title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=407 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Epiperipatus puri sp. nov., a new velvet worm from Atlantic Forest in Southeastern Brazil (Onychophora, Peripatidae) link: https://peerj.com/articles/15384 last-modified: 2023-10-02 description: Epiperipatus ohausi (Bouvier, 1900) is the first species known from Rio de Janeiro, and more than 120 years later a new species is described in the state of Rio de Janeiro (RJ). In this study, we describe the second species in the state of Rio de Janeiro, which we are naming in honor of the indigenous population called puri who resided in southeastern coastal Brazil. The species can be diagnosed mainly by large dorsal primary papillae close to the insertion of the legs drawing a light band from the anterior to the posterior region of the body, and large dorsal primary papillae alternating on the dorsal plicae. Moreover, they are recognized in vivo by the color of the diamond-shaped marks brownish orange on the dorsal portion of the body. Epiperipatus puri sp. nov. morphologically seems to be related to Epiperipatus acacioi (Marcus & Marcus, 1995) by the shape of the primary papillae apical piece and to E. ohausi by the resemblance of dorsal papillae. The phylogeny shows a close relationship between the new species and E. ohausi in a clade with a still undescribed species from Rio de Janeiro, Brazil located within the Atlantic Forest, one of the most threatened biomes in the world. creator: Cristiano Sampaio Costa creator: Amanda Cruz Mendes creator: Alessandro Ponce de Leão Giupponi uri: https://doi.org/10.7717/peerj.15384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Costa et al. title: Prediction models of macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression link: https://peerj.com/articles/15417 last-modified: 2023-10-02 description: BackgroundUndoubtedly, the importance of food and food security as one of the present and future challenges is not invisible to anyone. Nowadays, the development of methods for monitoring the nutrient content in crop products is an essential issue for implementing reasonable and logical soil properties management. The modeling technique can evaluate the soil properties of fields and study the subject of crop yield through soil management. This study aims to predict fruit yield and macro-nutrient content in plant organs of Cucumis melo in response to soil elements using support vector regression (SVR).MethodologyIn the spring of 2020, this study was done as a factorial test in a randomized complete block design with three replications. The first factor was the use of fertilizers in six levels: no fertilizer (control), cow manure (30 t ha−1), sheep manure (30 t ha−1), nanobiomic foliar application (2 l ha−1), silicone foliar application (3 l ha−1), and chemical fertilizer from urea, triple superphosphate, and potassium sulfate sources (200, 100, and 150 kg ha−1). In addition, four levels of vermicompost considering as the second factor: no vermicompost (control), 5, 10, and 15 t ha−1. Input data sets such as fruit yield and nitrogen, phosphorus, and potassium levels in the seeds, fruits, leaves, and roots are used to calibrate the probabilistic model of SP using SVR.ResultsAccording to the results, when the data sets of the nitrogen, phosphorus, and potassium in the fruit uses as input, the accuracy of these models was higher than 80.0% (R2 = 0.807 for predicting fruit nitrogen; R2 = 0.999 for fruit phosphorus; R2 = 0.968 for fruit potassium). Also, the results of the prediction models in response to soil elements showed that the soil nitrogen content ranged from 0.05 to 1.1%, soil phosphorus from 10 to 59 mg kg−1, and soil potassium from 180 to 320 mg kg−1, which offers a suitable macro-nutrient content in the soil. Likewise, the best fruit nitrogen content ranged from 1.27 to 4.33%, fruit phosphorus from 15.74 to 26.19%, fruit potassium from 15.19 to 19.67%, and fruit yield from 2.16 to 5.95 kg per plant obtained under NPK chemical fertilizers and using 15 t ha−1 of vermicompost.ConclusionsBecause the fruit values had the highest contribution in prediction than observed values, thus identified as the best plant organs in response to soil elements. Based on our findings, the importance of fruit phosphorus identifies as a determinant that strongly influenced melon prediction models. More significant values of soil elements do not affect increasing fruit yield and macro-nutrient content in plant organs, and excessive application may not be economical. Therefore, our studies provide an efficient approach with