title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=91 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Advancements in understanding and treating psoriasis: a comprehensive review of pathophysiology, diagnosis, and therapeutic approaches link: https://peerj.com/articles/19325 last-modified: 2025-04-29 description: Psoriasis is a chronic autoimmune disease affecting millions worldwide. This condition is characterized by scaly, red patches of skin that can be painful, itchy, and disfiguring. This non-contagious illness forms plaques and accelerates the dermal cell’s life cycle. This review provides a comprehensive overview of the current knowledge on psoriasis, covering its definition, prevalence, causes, pathogenesis, clinical features, diagnosis, and treatment options. The psychosocial impact of psoriasis on patients and their coping mechanisms is also explored. Biologic agents, which target specific cytokines involved in psoriasis pathogenesis, have revolutionized psoriasis treatment and have significantly improved patient outcomes. However, effective and safe treatments for moderate to severe psoriasis are still needed. Future research directions include the development of biomarkers for predicting disease severity and treatment response, investigating new therapeutic targets like the microbiome and epigenetics, and leveraging advancements in technology and genomics for deeper insights into psoriasis pathogenesis and treatment. This study summarizes the key aspects of psoriasis, including its epidemiology, pathophysiology, clinical traits, disease burden, and management. However, further research is needed to improve treatment outcomes and enhance the quality of life for patients affected by this complex condition. creator: Sai Chakith M. R. creator: Sushma Pradeep creator: Manu Gangadhar creator: Chaithra Maheshwari N. creator: Shuaib Pasha creator: Shiva Prasad Kollur creator: Nagashree S. creator: Chandan Shivamallu creator: Satish Allur Mallanna uri: https://doi.org/10.7717/peerj.19325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chakith M R et al. title: Urban ecosystem quality assessment based on the improved remote sensing ecological index link: https://peerj.com/articles/19297 last-modified: 2025-04-29 description: The remote sensing ecological index (RSEI) is an important tool for assessing ecosystem quality. However, its land surface temperature (LST) component poses challenges due to complex calculations and mismatched spatial resolution with other indicators. This study proposed an improved remote sensing ecological index (DRSEI). By replacing the LST component in RSEI with the difference index (DI) (representing PM2.5 concentration), the new index better reflects air pollution’s impact on ecosystem quality. The results demonstrated that DRSEI outperformed the RSEI in assessing ecosystem quality in Chongqing’s urban area. It exhibited three advantages: stronger correlation with the ecological index (EI), standard deviation values closer to EI’s baseline, and lower root mean square error. The applicability of the DRSEI and RSEI varied across different regions: the DRSEI proved to be more suitable for highly urbanized areas, whereas the RSEI performed better in suburban regions. Further analysis revealed that the spatial variability of indicators influenced their loadings in principal component analysis, thereby affecting ecosystem quality assessment results. This study emphasizes the importance of considering the spatial distribution of indicators when constructing ecological indices. The findings suggest DRSEI could effectively assess ecosystem quality in urbanized areas. This approach provides new insights for urban ecological monitoring and environmental management. creator: Guolin Zhang creator: Honghai Kuang uri: https://doi.org/10.7717/peerj.19297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang and Kuang title: Spatial planning model for optimizing conservation priorities for local community utilization on Arefi Island in the Raja Ampat Marine Protected Area (MPA) Southwest Papua, Indonesia link: https://peerj.com/articles/19292 last-modified: 2025-04-29 description: This study investigates the application of remote sensing technologies to identify the biophysical characteristics of marine ecosystems for spatial planning, focusing on optimal conservation scenarios within the Raja Ampat Marine Protected Area (MPA) on Arefi Island, Southwest Papua, Indonesia. Indigenous communities manage this area. WorldView-3 satellite imagery, combined with an object-based image analysis (OBIA) approach, was used to classify and map coastal ecosystems. A Marine Reserve Design using the Spatially Explicit Annealing (Marxan) model was applied to delineate conservation areas and propose zoning strategies. Based on ecological values (EV), three scenarios were tested to prioritize conservation features while ensuring sustainable ecosystem use. Image analysis revealed that Arefi Island’s coastal ecosystems cover 64.78 hectares, consisting of seagrass beds (45.41%), coral reefs (36.35%), and mangroves (18.24%), with a kappa accuracy of 0.82. Results indicate that EV3 selects the highest number of planning units, ensuring broader conservation coverage, while EV1 