title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=798 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Systematic review and meta-analysis on the effect of continuous subjective tinnitus on attention and habituation link: https://peerj.com/articles/12340 last-modified: 2021-11-26 description: BackgroundAttention and habituation are two domains known to play key roles in the perception and maintenance of tinnitus. The heterogeneous nature of tinnitus and the methodologies adopted by various studies make it difficult to generalize findings. The current review aims at assessing and synthesizing evidence on the possible roles of attention and habituation in continuous subjective tinnitus.MethodologyThe literature search included five databases (PubMed, Scopus, Web of Sciences, CINAHL and ProQuest) that resulted in 1,293 articles, published by July 2019. Studies on attention and/or habituation in individuals with tinnitus using either behavioural or electrophysiological tests were included in the review after a quality assessment.ResultsSeventeen studies on attention in tinnitus were included in the narrative synthesis. Two meta-analyses were performed to assess the role of attention in tinnitus using a behavioural methodology (z = 4.06; p < 0.0001) and P300 amplitude (z = 2.70; p = 0.007) with 531 participants. With respect to habituation, the review indicates the lack of quality articles for habituation inclusion in the narrative synthesis.ConclusionsThe review highlights that selective domains of attention were consistently impaired in individuals with tinnitus. Habituation, on the other hand, needs further exploration. creator: Harini Vasudevan creator: Kanaka Ganapathy creator: Hari Prakash Palaniswamy creator: Grant Searchfield creator: Bellur Rajashekhar uri: https://doi.org/10.7717/peerj.12340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vasudevan et al. title: Monitoring newt communities in urban area using eDNA metabarcoding link: https://peerj.com/articles/12357 last-modified: 2021-11-26 description: Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales. creator: Léo Charvoz creator: Laure Apothéloz-Perret-Gentil creator: Emanuela Reo creator: Jacques Thiébaud creator: Jan Pawlowski uri: https://doi.org/10.7717/peerj.12357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Charvoz et al. title: Quadriceps femoris cross-sectional area and specific leg strength: relationship between different muscles and squat variations link: https://peerj.com/articles/12435 last-modified: 2021-11-26 description: BackgroundThe aim was to determine the relationship between the cross-sectional area of the quadriceps femoris and strength performance in the deep and parallel barbell squat.MethodsThe sample included 16 university students (seven female, 24.1 ± 1.7 years). Muscle strength was expressed as external load, including the one-repetition maximum and the body mass segments involved (calculated according to Dempster’s method). The cross-sectional area of the quadriceps femoris muscles was determined using ultrasound, while leg muscle mass was measured using the Bioelectrical Impedance method.ResultsThe cross-sectional areas of the three vastii muscles and leg muscle mass showed moderate to strong correlation with external load in both squat types (r = 0.509–0.873). However, partial correlation (cross-sectional area of quadriceps femoris muscles were controlled) showed significant association only between leg muscle mass and deep squat (r = 0.64, p < 0.05). The cross-sectional area of the vastus lateralis showed a slightly higher correlation with external load in the parallel than in the deep squat (r = 0.67, p < 0.01 vs. r = 0.59, p < 0.05). The regression analysis extracted the vastus medialis cross-sectional area as the most important factor in manifesting strength (parallel squat: R2 = 0.569; deep squat: R2 = 0.499, both p < 0.01). The obtained results suggest that parallel squat strength depends mainly on the cross-sectional area of the vastii muscles, while it seems that the performance in the deep squat requires an additional engagement of the hip and back extensor muscle groups. creator: Filip Kojic creator: Saša Ðurić creator: Igor Ranisavljev creator: Stanimir Stojiljkovic creator: Vladimir Ilic uri: https://doi.org/10.7717/peerj.12435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kojic et al. title: treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data link: https://peerj.com/articles/12450 last-modified: 2021-11-26 description: The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/). creator: Cristian Román Palacios creator: April Wright creator: Josef Uyeda uri: https://doi.org/10.7717/peerj.12450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Román Palacios et al. title: The influence of storage time on ponazuril concentrations in feline plasma link: https://peerj.com/articles/12516 last-modified: 2021-11-26 description: BackgroundThe pharmacokinetics of ponazuril have been determined in several species; however, there is very little information on the stability of the drug after storage for long periods of time. This study was undertaken to determine the stability of ponazuril in plasma samples stored at −80 °C, which is the temperature