title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=927 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Meiogyne oligocarpa (Annonaceae), a new species from Yunnan, China link: https://peerj.com/articles/10999 last-modified: 2021-04-14 description: Meiogyne oligocarpa sp. nov. (Annonaceae) is described from Yunnan Province in Southwest China. It is easily distinguished from all previously described Meiogyne species by the possession of up to four carpels per flower, its bilobed, sparsely hairy stigma, biseriate ovules and cylindrical monocarps with a beaked apex. A phylogenetic analysis was conducted to confirm the placement of this new species within Meiogyne. Meiogyne oligocarpa represents the second species of Meiogyne in China: a key to the species of Meiogyne in China is provided to distinguish it from Meiogyne hainanensis. Paraffin sectioning was undertaken to study the anatomy of the corrugations on the inner petals of Meiogyne oligocarpa to verify whether they are glandular. creator: Bine Xue creator: Yun-Yun Shao creator: Chun-Fen Xiao creator: Ming-Fai Liu creator: Yongquan Li creator: Yun-Hong Tan uri: https://doi.org/10.7717/peerj.10999 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xue et al. title: A quantitative comparison of towed-camera and diver-camera transects for monitoring coral reefs link: https://peerj.com/articles/11090 last-modified: 2021-04-14 description: Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring. creator: Anna K. Cresswell creator: Nicole M. Ryan creator: Andrew J. Heyward creator: Adam N. H. Smith creator: Jamie Colquhoun creator: Mark Case creator: Matthew J. Birt creator: Mark Chinkin creator: Mathew Wyatt creator: Ben Radford creator: Paul Costello creator: James P. Gilmour uri: https://doi.org/10.7717/peerj.11090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cresswell et al. title: Design and evaluation of a simulated wound management course for postgraduate year one surgery residents link: https://peerj.com/articles/11104 last-modified: 2021-04-14 description: BackgroundIt is vital to cover wound management knowledge and operations in the early stages of resident training. With this in mind, a simulated wound management course for postgraduate year one surgery residents (PGY1s) was designed and its effectiveness was evaluated.MethodsA retrospective quasi-experimental method was used. PGY1s in 2014 constituted the control group, and PGY1s in 2015 and 2016 constituted the intervention group. The course given to the control group comprised didactic teaching followed by deliberate practice plus immediate personalized feedback. The newly designed course given to the intervention group was reconstructed and disassembled into four components according to the simulation-based mastery learning model, which were baseline test, interactive learning, basic skills practice, and reflective learning. The same performance assessments were used in the control and intervention group, including process measurement and outcome measurement.ResultsThe process measurement showed that the intervention group’s scores were significantly higher in the “dissociation of subcutaneous tissue” and “quality of suturing and knots”. The outcome measurement showed that the accuracy of debridement was greatly improved and both key and total suture numbers were significantly higher in the intervention group.ConclusionsSimulation-based mastery learning was incorporated into our proposed course framework, promoting the learning outcome of PGY1s. It has the potential to be adapted for other surgical training sites for residents in China. creator: Xin Qi creator: Rui He creator: Bing Wen creator: Qiang Li creator: Hongbin Wu uri: https://doi.org/10.7717/peerj.11104 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Qi et al. title: Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial link: https://peerj.com/articles/11174 last-modified: 2021-04-14 description: BackgroundDespite a consistent link between obesity and increased circulating levels of fibroblast growth factor-21 (FGF21), the effect of weight-loss interventions on FGF21 is not clear. We aimed to determine the short- and long-term effects of Roux-en-Y gastric bypass (RYGB) on intact plasma FGF21 levels and to test the hypothesis that RYGB, but not diet-induced weight loss, increases fasting and postprandial responses of FGF21.MethodTwenty-eight participants with obesity followed a low-calorie diet for 11 weeks. The 28 participants were randomized to undergo RYGB surgery at week 8 (RYGB group, n = 14), or to a control group scheduled for surgery at week 12 (n = 14). Fasting levels of intact, biologically active FGF21 (amino acids 1-181) and its postprandial responses to a mixed meal