title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=160 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A machine learning approach for identifying anatomical biomarkers of early mild cognitive impairment link: https://peerj.com/articles/18490 last-modified: 2024-12-13 description: BackgroundAlzheimer’s Disease (AD) poses a major challenge as a neurodegenerative disorder, and early detection is critical for effective intervention. Magnetic resonance imaging (MRI) is a critical tool in AD research due to its availability and cost-effectiveness in clinical settings.ObjectiveThis study aims to conduct a comprehensive analysis of machine learning (ML) methods for MRI-based biomarker selection and classification to investigate early cognitive decline in AD. The focus to discriminate between classifying healthy control (HC) participants who remained stable and those who developed mild cognitive impairment (MCI) within five years (unstable HC or uHC).Methods3-Tesla (3T) MRI data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and Open Access Series of Imaging Studies 3 (OASIS-3) were used, focusing on HC and uHC groups. Freesurfer’s recon-all and other tools were used to extract anatomical biomarkers from subcortical and cortical brain regions. ML techniques were applied for feature selection and classification, using the MATLAB Classification Learner (MCL) app for initial analysis, followed by advanced methods such as nested cross-validation and Bayesian optimization, which were evaluated within a Monte Carlo replication analysis as implemented in our customized pipeline. Additionally, polynomial regression-based data harmonization techniques were used to enhance ML and statistical analysis. In our study, ML classifiers were evaluated using performance metrics such as Accuracy (Acc), area under the receiver operating characteristic curve (AROC), F1-score, and a normalized Matthew’s correlation coefficient (MCC′).ResultsFeature selection consistently identified biomarkers across ADNI and OASIS-3, with the entorhinal, hippocampus, lateral ventricle, and lateral orbitofrontal regions being the most affected. Classification results varied between balanced and imbalanced datasets and between ADNI and OASIS-3. For ADNI balanced datasets, the naíve Bayes model using z-score harmonization and ReliefF feature selection performed best (Acc = 69.17%, AROC = 77.73%, F1 = 69.21%, MCC’ = 69.28%). For OASIS-3 balanced datasets, SVM with zscore-corrected data outperformed others (Acc = 66.58%, AROC = 72.01%, MCC’ = 66.78%), while logistic regression had the best F1-score (66.68%). In imbalanced data, RUSBoost showed the strongest overall performance on ADNI (F1 = 50.60%, AROC = 81.54%) and OASIS-3 (MCC’ = 63.31%). Support vector machine (SVM) excelled on ADNI in terms of Acc (82.93%) and MCC’ (70.21%), while naïve Bayes performed best on OASIS-3 by F1 (42.54%) and AROC (70.33%).ConclusionData harmonization significantly improved the consistency and performance of feature selection and ML classification, with z-score harmonization yielding the best results. This study also highlights the importance of nested cross-validation (CV) to control overfitting and the potential of a semi-automatic pipeline for early AD detection using MRI, with future applications integrating other neuroimaging data to enhance prediction. creator: Alwani Liyana Ahmad creator: Jose M. Sanchez-Bornot creator: Roberto C. Sotero creator: Damien Coyle creator: Zamzuri Idris creator: Ibrahima Faye uri: https://doi.org/10.7717/peerj.18490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ahmad et al. title: The bile acid metabolome in umbilical cord blood and meconium of healthy newborns: distinct characteristics and implications link: https://peerj.com/articles/18506 last-modified: 2024-12-13 description: ObjectiveTo characterize the bile acid metabolomic profiles of umbilical cord blood and meconium in healthy newborns.MethodsFifteen healthy newborns, which born in the Obstetrics Department of the Affiliated Hospital of Southwest Medical University between July 1 and August 31, 2023, were selected as study subjects. Umbilical cord blood and meconium samples were collected, and bile acid metabolomics were analyzed using ultra-high performance liquid chromatography-tandem mass spectrometry.ResultsThe ratio of primary to secondary bile acids in cord blood was significantly higher than in meconium [2.64 (2.49, 5.70) vs. 0.99 (0.37, 1.58), Z = −3.80, P < 0.05]. The ratio of unconjugated to conjugated bile acids was notably higher in cord blood than in meconium [0.14 (0.07, 0.18) vs. 0.01 (0.01, 0.04), Z = −3.88, P < 0.05]. The ratio of cholic acid to chenodeoxycholic acid in conjugated primary bile acids was significantly lower in cord blood than in meconium [0.59 (0.19, 0.75) vs. 2.21 (1.34, 3.04), Z = −4.21, P < 0.05], but the ratio of cholic acid to chenodeoxycholic acid in secondary bile acids was significantly higher in cord blood