Microbial community structure and carbon transformation characteristics of different aggregates in black soil
Background Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification. Methods In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2–5, 1–2, 0.5–1, 0.25–0.5, <0.25 mm, and bulk soil. Results The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25–0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25–0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil’s ability to fix carbon and nitrogen. Discussion There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25–0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.
Zhao et al. (2024) Microbial community structure and carbon transformation characteristics of different aggregates in black soil. PeerJ 12:e17269 https://doi.org/10.7717/peerj.17269
Plasma-based lipidomics reveals potential diagnostic biomarkers for esophageal squamous cell carcinoma: a retrospective study
Background Esophageal squamous cell carcinoma (ESCC) is highly prevalent and has a high mortality rate. Traditional diagnostic methods, such as imaging examinations and blood tumor marker tests, are not effective in accurately diagnosing ESCC due to their low sensitivity and specificity. Esophageal endoscopic biopsy, which is considered as the gold standard, is not suitable for screening due to its invasiveness and high cost. Therefore, this study aimed to develop a convenient and low-cost diagnostic method for ESCC using plasma-based lipidomics analysis combined with machine learning (ML) algorithms. Methods Plasma samples from a total of 40 ESCC patients and 31 healthy controls were used for lipidomics study. Untargeted lipidomics analysis was conducted through liquid chromatography-mass spectrometry (LC-MS) analysis. Differentially expressed lipid features were filtered based on multivariate and univariate analysis, and lipid annotation was performed using MS-DIAL software. Results A total of 99 differential lipids were identified, with 15 up-regulated lipids and 84 down-regulated lipids, suggesting their potential as diagnostic targets for ESCC. In the single-lipid plasma-based diagnostic model, nine specific lipids (FA 15:4, FA 27:1, FA 28:7, FA 28:0, FA 36:0, FA 39:0, FA 42:0, FA 44:0, and DG 37:7) exhibited excellent diagnostic performance, with an area under the curve (AUC) exceeding 0.99. Furthermore, multiple lipid-based ML models also demonstrated comparable diagnostic ability for ESCC. These findings indicate plasma lipids as a promising diagnostic approach for ESCC.
Chen et al. (2024) Plasma-based lipidomics reveals potential diagnostic biomarkers for esophageal squamous cell carcinoma: a retrospective study. PeerJ 12:e17272 https://doi.org/10.7717/peerj.17272
Variational Bayesian phylogenies through matrix representation of tree space
In this article, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the entries in a matrix, this allows us to represent a distribution over rooted time trees. Here, we demonstrate tree distributions can be represented accurately this way for a number of published tree distributions. Though such a representation does not map to unique trees, restriction to a subspace, in particular one we call a “cube”, makes the representation bijective at the cost of not being able to represent all possible trees. We introduce an algorithm “cubeVB” specifically for cubes and show through well calibrated simulation study that it is possible to recover parameters of interest like tree height and length. Although a cube cannot represent all of tree space, it is a great improvement over a single summary tree, and it opens up exciting new opportunities for scaling up Bayesian phylogenetic inference. We also demonstrate how to use a matrix representation of a tree distribution to get better summary trees than commonly used maximum clade credibility trees. An open source implementation of the cubeVB algorithm is available from https://github.com/rbouckaert/cubevb as the cubevb package for BEAST 2.
Bouckaert (2024) Variational Bayesian phylogenies through matrix representation of tree space. PeerJ 12:e17276 https://doi.org/10.7717/peerj.17276
Association between passing return-to-sport testing and re-injury risk in patients after anterior cruciate ligament reconstruction surgery: a systematic review and meta-analysis
Background Inconsistent results have been obtained regarding the association between return-to-sport (RTS) testing and the risk of subsequent re-injury following anterior cruciate ligament reconstruction (ACLR). We therefore conducted a systematic review and meta-analysis to assess the potential association between passing of RTS and the risk of re-injury for patients after ACLR. Methods This meta-analysis was registered in INPLASY with the registration number INPLASY202360027. The electronic databases MedLine, EmBase, and the Cochrane library were systematically searched to identify eligible studies from their inception up to September 2023. The investigated outcomes included knee injury, secondary ACL, contralateral ACL injury, and graft rupture. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using the random-effects model. Results A total number of nine studies involving 1410 individuals were selected for the final quantitative analysis. We noted that passing RTS test was not associated with the risk of subsequent knee injury (OR: 0.95; 95% CI: 0.28–3.21; P = 0.929), secondary ACL injury (OR: 0.98; 95% CI: 0.55–1.75; P = 0.945), and contralateral ACL injury (OR: 1.53; 95% CI: 0.63–3.71; P = 0.347). However, the risk of graft rupture was significantly reduced (OR: 0.49; 95% CI: 0.33–0.75; P = 0.001). Conclusions This study found that passing RTS test was not associated with the risk of subsequent knee injury, secondary ACL injury, and contralateral ACL injury, while it was associated with a lower risk of graft rupture. Thus, it is recommended that patients after ACLR pass an RTS test in clinical settings.
