Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental mueller matrices.

MOTIVATION: Imaging Mueller polarimetry has already proved its potential for biomedicine, remote sensing and metrology. The real-time applications of this modality require both video rate image acquisition and fast data post-processing algorithms. First, one must check the physical realizability of the experimental Mueller matrices in order to filter out non-physical data, ie to test the positive semi-definiteness of the 4 × 4 Hermitian coherency matrix calculated from the elements of corresponding Mueller matrix pixel-wise. For this purpose, we compared the execution time for the calculations of i) eigenvalues, ii) Cholesky decomposition, iii) Sylvester's criterion, and iv) coefficients of the characteristic polynomial (two different approaches) of the Hermitian coherency matrix, all calculated for the experimental Mueller matrix images (600 pixels × 700 pixels) of mouse uterine cervix. The calculations were performed using C ++ and Julia programming languages. RESULTS: Our results showed the superiority of the algorithm iv) based on the simplification via Pauli matrices over other algorithms for our dataset. The sequential implementation of latter algorithm on a single core already satisfies the requirements of real-time polarimetric imaging. This can be further amplified by the proposed parallelization (e.g., we achieve a 5-fold speed up on 6 cores). AVAILABILITY AND IMPLEMENTATION: The source codes of the algorithms and experimental data are available at https://github.com/pogudingleb/mueller_matrices.

Hydrolysis of Oligodeoxyribonucleotides on the Microarray Surface and in Solution by Catalytic Anti-DNA Antibodies in Systemic Lupus Erythematosus.

Anti-DNA antibodies are known to be classical serological hallmarks of systemic lupus erythematosus (SLE). In addition to high-affinity antibodies, the autoantibody pool also contains natural catalytic anti-DNA antibodies that recognize and hydrolyze DNA. However, the specificity of such antibodies is uncertain. In addition, DNA binding to a surface such as the cell membrane, can also affect its recognition by antibodies. Here, we analyzed the hydrolysis of short oligodeoxyribonucleotides (ODNs) immobilized on the microarray surface and in solution by catalytic anti-DNA antibodies from SLE patients. It has been shown that IgG antibodies from SLE patients hydrolyze ODNs more effectively both in solution and on the surface, compared to IgG from healthy individuals. The data obtained indicate a more efficient hydrolysis of ODNs in solution than immobilized ODNs on the surface. In addition, differences in the specificity of recognition and hydrolysis of certain ODNs by anti-DNA antibodies were revealed, indicating the formation of autoantibodies to specific DNA motifs in SLE. The data obtained expand our understanding of the role of anti-DNA antibodies in SLE. Differences in the recognition and hydrolysis of surface-tethered and dissolved ODNs need to be considered in DNA microarray applications.

C60 adduct with L-arginine as a promising nanomaterial for treating cerebral ischemic stroke.

The work aimed to investigate the biocompatibility and biological activity of the water-soluble fullerene adduct C60-Arg. It was found that the material is haemocompatible, is not cyto- and genotoxic, possesses pronounced antioxidant activity. Additionally, this paper outlines the direction of application of water-soluble fullerene adducts in the creation of neuroprotectors. It has been suggested that a putative mechanism of the protective action of the C60-Arg adduct is associated with its antioxidant properties, the ability to penetrate the blood-brain barrier, and release nitrogen monoxide as a result of the catabolism of L-arginine residues, which promote vascular relaxation. The action of the C60-Arg adduct was compared with the action of such an antioxidant as Edaravone, which is approved in Japan for the treatment of ischemic and haemorrhagic strokes.

Is a complete Mueller matrix necessary in biomedical imaging?

The advent of imagers with integrated linear polarization selectivity opens new opportunities for researchers interested in the polarization properties of biological tissues. In this Letter, we explore the mathematical framework necessary to obtain common parameters of interest: azimuth; retardance; and depolarization with reduced Mueller matrices that can be measured with the new instrumentation. We show that in the case of acquisition close to the tissue normal, simple algebraic analysis of the reduced form of the Mueller matrix yields results very close to those obtained with more complex decomposition algorithms applied to a complete Mueller matrix.

