Comparison of REMS, NEWS, qSOFA and SIRS criteria scales for sepsis prediction in patients with diagnosis “SARS-CoV-2, virus unidentified”: a retrospective observational study

Background. Despite ample research on the coronavirus infection sequence and therapy, the incidence of adverse outcomes remains very high. Sepsis stands among the major factors greatly complicating treatment and increasing the risk of death. A timely identification of highrisk sepsis patients is a cornerstone of effective sepsis prevention.Objectives. A comparative prognostic power assessment between the quick Sequential Organ Failure Assessment (qSOFA) scale, National Early Warning Score (NEWS), Initial Prehospital Rapid Emergency Medicine Score (REMS) and the Systemic Inflammatory Response Syndrome (SIRS) criteria for sepsis detection in anaesthetic intensive care patients with a diagnosis: SARS-CoV-2, virus unidentified.Methods. A retrospective observational study included 166 patients over 18-year age with unconfirmed infection (ICD-10 code U07.2). The qSOFA, NEWS, REMS and SIRS point estimates were obtained from each patient. The patients were retrospectively divided in two cohorts by sepsis presence (Sepsis-3 criteria) to determine the express scales power in evaluating the risk of sepsis (estimated as area under ROC curve, AUROC).Results. Data on 102 patients were included in the final analysis. Fifty-eight (57%) patients were terminal, and 55 (54%) developed sepsis. The estimates are as follows: NEWS — AUROC 0.848 [95% confidence interval (CI) 0.764–0.912], sensitivity 76.36% [95% CI 63.0–86.8], specificity 82.98% [95% CI 69.2–92.4], optimal cut-off threshold >5 points; qSOFA — AUROC 0.700 [95% CI 0.602–0.787], sensitivity 76.36% [95% CI 63.0–86.8], specificity 61.70% [95% CI 46.4–75.5], optimal cut-off threshold >0 points; REMS — AUROC 0.739 [95% CI 0.643–0.821], sensitivity 69.09% [95% CI 55.2–80.9], specificity 65.96% [95% CI 50.7–79.1], optimal cut-off threshold >5 points; SIRS criteria — AUROC 0.723 [95% CI 0.626–0.807], sensitivity 98.18% [95% CI 90.3–100.0], specificity 31.91% [95% CI 19.1–47.1], optimal cut-off threshold >0 points.Conclusion. The NEWS scale revealed a good prognostic power to estimate the risk of sepsis in patients with suspected COVID-19 disease. The qSOFA, REMS scales and SIRS criteria possess a good calibration capacity, albeit insufficient resolution, which limits their prognostic value

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site

Ингибирование процесса кристаллизации карбонатов кальция и магния полиакрилатом натрия

It is known that when water are used for technological purposes, in circulating water supply systems of enterprises as a coolant during continuous heating and cooling, the formation of insoluble precipitates, most often calcium carbonates, occurs on the walls of heat exchangers, which leads to a large number of problems, even production can be stopped for cleaning equipment. To prevent the formation of salts, it is necessary to use precipitation inhibitors. Sodium polyacrylate was investigated as a precipitation inhibitor. The composition, morphology and IR spectra of calcium carbonate precipitate obtained in the absence and in the presence of sodium polyacrylate were studied. It was established that the effect of sodium polyacrylate on the mechanism of crystallization of carbonate sediment depends on the pH of the initial solution. The results of IR spectroscopy, X-ray diffraction analysis and images obtained by electron microscopy indicate the participation of polymer molecules in the formation of the crystalline structure of the carbonate precipitate.Известно, что при использовании воды в технологических целях, в частности, в системах оборотного водоснабжения предприятий в качестве охлаждающей жидкости в процессе постоянного нагревания и охлаждения происходит образование нерастворимых осадков, чаще всего карбонатов кальция, на стенках теплообменников, что приводит к большому количеству проблем, вплоть до остановок производства для очистки оборудования. Для предотвращения образования отложений необходимо применять ингибиторы осадкообразования. В работе в качестве ингибитора осадкообразования исследовали полиакрилат натрия. Изучен состав, морфология, ИК-спектры осадка карбоната кальция, полученного в отсутствие и в присутствии полиакрилата натрия. Установлено, что влияние полиакрилата натрия на механизм кристаллизации карбонатного осадка зависит от рН исходного раствора. Результаты ИК-спектроскопии, РФА и снимки, полученные электронной микроскопией, свидетельствуют об участии молекул полимера в формировании кристаллической структуры карбонатного осадка

