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Deoxyribonucleic acid or DNA is one of the most fundamental molecules of life as it has the power to encode the basic structure of every living thing large or small, including us. Not only is DNA responsible for precisely describing every single aspect that makes us what we are, it also directly affects the world around us, every second of every day. Indeed, by unlocking the genetic code embedded in DNA we were already able to create new diagnostics that allow us to detect certain diseases before we can even detect the first symptoms. It allows us to create new, stronger crops that allow us to feed the worlds ever growing population. However, in spite of this newly acquired power to manipulate the very core of life itself we are ever so often reminded of the fact that mankind is still very much subjected to the ever evolving ‘source code’ of life rather than being in control of it. Indeed, many disease causing pathogens exchange DNA that provides them with the ability to withstand even the most powerful known antibiotics. Furthermore, many aspects of the genetic code still remain obfuscated by its complex nature and are very much out of reach of even the most modern sequencing technologies because these often rely on determining sequence information for a large population of DNA. Therefore, the search for genomic analysis strategies that allow us to investigate the code of life at the single molecule level are the next big frontier scientific research. Here, optical DNA mapping is one of the top contenders to address some of the long standing issues that remain with modern ‘next-generation’ sequencing technologies such as their inability to achieve long readout lengths and difficulties encountered when trying to detect long range structural variations in the genome. In optical mapping, fluorescent molecules are attached to the DNA in a sequence-specific manner. Through subsequent observation of surface deposited, contiguous DNA molecules with a fluorescent microscope, long range information about the sequence can be retrieved. The information content of such genomic maps is of course, less dense than in the case of sequencing approach. However, genomic DNA maps have already proven their worth by serving as scaffolds for sequencing based reconstructions of complex genomes. Furthermore, if the resolution of the microscopy imaging in mapping could be increased beyond the diffraction limit of 250 nm, which roughly corresponds to a map labeling density of one label every 700 to 800 base pairs, the information density of maps would also be increased drastically. Fortunately, recent years have seen an increasing number of developments in so called super-resolution microscopy methods. The founders of this field were even awarded the Nobel Prize in 2014. Stimulated emission depletion microscopy (STED) is one of such techniques and allows to produce images at resolutions exceeding 100 nm in an almost instantaneous way. The presented work aims to evaluate the applicability of STED for optical DNA mapping with an emphasis on optical map characterisation and differentiation. For this reason, STED based DNA mapping was attempted on reference DNA samples of two viruses, phage T7 and phage Lambda. Intensity profiles from DNA images obtained with STED were extracted and compared to in silico generated reference intensity profiles for these species. This work demonstrates that STED is applicable to optical DNA mapping but also that it provides a sufficient amount of information to allow for pattern recognition. Indeed, the correct specie was assessed to samples containing one specie. Furthermore, two populations could be distinguished in a sample composed of the two species showing that STED allows for DNA differentiation.

STED, super-resolution, DNA mapping, DNA imaging, optical mapping, DNA identification, DNA differentiation, fluorescence microscopy --- Physique, chimie, mathématiques & sciences de la terre > Chimie

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This Urological Cancer 2020 collection contains a set of multidisciplinary contributions to the extraordinary heterogeneity of tumor mechanisms, diagnostic approaches, and therapies of the renal, urinary tract, and prostate cancers, with the intention of offering to interested readers a representative snapshot of the status of urological research.

Research & information: general --- Biology, life sciences --- renal cell carcinoma --- iron --- macrophages --- chelation therapy --- urothelial carcinoma --- transcriptome --- microtubule --- MAP1B --- prognosis --- KLF5 --- androgen receptor --- cell proliferation --- tumorigenesis --- prostate cancer --- precision medicine --- whole genome sequencing --- optical mapping --- therapy --- prostate carcinoma --- prostate mpMRI --- machine learning --- artificial intelligence --- deep learning --- neural network --- angiogenesis --- angiogenic growth factors --- antiangiogenic therapy --- renal tumors --- prevention --- α1-adrenoceptor antagonists --- anoikis --- vascularity --- research model --- oncogenes --- tumor suppressor genes --- MR-guided --- radiotherapy --- MRgRT --- stereotactic ablative radiotherapy --- stereotactic ablative radiation therapy (SABR) --- renal cell cancer --- RCC --- online adaptive --- [68Ga]Ga-PSMA PET/CT --- dual-time point imaging --- delayed imaging --- biphasic imaging --- lesion positivity rate --- CXCL9 --- PD1 --- PD-L1 --- stage T1 NMIBC --- prostatic neoplasms/mortality --- prostatic neoplasms/epidemiology --- SEER Program --- bladder cancer --- transurethral resection --- en-bloc resection --- CPT1A --- fatty acids --- serine --- androgen response --- ROS --- oxidative stress --- DONSON --- Downstream Neighbor of SON --- biomarker --- metastatic spread --- diagnosis --- differential diagnosis --- histopathology --- immunohistochemistry --- stroma signature --- patient-derived xenografts --- n/a --- Research. --- Biology.

