title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=208 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly link: https://peerj.com/articles/18132 last-modified: 2024-11-08 description: Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics–particularly coding gene content and read recruitment profiles–were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses. creator: Garrett J. Smith creator: Theo A. van Alen creator: Maartje A.H.J. van Kessel creator: Sebastian Lücker uri: https://doi.org/10.7717/peerj.18132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Smith et al. title: Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus link: https://peerj.com/articles/18341 last-modified: 2024-11-08 description: A new species of Helicascus satunensis sp. nov. was collected on mature dead fruits of the Nypa palm in Satun Province, southern Thailand. Its morphological characteristics are similar to those of the genus Helicascus. Recently, a genus Helicascus with three species from marine habitats worldwide was studied. The morphology of this fungus was investigated and combined with multigene sequence analyzes of small subunit (SSU), large subunit (LSU), internal transcribed spacer (ITS) ribosomal DNA, translation elongation factor 1-alpha (TEF-1α) and RNA polymerase II (RPB2) genes. Morphologically, H. satunensis sp. nov. is characterized by semi-immersed, lenticular ascomata, multilocules, a bitunicate ascus and smooth, obovoid, dark brown ascospores that are one-septate and unequally two-celled. In addition, 3D visualization using synchrotron X-ray tomography was performed to investigate the interaction between fruiting body and substrata. Molecular phylogeny with multigene revealed that H. satunensis sp. nov. belongs to the family Morosphaeriaceae, order Pleosporales, class Dothideomycetes. Furthermore, H. satunensis sp. nov. forms a well-supported clade with Helicascus species described from marine habitats. Based on the unique morphological and molecular evidence, we propose this fungus, H. satunensis sp. nov., as a new species for Helicascus. creator: Sita Preedanon creator: Anupong Klaysuban creator: Satinee Suetrong creator: Oraphin Pracharoen creator: Waratthaya Promchoo creator: Tanuwong Sangtiean creator: Catleya Rojviriya creator: Jariya Sakayaroj uri: https://doi.org/10.7717/peerj.18341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Preedanon et al. title: YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines link: https://peerj.com/articles/18344 last-modified: 2024-11-08 description: BackgroundThe Internet has transformed global information access, particularly through platforms like YouTube, which launched in 1995 and has since become the second largest search engine worldwide with over two billion monthly users. While YouTube offers extensive educational content, including health topics like cardiopulmonary resuscitation (CPR) and basic life support (BLS), it also poses risks due to potential misinformation. Our study focuses on evaluating the accuracy of CPR and BLS videos on YouTube according to the latest 2020 American Heart Association (AHA) guidelines. This research aims to highlight inconsistencies and provide insights into improving YouTube as a reliable educational resource for both lay rescuers and healthcare professionals.MethodsIn this cross-sectional observational study, English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were searched using keywords related to CPR and basic life support. Videos were assessed for their source, duration, views, use of human or mannequin models, and mean assessment scores by two emergency medicine physicians. A third physician’s opinion was sought in cases of disagreement. The first assessment evaluated video validity based on specified information criteria, while the second assessed their ability to convey advanced medical information aligned with the 2020 AHA guidelines.ResultsIn this study, 201 English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were evaluated based on search terms related to CPR and BLS, resulting in 95 videos meeting inclusion criteria after excluding 106 due to various reasons. Most included videos were from healthcare professionals (49.5%), followed by anonymous sources (29.5%) and official medical organizations (21.1%). Video durations ranged widely from 43 to 6,019 seconds, with an average of 692 seconds. Videos featuring mannequins predominated (91.6%), followed by those using human subjects (5.3%) or both (3.2%). Healthcare professional and official medical organization videos scoring significantly higher than those of unknown origin (p = 0.001). Video length did not correlate significantly with view counts, although shorter videos under 5 minutes tended to have higher average views.DiscussionThe results presented in this study demonstrated that English-language videos on YouTube related to BLS and CPR, throughout the study period, did not conform to the 2020 AHA guidelines in terms of providing basic information for lay rescuers. Furthermore, healthcare professionals cannot obtain advanced medical knowledge through these videos. We recommend a professional oversight mechanism in health-related videos that does not tolerate such misinformation. creator: Merve Yazla creator: Tuba Şafak creator: Şakir Hakan Aksu creator: Kadiriye Savran creator: Rafet Fatih Aydogan creator: Mustafa Arslan creator: Abdullah Osman Koçak creator: Burak Katipoğlu uri: https://doi.org/10.7717/peerj.18344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yazla et al. title: Stable dominance of parasitic dinoflagellates in Antarctic sponges link: https://peerj.com/articles/18365 last-modified: 2024-11-08 description: BackgroundMarine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies.ResultsThe analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges.ConclusionsThe present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean. creator: Marileyxis R. López-Rodríguez creator: Catherine Gérikas Ribeiro creator: Susana Rodríguez-Marconi creator: Génesis Parada-Pozo creator: Maria Manrique-de-la-Cuba creator: Nicole Trefault uri: https://doi.org/10.7717/peerj.18365 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 López-Rodríguez et al. title: Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance link: https://peerj.com/articles/18371 last-modified: 2024-11-08 description: We investigated the convergent validity and intrasession reliability of force, velocity, and power (FVP) variables and the dynamic strength index (DSI) obtained from isometric midthigh pull (IMTP) and squat jump (SJ) testing. Fifteen male combat sports athletes (27 ± 5 years, 77 ± 9 kg, 1.76 ± 0.1 m, 14 ± 6% body fat) participated in a 2-days study. The first day involved testing familiarization, while the second was dedicated to IMTP and SJ testing. Maximal isometric force (Fiso) was obtained from IMTP, while mean force, mean velocity, jump height, and jump impulse (J) were gathered from SJ. To analyze the FVP, we calculated the linear relationship between force and velocity, which allowed us to obtain the slope of the relationship (SFV), the theoretical velocity at zero force (V0), and the theoretical maximal power (Pmax). DSI was obtained as a ratio from SJ peak force and Fiso. The convergent validity was investigated using Spearman’s ρ coefficients to assess the relationships between jump height and J with Fiso, V0, SFV, Pmax, and DSI. The intrasession reliability was assessed using intraclass correlation coefficients (ICC) and coefficient of variations (CV). All variables demonstrated acceptable reliability scores. ICC ranged from moderate to excellent, and the mean CV was <10%. We found a “very large” correlation between jump J and Pmax, while jump height was not correlated with any variable. In conclusion, the IMTP and SJ combination is a practical way to determine FVP producing capacities that can be reliably measured (intrasession). The Pmax, derived from FVP, was correlated with jump performance, which might evidence the convergent validity of the method. creator: Amilton Vieira creator: Rafael Cunha creator: Carlos Gonçalves creator: Juliano Dal Pupo creator: James Tufano uri: https://doi.org/10.7717/peerj.18371 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Vieira et al. title: Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis link: https://peerj.com/articles/18402 last-modified: 2024-11-08 description: BackgroundPhragmites australis is a common foundation species found in inland and brackish estuarine ecosystems. P. australis stands provide a wide range of habitats for wetland organisms and perform essential functions, such as nutrient cycling, pollutant filtration, wave energy reduction, and soil stabilization. However, excessive growth of P. australis can degrade the quality of wetland habitats, thereby reducing the functions of restored wetlands.MethodsIn this study, we investigated the effectiveness of vegetation management techniques, such as aboveground cutting and temporal inundation with varying depth and periodicity, in controlling the growth performance of P. australis and adjacent vegetation, Bolboschoenus planiculmis. Differences in growth responses to manipulated inundation stress between P. australis and B. planiculmis were measured.ResultsInundation stress of 10–50 cm caused significantly greater inhibition of growth performance in B. planiculmis compared to P. australis. The combination of aboveground-cutting and inundation treatments resulted in a significant inhibitory effect on the growth performance and survival rate of P. australis. The growth performance of P. australis, including stem volume and biomass, decreased and its mortality rate increased. Our manipulated experiment suggests a combined treatment approach of moderate inundation, such as 5–10 cm for 20–30 days, and aboveground cutting to manage the overgrowth of P. australis in restored brackish wetlands. creator: Hee-Sun Park creator: Ji Yoon Kim creator: Gu-Yeon Kim creator: Hyunbin Jo creator: Gea-Jae Joo uri: https://doi.org/10.7717/peerj.18402 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Park et al. title: Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections link: https://peerj.com/articles/18471 last-modified: 2024-11-08 description: BackgroundDetermining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses.MethodsIn this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology.ResultsA total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively.ConclusionOur study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection. creator: Xinyuan Liu creator: Zhitao Gan creator: Zengshun Lin creator: Xiaojun Lin creator: Jianying Yuan creator: Lili Rong creator: Jiachang Chen creator: Jun Liu creator: Yingzhen Li creator: Chaohui Hu uri: https://doi.org/10.7717/peerj.18471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation link: https://peerj.com/articles/18476 last-modified: 2024-11-08 description: BackgroundBreast cancer (BC) is one of most frequent female malignancies that poses multiple challenges in treatment and prevention. This study aimed to explore the role of miRNAs and their target genes during the BC progression.MethodsBased on the BC data (113 normal and 1,118 tumor samples) from the TCGA-BRCA dataset, a single-sample gene set enrichment analysis (ssGSEA) was applied to calculate the cancer migration scores, and weighted gene co-expression network analysis (WGCNA) were performed