga stage (p = 0.048 and p < 0.001). A positive correlation between HJURP and CENP-A was also observed. The presence of cytoplasmic CENP-A expression was correlated with a favorable overall survival (p = 0.03). CENP-A overexpression in survival analysis of TCGA TETs showed similar results. H3K4me3 expression was not associated with any clinicopathological parameters. Conclusions: Our results suggest a significant interaction between CENP-A and HJURP in TETs. Moreover, we confirmed the presence of a cytoplasmic CENP-A immunolocalization, suggesting also a possible favorable prognostic value of this specific immunostaining pattern.     

Circulating miRNA Expression Profiles and Machine Learning Models in Association with Response to Irinotecan-Based Treatment in Metastatic Colorectal Cancer

Colorectal cancer represents a leading cause of cancer-related morbidity and mortality. Despite improvements, chemotherapy remains the backbone of colorectal cancer treatment. The aim of this study is to investigate the variation of circulating microRNA expression profiles and the response to irinotecan-based treatment in metastatic colorectal cancer and to identify relevant target genes and molecular functions. Serum samples from 95 metastatic colorectal cancer patients were analyzed. The microRNA expression was tested with a NucleoSpin miRNA kit (Machnery-Nagel, Germany), and a machine learning approach was subsequently applied for microRNA profiling. The top 10 upregulated microRNAs in the non-responders group were hsa-miR-181b-5p, hsa-miR-10b-5p, hsa-let-7f-5p, hsa-miR-181a-5p, hsa-miR-181d-5p, hsa-miR-301a-3p, hsa-miR-92a-3p, hsa-miR-155-5p, hsa-miR-30c-5p, and hsa-let-7i-5p. Similarly, the top 10 downregulated microRNAs were hsa-let-7d-5p, hsa-let-7c-5p, hsa-miR-215-5p, hsa-miR-143-3p, hsa-let-7a-5p, hsa-miR-10a-5p, hsa-miR-142-5p, hsa-miR-148a-3p, hsa-miR-122-5p, and hsa-miR-17-5p. The upregulation of microRNAs in the miR-181 family and the downregulation of those in the let-7 family appear to be mostly involved with non-responsiveness to irinotecan-based treatment.     

Absence of Gut Microbiota Is Associated with RPE/Choroid Transcriptomic Changes Related to Age-Related Macular Degeneration Pathobiology and Decreased Choroidal Neovascularization

Studies have begun to reveal significant connections between the gut microbiome and various retinal diseases, including age-related macular degeneration (AMD). As critical supporting tissues of the retina, the retinal pigment epithelium (RPE) and underlying choroid play a critical role in retinal homeostasis and degeneration. However, the relationship between the microbiome and RPE/choroid remains poorly understood, particularly in animal models of AMD. In order to better elucidate this role, we performed high-throughput RNA sequencing of RPE/choroid tissue in germ-free (GF) and specific pathogen-free (SPF) mice. Furthermore, utilizing a specialized laser-induced choroidal neovascularization (CNV) model that we developed, we compared CNV size and inflammatory response between GF and SPF mice. After correction of raw data, 660 differentially expressed genes (DEGs) were identified, including those involved in angiogenesis regulation, scavenger and cytokine receptor activity, and inflammatory response—all of which have been implicated in AMD pathogenesis. Among lasered mice, the GF group showed significantly decreased CNV lesion size and microglial infiltration around CNV compared to the SPF group. Together, these findings provide evidence for a potential gut–RPE/choroidal axis as well as a correlation with neovascular features of AMD.     

Effect of Bladder Injection of OnabotulinumtoxinA on the Central Expression of Genes Associated with the Control of the Lower Urinary Tract: A Study in Normal Rats

To investigate a possible central mechanism of action of Botulinum toxin A (BoNT/A) following injection in the bladder, complementary to the acknowledged peripheral bladder effect, we studied changes in the expression of neuropeptides and receptors involved in lower urinary tract function in the spinal cord (SC) and dorsal root ganglia (DRG) of normal rats following BoNT/A bladder injection. Thirty-six Sprague-Dawley rats, divided into three groups of n = 12, received bladder injections of 2U or 5U OnabotulinumtoxinA (BOTOX^®), or saline. Six animals from each group were sacrificed on days 7 and 14. Expression of Tachykinin 1 (Tac1), capsaicin receptor (TRPV1), neuropeptide Y (NPY), proenkephalin (PENK) and muscarinic receptors M1, M2, M3, was evaluated in the bladder, L6-S1 DRG, and SC segments using real-time PCR and Western blotting. Real-time PCR revealed increased expression of NPY in all tissues except for SC, and increased TRPV1 and PENK expression in DRG and SC, whereas expression of Tac1, M1 and M2 was decreased. Less significant changes were noted in protein levels. These findings suggest that bladder injections of OnabotulinumtoxinA may be followed by changes in the expression of sensory, sympathetic and cholinergic bladder function regulators at the DRG/SC level.     

