title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=171 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Super Partition: fast, flexible, and interpretable large-scale data reduction in R link: https://peerj.com/articles/18580 last-modified: 2025-01-27 description: MotivationAs data sets increase in size and complexity with advancing technology, flexible and interpretable data reduction methods that quantify information preservation become increasingly important.ResultsSuper Partition is a large-scale approximation of the original Partition data reduction algorithm that allows the user to flexibly specify the minimum amount of information captured for each input feature. In an initial step, Genie, a fast, hierarchical clustering algorithm, forms a super-partition, thereby increasing the computational tractability by allowing Partition to be applied to the subsets. Applications to high dimensional data sets show scalability to hundreds of thousands of features with reasonable computation times.Availability and implementationSuper Partition is a new function within the partition R package, available on the CRAN repository (https://cran.r-project.org/web/packages/partition/index.html). creator: Katelyn J. Queen creator: Malcolm Barrett creator: Joshua Millstein uri: https://doi.org/10.7717/peerj.18580 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Queen et al. title: Beyond support: exploring the dynamic and static biomechanical changes induced by preventive ankle taping: a novel cross-sectional study link: https://peerj.com/articles/18472 last-modified: 2025-01-27 description: IntroductionIn sports, 80% of all ankle injuries are sprains of the external compartment. Functional bandages are usually used preventively, specially in individuals with a history of lateral ankle injuries. To this day, the actual benefits of such taping remain unknown as important modifications are introduced in the ankle biomechanics.ObjectiveThe aim of the present study is to describe the biomechanical processes underlying these effects, such as modification during stance times, balance, contact surface and maximum and average pressures in the rearfoot, forefoot and midfoot, using a sprain preventive taping for the external ankle compartment.MethodsAn observational, analytic, cross-sectional study was designed. Data from static and dynamic plantar pressures with a pressure platform and balance data assessed with the Y Balance Test (YBT) were analysed in 50 participants (age = 21.00 ± 2.34 years, weight = 71.11 ± 13.12 kg, height = 1.75 ± 00.9 m, BMI = 22.94 ± 2.50 kg/m2, foot size = 41.60 ± 3.00) with and without preventive functional taping for lateral ankle sprain (LAS).ResultsA statistically significant decrease in YBT was observed in the taped participants toward anterior (p = 0.001) and posterolateral (p = 0.005) motion. On the static measures at the pressure platform, an increase in peak pressure at the midfoot (p = 0.001), a decrease in the maximum pressure in the forefoot (p = 0.003) and a decrease in the contact surface in the rearfoot (p = 0.003) were recorded. Dynamic measures at the pressure platform analysis showed a statistically significant decrease in contact surface at the rearfoot (p = 0.001), an increase in mean pressure in both the midfoot (p = 0.044) and forefoot (p = 0.001) and a significant decrease in velocity in the forefoot (p = 0.003).ConclusionsIn conclusion, we observed that ankle taping led to increased peak pressures in the midfoot and decreased maximum pressures in the forefoot, indicating a shift in load distribution within the plantar surface. Simultaneously, a significant reduction in the velocity at the forefoot during dynamic tasks suggests that taping may alter natural gait dynamics, potentially affecting movement efficiency and stride characteristics. In addition, the application of ankle taping significantly altered balance, as evidenced by a decrease of YBT scores anterior and posterolateral directions. Prophylactic taping in patients with no prior history of LAS is not recommended. creator: María Bravo-Aguilar creator: Vanesa Abuín-Porras creator: María Blanco-Morales creator: Carlos Romero Morales creator: Jaime Almazán-Polo creator: Jorge Hugo Villafañe creator: Lorena Canosa-Carro uri: https://doi.org/10.7717/peerj.18472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bravo-Aguilar et al. title: The correlation of region-specific lifestyle and subjective perception of oral health with oral health-related quality of life among Tibetan early adolescents in Ganzi: a cross-sectional study link: https://peerj.com/articles/18842 last-modified: 2025-01-24 description: BackgroundThe oral health-related quality of life (OHRQoL) of Tibetan adolescents has been largely overlooked.AimThis cross-sectional study examined the association of region-specific lifestyle, subjective perception, and clinician conditions of oral health with Tibetan adolescents’ OHRQoL in Ganzi, Sichuan.MethodsThe OHRQoL was measured using standardized Child Oral Impacts on Daily Performances (sC-OIDP) scores. Binary logistic regression was used to explore the association between region-specific lifestyle, subjective perception of oral health, clinician oral health conditions (gingival bleeding on probing (BOP), dental calculus (DC), and decayed, missing, and filled