Thermodynamics and Kinetics of Unfolding of Antiparallel G-Quadruplexes in Anti-Thrombin Aptamers.

The process of unfolding of G-quadruplex structure in the RE31 DNA-aptamer and in its complex with thrombin under the action of the fluorescently labeled complementary oligonucleotides of varying length with formation of double-helix structures has been studied. It has been suggested that G-quadruplex unfolding involves formation of an intermediate complex with an oligonucleotide. Thermodynamic parameters and kinetics of unfolding of the free aptamer and its complex with thrombin differ. Extension of the oligonucleotide sequence complementary to G-quadruplex by two nucleotides to cover the so-called "hinge region" had little impact on the conformational transition of G-quadruplex of the free aptamer. However, a pronounced effect has been observed for the aptamer-protein complex. Most likely these differences could be explained by the thrombin-induced conformational transition of the aptamer involving the hinge region.

Digital histology of tissue with Mueller microscopy and FastDBSCAN.

We present the results of the automated post-processing of Mueller microscopy images of skin tissue models with a new fast version of the algorithm of density-based spatial clustering of applications with noise (FastDBSCAN) and discuss the advantages of its implementation for digital histology of tissue. We demonstrate that using the FastDBSCAN algorithm, one can produce the diagnostic segmentation of high resolution images of tissue by several orders of magnitude faster and with high accuracy (>97%) compared to the original version of the algorithm.

Drug Repurposing of the Unithiol: Inhibition of Metallo-ß-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections.

The increasing antibiotic resistance is a clinical problem worldwide. Numerous Gram-negative bacteria have already become resistant to the most widely used class of antibacterial drugs, ß-lactams. One of the main mechanisms is inactivation of ß-lactam antibiotics by bacterial ß-lactamases. Appearance and spread of these enzymes represent a continuous challenge for the clinical treatment of infections and for the design of new antibiotics and inhibitors. Drug repurposing is a prospective approach for finding new targets for drugs already approved for use. We describe here the inhibitory potency of known detoxifying antidote 2,3-dimercaptopropane-1-sulfonate (unithiol) against metallo-ß-lactamases. Unithiol acts as a competitive inhibitor of meropenem hydrolysis by recombinant metallo-ß-lactamase NDM-1 with the KI of 16.7 µM. It is an order of magnitude lower than the KI for l-captopril, the inhibitor of angiotensin-converting enzyme approved as a drug for the treatment of hypertension. Phenotypic methods demonstrate that the unithiol inhibits natural metallo-ß-lactamases NDM-1 and VIM-2 produced by carbapenem-resistant K. pneumoniae and P. aeruginosa bacterial strains. The 3D full atom structures of unithiol complexes with NDM-1 and VIM-2 are obtained using QM/MM modeling. The thiol group is located between zinc cations of the active site occupying the same place as the catalytic hydroxide anion in the enzyme-substrate complex. The sulfate group forms both a coordination bond with a zinc cation and hydrogen bonds with the positively charged residue, lysine or arginine, responsible for proper orientation of antibiotics upon binding to the active site prior to hydrolysis. Thus, we demonstrate both experimentally and theoretically that the unithiol is a prospective competitive inhibitor of metallo-ß-lactamases and it can be utilized in complex therapy together with the known ß-lactam antibiotics.

Spatial evolution of depolarization in homogeneous turbid media within the differential Mueller matrix formalism.

We show, through visible-range Mueller polarimetry, as well as numerical simulations, that the depolarization in a homogeneous turbid medium consisting of submicron spherical particles follows a parabolic law with the path-length traveled by light through the medium. This result is in full agreement with the phenomenological theory of the fluctuating medium within the framework of the differential Mueller matrix formalism. We further found that the standard deviations of the fluctuating elementary polarization properties of the medium depend linearly on the concentration of particles. These findings are believed to be useful for the phenomenological interpretation of polarimetric experiments, with special emphasis on biomedical applications.

Near-real-time Mueller polarimetric image processing for neurosurgical intervention.

