Data on the genome analysis of the wood-rotting fungus Steccherinum ochraceum LE-BIN 3174

In the present article, we report data on the whole-genome sequencing of wood-rotting (white-rot) fungus Steccherinum ochraceum LE-BIN 3174. The S. ochraceum LE-BIN 3174 genome consists of 770 scaffolds (N50 = 62,812 bp) with the total length of assembly ∼35 Mb. The structural annotation of the genome resulted in the prediction of 12,441 gene models, among which 181 were models of tRNA-coding genes, and 12,260 - protein-coding genes. The protein-coding genes were annotated with different databases (Pfam, InterPro, eggNOG, dbCAN, and MEROPS). The whole genome sequence and functional annotation provide an important information for the deep investigation of biochemical processes that take place during the late stages of wood decomposition by Basidiomycetes. The Whole Genome project of S. ochraceum LE-BIN 3174 had been deposited at DDBJ/ENA/GenBank under the accession RWJN00000000. The version described in this work is version RWJN00000000.1. For further interpretation of the data provided in this article, please refer to the research article "Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum" [1].

Signatures of Molecular Unification and Progressive Oxidation Unfold in Dissolved Organic Matter of the Ob-Irtysh River System along Its Path to the Arctic Ocean

The Ob-Irtysh River system is the seventh-longest one in the world. Unlike the other Great Siberian rivers, it is only slightly impacted by the continuous permafrost in its low flow. Instead, it drains the Great Vasyugan mire, which is the world largest swamp, and receives huge load of the Irtysh waters which drain the populated lowlands of the East Siberian Plain. The central challenge of this paper is to understand the processes responsible for molecular transformations of natural organic matter (NOM) in the Ob-Irtysh river system along the South-North transect. For solving this task, the NOM was isolated from the water samples collected along the 3,000 km transect using solid-phase extraction. The NOM samples were further analyzed using high resolution mass spectrometry and optical spectroscopy. The obtained results have shown a distinct trend both in molecular composition and diversity of the NOM along the South-North transect: the largest diversity was observed in the Southern "swamp-wetland" stations. The samples were dominated with humic and lignin-like components, and enriched with aminosugars. After the Irtysh confluence, the molecular nature of NOM has changed drastically: it became much more oxidized and enriched with heterocyclic N-containing compounds. These molecular features are very different from the aliphatics-rich permafrost NOM. They witnesses much more conservative nature of the NOM discharged into the Arctic by the Ob-Irtysh river system. In general, drastic reduction in molecular diversity was observed in the northern stations located in the lower Ob flow.

Source apportionment of circum-Arctic atmospheric black carbon from isotopes and modeling

Black carbon (BC) contributes to Arctic climate warming, yet source attributions are inaccurate due to lacking observational constraints and uncertainties in emission inventories. Year-round, isotope-constrained observations reveal strong seasonal variations in BC sources with a consistent and synchronous pattern at all Arctic sites. These sources were dominated by emissions from fossil fuel combustion in the winter and by biomass burning in the summer. The annual mean source of BC to the circum-Arctic was 39 ± 10% from biomass burning. Comparison of transport-model predictions with the observations showed good agreement for BC concentrations, with larger discrepancies for (fossil/biomass burning) sources. The accuracy of simulated BC concentration, but not of origin, points to misallocations of emissions in the emission inventories. The consistency in seasonal source contributions of BC throughout the Arctic provides strong justification for targeted emission reductions to limit the impact of BC on climate warming in the Arctic and beyond.

Optical coherence tomography-based angiography device with real-time angiography B-scans visualization and hand-held probe for everyday clinical use

This work is dedicated to the development of the OCT system with angiography for everyday clinical use. Two major problems were solved during the development: compensation of specific natural tissue displacements, induced by contact scanning mode and physiological motion of patients (eg, respiratory and cardiac motions) and online visualization of vessel cross-sections to provide feedback for the system operator.

Optical coherence tomography in gynecology: a narrative review

Modern gynecologic practice requires noninvasive diagnostics techniques capable of detecting morphological and functional alterations in tissues of female reproductive organs. Optical coherence tomography (OCT) is a promising tool for providing imaging of biotissues with high resolution at depths up to 2 mm. Design of the customized probes provides wide opportunities for OCT use in gynecology. This paper contains a retrospective insight into the history of OCT employment in gynecology, an overview of the existing gynecologic OCT probes, including those for combination with other diagnostic modalities, and state-of-the-art application of OCT for diagnostics of tumor and nontumor pathologies of female genitalia. Perspectives of OCT both in diagnostics and treatment planning and monitoring in gynecology are overviewed.

