title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=107 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: EcoNicheS: enhancing ecological niche modeling, niche overlap and connectivity analysis using the shiny dashboard and R package link: https://peerj.com/articles/19136 last-modified: 2025-03-28 description: EcoNicheS (https://github.com/armandosunny/EcoNicheS) is a comprehensive R package built on a Shiny dashboard that offers an intuitive and streamlined workflow for creating ecological niche models (ENMs) and landscape connectivity models. It incorporates tools for niche modeling, overlap analysis, and connectivity modeling, leveraging robust algorithms from the biomod2 suite. EcoNicheS is designed to simplify the technical complexities of ENMs, bridging the gap between advanced modeling techniques and user accessibility. The package offers an interactive interface for streamlined data input, model parameterization, and result visualization. Its comprehensive toolset includes occurrence data processing, pseudoabsence point generation, urbanization filters, and ecological connectivity modeling, distinguishing it from other platforms. EcoNicheS integrates innovative workflows with dynamic output visualizations while emphasizing reproducibility and comparability across statistical methods. Its practical applications span diverse research fields, including biogeography, epidemiology, evolutionary studies, climate change impacts, landscape connectivity, and biodiversity conservation. This versatility makes EcoNicheS a valuable resource for advancing in ecological and conservation science. creator: Armando Sunny creator: Clere Marmolejo creator: Rodrigo Vidal-López creator: Fredy A. Falconi-Briones creator: Ángela P. Cuervo-Robayo creator: René Bolom-Huet uri: https://doi.org/10.7717/peerj.19136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sunny et al. title: Is there hidden genetic variability in the species of Steindachneridion Garavello, 2005 (Siluriformes: Pimelodidae)? link: https://peerj.com/articles/18193 last-modified: 2025-03-28 description: BackgroundThe genus Steindachneridion, which includes large-sized freshwater pimelodid species, is endemic to the southeastern coastal drainages of South America, specifically the Paraná River and Uruguay River basins.MethodsIn this study, genetic analyses of mitochondrial DNA (mtDNA) D-loop were conducted on four species within this genus across their respective distributions: Steindachneridion scriptum (from the Tibagi and Uruguay rivers), S. melanodermatum (from the Iguaçu River), S. doceanum (from the Doce River), and S. parahybae (from the Paraíba do Sul River). Zungaro zungaro and Brachyplatystoma rousseauxii were employed as outgroups, and the topology was inferred using Bayesian Inference (BI) and maximum likelihood (ML) phylogenetic reconstruction techniques. Additionally, the sequences were analyzed to assess genetic diversity levels.ResultsIn contrast to the remaining species, which exhibited distinct species-specific clades, our data suggests that S. scriptum formed two sister clades, potentially representing distinct operational taxonomic units. Novel haplotypes were identified for each of the four species, further supporting the conclusions derived from the phylogenetic analysis. Overall, Steindachneridion species displayed high haplotype diversity paired with low nucleotide diversity, indicating a demographic expansion event after reduced effective population size. Nevertheless, genetic structure indexes were notably high. These findings suggest that the genetic diversity within these species may be underestimated, which has implications for both taxonomic classification and biological conservation strategies.ConclusionIn conclusion, the study of genetic diversity in four Steindachneridion species has revealed distinct molecular operational taxonomic units (MOTUs), which highlights the necessity for conservation efforts. The detection of new haplotypes and intraspecific variability emphasizes the urgency of implementing systematic conservation measures in the face of looming extinction threats. creator: Daniele Aparecida Matoso creator: Hallana Cristina Menezes da Silva creator: Augusto Luiz Ferreira Júnior creator: Fábio Porto-Foresti creator: Ricardo Utsunomia creator: Fernanda Dotti do Prado creator: Roberto Ferreira Artoni uri: https://doi.org/10.7717/peerj.18193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Matoso et al. title: Assessment of liquid media requirements for storing and evaluating respiratory cilia motility link: https://peerj.com/articles/19191 last-modified: 2025-03-27 description: Mucociliary clearance is critical for maintaining normal lung function. Respiratory cilia which drive mucociliary clearance are commonly studied by measuring cilia beat frequency (CBF). There is currently significant variation within the literature regarding what is a normal value for CBF, this may be due in part to the large variety of liquid media used to suspend, maintain, and image ciliated cells. This study aimed to conduct a thorough examination to assess how media choice influences respiratory cilia motility. To accomplish this, Adult C57/BL6 mouse trachea samples were incubated in eight commonly used liquid media including: Saline, Dulbecco’s Phosphate-Buffered Saline (DPBS), Hanks’ Balanced Salt Solution (HBSS), Medium 199 (M199), Dulbecco’s Modified Eagle’s Medium (DMEM), Roswell Park Memorial Institute Medium (RPMI), Minimum Essential Medium (MEM), and Leibovitz’s L-15 Medium (L-15); with or without 10% FBS supplementation. The effects of storage time (0–12 hours) and storage temperature (4 °C or room temperature) were also assessed. All media except saline were found to be equally effective in maintaining cilia function in airway samples that were freshly harvested and immediately imaged. Saline, however, significantly reduced the number of cells with motile cilia. A more complex pattern emerged when samples were stored before imaging. In saline, cilia function was significantly impaired after just one hour of storage. Samples stored in all other media showed strong maintenance of motile cilia function, with only minor changes. Notably, cilia function was better preserved with storage at 4 °C, while room temperature storage generally led to significant increases in CBF, especially in media containing FBS. Lastly, FBS supplementation was essential for maintaining cilia motility in L-15 media, as L-15 without FBS resulted in significant decreases in cilia motility following storage at either 4 °C or room temperature. In conclusion, saline should only be used if cilia are to be imaged immediately, as cilia stored in saline quickly lose motile function. All other commonly used media appear equally capable of maintaining motile cilia function for up to 12 hours when stored at 4 °C. Surprisingly, DPBS was just as effective as more expensive media in preserving ciliated samples. Storing ciliated tissue at room temperature generally leads to increased CBF, particularly in media containing FBS. Finally, L-15 media alone specifically requires the addition of 10% FBS to maintain cilia motility. These findings provide a valuable foundation for standardizing the handling, collection, and transport of ciliated samples for motile cilia assessment. creator: Richard Francis uri: https://doi.org/10.7717/peerj.19191 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Francis title: MicroRNA-99 family in cancer: molecular mechanisms for clinical applications link: https://peerj.com/articles/19188 last-modified: 2025-03-27 description: MicroRNAs (miRNAs) are a class of non-coding RNA sequences that regulate gene expression post-transcriptionally. The miR-99 family, which is highly evolutionarily conserved, comprises three homologs: miR-99a, miR-99b, and miR-100. Its members are under-expressed in most cancerous tissues, suggesting their cancer-repressing properties in multiple cancers; however, in some contexts, they also promote malignant lesion progression. MiR-99 family members target numerous genes involved in various tumor-related processes such as tumorigenesis, proliferation, cell-cycle regulation, apoptosis, invasion, and metastasis. We review the recent research on this family, summarize its implications in cancer, and explore its potential as a biomarker and cancer therapeutic target. This review contributes to the clinical translation of the miR-99 family members. creator: Yueyuan Wang creator: Dan Huang creator: Mingxi Li creator: Ming Yang uri: https://doi.org/10.7717/peerj.19188 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Assessment tools for attention deficits in patients with stroke: a scoping review across components and recovery phases link: https://peerj.com/articles/19163 last-modified: 2025-03-27 description: BackgroundAttention deficits are common in patients with stroke, making the assessment of attention functions crucial for improvement. A previous review reported on attention deficit assessments using specific components in patients with stroke. However, this study only included randomized controlled trials (RCTs) and did not encompass the attention assessments included in the observational study. Therefore, we reviewed and categorized the assessments used for attention deficits in patients with stroke according to specific attention components including RCTs and observational studies.MethodIn this study, we adhered to the scoping review guidelines. The population, concept, and context of this study were stroke; attention deficits, RCTs, observational studies, and assessments; and components (focused, selective, sustained, spatial, divided, visual, and auditory attention) and phase (acute, subacute, and chronic), respectively. Two reviewers independently screened articles at the title, abstract, and full-text levels based on inclusion and exclusion criteria using four databases and the Rayyan software. Furthermore, we identified the study design, sample size, duration since stroke onset, and assessment tools were identified.ResultsOut of 1,423 articles, we selected 35. The study designs included observational studies (80%) and RCTs (20%) and a total of 2,987 patients. The age range was 40.0 ± 7.7 to 83.6 ± 9.7 years. Twenty-four assessment tools were identified, mainly including the Trail Making Test Part A, Test of Everyday Attention, and other assessments (40%, 11.4%, and 62.8%, respectively). Regarding the five components of attention, there were 10 assessments were used each for sustained and selective attention (28.6%), and six each for alertness and divided attention (17.1%). Spatial attention was assessed using only one tool (2.9%).ConclusionsWe identified various assessment tools for analyzing attention deficit in patients with stroke and mapped them by component. This scoping review would be useful for selecting assessment methods for patients with stroke with attention deficits. creator: Katsuya Sakai creator: Takayuki Miyauchi creator: Junpei Tanabe uri: https://doi.org/10.7717/peerj.19163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sakai et al. title: Enhancing drought resilience in durum wheat: effect of root architecture and genotypic performance in semi-arid rainfed regions link: https://peerj.com/articles/19096 last-modified: 2025-03-27 description: BackgroundDeveloping drought-adapted genotypes is a primary goal for achieving resilient agriculture in the Mediterranean region. Durum wheat, a widely grown crop in the drylands of the Mediterranean basin, would significantly benefit from increased drought resistance.MethodsWe investigated a diverse set of 30 durum wheat varieties, including both local landraces and modern cultivars that have proven successful in Algeria. These varieties were evaluated in field trials over two consecutive years with contrasting rainfall patterns (one very dry, the other quite wet). Grain yield (PGY), yield components, and flag leaf characteristics such as area, canopy temperature, or rolling index were evaluated. Data from previous studies of root traits recorded on the same set of genotypes at seedling and adult growth stages were used to search for possible associations with grain yield and other agronomic traits measured in the current work.ResultsGenotypic variation was found for all traits measured under both conditions. Grain yield and aerial biomass were reduced by 76% (from 5.28 to 1.97 Mg ha−1) and 66% (from 15.94 to 3.80 Mg ha−1), respectively in the dry year, whereas the harvest index increased by 32%. The breeding history of the germplasm (cultivar vs. landrace) had a significant effect on the traits studied. Landraces showed higher biomass only under drought (4.27 vs. 3.63 Mg ha−1), whereas modern cultivars out-yielded landraces only under non-drought conditions (5.56 vs. 4.49 Mg ha−1). Promising associations were found between root and agronomic traits, especially with grain yield, indicating that a profuse (large root length) and shallow (wide root angle) root system was related to increased yield of modern cultivars only in the dry year, without penalizing yield in the wet year.ConclusionBreeding programs could improve grain yield under Algerian, semi-arid conditions, by making crosses between selected landraces with good growth potential under drought and modern cultivars, with high efficiency of biomass conversion into grain, and searching for lines with acceptable agronomic performance, which combine these desirable traits from landraces and modern cultivars, with the presence of shallow and profuse root systems. creator: Ridha Boudiar creator: Abdelhamid Mekhlouf creator: Yacine Bekkar creator: Meriem Yessaadi creator: Adel Bachir creator: Larbi Karkour creator: Ana Maria Casas creator: Ernesto Igartua uri: https://doi.org/10.7717/peerj.19096 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Boudiar et al. title: Bacterial community composition is an important predictor of surface soil fertility across different land use types: a case study in the Three Gorges Reservoir area link: https://peerj.com/articles/18959 last-modified: 2025-03-27 description: BackgroundSurface soil is a vital component of terrestrial ecosystems and is of great importance for primary productivity. In Zhangjiachong, a small watershed in Zigui County, central China, human activity and erosion cause extensive surface soil degradation. It is still unclear as to what extent human activity influences soil fertility and soil microorganisms in this area.MethodsSoil samples were collected, during spring and autumn, across a series of land use types with different levels of human activity. We assessed soil fertility and microbial communities using 16S rRNA gene sequencing and Biolog ECO-plates.ResultsThe results showed that higher levels of human activity were associated with lower soil fertility and microbial metabolic activity, in addition to higher bacterial diversity. Moreover, human activity had negative effects on the relative abundances of Proteobacteria and Acidobacteriota, which were the key drivers of surface soil fertility. Conversely, stronger human activity was associated with lower abundance of Actinobacteriota. This study suggested that human activity had a negative influence on surface soil fertility, and bacterial community composition could be a good predictor of surface soil fertility. creator: Lin Xu creator: Dandan Cheng creator: Liang Feng creator: Xuetian Lu creator: Sarah Ruffell creator: Hongmei Wang uri: https://doi.org/10.7717/peerj.18959 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu et al. title: Distribution, characteristics, and importance of particulate and mineral-associated organic carbon in China forest: a meta-analysis link: https://peerj.com/articles/19189 last-modified: 2025-03-26 description: BackgroundForest soil organic carbon (SOC) plays a critical role in the global carbon cycle, and increasing long-term forest carbon storage is essential for carbon sequestration. However, the distribution and drivers of mineral-associated (MAOC) and particulate organic carbon (POC) in forest soils at a continental scale remain poorly understood.MethodsUsing 540 data points from 59 studies related to POC, MAOC, and total SOC in China’s forests, we analyzed the distribution of POC and MAOC across forest type, soil depth and soil type, and further investigated their influencing factors.ResultsMAOC accounted for more