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The COVID-19 pandemic prompted rapid vaccine development and deployment worldwide. Despite widespread vaccination efforts, understanding the effectiveness of vaccines in hospitalized patients remains a critical concern. This retrospective cohort study, conducted at a tertiary healthcare centre in Serbia, tracked patients hospitalized during different waves of COVID-19 variants—Alpha, Delta, and Omicron. Data collection included demographics, comorbidities, symptoms, and vaccination status. Among 3593 patients, those with prior exposure to COVID-19 cases or hospital treatment showed higher positivity rates. Symptom prevalence varied across waves, with coughs persisting. Patients without chronic diseases were more frequent among those testing negative. Vaccine effectiveness varied, with Sinopharm demonstrating a 45.6% effectiveness initially and Pfizer-BioNTech showing an effectiveness of up to 74.8% within 0–84 days after the second dose. Mixed-dose strategies, notably Sinopharm as a primary dose followed by a Pfizer-BioNTech booster, suggested increased protection. Despite substantial vaccination availability, a significant portion of hospitalized patients remained unvaccinated. This study underscores the dynamic nature of vaccine effectiveness and advocates for booster strategies to address evolving challenges in combating COVID-19, particularly in hospitalized patients. [ABSTRACT FROM AUTHOR]

Toxoplasmosis, caused by the cosmopolitan protozoan Toxoplasma gondii, has particular implications during pregnancy due to the possible transmission of infection to the fetus. Very few studies have assessed seroprevalence and the risk factors for toxoplasmosis in healthy pregnant women. The aim of this study was to examine the seroprevalence of T. gondii infection in healthy pregnant women and to identify the associated risk factors for toxoplasmosis. The cross-sectional study involved 300 healthy pregnant women who came to the Institute for Blood Transfusion in Belgrade between November 2018 and February 2019 for routine blood group and Rh factor testing before delivery, who were also tested using serological screening for the presence of specific antibodies. Positives were further examined using enzyme immunoassay. Of the total sera of participants analyzed, 38 were positive for specific IgG, resulting in a seroprevalence rate of 12.7% (95% Confidence Interval (CI) 9.1–17.0%). All pregnant women presented negative anti-T. gondii IgM antibodies. The multivariate logistic regression analysis revealed that living in a house with a garden was independently associated with the risk of T. gondii infections, while eating chicken meat was connected with a lower risk compared to eating other types of meat with an odds ratio (OR) of 2.5 (95% CI 1.21–5.02) and an OR of 0.3 (95% CI 0.09–0.83), respectively. Although the prevalence of anti-T. gondii IgG antibodies is relatively low, it is essential to maintain and adapt evidence-based preventive measures for toxoplasmosis continually. [ABSTRACT FROM AUTHOR]

Green hydrogen produced by alkaline electrolysis is a promising solution to address the world's increasing energy demand while mitigating greenhouse gas emissions. However, the efficient and cost-effective production of green hydrogen via alkaline electrolysis requires improvements. This paper presents an in situ activation process that simplifies the alkaline electrolysis technology while enhancing the catalytic activity of electrodes for the hydrogen evolution reaction. The aim of this research is to enhance the energy efficiency of alkaline electrolysis and decrease the energy consumption for hydrogen production. To achieve this goal, ionic activators comprising Ni, Zn, and Mo were incorporated into the standard electrolyte solution. Our results demonstrate that the anticipated improvement in the catalytic activity of the d-metal combination, surpassing even that of precious metals, has been successfully attained. As a result, a 20% reduction in energy consumption (REC) for the hydrogen produced has been observed. The catalytic activity of the added activators for the hydrogen evolution reaction was discussed by analyzing the mechanism of the reaction via Tafel analysis and EIS techniques. These findings offer a promising approach to improve alkaline electrolysis and enhance the production of green hydrogen. [ABSTRACT FROM AUTHOR]

Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies long sequencing read datasets with different base error profiles sourced from three human cell lines, rice, and tomato. Here, we show that GoldRush achieves assembly scaffold NGA50 lengths of 18.3-22.2, 0.3 and 2.6 Mbp, for the genomes of human, rice, and tomato, respectively, and assembles each genome within a day, using at most 54.5 GB of random-access memory, demonstrating the scalability of our genome assembly paradigm and its implementation. Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. GoldRush departs from this paradigm, generating highly contiguous assemblies with linear time complexity and using an order of magnitude less RAM than state-of-the-art methods. [ABSTRACT FROM AUTHOR]

The capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However, single cell engineering is limited by the necessary molecular complexity and the accompanying metabolic burden of synthetic circuits. To overcome these limitations, synthetic biologists have begun engineering multicellular systems that combine cells with designed subfunctions. To further advance information processing in synthetic multicellular systems, we introduce the application of reservoir computing. Reservoir computers (RCs) approximate a temporal signal processing task via a fixed-rule dynamic network (the reservoir) with a regression-based readout. Importantly, RCs eliminate the need of network rewiring, as different tasks can be approximated with the same reservoir. Previous work has already demonstrated the capacity of single cells, as well as populations of neurons, to act as reservoirs. In this work, we extend reservoir computing in multicellular populations with the widespread mechanism of diffusion-based cell-to-cell signaling. As a proof-of-concept, we simulated a reservoir made of a 3D community of cells communicating via diffusible molecules and used it to approximate a range of binary signal processing tasks, focusing on two benchmark functions—computing median and parity functions from binary input signals. We demonstrate that a diffusion-based multicellular reservoir is a feasible synthetic framework for performing complex temporal computing tasks that provides a computational advantage over single cell reservoirs. We also identified a number of biological properties that can affect the computational performance of these processing systems. [ABSTRACT FROM AUTHOR]

In this experimental study, picosecond laser treatment was performed on a nickel-based superalloy Nimonic 263, aiming to investigate the surface effects induced by irradiation in different atmospheric conditions and, concerning changes in surface composition, regarding the possibility for improvement of its functionality. Besides the varying laser parameters, such as a number of pulses and pulse energy, environmental conditions are also varied. All surface modifications were carried out in standard laboratory conditions and a nitrogen- and argon-rich atmosphere. The resulting topography effects depend on the specific laser treatment and could be categorized as increased roughness, crater formation, and formation of the laser-induced periodic surface structures (LIPSS). Changes in the chemical surface composition are distinguished as the potential formation of the protective oxides/nitrides on the sample surface. Numerous characterization techniques analyse the resulting effects on the topography and surface parameters. The multi-response parametric optimization of the picosecond laser process was performed using an advanced statistical method based on Taguchi's robust parameter design. Finally, the optimal parameter conditions for Nimonic 263 modification are suggested. [ABSTRACT FROM AUTHOR]

Millions of patients acquire healthcare-associated infections (HAIs) every year, putting them at risk for serious complications and prolonged hospitalization. Point prevalence surveys (PPS), guided by the European Centre for Disease Prevention and Control framework, are one of the primary methods by which countries in the European Union conduct surveillance of HAIs. Serbia, though not in the EU, implemented this approach in its national PPS. The microbiological and antimicrobial resistance (AMR) analyses comprised patients in 61 out of 65 hospitals included in the fourth PPS conducted in November 2017. A total of 515/12,380 (4.2%) of the adult patients included in the PPS had at least one HAI, with intensive care units carrying the highest prevalence of 15.9%. Urinary tract and surgical site infections were the most frequently identified types of HAIs (23.9% and 23.0%, respectively). Enterobacterales comprised almost half (47.0%) of all causative agents, most notably Klebsiella spp. (16.7%). AMR was very high for most pathogens—80.5% of nonfermentative Gram-negative bacilli were resistant to carbapenems whereas 62.9% of Enterobacterales were resistant to third generation cephalosporins. The calculated AMR index of 61% is one of the highest in Europe. Further efforts are needed to reduce the burden of HAIs in Serbia that carry very high resistance rates to antibiotics currently used in clinical practice. [ABSTRACT FROM AUTHOR]

Background: De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers. Edges in this graph are established between nodes that overlap by k - 1 bases, and nodes along unambiguous walks in the graph are subsequently merged. The selection of k is influenced by multiple factors, and optimizing this value results in a trade-off between graph connectivity and sequence contiguity. Ideally, multiple k sizes should be used, so lower values can provide good connectivity in lesser covered regions and higher values can increase contiguity in well-covered regions. However, current approaches that use multiple k values do not address the scalability issues inherent to the assembly of large genomes. Results: Here we present RResolver, a scalable algorithm that takes a short-read de Bruijn graph assembly with a starting k as input and uses a k value closer to that of the read length to resolve repeats. RResolver builds a Bloom filter of sequencing reads which is used to evaluate the assembly graph path support at branching points and removes paths with insufficient support. RResolver runs efficiently, taking only 26 min on average for an ABySS human assembly with 48 threads and 60 GiB memory. Across all experiments, compared to a baseline assembly, RResolver improves scaffold contiguity (NGA50) by up to 15% and reduces misassemblies by up to 12%. Conclusions: RResolver adds a missing component to scalable de Bruijn graph genome assembly. By improving the initial and fundamental graph traversal outcome, all downstream ABySS algorithms greatly benefit by working with a more accurate and less complex representation of the genome. The RResolver code is integrated into ABySS and is available at https://github.com/bcgsc/abyss/tree/master/RResolver. [ABSTRACT FROM AUTHOR]

