A subgroup of light-driven sodium pumps with an additional Schiff base counterion.

Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.

[Russian study on brain aneurysm surgery: a continuation (RIHA II)]. / Rossiiskoe issledovanie po khirurgii anevrizm golovnogo mozga: prodolzhenie (RIKhA II).

OBJECTIVE: To assess the main performance indicators of neurosurgical departments in surgical treatment of cerebral aneurysms in the Russian Federation. MATERIAL AND METHODS: We analyzed 22 neurosurgical departments (19 regional and 3 federal hospitals) in 2017 and 2021. The study enrolled 6.135 patients including 3.160 ones in 2017 and 2.975 ones in 2021. We studied the features of surgical treatment of cerebral aneurysms in different volume hospitals and factors influencing postoperative outcomes. RESULTS: The number of surgeries for cerebral aneurysms decreased from 2.950 in 2017 to 2.711 in 2021. Postoperative mortality rate was 6.3% and 5.6%, respectively. The number of microsurgical interventions decreased from 60% in 2017 to 48% in 2021. The share of endovascular interventions increased from 40% to 52%, respectively. Endovascular embolization was accompanied by stenting in 55% of cases. Simultaneous revascularization was carried out in 2% of cases. In 2021, the number of patients undergoing surgery in acute period of hemorrhage increased to 70% (in 2017 - 61%). The number of hospitals performing more than 50 surgical interventions for cerebral aneurysms annually increased from 14 in 2017 to 17 in 2021. CONCLUSION: Certain changes in neurosurgical service occurred in 2021 compared to 2017. Lower number of surgical interventions for cerebral aneurysms, most likely caused by the COVID-19 pandemic, is accompanied by lower postoperative mortality. Endovascular interventions and revascularization techniques became more common. The number of surgeries in acute period after aneurysm rupture and hospitals performing more than 50 surgical interventions for cerebral aneurysms annually increased.

Berezin Quantization, Conformal Welding and the Bott-Virasoro Group.

Following Nag-Sullivan, we study the representation of the group Diff+(S1) of diffeomorphisms of the circle on the Hilbert space of holomorphic functions. Conformal welding provides triangular decompositions for the corresponding symplectic transformations. We apply Berezin formalism and lift this decomposition to operators acting on the Fock space. This lift provides quantization of conformal welding, gives a new representative of the Bott-Virasoso cocycle class, and leads to a surprising identity for the Takhtajan-Teo energy functional on Diff+(S1).

Interplay between structural changes, surface states and quantum confinement effects in semiconducting Mg2Si and Ca2Si thin films.

Ab initio techniques have been used to investigate structural changes in semiconducting Mg2Si and Ca2Si thin films (from 17 nm down to 0.2 nm corresponding to the 2D structure) along with band-gap variations due to quantum confinement. Cubic Mg2Si(111) thin films being dynamically stable at thicknesses (d) larger than 0.3 nm displayed an indirect band gap, the reduction of which with increasing d could be reasonably well described by the simple effective mass approximation. Only 2D Mg2Si has a unique structure because of the orthorhombic distortion and the direct band gap. Since the surface energy of cubic Ca2Si(111) films was lower with respect to any surface of the orthorhombic phase, which is the ground state for the Ca2Si bulk, the metastable in-bulk cubic phase in the form of thin films turned out to be preferable in total energy than any orthorhombic Ca2Si thin film for d < 3 nm. Sizable structural distortion and the appearance of surface states in the gap region of Ca2Si thin films with d < 3 nm could be the reason for an odd dependence of the band-gap variation on d.

Low noise distributed acoustic sensor for seismology applications.

A distributed acoustic sensor (a phase optical time-domain reflectometer) configuration with a low noise level in the hertz and sub-hertz frequency ranges is proposed. The sensor scheme uses a Mach-Zehnder interferometer to generate a dual-pulse probe signal and implements the frequency stabilization of a laser source using the same interferometer as a frequency etalon. The scheme simultaneously provides a low noise level owing to the compensation of the optical path difference of interfering backscattered fields and low drift of the output signal. It has been shown experimentally that the stabilization of the laser frequency provides up to 35 dB signal/noise gain in the sub-hertz frequencies, which are of interest for seismology. The applicability of the proposed scheme is demonstrated experimentally by teleseismic earthquakes recorded by a fiber-optic cable deployed on the seabed of the Black Sea.

Structural insights into light-driven anion pumping in cyanobacteria.

