title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=141 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Examining ozone effects on the tropical C4 crop Sorghum bicolor link: https://peerj.com/articles/18844 last-modified: 2025-01-20 description: Ozone (O3), a major air pollutant, can negatively impact plant growth and yield. While O3 impacts have been widely documented in crops such as wheat and soybean, few studies have looked at the effects of O3 on sorghum, a C4 plant and the fifth most important cereal crop worldwide. We exposed grain sorghum (Sorghum bicolor cv. HAT150843) to a range of O3 concentrations (daytime mean O3 concentrations ranged between 20 and 97 ppb) in open-top chambers, and examined how whole plant and leaf morphological traits varied in response to O3 exposure. Results showed no significant impact of realistic O3 exposure on whole plant biomass and its partitioning in sorghum. These findings suggest that sorghum is generally resistant to O3 and should be considered as a favourable crop in O3 polluted regions, while acknowledging further research is needed to understand the mechanistic basis of O3 tolerance in sorghum. creator: Mst Nahid Farha creator: Flossie Brown creator: Lucas A. Cernusak creator: Stephen Sitch creator: Alexander W. Cheesman uri: https://doi.org/10.7717/peerj.18844 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Farha et al. title: Prevalence of nasopharyngeal bacteria during naturally occurring bovine respiratory disease in commercial stocker cattle link: https://peerj.com/articles/18858 last-modified: 2025-01-20 description: Bovine respiratory disease (BRD) is one of the most common economic and health challenges to the beef cattle industry. Prophylactic use of antimicrobial drugs can alter the microbial communities in the respiratory tract. Considering that the bovine upper respiratory tract microbiome has been associated with generalized health, understanding the microenvironment that influences this microbiome may provide insights into the pathogenesis of BRD. This study aimed to determine temporal variation in nasopharyngeal (NP) microbiome in naturally occurring BRD in newly received stocker calves. Mixed breed steers (n = 40) were purchased from an auction market and housed in a commercial stocker farm. Clinical signs were used to identify BRD affected animals, and calves were categorized based on the number of treatments (NumTrt) received (0, 1, 2). On days 0, 7, 14, and 21, NP samples were collected, and subsequent DNA were isolated and sequenced. After sequencing, 16S rRNA V4 gene was amplified and utilized for NP bacterial determination. The difference in relative abundance based on day and NumTrt was measured using repeated measures ANOVA (PROC GLIMMIX; SAS 9.4). Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Verrucomicrobiota were the top phyla and Mycoplasma, Histophilus, Geobacillus, Saccharococcus, Lactobacillus, and Pasteurella were the top genera. In healthy calves, the relative abundance of Mycoplasma differed by day (P = 0.01), whereas on day 7, calves had five times greater abundance compared to day 0 (d 0: 0.06 ± 0.05; d 7: 0.30 ± 0.05). No differences were observed in the alpha diversity matrices based on day or NumTrt (P > 0.05). Results of this study suggest compositional variations in NP microbial populations occur during disease conditions. creator: Afroza Akter creator: Hannah Teddleton creator: Marc Caldwell creator: Gina Pighetti creator: Phillip R. Myer creator: Madison T. Henniger creator: Liesel Schneider creator: Elizabeth Shepherd uri: https://doi.org/10.7717/peerj.18858 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Akter et al. title: Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data link: https://peerj.com/articles/18212 last-modified: 2025-01-17 description: The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama. creator: Erick Arias creator: Andrew J. Crawford creator: Andreas Hertz creator: Gabriela Parra Olea uri: https://doi.org/10.7717/peerj.18212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Arias et al. title: What ‘unexplored’ means: mapping regions with digitized natural history records to look for ‘biodiversity blindspots’ link: https://peerj.com/articles/18511 last-modified: 2025-01-17 description: We examined global records of accessible natural history voucher collections (with publicly available data and reliable locality data) for terrestrial and freshwater vascular plants, fungi, freshwater fishes, birds, mammals, and herpetofauna (amphibians and reptiles) and highlight areas of the world that would be considered undersampled and sometimes called ‘unexplored’ (i.e., have relatively low, or no evidence of, past sampling efforts) under typical Western-scientific descriptions. We also question what ‘unexplored’ may mean in these contexts and explain how replacing the term in favor of more nuanced phrasing (e.g., ‘biodiversity blindspots,’ which emphasizes the lack of publicly available data about specimens) can mitigate future misunderstandings of natural history science. We also highlight geographic regions where there are