ntHash2: recursive spaced seed hashing for nucleotide sequences.

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.

Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy.

Locally advanced rectal cancer (LARC) presents a challenge in identifying molecular markers linked to the response to neoadjuvant chemoradiotherapy (nCRT). This study aimed to utilize a sensitive proteomic method, data-independent mass spectrometry (DIA-MS), to extensively analyze the LARC proteome, seeking individuals with favorable initial responses suitable for a watch-and-wait approach. This research addresses the unmet need to understand the response to treatment, potentially guiding personalized strategies for LARC patients. Post-treatment assessment included MRI scans and proctoscopy. This research involved 97 LARC patients treated with intense chemoradiotherapy, comprising radiation and chemotherapy. Out of 97 LARC included in this study, we selected 20 samples with the most different responses to nCRT for proteome profiling (responders vs. non-responders). This proteomic approach shows extensive proteome coverage in LARC samples. The analysis identified a significant number of proteins compared to a prior study. A total of 915 proteins exhibited differential expression between the two groups, with certain signaling pathways associated with response mechanisms, while top candidates had good predictive potential. Proteins encoded by genes SMPDL3A, PCTP, LGMN, SYNJ2, NHLRC3, GLB1, and RAB43 showed high predictive potential of unfavorable treatment outcome, while RPA2, SARNP, PCBP2, SF3B2, HNRNPF, RBBP4, MAGOHB, DUT, ERG28, and BUB3 were good predictive biomarkers of favorable treatment outcome. The identified proteins and related biological processes provide promising insights that could enhance the management and care of LARC patients.

RResolver: efficient short-read repeat resolution within ABySS.

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 [Formula: see text] 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 .

Quality of life following two different techniques of an open ventral hernia repair for large hernias: a prospective randomized study.

BACKGROUND: We compare the health-related quality of life (QoL) of patients with incision hernias before and after surgery with two different techniques. METHODS: In this prospective randomized study, the study population consisted of all patients who underwent the first surgical incisional hernias repair during the 1-year study period. Patients who met the criteria for inclusion in the study were randomized into two groups: the first group consisted of patients operated by an open Rives sublay technique, and the second group included patients operated by a segregation component technique. The change in the quality of life before and 6 months after surgery was assessed using two general (Short form of SF-36 questionnaires and European Quality of Life Questionnaire-EQ-5D-3L), and three specific hernia questionnaires (Hernia Related Quality of Life Survey-HerQles, Eura HS Quality of Life Scale-EuraHS QoL, and Carolinas Comfort Scale-CCS). RESULTS: A total of 93 patients were included in the study. Patients operated on by the Rives technique had a better role physical score before surgery, according to the SF-36 tool, although this was not found after surgery. The postoperative QoL measured with each scale of all questionnaires was significantly better after surgery. Comparing two groups of patients after surgery, only the pain domain of the EuraHS Qol questionnaire was worse in patients operated by a segregation component technique. CONCLUSION: Both techniques improve the quality of life after surgery. Generic QoL questionnaires showed no difference in the quality of life compared to repair technique but specific hernia-related questionnaires showed differences.

LongStitch: high-quality genome assembly correction and scaffolding using long reads.

BACKGROUND: Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. RESULTS: LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. CONCLUSIONS: Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch .

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.

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.

Prognostic Factors for Post-Recurrence Survival in Stage II and III Colorectal Carcinoma Patients.