teeth (DMFT)), and OHRQoL.ResultsIn total, 485 Tibetan adolescents were included. In relation to region-specific lifestyle, the factors associated with poorer OHRQoL were residence altitude of 3,300 m (compared to 1,400 m), buttered tea consumption by adolescents or mother, and being a boarding student. Regarding the subjective perception of oral health, adolescents that rated bad or very bad oral health or self-reported dental pain had poorer OHRQoL. Interestingly, clinician oral health conditions were not related to OHRQoL.ConclusionsThis study underscores the relationship between region-specific lifestyle, subjective oral health perceptions, and OHRQoL among Tibetan adolescents. Addressing these factors through tailored health initiatives can play a pivotal role in improving oral health outcomes and overall quality of life in remote regions like Ganzi. Future research should focus on longitudinal studies to better understand the causality and long-term impact of targeted interventions. creator: Shaoying Duan creator: Renjie Tang creator: Chenchen Zhang creator: Qianqian Su creator: Huiyu Yang creator: He Cai creator: Tao Hu uri: https://doi.org/10.7717/peerj.18842 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Duan et al. title: Single-cell analysis of Mycobacterium tuberculosis with diverse drug resistance using surface-enhanced Raman spectroscopy (SERS) link: https://peerj.com/articles/18830 last-modified: 2025-01-24 description: In this work, we investigated individual bacteria M. tuberculosis belonging to strains of the Beijing family with different drug sensitivity (sensitive, multi and extensive drug-resistant) by surface-enhanced Raman spectroscopy (SERS) in the fingerprint region. The latter is focused on the spectral bands, which correspond to a set of glutathione bands and DNA methylation patterns revealed due to 5-methylcytosine spectral biomarkers. It is shown that these spectral features can be correlated with drug sensitivity and DNA methylation. Thus, since this kind of diagnostics is fast and operates with individual cells, it can be considered a promising tool, which significantly shortens the time required for a strain’s type identification necessary to prescribe adequate therapy. creator: Andrey Zyubin creator: Anastasia Lavrova creator: Marine Dogonadze creator: Evgenii Borisov creator: Eugene B. Postnikov uri: https://doi.org/10.7717/peerj.18830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zyubin et al. title: A plant-derived biostimulant Aminolom Enzimatico® application stimulates chlorophyll content, electrolyte leakage, stomata density and root yield of radishes under salinity stress link: https://peerj.com/articles/18804 last-modified: 2025-01-24 description: Biostimulants stimulate plant growth and tolerance to salinity stress, which creates unfavorable conditions for plant growth from emergence to harvest; however, little is known about their roles in triggering salt tolerance. Therefore, the study aimed to determine how applying a foliar plant-derived biostimulant (Aminolom Enzimatico® 24%) affects the growth (leaf area, biomass weight, root diameter, root fresh weight, and water-soluble dry matter), physiology (chlorophyll content, electrolyte leakage, cell membrane stability, and relative water content), and stomata of the lower and upper parts of leaves in radish plants (Raphanus sativus L.) under salinity stress. Radish plantlets at 7 d old were irrigated with saline water (i.e., 50, 100, 150, and 200 mM NaCl), and the biostimulant was sprayed twice at 7 d intervals. Under salinity stress, increased water-soluble dry matter content was detected, along with reduced plant biomass weight, root fresh weight, and root diameter. Meanwhile, the foliar biostimulant increased the mean root fresh weight, biomass fresh weight, and leaf area by 12%, 13.6%, and 24% compared to the control, respectively. Increasing NaCl dramatically reduced leaf area and relative water content, whereas chlorophyll content and stomata densities on both sides of the leaves improved. By regulating physiological parameters and thereby promoting root and leaf growth, the biostimulant application improved the radish plants’ tolerance to salinity stress up to 100 mM NaCl. Spraying the biostimulant can also boost plant growth, root yield, and radish quality under moderate salinity stress. creator: Gamze Kaya uri: https://doi.org/10.7717/peerj.18804 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kaya title: Chitosan-DNA nanoparticles: synthesis and optimization for long-term storage and effective delivery link: https://peerj.com/articles/18750 last-modified: 2025-01-24 description: BackgroundChitosan nanoparticles (CsNPs) are an effective and inexpensive approach for DNA delivery into live cells. However, most CsNP synthesis protocols are not optimized to allow long-term storage of CsNPs without loss of function. Here, we describe a protocol for CsNP synthesis, lyophilization, and sonication, to store CsNPs and maintain transfection efficiency.MethodsThe size and zeta potential of CsNPs were analyzed by dynamic light scattering (DLS) and the morphology of CsNPs was assessed by transmission electron microscopy (TEM). HEK293 cells were transfected with CsNPs, and expression of H2B-CMV-mScarlet plasmid was assessed by flow cytometry. Confocal microscopy was