than 63% of total SOC in forest soils. Both POC and MAOC increase with forest age, with mixed forests showing faster growth compared to monoculture forests. The MAOC/SOC ratio decreases with forest age but increases with soil depth, demonstrating the dominance of MAOC in deeper soils. Importantly, MAOC content continuously increases with SOC, and exhibits no upper limit, suggesting the potential for persistent soil carbon accumulation. MAOC is closely associated to microbial biomass carbon, and POC is mainly related with plant litter biomass.ConclusionMAOC and POC are influenced by different environmental factors and display distinct distribution patterns across forest types and soil depths. Thus, differentiating their respective responses to climate change is essential. The carbon sequestration potential of forests in China remains far from saturation. creator: Hao Cheng creator: Yangui Su creator: Zhengyi Huang creator: Sinuo Lin creator: Jingyi Yan creator: Guopeng Wu creator: Gang Huang uri: https://doi.org/10.7717/peerj.19189 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cheng et al. title: Effects of pH, temperature and hydraulic disturbance on nitrogen release from sediments in the Sunxi River, Three Gorges Reservoir Area, China link: https://peerj.com/articles/19161 last-modified: 2025-03-26 description: To clarify the influence of changes in the overlying water environment on internal nitrogen release from reservoir sediments, we collected surface sediments at a depth of approximately 10 cm from the Sunxi River in the tail area of the Three Gorges Reservoir area for simulation experiments. By using orthogonal simulation experiments in the laboratory, we studied the effects of water pH, temperature and hydraulic disturbance on nitrogen release in the sediment and established a quantitative linear relationship between the nitrogen release rate from the sediment and the environmental factors of the overlying water. The results indicated that the average concentrations of total nitrogen (TN) and total phosphorus (TP) in the sediment were 430 mg/kg and 200 mg/kg, respectively. The sediment TN concentration had a very significant positive correlation with the sediment organic matter content (P < 0.001). The sediment TN, NO3-N and NH4-N release intensities gradually increased with increasing incubation time, with maximum release rates of 29.24 mg/((m2⋅d), 23.11 mg/(m2⋅d) and 4.32 mg/((m2⋅d), respectively. Range analysis revealed that the significance of the effects of environmental factors on sediment TN and NH4-N release were ranked as follows: temperature > pH > disturbance, and that of NO3-N release was ranked as pH > temperature > disturbance. Temperature plays the most important role in the behavior of different forms of nitrogen release from sediments. The capacity and potential for nitrogen release from sediments offer crucial insights for assessing the risks posed to the overlying water and highlighting the importance of these factors in water quality management and prediction in the reservoir area. creator: Yihong Ning creator: Bin Gao creator: Haiyan Wang creator: Wenning Hou uri: https://doi.org/10.7717/peerj.19161 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ning et al. title: Intermittent horizontal mattress suture in proximal anastomosis for acute type A aortic dissection: a retrospective study link: https://peerj.com/articles/19159 last-modified: 2025-03-26 description: ObjectiveTo compare intermittent horizontal mattress suture (IHMS) technique and conventional sandwich technique for proximal anastomosis in acute type A aortic dissection (ATAAD) surgery.MethodsPatients who underwent ATAAD repair in our hospital between December 2020 and February 2023 were selected for inclusion in the study. The number of patients treated with the IHMS technique for aortic root repair were matched with those who received the conventional sandwich technique by the same surgeon. Perioperative and postoperative outcomes were analyzed and compared between the two groups.ResultsThis study compared 44 patients in each group. The IHMS group had a shorter operation time than the sandwich group (6.07 h vs. 7.02 h, p = 0.018). The proximal anastomosis time (35.50 min vs. 40.00 min, p = 0.013), and extracorporeal circulation assistance time (70.00 min vs. 92.00 min, p < 0.001) were significantly reduced compared to the sandwich group. IHMS patients sustained less intraoperative blood loss (900 .00 mL vs. 1,500.00 mL, p = 0.005) and blood transfusion need (0 U vs. 0.75 U, p = 0.028) than patients in the sandwich group. Multivariate analysis revealed the IHMS technique to be independently associated with shorter suture time, less blood loss, and higher spontaneous heartbeat recovery. The IHMS group also had shorter durations of mechanical ventilation use, delirium, and hospital stay than the sandwich technique group. No statistically significant differences were found in postoperative morbidities during the follow-up period.ConclusionThe IHMS technique for the aortic root anastomosis is simple, feasible and effective, particularly in ATAAD surgery with intimal rupture near the sinus-tubular junction to preserve the aortic valve during anastomosis of the ascending aorta. creator: Jiajun Li creator: Yongzhi Zhou creator: Yucong Zhang creator: Xuegui Chen creator: Jing Wang creator: Xiang Wei creator: Min Hu uri: https://doi.org/10.7717/peerj.19159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al.