than in meconium [0.42 (0.21, 0.63) vs. 0.03 (0.01, 0.05), Z = −4.54, P < 0.05]. Only three primary bile acids (taurochenodeoxycholic acid, glycochenodeoxycholic acid, and glycochenodeoxycholic acid 3-glucoside in umbilical cord blood) were correlated with their downstream metabolites in meconium (with hyodesoxycholic acid (r = −0.66, P = 0.01), tauro-ω-muricholic acid (r = 0.52, P = 0.048) and ursodeoxycholic acid-7S (r = −0.53, P = 0.04), respectively). In meconium, most of primary bile acids were correlated with their downstream metabolites (P all < 0.05): cholic acid was positively correlated with 3-dehydrocholic acid, taurocholic acid was positively correlated with taurodeoxycholic acid and 3-dehydrocholic acid, glycocholic acid was positively correlated with 3-dehydrocholic acid, chenodeoxycholic acid was positively correlated with glycoursodeoxycholic acid, taurolithocholic acid, and 7-keto lithocholic acid and negatively correlated with isolithocholic acid. Taurochenodeoxycholic acid was positively correlated with taurohyodeoxycholic acid, tauroursodeoxycholic acid, glycoursodeoxycholic acid, taurolithocholic acid, tauro-ω-muricholic acid, and glycohyodeoxycholic acid, while glycochenodeoxycholic acid was positively correlated with tauroursodeoxycholic acid, glycoursodeoxycholic acid, taurolithocholic acid, and glycohyodeoxycholic acid, and negatively correlated with isolithocholic acid.ConclusionThe bile acid metabolites in umbilical cord blood and meconium differ significantly, and the downstream bile acid metabolites in meconium are predominantly correlated with their upstream bile acids in meconium, but not those bile acids in umbilical cord blood. These findings contribute to a better understanding of bile acid metabolism in utero and lay the foundation for future research in this topic. creator: Chunxia Lu creator: Zhiyong Gao creator: Siqi Zhang creator: Ke Du creator: Die Xu creator: Wenbin Dong creator: Yujiao Zhang creator: Xiaoping Lei uri: https://doi.org/10.7717/peerj.18506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lu et al. title: Stirring up the muck: the systematics of soft-sediment Fionidae (Nudibranchia: Aeolidina) from the tropical Indo-Pacific link: https://peerj.com/articles/18517 last-modified: 2024-12-13 description: The tropical Indo-Pacific aeolid nudibranchs of the Fionidae are poorly known and have not been studied in a concerted manner. Many undescribed species are found throughout the Indian and Pacific Oceans and are concentrated in the Coral Triangle. With the recent publication of a revised systematic arrangement of the Fionidae, documentation and description of new taxa of Fionidae is especially warranted. Here we describe Tenellia bughaw Kim & Gosliner sp. nov., Tenellia puti Kim & Gosliner sp. nov., Tenellia nakapila Kim & Gosliner sp. nov., Abronica payaso Kim & Gosliner, sp. nov. and Abronica turon Gosliner & Kim sp. nov. from the waters of the Coral Triangle. Their phylogenetic placement in Fionidae is reviewed using three genes: cytochrome oxidase I (COI), 16s rRNA, and histone 3 (H3) in a Bayesian and maximum likelihood framework. A redescription of Tenellia yamasui (Hamatani, 1993) is also provided to clarify its distinctiveness from T. bughaw and T. puti. This study confirms that all four known species of Abronica are characterized by having an acutely pointed curved penial stylet, thus confirming a unique morphological synapomorphy for members of this genus. A discussion on conflicts in the classification of fionid aeolid nudibranchs addresses concerns with extreme splitting based on novel innovations that emphasize evolutionary novelty over phyletic kinship. Instead, a more conservative approach is suggested, especially within the context of taxa that still have much undocumented primary diversity. creator: Ashley Y. Kim creator: Samantha A. Donohoo creator: Terrence M. Gosliner uri: https://doi.org/10.7717/peerj.18517 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Kim et al. title: Geographic variation and core microbiota composition of Anastrepha ludens (Diptera: Tephritidae) infesting a single host across latitudinal and altitudinal gradients link: https://peerj.com/articles/18555 last-modified: 2024-12-13 description: Anastrepha ludens is a pestiferous tephritid fly species exhibiting extreme polyphagy. It develops optimally in hosts rich in sugar but low nitrogen content. We studied the geographical influence on the composition of A. ludens’s larval and newly emerged adult gut microbiota in altitudinal (0–2,000 masl) and latitudinal (ca. 800 km from 17° to 22°N latitude) transects along the coastline of the state of Veracruz, Mexico. In the 16 collection sites, we only collected Citrus x aurantium fruit (238 samples of A. ludens larvae and adults, plus 73 samples of pulp) to control for host effect, hypothesizing that there exists a conserved core microbiota that would be dominated by nitrogen-fixing bacteria. We found that