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Objective: To compare the difference in failure rates between orthodontic brackets bonded with light-cured primer and those bonded without primer., Material and Methods: An electronic search of five databases and additional manual searches were performed until January 2024. Randomized and prospective non-randomized controlled trials directly comparing the bracket failure rate with and without primer. Two authors independently collected study characteristics by extracting outcome data from pre-defined sheets. After evaluating the risk of bias, the odds ratio and 95% confidence intervals (CIs) were calculated with random-effects models., Results: Four studies were evaluated using qualitative and quantitative analysis. The analysis included data from 199 patients (1691 brackets with primer and 1646 brackets without primer). Random effects of pooled meta-analysis demonstrated statistically significant differences in the bracket failure rates (odds ratio=1.50, p=0.010, [95% CI 1.10 to 2.05]). The risk of failure was 1.5 times greater when brackets were bonded without primer., Conclusion: The results should be interpreted in the context of the limited sample size, even though there was a substantial difference in the failure rates of brackets with and without a primer, favouring the use of a primer. Furthermore, the validity of the finding may be limited by potential variables such as patient factors, clinician expertise, and isolation. More extensive research is required to validate these findings (PROSPERO CRD42024593134)., (Copyright © 2024 CEO. Published by Elsevier Masson SAS. All rights reserved.)

Moth orchids ( Phalaenopsis spp.) are globally popular ornamental flowers. However, effective management strategies for Phalaenopsis leaf yellowing remain elusive, making the disease a challenging obstacle affecting moth orchids at various growth stages. This disease manifests as collar rot, leaf yellowing, leaf abscission, and eventually, plant death. The lack of effective management strategies is likely attributed to a limited understanding of the disease pathogenesis and pathogen dissemination pathways. Fusarium phalaenopsidis sp. nov. was established in this study to stabilize the classification status of Phalaenopsis leaf yellowing pathogens using molecular and morphological features. The genome of the holotype strain was sequenced and assembled, revealing its genome structures. Analyses of virulence-related elements, including transposon elements, secondary metabolite biosynthetic gene clusters, effectors, and secreted carbohydrate-active enzymes, shed light on the potential roles of three fast core chromosomes in virulence. Two species-specific primers were designed based on unique gene sequences of two virulence-related proteins through comparative genomics and BLAST screening. The specificity of these primers was validated using isolates of F. phalaenopsidis , non-target species in the Fusarium solani species complex, other Fusarium species complexes, and saprophytic fungi. These results are intended to accelerate the identification of the pathogens, facilitate the study of disease pathogenesis, and pave the way for elucidating pathogen dissemination pathways. Ultimately, they aim to contribute to the formulation of effective control strategies against Phalaenopsis leaf yellowing., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Tsao, Li, Tu, Nai, Lin and Wang.)

Multidrug resistance efflux pumps (MDREPs) in biofilm communities have become an increasingly expensive problem in clinical settings. Polymerase chain reaction (PCR)-based detection can be used to diagnose and characterize these genes, but this requires effective primer design to minimize false positives and negatives in test conclusions. A universal primer approach has previously been used to detect conserved core genes but not for accessory genes such as MDREPs. This study describes a guideline for the design of primers used in the detection of MDREP genes and an optimization approach for creating primers by using multiple sequence alignments to target conserved regions in silico , progressing from in silico to in vitro to generate working primers. Using this approach, this paper was able to generate primers to target sugE , a small multidrug resistance (SMR) protein found in microbial species. Primers were tested positively against synthetic DNA sequences but were inconsistent with DNA extracted from the organism of interest. Primer design informs the shortfalls of this detection technique and the difficulty in characterizing such genomic elements., Competing Interests: Human subjects: All authors have confirmed that this study did not involve human participants or tissue. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Hui et al.)

Nucleic acid tests (NATs) are considered as gold standard in molecular diagnosis. To meet the demand for onsite, point-of-care, specific and sensitive, trace and genotype detection of pathogens and pathogenic variants, various types of NATs have been developed since the discovery of PCR. As alternatives to traditional NATs (e.g., PCR), isothermal nucleic acid amplification techniques (INAATs) such as LAMP, RPA, SDA, HDR, NASBA, and HCA were invented gradually. PCR and most of these techniques highly depend on efficient and optimal primer and probe design to deliver accurate and specific results. This chapter starts with a discussion of traditional NATs and INAATs in concert with the description of computational tools available to aid the process of primer/probe design for NATs and INAATs. Besides briefly covering nanoparticles-assisted NATs, a more comprehensive presentation is given on the role CRISPR-based technologies have played in molecular diagnosis. Here we provide examples of a few groundbreaking CRISPR assays that have been developed to counter epidemics and pandemics and outline CRISPR biology, highlighting the role of CRISPR guide RNA and its design in any successful CRISPR-based application. In this respect, we tabularize computational tools that are available to aid the design of guide RNAs in CRISPR-based applications. In the second part of our chapter, we discuss machine learning (ML)- and deep learning (DL)-based computational approaches that facilitate the design of efficient primer and probe for NATs/INAATs and guide RNAs for CRISPR-based applications. Given the role of microRNA (miRNAs) as potential future biomarkers of disease diagnosis, we have also discussed ML/DL-based computational approaches for miRNA-target predictions. Our chapter presents the evolution of nucleic acid-based diagnosis techniques from PCR and INAATs to more advanced CRISPR/Cas-based methodologies in concert with the evolution of deep learning (DL)- and machine learning (ml)-based computational tools in the most relevant application domains., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A ( amoA ) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zhou, Liu, Liu, Liu, Xu and Li.)

We investigated a variant of measles virus that encodes three mismatches to the reverse priming site for a widely used diagnostic real-time RT-PCR assay; reduction of sensitivity was hypothesised. We examined performance of the assay in context of the variant using in silico data, synthetic RNA templates and clinical specimens. Sensitivity was reduced observed at low copy numbers for templates encoding the variant sequence. We designed and tested an alternate priming strategy, rescuing the sensitivity of the assay.