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This Urological Cancer 2020 collection contains a set of multidisciplinary contributions to the extraordinary heterogeneity of tumor mechanisms, diagnostic approaches, and therapies of the renal, urinary tract, and prostate cancers, with the intention of offering to interested readers a representative snapshot of the status of urological research.

renal cell carcinoma --- iron --- macrophages --- chelation therapy --- urothelial carcinoma --- transcriptome --- microtubule --- MAP1B --- prognosis --- KLF5 --- androgen receptor --- cell proliferation --- tumorigenesis --- prostate cancer --- precision medicine --- whole genome sequencing --- optical mapping --- therapy --- prostate carcinoma --- prostate mpMRI --- machine learning --- artificial intelligence --- deep learning --- neural network --- angiogenesis --- angiogenic growth factors --- antiangiogenic therapy --- renal tumors --- prevention --- α1-adrenoceptor antagonists --- anoikis --- vascularity --- research model --- oncogenes --- tumor suppressor genes --- MR-guided --- radiotherapy --- MRgRT --- stereotactic ablative radiotherapy --- stereotactic ablative radiation therapy (SABR) --- renal cell cancer --- RCC --- online adaptive --- [68Ga]Ga-PSMA PET/CT --- dual-time point imaging --- delayed imaging --- biphasic imaging --- lesion positivity rate --- CXCL9 --- PD1 --- PD-L1 --- stage T1 NMIBC --- prostatic neoplasms/mortality --- prostatic neoplasms/epidemiology --- SEER Program --- bladder cancer --- transurethral resection --- en-bloc resection --- CPT1A --- fatty acids --- serine --- androgen response --- ROS --- oxidative stress --- DONSON --- Downstream Neighbor of SON --- biomarker --- metastatic spread --- diagnosis --- differential diagnosis --- histopathology --- immunohistochemistry --- stroma signature --- patient-derived xenografts --- n/a --- Research. --- Biology.

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Optical technologies provide unique opportunities for the diagnosis of various pathological disorders. The range of biophotonics applications in clinical practice is considerably wide given that the optical properties of biological tissues are subject to significant changes during disease progression. Due to the small size of studied objects (from μm to mm) and despite some minimum restrictions (low-intensity light is used), these technologies have great diagnostic potential both as an additional tool and in cases of separate use, for example, to assess conditions affecting microcirculatory bed and tissue viability. This Special Issue presents topical articles by researchers engaged in the development of new methods and devices for optical non-invasive diagnostics in various fields of medicine. Several studies in this Special Issue demonstrate new information relevant to surgical procedures, especially in oncology and gynecology. Two articles are dedicated to the topical problem of breast cancer early detection, including during surgery. One of the articles is devoted to urology, namely to the problem of chronic or recurrent episodic urethral pain. Several works describe the studies in otolaryngology and dentistry. One of the studies is devoted to diagnosing liver diseases. A number of articles contribute to the studying of the alterations caused by diabetes mellitus and cardiovascular diseases. The results of all the presented articles reflect novel innovative research and emerging ideas in optical non-invasive diagnostics aimed at their wider translation into clinical practice.

