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Background Despite concerns about worsening pregnancy outcomes resulting from healthcare restrictions, economic difficulties and increased stress during the COVID-19 pandemic, preterm birth (PTB) rates declined in some countries in 2020, while stillbirth rates appeared stable. Like other shocks, the pandemic may have exacerbated existing socioeconomic disparities in pregnancy, but this remains to be established. Our objective was to investigate changes in PTB and stillbirth by socioeconomic status (SES) in European countries. Methods The Euro-Peristat network implemented this study within the Population Health Information Research Infrastructure (PHIRI) project. A common data model was developed to collect aggregated tables from routine birth data for 2015–2020. SES was based on mother’s educational level or area-level deprivation/maternal occupation if education was unavailable and harmonized into low, medium and high SES. Country-specific relative risks (RRs) of PTB and stillbirth for March to December 2020, adjusted for linear trends from 2015 to 2019, by SES group were pooled using random effects meta-analysis. Results Twenty-one countries provided data on perinatal outcomes by SES. PTB declined by an average 4% in 2020 {pooled RR: 0.96 [95% confidence intervals (CIs): 0.94–0.97]} with similar estimates across all SES groups. Stillbirths rose by 5% [RR: 1.05 (95% CI: 0.99–1.10)], with increases of between 3 and 6% across the three SES groups, with overlapping confidence limits. Conclusions PTB decreases were similar regardless of SES group, while stillbirth rates rose without marked differences between groups.

Stillbirth rates have stalled or increased in some European countries during the last decade. We investigate to what extent time-trends and between-country differences in stillbirth rates are explained by the changing prevalence of advanced maternal age and teenage pregnancies or multiple births. We analysed data on stillbirths and live births by maternal age and multiplicity from 2010 to 2021 in 25 European countries using Kitagawa decomposition to separate rate differences into compositional and rate components. Rates significantly decreased in six countries, but increased in two. Changes in maternal age structure reduced national stillbirth rates by a maximum of 0.04 per 1000 in the Netherlands and increased rates by up to 0.85 in Cyprus. Changes in the prevalence of multiple births decreased rates by up to 0.19 in the Netherlands and increased rates by up to 0.01 across multiple countries. Maternal age differences explained between 0.11 of the below-European average stillbirth rate in Belgium and 0.13 of the above-average rate in Ireland. Excluding Cyprus, differences in multiple births explained between 0.05 of the below-average rate in Malta and 0.03 of the above-average rate in Ireland. For most countries, the increase in advanced-age pregnancies contributed to rising stillbirth rates over time, while reductions in multiples led to decreases in rates. However, large parts of the trends remain unexplained by those factors. By 2021, neither factor explained the differences between countries, due to increased compositional uniformity and declining stillbirth risk for advanced maternal age.

Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.

Homocysteine (Hcy) and Hcy-thiolactone (HTL) affect fibrin clot properties and are linked to cardiovascular disease. Factors that influence fibrin clot properties and stroke are not fully understood. To study sulfur-containing amino acid metabolites, fibrin clot lysis time (CLT) and maximum absorbance (Abs max ) in relation to stroke, we analyzed plasma and urine from 191 stroke patients (45.0% women, age 68 ± 12 years) and 291 healthy individuals (59.7% women, age 50 ± 17 years). Plasma and urinary levels of sulfur-containing amino acid metabolites and fibrin clot properties were significantly different in stroke patients compared to healthy individuals. Fibrin CLT correlated with fibrin Abs max in healthy males (R 2  = 0.439, P  = 0.000), females (R 2  = 0.245, P  = 0.000), female stroke patients (R 2  = 0.187, P  = 0.000), but not in male stroke patients (R 2  = 0.008, P  = ns). Fibrin CLT correlated with age in healthy females but not males while fibrin Abs max correlated with age in both sexes; these correlations were absent in stroke patients. In multiple regression analysis in stroke patients, plasma (p)CysGly, pMet, and MTHFR A1298C polymorphism were associated with fibrin Abs max , while urinary (u)HTL, uCysGly, and pCysGly were significantly associated with fibrin CLT. In healthy individuals, uHTL and uGSH were significantly associated with fibrin Abs max , while pGSH, and CBS T833C 844ins68 polymorphism were associated with fibrin CLT. In logistic regression, uHTL, uHcy, pCysGly, pGSH, MTHFR C677T polymorphism, and Abs max were independently associated with stroke. Our findings suggest that HTL and other sulfur-containing amino acid metabolites influence fibrin clot properties and the risk of stroke.

