title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=574 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The morphology of the pulp chamber floor of permanent mandibular first and second molars in an Indian subpopulation—a descriptive cross-sectional study employing Pawar and Singh classification link: https://peerj.com/articles/14392 last-modified: 2022-11-29 description: BackgroundMandibular molars are multi-rooted teeth with a complex and strenuous root canal anatomy. Because there is relatively negligible literature describing the pulp chamber floor anatomy, predicting the exact anatomical layout and its variations is daunting. A thorough comprehension and knowledge of the same is required for efficacious endodontic treatment consequence. The purpose of this study was to characterise and ascertain the pulp chamber floor anatomy of permanent mandibular first (ManFMs) and second (ManSMs) molars in an Indian population.MethodsOn 2,134 extracted human mandibular first (ManFMs = 1,067) and second molars (ManSMs = 1,067), a descriptive cross-sectional investigation was executed. Cleaning and removal of hard and soft tissue debris were performed, followed by flattening the anatomical crown until the pupal architecture was uncovered. A stereomicroscope with a magnification of 4.5 magnification was used to investigate the pulpal anatomy. Statistical analysis was carried out using chi square test, with 95% confidence intervals and a p value of 0.05 considered statistically significant.ResultsThe majority of the ManFMs showed presence of three canal orifices in 57.73%, followed by four orifices 31.31%, five orifices 8.81%, and six orifices 2.15%. For ManSMs, majorly three orifices were found in 39.83% specimens, followed by two orifices in 37.39%, four orifices in 16.31%, and single root canal orifice was observed in 6.47%. The mesio-buccal, mesio-lingual, disto-buccal, disto-lingual canal orifices exhibited round and oval shapes in both ManFMs and ManSMs. The shape was predominantly oval with a single distal canal orifice (84.25% ManFMs and 74.16% ManSMs). In ManSMs, among the single root canal orifice, 66.66% were round in shape and 33.34% were C-shaped. In ManSMs with two root canal orifices, mesially 79.44% exhibited oval and 20.56% round shape. Distally, 74.16% were oval and 25.84% were round. The shapes of the access cavities for ManFMs were rectangular in 46.67% and triangular in 53.33%. For the ManSMs, the access cavities were triangular in 39.83%, rectangular in 16.31% and non-classified (others) in 43.86% of specimen. In both ManFMs and ManSMs, the pulp chamber floor morphology was predominately Y shaped (57.73% and 39.83%) according to the Pawar and Singh classification© of pulp chamber floor anatomy.ConclusionOur study indicated that the orifices on the pulp chamber floor are arranged in a typical manner, supporting the proposed categorization. Furthermore, description of the anatomical patterns of the pulp chamber guides the clinicians in chair-side treatment decisions. creator: Ajinkya M. Pawar creator: Shishir Singh uri: https://doi.org/10.7717/peerj.14392 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pawar and Singh title: The evolution of unique cranial traits in leporid lagomorphs link: https://peerj.com/articles/14414 last-modified: 2022-11-29 description: BackgroundThe leporid lagomorphs (rabbits and hares) are adapted to running and leaping (some more than others) and consequently have unique anatomical features that distinguish them from ochotonid lagomorphs (pikas) and from their rodent relatives. Two traits that have received some attention are fenestration of the lateral wall of the maxilla and facial tilting. These features are known to correlate with specialised locomotory form in that the faster running species will generally have fenestration that occupies the dorsal and the anteroventral surface of the maxillary corpus and a more acute facial tilt angle. Another feature is an intracranial joint that circumscribes the back of the skull, thought to facilitate skull mobility. This joint separates the anterior portion of the cranium (including the dentition, rostrum and orbit) from the posterior portion of the cranium (which encompasses the occipital and the auditory complex). Aside from the observation that the intracranial joint is absent in pikas (generalist locomotors) and appears more elaborate in genera with cursorial and saltatorial locomotory habits, the evolutionary history, biomechanical function and comparative anatomy of this feature in leporids lacks a comprehensive evaluation.MethodologyThe present work analysed the intracranial joint, facial tilting and lateral fenestration