title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=286 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of warm-up protocols using lower and higher loads on multiple-set back squat volume-load link: https://peerj.com/articles/17347 last-modified: 2024-07-09 description: BackgroundThe present study aimed to investigate the effects of post-activation performance enhancement (PAPE) after three warm-up protocols on back squat performance in trained men.MethodsFourteen resistance-trained men performed conditioning activity (CA) with high-load (HL-CA), low-load (LL-CA), or usual specific warm-up as a control (CON). HL-CA consisted of one set of three repetitions with 90% of one repetition maximum (RM); LL-CA consisted of one set of six repetitions with 45% of 1 RM performed at maximal velocity; CON involved eight repetitions with 45% of 1 RM at controlled velocity. The participant’s performance was measured using the total number of repetitions and volume load (reps × load × sets).ResultsThere were no significant differences between warm-up for the total number of repetitions (p = 0.17) or total volume load (p = 0.15). There was no difference between conditions for the number of repetitions (main condition effect; p = 0.17); however, participants achieved a significantly higher volume load after HL-PAPE than after CON for the first set (p = 0.04).ConclusionHigh or low equated-load CA used as warm-up strategies did not potentiate subsequent performance enhancement in multiple-set back squat exercise performed until muscle failure in comparison with usual warm-up. creator: Daniel Souza creator: Anderson Garcia Silva creator: Arthur Vale creator: Alana Pessoni creator: Luan Galvão creator: Murilo Augusto Araújo creator: Célio de Paula Júnior creator: Carlos Vieira creator: Amilton Vieira creator: Paulo Gentil uri: https://doi.org/10.7717/peerj.17347 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Souza et al. title: The role of melatonergic system in intervertebral disc degeneration and its association with low back pain: a clinical study link: https://peerj.com/articles/17464 last-modified: 2024-07-09 description: ObjectiveThe mechanisms of intervertebral disc degeneration (IVDD) in low back pain (LBP) patients are multiples. In this study, we attempt to investigate whether melatonergic system plays a potential role in IVDD patients with LBP by analyzing their clinical specimens. The fucus will be given to the correlation between the melatonin receptor expression and intervertebral disc tissue apoptosis.MethodsIn this clinical study, 107 lumbar intervertebral disc nucleus pulposus (NP) specimens from patients with LBP were collected with patients’ consents. The disc height (DH) discrepancy ratio, range of motion and sagittal parameters of the pathological plane were measured and Pfirrmann grade was used to classified the grades of IVDD level. Discs at grades 1–3 were served as normal control and grades 4–5 were considered as IVDD. The expression levels of melatonin receptor 1A (MT1) and 1B (MT2) were measured by immunohistochemistry. The apoptosis of NP was assessed using TUNEL staining. Their potential associations among MT1/2, DH, apoptosis, sagittal parameters with IVDD and LBP were evaluated with statistical analysis.ResultsThe incidence of IVDD was positively associated with age and negatively related to VAS scores for LBP (p < 0.001). Patients with higher degree of IVDD also have higher DH discrepancy ratio (p < 0.001), higher prevalence of lumbar instability (p = 0.003) and higher cell apoptosis compared to the control. Nevertheless, no statistically significant correlation was identified between Pfirrmann grade and lumbar sagittal parameters. MT1 and MT2 both were highly expressed in the NP tissues. Importantly, MT1 expression but not MT2 was significantly increased in the intervertebral disc tissue of patients with IVDD and its level correlated well with cell apoptosis level and the severity of IVDD as well as lower VAS scores for LBP.ConclusionThe highly elevated MT1 expression was found in NP tissues of patients with IVDD and LBP compared to the control. This phenomenon probably reflects the compensating response of the body to the pathological alteration of the IVDD and LBP. Therefore, these findings provide the novel information to use selective agonists of MT1 to target IVDD and LBP clinically. creator: Chong Chen creator: Zongyuan Deng creator: Zhengran Yu creator: Yifan Chen creator: Tao Yu creator: Changxiang Liang creator: Yongyu Ye creator: Yongxiong Huang creator: Feng-Juan Lyu creator: Guoyan Liang creator: Yunbing Chang uri: https://doi.org/10.7717/peerj.17464 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Assessing tooth wear progression in non-human primates: a longitudinal study using intraoral scanning technology link: https://peerj.com/articles/17614 last-modified: 2024-07-09 description: Intraoral scanners are widely used in a clinical setting for orthodontic treatments and tooth restorations, and are also useful for assessing dental wear and pathology progression. In this study, we assess the utility of using an intraoral scanner and associated software for quantifying dental tissue loss in non-human primates. An upper and lower second molar for 31 captive hamadryas baboons (Papio hamadryas) were assessed for dental tissue loss progression, giving