Transmembrane ion transport is a key process in living cells. Active transport of ions is carried out by various ion transporters including microbial rhodopsins (MRs). MRs perform diverse functions such as active and passive ion transport, photo-sensing, and others. In particular, MRs can pump various monovalent ions like Na+, K+, Cl-, I-, NO3-. The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp. PCC 7509 and is named Synechocystis halorhodopsin (SyHR). The structural study of SyHR may help to understand what makes an MR pump divalent ions. Here we present the crystal structure of SyHR in the ground state, the structure of its sulfate-bound form as well as two photoreaction intermediates, the K and O states. These data reveal the molecular origin of the unique properties of the protein (exceptionally strong chloride binding and proposed pumping of divalent anions) and sheds light on the mechanism of anion release and uptake in cyanobacterial halorhodopsins. The unique properties of SyHR highlight its potential as an optogenetics tool and may help engineer different types of anion pumps with applications in optogenetics.

Wild Animal Migration As a Potential Threat of Introduction of New Viruses into Russia.

The SARS-CoV-2 pandemic has shown how serious the problem of re-emerging zoonotic infections is for our existence. Migrations of animals, which are natural reservoirs of a particular virus, play a colossal role in the spread of pathogens to new territories. Examples are the migrations of both land animals (carnivores, rodents, and ungulates) and many marine mammals (pinnipeds and cetaceans). Yet the most interesting from the point of view of the speed and range of the spread of viral infections are migrations associated with flights. In nature, these can be migrations of insects, bats, and, of course, birds. Unfortunately, there are very few studies on the migration of these animals in Russia. Considering the problems related to climate change and other environmental factors, it is important to obtain up-to-date data on the changing animal migration routes and, as a consequence, to develop domestic equipment, particularly transmitters, to fix them.

Melting of crystallites in a solid porous matrix and the application limits of the Gibbs-Thomson equation.

A thermodynamic model is proposed to describe the melting of lamellar crystallite in a solid medium. This model includes a modification of the Gibbs-Thomson equation to make it applicable to the above-mentioned crystallites. The need for such modification is supported experimentally by studying the impact of the surroundings on the melting point of the crystallites. In particular, the application of the model to nanocrystals in open-porous systems makes it possible to determine the analytical relations for the melting point, the heat of melting, and the inverse effective size of the pores. The fitting of the experimental data with these functional relations then allows for the calculation of the nanocrystalline density, pressure in the nanocrystal, and difference in the surface tension coefficients at the nanocrystal-matrix interface and melt-matrix interface, as well as the difference in the surface entropies per unit area at the nanocrystal-matrix and melt-matrix interfaces.

Random jumps in the phase-OTDR response.

In the paper, we present a qualitative analysis of the dual-pulse phase optical time domain reflectometry (phase-OTDR) response to uniform and nonuniform propagating fiber strain. It is found that on average over all realizations of scattering centers the response of the dual-pulse phase-OTDR is linear with respect to an external perturbation. Meanwhile, individual responses contain random phase jumps, which are an intrinsic property of phase-OTDR. These jumps are the result of nonlinear responses of the scattering fiber segments and arise due to interference of random backscattered fields varying in time. Two types of phase jumps are considered: π jumps and 2π jumps; the first type is caused by the fading in phase-OTDR spatial channel, while the second type occurs when a nonuniform perturbation propagates along the fiber. The origin of the phase jumps is explained by considering the simulated response on the complex plane. It is shown that the distribution of 2π jumps can be well described by the Gaussian probability mass function (PMF), provided the number of 2π jumps is large. The conducted experiments on the registration of uniform and nonuniform fiber strain confirm the presence of the jumps in the phase-OTDR response.

Low incidence of human coronavirus among hospitalized children in Novosibirsk city, Russia during pre-pandemic period (2013-2020).

We investigated the incidence of 15 respiratory viruses among 2991 children with acute respiratory infections in Novosibirsk city, Russia, prior to the COVID-19 pandemic (2013-2020). Viral infections were detected in 72.5% cases. The incidence of human coronavirus was 2% (Alphacoronaviruses, 63%; Betacoronaviruses, 37%).

Development of a Purified Viral Preparation for Studies of COVID-19 (SARS-CoV-2) Biology.

Different methods for producing bulk quantities of concentrated and purified SARS-CoV-2 for the use as antigens and for the research into COVID-19 biology were tested.

Distributed strain and temperature sensing over 100 km using tunable-wavelength OTDR based on MEMS filters.

The possibility of distributed wide-range strain and temperature measurements in a 100 km long optical fiber using tunable-wavelength low-coherence optical time-domain reflectometer (OTDR) is demonstrated. The specified distance range is provided by employing two narrowband microelectromechanical system (MEMS) spectral filters tuned synchronously as well as by taking advantage of Raman amplification and amplification by remotely pumped erbium-doped fiber segments built into the fiber under test. With the time of a single measurement of 10 min and the spatial resolution of about 1 m, the measurement range reached 1000 µÉ› in strain units, which is equivalent to the temperature range of 110°C.