of the wall of the maxilla in the context of leporid evolutionary history using a Bayesian inference of phylogeny (18 genera, 23 species) and ancestral state reconstruction. These methods were used to gather information about the likelihood of the presence of these three traits in ancestral groups.ResultsOur phylogenetic analyses found it likely that the last common ancestor of living leporids had some facial tilting, but that the last common ancestor of all lagomorphs included in the dataset did not. We found that it was likely that the last common ancestor of living leporids had fenestration that occupies the dorsal, but not the anteroventral, surface of the maxillary corpus. We also found it likely that the last common ancestor of living leporids had an intracranial joint, but that the last common ancestor of all living lagomorphs did not. These findings provide a broader context to further studies of evolutionary history and will help inform the formulation and testing of functional hypotheses. creator: Amber P. Wood-Bailey creator: Philip G. Cox creator: Alana C. Sharp uri: https://doi.org/10.7717/peerj.14414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wood-Bailey et al. title: Superimposed vibration on suspended push-ups link: https://peerj.com/articles/14435 last-modified: 2022-11-29 description: BackgroundSuperimposition of vibration has been proposed in sports training using several devices and methods to enhance muscle activation and strength adaptations. Due to the popularity of suspension training, vibration systems have recently been developed to increase the effects of this training method. The present cross-sectional study aims to examine the effects of superimposing vibration on one of the most popular exercises in strength and conditioning programs: push-ups.MethodsTwenty-eight physically active men and women executed push-ups in three suspended conditions (non-vibration, vibration at 25 Hz, and vibration at 40 Hz). OMNI-Res scale was registered, and surface electromyographic signals were measured for the activity of the right and left external oblique, anterior deltoid, triceps brachii, sternal, and clavicular heads of the pectoralis major.ResultsA linear mixed model indicated a significant fixed effect for vibration at 25 Hz and 40 Hz on muscle activity. Suspended push-ups with superimposed vibration (25 Hz and 40 Hz) showed a significant higher activity on left (25 Hz: p = 0.036, d = 0.34; 40 Hz: p = 0.003, d = 0.48) and right external oblique (25 Hz: p = 0.004, d = 0.36; 40 Hz: p = 0.000, d = 0.59), anterior deltoid (25 Hz: p = 0.032, d = 0.44; 40 Hz: p = 0.003, d = 0.64), and global activity (25 Hz: p = 0.000, d = 0.55; 40 Hz: p = 0.000, d = 0.83) compared to non-vibration condition. Moreover, OMNI-Res significant differences were found at 25 Hz (6.04 ± 0.32, p = 0.000 d = 4.03 CI = 3.27, 4.79) and 40 Hz (6.21 ± 0.36 p = 0.00 d = 4.29 CI = 3.49, 5.08) compared to the non-vibration condition (4.75 ± 0.32).ConclusionSuperimposing vibration is a feasible strategy to enhance the muscle activity of suspended push-ups. creator: Bernat Buscà creator: Joan Aguilera-Castells creator: Jordi Arboix-Alió creator: Adrià Miró creator: Azahara Fort-Vanmeerhaeghe creator: Pol Huertas creator: Javier Peña uri: https://doi.org/10.7717/peerj.14435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Buscà et al. title: Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries link: https://peerj.com/articles/14449 last-modified: 2022-11-29 description: BackgroundIntra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes.ResultsIn this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis—dominant (N = 6, 21.8%); CST VII (Prevotella—dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 “taxa with high pathogenic potential” (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = −0.68, p < 2.2e−16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = −0.13, p = 0.1). However, at the individual level, Mycoplasma hominis exhibited moderate positive correlations with Gardnerella (r = 0.46, p = 2.6e−09) and Prevotella spp. (r = 0.47, p = 1.4e−09).ConclusionsThese findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-Lactobacillus-dominated CSTs. creator: Orville St. E. Roachford creator: Angela T. Alleyne creator: Karen E. Nelson uri: https://doi.org/10.7717/peerj.14449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Roachford et al. title: Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme link: https://peerj.com/articles/14479 last-modified: 2022-11-29 description: Melatonin is a multifunctional nontoxic bio-stimulant or signaling molecule, generally distributing in different animal and plant