Objectives: The peer review process is critical to maintaining quality, reliability, novelty, and innovation in the scientific literature. However, the teaching of scientific peer review is rarely a component of formal scientific or clinical training, and even the most experienced peer reviewers express interest in continuing education. The objective of this review article is to summarize the collective perspectives of experienced journal editors about how to be a good reviewer in a step-by-step guide that can serve as a resource for the performance of peer review of a scientific manuscript., Methods: This is a narrative review., Results: A review of the history and an overview of the modern-day peer review process are provided with attention to the role played by the reviewer, including important reasons for involvement in scientific peer review. The general components of a scientific peer review are described, and a model for how to structure a peer review report is provided. These concepts are also summarized in a reviewer checklist that can be used in real-time to develop and double-check one's reviewer report before submitting it., Conclusions: Peer review is a critically important service for maintaining quality in the scientific literature. Peer review of a scientific manuscript and the associated reviewer's report should assess specific details related to the accuracy, validity, novelty, and interpretation of a study's results. We hope that this article will serve as a resource and guide for reviewers of all levels of experience in the performance of peer review of a scientific manuscript., Competing Interests: Ahmad R. Sedaghat is Associate Editor for Laryngoscope Investigative Otolaryngology, Rhinology and International Forum of Allergy and Rhinology; Manuel Bernal‐Sprekelsen is Editor‐in‐Chief of European Archives of Otorhinolaryngology, receives speaker honorarium from Sanofi Spain, GSK Spain, and, as scientific advisor, from Bionorica, Germany; Wytske J. Fokkens is editor‐in‐chief of Rhinology and Associate Editor for Allergy; Timothy L. Smith is editor‐in‐chief of International Forum of Allergy and Rhinology; Michael G. Stewart is former editor‐in‐chief of Laryngoscope; Romaine F. Johnson is editor‐in‐chief of Laryngoscope Investigative Otolaryngology., (© 2024 The Authors. Laryngoscope Investigative Otolaryngology published by Wiley Periodicals LLC on behalf of The Triological Society.)

Turtlegrass virus X, which infects the seagrass Thalassia testudinum , is the only potexvirus known to infect marine flowering plants. We investigated potexvirus distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed to capture potexvirus diversity in terrestrial plants. The assay, which implements Potex-5 and Potex-2RC primers, successfully amplified a 584 nt RNA-dependent RNA polymerase (RdRp) fragment from TVX-infected seagrasses. Following validation, we screened 74 opportunistically collected, apparently healthy seagrass samples for potexviruses using this RT-PCR assay. The survey examined the host species T. testudinum , Halodule wrightii , Halophila stipulacea , Syringodium filiforme , Ruppia maritima , and Zostera marina . Potexvirus PCR products were successfully generated only from T. testudinum samples and phylogenetic analysis of sequenced PCR products revealed five distinct TVX sequence variants. Although the RT-PCR assay revealed limited potexvirus diversity in seagrasses, the expanded geographic distribution of TVX shown here emphasizes the importance of future studies to investigate T. testudinum populations across its native range and understand how the observed fine-scale genetic diversity affects host-virus interactions.

Background: The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels., Results: As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea., Conclusions: This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy ., (© 2024. The Author(s).)

The aim of this study was to evaluate the influence of weight ratio, the shape of the precursor particles, and the application of a phosphate-monomer-containing primer on the mechanical properties of polymer infiltrated ceramic networks (PICNs) using zinc oxide. Two different types of zinc oxide particles were used as precursors to produce zinc oxide networks by sintering, each with two different densities resulting in two different weight ratios of the PICNs. For each of these different networks, two subgroups were built: one involving the application of a phosphate-monomer-containing primer prior to the infiltration of Bis-GMA/TEGDMA and one without. Elastic modulus and flexural strength were determined by using the three-point bending test. Vertical substance loss determined by the chewing simulation was evaluated with a laser scanning microscope. There was a statistically significant influence of the type of precursor particles on the flexural strength and in some cases on the elastic modulus. The application of a primer lead to a significant increase in the flexural strength and in most cases also in the elastic modulus. A higher weight ratio of zinc oxide led to a significantly higher elastic modulus. Few statistically significant differences were found for the vertical substance loss. By varying the shape of the particles and the weight fraction of zinc oxide, the mechanical properties of the investigated PICN can be controlled. The use of a phosphate-monomer-containing primer strengthens the bond between the infiltrated polymer and the zinc oxide, thus increasing the strength of the composite.

Objectives: This in vitro study evaluated the effect of different colouring solutions and primer systems used in the bonding of brackets on enamel colour change and bond strength., Materials and Methods: 120 premolar teeth were divided into four main groups; brackets were bonded with 37% orthophosphoric acid + Transbond XT Primer in Group 1, 3 M Single Bond Universal in Group 2, Transbond Plus SEP in Group 3, and G-Premio Bond in Group 4. Each group was divided into three subgroups, and the teeth were placed in a cup containing coffee and tea mixture, in a cup containing cola and in distilled water. A bond strength test was applied to all teeth. Colour measurements of all teeth were performed at 2 different times: before bonding and after the bond strength test., Results: The average bond strength of the 37% orthophosphoric acid group was higher than that of the other groups. The effect of primer and solution groups on colour change was statistically significant (p = 0.001 and p = 0.023, respectively)., Conclusions: In this study, the bond strength was clinically sufficient in all primer groups. The highest colour change was observed when the tea-coffee solution and Transbond Plus SEP primer were used., Clinical Relevance: This study has identified enamel discoloration and bond strength from different colouring solutions and primer systems used for bonding braces, which can be used to inform clinicians and patients to achieve better treatment results., (© 2024. The Author(s).)

Purpose: Polyetheretherketone (PEEK) is a new polymeric material that has received significant attention in dentistry because of its mechanical properties, biocompatibility, and aesthetics. However, the bonding performance of PEEK to other materials is not preferable. This study aimed to analyze the variations in the surface characteristics of PEEK under the chemical action of primers containing different functional monomers or polymers and to evaluate the bonding performance of PEEK and dental cement., Methods: Disk-shaped PEEK samples were prepared by dental milling, blasting with alumina oxide, and covering with primers containing functional monomers or polymers. The surface characteristics of the samples were analyzed by microscopy and spectroscopy. The shear bond strength (SBS) between PEEK and dental cement, with and without thermocycling, was tested using a universal testing machine. Finally, the data were statistically analyzed and compared., Results: Functional monomers or polymers were successfully bonded to the surface of PEEK. This treatment significantly improved its hydrophilicity and surface free energy (P < 0.05). The primer containing pentaerythritol triacrylate had the highest SBS without thermocycling (13.89 MPa). Meanwhile, the primers containing urethane dimethacrylate (UDMA) and methyl methacrylate (MMA) (abbreviated as the HC group) showed the highest SBS and lowest reduction (25.51%) after thermocycling. Notably, all the testing groups achieved the ISO10477 standard of 5 MPa. After thermocycling, adhesive failure accounted for the largest proportion of failures in all the groups except the HC group., Conclusions: The chemical priming treatment can significantly improve the SBS of PEEK and dental cement. Moreover, a primer containing both UDMA and MMA can provide improved bonding for PEEK materials.