relatively few or no publicly available natural history records to raise awareness about habitats that might be worthy of future natural history research and conservation. A major finding is that many of the areas that appear ‘unexplored’ may be in countries whose collections are not digitized (i.e., they don’t have metadata such as GPS coordinates about their voucher specimens publicly available). We call for museums to prioritize digitizing those collections from these ‘biodiversity blindspots’ and for increased funding for museums to aid in these efforts. We also argue for increased scientific infrastructure so that more reference collections with vouchers can be kept in the countries of origin (particularly those countries lacking such infrastructure currently). creator: Laymon Ball creator: Sheila Rodríguez-Machado creator: Diego Paredes-Burneo creator: Samantha Rutledge creator: David A. Boyd creator: David Vander Pluym creator: Spenser Babb-Biernacki creator: Austin S. Chipps creator: Rafet Ç. Öztürk creator: Yahya Terzi creator: Prosanta Chakrabarty uri: https://doi.org/10.7717/peerj.18511 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ball et al. title: The pattern and burden of non-communicable diseases in armed conflict-exposed populations in Northeastern Nigeria link: https://peerj.com/articles/18520 last-modified: 2025-01-17 description: BackgroundThe risk of non-communicable diseases (NCDs) in conflict and post-conflict settings in Northeastern Nigeria has not been evaluated to date. As this region undergoes recovery, understanding the prevalence of NCDs, such as hypertension, diabetes, depression, and obesity, and the associated behavioral coping mechanisms, is crucial for developing tailored healthcare solutions. Therefore, this study aimed to assess the impact of conflict on the prevalence of NCDs in conflict-exposed areas in Northeastern Nigeria compared with non-conflict regions.MethodsThis study was an unmatched cross-sectional study. The participants were selected from inpatients and outpatients at general hospitals in Mubi (conflict-exposed) and Jada (non-conflict), which are local government areas in Adamawa, a state in Northeastern Nigeria. The study was conducted over four months, and data on various health indicators were collected. Multivariable binary logistic regression and complementary log regression were performed to investigate the effects of individual risk factors and regional settings on the prevalence of NCDs.FindingsA sample of 973 individuals from both locations was analyzed. The prevalence of hypertension, diabetes, abdominal obesity, and depression in the entire cohort was 22.92%, 5.04%, 44.19%, and 17.94%, respectively. The rates of hypertension and abdominal obesity in the conflict-exposed Mubi were lower, and the rate of depression was higher than those recorded in Jada. Females showed higher rates of hypertension, obesity, and depression than males. The residents of Mubi had lower odds of having abdominal obesity (adjusted odds ratio (aOR) = 0.18; 95% confidence interval (CI) [0.11–0.28]) but a higher risk of depression (incidence risk ratio (IRR) = 4.78; 95% CI [2.51–9.22]) than those in Jada. However, the participants affected by insurgency showed higher odds of having both abdominal obesity (aOR = 1.95; 95% CI [1.23–3.08]) and depression (IRR = 1.76; 95% CI [1.08–2.88]) than those who were not affected by the conflict.ConclusionsThe findings of this study underscore the urgent need for mental health support in conflict-affected regions and comprehensive healthcare strategies for the aging population. As adjustment of lifestyle factors is crucial for addressing NCDs, effective case management and food security are essential for reducing the risk of NCDs in conflict-exposed populations. creator: Roland I. Stephen creator: Jennifer A. Tyndall creator: Jamiu S. Olumoh creator: Malachy I. Okeke creator: Jacob A. Dunga creator: Tonde G. Elijah creator: Dillys M. Bello creator: Oyelola A. Adegboye creator: Jimmy A. Reyes uri: https://doi.org/10.7717/peerj.18520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Stephen et al. title: The relationship between steroid treatment and mortality in patients with COVID-19 followed up in an intensive care unit link: https://peerj.com/articles/18606 last-modified: 2025-01-17 description: AimOptimal treatment of the coronavirus disease (COVID-19) is still unclear. It has been reported that the use of different doses of corticosteroid treatments may reduce mortality. In our study, we aimed to find the effect of corticosteroid treatment dose on mortality of patients followed up in intensive care due to COVID-19.MethodsOur retrospective, descriptive and single-centre study included 102 patients diagnosed with COVID-19 who were followed up in intensive care unit, 28 of whom received pulse steroids and 74 of whom received high dose steroids. Laboratory values, duration of intensive care unit and mortality rates of the patients were evaluated.ResultsMortality was found to be statistically significantly lower in the group receiving pulse steroid compared to the group receiving high