Public health & preventive medicine --- chemoresistance --- cisplatin --- gray-level co-occurrence matrix --- ovarian adenocarcinoma --- optical densitometry --- liver diagnosis --- indocyanine green --- liver functional reserve --- optical density --- plasma disappearance rate --- cross-polarization optical coherence tomography (CP OCT) --- ultrasound --- urethral pain syndrome --- epithelial atrophy --- epithelial hyperplasia --- inflammation --- fibrosis --- image evaluation --- liver cancer --- endogenous fluorescence --- laser Doppler flowmetry --- blood perfusion --- minimally invasive interventions --- machine learning --- raman spectroscopy --- optical diagnostic --- periodontitis --- tooth tissues --- biophotonics --- calculus --- zebrafish --- embryonic development --- cardiovascular system --- in vivo imaging --- optical mapping --- non-invasive measurements --- shortwave-infrared light --- near-infrared light --- visible light --- fluorescence --- breast cancer --- duct --- visible human project --- Monte Carlo simulation --- voxelized media --- cross-polarization optical coherence tomography (CP-OCT) --- compressional optical coherence elastography (C-OCE) --- image assessment --- optical properties --- scattering theories --- circulatory system --- blood rheology --- red blood cell aggregation --- laser tweezers --- laser aggregometry --- digital capillaroscopy --- coronary heart disease --- diabetes mellitus --- optical diagnostics --- digital diaphanoscopy --- magnetic resonance imaging --- paranasal sinuses --- inflammatory diseases --- non-invasive optical diagnostics --- cumulative sum --- power spectrum --- heating test --- diabetes mellitus type 2 --- wearable blood flow sensors --- ortostatic test --- postural changes --- body position --- blood perfusion in forehead --- blood perfusion in wrists --- blood perfusion in shins --- blood perfusion oscillations --- vasomotions --- optics --- spectroscopy --- imaging --- diagnostics

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Optical technologies provide unique opportunities for the diagnosis of various pathological disorders. The range of biophotonics applications in clinical practice is considerably wide given that the optical properties of biological tissues are subject to significant changes during disease progression. Due to the small size of studied objects (from μm to mm) and despite some minimum restrictions (low-intensity light is used), these technologies have great diagnostic potential both as an additional tool and in cases of separate use, for example, to assess conditions affecting microcirculatory bed and tissue viability. This Special Issue presents topical articles by researchers engaged in the development of new methods and devices for optical non-invasive diagnostics in various fields of medicine. Several studies in this Special Issue demonstrate new information relevant to surgical procedures, especially in oncology and gynecology. Two articles are dedicated to the topical problem of breast cancer early detection, including during surgery. One of the articles is devoted to urology, namely to the problem of chronic or recurrent episodic urethral pain. Several works describe the studies in otolaryngology and dentistry. One of the studies is devoted to diagnosing liver diseases. A number of articles contribute to the studying of the alterations caused by diabetes mellitus and cardiovascular diseases. The results of all the presented articles reflect novel innovative research and emerging ideas in optical non-invasive diagnostics aimed at their wider translation into clinical practice.

chemoresistance --- cisplatin --- gray-level co-occurrence matrix --- ovarian adenocarcinoma --- optical densitometry --- liver diagnosis --- indocyanine green --- liver functional reserve --- optical density --- plasma disappearance rate --- cross-polarization optical coherence tomography (CP OCT) --- ultrasound --- urethral pain syndrome --- epithelial atrophy --- epithelial hyperplasia --- inflammation --- fibrosis --- image evaluation --- liver cancer --- endogenous fluorescence --- laser Doppler flowmetry --- blood perfusion --- minimally invasive interventions --- machine learning --- raman spectroscopy --- optical diagnostic --- periodontitis --- tooth tissues --- biophotonics --- calculus --- zebrafish --- embryonic development --- cardiovascular system --- in vivo imaging --- optical mapping --- non-invasive measurements --- shortwave-infrared light --- near-infrared light --- visible light --- fluorescence --- breast cancer --- duct --- visible human project --- Monte Carlo simulation --- voxelized media --- cross-polarization optical coherence tomography (CP-OCT) --- compressional optical coherence elastography (C-OCE) --- image assessment --- optical properties --- scattering theories --- circulatory system --- blood rheology --- red blood cell aggregation --- laser tweezers --- laser aggregometry --- digital capillaroscopy --- coronary heart disease --- diabetes mellitus --- optical diagnostics --- digital diaphanoscopy --- magnetic resonance imaging --- paranasal sinuses --- inflammatory diseases --- non-invasive optical diagnostics --- cumulative sum --- power spectrum --- heating test --- diabetes mellitus type 2 --- wearable blood flow sensors --- ortostatic test --- postural changes --- body position --- blood perfusion in forehead --- blood perfusion in wrists --- blood perfusion in shins --- blood perfusion oscillations --- vasomotions --- optics --- spectroscopy --- imaging --- diagnostics