title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=337 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Seasonal fluctuations of litter and soil Collembola and their drivers in rainforest and plantation systems link: https://peerj.com/articles/17125 last-modified: 2024-04-01 description: Rainforest conversion and expansion of plantations in tropical regions change local microclimate and are associated with biodiversity decline. Tropical soils are a hotspot of animal biodiversity and may sensitively respond to microclimate changes, but these responses remain unexplored. To address this knowledge gap, here we investigated seasonal fluctuations in density and community composition of Collembola, a dominant group of soil invertebrates, in rainforest, and in rubber and oil palm plantations in Jambi province (Sumatra, Indonesia). Across land-use systems, the density of Collembola in the litter was at a maximum at the beginning of the wet season, whereas in soil it generally varied little. The community composition of Collembola changed with season and the differences between land-use systems were most pronounced at the beginning of the dry season. Water content, pH, fungal and bacterial biomarkers, C/N ratio and root biomass were identified as factors related to seasonal variations in species composition of Collembola across different land-use systems. We conclude that (1) conversion of rainforest into plantation systems aggravates detrimental effects of low moisture during the dry season on soil invertebrate communities; (2) Collembola communities are driven by common environmental factors across land-use systems, with water content, pH and food availability being most important; (3) Collembola in litter are more sensitive to climatic variations than those in soil. Overall, the results document the sensitivity of tropical soil invertebrate communities to seasonal climatic variations, which intensifies the effects of the conversion of rainforest into plantation systems on soil biodiversity. creator: Winda Ika Susanti creator: Valentyna Krashevska creator: Rahayu Widyastuti creator: Christian Stiegler creator: Dodo Gunawan creator: Stefan Scheu creator: Anton M. Potapov uri: https://doi.org/10.7717/peerj.17125 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Susanti et al. title: Health and ecological risk of heavy metals in agricultural soils related to Tungsten mining in Southern Jiangxi Province, China link: https://peerj.com/articles/17200 last-modified: 2024-04-01 description: BackgroundDayu County, a major tungsten producer in China, experiences severe heavy metal pollution. This study evaluated the pollution status, the accumulation characteristics in paddy rice, and the potential ecological risks of heavy metals in agricutural soils near tungsten mining areas of Dayu County. Furthermore, the impacts of soil properties on the accumulation of heavy metals in soil were explored.MethodsThe geo-accumulation index (Igeo), the contamination factor (CF), and the pollution load index (PLI) were used to evaluate the pollution status of metals (As, Cd, Cu, Cr, Pb, Mo, W, and Zn) in soils. The ecological risk factor (RI) was used to assess the potential ecological risks of heavy metals in soil. The health risks and accumulation of heavy metals in paddy rice were evaluated using the health risk index and the translocation factor (TF), respectively. Pearson’s correlation coefficient was used to discuss the influence of soil factors on heavy metal contents in soil.ResultsThe concentrations of metals exceeded the respective average background values for soils (As: 10.4, Cd: 0.10, Cu: 20.8, Cr: 48.0, Pb: 32.1, Mo: 0.30, W: 4.93, Zn: 69.0, mg/kg). The levels of As, Cd, Mo, and tungsten(W) exceeded the risk screening values for Chinese agricultural soil contamination and the Dutch standard. The mean concentrations of the eight tested heavy metals followed the order FJ-S > QL > FJ-N > HL > CJ-E > CJ-W, with a significant distribution throughout the Zhangjiang River basin. Heavy metals, especially Cd, were enriched in paddy rice. The Igeo and CF assessment indicated that the soil was moderately to heavily polluted by Mo, W and Cd, and the PLI assessment indicated the the sites of FJ-S and QL were extremely severely polluted due to the contribution of Cd, Mo and W. The RI results indicated that Cd posed the highest risk near tungsten mining areas. The non-carcinogenic and total carcinogenic risks were above the threshold values (non-carcinogenic risk by HQ > 1, carcinogenic risks by CR > 1 × 10−4 a−1) for As and Cd. Correlation analysis indicated that K2O, Na2O, and CaO are main factors affecting the accumulation and migration of heavy metals in soils and plants. Our findings reveal significant contamination of soils and crops with heavy metals, especially Cd, Mo, and W, near mining areas, highlighting serious health risks. This emphasizes the need for