a total sample of 62 teeth. The animals are part of the Southwest National Primate Research Center and were all fed the same monkey-chow diet over their lifetimes. Two molds of each dentition were taken at either two- or three-year intervals, and the associated casts scanned using an intraoral scanner (Medit i700). Tissue loss was calculated in WearCompare by superimposition of the two scans followed by subtraction analysis. Four individuals had dental caries, and were assessed separately. The results demonstrate the reliability of these techniques in capturing tissue loss data, evidenced by the alignment consistency between scans, lack of erroneous tissue gain between scans, and uniformity of tissue loss patterns among individuals (e.g., functional cusps showing the highest degree of wear). The average loss per mm2 per year for all samples combined was 0.05 mm3 (0.04 mm3 for females and 0.08 mm3 for males). There was no significant difference in wear progression between upper and lower molars. Substantial variation in the amount of tissue loss among individuals was found, despite their uniform diet. These findings foster multiple avenues for future research, including the exploration of wear progression across dental crowns and arcades, correlation between different types of tissue loss (e.g., attrition, erosion, fractures, caries), interplay between tissue loss and microwear/topographic analysis, and the genetic underpinnings of tissue loss variation. creator: Ian Towle creator: Kristin L. Krueger creator: Raquel Hernando creator: Leslea J. Hlusko uri: https://doi.org/10.7717/peerj.17614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Towle et al. title: Effects of mating-type ratio imbalance on the degeneration of Cordyceps militaris subculture and preventative measures link: https://peerj.com/articles/17648 last-modified: 2024-07-09 description: The rapid degeneration of Cordyceps militaris strains during subculture represents a bottleneck problem that affects production stability. This study explored the mechanism underlying this degeneration in three production and three wild-type strains of Cordyceps militaris, isolating single-conidium strains from each. The effects of subculturing on fructification in both original and single mating-type strains were compared. Changes in the ratio of the two mating types were analyzed in both original and degenerated strains. Based on these findings, the two mating strains were paired in different ratios to determine their effects on fruiting. The resulting five strains were heterokaryotic strains with both MAT1-1 and MAT1-2 mating-type genes. Strain jb-2 was a single mating type (MAT1-1) mutant strain that produced stable fruiting bodies but failed to produce ascospores. It was found that the loss of or imbalance in mating types was the main reason for the rapid degeneration of fruiting traits during subculture and that this occurred randomly in the MAT1-1 and MAT1-2 types. The strains differed significantly in their stability during subculture. Fruiting was stable in the single mating-type Jb-2 strain, and the eleventh-generation fruited normally. There were differences in yield between the production and wild strains after inoculation with spawn containing different proportions of mating types. The production strain was more stable when inoculated with strains with mating-type ratios of 1:9 to 9:1 without affecting the yield. However, the yield of the wild-type strain xf-1 was positively correlated with the proportion of the MAT1-2 type, while the other two strains showed no correlations. Subculturing single mating-type mycelia separately and mixing them before production effectively mitigated degeneration during subculture. For Cordyceps militaris breeding, selecting strains containing both mating types, which are insensitive to the proportion of mating-type genes, enhanced stability in subculture and reduced the risk of mating-type loss. Direct breeding of specific single-mating type strains to induce fruiting is thus an effective breeding strategy. creator: Xin Wang creator: Xiu’E Li creator: Wenxu Qiu creator: Fangping Sa creator: Yetong Feng creator: Yupeng Ge creator: Shude Yang creator: Yu Liu creator: Jinzhong Xie creator: Wei Zhang creator: Weihuan Li creator: Xianhao Cheng uri: https://doi.org/10.7717/peerj.17648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Reliability and validity of “My Jump 2” application for countermovement jump free arm and interlimb jump symmetry in different sports of professional athletes link: https://peerj.com/articles/17658 last-modified: 2024-07-09 description: BackgroundVertical jumping is an important evaluation tool to measure muscle strength and power as well as lower limb symmetry. It is of practical importance and value to develop and utilize a portable and low-cost mobile application (APP) to evaluate jumping. The “My Jump 2” app is an iPhone camera-based application for measuring jumping movements, which is applied to the countermovement jump (CMJ) vertical jumps of the lower limbs of athletes in different sports. The validity of this application and previous versions applied to different forms of vertical jump tests has been preliminarily demonstrated in different population, which has an obvious progress in research. Therefore, the reliability and validity of the jump height, time of