Toxoplasmosis is a globally distributed parasitic zoonosis, affecting approximately one third of the human population. Epidemiological studies on toxoplasmosis conducted in Serbia so far have been focused on women of childbearing age, without a clear insight into the prevalence in the general population. We conducted a cross-sectional study in a representative sample of the healthy adult population consisting of 1095 blood donors of both genders to establish the prevalence and risk factors for Toxoplasma gondii infection. Data on the demographic and clinical characteristics of all study participants, as well as on their lifestyle habits, were collected by means of a questionnaire. The overall prevalence of infection was 20.5% (224/1095) and the avidity of the specific IgG antibodies detected was high in a vast majority of the seropositive donors (98.2%). Interestingly, the remaining 1.8% of the specific IgG positive samples were of borderline avidity (4/224), in complete absence of specific IgM. The multivariate logistic regression analysis showed that independent risk factors included age (from OR (95% CI) 1.9 (1.13–3.28) in the 30–39 age group, to 6.8 (3.27–14.24) in the age group of >60 years), suburban living (OR (95% CI) 2.2 (1.43–3.34)) and contact with soil (OR (95% CI) 1.4 (1.01–1.94)). This first large-scale study on toxoplasmosis in the general population in Serbia shows the lowest prevalence ever reported in this country. Moreover, the novel perspective on risk factors provides an updated basis for future prevention programs. [ABSTRACT FROM AUTHOR]

Copyright of Medical Journal / Medicinski Časopis is the property of Serbian Medical Society, Section Kragujevac and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: As the only non-European Union (EU) country, Serbia participated in a second point prevalence survey of healthcare-associated infections (HAIs) and antimicrobial use (AMU) organized by the European Centre for Disease Prevention and Control (ECDC) in the EU countries. Here, we aimed to estimate the prevalence of HAI and AMU in patients who had recently undergone a surgery and to compare risk profile, HAI rates, and AMU among surgical patients and non-surgical patients. Methods: A national PPS was performed in 65 Serbian acute-care hospitals, in November 2017. In this paper, the data of 61 hospitals for adult acute-care were analyzed. To ensure the comparability of study design we used the Serbian translation of ECDC case definitions and ECDC PPS protocol. The trained infection control staff, led by a hospital coordinator, reviewed medical records to identify HAI active at the time of the survey and AMU. Only inpatients admitted to the ward before 8 a.m. on the day if the survey were included. Results: A total of 12,478 patients from 61 hospitals for adult acute-care were eligible for inclusion in this study. Significantly higher proportions of surgical patients were female, belonged to the 60-to-79 age group, and were less severely ill. Also, extrinsic factors (invasive devices, hospitalization at the ICU, and prior antibiotics therapy) were more frequent in surgical patients. Prevalence of HAIs was higher among surgical patients (261/3626; 7.2%) than among non-surgical patients (258/8852; 2.9%) (p < 0.0001). The highest prevalence of all HAIs was noted in patients who had kidney transplantation (4/11; 36.4%), while SSIs were the most prevalent among patients who had peripheral vascular bypass surgery (3/15; 20.0%). Non-surgical patients received treatment for community-acquired infections in significantly higher proportion (2664/8852; 64.3) (p < 0.001). Surgical prophylaxis for more than 1 day was applied in 71.4% of surgical patients. Conclusion: We have provided an insight into the burden of HAIs and AMU among Serbia acute-care hospitals, and highlighted several priority areas and targets for quality improvement. [ABSTRACT FROM AUTHOR]

Copyright of Biologica Nyssana is the property of University of Nis, Department of Biology & Ecology, Faculty of Sciences & Mathematics and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short-read assembly with a draft long-read assembly and a draft assembly with an assembly from a closely related species. When scaffolding a human short-read assembly using the reference human genome or a long-read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using <11 GB of RAM. Compared to existing reference-guided scaffolders, ntJoin generates highly contiguous assemblies faster and using less memory. Availability and implementation ntJoin is written in C++ and Python and is freely available at https://github.com/bcgsc/ntjoin. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Motivation Spaced seeds are robust alternatives to k -mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research. Results ntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k -mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism. Availability and implementation ntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Copyright of Economics of Agriculture / Ekonomika Poljoprivrede is the property of Institute of Agricultural Economics (IAE) / Belgrade and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Works of the Faculty of Forestry University of Sarajevo is the property of Faculty of Forestry University of Sarajevo and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Over the years, alternative procedures to the Bond grindability test have been proposed aiming to avoid the need for the standard mill or to reduce and simplify the grinding procedure. Some of them use the standard mill, while others are based on a non-standard mill or computation techniques. Therefore, papers targeting to propose a better alternative claim to improve validity, to reduce test duration, or to propose simpler and faster alternative methods for determining the Bond work index (wi). In this review paper, a compilation and critical analysis of selected proposals is performed, concluding that some of the short procedures could be useful for control purposes, while the simulation-based procedures could be interesting within a process digitalisation strategy. [ABSTRACT FROM AUTHOR]