latitude triggered more significant changes in the gut microbiota than altitude. Northern and southernmost samples differed the most in microbiota composition, with a trade-off between Acetobacteraceae and Rhizobiaceae driving these differences. As hypothesized, the core microbiota in each sampling site, contained the functional group of nitrogen-fixing bacteria. We conclude that A. ludens larvae can acquire multiple diazotrophic symbionts along its wide distribution range where it infests fruit with a high C:N ratio in the pulp. creator: Martín Aluja creator: Daniel Cerqueda-García creator: Alma Altúzar-Molina creator: Larissa Guillén creator: Emilio Acosta-Velasco creator: Juan Conde-Alarcón creator: Andrés Moya uri: https://doi.org/10.7717/peerj.18555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Aluja et al. title: Temporal disruption in tuberculosis incidence patterns during COVID-19: a time series analysis in China link: https://peerj.com/articles/18573 last-modified: 2024-12-13 description: BackgroundDespite extensive knowledge of tuberculosis (TB) and its control, there remains a significant gap in understanding the comprehensive impact of the COVID-19 pandemic on TB incidence patterns. This study aims to explore the impact of COVID-19 on the pattern of pulmonary tuberculosis in China and examine the application of time series models in the analysis of these patterns, providing valuable insights for TB prevention and control.MethodsWe used pre-COVID-19 pulmonary tuberculosis (PTB) data (2007–2018) to fit SARIMA, Prophet, and LSTM models, assessing their ability to predict PTB incidence trends. These models were then applied to compare the predicted PTB incidence patterns with actual reported cases during the COVID-19 pandemic (2020–2023), using deviations between predicted and actual values to reflect the impact of COVID-19 countermeasures on PTB incidence.ResultsPrior to the COVID-19 outbreak, PTB incidence in China exhibited a steady decline with strong seasonal fluctuations, characterized by two annual peaks—one in March and another in December. These seasonal trends persisted until 2019. During the COVID-19 pandemic, there was a significant reduction in PTB cases, with actual reported cases falling below the predicted values. The disruption in PTB incidence appears to be temporary, as 2023 data indicate a gradual return to pre-pandemic trends, though the incidence rate remains slightly lower than pre-COVID levels. Additionally, we compared the fitting and forecasting performance of the SARIMA, Prophet, and LSTM models using RMSE (root mean squared error), MAE (mean absolute error), and MAPE (mean absolute percentage error) indexes prior to the COVID-19 outbreak. We found that the Prophet model had the lowest values for all three indexes, demonstrating the best fitting and prediction performance.ConclusionsThe COVID-19 pandemic has had a temporary but significant impact on PTB incidence in China, leading to a reduction in reported cases during the pandemic. However, as pandemic control measures relax and the healthcare system stabilizes, PTB incidence patterns are expected to return to pre-COVID-19 levels. The Prophet model demonstrated the best predictive performance and proves to be a valuable tool for analyzing PTB trends and guiding public health planning in the post-pandemic era. creator: Jiarui Zhang creator: Zhong Sun creator: Qi Deng creator: Yidan Yu creator: Xingyue Dian creator: Juan Luo creator: Thilakavathy Karuppiah creator: Narcisse Joseph creator: Guozhong He uri: https://doi.org/10.7717/peerj.18573 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhang et al. title: Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago link: https://peerj.com/articles/18584 last-modified: 2024-12-13 description: BackgroundModern workplace requirements in the banking sector require bankers to work on screens for more than 6 h a day, putting much stress and strain on their eyes, which leads to computer vision syndrome. Therefore, this study aimed to assess the prevalence of computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago.Methods and materialsA cross-sectional design was applied to collect data from 399 bankers between April and June 2023. The collected data was entered into Excel worksheets and later uploaded to SPSS for further analysis. A variable with a P-value of 0.25 in binary logistic regression is a candidate for multi-variable logistic regression analysis. Finally, a variable with a P-value of 0.05 was used to declare statistical significance.ResultsA total of 371 participants were enrolled in this study, leading to a response rate of 92.9%. Of the total participants, 277 (74.7%) had computer vision syndrome. Working in rural areas (AOR = 2.69; 95% CI [1.41–5.13]) and using eyesight glasses (AOR = 0.57; 95% CI [0.33–0.97]) was associated with computer vision syndrome.ConclusionDespite being easily preventable, computer vision syndrome is substantially