Novel pH-Sensitive Microbial Rhodopsin from Sphingomonas paucimobilis.

This work provides the first characteristics of the rhodopsin SpaR from Sphingomonas paucimobilis, aerobic bacteria associated with opportunistic infections. The sequence analysis of SpaR has shown that this protein has unusual DTS motif which has never reported in rhodopsins from Proteobacteria. We report that SpaR operates as an outward proton pump at low pH; however, proton pumping is almost absent at neutral and alkaline pH. The photocycle of this rhodopsin in detergent micelles slows down with an increase in pH because of longer Schiff base reprotonation. Our results show that the novel microbial ion transporter SpaR of interest both as an object for basic research of membrane proteins and as a promising optogenetic tool.

[Erosive and ulcerative lesions of gastrointestinal tract in patients with burns]. / Erozivno-yazvennye porazheniya zheludochno-kishechnogo trakta pri ozhogovoi travme.

OBJECTIVE: To analyze the incidence of erosive and ulcerative lesions of gastrointestinal tract in patients with burns, including those complicated by gastrointestinal bleeding, depending on severity of injury, complications of burn disease and treatment features. MATERIAL AND METHODS: Medical records of 1833 patients were reviewed. We have retrospectively analyzed symptoms of disease and incidence of gastrointestinal bleeding depending on treatment strategy in patients with identified erosive and ulcerative lesions of gastrointestinal tract. RESULTS: Risk of gastrointestinal erosions and ulcers, including those complicated by gastrointestinal bleeding, correlates with area and depth of burn damage, especially in patients with thermo-inhalation injury and infectious complications of burn disease. Proton pump inhibitors intake in patients with burns of up to 50% of body surface area (BSA) and deep lesions up to 40% of BSA is followed by less incidence of gastrointestinal bleeding compared to H2-histamine receptor blockers. At the same time, severe burns of more than 50% of BSA ensure high risk of gastrointestinal bleeding regardless antisecretory therapy. CONCLUSION: Endoscopy upon admission is recommended in all patients with burns ≥30% of BSA or deep lesions ≥20% of BSA, as well as severe thermo-inhalation injury. This approach ensures timely diagnosis of gastrointestinal lesions and their adequate treatment.

Nanoscale mobility mapping in semiconducting polymer films.

Local electrical properties of thin films of the polymer PTB7 are studied by conductive atomic force microscopy (C-AFM). Non-uniform nanoscale current distribution in the neat PTB7 film is revealed and connected with the existence of ordered PTB7 crystallites. The shape of local I-V curves is explained by the presence of space charge limited current. We modify an existing semi-empirical model for estimation of the nanoscale hole mobility from our experimental C-AFM measurements. The procedure of nanoscale charge mobility estimation was described and applied to the PTB7 films. The calculated average C-AFM hole mobility is in good agreement with macroscopic values reported for this material. Mapping of nanoscale hole mobility was achieved using the described procedure. Local mobility values, influenced by nanoscale structure, vary more than two times in value and have a root-mean-square value 0.22 × 10-8 m2/(Vs), which is almost 20% from average hole mobility.

[Frequency of occurrence and risk factors for acute kidney injury after radical cystectomy].

INTRODUCTION: Various studies have revealed the negative impact of surgery or related factors on the risk of acute kidney injury (AKI). The risk factors and 6-months outcomes in patients with clinical or subclinical manifestations of AKI after radical cystectomy were analyzed. MATERIALS AND METHODS: This prospective study included patients with normal renal function who underwent radical cystectomy. Urine and serum samples were collected to measure the level of neutrophil gelatinase-associated lipocalin (NGAL). RESULTS: Of the 186 patients, 43 (23.1%) had AKI in the postoperative period. The most reliable predictor was the concentration of NGAL in the urine 12 hours after surgery (threshold value of 156.87 ng/ml). In 53 (28.5%) patients with NGAL higher than this value, subclinical AKI was diagnosed. Patients with clinical AKI and patients with subclinical AKI were allocated to the AKI group. Independent risk factors for postoperative AKI were age and obesity. After 6 months the glomerular filtration rate (GFR) in the group with AKI was significantly lower than in the control group, although the baseline GFR was similar. CONCLUSION: Determination of NGAL concentration in urine is recommended for early diagnosis of postoperative AKI, as well as for predicting the functional state of the kidneys 6 months after oncourological procedures. A significant proportion of patients developed subclinical AKI; in this group there was a worse renal outcome in comparison with the group without AKI.

