World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens
Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.
Ion et al. (2024) World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens. PeerJ 12:e18229 https://doi.org/10.7717/peerj.18229
The impact of scabies in tent cities in Kahramanmaraş after the Turkish earthquakes: oral pharmacologic treatment efficacy
Background Our study was conducted to determine the impact of scabies in people living in collective living areas such as tent cities and container cities after the February 6 Kahramanmaraş earthquakes and to show the effectiveness of oral ivermectin treatment on scabies cases because topical treatments could not be used in this period when access to water was limited. Methods Among 233 patients diagnosed and treated with scabies in tent and container cities, 192 patients who met the criteria were included in the study. Descriptive statistics were given as number (n), percentage (%), mean, median, standard deviation (SD). In the comparison of categorical data, the chi-square test was applied; in the comparison of numerical data ANOVA analyses was applied. Results A total of 192 scabies patients (82.4%), 47.9% (N:92) of whom were women, were included in the study. The frequency of scabies in the total population in tent cities and container cities was found to be at least 0.54%. The most common symptoms were pruritis (99.0%) and rash (97.9%). The most common sites of lesion involvement were the umbilicus (87.0.%), forearm (75.0%), and back (70.3%). After the first dose of ivermectin, 159 (82.8%) patients showed complete recovery, while 30 (15.6%) patients showed partial recovery. 3 (1.6%) patients showed no improvement. After the second dose of ivermectin, 173 (90.1%) patients showed complete recovery. There were two (1.0%) patients who did not show improvement after two doses. Due to the deterioration of urban infrastructure after devastating earthquakes, the irregularity of mass living areas, the lack of hygiene conditions, and the difficulty of accessing clean, usable water, oral ivermectin may be the first choice for treatment in terms of ease of use and effectiveness.
Beyoğlu et al. (2024) The impact of scabies in tent cities in Kahramanmaraş after the Turkish earthquakes: oral pharmacologic treatment efficacy. PeerJ 12:e18242 https://doi.org/10.7717/peerj.18242
Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities
Background Root plays an important role in the growth and development of fruit trees; however, the molecular mechanisms behind the differences among rootstock varie-ties remain unclear. Methods This study examined the effects of different rootstocks on root structure and the endogenous hormone content of 1-year old apple seedlings in combinations of Tianhong 2 (T2)/Malus robusta (HT), T2/G935, and T2/Jizhen 2 (J2). Results The results showed that the T2/HT treatment had greater root length, surface area, volume, average diameter, tips and forks, followed by G935 and J2. In T2/HT leaves and roots, the indole-3-acetic acid (IAA) and gibberellins (GA3) levels were highest, and the abscisic acid (ABA) levels were the lowest. A root transcriptome analysis detected 10,064, 10,511, and 8,719 differentially expressed genes in T2/HT vs. T2/G935, T2/HT vs. T2/J2, and T2/J2 vs. T2/G935, respectively. The analysis of Gene Ontology (GO) terms indicated a significant enrichment in biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that plant hormone signaling, MAPK signaling pathway–plant, and plant–pathogen interaction played important roles in differences in the rooting ability of different rootstocks. In addition, some key differential genes were associated with root growth and development and were involved in these metabolic pathways. This study is important for enriching theoretical studies of fruit tree roots.
Li et al. (2024) Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities. PeerJ 12:e18244 https://doi.org/10.7717/peerj.18244
Association of serum Metrnl levels and high-density lipoprotein cholesterol in patients with type 2 diabetes mellitus: a cross-sectional study
Purpose Meteorin-like (Metrnl) is a novel adipokine which is highly expressed in adipose tissue and has a beneficial effect on glucose and lipid metabolism. High density lipoprotein cholesterol (HDL-C) is well recognized to be inversely associated with cardiovascular events. However, the relationship between serum Metrnl levels and HDL-C in the type 2 diabetes mellitus (T2DM) remains unclear. Therefore, the present study aimed to evaluate the association of serum Metrnl with HDL-C levels in T2DM. Materials and Methods Eighty participants with T2DM were included in this cross-sectional study. They were divided into two groups according to HDL-C levels: Group1 (lower HDL-C group): HDL-C < 1.04 mmol/L; Group2 (higher HDL-C group): HDL-C ≥ 1.04 mmol/L. Serum Metrnl levels were measured by enzyme-linked immunosorbent assay (ELISA). Results As compared with lower HDL-C levels groups, serum Metrnl levels were significantly higher in the group with higher HDL-C. Binary logistic regression analysis showed serum Metrnl levels were positively associated with HDL-C group after adjustment with sex, age, body mass index (BMI), mean arterial pressure (MAP), fasting blood glucose (FPG), triglyceride (TG). Furthermore, serum Metrnl levels were inversely correlated with insulin resistance index (HOMA-IR). HDL-C levels were lowest in the group with the lowest Metrnl levels group and remained positively associated with Metrnl after adjustment for sex, age, BMI, TG, and HOMA-IR by using multivariate logistic regression analysis. Conclusion Serum Metrnl levels were positively associated with HDL-C levels in patients with T2DM.This suggests that increasing serum Metrnl levels maybe a candidate for improving lipid metabolism and preventing cardiovascular events in T2DM. Registry and the Registration No. of the Study/Trial The study was registered in the Chinese clinical trial registry (ChiCTR- 2100047148).