prevalent among bankers in Trinidad. The use of eye-sight glasses and the working area are significantly associated with computer vision syndrome. Therefore, it is necessary to improve workplace practices by encouraging the use of anti-glare screens and glasses for employees who work long hours on the computer. creator: Kingsley Ekemiri creator: Devonte McKnight creator: Chioma Ekemiri creator: Ngozika Ezinne creator: Henrietta Ashang creator: Virginia Victor creator: Osaze Okonedo creator: Ayishetu Oshoke Shuaibu creator: Robin Seemongal-Dass uri: https://doi.org/10.7717/peerj.18584 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ekemiri et al. title: Companion animal foster caregiving: a scoping review exploring animal and caregiver welfare, barriers to caregiver recruitment and retention, and best practices for foster care programs in animal shelters link: https://peerj.com/articles/18623 last-modified: 2024-12-13 description: Each year, millions of animals enter animal shelters across the United States and are met with a variety of potential stressors that can negatively impact their experience, including noise, confinement, and social isolation. Foster care, a unique form of human–animal interaction, is increasingly understood to be an effective tool for improving welfare by allowing animals to escape the stressors of the shelter, providing an environment that allows for greater social interaction, and offering opportunities for improved health and behavior. This review includes 42 published articles, reports, master’s theses, and doctoral dissertations that have previously evaluated companion animal foster care programs. While scientific literature in this area has increased over the last decade, no review of the research exploring companion animal fostering has been published. Here, we examine foster care programs and their effects on human and animal welfare, evaluate the successes and challenges of supporting shelter foster care programs, recommend best practices for programmatic success, illuminate discrepancies in equity and diversity of caregiver engagement, and offer directions for future research in animal foster caregiving. The examinations in this review conclude that fostering provides both proximate (i.e., physiological and behavioral) and distal (i.e., length of stay and adoption outcomes) welfare benefits for shelter animals as well as their caregivers. Companion animal foster care programs may be further improved by providing greater caregiver support and increasing the diversity and extent of community engagement. Meanwhile, scientific investigations should explore lesser-researched components of foster care programs that are not yet well understood. creator: Grace E. Phillips creator: Lisa M. Gunter uri: https://doi.org/10.7717/peerj.18623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Phillips and Gunter title: A comparative study on leaf anatomy and photosynthetic characteristics of different growth stages of Horsfieldia hainanensis link: https://peerj.com/articles/18640 last-modified: 2024-12-13 description: The rare and endangered wild plant, Horsfieldia hainanensis, has been listed as a second-level key protected plant in China. Currently, its habitat is severely damaged, and the population has dramatically declined, necessitating urgent intervention for protection. In this study, the aim was to explore the correlations and differences from the perspectives of photosynthetic characteristics and leaf structure, providing scientific references for in-situ conservation and ex-situ cultivation. The results revealed the following: (1) The maximum net photosynthetic rate (Pmax) and light saturation point (LSP) of mature trees were significantly higher than those of seedlings, while the light compensation point (LCP), CO2 compensation point (CCP), and CO2 saturation point (CSP) were significantly lower in seedlings. (2) The average daily net photosynthetic rate of mature trees was significantly higher than that of seedlings. When both mature trees and seedlings exhibited a “midday depression” phenomenon, accompanied by an increase in intercellular CO2 concentration (Ci), it indicated that the “midday depression” was caused by non-stomatal limiting factors. (4) Both mature trees and seedlings showed peak values of water use efficiency (WUE) under low light conditions. Mature trees had smaller upper and lower epidermis thickness but larger leaf thickness, and their leaf structure, characterized by well-developed palisade and spongy tissues, conformed to the cellular structure adaptations for low light. Therefore, both were more adapted to low light conditions. (5) The stomatal density (SD) and individual stomatal area (SA) of seedlings were significantly higher than those of mature trees. (6) The total chlorophyll content of mature trees was significantly higher than that of seedlings, while the chlorophyll a/chlorophyll b ratio was significantly lower in mature trees