This review offers an accessible primer to social neuroscientists interested in neural networks. It begins by providing an overview of key concepts in deep learning. It then discusses three ways neural networks can be useful to social neuroscientists: (i) building statistical models to predict behavior from brain activity; (ii) quantifying naturalistic stimuli and social interactions; and (iii) generating cognitive models of social brain function. These applications have the potential to enhance the clinical value of neuroimaging and improve the generalizability of social neuroscience research. We also discuss the significant practical challenges, theoretical limitations and ethical issues faced by deep learning. If the field can successfully navigate these hazards, we believe that artificial neural networks may prove indispensable for the next stage of the field's development: deep social neuroscience., (© The Author(s) 2024. Published by Oxford University Press.)

Ensuring a secure bond between a framework structure and layering composite resin veneer is essential for a long-lasting dental restoration. A variety of primer systems are available to facilitate the adhesive bonding. Nevertheless, the growing preference for efficiency and simplicity in dentistry has made the one-bottle universal primers a desirable option. This study aims to compare the effectiveness of universal primers on the shear bond strength (SBS) of base metal alloy (BMA) and zirconia to layering composite resin. Each 160 BMA and zirconia 20 × 10 × 5 mm test specimen was fabricated. Eight different primers (SunCera Metal Primer, Metal Primer Z, Reliance Metal Primer, Alloy Primer, MKZ Primer, Monobond Plus, ArtPrime Plus, and Clearfil Ceramic Primer Plus) were applied to 20 specimens in each group. Subsequently, a 5 × 2 mm composite resin build-up was applied. SBS tests were performed after 24 h of water storage and after thermocycling (25,000 cycles, 5-55 °C). On BMA, after water storage for 24 h, the bond strength values ranged from 26.53 ± 3.28 MPa (Metal Primer Z) to 29.72 ± 2.00 MPa (MKZ Primer), while after thermocycling, bond strength values ranged from 25.19 ± 1.73 MPa (MKZ Primer) to 27.69 ± 2.37 MPa (Clearfil Ceramic Primer Plus). On a zirconia base, after 24 h, the bond strengths values ranged from 22.63 ± 2.28 MPa (Reliance Primer) to 29.96 ± 2.37 MPa (MKZ Primer) and from 23.77 ± 3.86 MPa (Metal Primer Z) to 28.88 ± 3.09 MPa (Monobond Plus) after thermocycling. While no significant difference in bond strength was found between the primers on the BMA base, five primer combinations differed significantly from each other on zirconia ( p = 0.002-0.043). All primers achieved a bond strength greater than 23 MPa on both framework materials after thermocycling. Thus, all primers tested can be applied to both framework materials with comparable results.

Background: The aim of this study was to evaluate the effect of separately curing the unfilled resin for increased bond strength of the orthodontic brackets as the literature shows both studies that support and contradict this aspect., Methodology: The sample consisted of 120 specimens randomly grouped into four of 30. The tooth was cleaned of tissue and debris and stored in a distilled water solution until the procedures of bonding. The surface of the enamel was conditioned with pumice, and acrylic blocks were designed for the tooth to be mounted onto them. The buccal surfaces of all the teeth were prepared by etching the enamel with 37% phosphoric acid for a time period of 30 seconds and washed for 20 seconds under running water. Stainless steel brackets (Victory Series™ MBT, 0.022 Slot) were used for all the samples in the study, and the bonding procedure was conducted on the same day for all the groups. The artificial saliva was used for the storage of samples for 24 h after bonding, and shear bond strength testing was conducted using an Instron machine in shear or peel mode at a crosshead speed., Results: The highest mean bond strength calculated was for the conventional technique (17.45 mpa), while it was the lowest for no primer adhesive (11.21 mpa). Group IV had a greater distribution of ARI scores than groups I, II, and III., Conclusion: Group IV achieved the highest bond strength when compared to other groups, with an ARI score of 3. Group III had less bond strength, likely due to incomplete curing of the primer due to insufficient exposure to light. Transbond XT can be used without primer, making bonding, debonding, and cleaning procedures easy and less time-consuming., Competing Interests: There are no conflicts of interest., (Copyright: © 2024 Journal of Pharmacy and Bioallied Sciences.)

Background: Nanosized antibacterial agents can be used to prevent biofilm buildup on orthodontic appliances and auxiliaries, limiting microbial adherence and preventing caries. Nanoparticles (NPs) can enhance the antibacterial properties of orthodontic materials due to their smaller particle size and larger surface area., Materials and Methods: The study's material analysis was divided into four groups, numbered I through IV, using Transbond XT Primer as a control and modifying group I by adding various antibacterial agents. 98.1 g of mutans-sanguis agar was dissolved in 1,000 ml of warm distilled water and autoclaved for 15 minutes at 121°C and 15 lb pressure. 176 disk specimens of 6 mm in diameter were created, sterilized in an autoclave, and heated to 60°C in a hot air oven for 1 hour. Ten milliliters of primer containing different antimicrobial agents was applied to the sterilized disks. Four petri plates were used for each concentration, with 16 disks in each group. 44 petri plates in all were utilized., Results: The orthodontic primer modified by the addition of antibacterial agents showed a significantly increased antimicrobial activity, and nanobenzalkonium chloride (BAC) at 5% concentration showed the highest antimicrobial efficacy among all groups. Nanohydroxyapatite showed the least., Conclusion: Within the confines of the current investigation, it was determined that the addition of antibacterial agents had significantly higher antimicrobial activity and BAC at 5% concentration had the highest antimicrobial efficacy of all the groups., Competing Interests: There are no conflicts of interest., (Copyright: © 2024 Journal of Pharmacy and Bioallied Sciences.)

This laboratory study was conducted to evaluate and compare the resin bond strength of different adhesive resin systems in different combinations and the durability of their bonds with zirconia ceramic., Materials and Methods: One hundred and twenty-eight specimens were milled from 3Y-TZP zirconia ceramic. The bonding surfaces of all disks were wet polished, steam cleaned, airborne-particle abraded and ultrasonically cleaned in 99% isopropanol. The specimens were randomly divided into four main groups according to the applied resin system; two conventional and two self-adhesive systems were used. Each group was further subdivided into two subgroups; the first was conditioned with the specified primer for conventional luting resins or not conditioned for the self-adhesive systems, whereas the second subgroup of each was conditioned with the same phosphate monomer-containing primer (Alloy Primer). The zirconia specimens were adhesively bonded, using the allocated luting resin, to plexiglass tubes filled with self-curing composite resin (Clearfil FII). Half of the specimens of each subgroup were stored in distilled water at 37 °C for 3 days, whereas the other half were subjected to artificial aging, 150 days of storage and additional thermal cycling. Thereafter, all specimens were subjected to TBS testing using a universal testing machine. Statistical analysis was conducted using two-way ANOVA followed by separate one-way ANOVAs. The Games-Howell post-hoc test was applied for pairwise comparisons., Results: All specimens survived storage with thermal cycling. The mean TBS values ranged from a minimum of 43.4 ± 5.0 MPa to a maximum of 66.4 ± 3.5 after 3 days and from a minimum of 13.6 ± 2.5 MPa to a maximum of 50.1 ± 9.4 MPa after 150 days., Conclusions: Artificial aging had a significantly negative effect on all test groups. The chosen adhesive-resin system had a significant effect on the resulting TBS values. The highest TBS values were achieved for the self-adhesive luting resin G-Cem One but were statistically comparable to the results obtained for the dual-cure luting resin G-Cem LinkForce.

