Risk assessment of psychiatric complications in infectious diseases: CALCulation of prognostic indices on example of COVID-19.

Introduction: Factors such as coronavirus neurotropism, which is associated with a massive increase in pro-inflammatory molecules and neuroglial reactivity, along with experiences of intensive therapy wards, fears of pandemic, and social restrictions, are pointed out to contribute to the occurrence of neuropsychiatric conditions. Aim: The aim of this study is to evaluate the role of COVID-19 inflammation-related indices as potential markers predicting psychiatric complications in COVID-19. Methods: A total of 177 individuals were examined, with 117 patients from a temporary infectious disease ward hospitalized due to COVID-19 forming the experimental group and 60 patients from the outpatient department showing signs of acute respiratory viral infection comprising the validation group. The PLR index (platelet-to-lymphocyte ratio) and the CALC index (comorbidity + age + lymphocyte + C-reactive protein) were calculated. Present State Examination 10, Hospital Anxiety and Depression Scale, and Montreal Cognitive Assessment were used to assess psychopathology in the sample. Regression and Receiver operating characteristic (ROC) analysis, establishment of cutoff values for the COVID-19 prognosis indices, contingency tables, and comparison of means were used. Results: The presence of multiple concurrent groups of psychopathological symptoms in the experimental group was associated (R² = 0.28, F = 5.63, p < 0.001) with a decrease in the PLR index and a simultaneous increase in CALC. The Area Under Curve (AUC) for the cutoff value of PLR was 0.384 (unsatisfactory). For CALC, the cutoff value associated with an increased risk of more psychopathological domains was seven points (sensitivity = 79.0%, specificity = 69.4%, AUC = 0.719). Those with CALC > 7 were more likely to have disturbances in orientation (χ² = 13.6; p < 0.001), thinking (χ² = 7.07; p = 0.008), planning ability (χ² = 3.91; p = 0.048). In the validation group, an association (R²McF = 0.0775; p = 0.041) between CALC values exceeding seven points and the concurrent presence of pronounced anxiety, depression, and cognitive impairments was demonstrated (OR = 1.52; p = 0.038; AUC = 0.66). Discussion: In patients with COVID-19, the CALC index may be used for the risk assessment of primary developed mental disturbances in the context of the underlying disease with a diagnostic threshold of seven points.

Seasonal Diet Changes and Trophic Links of Cold-Water Fish (Coregonus albula) within a Northern Lake Ecosystem.

The seasonal feeding patterns of the cold-adapted fish, Coregonus albula, are poorly studied in high-latitude lakes but could provide insight for predicting the effects of global warming. We examined vendace's diet composition, traced the carbon and nitrogen isotope ratios from producers to consumers in the food web, and estimated vendace's trophic position in a subarctic lake (the White Sea basin). Results showed the vendace to be a typical euryphagous fish, but clear seasonal differences were found in the relative importance of plankton and benthos in the diet. The vendace consumed primarily benthic amphipods in the summer, planktonic cladocerans in the autumn, and copepods in the winter-spring (under ice); larvae of aquatic insects were the second-most important food items throughout the year. Because of the substantial proportion of fish embryos in its diet, the vendace had a trophic position similar to that of a predatory fish (perch). The Bayesian food source-mixing model revealed that the majority of vendace energy derives from planktonic copepods. The dominant Cyclops had the lowest carbon isotope values, suggesting a carbon-depleted diet typical for methanotrophic bacteria, as its probable food source was in a lake under ice. Understanding the feeding patterns of vendace provides information to better predict the potential biotic effects of environmental change on lake ecosystems.

Experimental detection of conformational transitions between forms of DNA: problems and prospects.

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.

Increased importance of cool-water fish at high latitudes emerges from individual-level responses to warming.

High latitude ecosystems are experiencing the most rapid warming on earth, expected to trigger a diverse array of ecological responses. Climate warming affects the ecophysiology of fish, and fish close to the cold end of their thermal distribution are expected to increase somatic growth from increased temperatures and a prolonged growth season, which in turn affects maturation schedules, reproduction, and survival, boosting population growth. Accordingly, fish species living in ecosystems close to their northern range edge should increase in relative abundance and importance, and possibly displace cold-water adapted species. We aim to document whether and how population-level effects of warming are mediated by individual-level responses to increased temperatures, shift community structure, and composition in high latitude ecosystems. We studied 11 cool-water adapted perch populations in communities dominated by cold-water adapted species (whitefish, burbot, and charr) to investigate changes in the relative importance of the cool-water perch during the last 30 years of rapid warming in high latitude lakes. In addition, we studied the individual-level responses to warming to clarify the potential mechanisms underlying the population effects. Our long-term series (1991-2020) reveal a marked increase in numerical importance of the cool-water fish species, perch, in ten out of eleven populations, and in most fish communities perch is now dominant. Moreover, we show that climate warming affects population-level processes via direct and indirect temperature effects on individuals. Specifically, the increase in abundance arises from increased recruitment, faster juvenile growth, and ensuing earlier maturation, all boosted by climate warming. The speed and magnitude of the response to warming in these high latitude fish communities strongly suggest that cold-water fish will be displaced by fish adapted to warmer water. Consequently, management should focus on climate adaptation limiting future introductions and invasions of cool-water fish and mitigating harvesting pressure on cold-water fish.