and remained below three in both cases. In summary, the photosynthetic capacity and light adaptability of mature trees are stronger than those of seedlings, but both mature trees and seedlings exhibit shade-tolerant characteristics. For in-situ conservation, it is possible to promote the growth and development of seedlings by appropriately employing artificial “windowing” or shading methods based on the actual growth environment of the seedlings. In the case of ex-situ cultivation, seedlings should be provided with appropriate shading initially, while ensuring sufficient moisture and CO2 concentration. As the plants grow, the shading intensity can be gradually reduced. Once the plants reach maturity, they have a broader range of light adaptability and can be transplanted to environments with less shading. creator: Jianwang Xu creator: Jianmin Tang creator: Haolong Jiang creator: Rong Zou creator: Xiao Wei uri: https://doi.org/10.7717/peerj.18640 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Xu et al. title: N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review link: https://peerj.com/articles/18645 last-modified: 2024-12-13 description: N6-methyladenosine (m6A) is the most abundant internal messenger RNA modification in eukaryotes, influencing various physiological and pathological processes by regulating RNA metabolism. Numerous studies have investigated the role of m6A in inflammatory responses and inflammatory diseases. In this study, VOSviewer and Citespace were used to perform bibliometric analysis to systematically evaluating the current landscape of research on the association between m6A and inflammation. The literature was sourced from the Web of Science Core Collection, with characteristics including year, country/region, institution, author, journal, citation, and keywords. According to the bibliometric analysis results of keywords, we present a narrative summary of the potential mechanisms by which m6A regulates inflammation. The results showed that the key mechanisms by which m6A modulates inflammation include apoptosis, autophagy, oxidative stress, immune cell dysfunction, and dysregulation of signaling pathways. creator: Zewen Li creator: Yongfeng Lao creator: Rui Yan creator: Xin Guan creator: Yanan Bai creator: Fuhan Li creator: Zhilong Dong uri: https://doi.org/10.7717/peerj.18645 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Isolation and identification of serotonin compound from banana hump: a reproductive stimulant for tiger shrimp Penaeus monodon broodstock enhancement link: https://peerj.com/articles/18670 last-modified: 2024-12-13 description: BackgroundThe banana plant is claimed to contain a serotonin compound that has the potential to stimulate and improve the reproductive performance of crustacean species. This study aimed to isolate and characterize the serotonin compound from the banana hump and its application to enhance the reproductive performance of tiger shrimp broodstock.MethodsBanana hump as a part of the plant was extracted by using the maceration technique. The chemical structure of the serotonin compound was identified and characterized based on spectroscopic data, including high-performance liquid chromatography (HPLC), ultraviolet-visible (UV-Vis) spectroscopy, and infrared (IR) spectroscopy, and a comparison was made with the standard compound and the literature. The extract herb in a dose of 50 µg/g body weight was injected into the tiger shrimp broodstock in four-time administrations. During 2 months of broodstock gonadal maturation, the parameters of molting, reproduction, and gene expression related to reproduction were observed.ResultsBased on the chemical structure analysis, the stimulant component of the banana hump was identified as a serotonin compound (5-hydroxytryptamine) at a concentration of 0.7% of dry weight. The number of spawned broodstock was higher in the serotonin extract treatment (60%) than in the control treatment (40%), and the broodstock injected serotonin spawned up to the second re-maturation. In contrast, no re-maturation was obtained in the control treatment. The egg number was significantly higher using the serotonin extract (286,550 ± 46,402 eggs) than the control shrimp (148,585 ± 23,647 eggs), in which the serotonin extract treatment showed a comparatively larger egg diameter number. The higher expression of the genes related to female and male reproduction was observed in the tiger shrimp injected with serotonin extract than in the control treatment. creator: Andi Parenrengi creator: Emma Suryati creator: Rachman Syah creator: Andi Tenriulo creator: Samuel Lante creator: Elmi Nurhaidah Zainuddin creator: Ratu Siti Aliah creator: Nuril Farizah creator: Agus Nawang creator: Sulaeman Sulaeman creator: Makmur Makmur creator: Rosmiati Rosmiati creator: Gunarto Gunarto creator: Herlinah Herlinah uri: https://doi.org/10.7717/peerj.18670 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Parenrengi et al.