Background Machine learning techniques are known to be a powerful way of distinguishing microRNA hairpins from pseudo hairpins and have been applied in a number of recognised miRNA search tools. However, many current methods based on machine learning suffer from some drawbacks, including not addressing the class imbalance problem properly. It may lead to overlearning the majority class and/or incorrect assessment of classification performance. Moreover, those tools are effective for a narrow range of species, usually the model ones. This study aims at improving performance of miRNA classification procedure, extending its usability and reducing computational time. Results We present HuntMi, a stand-alone machine learning miRNA classification tool. We developed a novel method of dealing with the class imbalance problem called ROC-select, which is based on thresholding score function produced by traditional classifiers. We also introduced new features to the data representation. Several classification algorithms in combination with ROC-select were tested and random forest was selected for the best balance between sensitivity and specificity. Reliable assessment of classification performance is guaranteed by using large, strongly imbalanced, and taxon-specific datasets in 10-fold cross-validation procedure. As a result, HuntMi achieves a considerably better performance than any other miRNA classification tool and can be applied in miRNA search experiments in a wide range of species. Conclusions Our results indicate that HuntMi represents an effective and flexible tool for identification of new microRNAs in animals, plants and viruses. ROC-select strategy proves to be superior to other methods of dealing with class imbalance problem and can possibly be used in other machine learning classification tasks. The HuntMi software as well as datasets used in the research are freely available at http://lemur.amu.edu.pl/share/HuntMi/ .

Cystathionine β-synthase (CBS)-deficient patients are prone to vascular thrombosis. In contrast, Cbs −/− mice show no abnormalities in blood coagulation. To identify molecular basis underlying these disparately different thrombotic phenotypes, we analyzed plasma proteomes of Cbs −/− vs. Cbs +/+ mice (8-month-old, 12/group, sex-matched) and CBS −/− vs. CBS +/+ humans (37 ± 7-year-old, 10–14/group, sex-matched) using label-free mass spectrometry. We identified 117 and 41 differentiating plasma proteins in Cbs −/− mice and CBS −/− humans, respectively. Twenty-one proteins were shared between CBS −/− humans and Cbs −/− mice, with sixteen changed in the opposite direction. Proteins involved in blood coagulation and complement/coagulation cascades represented a greater fraction of the differentiating proteins in CBS −/− patients (51%) than in Cbs −/− mice (21%). Top canonical pathways, identified by Ingenuity Pathways Analysis, such as LXR/RXR, FXR/RXR activation (− log[ P -value] = 30–31) and atherosclerosis signaling (− log[ P -value] = 10–11) were similarly affected in Cbs −/− mice and CBS −/− humans. The Coagulation System was affected stronger in CBS −/− humans than in Cbs −/− mice (− log[ P -value] = 15 vs. 10, respectively) while acute phase response and complement system were affected stronger in Cbs −/− mice (− log[ P -value] = 33 and 22, respectively) than in humans (− log[ P -value] = 22 and 6, respectively). Other pathways, including IL-7 signaling and B cell development were affected only in Cbs −/− mice. Taken together, our findings suggest that differences in these processes, in particular in the Coagulation System, could account for the thrombotic phenotype in CBS −/− patients and the absence of thrombosis in Cbs −/− mice. Overall, our findings suggest that Cbs −/− mice have a better adaptive response to protect from prothrombotic effects of hyperhomocysteinemia than CBS −/− humans.

Water deficit affects the growth as well as physiological and biochemical processes in plants. The aim of this study was to determine differences in physiological and biochemical responses to drought stress in two wheat cultivars—Chinese Spring (CS) and SQ1 (which are parents of a mapping population of doubled haploid lines)—and to relate these responses to final yield and agronomic traits. Drought stress was induced by withholding water for 14 days, after which plants were re-watered and maintained until harvest. Instantaneous gas exchange parameters were evaluated on the 3rd, 5th, 10th, and 14th days of seedling growth under drought. After 14 days, water content and levels of chlorophyll a+b, carotenoids, malondialdehyde, soluble carbohydrates, phenolics, salicylic acid, abscisic acid (ABA), and polyamines were measured. At final maturity, yield components (grain number and weight), biomass, straw weight, and harvest index were evaluated. Physiological and biochemical parameters of CS responded more than those of SQ1 to the 14-day drought, reflected in a greater reduction in final biomass and yield in CS. Marked biochemical differences between responses of CS and SQ1 to the drought were found for soluble carbohydrates and polyamines. These would be good candidates for testing in the mapping population for the coincidence of the genetic control of these traits and final biomass and yield.