Zhou et al. (2024) Association between passing return-to-sport testing and re-injury risk in patients after anterior cruciate ligament reconstruction surgery: a systematic review and meta-analysis. PeerJ 12:e17279 https://doi.org/10.7717/peerj.17279
Anodal transcranial direct current stimulation enhances response inhibition and attention allocation in fencers
Background The aim of this study is to investigate the acute effects of anodal transcranial direct current stimulation (tDCS) on reaction time, response inhibition and attention in fencers. Methods Sixteen professional female fencers were recruited, and subjected to anodal tDCS and sham stimulation in the primary motor area (M1) one week apart in a randomized, crossover, single-blind design. A two-factor analysis of variance with repeated measures was used to analyze the effects of stimulation conditions (anodal stimulation, sham stimulation) and time (pre-stimulation, post-stimulation) on reaction time, response inhibition, and attention in fencers. Results The study found a significant improvement in response inhibition and attention allocation from pre-stimulation to post-stimulation following anodal tDCS but not after sham stimulation. There was no statistically significant improvement in reaction time and selective attention. Conclusions A single session of anodal tDCS could improve response inhibition, attention allocation in female fencers. This shows that tDCS has potential to improve aspects of an athlete’s cognitive performance, although we do not know if such improvements would transfer to improved performance in competition. However, more studies involving all genders, large samples, and different sports groups are needed in the future to further validate the effect of tDCS in improving the cognitive performance of athletes.
Dai et al. (2024) Anodal transcranial direct current stimulation enhances response inhibition and attention allocation in fencers. PeerJ 12:e17288 https://doi.org/10.7717/peerj.17288
Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities
Background Oat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat. Methods Therefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat. Results We observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,000-grain weight can serve as important indicators for evaluating oat stem lodging resistance. We also noted that planting density affected grain yield both directly and indirectly (by affecting lodging); high density increased lodging rate and decreased grain yield, mainly by reducing 1,000-grain weight. Nonetheless, there was no significant relationship between lodging and grass yield. As appropriate planting density can increase the yield while maintaining good lodging resistance, in this study, 4.5×106 plants/ha (D2) was found to be the best planting density for oat in terms of lodging resistance and grass and grain yield. These findings can be used as a reference for oat planting.
Liu et al. (2024) Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities. PeerJ 12:e17310 https://doi.org/10.7717/peerj.17310
Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney
This review discusses the importance of homeostasis with a particular emphasis on the acid-base (AB) balance, a crucial aspect of pH regulation in living systems. Two primary organ systems correct deviations from the standard pH balance: the respiratory system via gas exchange and the kidneys via proton/bicarbonate secretion and reabsorption. Focusing on kidney functions, we describe the complexity of renal architecture and its challenges for experimental research. We address specific roles of different nephron segments (the proximal convoluted tubule, the loop of Henle and the distal convoluted tubule) in pH homeostasis, while explaining the physiological significance of ion exchange processes maintained by the kidneys, particularly the role of bicarbonate ions (HCO3−) as an essential buffer system of the body. The review will be of interest to researchers in the fields of physiology, biochemistry and molecular biology, which builds a strong foundation and critically evaluates existing studies. Our review helps identify the gaps of knowledge by thoroughly understanding the existing literature related to kidney acid-base homeostasis.
Gantsova et al. (2024) Mechanisms and physiological relevance of acid-base exchange in functional units of the kidney. PeerJ 12:e17316 https://doi.org/10.7717/peerj.17316
Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey
Background Thailand recently decriminalized (de facto legalized) cannabis use and sales. However, nationally representative data are scarce with regard to cannabis use behaviors and its association with cannabis outlet density. The objectives of this study are: (1) to describe the prevalence of cannabis use behaviors and cannabis use disorder among the general adult population of Thailand; (2) to describe the extent that the density of cannabis outlets is associated with cannabis use behaviors, cannabis use disorder, and the amount of cannabis smoked per day. Methods We conducted a community-based cross-sectional study in 11 provinces and the Bangkok Metropolitan Area. Participants were residents of sampled communities aged 20 years or older. We requested literate participants to self-administer the questionnaire and interviewed participants who could not read. We analyzed data using descriptive statistics with sampling weight adjustments and multivariate logistic regression analyses. Results The prevalence of current cannabis use was 15 percent. At a 400-m radius, participants who reported three cannabis outlets had 4.2 times higher odds of being current users than participants who reported no outlet (Adjusted OR = 4.82; 95% CI [3.04–7.63]). We found no association between outlet density and hazardous cannabis use or cannabis use disorder, nor association with the amount of cannabis use among cannabis smokers. Discussion and Conclusion The patterns of association between outlet density and cannabis use behaviors were inconsistent. Furthermore, limitations regarding outlet density measurement and lack of temporality should be considered as caveats in the interpretation of the study findings.