most commonly used in the author’s laboratory.MethodSpiked plasma samples (0.3, 7.5, and 15 µg/mL) were stored at −80 °C for three months. Analysis occurred on the first day and then once a week for the following twelve weeks. The drug was extracted using a chloroform extraction and separated by high performance liquid chromatography using ultraviolet detection.ResultsThere was no loss of drug for any concentration for the first four weeks of storage. There was an average loss of less than 5% from day 35 through day 70 and an average loss of 6% on day 77 and 84. The data suggest that ponazuril is stable for 4 weeks when stored at −80 °C and undergoes minimal loss in the remaining 8 weeks. creator: Sherry Cox creator: Lainey Harvill creator: Sarah Singleton creator: Joan B. Bergman creator: Becky DeBolt uri: https://doi.org/10.7717/peerj.12516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cox et al. title: Nutritional properties of selected superfood extracts and their potential health benefits link: https://peerj.com/articles/12525 last-modified: 2021-11-26 description: BackgroundThe term ‘superfoods’ is used to market foods considered to have significant health benefits. ‘Superfoods’ are claimed to prevent diseases as well as improving overall health, though the lack of explicit criteria means that any food can be labelled ‘super’ without support from scientific research. Typically, these ‘superfoods’ are rich in a particular nutrient for example antioxidants or omega-3 fatty acids. The objective of this study was to investigate the nutritional properties of a selection of superfood seeds: flax, chia, hulled sunflower and two types of processed hemp seeds and determine whether they may have potential health benefits.MethodsWe developed a simple aqueous extraction method for ground seeds and analysed their composition by mineral, protein and monosaccharide analyses. Cell viability assays were performed on Caco-2 and IEC-6 intestinal epithelial cells using increasing doses of the prepared extracts.ResultsIncreased cell viability was observed in both cell lines with increasing concentrations of the flax seed, chia seed or hulled sunflower extracts (P < 0.05). Compositional analyses revealed the presence of polysaccharides, proteins and essential minerals in the aqueous extracts and in vitro assays showed sunflower had the highest antioxidant activity. However, differences in extract composition and antioxidant properties could not be directly related to the observed increase in cell viability suggesting that other components in the extracts may be responsible. Future studies will further characterize these extracts and investigate whether they are beneficial for gastrointestinal health. creator: Jacqueline P. Barsby creator: James M. Cowley creator: Shalem Y. Leemaqz creator: Jessica A. Grieger creator: Daniel R. McKeating creator: Anthony V. Perkins creator: Susan E. P. Bastian creator: Rachel A. Burton creator: Tina Bianco-Miotto uri: https://doi.org/10.7717/peerj.12525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Barsby et al. title: Application of ultrasound guidance in the oral and maxillofacial nerve block link: https://peerj.com/articles/12543 last-modified: 2021-11-26 description: IntroductionNerve block technology is widely used in clinical practice for pain management. Conventional nerve localization methods, which only rely on palpation to identify anatomical landmarks, require experienced surgeons and can be risky. Visualization technologies like ultrasound guidance can help prevent complications by helping surgeons locate anatomical structures in the surgical area and by guiding the operation using different kinds of images. There are several important and complex anatomical structures in the oral and maxillofacial regions. The current article reviews the application of ultrasound guidance in oral and maxillofacial nerve blocks.MethodsWe searched the literature on the use of ultrasound guidance for the main nerve block techniques in the oral and maxillofacial regions using both PubMed and MEDLINE and summarized the findings.Results and DiscussionA review of the literature showed that ultrasound guidance improves the safety and effectiveness of several kinds of puncture procedures, including nerve blocks. There are two approaches to blocking the mandibular nerve: intraoral and extraoral. This review found that the role of ultrasound guidance is more important in the extraoral approach. There are also two approaches to the blocking of the maxillary nerve and the trigeminal ganglion under ultrasound guidance: the superazygomatic approach and the infrazygomatic approach. The infrazygomatic approach can be further divided into the anterior approach and the posterior approach. It is generally believed that the anterior approach is safer and more effective. This review found that the effectiveness and safety of most oral and maxillofacial nerve block operations can be improved through the use of ultrasound guidance. creator: Zhiwei Cao creator: Kun Zhang creator: Liru Hu creator: Jian Pan uri: https://doi.org/10.7717/peerj.12543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cao et al. title: Prediction of early recurrence and response to adjuvant Sorafenib for