C-B-A Test of DNA Force Fields.

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.

The Mind-Body Problem in the Context of Neuropsychiatric Symptoms in Patients with Coronavirus Disease 2019.

Objective: This study is to determine the possible pathophysiological parameters associated with the development of anxiety and impaired consciousness in patients with acute coronavirus disease (COVID-19). Methods: Descriptive pathophysiological and pathopsychological data was collected from 89 patients hospitalized due to COVID-19 across 7 infectious hospitals, where 14 trainees in psychiatry and neurology collected data from December 2020 to June 2021. Contingency tables and logistic regression analyses were made to reveal associations and to detect predictors of patients' states of anxiety or impaired consciousness. Results: Anxiety and impaired consciousness were observed in 28 patients (31.50%); 22 (25.00%) presented with anxiety symptoms, and 7 (7.90%) had impaired consciousness. The degree of their association was low (Fisher's exact = 0.675 (df = 1), P = .495). Different pathophysiological mechanisms were shown to determine the development of anxiety or impaired consciousness within COVID-19. Predictors of anxiety were oxygen saturation (OR = 1.26; 95% CI, 1.04-1.54; P = .021), cardiovascular disorders (OR = 0.14; 95% CI, 0.04-0.52; P = .003), disorders of the nervous system (OR = 0.05; 95% CI, 0.01-0.84; P = .038), and urogenital system (OR = 0.13; 95% CI, 0.02-0.87; P = .035). The predictive power of the model was 80.23% (P ≤ .001). The development of impaired consciousness was associated with age (OR = 1.11; 95% CI, 1.01-1.21; P = .025) and C-reactive protein level (OR = 1.02; 95% CI, 0.99-1.04; P = .060), and the predictive power of the model was 94.52% (P ≤ .001). Conclusion: The prevalence of psychopathological disorders associated with acute COVID-19 was high: n = 28 (31.50%) for anxiety and impaired consciousness. Moreover, a 1.00% increase in the saturation index was associated with a 1.3-fold increase in the patient's risk of developing anxiety. Thus, anxiety symptoms may be considered within a personality rather than an infectious-inflammatory response to COVID-19.

Mental State of Inpatients With COVID-19: A Computational Psychiatry Approach.

Background: The overload of healthcare systems around the world and the danger of infection have limited the ability of researchers to obtain sufficient and reliable data on psychopathology in hospitalized patients with coronavirus disease 2019 (COVID-19). The relationship between severe acute respiratory syndrome with the coronavirus 2 (SARS-CoV-2) infection and specific mental disturbances remains poorly understood. Aim: To reveal the possibility of identifying the typology and frequency of psychiatric syndromes associated with acute COVID-19 using cluster analysis of discrete psychopathological phenomena. Materials and Methods: Descriptive data on the mental state of 55 inpatients with COVID-19 were obtained by young-career physicians. Classification of observed clinical phenomena was performed with k-means cluster analysis of variables coded from the main psychopathological symptoms. Dispersion analysis with p level 0.05 was used to reveal the clusters differences in demography, parameters of inflammation, and respiration function collected on the basis of the original medical records. Results: Three resulting clusters of patients were identified: (1) persons with anxiety; disorders of fluency and tempo of thinking, mood, attention, and motor-volitional sphere; reduced insight; and pessimistic plans for the future (n = 11); (2) persons without psychopathology (n = 37); and (3) persons with disorientation; disorders of memory, attention, fluency, and tempo of thinking; and reduced insight (n = 7). The development of a certain type of impaired mental state was specifically associated with the following: age, lung lesions according to computed tomography, saturation, respiratory rate, C-reactive protein level, and platelet count. Conclusion: Anxiety and/or mood disturbances with psychomotor retardation as well as symptoms of impaired consciousness, memory, and insight may be considered as neuropsychiatric manifestations of COVID-19 and should be used for clinical risk assessment.