The paper presents the research results obtained in the process of oxidative coupling of methane, in which unpurified biogas was used as the feedstock. Biogas obtained from two kinds of biomass materials, i.e., plant materials (potato and beet pulp, Corn-Cob-Mix—biogas 1) and animal waste (waste from fish filleting—biogas 2) was considered. The influence of temperature, the ratio of methane/oxygen and total flows of feedstock on the catalytic performance in oxidative coupling of methane process was investigated. Comparative tests were carried out using pure methane and a mixture of methane-carbon dioxide to simulate the composition of biogas 2. The process was carried out in the presence of an Mn-Na2WO4/SiO2 catalyst. Fresh and used catalysts were characterised by means of powder X-ray diffraction, X-ray photoelectron spectroscopy, and low-temperature nitrogen adsorption techniques. In oxidative coupling of methane, the type of raw material used as the source of methane has a small effect on methane conversion (the differences in methane conversion are below 3%), but a significant effect on the selectivity to C2. Depending on the type of raw material, the differences in selectivity to C2 reach as high as 9%. However, the Mn-Na2WO4/SiO2 catalyst operated steadily in the tested period of time at any feedstock composition. Moreover, it was found that CO2, which is the second main component of biogas in addition to methane, has an effect on catalytic performance. Comparative results of catalytic tests indicate that the CO2 effect varies with temperature. Below 1073 K, CO2 exerts a small poisoning effect on methane conversion, while above this temperature the negative effect of CO2 disappears. In the case of selectivity to C2+, the negative effect of CO2 was observed only at 1023 K. At higher temperatures, CO2 enhances selectivity to C2+. The effect of CO2 was established by correlating the catalytic results with the temperature programmed desorption of CO2 investigation. The poisoning effect of CO2 was connected with the formation of surface Na2CO3, whose concentration depends on temperature.

Staphylococcus aureus is considered one of the leading pathogens responsible for infections in humans and animals. The heterogeneous nature of diseases caused by these bacteria is due to the occurrence of multiple strains, differentiated by several mechanisms of antibiotic resistance and virulence factors. One of these is the ability to form biofilm. Biofilm-associated bacteria exhibit a different phenotype that protects them from external factors such as the activity of immune system or antimicrobial substances. Moreover, it has been shown that the majority of persistent and recurrent infections are associated with the presence of the biofilm. Omiganan, an analog of indolicidin - antimicrobial peptide (AMP) derived from bovine neutrophil granules, was found to exhibit high antistaphylococcal and antibiofilm potential. Furthermore, its analog with a reversed sequence (retro-omiganan) was found to display enhanced activity against a variety of pathogens. Based on experience of our group, we found out that counterion exchange can improve the antistaphylococcal activity of AMPs. The aim of this study was to investigate the activity of both compounds against S. aureus biofilm under flow conditions. The advantage of this approach was that it offered the opportunity to form and characterize the biofilm under more controlled conditions. To do this, unique flow cells made of polydimethylsiloxane (PDMS) were developed. The activity against pre-formed biofilm as well as AMPs-treated bacteria was measured. Also, the incorporation of omiganan and retro-omiganan into the channels was conducted to learn whether or not it would inhibit the development of biofilm. The results of the microbiological tests ultimately confirmed the high potential of the omiganan and its retro-analog as well as the importance of counterion exchange in terms of antimicrobial examination. We found out that retro-omiganan trifluoroacetate had the highest biofilm inhibitory properties, however, acetates of both compounds exhibited the highest activity against planktonic and biofilm cultures. Moreover, the developed methodology of investigation under flow conditions allows the implementation of the studies under flow conditions to other compounds.

Mining, water-reservoir impoundment, underground gas storage, geothermal energy exploitation and hydrocarbon extraction have the potential to cause rock deformation and earthquakes, which may be hazardous for people, infrastructure and the environment. Restricted access to data constitutes a barrier to assessing and mitigating the associated hazards. Thematic Core Service Anthropogenic Hazards (TCS AH) of the European Plate Observing System (EPOS) provides a novel e-research infrastructure. The core of this infrastructure, the IS-EPOS Platform (tcs.ah-epos.eu) connected to international data storage nodes offers open access to large grouped datasets (here termed episodes), comprising geoscientific and associated data from industrial activity along with a large set of embedded applications for their efficient data processing, analysis and visualization. The novel team-working features of the IS-EPOS Platform facilitate collaborative and interdisciplinary scientific research, public understanding of science, citizen science applications, knowledge dissemination, data-informed policy-making and the teaching of anthropogenic hazards related to georesource exploitation. TCS AH is one of 10 thematic core services forming EPOS, a solid earth science European Research Infrastructure Consortium (ERIC) ( www.epos-ip.org ).