immediate remedial actions and the implementation of stringent environmental policies to safeguard health and the environment. creator: Jinhu Lai creator: Yan Ni creator: Jinying Xu creator: Daishe Wu uri: https://doi.org/10.7717/peerj.17200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lai et al. title: Spatial habitat suitability prediction of essential oil wild plants on Indonesia’s degraded lands link: https://peerj.com/articles/17210 last-modified: 2024-04-01 description: BackgroundEssential oils are natural products of aromatic plants with numerous uses. Essential oils have been traded worldwide and utilized in various industries. Indonesia is the sixth largest essential oil producing country, but land degradation is a risk to the continuing extraction and utilization of natural products. Production of essential oil plants on degraded lands is a potential strategy to mitigate this risk. This study aimed to identify degraded lands in Indonesia that could be suitable habitats for five wild native essential oil producing plants, namely Acronychia pedunculata (L.) Miq., Baeckea frutescens L., Cynometra cauliflora L., Magnolia montana (Blume) Figlar, and Magnolia sumatrana var. glauca (Blume) Figlar & Noot using various species distribution models.MethodsThe habitat suitability of these species was predicted by comparing ten species distribution models, including Bioclim, classification and regression trees (CART), flexible discriminant analysis (FDA), Maxlike, boosted regression trees (BRT), multivariate adaptive regression splines (MARS), generalized linear models (GLM), Ranger, support vector machine (SVM), and Random Forests (RF). Bioclimatic, topographic and soil variables were used as the predictors of the model habitat suitability. The models were evaluated according to their AUC and TSS metrics. Model selection was based on ranking performance. The total suitable area for five native essential oil producing plants in Indonesia’s degraded lands was derived by overlaying the models with degraded land locations.ResultsThe habitat suitability model for these species was well predicted with an AUC value >0.8 and a TSS value >0.7. The most important predictor variables affecting the habitat suitability of these species are mean temperature of wettest quarter, precipitation seasonality, precipitation of warmest quarter, precipitation of coldest quarter, cation exchange capacity, nitrogen, sand, and soil organic carbon. C. cauliflora has the largest predicted suitable area, followed by M. montana, B. frutescens, M. sumatrana var. glauca, and A. pedunculata. The overlapping area between predictive habitat suitability and degraded lands indicates that the majority of degraded lands in Indonesia’s forest areas are suitable for those species.ConclusionThe degraded lands predicted as suitable habitats for five native essential oil producing plants were widely spread throughout Indonesia, mostly in its main islands. These findings can be used by the Indonesian Government for evaluating policies for degraded land utilization and restorations that can enhance the lands’ productivity. creator: Elga Renjana creator: Elok Rifqi Firdiana creator: Melisnawati H. Angio creator: Linda Wige Ningrum creator: Intani Quarta Lailaty creator: Apriyono Rahadiantoro creator: Irfan Martiansyah creator: Rizmoon Zulkarnaen creator: Ayyu Rahayu creator: Puguh Dwi Raharjo creator: Ilham Kurnia Abywijaya creator: Didi Usmadi creator: Rosniati Apriani Risna creator: Wendell P. Cropper, Jr creator: Angga Yudaputra uri: https://doi.org/10.7717/peerj.17210 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Renjana et al. title: Higher body condition with infection by Haemoproteus parasites in Bananaquits (Coereba flaveola) link: https://peerj.com/articles/16361 last-modified: 2024-03-29 description: Parasite transmission is a heterogenous process in host-parasite interactions. This heterogeneity is particularly apparent in vector-borne parasite transmission where the vector adds an additional level of complexity. Haemosporidian parasites, a widespread protist, cause a malaria-like disease in birds globally, but we still have much to learn about the consequences of infection to hosts’ health. In the Caribbean, where malarial parasites are endemic, studying host-parasites interactions may give us important insights about energetic trade-offs involved in malarial parasites infections in birds. In this study, we tested the consequences of Haemoproteus infection on the Bananaquit, a resident species of Puerto Rico. We also tested for potential sources of individual heterogeneity in the consequences of infection such as host age and sex. To quantify the consequences of infection to hosts’ health we compared three complementary body condition indices between infected and uninfected individuals. Our results showed that Bananaquits infected by Haemoproteus had higher body condition