Variability of the DNA Backbone Geometry in DNA-Protein Complexes: Experimental Data Analysis.

We have analyzed and compared the available experimental data (PDB) on the backbone geometry of the DNA in solution (NMR), in crystals (X-rays), and in complexes with proteins (X-rays and cryo-electron microscopy). The deoxyribose (pseudorotational angle τ0) and ε/ζ (BI-BII transition in phosphates) flexibilities are practically the same in the four samples. The α/γ mobility is minimal in crystalline DNA: on the histograms, there is one canonical and one noncanonical t/t peak. The α/γ mobility increases in DNA solutions (three more noncanonical peaks) and is maximal in DNA-protein complexes (another additional peak). On a large amount of data, we have confirmed that the three main degrees of freedom of the sugar-phosphate backbone are "orthogonal": changes in any of the angles τ0, (ζ-ε), and (γ-α) occur, as a rule, at a constant (usually canonical) value of any other. In the DNA-protein complexes, none of the geometrical parameters commonly used to distinguish the A and B forms of DNA, except for Zp and its simpler analog Zp', show an unambiguous correlation with τ0. Proteins, binding to DNA, in 59% of cases change the local shape of the helix up to the characteristic of the A-form without switching the deoxyribose conformation from south to north. However, we have found simple local characteristics of one nucleotide that correlate with the angles τ0 and (ζ-ε). These are the angles C3'C1'N* and C4'C3'P(2), respectively. They are orthogonal in DNA-protein complexes exactly as the pair τ0 and (ζ-ε). Most characteristics of DNA in complexes with proteins are the same in X-ray and in cryo-EM data, except for the histogram for the angle τ0. We offer a possible explanation for this difference. We also discuss the artifacts on the ε/ζ histogram for DNA in solutions caused by the currently used NMR refinement protocols.

Occurrence of fish species in the inland water of Murmansk Region (Russia): research in 1972-2021.

BACKGROUND: Knowledge about the distribution of organisms on Earth is important backbone of biological sciences and especially for deeper understanding of biogeography. However, much of the existing distributional data are scattered throughout a multitude of sources (including in different languages), such as taxonomic publications, checklists and natural history collections and often, bringing them together is difficult. Development of the digital storage facilities may prevent loss of important data (Ruchin et al. 2020). Project GBIF is a good example of a successful data storage facility, which allows investigators to publish biodiversity data in one safe place in one uniform format. Our dataset describes the degree of the investigation of the fish fauna of the inland water of the Murmansk Region. Murmansk Region is a Euro-Arctic Region with a heterogeneous landscape, which determines diversity of the habitats for the fish occurrence. Our dataset contains valid information about distribution of the fish species. This dataset was built upon information obtained by the members of a Laboratory of the aquatic ecosystems of the Institute of North Industrial Ecology Problems of Kola Science Center of the Russian Academy of Science (INEP KSC RAS). The dataset includes 18,509 records about 16 fish species from 14 genera (eight families) collected from 1972 to 2021. A total of 67 water bodies from 15 different basins (rivers from basins of the White and Barents Seas) was screened in order to characterise ichthyocenoses. The main purpose of publishing a database is to make our data available in the global biodiversity system to a wide range of users. The data can be used by researchers, as well as helping the authorities to manage their territory more efficiently. NEW INFORMATION: All occurrences are published in GBIF for the first time. We would like to make this data available to everyone by adding it in the global biodiversity database (GBIF).

Multicenter study of serotype distribution of Streptococcus pneumoniae nasopharyngeal isolates from healthy children in the Russian Federation after introduction of PCV13 into the National Vaccination Calendar.

Russia introduced PCV13 in 2014. We studied the serotype composition of S. pneumoniae isolated from the nasopharynx of healthy children younger than 6 years in St. Petersburg, Smolensk, Perm, Krasnoyarsk, Khanty-Mansiysk and Khabarovsk, between 2016 and 2018. 2.4% of children had completed a 3-dose course of PCV13, while 25.6% had received 1 or 2 doses. Pneumococcal DNA detection by PCR demonstrated S. pneumoniae in 37.2% of samples with regional variation between sites (27.3 to 56.9%). There was little difference between vaccinated, partially vaccinated and un-vaccinated children. Children who had received at least 1 dose of PCV13 had lower carriage rates of vaccine serotypes than their unvaccinated peers (49.9 vs. 61.4%; p < 0.001). Children who had received at least 1 dose of PCV13 showed increased carriage rates of non-vaccine serotypes (50 vs 38.6%; P < 0.001). Especially serogroup 15AF was more prevalent among fully immunized children than among their peers (12.5 vs 2.7%; P < 0.05).

Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.

Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.