using the WGCNA R package, with a focus on the set of genes associated with cancer migration. Key modules and hub genes related to cell migration and signaling pathways were identified. Survival analysis of hub genes was conducted using the survminer R package, and prediction of regulatory miRNAs were performed to analyze their impact on BC prognosis. In addition, the BC cell lines MCF-7 and MDA-MB-231 were used to further explore the effect of hsa-miR-1972 mimics on the gene expression and angiogenic factor regulation.ResultsThe study classified important modules (MEblue, MEmagenta, MEpink, and MEfloralwhite) associated with cell migration and identified three hub genes, namely, MRPL20, COL4A1 and VWF. Survival analysis showed that certain hub genes with a low expression were related to a poor prognosis, whereas low-expressed COL4A1 and VWF were related to better survival outcomes. We also found that hsa-miR-1972 mimics significantly downregulated critical genes involved in BC metastasis and angiogenesis and effectively inhibited the proliferation of BC cell lines, showing a strong therapeutic potential. Manipulation of VWF expression in cells overexpressing hsa-miR-1972 had significant effects on the malignant markers and angiogenic factors, suggesting a novel therapeutic direction for BC treatment.ConclusionOur study highlighted the complex interplay of genetic factors in BC progression as well as the therapeutic potential of targeting specific miRNAs and their related hub genes. These findings provided novel insights into the pathogenesis of BC and suggested new direction for the therapeutic development for the cancer. creator: Changjiang Yu creator: Tao Zhang creator: Fan Chen creator: Zhenyang Yu uri: https://doi.org/10.7717/peerj.18476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022 link: https://peerj.com/articles/18187 last-modified: 2024-11-07 description: Black carbon (BC) is a pollutant produced by the combustion of fossil fuels and biomass fuels, which has a huge impact on regional climate, atmospheric environment, and human health. In this study, based on MERRA-2 reanalysis data and ground-based observation data, the Mann-Kendall (MK) test and random forest (RF) model were used to explore the spatiotemporal variation characteristics of atmospheric BC concentration in Xinjiang, China and its correlation with meteorological and environmental covariates in 2010–2022. The results showed that the use of MERRA-2 reanalysis data to explore the spatiotemporal variation characteristics of BC concentration in Xinjiang had high reliability (relative average deviation (RAD) = 0.65). From 2010 to 2022, the annual average concentration of atmospheric BC in Xinjiang was 195.40 ± 15.55 ng/m3, and the multi-year average change rate was −0.05%. The winter season had the highest atmospheric BC concentration (145.52 ± 39.31 ng/m3), followed by autumn (124.95 ± 28.82 ng/m3), spring (74.05 ± 9.96 ng/m3), and summer (73.41 ± 5.69 ng/m3). The atmospheric BC concentration had a significant spatial variation, showing two high-BC-concentration areas on the northern slope of the Tianshan Mountains (centered on Urumqi-Changji-Shihezi region) and the urban agglomeration around the Tarim Basin (centered on Kashgar). The RF model analysis showed that meteorological factors including snow depth, surface temperature, and humidity as well as environmental factors including NO2, PM10, and SO2 were the main factors affecting the BC concentration. This work is of great significance for clarifying the accumulation and spatial distribution characteristics of atmospheric BC in northwest China and the factors influencing the atmospheric BC concentration, and helps to raise public attention to the increasingly serious climate change and public health problems caused by BC. creator: Xiang Xie creator: Zhujun Zhao creator: Shuting Li creator: Zhongqi Lu creator: Lijuan Chen creator: Jiangjiang Cai uri: https://doi.org/10.7717/peerj.18187 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xie et al. title: High variability in the attractiveness of municipally-planted decorative plants to insects link: https://peerj.com/articles/17762 last-modified: 2024-11-06 description: Insect populations are declining globally. A major driver of this decline is land use change, including urbanisation. However, urban environments can also offer a wide range of floral resources to pollinators, through ornamental plantings, but these can vary widely in their attractiveness to insects. Often, the largest single planter of ornamental plants in an urban area is the municipality. Here we evaluated the decorative plantings carried out by the city municipality of Regensburg, Germany, by systematically surveying insect visitations on different plant types in late summer, when forage is often limited for pollinators. We found a 130-fold difference from the least to the most attractive plants, and high variation in which insect groups were attracted to which plants. While honey bees, which are not a conservation concern, were the most common insect visitors, some decorative plants attracted a very large proportion of wild bees, flies, and wasps. Our results demonstrate that there is great scope for increasing the supply of urban forage to pollinators in general, and specific groups in particular, without requiring new decorative plant types to be sourced or planted. We argue that providing local evidence-based guidance to municipalities offers a quick and potentially cost-neutral method for supporting urban insect populations. creator: Tomer J. Czaczkes creator: Carsten Breuss creator: Christoph Kurze uri: https://doi.org/10.7717/peerj.17762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Czaczkes et al.