Wichaidit et al. (2024) Density of cannabis outlets vs. cannabis use behaviors and prevalent cannabis use disorder: findings from a nationally-representative survey. PeerJ 12:e17317 https://doi.org/10.7717/peerj.17317
Combining multisensor images and social network data to assess the area flooded by a hurricane event
In this study, multisensor remote sensing datasets were used to characterize the land use and land covers (LULC) flooded by Hurricane Willa which made landfall on October 24, 2018. The landscape characterization was done using an unsupervised K-means algorithm of a cloud-free Sentinel-2 MultiSpectral Instrument (MSI) image, acquired during the dry season before Hurricane Willa. A flood map was derived using the histogram thresholding technique over a Synthetic Aperture Radar (SAR) Sentinel-1 C-band and combined with a flood map derived from a Sentinel-2 MSI image. Both, the Sentinel-1 and Sentinel-2 images were obtained after Willa landfall. While the LULC map reached an accuracy of 92%, validated using data collected during field surveys, the flood map achieved 90% overall accuracy, validated using locations extracted from social network data, that were manually georeferenced. The agriculture class was the dominant land use (about 2,624 km2), followed by deciduous forest (1,591 km2) and sub-perennial forest (1,317 km2). About 1,608 km2 represents the permanent wetlands (mangrove, salt marsh, lagoon and estuaries, and littoral classes), but only 489 km2 of this area belongs to aquatic surfaces (lagoons and estuaries). The flooded area was 1,225 km2, with the agricultural class as the most impacted (735 km2). Our analysis detected the saltmarsh class occupied 541 km2in the LULC map, and around 328 km2 were flooded during Hurricane Willa. Since the water flow receded relatively quickly, obtaining representative imagery to assess the flood event was a challenge. Still, the high overall accuracies obtained in this study allow us to assume that the outputs are reliable and can be used in the implementation of effective strategies for the protection, restoration, and management of wetlands. In addition, they will improve the capacity of local governments and residents of Marismas Nacionales to make informed decisions for the protection of vulnerable areas to the different threats derived from climate change.
Hernández-Guzmán et al. (2024) Combining multisensor images and social network data to assess the area flooded by a hurricane event. PeerJ 12:e17319 https://doi.org/10.7717/peerj.17319
The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area
Environmental heterogeneity poses a significant influence on the functional characteristics of species and communities at local scales. Environmental transition zones, such as at the savanna-forest borders, can act as regions of ecological tension when subjected to sharp variations in the microclimate. For ectothermic organisms, such as lizards, environmental temperatures directly influence physiological capabilities, and some species use different thermoregulation strategies that produce varied responses to local climatic conditions, which in turn affect species occurrence and community dynamics. In the context of global warming, these various strategies confer different types of vulnerability as well as risks of extinction. To assess the vulnerability of a species and understand the relationships between environmental variations, thermal tolerance of a species and community structure, lizard communities in forest-savanna transition areas of two national parks in the southwestern Amazon were sampled and their thermal functional traits were characterized. Then, we investigated how community structure and functional thermal variation were shaped by two environmental predictors (i.e., microclimates estimated locally and vegetation structure estimated from remote sensing). It was found that the community structure was more strongly predicted by the canopy surface reflectance values obtained via remote sensing than by microclimate variables. Environmental temperatures were not the most important factor affecting the occurrence of species, and the variations in ecothermal traits demonstrated a pattern within the taxonomic hierarchy at the family level. This pattern may indicate a tendency for evolutionary history to indirectly influence these functional features. Considering the estimates of the thermal tolerance range and warming tolerance, thermoconformer lizards are likely to be more vulnerable and at greater risk of extinction due to global warming than thermoregulators. The latter, more associated with open environments, seem to take advantage of their lower vulnerability and occur in both habitat types across the transition, potentially out-competing and further increasing the risk of extinction and vulnerability of forest-adapted thermoconformer lizards in these transitional areas.
Souza-Oliveira et al. (2024) The role of environmental gradients and microclimates in structuring communities and functional groups of lizards in a rainforest-savanna transition area. PeerJ 12:e16986 https://doi.org/10.7717/peerj.16986