selects the fewest. EV2 is the most budget-friendly option with the lowest cost, whereas EV3 is the most expensive. Ecological Scenario II provided a balanced approach, allocating larger areas for local community use while preserving conservation integrity. Moreover, sensitivity analysis confirmed that a conservation objective targeting 40% of the total area (EV II) is the most effective model for Arefi Island. The zoning breakdown under this scenario includes a core zone of 19.53 hectares, a utilization zone of 15.96 hectares, a sustainable fisheries zone of 15.67 hectares, and other zones covering 92.89 hectares. This study highlights the effectiveness of remote sensing and spatial planning tools, such as Marxan, in marine conservation within indigenously managed areas, emphasizing the importance of balancing conservation efforts with sustainable community use for future planning. creator: Mulyanto Darmawan creator: Debora Christi Simamora creator: Irmadi Nahib creator: Fadhlullah Ramadhani creator: Dewayany Sutrisno creator: Fahmi Amhar creator: Muhammad Ramdhan creator: Sitarani Safitri creator: Bayu Sutejo creator: Samsul Arifin creator: Syamsul Bahri Agus uri: https://doi.org/10.7717/peerj.19292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Darmawan et al. title: Comparative transcriptome analysis of emerging young and mature leaves of Bienertia sinuspersici, a single-cell C4 plant link: https://peerj.com/articles/19282 last-modified: 2025-04-29 description: BackgroundEfficient carbon capture by plants is crucial to meet the increasing demands for food, fiber, feed, and fuel worldwide. One potential strategy to improve the photosynthetic performance of plants is the conversion of C3-type crops to C4-type crops, enabling them to perform photosynthesis at higher temperatures and with less water. C4-type crops, such as corn, possess a distinct Kranz anatomy, where photosynthesis occurs in two distinct cell types. Remarkably, Bienertia sinuspersici is one of the four known land plant species that perform C4 photosynthesis within a single cell. This unique single-cell C4 (SCC4) anatomy is characterized by dimorphic chloroplasts and corresponding intracellular biochemistry. Because young, emergent Bienertia leaves first exhibit C3anatomy and then differentiate into the C4 anatomy as the leaves mature, Bienertia represents an excellent system to explore the basis for a C3 to C4 transition.MethodsTo gain insight into the genes and pathways associated with the C3 to C4 transition between emerging young and mature Bienertia sinuspersici leaves, a comparative transcriptome analysis was conducted in which global gene expression and gene ontologies were compared between the two stages.ResultsIn the emergent leaf, differentially expressed genes and enrichment of ontologies associated with the cell cycle and cytoskeletal dynamics were observed, while the mature leaf displayed enrichment of processes associated with photosynthesis and cellular energetics. Additionally, numerous transcription factors (TFs) associated with metabolic homeostasis, hormone and stress signaling, and developmental regulation were expressed throughout development, with unique TF expression profiles at each stage. These data expand our insights into the molecular basis of Binertia’s unique cellular compartmentalization, chloroplast dimorphism, and single-cell C4 biochemistry and provide information that will be useful in the ongoing efforts to transform C3-type crops into C4 type. creator: Richard M. Sharpe creator: Seanna Hewitt creator: Gerald Edwards creator: Amit Dhingra uri: https://doi.org/10.7717/peerj.19282 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sharpe et al. title: Extraordinarily corrupt or statistically commonplace? Reproducibility crises may stem from a lack of understanding of outcome probabilities link: https://peerj.com/articles/18972 last-modified: 2025-04-29 description: Reports of crises of reproducibility have abounded in the scientific and popular press, and are often attributed to questionable research practices, lack of rigor in protocols, or fraud. On the other hand, it is a known fact that—just like observations in a single biological experiment—outcomes of biological replicates will vary; nevertheless, that variability is rarely assessed formally. Here I argue that some instances of failure to replicate experiments are in fact failures to properly describe the structure of variance. I formalize a hierarchy of distributions that represent the system-level and experiment-level effects, and correctly account for the between-and within-experiment variances, respectively. I also show that this formulation is straightforward to implement and generalize through Bayesian hierarchical models, although it doesn’t preclude the use of Frequentist models. One of the main results of this approach is that a set of repetitions of an experiment, instead of being described by irreconcilable string of significant/nonsignificant results, are described and consolidated as a system-level distribution. As a corollary, stronger statements about a system can only be made by analyzing a number of replicates, so I argue that scientists should refrain from making them based on individual experiments. creator: Caetano Souto-Maior uri: https://doi.org/10.7717/peerj.18972 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Response of soil pH to biochar application in farmland across China: a meta-analysis link: https://peerj.com/articles/19400 last-modified: 2025-04-28 description: BackgroundBiochar, an alkaline material derived from agricultural and forestry waste, can ameliorate soil quality by adjusting soil pH. However, various types of biochar have distinct effects on soil pH due to diversity in feedstock type, pyrolysis temperature, and application rate.MethodTherefore, a meta-analysis was conducted with 598 paired comparisons obtained from 104 published studies (January 2010–July 2022) to comprehensively depict the response of soil pH to biochar in farmland systems across China.ResultThe results showed that adding biochar significantly increased the acid soils’ pH. Still, its effects on neutral and alkaline soils varied depending on the biochar’s pH and the soil’s initial pH. The pH of acid and neutral soils was raised by 5–10% straw biochar (600–800 °C and 400–600 °C, respectively). In alkaline soils, 5–10% other biochar (200–400 °C) raised pH, while 1–5% straw biochar (200–400 °C) reduced it. The findings underscore the importance of biochar pH and initial soil pH in the divergent consequences of biochar application in farmland systems, and both factors should be considered to choose the optimal biochar type for acid, neutral, and alkaline soils. creator: Jia Yao creator: Xueren Wang creator: Mei Hong creator: Hui Gao creator: Shixiang Zhao uri: https://doi.org/10.7717/peerj.19400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yao et al. title: Association between fetal sex and metabolic syndrome in women aged 40 years and older: the REACTION study link: https://peerj.com/articles/19380 last-modified: 2025-04-28 description: IntroductionThis study aimed to investigate whether fetal sex influences the risk of metabolic syndrome (MetS) in women in China.Materials and MethodsA cohort of 3,758 Chinese women, each having given birth to only one child and aged 40 years or older, was included in the study. Registry data on all pregnancies and miscarriages were collected for each participant. This retrospective cohort study aimed to determine whether fetal sex was associated with metabolic syndrome. MetS was defined as meeting at least three of the following five criteria: impaired insulin metabolism, reduced glucose tolerance, hypertension, dyslipidemia, and large waist circumference.ResultsAmong the 3,758 women aged 40 years and older in Luzhou City, 1,018 (27.1%) developed MetS. Mothers who had carried a male fetus had higher triglyceride (TG) and total cholesterol (TC) levels and a greater prevalence of diabetes than those who had carried a female fetus (P < 0.05). Although the incidence of MetS was higher in women who had carried a male fetus than in those who had carried a female fetus, the difference was not statistically significant (P > 0.05). Notably, MetS was significantly less prevalent in premenopausal women than in postmenopausal women, irrespective of fetal sex (P < 0.05). In the postmenopausal subgroup, the incidence of MetS was significantly higher in women who had carried a male fetus compared to those who had carried a female fetus (P < 0.05).ConclusionsOur study found no significant association between fetal sex and MetS in Chinese women aged 40 years and older. However, among postmenopausal women, the incidence of MetS was significantly higher in those who had carried a male fetus. Greater attention should be given to postmenopausal women with a history of carrying a male fetus, and early preventive measures should be implemented to reduce the risk of related chronic diseases. creator: Qian Xie creator: Ruoqing Li creator: Qin Wan creator: Nanwei Tong uri: https://doi.org/10.7717/peerj.19380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins link: https://peerj.com/articles/19370 last-modified: 2025-04-28 description: BackgroundGenes are continually formed and lost as a genome evolves. However, new genes may tend to appear during specific evolutionary epochs rather than others, or disappear together in a more recent organismal clade. Methods to identify gene origination might simply use the last common ancestor to contain an ortholog as the putative gene origination point, or use a heuristic threshold that allows for a certain amount of missing orthologs in the cohort of species examined. Here, to avoid such issues, an alternative approach based on the clustering of phylogenetic profiles is applied, and the results are examined for any evidence of epochal trends in gene origination, and associated trends in specific sequence traits or functional associations.MethodsA phylogenetic profile is simply an array indicating the presence or absence of a gene in a list of species. These profiles were compared and clustered to discern patterns in gene occurrences across >800 fungal species, centering the analysis on the budding yeast Saccharomyces cerevisiae.ResultsClear epochs of gene origination were observed linked to the last common ancestors of Saccharomycetaceae and Saccharomycetes, and also to Fungi and earlier ancestors. These trends are independent of the proteome