title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=587
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Primate tooth crown nomenclature revisited
link: https://peerj.com/articles/14523
last-modified: 2023-01-12
description: Cusp patterning on living and extinct primate molar teeth plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. These studies rely on a system of nomenclature that can accurately identify and distinguish between the various structures of the crown surface. However, studies at the enamel-dentine junction (EDJ) of some primate taxa have demonstrated a greater degree of cusp variation and expression at the crown surface than current systems of nomenclature allow. In this study, we review the current nomenclature and its applicability across all the major primate clades based on investigations of mandibular crown morphology at the enamel-dentine junction revealed through microtomography. From these observations, we reveal numerous new patterns of lower molar accessory cusp expression in primates. We highlight numerous discrepancies between the expected patterns of variation inferred from the current academic literature, and the new patterns of expected variation seen in this study. Based on the current issues associated with the crown nomenclature, and an incomplete understanding of the precise developmental processes associated with each individual crown feature, we introduce these structures within a conservative, non-homologous naming scheme that focuses on simple location-based categorisations. Until there is a better insight into the developmental and phylogenetic origin of these crown features, these categorisations are the most practical way of addressing these structures. Until then, we also suggest the cautious use of accessory cusps for studies of taxonomy and phylogeny.
creator: Simon A. Chapple
creator: Matthew M. Skinner
uri: https://doi.org/10.7717/peerj.14523
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Chapple and Skinner

title: Models of ultrasonic radiomics and clinical characters for lymph node metastasis assessment in thyroid cancer: a retrospective study
link: https://peerj.com/articles/14546
last-modified: 2023-01-12
description: BackgroundPreoperative prediction of cervical lymph node metastasis in papillary thyroid carcinoma provided a basis for tumor staging and treatment decision. This study aimed to investigate the utility of machine learning and develop different models to preoperatively predict cervical lymph node metastasis based on ultrasonic radiomic features and clinical characteristics in papillary thyroid carcinoma nodules.MethodsData from 400 papillary thyroid carcinoma nodules were included and divided into training and validation group. With the help of machine learning, clinical characteristics and ultrasonic radiomic features were extracted and selected using randomforest and least absolute shrinkage and selection operator regression before classified by five classifiers. Finally, 10 models were built and their area under the receiver operating characteristic curve, accuracy, sensitivity, specificity, positive predictive value and negative predictive value were measured.ResultsAmong the 10 models, RF-RF model revealed the highest area under curve (0.812) and accuracy (0.7542) in validation group. The top 10 variables of it included age, seven textural features, one shape feature and one first-order feature, in which eight were high-dimensional features.ConclusionsRF-RF model showed the best predictive performance for cervical lymph node metastasis. And the importance features selected by it highlighted the unique role of higher-dimensional statistical methods for radiomics analysis.
creator: Hui Zhu
creator: Bing Yu
creator: Yanyan Li
creator: Yuhua Zhang
creator: Juebin Jin
creator: Yao Ai
creator: Xiance Jin
creator: Yan Yang
uri: https://doi.org/10.7717/peerj.14546
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhu et al.