The prerequisite for successful HLA genotyping is the integrity of the large allele reference database IPD-IMGT/HLA. Consequently, it is in the laboratories' best interest that the data quality of submitted novel sequences is high. However, due to its long and variable length, the gene HLA-DRB1 presents the biggest challenge and as of today only 16% of the HLA-DRB1 alleles in the database are characterized in full length. To improve this situation, we developed a protocol for long-range PCR amplification of targeted HLA-DRB1 alleles. By subsequently combining both long-read and short-read sequencing technologies, our protocol ensures phased and error-corrected sequences of reference grade quality. This dual redundant reference sequencing (DR2S) approach is of particular importance for correctly resolving the challenging repeat regions of DRB1 intron 1. Until today, we used this protocol to characterize and submit 384 full-length HLA-DRB1 sequences to IPD-IMGT/HLA., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The peer-review component of the editorial process is designed to facilitate quality control, legitimize scientific research, and self-regulate scientific communities. Even though serving as a reviewer undoubtedly has direct and indirect benefits, the peer-review system and the methods of teaching scholars to conduct reviews are nascent and relatively underdeveloped. This article describes the peer-review process and provides recommendations for writing reviews for scientific journals. The recommendations were developed based on the expertise and preferences of editors in chief and associate editors for behavior-analytic journals (Cengher & LeBlanc, 2024), and they include honoring your responsibility, knowing your audience, being constructive and kind, and carefully evaluating the merits of the study or review. These guidelines may serve as a primer for scholars who want to conduct reviews for scientific journals in behavior analysis., (© 2023 Society for the Experimental Analysis of Behavior (SEAB).)

Background: The era of using adhesives to fix brackets began in the 70s of the last century. There are eight generations of foreign-made adhesive systems for the restoration of teeth. However, until now, in orthodontics, the development of domestic adhesive systems with improved properties of adhesion of brackets to tooth enamel still important, especially in the posterior teeth., Objective: The purpose of this work was to study the shear strength of fifth generation domestic adhesive between metal brackets and the enamel of molar teeth in laboratory conditions., Material and Methods: The study included 17 specimens of extracted maxillary molars embedded in acrylic resin blocks. Brackets from G&H Orthodontics (G&H Wire Company, USA) were fixed to the tooth enamel using the domestic Compofix (ortho) set. The enamel was treated with etching gel (37% phosphoric acid) for 30 seconds. Then the gel was washed off with water and the surface of the enamel was thoroughly dried. A primer was applied to the prepared surface with an applicator, inflated with a weak air flow for 5-10 seconds and photopolymerized for 20 seconds. The surface of the bracket was treated with degreaser, then a thin layer of adhesive was applied, and the sample was fixed to the enamel. Excess material was removed with an applicator. The samples were photopolymerized for 20 sec. Then, the shear bond strength of the adhesive was determined according to the method of GOST 31574-2012 on a (Zwick/Roell Z010 testing machine, Zwick, Germany)., Results: The shear strength of the adhesive joint obtained during the test is 13.54±1.01 MPa, the average value of the index of adhesive residues on the surface of the bracket was 23%±4%, which corresponds to the standard average values according to GOST., Conclusion: The tested domestic adhesive system of the fifth generation can be recommended for the practical work of an orthodontist.

(3-Aminopropyl)triethoxysilane (APTES) silane possesses one terminal amine group and three ethoxy groups extending from each silicon atom, acting as a crucial interface between organic and inorganic materials. In this study, after APTES was deposited on the aluminum alloy AA2024-T3 as a primer for an optional top coating with polystyrene (PS), its role with regard to stability as a protection layer and interaction with the topcoat were studied via combinatorial experimentation. The aluminum alloy samples primed with APTES under various durations of concentrated vapor deposition (20, 40, or 60 min) with an optional post heat treatment and/or PS topcoat were comparatively characterized via electrochemical impedance spectroscopy (EIS) and surface energy. The samples top-coated with PS on an APTES layer primed for 40 min with a post heat treatment revealed excellent performance regarding corrosion impedance. A primed APTES surface with higher surface energy accounted for this higher corrosion impedance. Based on the SEM images and the surface energy calculated from the measured contact angles on the APTES-primed surfaces, four mechanisms are suggested to explain that the good protection performance of the APTES/PS coating system can be attributed to the enhanced wettability of PS on the cured APTES primer with higher surface energy. The results also suggest that, in the early stages of exposure to the corrosion solution, a thinner APTES primer (deposited for 20 min) enhances protection against corrosion, which can be attributed to the hydrolytic stability and hydrolyzation/condensation of the soaked APTES and the dissolution of the naturally formed aluminum oxide pre-existing in the bare samples. An APTES primer subjected to additional heat treatment will increase the impedance of the coating system significantly. APTES, and silanes, in general, used as adherent agents or surface modifiers, have a wide range of potential applications in micro devices, as projected in the Discussion section.

Purpose and Methods: The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation., Results: LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database., Conclusion: LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany.)

This study aimed to assess the ability of language learning models (LLMs), specifically GPT-3.5 (Chat Generative Pre-trained Transformer 3.5) and GPT-4 (Chat Generative Pre-trained Transformer 3.5), in designing primers for diagnostic polymerase chain reaction (PCR) of the monkeypox virus (MPXV). Five primer pairs were generated by each LLM, and their thermodynamic properties and specificity were analysed post-hoc using commonly used software. The LLMs demonstrated ability in sequence generation and predicting melting temperatures (Tm), but their accuracy in predicting GC content was suboptimal, necessitating further investigation. Results indicated that, of the total primer pairs, only three designed by GPT-4 and two by GPT-3.5 could theoretically form a PCR product, but only one pair demonstrated suitable parameters for experimental validation. This preliminary exploration suggests that while LLMs have a potential in aiding primer design, their accuracy needs improvement to match current deterministic, rule-based tools used in the field. Consequently, manual intervention remains a crucial step in PCR primer design., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Jorapur et al.)