Zhou et al. (2024) Association of serum Metrnl levels and high-density lipoprotein cholesterol in patients with type 2 diabetes mellitus: a cross-sectional study. PeerJ 12:e18264 https://doi.org/10.7717/peerj.18264
Ultra-rapid detection of nuclear protein of severe fever with thrombocytopenia syndrome virus by colloidal gold immunochromatography assay
In 2009, severe fever with thrombocytopenia syndrome virus (SFTSV), also known as the Dabie bandavirus (DBV), was first discovered in Henan, China. It is a tick-borne zoonotic virus with a fatality rate ranging from 6% to 30%. Currently, we lack safe and effective vaccines or antiviral drugs to treat SFTSV infection. Therefore, the development of a specific, sensitive, and cost-effective detection method is crucial. Using inactivated SFTSV and recombinant SFTSV nucleocapsid protein (SFTSV-NP), we repeatedly immunized mice with different adjuvants and obtained two monoclonal antibodies against SFTSV-NP, which were used to develop a colloidal gold immunochromatographic assay (ICA) rapid test kit for SFTSV. Compared with nucleic acid testing (gold standard), the ICA test strips are 97.67% accurate in testing clinical serum samples (36 cases of clinical serum samples and seven cases of whole blood samples). The test kit was 100% accurate in detecting different SFTSV strains. No false-positive results were generated when detecting other arboviruses. Therefore, our developed SFTSV test kit conveniently, rapidly, and effectively detects SFTSV.
Huang et al. (2024) Ultra-rapid detection of nuclear protein of severe fever with thrombocytopenia syndrome virus by colloidal gold immunochromatography assay. PeerJ 12:e18275 https://doi.org/10.7717/peerj.18275
A small venomous reptile from the Late Triassic (Norian) of the southwestern United States
Reptile feeding strategies encompass a wide variety of diets and accompanying diversity in methods for subduing prey. One such strategy, the use of venom for prey capture, is found in living reptile clades like helodermatid (beaded) lizards and some groups of snakes, and venom secreting glands are also present in some monitor lizards and iguanians. The fossil record of some of these groups shows strong evidence for venom use, and this feeding strategy also has been hypothesized for a variety of extinct reptiles (e.g., archosauromorphs, anguimorphs, and a sphenodontian). However, evidence of systems for venom delivery in extinct groups and its evolutionary origins has been scarce, especially when based on more than isolated teeth. Here, we describe a potentially venomous new reptile, Microzemiotes sonselaensis gen. et sp. nov., from a partial left dentary recovered from the Sonsela Member of the Chinle Formation (middle Norian, Upper Triassic) of northeastern Arizona, U.S.A. The three dentary teeth have apices that are distally reclined relative to their bases and the tip of the posteriormost tooth curves mesially. The teeth show subthecodont implantation and are interspaced by empty sockets that terminate above the Meckelian canal, which is dorsoventrally expanded posteriorly. Replacement tooth sockets are positioned distolingually to the active teeth as in varanid-like replacement. We identify this new specimen as a diapsid reptile based on its monocuspid teeth that lack carinae and serrations. A more exclusive phylogenetic position within Diapsida is not well supported and remains uncertain. Several features of this new taxon, such as the presence of an intramandibular septum, are shared with some anguimorph squamates; however, these likely evolved independently. The teeth of the new taxon are distinctively marked by external grooves that occur on the entire length of the crown on the labial and lingual sides, as seen in the teeth of living beaded lizards. If these grooves are functionally similar to those of beaded lizards, which use the grooves to deliver venom, this new taxon represents the oldest known reptile where venom-conducting teeth are preserved within a jaw. The teeth of the new species are anatomically distinct from and ~10x smaller than those of the only other known Late Triassic hypothesized venomous reptile, Uatchitodon, supporting venom use across multiple groups of different body size classes. This new species represents the third Late Triassic reptile species to possibly have used envenomation as a feeding (and/or defensive) strategy, adding to the small number of venomous reptiles known from the Mesozoic Era.
Burch et al. (2024) A small venomous reptile from the Late Triassic (Norian) of the southwestern United States. PeerJ 12:e18279 https://doi.org/10.7717/peerj.18279
Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland
Background The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem. Methods High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure. Results S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors. Conclusions Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.