dose steroid. In multivariate logistic regression analysis, age and pulse steroid were found to be independent predictors of mortality. According to this analysis, each 10-year increase in age increased mortality by 4.8%, whereas pulse steroid decreased mortality by 79.4%.ConclusionIn our study, we found that mortality was statistically significantly lower in the group of patients receiving pulse steroids than in the group receiving high dose steroids. We found that the number of patients using pulse steroids was statistically significantly lower in the group with mortality. We found that age and pulse steroid independently determined the patients with mortality. creator: Huseyin Ali Ozturk creator: Fatih Necip Arici uri: https://doi.org/10.7717/peerj.18606 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ozturk and Arici title: Body size prediction in scorpions: a phylogenetic comparative examination of linear measurements of individual body parts link: https://peerj.com/articles/18621 last-modified: 2025-01-17 description: Body size has always been the focus of several ecological studies due to its undeniable influence on other life-history traits. The conventional representation of body size in arthropods typically relies on linear measures, such as total body length, or the length of specific body parts that can be used to represent body size. While these measures offer simplicity over more complicated alternatives (e.g., dry mass), technical problems persist for arthropods with complex body structures, as is the case for scorpions. In these animals, accurate measurements often require extensive handling, including the stretching of body parts. In light of the difficulties associated with directly measuring total length and carapace length in scorpions (two prevalent proxies for body size in the group), this study evaluates the ability of seven simple linear measurements in predicting length measures of boy size in scorpions under a phylogenetic framework. Predictive equations derived from phylogenetic mixed linear models fitted under Bayesian framework were implemented in custom R functions that can be applied for size prediction in a wide range of scorpions. Overall, accurate predictions of total length and carapace length could be achieved using any of the studied traits as single predictors. However, the most accurate predictions for total length were obtained using the length of metasomal segment V, while the best predictions for carapace length were achieved using telson length. The addition of a secondary predictor had low impact on the quality of the size predictions, indicating that increasing model complexity by incorporating additional predictors is not necessary to achieve accurate size estimates. Technical advantages and limitations associated with each linear measurement are discussed. In conclusion, this study broadens the repertoire of methods available for accurately estimating body size in scorpions, particularly in instances where body size information can only be obtained indirectly through allometric relationships. creator: Stênio Í. A. Foerster uri: https://doi.org/10.7717/peerj.18621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Foerster title: Optimizing soil health through activated acacia biochar under varying irrigation regimes and cultivars for sustainable wheat cultivation link: https://peerj.com/articles/18748 last-modified: 2025-01-17 description: Wheat, a staple food crop globally, faces the challenges of limited water resources and sustainable soil management practices. The pivotal elements of the current study include the integration of activated acacia biochar (AAB) in wheat cultivation under varying irrigation regimes (IR). A field trial was conducted in the Botanical Garden, University of the Punjab, Lahore during 2023–2024, designed as a split-split-plot arrangement with RCBD comprising three AAB levels (0T, 5T, and 10T, T = tons per hectare) three wheat cultivars (Dilkash-2020, Akbar-2019, and FSD-08) receiving five IR levels (100%, 80%, 70%, 60%, and 50% field capacity). Biochar amended soil showed improved BET surface area, pore size, and volume. Carbon recovery (45%) and carbon sequestration capacity (49%) of 10T-AAB amended soil were better than non-amended soil (0.43% and 0.13%, respectively). The 10T-AAB amendment significantly improved the soil’s microporosity and water retention capacity, increasing it by 1.1 and 2.2 times, respectively. Statistical analysis showed that a reduction in IR negatively affected plant growth and yield. The 10T-AAB levels significantly increased sugar contents (14%), relative water content (10–28%), membrane stability index (27–55%), and photosynthetic pigments (18–26%) of wheat leaves under deficit irrigation among all the cultivars. Maximum stress markers (catalase, proline, peroxidase, and superoxide dismutase) were observed from Akbar under 50% irrigation with 0T-AAB, and the least were observed from 50% irrigated Dilkash-2020 with 10T-AAB amended soil. Among cultivars, Dilkash-2020 was observed to be the best for maximum yield, followed by FSD-08 and Akbar-2019, respectively. When