High-resolution structural insights into the heliorhodopsin family.

Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.

[Nephroprotective effect of calcium channel blocker lercanidipine in treatment of patients with urolithiasis and urinary tract obstruction and monitoring of the serum cytokine profile].

OBJECTIVE: to evaluate the nephroprotective effect of lercanidipine, its effect on the dynamics of creatinine clearance and blood cytokine levels in patients with nephrolithiasis with obstructive uropathy during renal drainage. MATERIAL AND METHODS: 66 patients were included in the study with concretions of the pelvic segment and the presence of obstruction according to instrumental methods of examination. In order to prevent the occurrence of infectious complications before lithotripsy patients the first stage was performed installation of nephrostomic drainage, followed by antibacterial, anti-inflammatory therapy. Patients were divided into 2 groups: the first (33 patients) received standard therapy, the second (33 people) additionally received lercanidipine at a dose of 10 mg per day for 1 month. Determined the concentration of IL-8, VEGF, MCP-1, G-CSF and GM-CSF in the blood serum by the method of solid-phase ELISA. The glomerular filtration rate was calculated using the CKD-EPI formula. All studies were performed at the preoperative stage, on 7, 14, 21 and 28 days after renal drainage. RESULTS: In the appointment of lercanidipine, there was a more rapid decrease in levels of IL-8, VEGF, MS-1, GM-CSF in serum (21 days), and an improvement in renal function, compared with the group that did not receive nephroprotective therapy. CONCLUSION: The administration of lercanidipine may contribute to a more rapid recovery of renal function and normalization of blood cytokine levels. This drug can be used in the complex treatment of patients with nephrolithiasis with obstructive uropathy.

[Optimized approach to the surgical treatment of patients with large and giant postoperative ventral hernia]. / Khirurgicheskoe lechenie patsientov s bol'shimi i gigantskimi posleoperatsionnymi ventral'nymi gryzhami.

OBJECTIVE: To optimize surgical approach in patients with large and giant postoperative ventral hernias through an analysis of early and long-term results of modern techniques of hernia repair. MATERIAL AND METHODS: There were 680 patients with postoperative ventral hernia over a 15-year period who underwent surgery in the Sklifosovsky Research Institute for Emergency Care and Medical Unit of the Ministry of Internal Affairs (445 (65.4%) women, 235 (34.6%) men). Mean age of patients was 63.2±14.2 years. Middle and elderly (employable) age patients (45-74 years) prevailed in the study (n=510, 75%). Hernia repair using «sublay¼ technique was performed in 490 (72%) patients without severe comorbidities and relative volume of hernial protrusion up to 18%. Submuscular-inlay technique was used in 95 (14%) patients with significant comorbidities and those over 50 years old or with a relative volume of hernial protrusion over 18%. We have applied a modified repair technique for the last 3 years in 5 (0.75%) patients with a giant postoperative ventral hernia and anterior abdominal tissue deficiency (partial or complete absence of some anatomical structures, for example, rectus muscle). A hybrid technology was applied in 12 patients with severe concomitant diseases, hernias W2 according to European qualifications or recurrent hernias, significant adhesions in the abdominal cavity or hernial sac. RESULTS: Early postoperative wound complications occurred in 27 (5.5%) patients including hematoma (n=12, 2.5%), infiltration (n=7, 1.4%), wound suppuration (n=8, 1.6%). Other complications were observed in 6 (1.2%) patients: pneumonia, pulmonary embolism, intestinal obstruction. Lethal outcomes were absent. Recurrences in long-term period were found in 18 (3.7%) patients. Submuscular-inlay technique of hernia repair was followed by early postoperative wound complications in 5 (5.1%) patients including hematoma (n=3, 3.2%), infiltration (n=1, 1%), wound suppuration (n=1, 1%). There was no mortality. No other early postoperative complications were observed. Recurrences were detected in 5 (5.2%) patients. Preoperative intra-abdominal pressure was 7-10 mm Hg in all patients with tissue deficit. This value did not exceed 12 mm Hg after repair due to creation of a «specified diastasis¼. Lethal outcomes were absent. There were no early and long-term recurrences or wound complications. Analysis of early and long-term results of the modified hybrid repair of the anterior abdominal wall did not reveal recurrences, local and systemic complications. Persistent minor diastasis between rectus muscles reinforced with a mesh implant was observed in 3 (25%) out of 12 patients. CONCLUSION: Thus, optimized and personalized approach in patients with large and giant postoperative ventral hernias considers all intra- and postoperative risk factors.