Current rates and mechanisms of subsea permafrost degradation in the East Siberian Arctic Shelf

The rates of subsea permafrost degradation and occurrence of gas-migration pathways are key factors controlling the East Siberian Arctic Shelf (ESAS) methane (CH₄) emissions, yet these factors still require assessment. It is thought that after inundation, permafrost-degradation rates would decrease over time and submerged thaw-lake taliks would freeze; therefore, no CH₄ release would occur for millennia. Here we present results of the first comprehensive scientific re-drilling to show that subsea permafrost in the near-shore zone of the ESAS has a downward movement of the ice-bonded permafrost table of ∼14 cm year⁻¹ over the past 31–32 years. Our data reveal polygonal thermokarst patterns on the seafloor and gas-migration associated with submerged taliks, ice scouring and pockmarks. Knowing the rate and mechanisms of subsea permafrost degradation is a prerequisite to meaningful predictions of near-future CH₄ release in the Arctic.

The rate of subsea permafrost degradation is a key factor controlling marine methane emissions in the Arctic. Here, using re-drilled boreholes, the authors show that the ice-bonded permafrost table in the near-shore East Siberian Arctic Shelf has deepened by ∼14 cm per year over the past 31–32 years.

Siberian Arctic black carbon sources constrained by model and observation

Black carbon (BC) in haze and deposited on snow and ice can have strong effects on the radiative balance of the Arctic. There is a geographic bias in Arctic BC studies toward the Atlantic sector, with lack of observational constraints for the extensive Russian Siberian Arctic, spanning nearly half of the circum-Arctic. Here, 2 y of observations at Tiksi (East Siberian Arctic) establish a strong seasonality in both BC concentrations (8 ng⋅m-3 to 302 ng⋅m-3) and dual-isotope-constrained sources (19 to 73% contribution from biomass burning). Comparisons between observations and a dispersion model, coupled to an anthropogenic emissions inventory and a fire emissions inventory, give mixed results. In the European Arctic, this model has proven to simulate BC concentrations and source contributions well. However, the model is less successful in reproducing BC concentrations and sources for the Russian Arctic. Using a Bayesian approach, we show that, in contrast to earlier studies, contributions from gas flaring (6%), power plants (9%), and open fires (12%) are relatively small, with the major sources instead being domestic (35%) and transport (38%). The observation-based evaluation of reported emissions identifies errors in spatial allocation of BC sources in the inventory and highlights the importance of improving emission distribution and source attribution, to develop reliable mitigation strategies for efficient reduction of BC impact on the Russian Arctic, one of the fastest-warming regions on Earth.

The East Siberian Arctic Shelf: towards further assessment of permafrost-related methane fluxes and role of sea ice

Sustained release of methane (CH(4)) to the atmosphere from thawing Arctic permafrost may be a positive and significant feedback to climate warming. Atmospheric venting of CH(4) from the East Siberian Arctic Shelf (ESAS) was recently reported to be on par with flux from the Arctic tundra; however, the future scale of these releases remains unclear. Here, based on results of our latest observations, we show that CH(4) emissions from this shelf are likely to be determined by the state of subsea permafrost degradation. We observed CH(4) emissions from two previously understudied areas of the ESAS: the outer shelf, where subsea permafrost is predicted to be discontinuous or mostly degraded due to long submergence by seawater, and the near shore area, where deep/open taliks presumably form due to combined heating effects of seawater, river run-off, geothermal flux and pre-existing thermokarst. CH(4) emissions from these areas emerge from largely thawed sediments via strong flare-like ebullition, producing fluxes that are orders of magnitude greater than fluxes observed in background areas underlain by largely frozen sediments. We suggest that progression of subsea permafrost thawing and decrease in ice extent could result in a significant increase in CH(4) emissions from the ESAS.

Criteria for pathology recognition in optical coherence tomography of fallopian tubes

An increase of infertility and chronic pelvic pains syndrome, a growing level of latent diseases of this group, as well as a stably high percentage (up to 25% for infertility and up to 60% for the chronic pelvic pains syndrome) of undetermined origin raises the requirement for novel introscopic diagnostic techniques. We demonstrate abilities of optical coherence tomography (OCT) as a complementary technique to laparoscopy in diagnostics of fallopian tubes pathologies. We have acquired OCT images of different parts of fallopian tubes in norm and with morphologically proven pathology. Based on comparative analysis of the OCT data and the results of histological studies, we have worked out the subjective OCT criteria for distinguishing between unaltered and pathologic tissues. The developed criteria are verified in blind recognition tests. Diagnostic efficacy of OCT diagnostics in the case ofpelvic inflammatory diseases has been statistically evaluated, and high diagnostic accuracy (88%) is shown. Basing of the subjective criteria, an attempt to develop independent criteria aimed for automated recognition of pathological states in fallopian tubes is undertaken. Enhanced diagnostic accuracy (96%) of the developed independent criteria is demonstrated.