Wang et al. (2024) Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland. PeerJ 12:e18291 https://doi.org/10.7717/peerj.18291
Identification of an additive interaction using parameter regularization and model selection in epidemiology
Background In epidemiology, indicators such as the relative excess risk due to interaction (RERI), attributable proportion (AP), and synergy index (S) are commonly used to assess additive interactions between two variables. However, the results of these indicators are sometimes inconsistent in real world applications and it may be difficult to draw conclusions from them. Method Based on the relationship between the RERI, AP, and S, we propose a method with consistent results, which are achieved by constraining $e^{\theta_3}-e^{\theta_1}-e^{\theta_2}+1=0$eθ3−eθ1−eθ2+1=0 , and the interpretation of the results is simple and clear. We present two pathways to achieve this end: one is to complete the constraint by adding a regular penalty term to the model likelihood function; the other is to use model selection. Result Using simulated and real data, our proposed methods effectively identified additive interactions and proved to be applicable to real-world data. Simulations were used to evaluate the performance of the methods in scenarios with and without additive interactions. The penalty term converged to 0 with increasing λ, and the final models matched the expected interaction status, demonstrating that regularized estimation could effectively identify additive interactions. Model selection was compared with classical methods (delta and bootstrap) across various scenarios with different interaction strengths, and the additive interactions were closely observed and the results aligned closely with bootstrap results. The coefficients in the model without interaction adhered to a simplifying equation, reinforcing that there was no significant interaction between smoking and alcohol use on oral cancer risk. Conclusion In summary, the model selection method based on the Hannan-Quinn criterion (HQ) appears to be a competitive alternative to the bootstrap method for identifying additive interactions. Furthermore, when using RERI, AP, and S to assess the additive interaction, the results are more consistent and the results are simple and easy to understand.
Hu et al. (2024) Identification of an additive interaction using parameter regularization and model selection in epidemiology. PeerJ 12:e18304 https://doi.org/10.7717/peerj.18304
The relationship between functional movement patterns, dynamic balance and ice speed and agility in young elite male ice hockey players
Background Understanding the relationship between the functional state of the musculoskeletal system and skating performance in ice hockey players is essential, as it can provide valuable insights for the development of training programs tailored to the specific needs of athletes. This study investigated the relationship between functional movement patterns, dynamic balance, and ice speed and agility in young elite male ice hockey players. Methods The study involved sixty elite male ice hockey players aged 14 to 18 years, with an average age of 15.9 ± 0.85 years and training experience ranging from 7 to 9 years. Functional movement patterns were evaluated using the Functional Movement Screen™ (FMSTM). Dynamic balance was assessed using the lower quarter Y-Balance test (YBT-LQ). Fitness tests on ice were conducted using a professional Smart Speed measurement system. Results Negative correlations were found between the in-line lunge and the results of the 5-m forward (rho = −0.31, p = 0.018) and 5-m backward (rho = −0.27, p = 0.040), as well as between the hurdle step and the 30-m forward skating test result (rho = −0.26, p = 0.043). Positive correlations were observed between shoulder mobility and both forward (5-m: rho = 0.27, p = 0.035) and backward skating results (5-m: rho = 0.35, p = 0.006; 30-m: rho = 0.26, p = 0.047), and between active straight leg rise and both the 5-m forward skating (rho = 0.38, p = 0.002) and agility tests (rho = 0.39, p = 0.002). The study also revealed positive correlations between the magnitude of asymmetries in the anterior reach distance of the right and left legs and the results of 5-m forward (rho = 0.34, p = 0.009) and backward skating (rho = 0.32, p = 0.013). Additionally, a positive correlation was found between the agility test and the magnitude of asymmetries in the posteromedial reach distance (r = 0.32, p = 0.012) as well as the composite YBT score (r = 0.28, p = 0.031). Negative correlations were found between normalized reach distances in the YBT-LQ and performance outcomes in both forward and backward skating, as well as in the agility test, indicating that greater reach distance corresponds to faster skating. Conclusions These findings suggest the potential impact of balance and hip mobility on skating speed and agility and emphasize the importance of symmetry for optimal performance among ice hockey players.
Grabara et al. (2024) The relationship between functional movement patterns, dynamic balance and ice speed and agility in young elite male ice hockey players. PeerJ 12:e18092 https://doi.org/10.7717/peerj.18092
Applications of dry chain technology to maintain high seed viability in tropical climates
Seed storage life in tropical areas is shortened by high humidity and temperature and the general inaccessibility to dehumidifying and refrigeration systems, resulting in rapid decreases in seed viability in storage as well as a high incidence of fungal and insect infestations. The dry chain, based on rapid and deep drying of seeds after harvest followed by packaging in moisture-proof containers, has been proposed as an effective method to maintain seed quality during medium-term storage in humid climates, even without refrigeration. In addition, seed drying with zeolite drying beads can be more effective and economical than sun or heated-air drying under these warm, humid conditions. In this paper, we review recent published literature regarding the dry chain, considering different crop species, storage environments and seed traits. In addition, we provide new original data on the application of dry chain methods and their implementation at larger scales in South Asia, Latin America and Pacific Island Countries. The clear conclusion is that the combination of reusable drying beads and waterproof storage containers enables the implementation of the dry chain in tropical climates, enhancing seed viability and quality in storage of many crop species. The dry chain approach can therefore significantly enhance seed security for farmers in many tropical countries. Finally, we propose actions and strategies that could guide further scaling-up implementation of this technology.
Guzzon et al. (2024) Applications of dry chain technology to maintain high seed viability in tropical climates. PeerJ 12:e18146 https://doi.org/10.7717/peerj.18146