potentially high accuracy to estimate fruit yield and macro-nutrient in the fruits of Cucumis melo in response to soil elements and cause a saving in the amount of fertilizer during the growing season. creator: Abbas Keshtehgar creator: Mahdi Dahmardeh creator: Ahmad Ghanbari creator: Issa Khammari uri: https://doi.org/10.7717/peerj.15417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Keshtehgar et al. title: Mitochondrial sequence data reveal population structure within Pustulosa pustulosa link: https://peerj.com/articles/15974 last-modified: 2023-10-02 description: Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system. creator: David Rodriguez creator: Stephen F. Harding creator: Shashwat Sirsi creator: Kelly McNichols-O’Rourke creator: Todd Morris creator: Michael R. J. Forstner creator: Astrid N. Schwalb uri: https://doi.org/10.7717/peerj.15974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodriguez et al. title: Assessing the magnitude of changes from protocol to publication—a survey on Cochrane and non-Cochrane Systematic Reviews link: https://peerj.com/articles/16016 last-modified: 2023-10-02 description: ObjectiveTo explore differences between published reviews and their respective protocols in a sample of 97 non-Cochrane Systematic Reviews (non-CSRs) and 97 Cochrane Systematic Reviews (CSRs) in terms of PICOS (Patients/Population, Intervention, Comparison/Control, Outcome, Study type) elements and the extent to which they were reported.Study Design and SettingWe searched PubMed and Cochrane databases to identify non-CSRs and CSRs that were published in 2018. We then searched for their corresponding Cochrane or PROSPERO protocols. The published reviews were compared to their protocols. The primary outcome was changes from protocol to review in terms of PICOS elements.ResultsWe identified a total of 227 changes from protocol to review in PICOS elements, 1.11 (Standard Deviation (SD), 1.22) changes per review for CSRs and 1.23 (SD, 1.12) for non-CSRs per review. More than half of each sub-sample (54.6% of CSRs and 67.0% of non-CSRs) (Absolute Risk Reduction (ARR) 12.4% [−1.3%; 26.0%]) had changes in PICOS elements. For both subsamples, approximately a third of all changes corresponded to changes related to primary outcomes. Marked differences were found between the sub-samples for the reporting of changes. 95.8% of the changes in PICOS items were not reported in the non-CSRs compared to 42.6% in the CSRs (ARR 53.2% [43.2%; 63.2%]).ConclusionCSRs showed better results than non-CSRs in terms of the reporting of changes. Reporting of changes from protocol needs to be promoted and requires general improvement. The limitations of this study lie in its observational design. Registration: https://osf.io/6j8gd/. creator: Maximilian Siebert creator: Laura Caquelin creator: Meisser Madera creator: Roberto Acosta-Dighero creator: Florian Naudet creator: Marta Roqué uri: https://doi.org/10.7717/peerj.16016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Siebert et al. title: Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort link: https://peerj.com/articles/16033 last-modified: 2023-10-02 description: Genetic heterogeneity influences the prognosis and therapy of breast cancer. The cause of disease progression varies and can be addressed individually. To identify the mutations and their impact on disease progression at an individual level, we sequenced exome and transcriptome from matched normal-tumor samples. We utilised DawnRank to prioritise driver genes and identify specific mutations in Indian patients. Mutations in the C3 and HLA genes were identified as drivers of disease progression, indicating the involvement of the innate immune system. We performed immune profiling on 16 matched normal/tumor samples using CIBERSORTx. We identified CD8+ve T cells, M2 macrophages, and neutrophils to be enriched in luminal A and T cells CD4+naïve, natural killer (NK) cells activated, T follicular helper (Tfh) cells, dendritic cells activated, and neutrophils in triple-negative breast cancer (TNBC) subtypes. Weighted gene co-expression network analysis (WGCNA) revealed activation of T cell-mediated response in ER positive samples and Interleukin and Interferons in ER negative samples. WGCNA analysis also identified unique pathways for each individual, suggesting that rare mutations/expression signatures can be used to design personalised treatment. creator: Snehal Nirgude creator: Sagar Desai creator: Vartika Khanchandani creator: Vidhyavathy Nagarajan creator: Jayanti Thumsi creator: Bibha Choudhary uri: https://doi.org/10.7717/peerj.16033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nirgude et al. title: The value of dual-energy computed tomography (DECT) in the diagnosis of urinary calculi: a systematic review and meta-analysis of retrospective studies link: https://peerj.com/articles/16076 last-modified: 2023-10-02 description: ObjectiveDual-energy computed tomography (DECT) imaging technology opens a new idea and method for analyzing stone composition, which can obtain several quantitative parameters reflecting tissue-related information and energy images different from traditional images. However, the application of DECT in diagnosing urinary calculi remains unknown. This study aims to evaluate the value of DECT in diagnosing urinary calculi by meta-analysis.MethodsPubMed, EMBASE, Web of Science, and the Cochrane Library were searched to articles published from the establishment of the databases to April 18, 2023. We reviewed the articles on the diagnosis of urinary calculi detected by DECT, established standards, screened the articles, and extracted data. Two researchers carried out data extraction and the Cohen’s unweighted kappa was estimated for inter-investigator reliability. The quality of the literature was evaluated by the diagnostic test accuracy quality evaluation tool (QUADAS-2). The heterogeneity and threshold effects were analyzed by Meta-Disc 1.4 software, and the combined sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic ratio were calculated. The combined receiver-operating characteristic (ROC) curve was drawn, and the value of DECT in the diagnosis of urinary calculi was evaluated by the area under the curve (AUC). The meta-analysis was registered at PROSPERO (CRD42023418204).ResultsOne thousand and twenty-seven stones were detected in 1,223 samples from 10 diagnostic tests. The analyzed kappa alternated between 0.78-0.85 for the document’s retrieval and detection procedure. The sensitivity of DECT in the diagnosis of urinary calculi was 0.94 (95% CI [0.92–0.96]). The positive likelihood ratio (PLR) of DECT in the diagnosis of urinary stones was 0.91 (95% CI [0.88–0.94]), and the negative likelihood ratio (NLR) was 0.08 (95% CI [0.05–0.11]). The specificity of DECT for detecting urinary calculi was 0.91 (95% CI [0.88–0.94]). The area under the curve of the summary receiver operator characteristic (SROC) was 0.9875. The sensitivity of dual-energy CT in the diagnosis of urinary calculi diameter <3 mm was 0.94 (95% CI [0.91–0.96]). The PLR of DECT in the diagnosis of urinary stones diameter <3 mm was 10.79 (95% CI [5.25 to 22.17]), and the NLR was 0.08 (95% CI [0.05–0.13]). The specificity of DECT for detecting urinary calculi <3 mm was 0.91 (95% CI [0.87–0.94]). The SROC was 0.9772.ConclusionThe DECT has noble application value in detecting urinary calculi. creator: Peipei Feng creator: Guochao Li creator: Peng Liang uri: https://doi.org/10.7717/peerj.16076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Feng et al. title: Standardization of in situ coral bleaching measurements highlights the variability in responses across genera, morphologies, and regions link: https://peerj.com/articles/16100 last-modified: 2023-10-02 description: Marine heatwaves and regional coral bleaching events have become more frequent and severe across the world’s oceans over the last several decades due to global climate change. Observational studies have documented spatiotemporal variation in the responses of reef-building corals to thermal stress within and among taxa across geographic scales. Although many tools exist for predicting, detecting, and quantifying coral bleaching, it remains difficult to compare bleaching severity (e.g., percent cover of bleached surface areas) among studies and across species or regions. For this review, we compiled over 2,100 in situ coral bleaching observations representing 87 reef-building coral genera and 250 species of common morphological groups from a total of 74 peer-reviewed scientific articles, encompassing three broad geographic regions (Atlantic, Indian, and Pacific Oceans). While bleaching severity was found to vary by region, genus, and morphology, we found that both genera and morphologies responded differently to thermal stress across regions. These patterns were complicated by (i) inconsistent methods and response metrics across studies; (ii) differing ecological scales of observations (i.e., individual colony-level vs. population or community-level); and (iii) temporal variability in surveys with respect to the onset of thermal stress and the chronology of bleaching episodes. To improve cross-study comparisons, we recommend that future