were assessed at week 7 and 11, and 78 weeks (18 months) after RYGB.ResultsAt week 11 (3 weeks after RYGB), postprandial responses of intact FGF21 were enhanced in participants undergoing surgery at week 8 (change from week 7 to 11: P = 0.02), whereas no change was found in non-operated control participants in similar negative energy balance (change from week 7 to 11: P = 0.81). However, no between-group difference was found (P = 0.27 for the group-week-time interaction). Fasting, as well as postprandial responses in intact FGF21, were unchanged 18 months after RYGB when both the RYGB and control group were collapsed together (change from week 7 to 78 weeks after RYGB: P = 0.17).ConclusionPostprandial intact FGF21 levels were enhanced acutely after RYGB whereas no signs of sustained changes were found 18 months after surgery. When comparing the acute effect of RYGB with controls in similar negative energy balance, we failed to detect any significant differences between groups, probably due to the small sample size and large inter-individual variations, especially in response to surgery. creator: Mette S. Nielsen creator: Susanna Søberg creator: Julie B. Schmidt creator: Anne Chenchar creator: Anders Sjödin creator: Matthew P. Gillum uri: https://doi.org/10.7717/peerj.11174 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Nielsen et al. title: Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions link: https://peerj.com/articles/11207 last-modified: 2021-04-14 description: BackgroundHepatitis B virus (HBV) pregenomic RNA (pgRNA) has gained increasing attention owing to its role in replication of covalently closed circular DNA (cccDNA) in HBV. This marker has the potential to be used in clinical programs aimed to manage HBV infections. However, several reports on HBV pgRNA levels in clinical cases have conflicting results. RNA is easily degraded when exposed to heat and other environmental stressors. However, the stability of HBV pgRNA, during blood sample collection before the standard automated quantification, has never been estimated. This study aimed to demonstrate the effect of two different temperature conditions and storage durations on the stability of HBV pgRNA.MethodBlood from forty patients with chronic hepatitis B infection, who also showed evidence of active HBV DNA replication, was collected and processed within 2 h of collection. Plasma from each patient was divided and stored at 4 °C and 25 °C (room temperature) for six different storage durations (0, 2, 6, 12, 24, and 48 h) and subsequently transferred to −80 °C for storage. The effect of multiple cycles of freezing and thawing of plasma at −20 °C or −80 °C was evaluated using samples from ten patients. Quantification of pgRNA from the samples was performed simultaneously, using the digital polymerase chain reaction (dPCR) method. The differences in pgRNA levels at baseline and each time point were compared using generalized estimating equation (GEE). A change greater than 0.5 log10 copies/mL of pgRNA is considered clinically significant. Statistical analyses were conducted using Stata 16.0.ResultsThe mean HBV pgRNA level in the initially collected plasma samples was 5.58 log10copies/mL (ranging from 3.08 to 8.04 log10 copies/mL). The mean pgRNA levels in samples stored for different time periods compared with the initial reference sample (time 0) significantly decreased. The levels of pgRNA for 6, 12, 24, and 48 h of storage reduced by −0.05 log10 copies/mL (95% confidence interval (CI) −0.095 to −0.005, p = 0.03), −0.075 log10 copies/mL (95% CI [−0.12 to −0.03], p = 0.001), −0.084 log10 copies/mL (95% CI [−0.13 to −0.039], p =  < 0.001), and −0.120 log10 copies/mL (95% CI [−0.17 to −0.076], p =  < 0.001), respectively. However, these changes were below 0.5 log10 copies/mL and thus were not clinically significant. Compared with the samples stored at 4 °C, there were no significant differences in pgRNA levels in samples stored at 25 °C for any of the storage durations (−0.01 log10 copies/mL; 95% CI [−0.708 to 0.689], p = 0.98). No significant difference in the levels of pgRNA was observed in the plasma samples, following four freeze-thaw cycles at −20 °C and −80 °C.ConclusionThe plasma HBV pgRNA level was stable at 4 °C and at room temperature for at least 48 h and under multiple freeze-thaw cycles. Our results suggest that pgRNA is stable during the process of blood collection, and therefore results of pgRNA quantification are reliable. creator: Pakkapon Rattanachaisit creator: Sirinporn Suksawatamnuay creator: Supachaya Sriphoosanaphan creator: Kessarin Thanapirom creator: Panarat Thaimai creator: Nipaporn Siripon creator: Sukanya Sittisomwong creator: Yong Poovorawan creator: Piyawat Komolmit uri: https://doi.org/10.7717/peerj.11207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rattanachaisit et al. title: Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests link: https://peerj.com/articles/11214 last-modified: 2021-04-14 description: The fish embryo test (FET) is an alternative to the classic freshwater toxicity test used to assess environmental hazards and risks to fish. This test has been standardized and adopted by the Organization for Economic and Cooperation and Development (OECD). As salinity may affect the substances’ toxicity, we describe the development of an alternative euryhaline test species for embryonic ecotoxicological tests: the Brazilian silverside Atherinella brasiliensis (Quoy & Gaimard, 1825). This species is broadly distributed along the coast of South America and is able to inhabit a broad range of environmental and saline conditions. Ours is the first study on the maintenance of a native South American species for natural reproduction and the generation of embryos for tests. The embryos used are transparent and possess fluorescent cells which have only been seen in a few species and which may be used as markers, making it an alternative assessment tool for the lethal and sublethal substances in marine and estuarine environments. We provide a detailed description and analysis of embryonic development under different salinities and temperatures. The embryos and larvae developed in similar ways at different salinities, however as temperatures increased, mortality also increased. We considered the effects of the reference toxicants Zn2+ and SDS using a protocol similar to the FET that was standardized for zebrafish. Brazilian silverside embryos are as sensitive as freshwater, or euryhaline fish, to the surfactant but are more resistant to metals prior to hatching. We were able to show the advantages of the Brazilian silverside as a model for a marine fish embryo test (FETm) with high levels of reproducibility and little contaminated waste. creator: Natália Martins Feitosa creator: Emiliano Nicolas Calderon creator: Rhennã Nascimento da Silva creator: Sônia Lopes Rezende de Melo creator: Jackson Souza-Menezes creator: Rodrigo Nunes-da-Fonseca creator: Márcia Vieira Reynier uri: https://doi.org/10.7717/peerj.11214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Feitosa et al. title: Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq link: https://peerj.com/articles/11215 last-modified: 2021-04-14 description: Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly, the alcohol metabolic process biological category had the highest number of upregulated genes, and the enzyme group in this category may play an important role in the mechanisms of secondary metabolite detoxification. Hydrolytic enzymes, such as endoglucanases and a pectate lyase, were also identified, as well as some proteases. In conclusion, our research was conducted mainly to explain how the vascular tissue of a recognized host of the ambrosia complex responds during F. kuroshium infection since Fusarium dieback is an ambrosia beetle-vectored disease and many variables facilitate its establishment. creator: Claudia-Anahí Pérez-Torres creator: Enrique Ibarra-Laclette creator: Eric-Edmundo Hernández-Domínguez creator: Benjamín Rodríguez-Haas creator: Alan-Josué Pérez-Lira creator: Emanuel Villafán creator: Alexandro Alonso-Sánchez creator: Clemente de Jesús García-Ávila creator: José-Abrahán Ramírez-Pool creator: Diana Sánchez-Rangel uri: https://doi.org/10.7717/peerj.11215 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pérez-Torres et al. title: Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils link: https://peerj.com/articles/11236 last-modified: 2021-04-14 description: Dental material attributed to Palaeoloxodon huaihoensis from the Middle to Late Pleistocene were recovered over decades from the Penghu Channel during commercial fisheries activities. The National Museum of Nature Science (NMNS) has a collection of such dental material, which differs in size and morphology and likely represents ontogenetic variation and growth trajectory of various age groups of P. huaihoensis. However, little is known regarding age determination. By using length of dental material, enamel thickness (ET), and plate counts, we established the method to distinguish the age of the species, which is directly derived from the extant African forest elephant Loxodonta africana. When measuring signs of allometric growth, we found that in both the upper and lower jaws, tooth width was correlated negatively with lamellar frequency but positively with ET. In the same age group, the number of lamellae was higher in P. huaihoensis than in L. africana. The reconstructed age distribution indicated