PURPOSE: Wide-field imaging Mueller polarimetry is a revolutionary, label-free, and non-invasive modality for computer-aided intervention; in neurosurgery, it aims to provide visual feedback of white matter fibre bundle orientation from derived parameters. Conventionally, robust polarimetric parameters are estimated after averaging multiple measurements of intensity for each pair of probing and detected polarised light. Long multi-shot averaging, however, is not compatible with real-time in vivo imaging, and the current performance of polarimetric data processing hinders the translation to clinical practice. METHODS: A learning-based denoising framework is tailored for fast, single-shot, noisy acquisitions of polarimetric intensities. Also, performance-optimised image processing tools are devised for the derivation of clinically relevant parameters. The combination recovers accurate polarimetric parameters from fast acquisitions with near-real-time performance, under the assumption of pseudo-Gaussian polarimetric acquisition noise. RESULTS: The denoising framework is trained, validated, and tested on experimental data comprising tumour-free and diseased human brain samples in different conditions. Accuracy and image quality indices showed significant ( p < 0.05 ) improvements on testing data for a fast single-pass denoising versus the state-of-the-art and high polarimetric image quality standards. The computational time is reported for the end-to-end processing. CONCLUSION: The end-to-end image processing achieved real-time performance for a localised field of view ( ≈ 6.5 mm 2 ). The denoised polarimetric intensities produced visibly clear directional patterns of neuronal fibre tracts in line with reference polarimetric image quality standards; directional disruption was kept in case of neoplastic lesions. The presented advances pave the way towards feasible oncological neurosurgical translations of novel, label-free, interventional feedback.

Characterization of Polarimetric Properties in Various Brain Tumor Types Using Wide-Field Imaging Mueller Polarimetry.

Neuro-oncological surgery is the primary brain cancer treatment, yet it faces challenges with gliomas due to their invasiveness and the need to preserve neurological function. Hence, radical resection is often unfeasible, highlighting the importance of precise tumor margin delineation to prevent neurological deficits and improve prognosis. Imaging Mueller polarimetry, an effective modality in various organ tissues, seems a promising approach for tumor delineation in neurosurgery. To further assess its use, we characterized the polarimetric properties by analysing 45 polarimetric measurements of 27 fresh brain tumor samples, including different tumor types with a strong focus on gliomas. Our study integrates a wide-field imaging Mueller polarimetric system and a novel neuropathology protocol, correlating polarimetric and histological data for accurate tissue identification. An image processing pipeline facilitated the alignment and overlay of polarimetric images and histological masks. Variations in depolarization values were observed for grey and white matter of brain tumor tissue, while differences in linear retardance were seen only within white matter of brain tumor tissue. Notably, we identified pronounced optical axis azimuth randomization within tumor regions. This study lays the foundation for machine learning-based brain tumor segmentation algorithms using polarimetric data, facilitating intraoperative diagnosis and decision making.

Polarimetric imaging of uterine cervix: a case study.

We present a preliminary investigation of macroscopic polarimetric imaging of uterine cervix. Orthogonal state contrast (OSC) images of healthy and anomalous cervices have been taken in vivo at 550 nm. Four ex vivo cervix samples have been studied in full Muller polarimetry, at 550 nm and 700 nm, and characterized in detail by standard pathology. One sample was totally healthy, another one carried CIN lesions at very early stage (CIN1) in its visible exocervical region, while for the other two samples more advanced (CIN3) lesions were present, together with visible glandular epithelium (ectropion). Significant birefringence has been observed in the healthy regions of all six samples, both in vivo and ex vivo. Standard treatments of the Mueller images of the ex vivo samples allowed to quantify both retardation and depolarization. Retardation reached 60° in healthy regions, and disappeared in the anomalous regions of the other three ex vivo samples. The depolarization power was largest in healthy regions, and lower in CINs and ectropion. Possible origins of the observed effects are briefly discussed.

Not choosing pathology: An essay-based survey of first-year clinical residents.