hepatocellular carcinoma after resection link: https://peerj.com/articles/12554 last-modified: 2021-11-26 description: BackgroundEarly recurrence of hepatocellular carcinoma (HCC) is a major obstacle to improving the prognosis, and no widely accepted adjuvant therapy guideline for patients post-liver resection is available. Currently, all available methods and biomarkers are insufficient to accurately predict post-operation HCC patients’ risk of early recurrence and their response to adjuvant therapy.MethodsIn this study, we downloaded four gene expression datasets (GSE14520, GSE54236, GSE87630, and GSE109211) from the Gene Expression Omnibus database and identified 34 common differentially expressed genes associated with HCC dysregulation and response to adjuvant sorafenib. Then, we constructed a novel 11-messenger RNA predictive model by using ROC curves analysis, univariate Cox regression analysis, and LASSO Cox regression analysis. Furthermore, we validated the predictive values of the risk model in GSE14520 and TCGA-LIHC cohorts by using Kaplan–Meier survival analysis, multivariable Cox regression analysis, and decision curve analysis, respectively.ResultsThe risk score model could identify patients with a high risk of HCC recurrence at the early stage and could predict the response of patients to adjuvant sorafenib. Patients with a high risk score had a worse recurrence rate in training cohorts (2-year: p < 0.0001, hazard ratio (HR): 4.658, confidence interval 95% CI [2.895–7.495]; 5-year: p < 0.0001, HR: 3.251, 95% CI [2.155–4.904]) and external validation cohorts (2-year: p < 0.001, HR: 3.65, 95% CI [2.001–6.658]; 5-year: p < 0.001, HR: 3.156, 95% CI [1.78–5.596]). The AUC values of the risk score model for predicting tumor early recurrence were 0.746 and 0.618, and that of the risk score model for predicting the response to adjuvant sorafenib were 0.722 and 0.708 in the different cohort, respectively. Multivariable Cox regression analysis and decision curve analysis also showed that the risk score model was superior to and independent of other clinicopathologic characteristics. Moreover, the risk score model had excellent abilities to predict the overall survival and HCC recurrence of patients with the same tumor stage category.ConclusionsOur risk model is a reliable and superior predictive tool. With this model, we could optimize the risk stratification based on early tumor recurrence and could evaluate the response of patients to adjuvant sorafenib after liver resection. creator: Liming Zheng creator: Xi Gu creator: Guojun Zheng creator: Xin Li creator: Meifang He creator: Longgen Liu creator: Xike Zhou uri: https://doi.org/10.7717/peerj.12554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zheng et al. title: Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks link: https://peerj.com/articles/12446 last-modified: 2021-11-25 description: BackgroundWhole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality.MethodsRaw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters.ResultsAssembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads.ConclusionsPHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies. creator: Darlene D. Wagner creator: Heather A. Carleton creator: Eija Trees creator: Lee S. Katz uri: https://doi.org/10.7717/peerj.12446 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2021 Wagner et al. title: Identification and functional analysis of bacteria in sclerotia of Cordyceps militaris link: https://peerj.com/articles/12511 last-modified: 2021-11-25 description: BackgroundCordyceps militaris is a fungus that parasitizes insects. Compounds from C. militaris are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of C. militaris. However, the community structure of microorganisms in samples from different places may be different, and their corresponding ecological functions require experimental verification.MethodsWe used high-throughput sequencing technology to analyze bacterial 16S rRNA gene sequences in sclerotia of three samples of C. militaris from Liaoning Province, China. We isolated, identified and verified the function of culturable bacterial strains from the sclerotia.ResultsPseudomonas, Pedobacter, Sphingobacterium, and Serratia were the dominant bacterial genera in the sclerotia. And function prediction showed that Pseudomonas and Pedobacter could be heterotrophic, Sphingobacterium could decompose urea, and Serratia could reduce nitrate. Two strains of bacteria isolated from the sclerotia of C. militaris, N-2 and N-26, were identified as Stenotrophomonas maltophilia and Pseudomonas baetica, respectively, based on culture and biochemical characteristics. When these isolated strains were co-cultured with C. militaris, the mycelium biomass and mycelium pellet diameter decreased, and the content of extracellular polysaccharide increased. Strain N-26 decreased the cordycepin content in C. militaris.ConclusionsBacteria in sclerotia have an important effect on the growth of C. militaris and the production of its metabolites. creator: Li Luo creator: Jiaxi Zhou creator: Zhongshun Xu creator: Jingqiang Guan creator: Yingming Gao creator: Xiao Zou uri: https://doi.org/10.7717/peerj.12511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Luo et al.