organs for invigorating numerous physiological processes against abiotic stresses. In this study, we investigated the potential impact of melatonin on the cyanobacterium Nostoc flagelliforme when exposed to salt stress according to some biochemical and physiological parameters, such as relative electrolyte leakage, PSII activity, and photosynthetic pigments including chlorophyll a, phycocyanobilin, and phycoerythrobilin. We found that melatonin could also maintain K+ homeostasis in salt-stressed N. flagelliforme. These above results confirmed melatonin had multiple functions in hyperosmotic stress and ion stress caused by salinity. Notably, we observed melatonin could regulate the reactive oxygen species (ROS) signal and distinctly decrease the content of hydrogen peroxide and superoxide anion in salt-stressed cells, which were largely attributed to the increased antioxidant enzymes activities including catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase. Finally, qRT-PCR analysis showed that melatonin stimulated the expression of antioxidant genes (NfCAT, NfSOD, and NfGR). In general, our findings demonstrate melatonin has beneficial effects on N. flagelliforme under salt stress by intensively regulating antioxidant system. creator: Xiaolong Yuan creator: Jing An creator: Tao Zheng creator: Wenjian Liu uri: https://doi.org/10.7717/peerj.14479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yuan et al. title: Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing? link: https://peerj.com/articles/14178 last-modified: 2022-11-28 description: Fish populations that bear considerable pressure levels tend to show a decline in the average size of individuals, with the small and unexploited species replacing the large and exploited ones. It is important to carry on with their characterization in areas where they are becoming an important source of food for local human populations. An example of such species are parrotfishes, whose responses to external factors such as fishing need to be understood and predicted. In this study, we used a diver-operated stereo-video to examine individual body size, sex ratios and proportion of species of the parrotfish assemblage and analyze them on a qualitative fishing pressure gradient at four oceanic islands in the Colombian Caribbean. We reported over 10,000 occurrences of eleven parrotfish species, of which we estimated the total length of over 90%, grouping them into three size categories (large, medium, and small). Our data showed a spatial variation of parrotfishes’ abundances, biomass, and individual body size. Observed differences are size-category-dependent throughout the qualitative fishing pressure. In general, the medium-bodied species had smaller sizes, lower abundances, and thus lower contribution to the total parrotfish biomass at the most heavily fished island. Unexpectedly, we found evidence of possible indirect effects over the small-bodied species Scarus iseri and Scarus taeniopterus with significantly greater abundances, and larger sizes of males of S. iseri, at the higher fishing pressure sites. Overall, our data highlights the extent of the spatial variation in the parrotfish communities at relatively short distances, and present new insights into the responses of parrotfish species on a spectrum of body sizes along a gradient of human pressure. creator: Natalia Rivas creator: Arturo Acero P. creator: José Tavera uri: https://doi.org/10.7717/peerj.14178 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rivas et al. title: Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression link: https://peerj.com/articles/14285 last-modified: 2022-11-28 description: Colorectal carcinoma (CRC) is the second most frequent cancer worldwide. MiR-491-3p, a tumor-suppressive microRNA (miRNA, miR), has been revealed to be abnormally expressed in CRC tissues. Meanwhile, up-regulated ubiquitous mitochondrial creatine kinase (uMtCK) contributes to CRC cell proliferation. Here we aim to explore whether aberrant miR-491-3p expression promotes CRC progression through regulating uMtCK. To this end, miR-491-3p and uMtCK levels were assessed in CRC tissues using quantitative real-time PCR (qRT-PCR). The biological roles of miR-491-3p and uMtCK in regulating CRC growth were evaluated using colony formation assay and mouse Xenograft tumour model. We found that miR-491-3p expression was decreased in CRC tissues compared with matched para-cancerous tissues, whereas uMtCK expression was increased. Functionally, miR-491-3p overexpression repressed SW480 cell growth, whereas miR-491-3p depletion accelerated SW620 cell proliferation and growth. Inversely, uMtCK positively regulated CRC cell