OBJECTIVES: Health care systems worldwide are facing a shortage in the pathology workforce that could negatively affect health care services, particularly oncology. To address this potential shortfall, the pathology community must identify the reasons why graduating students are not choosing pathology as a specialty. METHODS: We analyzed 226 free-text essay responses submitted by nonpathology residents at a teaching hospital. We used a general inductive approach and quantitative analysis to identify the barriers that prevent medical college graduates from choosing pathology as a specialty. RESULTS: Residents at our institution view pathology similar to residents from other countries, with the main obstacles to choosing pathology as a specialty being a perception that it lacks practical application to patient care or provides "no real help" and has a lack of patient interaction. In Russia specifically, there is a focus on the perceived negative aspects of autopsy as a barrier to selecting pathology. Less significant factors that may be based more on stereotypes than reality include the expectation that the work is not engaging, the emotional burden, and the occupational risks. CONCLUSIONS: For medical students who place less importance on patient interaction, addressing these secondary factors could help select potential pathologists during students' undergraduate years.

Polarimetric imaging for cervical pre-cancer screening aided by machine learning: ex vivo studies.

Significance: Wide-field imaging Mueller polarimetry is an optical imaging technique that has great potential to become a reliable, fast, non-contact in vivo imaging modality for the early detection of, e.g., deceases and tissue structural malformations, such as cervical intraepithelial neoplasia, in both clinical and low-resource settings. On the other hand, machine learning methods have established themselves as a superior solution in image classification and regression tasks. We combine Mueller polarimetry and machine learning, critically assess the data/classification pipeline, investigate the bias arising from training strategies, and demonstrate how higher levels of detection accuracy can be achieved. Aim: We aim to automate/assist with diagnostic segmentation of polarimetric images of uterine cervix specimens. Approach: A comprehensive capture-to-classification pipeline is developed in house. Specimens are acquired and measured with imaging Mueller polarimeter and undergo histopathological classification. Subsequently, a labeled dataset is created within tagged regions of either healthy or neoplastic cervical tissues. Several machine learning methods are trained utilizing different training-test-set-split strategies, and their corresponding accuracies are compared. Results: Our results include robust measurements of model performance with two approaches: a 90:10 training-test-set-split and leave-one-out cross-validation. By comparing the classifier's accuracy directly with the ground truth obtained during histology analysis, we demonstrate how conventionally used shuffled split leads to an over-estimate of true classifier performance (0.964±0.00). The leave-one-out cross-validation, however, leads to more accurate performance (0.812±0.21) with respect to newly obtained samples that were not used to train the models. Conclusions: Combination of Mueller polarimetry and machine learning is a powerful tool for the task of screening for pre-cancerous conditions in cervical tissue sections. Nevertheless, there is a inherent bias with conventional processes that can be addressed using more conservative classifier training approaches. This results in overall improvements of the sensitivity and specificity of the developed techniques for "unseen" images.

Impact of corpus callosum fiber tract crossing on polarimetric images of human brain histological sections: ex vivo studies in transmission configuration.

Significance: Imaging Mueller polarimetry is capable to trace in-plane orientation of brain fiber tracts by detecting the optical anisotropy of white matter of healthy brain. Brain tumor cells grow chaotically and destroy this anisotropy. Hence, the drop in scalar retardance values and randomization of the azimuth of the optical axis could serve as the optical marker for brain tumor zone delineation. Aim: The presence of underlying crossing fibers can also affect the values of scalar retardance and the azimuth of the optical axis. We studied and analyzed the impact of fiber crossing on the polarimetric images of thin histological sections of brain corpus callosum. Approach: We used the transmission Mueller microscope for imaging of two-layered stacks of thin sections of corpus callosum tissue to mimic the overlapping brain fiber tracts with different fiber orientations. The decomposition of the measured Mueller matrices was performed with differential and Lu-Chipman algorithms and completed by the statistical analysis of the maps of scalar retardance, azimuth of the optical axis, and depolarization. Results: Our results indicate the sensitivity of Mueller polarimetry to different spatial arrangement of brain fiber tracts as seen in the maps of scalar retardance and azimuth of optical axis of two-layered stacks of corpus callosum sections The depolarization varies slightly (<15%) with the orientation of the optical axes in both corpus callosum stripes, but its value increases by 2.5 to 3 times with the stack thickness. Conclusions: The crossing brain fiber tracts measured in transmission induce the drop in values of scalar retardance and randomization of the azimuth of the optical axis at optical path length of 15 µm. It suggests that the presence of nerve fibers crossing within the depth of few microns will be also detected in polarimetric maps of brain white matter measured in reflection configuration.