Comprehensive analysis of the 5-HTTLPR allelic polymorphism effect on behavioral and neurophysiological indicators of executive control in people from different ethnic groups in Siberia

The allelic polymorphism of the serotonin transporter’s gene 5-HTTLPR is considered as one of the factors determining an individual genetic predisposition to the development of a wide range of affective disorders, including depression. Many studies have shown that the climatic and social conditions of people’s life can have a significant impact on the connections of 5-HTTLPR with the risk of depression. The stop-signal paradigm (SSP) is an experimental method allowing evaluating an individual ability to the self-control of behavior in a changing environment. In the SSP experiment, a subject should either press one of several buttons quickly after the appearance of the target stimuli or suppress the already started movement if an inhibitory signal follows the target stimulus. The aim of this study is a research of associations between the allelic the 5-HTTLPR polymorphism and the individual scores of the personal anxiety level, as well as the behavioral and neurophysiological indicators of the ability to self-control over motor reactions in the SSP. The study was conducted among people from three ethno-regional groups: healthy Caucasoids from Novosibirsk, the Mongoloid groups of the indigenous population of the Tuva Republic and Sakha Republic (Yakutia). Genetic, ethnographic, and psychological influences on an individual’s ability to control motor responses were compared. The amplitude of the premotor peak of the evoked brain potential was used as a neurophysiological marker of the person’s readiness to the execution of target-directed activity. It was revealed that the frequency of the S-allele polymorphism 5-HTTLPR was significantly higher for both mongoloid groups compared to the Caucasoids. The S/S genotype was associated with an increased level of personal anxiety and at the same time with a better ability to the self-control of behavior in the SSP experiment. Anxiety level, participants’ sex, ethnicity, and allelic polymorphism 5-HTTLPR had a statistically significant effect on the amplitude of the premotor readiness potential recorded under the SSP conditions in the frontal and parietal-occipital cortical regions. Our data support the hypothesis that the S/S genotype of the 5-HTTLPR polymorphism may be associated with more success in adapting to the climatic conditions connected with high life risk in comparison to L/L and L/S genotypes

cisRED: a database system for genome-scale computational discovery of regulatory elements

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally

Получение сополимеров терпенов с метакриловой кислотой и их влияние на устойчивость неорганических дисперсий в присутствии катионных поверхностно-активных веществ

Copolymers of methacrylic acid and natural terpene monomers (α-pinene; β-pinene; ∆3-karene) with the molecular weight of (0.3–0.5)∙104 and a content of carboxyl groups of 14.5–16.3 % were synthesized. For the synthesized copolymers, hydrodynamic radius and the Kuhn segment, which characterizes flexibility of a polymer chain, were determined, as well as the Huggins constant in aqueous and saline solutions, and concentration regions for formation of supramolecular structures. In the presence of a cationic surfactant (benzetonium chloride, Hyamine), depending on the concentration of copolymers in the system, polymer-surfactant complexes were formed in soluble and insoluble forms. It has been shown that the effectiveness of the stabilizing action of soluble complexes with respect to an aqueous dispersion of calcium carbonate increases with an increase in the content of nonpolar groups in the polymer chain. A cationic surfactant (Hyamine) has been proposed as a precipitant in the method for the quantitative determination of carboxyl-containing polymers in aqueous and saline media. Синтезированы сополимеры на основе метакриловой кислоты и природных терпеновых мономеров (α-пинен, β-пинен, ∆3-карен) с молекулярной массой (0,3–0,5)∙104 и содержанием карбоксильных групп 14,5–16,3 %. Для синтезированных сополимеров определены гидродинамический радиус и сегмент Куна, характеризующий гибкость полимерной цепи, константа Хаггинса в водном и солевом растворах, концентрационные области формирования надмолекулярных структур. В присутствии катионного ПАВ (бензетония хлорид, Hyamine) в зависимости от концентрации сополимеров в системе образуются комплексы «полимер–ПАВ» в растворимой и нерастворимой формах. Показано, что эффективность стабилизирующего действия растворимых комплексов в отношении водной дисперсии карбоната кальция возрастает с увеличением содержания неполярных групп в полимерной цепи. Катионный ПАВ (Hyamine) предложен в качестве осадителя в методе количественного определения карбоксилсодержащих полимеров в водной и солевой средах.