A variety of rodent ceca are parasitized by Tritrichomonas muris ( T. muris ), a flagellated protozoan. To date, there are no ideal methods for the detection of T. muris infections in laboratory mice; thus, new molecular methodologies for its specific detection need to be developed. In this study, using staining and SEM, it was observed that T. muris has a pear-shaped body and contains three anterior flagella. A nested PCR system with novel specific primers was designed based on the conserved regions of the SSU rRNA gene of T. muris . The nested PCR system for T. muris showed good specificity and high sensitivity for at least 100 T. muris trophozoites/mL and 0.1 ng/μL of fecal genomic DNA, which means that 176 trophozoites per gram of mouse feces could be detected. When using this nested PCR system, the detection rate was 18.96% (58/306), which was higher than the detection rate of 14.05% (43/306) detected via smear microscopy in fecal samples from five mouse strains. The sensitivity and specificity of nested PCR in detecting T. muris was found to be 100%, and it demonstrated a 26% increase in diagnostic sensitivity compared to the smear microscopy method in the present study. In conclusion, the nested PCR developed with novel primers based on the SSU rRNA gene of T. muris has good accuracy, specificity, and sensitivity for the detection of T. muris infections in laboratory mice.

Conventional PCR provides Leishmania species characterization with even a small amount of biological material. Species-specific primers have been a widely used alternative; however, nonspecific amplifications are a reality, interfering with PCR efficiency. In endemic areas with multiple etiological agents for leishmaniasis, there is a requirement for higher specificity of primers. This study evaluates 3 pairs of primers described for the identification and characterization of Leishmania infantum. Primers RV1/RV2, LEISH1/LEISH2, and FLC2/RLC2 were used with the DNA of L. infantum, Leishmania amazonensis, and Leishmania braziliensis. An initial temperature curve was performed (52-62 C) to determine the optimal annealing temperature, followed by a dilution curve of Leishmania DNA (500 pg/μl, 50 pg/μl, 5 pg/μl, 500 fg/μl, 50 fg/μl, 5 fg/μl, and 0.5 fg/μl) to be used for analytical sensitivity. RV1/RV2 PCR amplified L. infantum and L. amazonensis at all analyzed temperatures; LEISH1/LEISH2 PCR amplified all 3 species of Leishmania, although at some temperatures L. infantum was specifically amplified, and, finally, FLC2/RLC2 PCR amplified only L. infantum at all temperatures analyzed. In terms of sensitivity, RV1/RV2 PCR detected 1 fg of L. infantum DNA and 100 pg of L. amazonensis DNA; LEISH1/LEISH2 PCR detected 1 fg of L. infantum DNA, 100 fg of L. amazonensis DNA, and 10 fg of L. braziliensis DNA; and FLC2/RLC2 PCR detected 10 fg of L. infantum DNA. Thus, PCR with FLC2/RLC2 primers is best suited for the molecular characterization of L. infantum, especially in areas where there is an incidence of more than 1 Leishmania species, such as South America., (© American Society of Parasitologists 2023.)

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them., (© 2023 The Authors. Molecular Oral Microbiology published by John Wiley & Sons Ltd.)

Bluetongue is a non-contagious viral disease causing significant economic losses throughout the world. The bluetongue vectors Culicoides oxystoma and Culicoides actoni, which play a significant role in the transmission of various pathogens, are distributed across different geographical realms. Adults are minute in size with wide phenotypic variation, so morphology-based species identification is severely constrained by preparatory time and shortage of taxonomic expertise. To make the identification process rapid and effective, a specific primer was designed for the identification of C. actoni based on the multiple sequence alignment of ITS1 sequences of 11 Culicoides species. Along with this, a refined version of existing C. oxystoma specific primer was proposed. The primer sets distinguished C. oxystoma and C. actoni from a pooled sample consisting of other Culicoides species as well as closely related genera such as Forcipomyia and Alluaudomyia. Our findings suggest that the primers were species specific, sensitive and have potential to discriminate vector species C. oxystoma and C. actoni from pooled samples. To the best of our knowledge, these are the first ITS1 sequences generated and submitted in GenBank for Culicoides innoxius, Culicoides shortti, Culicoides palpifer and Culicoides anophelis and the first for Culicoides peregrinus, Culicoides fulvus and C. actoni from India., (© 2023 Royal Entomological Society.)

Background Acinetobacter calcoaceticus baumannii (ACB) complex has become a major concern nowadays because of its increasing involvement in several severe infections associated with catheter-related bloodstream and urinary tract infections, ventilator-associated pneumonia, cerebrospinal shunt-related meningitis, and wound infections. Multiple drug-resistant (MDR) ACB cases have been described with an increasing trend where at least it is resistant to a minimum of three antimicrobial groups. The mortality rate associated with A. baumannii is significantly higher than all Acinetobacter  spp. isolates with the most prevalence seen in India and Thailand. The rapid spread of high resistance to most potent antimicrobial drugs is due to its ability to incorporate resistance determinants despite multifactorial reasons such as alteration in permeability of cell membrane by either losing expression of outer membrane porins or excess production of efflux pumps. This study aims to characterize resistance determinants responsible for MDR at the genetic level and emphasizes the use of genotyping in routine diagnosis as genotype analysis is reliable and valid. Methodology A total of 289 ACB complex clinical isolates were included in this study. The study for species-level identification of A. baumannii was conducted at the Department of Microbiology, IQ City Medical College Hospital, Durgapur, West Bengal. In addition, the detection of encoded genes associated with class A-extended spectrum beta-lactamases (i.e., CTX-M , KPC , SHV , and TEM genes), class B-metallo-β-lactamases (i.e., IMP , NDM , and VIM genes), Class C-AmpC cephalosporinase, and classD-OXA carbapenemases (i.e., bla OXA-10/11 , bla OXA-24 , bla OXA-48 , bla OXA-58 , bla OXA-143 , and bla OXA-235  was done using real-time polymerase chain reaction. Results All 289 non-repetitive ACB complex clinical isolates were confirmed as A. baumannii , of which 277 (96%) isolates were MDR. There were no findings of bla CTX-M , bla KPC , bla SHV , bla TEM , bla IMP , bla VIM , bla AmpC , bla OXA-10/11 , bla OXA-24 , bla OXA-48 , bla OXA-58 , bla OXA-143 , and bla OXA-235 genes in our study. However, there were four (1.44%) positive findings of the bla NDM gene. All MDR isolates (n = 277) were positive for the bla OXA-51 gene. In addition, bla OXA-23 was positive in 269 (97.12%) isolates. Conclusions The oxacillinase production corresponding to bla OXA-23 and bla OXA-51 were the most prevalent antibiotic resistance determinants among MDR A. baumannii  in our study. Four (1.44%) isolates had the multiple genes bla OXA-51 , bla OXA-23 , and bla NDM that shows the coexistence of diverse genetic elements involved in MDR A. baumannii , resulting in total resistance except for a few potent drugs such as colistin and tigecycline. Genotyping is helpful in determining the contribution of the isolates in understanding their association with encoded genes, which, in turn, helps in designing effective surveillance and control strategies in the management of such MDR isolates., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Longjam et al.)