flight parameters and symmetry of the CMJ vertical jump of athletes in different sports are needed to be verified by more experiments.PurposeThe purpose of this study is to verify whether “My Jump 2” can effectively and reliably assess jump height, flight practice and lower limb symmetry in CMJAM (countermovement jump free arm) tests in fencing, swimming and diving athletes.MethodsSeventy-nine fencers, swimmers and divers with training experience participated in this study. They completed a total of three CMJAM vertical jump and lower limb symmetry tests in 1 day, while being assessed by using the “My Jump 2” application and a force platform. The intra-group correlation coefficient (ICC) was used to verify reliability, while the Cronbach’s alpha and coefficient of variation (CV%) was used to analyze the stability of the CMJAM vertical jump test over three jumps. The Pearson correlation coefficient was used to verify the strength of the relationship between methods (i.e., concurrent validity), and the Bland-Altman plot was used to represent consistency, meanwhile, the t-test was used to determine the systematic bias between methods.ResultsCompared with the force platform, the cumulative height values of the total number of jumps (r = 0.999; p = 0.000), the cumulative time to vacate (r = 0.999; p = 0.000) for the CMJAM test obtained by the “My Jump 2” application, the height (ICC = 0.999–1, p = 0.000), the time to vacate flight (ICC = 0.999–1, p = 0.000), contact time symmetry (ICC = 0.976–0.994, p = 0.000), and flight time symmetry (ICC = 0.921–0.982, p = 0.000), respectively. Showed high correlation between the results of “my jump 2” app and the force platform.ConclusionThe “My Jump 2” application is a valid tool to assess CMJAM vertical jump and lower limb symmetry in fencing, swimming and diving athletes with training experience. creator: Yong Peng creator: Shaotong Sun creator: Yudi Wang creator: Ya xuan Qin creator: Di Qin uri: https://doi.org/10.7717/peerj.17658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Peng et al. title: The ‘Erlenmeter’: a low-cost, open-source turbidimeter for no-sampling phenotyping of microorganism growth link: https://peerj.com/articles/17659 last-modified: 2024-07-09 description: This work presents a low-cost, open-source turbidimeter, the ‘Erlenmeter’, designed to monitor the growth of microorganisms in batch cultures. It is easy to build, based exclusively on inexpensive off-the-shelf electronic components and 3D-printed parts. The Erlenmeter allows measuring the optical density of cultures on standard Erlenmeyer flasks without the need to open the flasks to collect aliquots, ensuring speed, minimal use of consumables, and elimination of the risk of contamination. These features make it particularly well-suited not just for routine research assays but also for experimental teaching. Here we illustrate the use of the Erlenmeter turbidimeter to record the growth of the microalga Phaeodactylum tricornutum, of the bacterium Escherichia coli, and of the yeast Saccharomyces cerevisiae, model organisms that are widely used in research and teaching. The Erlenmeter allows a detailed characterization of the growth curves of all organisms, confirming its usefulness for studying microbial populations dynamics both for research purposes and in classroom settings. creator: João Serôdio creator: Alexandra Bastos creator: Silja Frankenbach creator: Jörg C. Frommlet creator: Ana Cristina Esteves creator: Henrique Queiroga uri: https://doi.org/10.7717/peerj.17659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Serôdio et al. title: Innovative infrastructure to access Brazilian fungal diversity using deep learning link: https://peerj.com/articles/17686 last-modified: 2024-07-09 description: In the present investigation, we employ a novel and meticulously structured database assembled by experts, encompassing macrofungi field-collected in Brazil, featuring upwards of 13,894 photographs representing 505 distinct species. The purpose of utilizing this database is twofold: firstly, to furnish training and validation for convolutional neural networks (CNNs) with the capacity for autonomous identification of macrofungal species; secondly, to develop a sophisticated mobile application replete with an advanced user interface. This interface is specifically crafted to acquire images, and, utilizing the image recognition capabilities afforded by the trained CNN, proffer potential identifications for the macrofungal species depicted therein. Such technological advancements democratize access to the Brazilian Funga, thereby enhancing public engagement and knowledge dissemination, and also facilitating contributions from the populace to the expanding body of knowledge concerning the conservation of macrofungal species of Brazil. creator: Thiago Chaves creator: Joicymara Santos Xavier creator: Alfeu Gonçalves dos Santos creator: Kelmer Martins-Cunha creator: Fernanda Karstedt creator: Thiago Kossmann creator: Susanne Sourell creator: Eloisa Leopoldo creator: Miriam Nathalie Fortuna Ferreira creator: Roger Farias creator: Mahatmã Titton creator: Genivaldo Alves-Silva creator: Felipe Bittencourt creator: Dener Bortolini creator: Emerson L. Gumboski creator: Aldo von Wangenheim creator: Aristóteles Góes-Neto creator: Elisandro Ricardo Drechsler-Santos uri: https://doi.org/10.7717/peerj.17686 