and genome-assembly quality of the underlying data. Clusters of phylogenetic profiles demonstrated some significant functional associations, such as to cellular spore formation and chromosome segregation in genes originating in Saccharomycetaceae. The phylogenetic profile clustering analysis enabled detection of parameter-independent trends in intrinsic disorder, prion-like composition and gene uniqueness as a function of epochal gene age. For example: new proteins with prion-like domains have arisen at a similar rate for most of fungal evolution centred on S. cerevisiae; the most proteins with mild intrinsic disorder have appeared during the early Saccharomycetaceae epoch rather than more recently, and very recently formed genes are the least likely to be single-copy (i.e., ‘unique’ yeast proteins).ConclusionsFor individual proteins, the profile cluster data generated here are useful for investigating experimental hypotheses, since they provide evidence for functional linkages that have yet to be discerned. creator: Paul M. Harrison uri: https://doi.org/10.7717/peerj.19370 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Harrison title: Genetic variations of the SHFL gene associated with hepatitis C virus (HCV) infection in Yunnan population link: https://peerj.com/articles/19367 last-modified: 2025-04-28 description: Hepatitis C virus (HCV) infection led to hepatitis C, and even cirrhosis and hepatocellular carcinoma. The SHFL gene belonged to interferon (IFN)-stimulated genes (ISGs) and was identified to inhibit different viruses, including HCV. Whether genetic variations of the SHFL gene was associated with HCV infection was unclear. We collected 347 HCV patients and 448 general controls to genotype three SNPs in the SHFL gene, and analyzed the association between genotypes of SNPs and HCV infection, biochemical indices and disease progression of HCV patients. The results showed that genotype AT of rs77076061 (P = 0.033, OR = 1.515), AG of rs1979262 (P = 0.001, OR = 2.076), and CT of rs12611087 (P = 0.0002, OR = 1.844) were risk factors for HCV infection in Yunnan population. However, genotype TT of rs77076061 (78.1%), GG of rs1979262 (83.9%), and CC of rs12611087 (67.7%) showed statistically lower frequencies in HCV patients than that in controls. No association was found between genotypes of SNPs and biochemical indices or disease progression of patients. Functional prediction and structure alteration of RNA regions contained each single nucleotide polymorphism (SNP) suggested that these genetic variations might influence HCV infection by changing RNA structure. This study firstly investigated the association between genetic variants in the SHFL gene and HCV infection. creator: Mengren Cun creator: Xingcui Gao creator: Shuwei Dong creator: A-Mei Zhang uri: https://doi.org/10.7717/peerj.19367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cun et al. title: Construction of a novel five programmed cell death-related gene signature as a promising prognostic model for triple negative breast cancer link: https://peerj.com/articles/19359 last-modified: 2025-04-28 description: BackgroundTriple negative breast cancer (TNBC) is a more aggressive subtype of breast cancer that usually progresses rapidly, develops drug resistance, metastasis, and relapses, and remains a challenge for clinicians to treat. Programmed cell death (PCD), a conserved mechanism of cell suicide controlled by various pathways, contributed to carcinogenesis and cancer progression. Nevertheless, the prognostic significance of PCD-related genes in TNBC remains largely unclear, and more accurate prognostic models are urgently needed.MethodsGene expression profiles and clinical information of TNBC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis were used to establish the PCD-related gene signature. Kaplan-Meier plotter, receiver operating characteristic curves, and nomogram were applied to validate the prognostic value of the gene signature. Gene set enrichment analysis was carried out to investigate the pathways and molecular functions.ResultsFive PCD-related genes including SEPTIN3, SCARB1, CHML, SYNM, and COL5A3 were identified to establish the PCD-related risk score for TNBC patients. Patients stratified into high-risk or low-risk group showed significantly different survival outcome, immune infiltration, and drug susceptibility. Kaplan-Meier and receiver operating characteristic curves showed a good performance for survival prediction in different cohorts. Gene set enrichment analysis revealed that the five-gene signature was associated with tumor metabolism, cancer cell proliferation, invasion and metastasis, and tumor microenvironment. Nomogram including the five-gene signature was established.ConclusionA novel five PCD-related gene signature and nomogram could be used for prognostic prediction in TNBC. The present work might offer useful insights in digging sensitive and effective biomarkers for TNBC prognosis prediction and establishing accurate prognostic model in clinical management. creator: Quanfeng Shao creator: Hai-yan Gao creator: Zi-ying Wang creator: Yu-ling Qian creator: Wei-xian Chen uri: https://doi.org/10.7717/peerj.19359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shao et al.