than uninfected individuals. This result was consistent among the three body condition indices. Still, we found no clear evidence that this effect was mediated by host age or sex. We discuss a set of non-mutually exclusive hypotheses that may explain this pattern including metabolic syndrome, immunological responses leading to host tolerance or resistance to infection, and potential changes in consumption rates. Overall, our results suggest that other mechanisms, may drive the consequences of avian malarial infection. creator: Nicole A. Gutiérrez-Ramos creator: Miguel A. Acevedo uri: https://doi.org/10.7717/peerj.16361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gutiérrez-Ramos and Acevedo title: Factors associated with intention to be vaccinated with the COVID-19 booster dose: a cross-sectional study in Peru link: https://peerj.com/articles/16727 last-modified: 2024-03-29 description: IntroductionThe pandemic of COVID-19 continues to impact people worldwide, with more than 755 million confirmed cases and more than 6.8 million reported deaths. Although two types of treatment, antiviral and immunomodulatory therapy, have been approved to date, vaccination has been the best method to control the spread of the disease.ObjectiveTo explore factors associated with the intention to be vaccinated with the COVID-19 booster dose in Peru.Material and MethodsCross-sectional study, using virtual and physical surveys of adults with two or more doses of COVID-19 vaccine, where the dependent variable was the intention to be vaccinated (IBV) with the booster dose. We calculated prevalence ratios with 95% confidence intervals, using generalized linear models of the Poisson family with robust varying, determining associations between sociodemographic, clinical, and booster dose perception variables.ResultsData from 924 adults were analyzed. The IBV of the booster doses was 88.1%. A higher prevalence was associated with being male (aPR = 1.05; 95% CI [1.01–1.10]), having a good perception of efficacy and protective effect (PR = 3.69; 95% CI [2.57–5.30]) and belonging to the health sector (PR = 1.10; 95% CI [1.04–1.16]). There was greater acceptance of the recommendation of physicians and other health professionals (aPR = 1.40; 95% CI [1.27–1.55]).ConclusionsFactors associated with higher IBV with booster dose include male gender, health sciences, physician recommendation, and good perception of efficacy. creator: Rodrigo Camacho-Neciosup creator: Ericka N. Balcazar-Huaman creator: Margarita L. Alvarez-Vilchez creator: Janith P. De la Cruz-Galán creator: Yubely Gálvez-Guadalupe creator: Edwin D. Garcia-Muñoz creator: Greysi Cerron-Daga creator: Virgilio E. Failoc-Rojas creator: Mario J. Valladares-Garrido uri: https://doi.org/10.7717/peerj.16727 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Camacho-Neciosup et al. title: On the elephant trails: habitat suitability and connectivity for Asian elephants in eastern Indian landscape link: https://peerj.com/articles/16746 last-modified: 2024-03-29 description: Identifying suitable habitats and conserving corridors are crucial to the long-term conservation of large and conflict-prone animals. Being a flagship species, survival of Asian elephants is threatened by human-induced mortality and habitat modification. We aimed to assess the habitat suitability and connectivity of the Asian elephant Elephas maximus Linnaeus, 1758 habitat in the state of Odisha in eastern India. We followed the ensemble of spatial prediction models using species presence data and five environmental variables. We used least-cost path and circuit theory approaches to identify the spatial connectivity between core habitats for Asian elephants. The results revealed that normalized difference vegetation index (NDVI; variable importance 42%) and terrain ruggedness (19%) are the most influential variables for predicting habitat suitability of species within the study area. Our habitat suitability map estimated 14.6% of Odisha’s geographical area (c. 22,442 km2) as highly suitable and 13.3% (c. 20,464 km2) as moderate highly suitable. We identified 58 potential linkages to maintain the habitat connectivity across study area. Furthermore, we identified pinch points, bottlenecks, and high centrality links between core habitats. Our study offers management implications for long-term landscape conservation for Asian elephants in Odisha and highlights priority zones that can help maintain spatial links between elephant habitats. creator: Himanshu Shekhar Palei creator: Ashish Kumar Jangid creator: Dhamdhere Dhanraj Hanumant creator: Nimain Charan Palei creator: Arun Kumar Mishra uri: https://doi.org/10.7717/peerj.16746 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Palei et al. title: An androgen receptor-based signature to predict prognosis and identification of ORC1 as a therapeutical target for prostate adenocarcinoma link: https://peerj.com/articles/16850 last-modified: 2024-03-29 description: BackgroundAberrant activation of androgen receptor (AR) signaling plays a crucial role in the progression of prostate adenocarcinoma (PRAD) and contributes significantly to the development of enzalutamide resistance. In this study, we aimed to identify a novel AR-driven signature that can predict prognosis and endows potentially reveal novel therapeutic targets for PRAD.MethodsThe Seurat package was used to preprocess the single-cell RNA sequencing (scRNA-seq). Differentially expressed genes were visualized using limma and pheamap packages. LASSO and multi-variate Cox regression models were established using glmnet package. The package “Consensus Cluster Plus” was utilized to perform the consensus clustering analysis. The biological roles of origin recognition complex subunit 1 (ORC1) in PRAD were determined by gain- and loss-of-function studies in vitro and in vivo.ResultWe characterized the scRNA-seq data from GSE99795 and identified 10 AR-associated genes (ARGs). The ARGs model was trained and validated in internal and external cohorts. The ARGs were identified as an independent hazard factor in PRAD and correlated with clinical risk characteristics. In addition, the ARGs were found to be correlated with somatic tumor mutation burden (TMB) levels. Two groups that have distinct prognostic and molecular features were identified through consensus clustering analysis. ORC1 was identified as a critical target among these ARGs, and it ORC1 promoted proliferation and stem-like properties of PRAD cells. Chromatin immunoprecipitation (ChIP)-qPCR assay confirmed that AR could directly bind the promoter of ORC1. Activated AR/ORC1 axis contributed to enzalutamide resistance, and targeting ORC1 rendered PRAD cells more susceptible to enzalutamide.ConclusionsThis study defines an AR-driven signature that AR activates ORC1 expressions to promote PRAD progression and enzalutamide resistance, which may provide novel targets for PRAD treatment. creator: Linjin Li creator: Dake Chen creator: Xiang Chen creator: Jianlong Zhu creator: Wenshuo Bao creator: Chengpeng Li creator: Feilong Miao creator: Rui Feng uri: https://doi.org/10.7717/peerj.16850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: First record of Apanteles hemara (N.) on Leucinodes orbonalis Guenée and biodiversity of Hymenoptera parasitoids on Brinjal link: https://peerj.com/articles/16870 last-modified: 2024-03-29 description: The brinjal fruit and shoot borer (BFSB), Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), is a very detrimental pest that causes significant economic losses to brinjal crop worldwide. Infested brinjal fruits were collected from vegetable fields located at the ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India, during two consecutive seasons (2021–2022). The larvae of the pest were brought to the laboratory and reared under controlled conditions of 25 ± 0.5 °C and 70 ± 5% relative humidity, for the emergence of parasitoids. In addition, the survey of Hymenoptera parasitoids in brinjal was conducted utilizing a sweep net and yellow pan trap over the course of two seasons. The results reveal that five parasitoid species were emerged from L. orbonalis viz., Apanteles hemara Nixon, 1965, Bracon greeni Ashmead 1896 (Hymenoptera: Braconidae), Goryphus nursei (Cameron, 1907), Trathala flavoorbitalis (Cameron, 1907) (Hymenoptera: Ichneumonidae) and Spalangia gemina Boucek 1963 (Hymenoptera: Spalangiidae). Out of these, A. hemara and S. gemina were documented as new occurrences in Delhi. Additionally, A. hemara was recorded for the first time as a parasite on L. orbonalis. Trathala flavoorbitalis was observed during both seasons and exhibited higher parasitism reaching 15.55% and 18.46% in July and August 2022, respectively. However, the average parasitism (%) recorded by A. hemara, B. greeni, G. nursei, T. flavoorbitalis and S. gemina was 3.10%, 1.76%, 1.10%, 9.28% and 1.20% respectively. Furthermore, the findings showed a significant (p ≤ 0.01) strongly positive correlation between fruit infestation (%) by L. orbonalis and parasitism (%). The survey indicates the presence of a broad group (19 families and 60 species) of Hymenoptera parasitoids in the brinjal crop ecosystem in Delhi which could be valuable in biological control. In light of these results, this study revealed that A. hemara and other parasitoids identified in this study alongside T. flavoorbitalis would be ideal biocontrol agents within the integrated pest management (IPM) program of BFSB in Delhi. creator: Hager M. M. Saleh creator: Areej A. Al-Khalaf creator: Maha Abdullah Alwaili creator: Debjani Dey uri: https://doi.org/10.7717/peerj.16870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Saleh et al. title: Vocal repertoire of Microhyla nilphamariensis from Delhi and comparison with closely related M. ornata populations from the