title: The impact of hypertension on the prognosis of patients with hypertrophic cardiomyopathy: a single-center retrospective study
link: https://peerj.com/articles/14614
last-modified: 2023-01-12
description: BackgroundHypertrophic cardiomyopathy (HCM) and hypertension coexist fairly frequently in clinical practice. However, the evidence about the impact of hypertension on the prognosis of HCM is limited. The present study aims to investigate the impact of hypertension on the prognosis of HCM patients.MethodsA total of 468 HCM patients were enrolled, and patients were divided into hypertension group (31.8%) and non-hypertension group (68.2%). The primary study endpoint was HCM-related death, consisting of heart failure (HF)-related death, stroke-related death and sudden cardiac death (SCD). Associations between hypertension and HCM-related death were analyzed by Cox regression models with the use of propensity score matching (PSM) as primary analysis.ResultsThere were 55 HCM-related death during a median follow-up time of 4.6 years, and the mortality rate was 2.53 per 100 person years. Kaplan-Meier analysis based on the crude cohort or PSM cohort revealed no significant difference regarding the HCM-related death between the two groups. In the crude cohort, both univariable and multivariable Cox regression analysis indicated that hypertension was not significantly associated with HCM-related death with hazard ratios (HR) at 0.74 (95% CI [0.40–1.36], p value: 0.329) and 0.77 (95% CI [0.35–1.71], p value: 0.521), respectively. Similarly, no strong evidence for an association was observed between hypertension and HCM-related death in the PSM cohort with unadjusted HR at 0.90 (95% CI [0.34–2.41]; p value: 0.838) and adjusted HR at 0.77 (95% CI [0.35–1.71]; p value: 0.521), respectively. Other propensity score methods, including overlap weighting and inverse probability treatment weighting demonstrated similar results. Sensitivity analysis also indicated that the concomitant hypertension did not significantly increase the risk of HF-related death, stroke-related death or SCD in HCM patients.ConclusionHCM-related death did not significantly differ between hypertension and non-hypertension groups, suggesting a negative impact of hypertension on the clinical prognosis of HCM patients.
creator: Ziqiong Wang
creator: Yi Zheng
creator: Haiyan Ruan
creator: Liying Li
creator: Muxin Zhang
creator: Linjia Duan
creator: Sen He
uri: https://doi.org/10.7717/peerj.14614
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study
link: https://peerj.com/articles/14615
last-modified: 2023-01-12
description: BackgroundPrevious studies suggested that bone metastasis has a significant effect on the time of progression to metastatic castration-resistant prostate cancer (CRPC) for newly diagnosed de novo bone metastatic hormone-sensitive prostate cancer (mHSPC). Nevertheless, the effect of different bone metastasis sites was not fully evaluated. This study aimed to develop and validate a novel bone metastatic risk model.MethodsWe enrolled 122 patients who were newly diagnosed with de novo bone metastatic prostate cancer following primary androgen deprivation based therapy at our institution from January 2008 to June 2021. The metastatic bone sites were classified into six sites: skull; cervical, thoracic, and lumbar vertebrae; chest (ribs and sternum); pelvis; upper limbs; and lower limbs. We calculated the bone metastatic score (BMS) for each site: 0 points were assigned for non-metastasis and 1 point was assigned for metastasis. The X-tile was adopted to acquire optimal cutoff points of BMS. We defined high-risk group (HRG) as BMS ≥ 3 and low-risk group (LRG) as BMS < 3. The new bone risk stratification was validated by calculating the area under the receiver operating characteristic curve (AUC). Subsequently, the relevant clinical prognostic variables were added to construct a predictive nomogram for predicting CRPC.ResultsThe median patient age was 73 years. Most patients had Gleason score ≤8 (93 cases, 76.2%). The median follow-up duration was 11.5 months (range: 2–92 months). Eighty-six patients progressed to CRPC during the follow-up. The most common bone metastatic site was the pelvis (90.2%). The median BMS was 4. Seventy-six patients had HRG, while forty-six had LRG. The 1-, 2-, and 3-year AUCs for H/LRG were 0.620, 0.754, and 0.793, respectively. The HRG was associated with earlier time to CRPC. A nomogram based on four parameters (Gleason score, H/LRG, prostate-specific antigen [PSA] nadir, and time to PSA nadir) was developed to predict CRPC. Internal validation using bootstrapping demonstrated good accuracy for predicting the CRPC (C-index: 0.727). The calibration analysis demonstrated that the model performed well.ConclusionWe established a novel H/LRG risk model for newly diagnosed de novo bone metastatic prostate cancer, which provided evidence to support clinical decision-making.
creator: Yang Zhang
creator: Junqi Wang
creator: Li Ding
creator: Yuxin Zheng
creator: Chuang Wu
creator: Kun Wang
creator: Wentao Xia
creator: Peng Ge
uri: https://doi.org/10.7717/peerj.14615
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhang et al.

title: Modulation of lower limb muscles and trajectory correction in the bipedal stance during visual perturbation
link: https://peerj.com/articles/14631
last-modified: 2023-01-12
description: The ability to actively track posture using visual targets as indicators is important for improving impairments in whole-body coordination, and accurate visual feedback on tasks is considered effective in promoting sensory-motor integration and behavioral success. In the present study, we examined inter- and intramuscular modulation between the two lower limbs in response to visual perturbation. Sixteen healthy young subjects (age: 21.3 ± 0.7 years) were asked to move their weight back and forth while tracking a visual target displayed on a monitor in front of them for 30 s. Three types of target movements were examined: a sinusoidal wave (i.e., a predictable pattern), more complex patterns (random), and no movement (stationary). Electromyography (EMG) was used to assess intra- and intermuscular coherence modulation of the plantar flexor muscles (right and left soleus and right and left medial gastrocnemius). The ability to adjust posture to follow the target signal was assessed using a stabilometer. Inter- and intramuscular coherence increased during the visual perturbation task compared to the stationary task. In addition, left-right differences in lower limb modulation were observed during the visual perturbation task. Furthermore, interlimb coherence was related to the motor accuracy of tracking. The muscles of both lower limbs cooperated in response to visual perturbation, suggesting that these muscles control visually induced anteroposterior postural sway. Since such visual perturbations promote coordination between both lower extremities, this relationship may indicate the potential for rehabilitation training to help individuals acquire and improve the motor functions necessary to efficiently and stably perform activities of daily living.
creator: Tadayoshi Minamisawa
creator: Noboru Chiba
creator: Eizaburo Suzuki
uri: https://doi.org/10.7717/peerj.14631
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Minamisawa et al.