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chaves et al. title: Integrative analysis of the transcriptome and metabolome provides insights into polysaccharide accumulation in Polygonatum odoratum (Mill.) Druce rhizome link: https://peerj.com/articles/17699 last-modified: 2024-07-09 description: BackgroundPolygonatum odoratum (Mill.) Druce is a traditional Chinese herb that is widely cultivated in China. Polysaccharides are the major bioactive components in rhizome of P. odoratum and have many important biological functions.MethodsTo better understand the regulatory mechanisms of polysaccharide accumulation in P. odoratum rhizomes, the rhizomes of two P. odoratum cultivars ‘Y10’ and ‘Y11’ with distinct differences in polysaccharide content were used for transcriptome and metabolome analyses, and the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified.ResultsA total of 14,194 differentially expressed genes (DEGs) were identified, of which 6,689 DEGs were down-regulated in ‘Y10’ compared with those in ‘Y11’. KEGG enrichment analysis of the down-regulated DEGs revealed a significant enrichment of ‘starch and sucrose metabolism’, and ‘amino sugar and nucleotide sugar metabolism’. Meanwhile, 80 differentially accumulated metabolites (DAMs) were detected, of which 52 were significantly up-regulated in ‘Y11’ compared to those in ‘Y10’. The up-regulated DAMs were significantly enriched in ‘tropane, piperidine and pyridine alkaloid biosynthesis’, ‘pentose phosphate pathway’ and ‘ABC transporters’. The integrated metabolomic and transcriptomic analysis have revealed that four DAMs, glucose, beta-D-fructose 6-phosphate, maltose and 3-beta-D-galactosyl-sn-glycerol were significantly enriched for polysaccharide accumulation, which may be regulated by 17 DEGs, including UTP-glucose-1-phosphate uridylyltransferase (UGP2), hexokinase (HK), sucrose synthase (SUS), and UDP-glucose 6-dehydrogenase (UGDH). Furthermore, 8 DEGs (sacA, HK, scrK, GPI) were identified as candidate genes for the accumulation of glucose and beta-D-fructose 6-phosphate in the proposed polysaccharide biosynthetic pathways, and these two metabolites were significantly associated with the expression levels of 13 transcription factors including C3H, FAR1, bHLH and ERF. This study provided comprehensive information on polysaccharide accumulation and laid the foundation for elucidating the molecular mechanisms of medicinal quality formation in P. odoratum rhizomes. creator: Gen Pan creator: Jian Jin creator: Hao Liu creator: Can Zhong creator: Jing Xie creator: Yuhui Qin creator: Shuihan Zhang uri: https://doi.org/10.7717/peerj.17699 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pan et al. title: Cancer histology in metastatic lymph node predicts prognosis in patients with node-positive stage IV colorectal cancer link: https://peerj.com/articles/17702 last-modified: 2024-07-09 description: BackgroundAppropriate prognostic indicators are required for patients with stage IV colorectal cancer (CRC). Lymph node metastasis mainly involves four histological types of CRC. Some metastatic lymph nodes (mLNs) showing cribriform carcinoma are associated with distant metastasis in patients with node-positive CRC and are correlated with recurrence and survival in stage III disease. However, the significance of mLN histology in the prognosis of patients with node-positive stage IV disease remains unclear.MethodsWe enrolled 449 consecutive patients with CRC who underwent primary tumor resection with lymph node dissection between January 2011 and November 2018. This study included 88 patients with node-positive stage IV CRC and synchronous or metachronous distant metastases. We retrospectively investigated the association between cancer histology in the mLNs based on our classification and cancer-specific survival (CSS) in patients with node-positive stage IV CRC.ResultsKaplan-Meier analysis showed that CSS was better in patients with CRC and all the mLNs showing tubular-type carcinoma. In contrast, patients with at least some mLNs showing poorly differentiated-type carcinoma had poor prognosis. Multivariate analysis showed that “all mLNs showing tubular-type carcinoma” was an independent good prognostic factor for CSS in patients with node-positive stage IV CRC. In addition, “at least some mLNs showing poorly differentiated-type carcinoma” was an independent poor prognostic factor for CSS in patients with node-positive stage IV disease.ConclusionsThe histological type of the mLN may indicate a better or poor prognosis for patients with stage IV CRC. creator: Shozo Yokoyama creator: Takashi Watanabe creator: Shuichi Matsumura creator: Masato Tamiya creator: Shotaro Nagano creator: Yuya Hori uri: https://doi.org/10.7717/peerj.17702 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yokoyama et al. title: A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures link: https://peerj.com/articles/17710 last-modified: 2024-07-09 description: As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds. creator: Jundie Zhai creator: You Wang creator: Boyu Tang creator: Sisi Zheng creator: Shunfu He creator: Wenxin Zhao creator: Jun Lin creator: Feng Li creator: Yuzi Bao creator: Zhuoma Lancuo creator: Chuanfa Liu creator: Wen Wang uri: https://doi.org/10.7717/peerj.17710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhai et al.