A privacy-aware access control model for distributed network monitoring

In this paper, we introduce a new access control model that aims at addressing the privacy implications surrounding network monitoring. In fact, despite its importance, network monitoring is natively leakage-prone and, moreover, this is exacerbated due to the complexity of the highly dynamic monitoring procedures and infrastructures, that may include multiple traffic observation points, distributed mitigation mechanisms and even inter-operator cooperation. Conceived on the basis of data protection legislation, the proposed approach is grounded on a rich in expressiveness information model, that captures all the underlying monitoring concepts along with their associations. The model enables the specification of contextual authorisation policies and expressive separation and binding of duty constraints. Finally, two key innovations of our work consist in the ability to define access control rules at any level of abstraction and in enabling a verification procedure, which results in inherently privacy-aware workflows, thus fostering the realisation of the Privacy by Design vision.     

Investigation of the antioxidant properties of Ferula orientalis L. using a suitable extraction procedure

The present work examines the in vitro antioxidant properties of the essential oil and various extracts prepared from the herbal parts of Ferula orientalis A. (Apiaceae). The highest 2,2-diphenyl-l-picrylhydrazyl (DPPH) radical-scavenging activity was found in the polar extract, e.g. methanol–water (1:1), obtained from non-deodorised materials with IC₅₀ values at 99.1 μg/ml. In the β-carotene/linoleic acid assay, the deodorised acetone extract exhibited stronger activity than the polar one. The relative antioxidant activities (RAA%) of the extracts ranged from 10.1% to 76.1%, respectively. Extraction with methanol–water (1:1) mixture was concluded to be the most appropriate method in terms of higher extract yield, as well as effectiveness, observed in both assays. Although the essential oil showed antioxidative potential, it was not as strong as that of positive control (BHT). GC/MS analysis of the essential oil resulted in the identification of 39 compounds, β-phellandrene (23.6%), (E)-β-ocimene (13.8%), α-pinene (12.5%), α-phellandrene (11.5%) and dehydro-sesquicineole (10.1%) being the major components.     

Multiscale modeling for image analysis of brain tumor studies

Image-based modeling of tumor growth combines methods from cancer simulation and medical imaging. In this context, we present a novel approach to adapt a healthy brain atlas to MR images of tumor patients. In order to establish correspondence between a healthy atlas and a pathologic patient image, tumor growth modeling in combination with registration algorithms is employed. In a first step, the tumor is grown in the atlas based on a new multiscale, multiphysics model including growth simulation from the cellular level up to the biomechanical level, accounting for cell proliferation and tissue deformations. Large-scale deformations are handled with an Eulerian approach for finite element computations, which can operate directly on the image voxel mesh. Subsequently, dense correspondence between the modified atlas and patient image is established using nonrigid registration. The method offers opportunities in atlas-based segmentation of tumor-bearing brain images as well as for improved patient-specific simulation and prognosis of tumor progression.     

Genetic Tuning of Iron Oxide Nanoparticle Size,Shape, and Surface Properties in Magnetospirillum magneticum

Different applications require iron oxide nanoparticles (IONPs) of varying size, shape, crystallinity, and surfaces that can be controlled through the synthesis reaction conditions. Under ambient conditions, Magnetospirillum magneticum AMB-1 builds uniform Fe₃O₄ IONPs with shapes and crystal forms difficult to achieve with chemical synthesis. Genetic engineering can be used to change their properties, but there are few tools to fine-tune expression over a wide range. To this end, ribosome binding sites, minimal constitutive promoters, and inducible systems (IPTG, aTc, and OC6) with large dynamic range are designed. These are used to control M. magneticum genes that affect IONP properties, including size (mamC), morphology (mms6), chain length (mamK), and surface coating (mamC fusions). These systems increase the fraction of IONPs that are less than 30 nm, produce rounded particles, and lead to the production of intracellular chains with 24 or more IONPs. In addition, the R5 peptide from diatoms is found to silica coat the surface of metal oxide nanoparticles (Fe, Ti, Ta, Hf) and can be genetically directed to the IONP surface. This work demonstrates the genetic control of IONP properties, but also highlights the robustness of the system, which complicates genetic engineering to produce radically different particles and structures.