Background and objectives: This study aimed to evaluate prognostic factors for post-recurrence survival in local and locally advanced colorectal cancer patients. Materials and Methods: A total of 273 patients with stage III and high-risk stage II colorectal cancer were prospectively enrolled. All patients underwent operative treatment of the primary tumor and adjuvant fluorouracil-based chemotherapy. Results: Over the three-year period (2008-2010), a cohort of 273 patients with stage III and high-risk stage II colorectal cancer had been screened. During follow up, 105 (38.5%) patients had disease recurrence. Survival rates 1-, 3- and 5-year after recurrence were 53.9, 18.2 and 6.5%, respectively, and the median post-recurrence survival time was 13 months. Survival analysis showed that age at diagnosis (p < 0.01), gender (p < 0.05), elevated postoperative Ca19-9 (p < 0.01), tumor histology (adenocarcinoma vs. mucinous vs. signet ring tumors, p < 0.01) and tumor stage (II vs. III, p < 0.05) had a significant influence on post-recurrence survival. Recurrence interval and metastatic site were not related to survival following recurrence. Multivariate analysis showed that older age (HR 2.43), mucinous tumors (HR 1.51) and tumors expressing Ca19-9 at baseline (HR 3.51) were independently associated with survival following recurrence. Conclusions: Baseline patient and tumor characteristics largely predicted patient outcomes after disease recurrence. Recurrence intervals in local and locally advanced colorectal cancer were not found to be prognostic factors for post-recurrence survival. Older age, male gender, stage III and mucinous histology were poor prognostic factors after the disease had recurred. Stage II patients had remarkable post-recurrence survival compared to stage III patients.

Epidemiology and risk factors for multi-drug resistant hospital-acquired urinary tract infection in patients with liver cirrhosis: single center experience in Serbia.

BACKGROUND: Cirrhosis-associated immune dysfunction syndrome (CAIDS) has been identified in patients with liver cirrhosis (LC), predisposing them to a wide variety of infections. In patients with LC, healthcare-associated infections involving multi-drug resistant (MDR) bacteria have increased significantly over the last decades. Among them, hospital-acquired urinary tract infections (HA-UTI) are the most common. This study aimed to investigate the rates of antimicrobial resistance among patients with LC and HA-UTI and to determine risk factors associated with their development among patients hospitalized in tertiary care facility in Serbia. METHODS: This retrospective study included 65 hospitalized patients with LC who had developed HA-UTI. We examined the epidemiology of these infections concerning resistance to the most commonly used antimicrobials and patient-specific risk factors associated with HA-UTI development by MDR pathogens. RESULTS: The most frequently isolated organisms were Enterococcus spp. (n = 34, 52.3%), Klebsiella spp. (n = 10, 15.4%), and E.coli (n = 6, 9.2%). Thirty-five isolates (53.8%) were identified as MDR, and 30 (46.2%) were non-MDR.We found a statistically significant difference in the distribution of MDR and non-MDR strains, based on Gram staining, with the majority of Gram-negative pathogens being MDR (p = 0.005). We identified age ≥ 65 years (p = 0.007), previous use of cephalosporins as empiric therapy (p = 0.042), and the presence of hepatic encephalopathy (p = 0.011) as independent risk factors for the development of MDR UTIs. CONCLUSION: This is the first study from Serbia and the Balkans concerning the changing epidemiology of MDR UTI in patients with LC. Our study showed that more than half of HA-UTI was caused by MDR and the most common pathogen was Enterococcus spp. The overall resistance to ceftriaxone was 92%. Our findings underscore the need for institutions to individualize protocols for treatment of hospital-acquired infections, particularly in immunocompromised populations.

Simple One-Pot Synthesis of Fully Biobased Unsaturated Polyester Resins Based on Itaconic Acid.

For the preparation of fully biobased unsaturated polyester resins (UPRs), the replacement of styrene with alternate nonpetroleum-based monomers turned out to be one of the most challenging tasks. Its complexity lies in the fact that reactive diluents (RD) have to have low viscosity and volatility, good compatibility with prepolymer, and capability to homopolymerize and copolymerize with its unsaturations. In this context, we directed our efforts to develop fully biobased UPRs using the dialkyl itaconates as an alternative to styrene. Therefore, a series of 100% biobased UPRs were prepared from itaconic acid and 1,2-propandiol and diluted by dialkyl itaconates. The resins were characterized by Fourier transform infrared spectroscopy, NMR, volatility, and viscosity measurements, while the cured samples were characterized by dynamic mechanical properties, thermomechanical analysis, thermogravimetric analysis data, and tensile tests. The influence of RD structure on the properties of cured samples was discussed in detail. It was shown that the prepared resins had evaporation rates of dialkyl itaconates of several orders of magnitude less compared to styrene. The cured resins with dimethyl itaconate showed comparable or even better thermal and mechanical properties compared to the one with styrene. This investigation showed that itaconic acid and dialkyl itaconates are promising bioresources for the preparation of fully biobased UPRs for mass consumption.

p21 does, but p53 does not predict pathological response to preoperative chemoradiotherapy in locally advanced rectal cancer.