Food authentication is a mandatory effort to assure the fair-trade. This study developed a duplex polymerase chain reaction (PCR) from the NADH dehydrogenase subunit 2 ( ND2 ) gene to amplify specific segments of a cattle and porcine DNA. A universal forward primer composed of nineteen base pairs (bp) (3'-CCAAACACAACTCCGAAAA-5') and species-specific reverse primers composed of twenty (3'-CCAAACACAACTCCGAAAA-5') and twenty-one (3'-TGGCAAGAATTAGGACGGTTA-5') bp were used to limit the amplified DNA segment for porcine and cattle. The PCR reaction would generate a product with a profile of 168 and 227 bp, respectively. To investigate the accuracy and limit of detection, an in vitro experiment was conducted using simplex and duplex PCR on commercial meatballs randomly purchased from a commercial market in Surakarta, Indonesia. The findings of this study indicated that ND2 could be used as an alternative genetic marker for the identification of porcine and beef species in meat-derived products., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

It is critical that breweries of all sizes routinely monitor the microbiome of their process to limit financial losses due to microbial contamination. Contamination by beer-spoiling microbes (BSMs) at any point during the brewing process may lead to significant losses for breweries if gone undetected and allowed to spread. Testing and detection of BSMs must be routine and rapid, and because even small breweries need the capability of BSM detection and identification, the method also needs to be affordable. Lactic acid bacteria (LAB) are responsible for most spoilage incidents, many of which have been shown to enter the viable but nonculturable (VBNC) state under conditions present in beer such as cold or oxidative stress. These bacteria are invisible to traditional methods of detection using selective media. This article describes several methods of BSM detection and identification that may be useful in the majority of craft breweries. While there are several genomic methods that meet some or many qualifications of being useful in craft breweries, real-time quantitative polymerase chain reaction (qPCR) currently best meets the desired method characteristics and holds the most utility in this industry, specifically SYBR Green qPCR. qPCR is a targeted method of detection and identification of microbes that is affordable, rapid, specific, sensitive, quantitative, and reliable, and when paired with valid DNA extraction techniques can be used to detect BSMs, including those in the VBNC state., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher., (Copyright © 2023 Oldham and Held.)

Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1-V2, V1-V3, V3-V4, V4-V5, V5-V7 and V6-V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1-V2, V3-V4, and V4-V5 regions generated more than 90% of the original input sequences. Primers targeting the V1-V2 and V1-V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1-V2 and V3-V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1-V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for Streptococcus than V3-V4 primers. In conclusion, primers targeting the V1-V2 region of 16S rRNA showed the best performance for oral microbiome studies. In addition, the study demonstrates the need for careful PCR primer selections.

Myxobacteria have potential application value in developing new antibiotics and environmental protection. In this study, in order to establish a more suitable method for diversity studies of myxobacteria, the effects of primers, polymerase chain reaction (PCR) approaches and sample preservation methods on the results were compared by Illumina high-throughput sequencing. The results showed that the relative abundance and operational taxonomic unit (OTU) ratio of myxobacteria amplified by the universal primers accounted for 0.91-1.85% and 2.82-4.10% of total bacteria, indicating that myxobacteria were the dominant bacteria both in population and species numbers. The relative abundance and OTU number and ratio of myxobacteria amplified by the myxobacteria semi-specific primers were significantly higher than those amplified by the universal primers, of which the primer pair W2/802R specifically amplified myxobacteria of suborder Cystobacterineae, while the primer pair W5/802R mainly amplified myxobacteria of suborder Sorangineae and also amplified more species of suborder Nannocystineae at the same time. Among three PCR approaches, the relative abundance and OTU ratio of myxobacteria amplified by the touch-down PCR were the highest. More myxobacterial OTUs were detected in most dried samples. In conclusion, the combination of the myxobacteria semi-specific primer pairs W2/802R and W5/802R, touch-down PCR, and dry preservation of samples were more conducive to diversity studies of myxobacteria., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflicts of interest, and manuscript is approved by all authors for publication. This article does not contain any studies with human participants or animals performed by any of the authors., (Copyright © 2023. Published by Elsevier B.V.)

Objectives: To determine the effect of an extra hydrophobic resin layer (EHL) on the bond strength and durability of three different pH one-step universal adhesives (UAs) utilized in self-etch (SE) mode, and to explore whether UAs can be used as a primer in two-step bonding system., Methods: Three different pH UAs were utilized: G-Premio Bond (GPB), Scotchbond Universal (SBU), All-Bond Universal (ABU), while the bonding agent of Clearfil SE Bond 2 (SE2) was selected as the EHL. For the EHL groups, EHL was applied after the air blow of each UA and before light curing. The microtensile bond strength (μTBS), fracture modes, interfacial structures and nanoleakage (NL) were evaluated after 24 h water storage and after 15,000 thermal cycling (TC). Elastic modulus (EM) and hardness (H) was tested by a nanoindenter after 24 h., Results: Significantly higher μTBS was achieved in the GPB+EHL group compared with GPB both at 24 h and after 15,000 TC, while the additional use of EHL did not improve the μTBS of SBU and ABU significantly both at 24 h and after 15,000 TC. GPB+EHL demonstrated lower NL than GPB. The mean EM and H of the adhesive layer in GPB+EHL was significantly decreased compared with GPB., Conclusions: The results indicated that the bond strength and durability of low pH one-step UA (GPB) were significantly improved by additional application of EHL both at 24 h and after 15,000 TC, while no significant improvement was observed for ultra-mild one-step UAs (SBU and ABU)., Clinical Significance: This study indicates that GPB can be used as a primer in a two-step bonding system, while SBU and ABU may not be as effective. These findings may help guide clinicians in selecting the appropriate UAs and bonding techniques for different clinical scenarios., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Psychotherapy manuals are critical to the dissemination of psychotherapy treatments. Psychotherapy manuals typically serve several purposes, including, but not limited to, establishing new psychotherapy treatments, training providers, disseminating treatments to those who deliver them, and providing guidelines to deliver treatments with fidelity. Yet, the proliferation of psychotherapy manuals has not been well-understood, and no work has aimed to assess or review the existing landscape of psychotherapy manuals. Little is known about the breadth, scope, and foci of extant psychotherapy manuals., Objective: This scoping review aims to identify and explore the landscape of existing book-based psychotherapy manuals. This review aims to specify the defining characteristics (ie, foci, clinical populations, clinical targets, treatment type, treatment modality, and adaptations) of existing book-based psychotherapy manuals. Further, this review will demonstrate how this information, and psychotherapy manuals more broadly, has changed over time. This project aims to make a novel contribution that will have critical implications for current methods of developing, aggregating, synthesizing, and translating knowledge about psychotherapeutic treatments., Methods: This scoping review will review book-based psychotherapy manuals published from 1950 to 2022.This scoping review will be informed by guidance from the Joanna Briggs Institute Scoping Review Methodology Group and prior scoping reviews. Traditional search and application programming interface-based search methods will be used with search terms defined a priori to identify relevant results using 3 large book databases: Google Books, WorldCat, and PsycINFO. This review will leverage machine learning methods to enhance and expedite the screening process. Primary screening of results will be conducted by at least 2 authors. Data will be extracted and double-coded by research assistants using an iteratively defined codebook., Results: The search process produced 78,600 results, which were then iteratively deduplicated. Following deduplication, 50,583 results remained. The scoping review is expected to identify common elements of psychotherapy manuals, establish how the foci and content of manuals have changed over time, and illustrate coverage and gaps in the landscape of psychotherapy manuals. Results from this scoping review will be critical for future work focused on developing, aggregating, synthesizing, and disseminating knowledge about psychotherapeutic treatments., Conclusions: This review will provide knowledge about the vast landscape of psychotherapy manuals that exist. Findings from this study will inform future efforts to develop, aggregate, synthesize, and translate knowledge about psychotherapeutic treatments., International Registered Report Identifier (irrid): DERR1-10.2196/47708., (©Katherine Wislocki, Mai-Lan Tran, Emily Petti, Rosa Hernandez-Ramos, David Cenkner, Miranda Bridgwater, Ghazal Naderi, Leslie Walker, Alyson K Zalta. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 30.06.2023.)