western coast of India and Sri Lanka link: https://peerj.com/articles/16903 last-modified: 2024-03-29 description: Advertisement calls in frogs have evolved to be species-specific signals of recognition and are therefore considered an essential component of integrative taxonomic approaches to identify species and delineate their distribution range. The species rich genus Microhyla is a particularly challenging group for species identification, discovery and conservation management due to the small size, conserved morphology and wide distribution of its members, necessitating the need for a thorough description of their vocalization. In this study, we provide quantitative description of the vocal behaviour of Microhyla nilphamariensis, a widely distributed south Asian species, from Delhi, India, based on call recordings of 18 individuals and assessment of 21 call properties. Based on the properties measured acrossed 360 calls, we find that a typical advertisement call of M. nilphamariensis lasts for 393.5 ±  57.5 ms, has 17 pulses on average and produce pulses at rate of 39 pulses/s. The overall call dominant frequency was found to be 2.8 KHz and the call spectrum consisted of two dominant frequency peaks centered at 1.6 KHz and 3.6 KHz, ranging between 1.5–4.1 KHz. Apart from its typical advertisement call, our study also reveals the presence of three ‘rare’ call types, previously unreported in this species. We describe variability in call properties and discuss their relation to body size and temperature. We found that overall dominant frequency 1 (spectral property) was found to be correlated with body size, while first pulse period (temporal property) was found to be correlated with temperature. Further, we compare the vocal repertoire of M. nilphamariensis with that of the congener Microhyla ornata from the western coast of India and Sri Lanka and also compare the call properties of these two populations of M. ornata to investigate intra-specific call variation. We find statistically significant differentiation in their acoustic repertoire in both cases. Based on 18 call properties (out of 20), individuals of each locality clearly segregate on PCA factor plane forming separate groups. Discriminant function analysis (DFA) using PCA factors shows 100% classification success with individuals of each locality getting classified to a discrete group. This confirms significant acoustic differentiation between these species as well as between geographically distant conspecifics. The data generated in this study will be useful for comparative bioacoustic analysis of Microhyla species and can be utilized to monitor populations and devise conservation management plan for threatened species in this group. creator: Megha Srigyan creator: Abdus Samad creator: Abhishek Singh creator: Jyotsna Karan creator: Abhishek Chandra creator: Pooja Gokhale Sinha creator: Vineeth Kumar creator: Sandeep Das creator: Ashish Thomas creator: Robin Suyesh uri: https://doi.org/10.7717/peerj.16903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Srigyan et al. title: Predicting central cervical lymph node metastasis in papillary thyroid microcarcinoma using deep learning link: https://peerj.com/articles/16952 last-modified: 2024-03-29 description: BackgroundThe aim of this study is to design a deep learning (DL) model to preoperatively predict the occurrence of central lymph node metastasis (CLNM) in patients with papillary thyroid microcarcinoma (PTMC).MethodsThis research collected preoperative ultrasound (US) images and clinical factors of 611 PTMC patients. The clinical factors were analyzed using multivariate regression. Then, a DL model based on US images and clinical factors was developed to preoperatively predict CLNM. The model’s efficacy was evaluated using the receiver operating characteristic (ROC) curve, along with accuracy, sensitivity, specificity, and the F1 score.ResultsThe multivariate analysis indicated an independent correlation factors including age ≥55 (OR = 0.309, p < 0.001), tumor diameter (OR = 2.551, p = 0.010), macrocalcifications (OR = 1.832, p = 0.002), and capsular invasion (OR = 1.977, p = 0.005). The suggested DL model utilized US images achieved an average area under the curve (AUC) of 0.65, slightly outperforming the model that employed traditional clinical factors (AUC = 0.64). Nevertheless, the model that incorporated both of them did not enhance prediction accuracy (AUC = 0.63).ConclusionsThe suggested approach offers a reference for the treatment and supervision of PTMC. Among three models used in this study, the deep model relied generally more on image modalities than the data modality of clinic records when making the predictions. creator: Yu Wang creator: Hai-Long Tan creator: Sai-Li Duan creator: Ning Li creator: Lei Ai creator: Shi Chang uri: https://doi.org/10.7717/peerj.16952 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al.