surveys prioritize measuring bleaching in the same individual coral colonies over time and incorporate the severity and timing of warming into their analyses. By reevaluating and standardizing the ways in which coral bleaching is quantified, researchers will be able to track responses to marine heatwaves with increased rigor, precision, and accuracy. creator: Adi Khen creator: Christopher B. Wall creator: Jennifer E. Smith uri: https://doi.org/10.7717/peerj.16100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khen et al. title: Different patterns of foreground and background processing contribute to texture segregation in humans: an electrophysiological study link: https://peerj.com/articles/16139 last-modified: 2023-10-02 description: BackgroundFigure-ground segregation is a necessary process for accurate visual recognition. Previous neurophysiological and human brain imaging studies have suggested that foreground-background segregation relies on both enhanced foreground representation and suppressed background representation. However, in humans, it is not known when and how foreground and background processing play a role in texture segregation.MethodsTo answer this question, it is crucial to extract and dissociate the neural signals elicited by the foreground and background of a figure texture with high temporal resolution. Here, we combined an electroencephalogram (EEG) recording and a temporal response function (TRF) approach to specifically track the neural responses to the foreground and background of a figure texture from the overall EEG recordings in the luminance-tracking TRF. A uniform texture was included as a neutral condition. The texture segregation visual evoked potential (tsVEP) was calculated by subtracting the uniform TRF from the foreground and background TRFs, respectively, to index the specific segregation activity.ResultsWe found that the foreground and background of a figure texture were processed differently during texture segregation. In the posterior region of the brain, we found a negative component for the foreground tsVEP in the early stage of foreground-background segregation, and two negative components for the background tsVEP in the early and late stages. In the anterior region, we found a positive component for the foreground tsVEP in the late stage, and two positive components for the background tsVEP in the early and late stages of texture processing.DiscussionIn this study we investigated the temporal profile of foreground and background processing during texture segregation in human participants at a high time resolution. The results demonstrated that the foreground and background jointly contribute to figure-ground segregation in both the early and late phases of texture processing. Our findings provide novel evidence for the neural correlates of foreground-background modulation during figure-ground segregation in humans. creator: Baoqiang Zhang creator: Saisai Hu creator: Tingkang Zhang creator: Min Hai creator: Yongchun Wang creator: Ya Li creator: Yonghui Wang uri: https://doi.org/10.7717/peerj.16139 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Long non-coding RNA NMRAL2P promotes glycolysis and reduces ROS in head and neck tumors by interacting with the ENO1 protein and promoting GPX2 transcription link: https://peerj.com/articles/16140 last-modified: 2023-10-02 description: BackgroundMetabolic reprogramming is a key marker in the occurrence and development of tumors. This process generates more reactive oxygen species (ROS), promoting the development of oxidative stress. To prevent ROS from harming tumor cells, tumor cells can increase the production of reducing agents to counteract excessive ROS. NMRAL2P has been shown to promote the production of reductive mRNA and plays an important role in the process of oxidative stress.MethodsIn this study, the clinical data and RNA sequencing of head and neck tumors were obtained from The Cancer Genome Atlas data set. The long non-coding RNA (LncRNA) related to oxidative stress were then identified using differential and correlation analyses. The differential expression and prognosis of the identified lncRNA were then verified using samples from the library of the Second Hospital of Hebei Medical University. Only NMRAL2P was substantially expressed in cancer tissues and predicted a poor prognosis. The tumor-promoting impact of NMRAL2P was then confirmed using in vitro functional assays. The data set was then split into high- and low-expression subgroups based on the median gene expression of NMRAL2P to obtain the mRNA that had a large difference between the