Background: Infectious diseases of young and adult birds with respiratory syndrome are a significant deterrent to the development of industrial poultry farming due to decreased productivity and significant mortality. The only effective method of combating viral diseases is timely and targeted vaccination, which largely depends on laboratory diagnostic results., Aim: This article aims to study the real-time reverse transcription polymerase chain reaction, (RT-PCR) which has the prospect of more effective diagnosis of vaccine strains of chicken infectious bronchitis and Newcastle disease., Methods: The fastest and most accurate method for the differential diagnosis of pathogens in an associative viral infection is RT-PCR. The method proposed in the article for selecting primers for amplification made it possible to use this method for the simultaneous interspecies differential diagnosis of two or more viral agents, significantly accelerating their diagnosis., Results: The correlation of the nucleotide sequence obtained from sequencing to a specific virus strain is complicated by the lack of a single nomenclature mechanism for separating genetic groups., Conclusion: The results of this study will allow easy and fast typing of sequences into known and databased virus strains and avoid further confusion in the nomenclature of genetic groups in the future.

Artificial intelligence has become ubiquitous. Machine learning, a branch of artificial intelligence, leads the current technological revolution through its remarkable ability to learn and perform on data sets of varying types. Machine learning applications are expected to change contemporary medicine as they are brought into mainstream clinical practice. In the field of cardiac arrhythmia and electrophysiology, machine learning applications have enjoyed rapid growth and popularity. To facilitate clinical acceptance of these methodologies, it is important to promote general knowledge of machine learning in the wider community and continue to highlight the areas of successful application. The authors present a primer to provide an overview of common supervised (least squares, support vector machine, neural networks and random forest) and unsupervised (k-means and principal component analysis) machine learning models. The authors also provide explanations as to how and why the specific machine learning models have been used in arrhythmia and electrophysiology studies., Competing Interests: Disclosure: The authors have no conflicts of interest to declare. Funding: This project was supported by National Institutes of Health Grant No. R01HL142496., (Copyright © 2023, Radcliffe Cardiology.)

Background: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain., Results: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively., Conclusions: Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP&#95;F048-OP&#95;R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP&#95;F051-OP&#95;R030 (4-7; 514-1079), and KP&#95;F048-OP&#95;R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP&#95;F066-KP&#95;R013 (5-6; 784-undefined), KP&#95;F020-KP&#95;R013 (3-6; 518-undefined), and OP&#95;F114-KP&#95;R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP&#95;F020-KP&#95;R032 (4-5; 518-801), OP&#95;F114-KP&#95;R031 (3-5; 340-801), and OP&#95;F066-OP&#95;R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract., (© 2023. The Author(s).)

Aim: The present study aimed to assess the antimicrobial effects of orthodontic primer containing nano-propolis against the cariogenic bacteria in а rat model., Materials and Methods: Transbond XT orthodontic primer containing 0%, 1%, 5%, and 10% nano-propolis was experimentally prepared in-house. The Wistar rats we used in the study were randomly divided into four groups and their oral cavities were colonized with Streptococcus mutans, Streptococcus sanguinis, and Lactobacillus acidophilus. After anesthetizing the rats, one drop (10 µL) of primer containing different concentrations of nano-propolis was applied to the labial surface of the maxillary incisor and light-cured. The orthodontic composite was applied on the primer and light-cured. One drop (10 µL) of primer containing the same concentrations of nano-propolis was again applied on the surface of composite and light-cured. The number of S. mutans, S. sanguinis, and L. acidophilus colonies in the saliva of rats was quantified at 24 h, at days 4 and 7 using plate counting., Results: Primer containing 1%, 5%, and 10% of nano-propolis significantly reduced the S. mutans colony count at 24 h compared with the control group (p<0.05). At day 4, the mean S. mutans colony counts in the 5% and 10% nano-propolis groups were significantly lower than that in the control group (p<0.05). Primer containing 1%, 5%, and 10% (all (p<0.05) of nano-propolis significantly reduced the L. acidophilus at 24 hours. Also, at day 4 the mean L. acidophilus colony counts in the 5% and 10% nano-propolis groups were significantly lower than that in the control group (p<0.05). At 24 h and 4 days, the mean S. sanguinis colony count in the 1%, 5%, and 10% nano-propolis group was significantly lower than that in the control group (p<0.05). No significant difference was observed in the presence of all concentrations of nano-propolis at day 7 (p>0.05)., Conclusions: Orthodontic primer containing nano-propolis significantly reduced the colony count of cariogenic bacteria in a rat model., (This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP&#95;F048-OP&#95;R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP&#95;F018-KP&#95;R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP&#95;F114-OP&#95;R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.

Primer is widely used to prepare bonding of chlorinated poly(vinyl chloride) (CPVC) pipe. The study examined the influences of primer and its major component, acetone, on CPVC's mechanical properties. Two types of CPVC product, sheet and pipe, were used in the mechanical testing. Sheet specimens were immersed in acetone or primer for 40 and 10 min, respectively, i.e., the maximum allowable time without mass loss, and then dried in air before the mechanical testing. Pipe (ring) specimens were treated either through immersion in acetone or primer for 30 min or in contact with these solvents locally on the inner surface for 2.5 h, and then air dried for 10.5 days before the mechanical testing. Results showed that CPVC's strength decreased after the absorption of these solvents, and air dry could remove acetone but not completely primer. The study also showed that pipe specimens by local contact with primer could generate brittle fracture. In view that sheet specimens always fractured in a ductile manner, brittle fracture of the pipe specimens could not be caused by CPVC degradation. Rather, strength decrease in the local region could provide a plausible explanation for the brittle fracture behavior, though further investigation is needed., Competing Interests: The authors declare no conflict of interest.