title: Heat treatment-induced autophagy promotes breast cancer cell invasion and metastasis via TGF-β2-mediated epithelial-mesenchymal transitions
link: https://peerj.com/articles/14640
last-modified: 2023-01-12
description: BackgroundInsufficient thermal ablation can accelerate malignant behaviors and metastases in some solid tumors, and epithelial-mesenchymal transition (EMT) and autophagy are involved in tumor metastasis. It has been found that TGF-β2 which belongs to the family of transforming growth factors often associated with cancer cell invasiveness and EMT. However, whether the interactions between autophagy and TGF-β2 induce EMT in breast cancer (BC) cells following insufficient microwave ablation (MWA) remains unclear.MethodsBC cells were treated with sublethal heat treatment to simulate insufficient MWA, and the effects of heat treatment on the BC cell phenotypes were explored. CCK-8, colony formation, flow cytometry, Transwell, and wound healing assays were performed to evaluate the influence of sublethal heat treatment on the proliferation, apoptosis, invasion, and migration of BC cells. Western blotting, real-time quantitative PCR, immunofluorescence, and transmission electron microscopy were carried out to determine the changes in markers associated with autophagy and EMT following sublethal heat treatment.ResultsResults showed that heat treatment promoted the proliferation of surviving BC cells, which was accompanied by autophagy induction. Heat treatment-induced autophagy up-regulated TGF-β2/Smad2 signaling and promoted EMT phenotype, thereby enhancing BC cells’ migration and invasion abilities. An increase or decrease of TGF-β2 expression resulted in the potentiation and suppression of autophagy, as well as the enhancement and abatement of EMT. Autophagy inhibitors facilitated apoptosis and repressed proliferation of BC cells in vitro, and thwarted BC cell tumor growth and pulmonary metastasis in vivo.ConclusionHeat treatment-induced autophagy promoted invasion and metastasis via TGF-β2/Smad2-mediated EMTs. Suppressing autophagy may be a suitable strategy for overcoming the progression and metastasis of residual BC cells following insufficient MWA.
creator: Zhennan Li
creator: Cheng Lu
creator: Fengliang Wang
creator: Haowei Guo
creator: Zhipeng Wang
creator: Hong Yin
creator: Jian Li
uri: https://doi.org/10.7717/peerj.14640
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Li et al.

title: The circadian calling activity of a lebinthine cricket with high-frequency calls is unaffected by cicada choruses in the day
link: https://peerj.com/articles/14641
last-modified: 2023-01-12
description: BackgroundMany factors can influence circadian rhythms in animals. For acoustically communicating species, both abiotic cues (such as light and temperature) and biotic cues (such as the activity of other animals), can influence the timing of signalling activity. Here we compare the 24-h singing activity of the cricket Lebinthus luae in the laboratory and field to assess whether the presence of other singing insects influences circadian rhythm.MethodsAcoustic monitors were placed in four localities in Singapore and the number of L. luae calls were counted for 10 min of each hour. Individuals from the same localities were captured and recorded in the laboratory in silence but with similar abiotic conditions (temperature and light cycle) as they experience in the field, and the number of calls over 24 h was quantified.ResultsThe 24-h pattern of L. luae singing was not significantly different between laboratory and field recordings. Singing activity peaked in the morning, with a secondary peak in the afternoon and a smaller peak at night. In the field, L. luae sang in the same locations and at the same time as diurnally singing cicadas, suggesting that the sympatric cicada chorus did not affect the circadian rhythm of communication in this species. Acoustic niche partitioning could potentially explain the ability of this cricket to call alongside cicadas: L. luae sings at higher frequencies than sympatric cicadas, unlike nocturnally singing cricket species that overlap with cicadas in frequency.
creator: Ming Kai Tan
creator: Tony Robillard
creator: Hannah ter Hofstede
uri: https://doi.org/10.7717/peerj.14641
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Tan et al.