two groups, and examine the mechanism of NMRAL2P on GPX2 using quantitative real-time PCR, RNA binding protein immunoprecipitation assay, and chromatin immunoprecipitation. Mass spectrometry was used to identify NMRAL2P-binding proteins and western blotting was used to investigate probable mechanisms.ResultsThe lncRNA NMRAL2P is associated with oxidative stress in head and neck tumors. In vitro functional assays showed that the gene has a cancer-promoting effect, increasing lactic acid and superoxide dismutase production, and reducing the production of ROS and malondialdehyde. NMRAL2P promotes the transcription of GPX2 by binding to transcription factor Nrf2. The gene also inhibits the degradation of ENO1, a crucial enzyme in glycolysis, by binding to protein ENO1.ConclusionsThis study shows that NMRAL2P can promote glycolysis and reduce the harm to tumor cells caused by ROS. The gene can also be used as a possible target for the treatment of head and neck tumors. creator: Qian Nie creator: Huan Cao creator: JianWang Yang creator: Tao Liu creator: BaoShan Wang uri: https://doi.org/10.7717/peerj.16140 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nie et al. title: Anti-methicillin-resistant Staphylococcus aureus and antibiofilm activity of new peptides produced by a Brevibacillus strain link: https://peerj.com/articles/16143 last-modified: 2023-10-02 description: BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is listed as a highly prioritized pathogen by the World Health Organization (WHO) to search for effective antimicrobial agents. Previously, we isolated a soil Brevibacillus sp. strain SPR19 from a botanical garden, which showed anti-MRSA activity. However, the active substances were still unknown.MethodsThe cell-free supernatant of this bacterium was subjected to salt precipitation, cation exchange, and reversed-phase chromatography. The antimicrobial activity of pure substances was determined by broth microdilution assay. The peptide sequences and secondary structures were characterized by tandem mass spectroscopy and circular dichroism (CD), respectively. The most active anti-MRSA peptide underwent a stability study, and its mechanism was determined through scanning electron microscopy, cell permeability assay, time-killing kinetics, and biofilm inhibition and eradication. Hemolysis was used to evaluate the peptide toxicity.ResultsThe pure substances (BrSPR19-P1 to BrSPR19-P5) were identified as new peptides. Their minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) against S. aureus and MRSA isolates ranged from 2.00 to 32.00 and 2.00 to 64.00 µg/mL, respectively. The sequence analysis of anti-MRSA peptides revealed a length ranging from 12 to 16 residues accompanied by an amphipathic structure. The physicochemical properties of peptides were predicted such as pI (4.25 to 10.18), net charge at pH 7.4 (−3 to +4), and hydrophobicity (0.12 to 0.96). The CD spectra revealed that all peptides in the water mainly contained random coil structures. The increased proportion of α-helix structure was observed in P2−P5 when incubated with SDS. P2 (NH2-MFLVVKVLKYVV-COOH) showed the highest antimicrobial activity and high stability under stressed conditions such as temperatures up to 100 °C, solution of pH 3 to 10, and proteolytic enzymes. P2 disrupted the cell membrane and caused bacteriolysis, in which its action was dependent on the incubation time and peptide concentration. Antibiofilm activity of P2 was determined by which the half-maximal inhibition of biofilm formation was observed at 2.92 and 4.84 µg/mL for S. aureus TISTR 517 and MRSA isolate 2468, respectively. Biofilm eradication of tested pathogens was found at the P2 concentration of 128 µg/mL. Furthermore, P2 hemolytic activity was less than 10% at concentrations up to 64 µg/mL, which reflected the hemolysis index thresholds of 32.ConclusionFive novel anti-MRSA peptides were identified from SPR19. P2 was the most active peptide and was demonstrated to cause membrane disruption and cell lysis. The P2 activity was dependent on the peptide concentration and exposure time. This peptide had antibiofilm activity against tested pathogens and was compatible with human erythrocytes, supporting its potential use as an anti-MRSA agent in this post-antibiotic era. creator: Abiodun Ogunsile creator: Nuttapon Songnaka creator: Somchai Sawatdee creator: Monthon Lertcanawanichakul creator: Sucheewin Krobthong creator: Yodying Yingchutrakul creator: Jumpei Uchiyama creator: Apichart Atipairin uri: https://doi.org/10.7717/peerj.16143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ogunsile et al.