PURPOSE: Preoperative chemoradiotherapy (CRT) is the standard treatment option in locally advanced rectal cancer. The tumor response is assessed through tumor and nodal downstaging and the tumor regression grade. Currently, there is no method to predict a tumor response to CRT. We aimed to evaluate whether p21 and p53 expressions could be a reliable predictors of pathological response to CRT. METHODS: Fifty patients with locally advanced rectal cancer were treated with preoperative radiotherapy combined with mitomycin C and capecitabine. p21 and p53 immumohistochemical staining was performed on pretreatment biopsies and the results were compared with tumor regression according to grading systems by Dworak (TRG grades) and by Wheeler (RCRG grades). RESULTS: Testing RCRG grades in relation to p21 expression showed statistically significant difference (p=0.021). RCRG 3 (poor response) was more frequent in the group of patients with low p21. According to Dworak, grade 4 (complete regression) was more frequent in the group of patients with positive p21 expression (p=0.032). Significant difference in p21 expression in grade 4 group compared with all other grade groups was also found (p=0.007). Patients with immune expression of p21 had significantly higher percentage of complete regression in comparison to the patients with low expression of p21. We haven't found any correlation between p53 expression and histopathological (HP) as well as regression grades. CONCLUSION: According to both grading systems, our results suggest that p53 expression does not, but p21 expression does predict pathological response to preoperative CRT.

Vaccine Effectiveness against SARS-CoV-2 Infection during the Circulation of Alpha, Delta, or Omicron Variants: A Retrospective Cohort Study in a Tertiary Hospital in Serbia.

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.

Computational capabilities of a multicellular reservoir computing system.

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.

Young-Onset Colorectal Cancer in Serbia: Tertiary Cancer Center Experience.

Purpose: Early-onset colorectal cancer (CRC) is a growing problem. The aim of the study was to identify adolescent and young adult (AYA) patients with CRC in Serbia, treated in the single tertiary cancer center. Materials and Methods: This is a retrospective study that included only AYA patients (ages 18-39 years) with histologically confirmed CRC. In 11 year (2009-2019), 109 patients were identified from a single-institution database and their clinical variables and outcomes were analyzed. Results: The prevalence of a positive family history of CRC was 12.8%. Presenting symptoms were not different than traditional CRC. More than a quarter were diagnosed as an emergency. Left-sided tumors were diagnosed in 83.4% and mucinous tumors were recorded in one-third of the patients. Postoperatively patients mainly were in PS0-1 (97%). Patients presented as stages II (18.3%), III (47.7%), and IV (33.9%). The recurrence rate in local stages was 50%. Surgical treatment of localized metastatic disease was performed in almost half of the stage IV patients. Median disease-free survival for patients with the recurrent disease was 11.8 months. Median overall survival (OS) for the local and metastatic stage was 64.3 and 20.5 months, respectively. Survival analysis showed that performance status, bowel obstruction, N2 status, local invasions, disease stage, and surgery in stage IV had a statistically significant influence on OS. Conclusion: Serbian AYA CRC patients are of good general condition, with advanced left-sided tumors, common mucinous histology, and inverse histology features. Surgery in metastatic disease provided long-term survival. The outcome of the patient is influenced by a late diagnosis, inverse histological features, and treatment provided.

ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads.

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection Basic Protocol 2: ntLink scaffolding with gap-filling Basic Protocol 3: Running in-code iterations of ntLink scaffolding Alternate Protocol 1: Generating long-read to contig mappings with ntLink Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long Support Protocol: Installing ntLink.