title: Modeling geographic distribution of arbuscular mycorrhizal fungi from molecular evidence in soils of Argentinean Puna using a maximum entropy approach
link: https://peerj.com/articles/14651
last-modified: 2023-01-12
description: The biogeographic region of Argentinean Puna mainly extends at elevations higher than 3,000 m within the Andean Plateau and hosts diverse ecological communities highly adapted to extreme aridity and low temperatures. Soils of Puna are typically poorly evolved and geomorphology is shaped by drainage networks, resulting in highly vegetated endorheic basins and hypersaline basins known as salar or salt flats. Local communities rely on soil fertility for agricultural practices and on pastures for livestock rearing. From this perspective, investigating the scarcely explored microbiological diversity of these soils as indicators of ecosystems functioning might help to predict the fragility of these harsh environments. In this study we collected soil samples from 28 points, following a nested design within three different macro-habitats, i.e., Puna grassland, hypersaline salar and family-run crop fields. Total fungi and arbuscular mycorrhizal fungi (AMF) occurrence were analyzed using eDNA sequencing. In addition, the significance of soil salinity and organic matter content as significant predictors of AMF occurrence, was assessed through Generalized Linear Mixed Modeling. We also investigated whether intensive grazing by cattle and lama in Puna grasslands may reduce the presence of AMF in these highly disturbed soils, driving or not major ecological changes, but no consistent results were found, suggesting that more specific experiments and further investigations may address the question more specifically. Finally, to predict the suitability for AMF in the different macro-habitats, Species Distribution Modeling (SDM) was performed within an environmental coherent area comprising both the phytogeographic regions of Puna and Altoandino. We modeled AMF distribution with a maximum entropy approach, including bioclimatic and edaphic predictors and obtaining maps of environmental suitability for AMF within the predicted areas. To assess the impact of farming on AMF occurrence, we set a new series of models excluding the cultivated Chaupi Rodeo samples. Overall, SDM predicted a lower suitability for AMF in hypersaline salar areas, while grassland habitats and a wider temperature seasonality range appear to be factors significantly related to AMF enrichment, suggesting a main role of seasonal dynamics in shaping AMF communities. The highest abundance of AMF was observed in Vicia faba crop fields, while potato fields yielded a very low AMF occurrence. The models excluding the cultivated Chaupi Rodeo samples highlighted that if these cultivated areas had theoretically remained unmanaged habitats of Puna and Altoandino, then large-scale soil features and local bioclimatic constraints would likely support a lower suitability for AMF. Using SDM we evidenced the influence of bioclimatic, edaphic and anthropic predictors in shaping AMF occurrence and highlighted the relevance of considering human activities to accurately predict AMF distribution.
creator: Davide Nepote Valentin
creator: Samuele Voyron
creator: Florencia Soteras
creator: Hebe Jorgelina Iriarte
creator: Andrea Giovannini
creator: Erica Lumini
creator: Mónica A. Lugo
uri: https://doi.org/10.7717/peerj.14651
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Nepote Valentin et al.

title: Genome-wide identification of MAXs genes for strigolactones synthesis/signaling in solanaceous plants and analysis of their potential functions in tobacco
link: https://peerj.com/articles/14669
last-modified: 2023-01-12
description: The more axillary growth (MAX) gene family is a group of key genes involved in the synthesis and signal transduction of strigolactones (SLs) in plants. Although MAX genes play vital roles in plant growth and development, characterization of the MAX gene family has been limited in solanaceous crops, especially in tobacco. In this study, 74 members of the MAX family were identified in representative Solanaceae crops and classified into four groups. The physicochemical properties, gene structure, conserved protein structural domains, cis-acting elements, and expression patterns could be clearly distinguished between the biosynthetic and signal transduction subfamilies; furthermore, MAX genes in tobacco were found to be actively involved in the regulation of meristem development by responding to hormones. MAX genes involved in SL biosynthesis were more responsive to abiotic stresses than genes involved in SL signaling. Tobacco MAX genes may play an active role in stress resistance. The results of this study provide a basis for future in-depth analysis of the molecular mechanisms of MAX genes in tobacco meristem development and stress resistance.
creator: Lixianqiu Wang
creator: Bingjie Li
creator: Changbo Dai
creator: Anming Ding
creator: Weifeng Wang
creator: Haoqi Shi
creator: Mengmeng Cui
creator: Yuhe Sun
creator: Jing Lv
uri: https://doi.org/10.7717/peerj.14669
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Wang et al.

title: Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe
link: https://peerj.com/articles/14684
last-modified: 2023-01-12
description: When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes—especially tet(M)—were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas.
creator: Kazuaki Matsui
creator: Takeshi Miki
uri: https://doi.org/10.7717/peerj.14684
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Matsui and Miki