Recent years have witnessed an increased prevalence of intrinsic and acquired beta-lactamase-producing bacteria, severely limiting human and veterinary medicine therapeutic options. The present study aimed to design specific oligonucleotides for rapid PCR detection of the cephalosporinase-encoding gene blaEC (BlaEC family class C beta-lactamase). A total of three primers were designed to detect 2281 variants of the blaEC gene and two sets of primer pairs were also tested against DNA from 11 strains. The study indicates that the proposed primers should be able to detect 100% of all described blaEC genes in different bacterial strains and monitor their spread. After comparing the amino acid sequences, a phylogenetic tree was created based on the presence of conserved amino acids and homologous motifs. More than 24 760 mutations in BlaEC enzymes have been identified. The mutations involving 371 amino acid positions and these hotspots can change the structure and activity of the monitored enzymes. We predicted several BlaEC enzymes with a broadened substrate activity against higher-generation cephalosporins., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

From its discovery in Malaysia in the late 1990s, the spillover of the Nipah virus from its pteropid reservoir into the human population has resulted in sporadic outbreaks of fatal encephalitis and respiratory disease. In this chapter, we revise a previously described quantitative reverse transcription polymerase chain reaction method, which now utilizes degenerate nucleotides at certain positions in the probe and the reverse primer to accommodate the sequence heterogeneity observed within the Nipah henipavirus species., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process., Competing Interests: The authors declare that they have no competing interests., (© 2022 Moll and Hoppe.)

Performing a PCR often does not teach students what happens in a PCR. This kinesthetic, hands-on exercise allows students to simulate by hand the steps of a PCR. Each step of the first two cycles is modeled with template DNA and primers formed from paper, with additional newly synthesized DNA strands written in chalk. At the end of the exercise, students design primers to amplify the chosen sequence. They also attain a greater understanding of the restrictions that limit DNA polymerase activity, which are of general importance to molecular biology., Competing Interests: The author declares no conflict of interest., (Copyright © 2022 Heineman.)

Purpose: The purpose of this study was to assess the effect of aging and alumina-particle air abrasion at different pressures on the bond strength of two luting composites to a translucent 3Y-TZP zirconia., Materials and Methods: Half of the 192 disk-shaped zirconia specimens were aged in an autoclave (group A) for 20 h (134°C, 2 bar), and the other half was not aged (group N). For each group, a different surface treatment was applied: as-sintered (group SIN), alumina-particle air abrasion either at 1 bar (group 1B) or at 2.5 bar (group 2.5B). Disks were bonded to Plexiglas tubes filled with composite resin using a phosphate monomer-based luting composite (group SA) or with a separate phosphate monomer containing primer before using a phosphate-monomer-free luting composite (group V5). All specimens were subjected to tensile bond strength testing (TBS) before and after thermocycling., Results: There were no statistically significant differences caused by autoclave aging for the test groups before thermocycling, except for the A-SIN-SA group, where the TBS decreased significantly. The variation of the aluminaparticle air abrasion pressure showed no statistically significant effect, except in the N-1B-V5 group, where TBS was significantly lower than N-2.5B-V5. After thermocycling, the TBS of most groups decreased significantly. Specimens of the primer group, which were abraded at 1 bar, showed a significant decrease in TBS in comparison with alumina-particle air abrasion at 2.5 bar., Conclusion: Twenty hours of autoclave aging had almost no influence on the bond strength of the test groups. For the primer/resin bonding system, higher pressure during alumina-particle air abrasion might help obtain a higher and more durable bond strength to zirconia.

The effect of a surface pre-reacted glass ionomer (S-PRG)-containing sealant on the demineralization inhibition and remineralization of intact enamel adjacent to the sealant material was investigated. BeautiSealant (BTS, S-PRG sealant, Shofu), Teeth Mate F-12.0 (TMF, fluoride-releasing sealant, Kuraray Noritake Dental), and an experimental silica-filler sealant were investigated. After pH cycling for 10 days, the enamel surface adjacent to the sealant material was observed using confocal laser microscopy and scanning electron microscopy. The polymerized sealant disks were immersed in a demineralized solution (pH: 4.3) to measure pH change. The enamel specimens with polymerized sealant disks were additionally immersed in demineralized solution, followed by energy-dispersive X-ray spectroscopy. The demineralized area of BTS was significantly smaller than that of TMF and SS (p < 0.05). The surfaces adjacent to the sealant of TMF and SS were demineralized, while the surface of BTS was comparatively intact. An increase in pH values were observed in the BTS and TMF groups. Enamel surfaces presented an inhibition of demineralization for BTS and TMF, but not for SS. Fluoride uptake from the polymerized sealant was greater for BTS than for TMF. The S-PRG-containing sealant showed a buffering ability, demineralization inhibition, promotion of remineralization, and it can be advised for clinical applications.

The combination of two dissimilar materials has always been a serious problem in dentistry. In order to meet this challenge, it is necessary to combine both chemical methods (treatment with silanes, (meth)acrylic functional monomers) and the development of the surface of the joined material in a physical way, e.g., by sandblasting with alumina, alumina with silica, acid etching, the use of lasers and other means. The purpose of this literature review is to present all methods of joining dental composites with other materials such as ceramics, metal, another composite material. This review covers articles published within the period 2012-2022 in journals indexed in the PubMed database, written in English and describing joining different dental materials to each other. All the critical steps of new joint preparation have been addressed, including proper cleaning of the joint surface, the application of appropriate primers capable of forming a chemical bond between ceramics, zirconium oxide or metals and alloys, and finally, the application of new composite materials.

Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. Clinostomum complanatum is a digenetic zoonotic parasite harbouring the intestine and body cavity of the fishes. 19 human incidences of Clinostomum complanatum infection have been reported to cause pharyngitis and lacramalitis from Japan, Thailand and Korea. Hence, adequate yet effective diagnosis is an issue. Designing primers used in the amplification of genes with adequate specificity and efficiency is of help in diagnosis. Hence, we describe primer design for cox-1 gene from the helminth parasite, Clinostomum complanatum parasitizing the intestine of fish Channastriata (Snakehead murrel). Thus, these designed primers set will be of further use in the wet lab for amplification of concerned gene or DNA fragment., Competing Interests: The authors declare that they have no conflict of interest., (© 2022 Biomedical Informatics.)