Extensive methane venting to the atmosphere from sediments of the East Siberian Arctic Shelf

Remobilization to the atmosphere of only a small fraction of the methane held in East Siberian Arctic Shelf (ESAS) sediments could trigger abrupt climate warming, yet it is believed that sub-sea permafrost acts as a lid to keep this shallow methane reservoir in place. Here, we show that more than 5000 at-sea observations of dissolved methane demonstrates that greater than 80% of ESAS bottom waters and greater than 50% of surface waters are supersaturated with methane regarding to the atmosphere. The current atmospheric venting flux, which is composed of a diffusive component and a gradual ebullition component, is on par with previous estimates of methane venting from the entire World Ocean. Leakage of methane through shallow ESAS waters needs to be considered in interactions between the biogeosphere and a warming Arctic climate.

Endoscopic OCT with forward-looking probe: clinical studies in urology and gastroenterology

In the current paper we present results of application of endoscopic time-domain OCT (EOCT) with lateral scanning by forward looking miniprobe. We analysed material of clinical studies of 554 patients: 164 patients with urinary bladder pathology, and 390 with gastrointestinal tract pathology. We reviewed the materials obtained in different clinics using the OCT device elaborated at the Institute of Applied Physics. We demonstrate results of EOCT application in detection of early cancer and surgery guidance, examples of combined use of OCT and fluorescence imaging. As a result, we show the diagnostic accuracy of EOCT in specific clinical tasks. The sensitivity of EOCT cancer determination in Barrett's esophagus is from 71% to 85% at different stages of neoplasia with specificity 68% for all stages. As for bladder carcinoma, the sensitivity and specificity are 85% and 68%, respectively. In colon dysplasia EOST demonstrates high efficacy: sensitivity 92% and specificity 84%.

Endoscopic OCT with forward-looking probe: clinical studies in urology and gastroenterology

In the current paper we present results of application of endoscopic time-domain OCT (EOCT) with lateral scanning by forward looking miniprobe. We analysed material of clinical studies of 554 patients: 164 patients with urinary bladder pathology, and 390 with gastrointestinal tract pathology. We reviewed the materials obtained in different clinics using the OCT device elaborated at the Institute of Applied Physics. We demonstrate results of EOCT application in detection of early cancer and surgery guidance, examples of combined use of OCT and fluorescence imaging. As a result, we show the diagnostic accuracy of EOCT in specific clinical tasks. The sensitivity of EOCT cancer determination in Barrett's esophagus is from 71% to 85% at different stages of neoplasia with specificity 68% for all stages. As for bladder carcinoma, the sensitivity and specificity are 85% and 68%, respectively. In colon dysplasia EOST demonstrates high efficacy: sensitivity 92% and specificity 84%.

Endoscopic applications of optical coherence tomography

We report results of application of our endoscopic optical coherence tomography (EOCT) system in clinical experiments to image human internal organs. Based on the experience of studying more than 100 patients, we make first general conclusions on the place and capabilities of this method in diagnosing human mucous membranes. It is demonstrated that EOCT can serve for several clinical purposes such as performing directed biopsy, monitoring functional states of human body, guiding surgical and other treatments and monitoring post-operative recovery processes. We show that applications of OCT are more informative in the case of internal organs covered by epithelium separated from underlying stroma by a smooth basal membrane and therefore concentrate on the results of the EOCT study of three internal organs, namely of larynx, bladder, and uterine cervix. Finally, we report first examination of internal organs in abdomen with the use of laparoscopic OCT.

In vivo endoscopic OCT imaging of precancer and cancer states of human mucosa

First results of endoscopic applications of optical coherence tomography for in vivo studies of human mucosa in respiratory, gastrointestinal, urinary and genital tracts are presented. A novel endoscopic OCT (EOCT) system has been created that is based on the integration of a sampling arm of an all-optical-fiber interferometer into standard endoscopic devices using their biopsy channel to transmit low-coherence radiation to investigated tissue. We have studied mucous membranes of esophagus, larynx, stomach, urinary bladder, uterine cervix and body as typical localization for carcinomatous processes. Images of tumor tissues versus healthy tissues have been recorded and analyzed. Violations of well-defined stratified healthy mucosa structure in cancered tissue are distinctly seen by EOCT, thus making this technique promising for early diagnosis of tumors and precise guiding of excisional biopsy.