no difference in the upper or lower jaw. Notably, within our sample, P. huaihoensis is skewed towards adult and older individuals with median age between 33–34.5 years and differed significantly from that of Mammuthus primigenius in the European Kraków Spadzista site. This age distribution pattern is speculated to be related to the harsh environmental conditions and intense intraspecific competition among P. huaihoensis during the last ice age. creator: Jia-Cih Kang creator: Chien-Hsiang Lin creator: Chun-Hsiang Chang uri: https://doi.org/10.7717/peerj.11236 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kang et al. title: Temporal inversion of the acid-base equilibrium in newborns: an observational study link: https://peerj.com/articles/11240 last-modified: 2021-04-14 description: BackgroundA considerable fraction of newborn infants experience hypoxia-ischaemia and metabolic acidosis at birth. However, little is known regarding the biological response of newborn infants to the pH drift from the physiological equilibrium. The aim of this study was to investigate the relationship between the pH drift at birth and postnatal acid-base regulation in newborn infants.MethodsClinical information of 200 spontaneously breathing newborn infants hospitalised at a neonatal intensive care centre were reviewed. Clinical variables associated with venous blood pH on days 5–7 were assessed.ResultsThe higher blood pH on days 5–7 were explained by lower cord blood pH (−0.131, −0.210 to −0.052; regression coefficient, 95% confidence interval), greater gestational age (0.004, 0.002 to 0.005) and lower partial pressure of carbon dioxide on days 5–7 (−0.005, −0.006 to −0.004) (adjusted for sex, postnatal age and lactate on days 5–7).ConclusionIn relatively stable newborn infants, blood pH drift from the physiological equilibrium at birth might trigger a system, which reverts and over-corrects blood pH within the first week of life. Given that the infants within the study cohort was spontaneously breathing, the observed phenomenon might be a common reaction of newborn infants to pH changes at birth. creator: Yuko Mizutani creator: Masahiro Kinoshita creator: Yung-Chieh Lin creator: Satoko Fukaya creator: Shin Kato creator: Tadashi Hisano creator: Hideki Hida creator: Sachiko Iwata creator: Shinji Saitoh creator: Osuke Iwata uri: https://doi.org/10.7717/peerj.11240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mizutani et al. title: Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways link: https://peerj.com/articles/11259 last-modified: 2021-04-14 description: BackgroundLaryngeal squamous cell carcinoma (LSCC) is the second most aggressive head and neck squamous cell carcinoma. Although much work has been done to optimize its treatment, patients with LSCC still have poor prognosis. Therefore, figuring out differentially expressed genes (DEGs) contained in the progression of LSCC and employing them as potential therapeutic targets or biomarkers for LSCC is extremely meaningful.MethodsOverlapping DEGs were screened from two standalone Gene Expression Omnibus datasets, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. By applying STRING and Cytoscape, a protein–protein network was built, and module analysis was carried out. The hub genes were selected by maximal clique centrality with the CytoHubba plugin of Cytoscape. UALCAN and GEPIA data were examined to validate the gene expression findings. Moreover, the connection of the hub genes with LSCC patient overall survival was studied employing The Cancer Genome Atlas. Then, western blot, qRT-PCR, CCK-8, wound healing and transwell assays were bring to use for further verify the key genes.ResultsA total of 235 DEGs were recorded, including 83 upregulated and 152 downregulated genes. A total of nine hub genes that displayed a high degree of connectivity were selected. UALCAN and GEPIA databases verified that these genes were highly expressed in LSCC tissues. High expression of the SPP1, SERPINE1 and Matrix metalloproteinases 1 (MMP1) genes was connected to worse prognosis in patients with LSCC, according to the GEPIA online tool. Western blot and qRT-PCR testify SPP1, SERPINE1 and MMP1 were upregulated in LSCC cells. Inhibition of SPP1, SERPINE1 and MMP1 suppressed cell proliferation, invasion and migration.ConclusionThe work here identified effective and reliable diagnostic and prognostic molecular biomarkers by unified bioinformatics analysis and experimental verification, indicating novel and necessary therapeutic targets for LSCC. creator: Jinhua Ma creator: Xiaodong Hu creator: Baoqiang Dai creator: Qiang Wang creator: Hongqin Wang uri: https://doi.org/10.7717/peerj.11259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ma et al.