compared to other IR levels, 10T-AAB amended soil had the highest yield enhancement (12, 11, and 9.2 times for Dilkash-2020, FSD-08, and Akbar-2019, respectively). Hence, AAB enhanced wheat production by improving soil properties, drought resilience, and yield attributes. creator: Lubaba Komal creator: Summera Jahan creator: Atif Kamran creator: Abeer Hashem creator: Graciela Dolores Avila-Quezada creator: Elsayed Fathi Abd_Allah uri: https://doi.org/10.7717/peerj.18748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Komal et al. title: The role of fMRI in the mind decoding process in adults: a systematic review link: https://peerj.com/articles/18795 last-modified: 2025-01-17 description: BackgroundFunctional magnetic resonance imaging (fMRI) has revolutionized our understanding of brain activity by non-invasively detecting changes in blood oxygen levels. This review explores how fMRI is used to study mind-reading processes in adults.MethodologyA systematic search was conducted across Web of Science, PubMed, and Google Scholar. Studies were selected based on strict inclusion and exclusion criteria: peer-reviewed; published between 2000 and 2024 (in English); focused on adults; investigated mind-reading (mental state decoding, brain-computer interfaces) or related processes; and employed various mind-reading techniques (pattern classification, multivariate analysis, decoding algorithms).ResultsThis review highlights the critical role of fMRI in uncovering the neural mechanisms of mind-reading. Key brain regions involved include the superior temporal sulcus (STS), medial prefrontal cortex (mPFC), and temporoparietal junction (TPJ), all crucial for mentalizing (understanding others’ mental states).ConclusionsThis review emphasizes the importance of fMRI in advancing our knowledge of how the brain interprets and processes mental states. It offers valuable insights into the current state of mind-reading research in adults and paves the way for future exploration in this field. creator: Sahal Alotaibi creator: Maher Mohammed Alotaibi creator: Faisal Saleh Alghamdi creator: Mishaal Abdullah Alshehri creator: Khaled Majed Bamusa creator: Ziyad Faiz Almalki creator: Sultan Alamri creator: Ahmad Joman Alghamdi creator: Mohammed Alhazmi creator: Hamid Osman creator: Mayeen U. Khandaker uri: https://doi.org/10.7717/peerj.18795 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alotaibi et al. title: The effectiveness of arbuscular mycorrhizal fungal species (Funneliformis mosseae, Rhizophagus intraradices, and Claroideoglomus etunicatum) in the biocontrol of root and crown rot pathogens, Fusarium solani and Fusarium mixture in pepper link: https://peerj.com/articles/18438 last-modified: 2025-01-16 description: This study evaluated the effectiveness of arbuscular mycorrhizal fungi (AMF) species, including Funneliformis mosseae (FM), Rhizophagus intraradices (RI), Claroideoglomus etunicatum (CE), and a Mycorrhizal mix (MM) comprising these three species, on pepper plants (Capsicum annuum L.) inoculated with two isolates of Fusarium solani (48-F. solani and 18-F. solani) and two isolates of Fusarium mix (50-F. mixture and 147-F. mixture). Analysis of variance (ANOVA)-Tukey statistics revealed that the effects of AMF inoculations on morphological parameters, disease severity, root colonization, and total spore numbers in pathogen-infected plants varied significantly depending on the AMF species and pathogen group. AMF colonization significantly reduced disease severity, with disease inhibition (DI) reaching up to 58%, depending on the specific pathogen. However, there were a few instances where the application of AMF did not lead to a reduction in disease severity. Single AMF species were more effective in enhancing the growth of pathogen-treated host plants and suppressing disease compared to the mixed AMF. The mixed AMF was only more effective in balancing pathogen-induced decreases in plant nutrients (Copper (Cu), Magnesium (Mg), Zinc (Zn), and Phosphorus (P)). Among the compared mycorrhizae, C. etunicatum (CE) was the most effective in disease suppression due to its relatively more positive effects on plant root structure, increasing root fresh weight by up to 49% in the CE+pathogen plant group compared to the control group. Root colonization rates were generally higher in plants treated with both mycorrhiza and pathogens compared to plants treated with mycorrhiza alone. Overall, the curative effects of AMFs on plants following pathogen application varied concurrently with disease severity rates caused primarily by pathogens. AMFs demonstrated greater efficacy in combating 18-F. solani, which causes less severe plant disease. However, the effectiveness of AMFs was comparatively lower against 48-F. solani and 147-F. mix., which cause more severe plant disease. This indicates that the efficacy of AMFs varies depending on the specific strain of Fusarium solani, with better results observed against strains that cause less severe plant disease. creator: Ayşin Bilgili uri: https://doi.org/10.7717/peerj.18438 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bilgili