Effects of formalin fixation on polarimetric properties of brain tissue: fresh or fixed?

Significance: Imaging Mueller polarimetry (IMP) appears as a promising technique for real-time delineation of healthy and neoplastic tissue during neurosurgery. The training of machine learning algorithms used for the image post-processing requires large data sets typically derived from the measurements of formalin-fixed brain sections. However, the success of the transfer of such algorithms from fixed to fresh brain tissue depends on the degree of alterations of polarimetric properties induced by formalin fixation (FF). Aim: Comprehensive studies were performed on the FF induced changes in fresh pig brain tissue polarimetric properties. Approach: Polarimetric properties of pig brain were assessed in 30 coronal thick sections before and after FF using a wide-field IMP system. The width of the uncertainty region between gray and white matter was also estimated. Results: The depolarization increased by 5% in gray matter and remained constant in white matter following FF, whereas the linear retardance decreased by 27% in gray matter and by 28% in white matter after FF. The visual contrast between gray and white matter and fiber tracking remained preserved after FF. Tissue shrinkage induced by FF did not have a significant effect on the uncertainty region width. Conclusions: Similar polarimetric properties were observed in both fresh and fixed brain tissues, indicating a high potential for transfer learning.

Robustness of the wide-field imaging Mueller polarimetry for brain tissue differentiation and white matter fiber tract identification in a surgery-like environment: an ex vivo study.

During neurooncological surgery, the visual differentiation of healthy and diseased tissue is often challenging. Wide-field imaging Muller polarimetry (IMP) is a promising technique for tissue discrimination and in-plane brain fiber tracking in an interventional setup. However, the intraoperative implementation of IMP requires realizing imaging in the presence of remanent blood, and complex surface topography resulting from the use of an ultrasonic cavitation device. We report on the impact of both factors on the quality of polarimetric images of the surgical resection cavities reproduced in fresh animal cadaveric brains. The robustness of IMP is observed under adverse experimental conditions, suggesting a feasible translation of IMP for in vivo neurosurgical applications.

High-Molecular-Weight Plasmids Carrying Carbapenemase Genes blaNDM-1, blaKPC-2, and blaOXA-48 Coexisting in Clinical Klebsiella pneumoniae Strains of ST39.

BACKGROUND: Klebsiella pneumoniae, a member of the ESKAPE group of bacterial pathogens, has developed multi-antimicrobial resistance (AMR), including resistance to carbapenems, which has increased alarmingly due to the acquisition of carbapenemase genes located on specific plasmids. METHODS: Four clinical K. pneumoniae isolates were collected from four patients of a neuro-intensive care unit in Moscow, Russia, during the point prevalence survey. The AMR phenotype was estimated using the Vitec-2 instrument, and whole genome sequencing (WGS) was done using Illumina and Nanopore technologies. RESULTS: All strains were resistant to beta-lactams, nitrofurans, fluoroquinolones, sulfonamides, aminoglycosides, and tetracyclines. WGS analysis revealed that all strains were closely related to K. pneumoniae ST39, capsular type K-23, with 99.99% chromosome identity. The novelty of the study is the description of the strains carrying simultaneously three large plasmids of the IncHI1B, IncC, and IncFIB groups carrying the carbapenemase genes of three types, blaOXA-48, blaNDM-1, and blaKPC-2, respectively. The first of them, highly identical in all strains, was a hybrid plasmid that combined two regions of the resistance genes (blaOXA-48 and blaTEM-1 + blaCTX-M-15 + blaOXA-1 + catB + qnrS1 + int1) and a region of the virulence genes (iucABCD, iutA, terC, and rmpA2::IS110). CONCLUSION: The spread of K. pneumoniae strains carrying multiple plasmids conferring resistance even to last-resort antibiotics is of great clinical concern.

Multidrug-Resistant and Extensively Drug-Resistant Acinetobacter baumannii Causing Nosocomial Meningitis in the Neurological Intensive Care Unit.

Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013-2020. The death rate was 37.8%. Strain susceptibility to antimicrobials was determined on the Vitek-2 instrument. Whole-genome sequencing was conducted using Illumina technology; the sequence types (ST), capsular types (KL), lipooligosaccharide outer core locus (OCL), antimicrobial resistance genes, and virulence genes were identified. The prevalent ST was ST2, belonging to the international clone IC2, and rarer, ST1, ST19, ST45, ST78, ST106, and ST400, with prevalence of KL9 and OCL1. Twenty-nine strains belonged to multidrug-resistant (MDR) and eight extensively drug-resistant (XDR) categories. Genes conferring resistance to beta-lactams (blaPER, blaGES, blaADC, blaCARB, blaCTX-M, blaTEM, and blaOXA-types), aminoglycosides (aac, aad, ant, aph, and arm), tetracyclines (tet), macrolides (msr and mph), phenicols (cml, cat, and flo), sulfonamides (dfr and sul), rifampin (arr), and antiseptics (qac) were identified. Virulence genes of nine groups (Adherence, Biofilm formation, Enzymes, Immune evasion, Iron uptake, Regulation, Serum resistance, Stress adaptation, and Antiphagocytosis) were detected. The study highlights the heterogeneity in genetic clones, antimicrobial resistance, and virulence genes variability among the agents of A. baumannii meningitis, with the prevalence of the dominant international clone IC2.

Neuroprotective and memory enhancing properties of a dual agonist of the FGF receptor and NCAM.

The fibroblast growth factor receptor (FGFR) plays a vital role in the development of the nervous system regulating a multitude of cellular processes. One of the interaction partners of the FGFR is the neural cell adhesion molecule (NCAM), which is known to play an important role in neuronal development, regeneration and synaptic plasticity. Thus, simultaneous activation of FGFR- and NCAM-mediated signaling pathways may be expected to affect processes underlying neurodegenerative diseases. We here report the identification of a peptide compound, Enreptin, capable of interacting with both FGFR and NCAM. We demonstrate that this dual specificity agonist induces phosphorylation of FGFR and differentiation and survival of primary neurons in vitro, and that these effects are inhibited by abrogation of both NCAM and FGFR signaling pathways. Furthermore, Enreptin crosses the blood-brain barrier after subcutaneous administration, enhances long-term memory in normal mice and ameliorates memory deficit in mice with induced brain inflammation. Moreover, Enreptin reduces cognitive impairment and neuronal death induced by Aß25-35 in a rat model of Alzheimer's disease, and reduces the mortality rate and clinical signs of experimental autoimmune encephalomyelitis in rats. Thus, Enreptin is an attractive candidate for the treatment of neurological diseases.

The neural cell adhesion molecule-derived peptide FGL facilitates long-term plasticity in the dentate gyrus in vivo.

The neural cell adhesion molecule (NCAM) is known to play a role in developmental and structural processes but also in synaptic plasticity and memory of the adult animal. Recently, FGL, a NCAM mimetic peptide that binds to the Fibroblast Growth Factor Receptor 1 (FGFR-1), has been shown to have a beneficial impact on normal memory functioning, as well as to rescue some pathological cognitive impairments. Whether its facilitating impact may be mediated through promoting neuronal plasticity is not known. The present study was therefore designed to test whether FGL modulates the induction and maintenance of synaptic plasticity in the dentate gyrus (DG) in vivo. For this, we first assessed the effect of the FGL peptide on synaptic functions at perforant path-dentate gyrus synapses in the anesthetized rat. FGL, or its control inactive peptide, was injected locally 60 min before applying high-frequency stimulation (HFS) to the medial perforant path. The results suggest that although FGL did not alter basal synaptic transmission, it facilitated both the induction and maintenance of LTP. Interestingly, FGL also modified the heterosynaptic plasticity observed at the neighboring lateral perforant path synapses. The second series of experiments, using FGL intracerebroventricular infusion in the awake animal, confirmed its facilitating effect on LTP for up to 24 h. Our data also suggest that FGL could alter neurogenesis associated with LTP. In sum, these results show for the first time that enhancing NCAM functions by mimicking its heterophilic interaction with FGFR facilitates hippocampal synaptic plasticity in the awake, freely moving animal.