used to visualize post-transfection gene expression. Time, volume, and effect of sonication were tested to optimize the lyophilization process.ResultsDLS and TEM analysis indicated amine groups on chitosan to phosphate groups on DNA (N:P) ratios yielded smaller CsNPs sizes. Transfection efficiency, measured by FACS and confocal microscopy, peaked at N:P ratios of 2:1 and 3:1 for both fresh and lyophilized CsNPs. Chitosan/DNA complexes remained stable in solution for at least 72 h at a ratio ≥2:1 as assessed by agarose gel electrophoresis. A lower surface charge with lower N:P ratios was indicated by zeta potential measurements. Lyophilized CsNPs lost 50% transfection efficiency compared to those freshly made. In contrast, sonication of lyophilized CsNPs restored their transfection efficiency to the level of fresh CsNPs. Sonicated CsNPs maintained spherical morphology, while unsonicated CsNPs showed aggregates. Cytotoxicity assays revealed high cell viability (>90%) after CsNPs transfection for a ratio of 2:1 or 3:1.ConclusionThis optimized CsNPs synthesis protocol opens the possibility of long-term storage for CsNPs, which would provide broader applications of this technology. creator: Aigul Raimbekova creator: Ulpan Kart creator: Akbayan Yerishova creator: Timur Elebessov creator: Sergey Yegorov creator: Tri Thanh Pham creator: Gonzalo Hortelano uri: https://doi.org/10.7717/peerj.18750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Raimbekova et al. title: Geochemical signatures and nanomechanical properties of echinoid tests from nearshore habitats of Florida: environmental and physiological controls on echinoid biomineralization link: https://peerj.com/articles/18688 last-modified: 2025-01-24 description: The mechanisms that regulate minor and trace element biomineralization in the echinoid skeleton can be primarily controlled biologically (i.e., by the organism and its vital effects) or by extrinsic environmental factors. Assessing the relative role of those controls is essential for understanding echinoid biomineralization, taphonomy, diagenesis, and their potential as geochemical archives. In this study, we (1) contrast geochemical signatures of specimens collected across multiple taxa and environmental settings to assess in situ the effects of environmental and physiological factors on skeletal biomineralogy; and (2) analyze the nanomechanical properties of the echinoid skeleton to assess potential linkages between magnesium/calcium (Mg/Ca) ratios and skeletal nanohardness. Live specimens of sand dollars and sea biscuits (Mellita tenuis, Encope spp., Leodia sexiesperforata, and Clypeaster subdepressus) were collected from three different salinity regimes: (1) a coastal region of Cedar Key influenced by freshwater input from Suwannee River, with low and fluctuating salinity; (2) St. James Bay with less fluctuating, higher salinity; and (3) Florida Keys with stable, fully marine salinity conditions. No clear relationship was found between the bulk skeletal barium/calcium (Ba/Ca), zinc/calcium (Zn/Ca), sodium/calcium (Na/Ca), cadmium/calcium (Cd/Ca), copper/calcium (Cu/Ca), phosphorous/calcium (P/Ca), lead/calcium (Pb/Ca), boron/calcium (B/Ca), manganese/calcium (Mn/Ca) ratios pooled across all taxa. In contrast, bulk Mg/Ca, strontium/calcium (Sr/Ca), sulfur/calcium (S/Ca) and lithium/calcium (Li/Ca) ratios exhibited notable differences between the three regions, indicating that distribution of these elements can be at least partly influenced by environmental factors such as salinity. However, such patterns were highly variable across taxa and regions, indicating that both environmental and physiological factors influenced geochemical signatures to varying degrees, depending on the species and environmental setting. In addition, regardless of species identity, different types of stereom within single tests were characterized by distinct skeletal Mg/Ca ratios and nanohardness. The inner galleried and coarse labyrinthic stereom typically exhibited a lower Mg/Ca ratio and nanohardness than the outer imperforate stereom layer that locally forms tubercles. Such heterogeneity in Mg distribution within single specimens cannot be ascribed solely to environmental changes, indicating that these echinoids actively regulate their intraskeletal Mg content: the higher magnesium concentration at the tubercles relative to that of the underlying stereom may be interpreted as a strategy for enhancing their mechanical strength to withstand surface friction and wear. The results suggest that the trace element composition of echinoid tests is a complex outcome of environmental and physiological factors. creator: Przemysław Gorzelak creator: Luis Torres Jr. creator: Dorota Kołbuk creator: Tobias B. Grun creator: Michał Kowalewski uri: https://doi.org/10.7717/peerj.18688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gorzelak et al. title: Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community—Leishan County, Guizhou Province, Southwest China link: https://peerj.com/articles/18683 last-modified: 2025-01-24 description: BackgroundCamellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region’s economic sustainability.MethodsThis study selected tea plantations with different tea planting durations of 3–5 years (Y5), 12–16 years (Y15), 18–22 years (Y20), 40–42 years (Y40), and 48–50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0–20 cm and 20–40 cm soil layers, respectively.ResultsCompared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota, Chloroflexi, Proteobacteria, and Actinobacteriota in the tea garden. FAPROTAX analysis highlighted aerobic and anaerobic chemoheterotrophy, cellulolysis, and nitrogen fixation as key bacterial functions. POC and MBC significantly influenced bacterial community structure. In conclusion, tea plantation soil exhibited the highest organic carbon content at 40 years of tea planting, indicating strong carbon accumulation capacity. However, soil acidification in the tea plantation may affect changes in organic carbon and bacterial community. Therefore, in the tea planting process, it is necessary to improve the management system of tea plantations to ensure the maintenance of a good ecological environment in the tea plantation soil, thus achieving sustainable development of the tea industry in the region. creator: Yingge Shu creator: Shan Xie creator: Hong Fan creator: Chun Duan creator: Yuansheng Liu creator: Zuyong Chen uri: https://doi.org/10.7717/peerj.18683 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shu et al. title: The influence of physical activity levels on lactate production during squat training using a functional electromechanical dynamometer link: https://peerj.com/articles/18215 last-modified: 2025-01-24 description: ObjectiveThis study aimed to determine the association between changes in lactate production and levels of physical activity in a group of healthy young adults in response to two squat training protocols.Material and methodsTwenty-nine students majoring in Sports Science willingly participated in this study. Participants visited the lab four times within a two-week period, ensuring at least 48 h between visits. In each session, they completed three sets of 12 repetitions at 75% 1RM and three sets of 30 repetitions at 50% of maximum strength, with the order of protocols being randomized.ResultsIn the regression analysis, there was a significant positive association between lactate delta changes immediately post-squat at 50% of maximum strength at session 2 with the variable “sex: women” (β: 3.02, 95% CI [−0.18–0.30], p = 0.047) and BMI (kg/m2). Age exhibited a positive association (β: 0.19, 95% CI [0.02–0.36], p = 0.032) with lactate delta changes immediately post-squat at 75% of maximum strength at session 2. There was also a significant inverse association between lactate delta changes at 10 min post-squat test exercise at 75% of maximum strength at session 1 and 2, and vigorous physical activity (−0.01, 95% CI [−0.02–0.00], p = 0.046).ConclusionIn summary, this study provides valuable insights into the association between lactate production and physical activity levels in young, healthy adults undergoing different squat training protocols. These findings suggest that intense physical activity may be associated with lower lactate production, indicating greater metabolic efficiency. In addition, sex differences in metabolic responses were observed, emphasizing the importance of personalized approaches in program design. creator: Indya del-Cuerpo creator: Daniel Jerez-Mayorga creator: Luis Javier Chirosa-Ríos creator: Felipe Caamaño-Navarrete creator: Pedro Delgado-Floody uri: https://doi.org/10.7717/peerj.18215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 del-Cuerpo et al. title: Analysing head and trunk motion in the judo osoto-gari technique: relationship to sweeping-leg velocity link: https://peerj.com/articles/18862 last-modified: 2025-01-23 description: BackgroundOsoto-gari is a leg throw technique that primarily relies on the hip extension to initiate the sweeping motion of the leg. A high sweep contact velocity is a crucial factor in efficiently executing this technique. While some literature emphasises whole-body coordination in the leg-sweeping action, the roles of trunk and head motion remain unclear. This study investigates head and trunk movements (including the pelvic and upper torso) contributing to higher leg-sweep velocities when executing the judo osoto-gari.MethodsKinematic data were collected from 17 male black-belt judokas using a motion capture system (250 Hz). Pearson product-moment correlation and stepwise linear regression were used to identify kinematic variables linked to the sweeping-leg velocity at sweep contact (SC).ResultsSix out of twenty-four variables correlated with sweeping-leg velocity at SC. A stepwise regression model (adjusted R2 = 0.53, p = 0.009) predicted sweeping-leg velocity based on head-tilt angle at maximum sweeping-leg height (MSH) and SC, head-tilt angular velocity at MSH, and trunk-tilt angular velocity at MSH.ConclusionsThe findings of this study indicate that (1) increasing the forward angle of the head aids the visual system in rapidly processing spatial information about the target position, thus facilitating the execution of the leg sweep, and (2) a greater forward-tilt rotation of the head, which leads to rapid trunk rotation, is conducive to enhancing sweeping-leg velocity. creator: Lingjun Liu creator: Tatsuya Deguchi creator: Mitsuhisa Shiokawa creator: Kazuto Hamaguchi creator: Masahiro Shinya uri: https://doi.org/10.7717/peerj.18862 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al.