proliferation. Mechanistically, miR-491-3p post-transcriptionally downregulated uMtCK expression by binding to 3’-UTR of uMtCK. Consequently, restoring uMtCK expression markedly eliminated the role of miR-491-3p in suppressing CRC growth. Collectively, miR-491-3p functions as a tumour suppressor gene by repressing uMtCK, and may be a potential target for CRC treatment. creator: Xingkui Tang creator: Yukun Lin creator: Jialin He creator: Xijun Luo creator: Junjie Liang creator: Xianjun Zhu uri: https://doi.org/10.7717/peerj.14285 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tang et al. title: A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors link: https://peerj.com/articles/14432 last-modified: 2022-11-28 description: BackgroundRecent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted.MethodsThe potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration.ResultsUsing the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. Moreover, as demonstrated by CCK-8 and Edu assays, RRM2 was an oncogene in liver cancer cells. We confirmed for the first time that RRM2 was significantly upregulated by HBx, suggesting that RRM2 may be a key regulator of LIHC induced by HBV. IHC analysis validated the upregulated expression of RRM2 protein and its correlation with immune infiltration makers in a LIHC patient cohort.ConclusionRRM2 may be a valuable molecular biomarker for predicting prognosis and immunotherapeutic efficacy in pan-cancer, particularly in LIHC. creator: Yaqun Li creator: Wenhuan Fu creator: Zikai Geng creator: Yun Song creator: Xionggang Yang creator: Tianye He creator: Jian Wu creator: Bin Wang uri: https://doi.org/10.7717/peerj.14432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study link: https://peerj.com/articles/14437 last-modified: 2022-11-28 description: BackgroundAnastomotic leakage remains one of the most common serious complications after rectal cancer surgery. How to predict its occurrence and prevent it remains largely elusive.ObjectiveThis study aimed to identify the risk factors of anastomotic leakage and construct a nomogram for predicting postoperative anastomotic leakage in patients with rectal cancer.MethodsThe data of 406 patients with rectal cancer after gastrointestinal surgery in the Third Affiliated Hospital of Sun Yat-sen University from January 2011 to May 2020 were collected (243 in the training set and 163 in the testing set). Logistic regression was applied to determine the risk factors of postoperative anastomotic leakage of rectal cancer, and a nomogram prediction model was thus established. Predictive performance of the nomogram was evaluated by C-index and area under the receiver-operating characteristic (ROC) curve.ResultsLogistic regression analysis showed that preoperative bowel obstruction (odds ratio [OR] = 12.846, 95% confidence interval CI [1.441–114.54], p = 0.022) and early first defecation after surgery (OR = 0.501, 95% CI [0.31–0.812], p = 0.005) were independent risk factors, which could be used to develop a nomogram to predict the occurrence of anastomotic leakage accurately. The evaluation of the prediction model shows that the C-index value of the model was 0.955, the area under the ROC curve (AUC) of the training set was 0.820, and the testing set was 0.747, whereas the optimal cut-off point based on the nomogram score was 174.6.ConclusionThis nomogram had a good prediction ability for postoperative anastomotic leakage in patients with rectal cancer. It can provide a reference for perioperative treatment and the selection of surgical methods to promote individualized and accurate treatment. creator: Tingzhen Li creator: Jianglong Huang creator: Purun Lei creator: Xiaofeng Yang creator: Zehong Chen creator: Peng Chen creator: Jiancheng Zhai creator: Xuefeng Guo creator: Hongbo Wei uri: https://doi.org/10.7717/peerj.14437 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule link: https://peerj.com/articles/14446 last-modified: 2022-11-28 description: BackgroundSuitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution.MethodologyWe integrated climate-based ecological niche models with information about topography and rivers’ network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85).ResultsCurrent weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a ‘belt’ connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe.ConclusionsThe outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats. creator: Mattia Iannella creator: Urbana Masciulli creator: Francesco Cerasoli creator: Michele Di Musciano creator: Maurizio Biondi uri: https://doi.org/10.7717/peerj.14446 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Iannella et al.