Structural and Functional Picosecond Laser Modification of the Nimonic 263 Superalloy in Different Environmental Conditions and Optimization of the Irradiation Process.

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.

Enhanced Catalytic Activity and Energy Savings with Ni-Zn-Mo Ionic Activators for Hydrogen Evolution in Alkaline Electrolysis.

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.

Factors Associated with Toxoplasma gondii Seroprevalence in Pregnant Women: A Cross-Sectional Study in Belgrade, Serbia.

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.

Changes in Attitudes toward COVID-19 Vaccination and Vaccine Uptake during Pandemic.

The epidemic control approach was based on non-pharmacological measures in the first year of the COVID-19 pandemic, followed by vaccine uptake in the second year. Vaccine uptake depends on the individual attitude toward vaccination. The aim was to assess the changes in attitudes regarding COVID-19 vaccine protection during the pandemic and to determine the vaccination uptake concerning these attitudes. A panel study on COVID-19 vaccine attitudes and vaccination against COVID-19 was conducted in Belgrade, Serbia. The first survey was carried out in May−June 2020, and the second survey was organized in August−September 2021. During the baseline testing performed in 2020, 64.4% of respondents believed that the future vaccine against COVID-19 could protect against the COVID-19 disease, while 9.7% thought that it could not, and 25.9% were unsure. One year later, in the second survey, the percentage of participants with positive attitudes was slightly lower (64.7% vs. 62.5%). However, negative attitudes turned positive in 34% of cases, and 28.9% became unsure about vaccine protection (p < 0.001). Out of the 390 participants included in the study, 79.7% were vaccinated against COVID-19 until follow-up. There is a statistically significant difference in vaccination uptake compared to the baseline attitude about the protection of the COVID-19 vaccine. The main finding of our study is that the majority of participants who were vaccine hesitant during the baseline testing changed their opinion during the follow-up period. Additionally, the baseline attitude about the protection of the COVID-19 vaccine has been shown to be a potential determinant of vaccination uptake.

Incidence and Risk Factors for Clostridioides difficile Infections in Non-COVID and COVID-19 Patients: Experience from a Tertiary Care Hospital.

(1) Background: The aim of this study was to assess the incidence and the risk factors for healthcare-associated Clostridioides difficile infection (HA-CDI) in patients with COVID-19 and without this infection. (2) Methods: A single-center, prospective observational study was conducted at the University Clinical Hospital Center in Belgrade, Serbia, from January 2019 to December 2021. The entire hospital was a COVID-dedicated hospital for 12 months during the study period. The incidence density rates and risk factors for HA-CDI in patients with and without COVID-19 are presented. (3) Results: The incidence rates of HA-CDIs were three times higher in patients with COVID-19. The HA-CDI-COVID-patients were younger (69.9 ± 12.6 vs. 72.5 ± 11.6; p = 0.017), admitted from another hospital (20.5% vs. 2.9; p < 0.001), had antimicrobial therapy before CDI (99.1% vs. 91.3%, p < 0.001), received two or more antibiotics (p = 0.030) during a longer period (p = 0.035), received proton pump inhibitors (95.9% vs. 50.0%, p < 0.001) during a longer period (p = 0.012) and steroids (32.8% vs. 20.4%, p < 0.001). During the last month before their current hospitalization, a higher percentage of patients without COVID-19 disease were hospitalized in our hospital (p < 0.001). Independent predictors for HA-CDIs in patients with COVID-19 were admission from another hospital (p = 0.003), the length of antibiotic administration (0.020), and the use of steroids in therapy (p < 0.001). The HA-CDI predictors in the non-COVID patients were older age (p = 0.017), advanced-stage renal failure (p = 0.005), chemotherapy (p = 0.003), and a low albumin level (0.005). (4) Conclusion: Higher incidence rates of HAI-CDIs in COVID-19 patients did not occur due to reduced infection control precautions and hygiene measures but due to antibiotic therapy and therapy with other drugs used during the pandemic.

Linear time complexity de novo long read genome assembly with GoldRush.

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.