Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
The influence of nutrient availability on transpiration is not well understood, in spite of the importance of transpiration to forest water budgets. Soil nutrients have the potential to affect tree water use through indirect effects on leaf area or stomatal conductance. For example, following addition of calcium silicate to a watershed at Hubbard Brook, in New Hampshire, streamflow was reduced for 3 years, which was attributed to a 25% increase in evapotranspiration associated with increased foliar production. The first objective of this study was to quantify the effect of nutrient availability on sap flux density in a nitrogen, phosphorus, and calcium addition experiment in New Hampshire in which tree diameter growth, foliar chemistry, and soil nutrient availability had responded to treatments. We measured sap flux density in American beech (Fagus grandifolia, Ehr.), red maple (Acer rubrum L.), sugar maple (Acer saccharum Marsh.), white birch (Betula papyrifera Marsh.), or yellow birch (Betula alleghaniensis Britton.) trees, over five years of experiments in five stands distributed across three sites. In 2018, 3 years after a calcium silicate addition, sap flux density averaged 36% higher in trees in the treatment than the control plot, but this effect was not very significant (p = 0.07). Our second objective was to determine whether this failure to detect effects with greater statistical confidence was due to small effect sizes or high variability among trees. We found that tree-to-tree variability was high, with coefficients of variation averaging 39% within treatment plots. Depending on the species and year of the study, the minimum difference in sap flux density detectable with our observed variability ranged from 46% to 352%, for a simple ANOVA. We analyzed other studies reported in the literature that compared tree water use among species or treatments and found detectable differences ranging from 16% to 78%. Future sap flux density studies could benefit from power analyses to guide sampling intensity. Including pretreatment data, in the case of manipulative studies, would also increase statistical power.
Rice et al. (2022) Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest. PeerJ 10:e14410 https://doi.org/10.7717/peerj.14410
Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.
Chen et al. (2022) Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics. PeerJ 10:e14441 https://doi.org/10.7717/peerj.14441
Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
The establishment of new symbiotic interactions between introduced species may facilitate invasion success. For instance, tawny crazy ant (Nylanderia fulva Mayr) is known to be an opportunistic tender of honeydew producing insects and this ants’ symbiotic interactions have exacerbated agricultural damage in some invaded regions of the world. The invasive sorghum aphid (Melanaphis sorghi Theobald) was first reported as a pest in the continental United States–in Texas and Louisiana–as recent as 2013, and tawny crazy ant (TCA) was reported in Texas in the early 2000s. Although these introductions are relatively recent, TCA workers tend sorghum aphids in field and greenhouse settings. This study quantified the tending duration of TCA workers to sorghum aphids and the impact of TCA tending on aphid biomass. For this study aphids were collected from three different host plant species (i.e., sugarcane, Johnson grass, and sorghum) and clone colonies were established. Sorghum is the main economic crop in which these aphids occur, hence we focused our study on the potential impacts of interactions on sorghum. Quantification of invasive ant-aphid interactions, on either stems or leaves of sorghum plants, were conducted in greenhouse conditions. Our results show that although these two invasive insect species do not have a long coevolutionary history, TCA developed a tending interaction with sorghum aphid, and aphids were observed excreting honeydew after being antennated by TCA workers. Interestingly, this relatively recent symbiotic interaction significantly increased overall aphid biomass for aphids that were positioned on stems and collected from Johnson grass. It is recommended to continue monitoring the interaction between TCA and sorghum aphid in field conditions due to its potential to increase aphid populations and sorghum plant damage.
Holt et al. (2022) Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi). PeerJ 10:e14448 https://doi.org/10.7717/peerj.14448
Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
Background Insufficient low temperatures in winter and soil residues caused by paclobutrazol (PBZ) application pose a considerable challenge for mango floral induction (FI). Gibberellin inhibitors SPD (compound of mepiquat chloride, prohexadione-calcium and uniconazole) had a significant influence on enhancing the flowering rate and yield of mango for two consecutive years (2020–2021). Researchers have indicated that FI is regulated at the metabolic level; however, little is known about the metabolic changes during FI in response to SPD treatment. Methods Here, ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based widely targeted metabolomic analysis was carried out to assess the metabolic differences in the mango stem apex during different stage of mango FI (30, 80, 100 days after SPD/water treatment). Results A total of 582 compounds were annotated and 372 metabolites showed two-fold differences in abundance (variable importance in projection, VIP ≥ 1 and fold change, FC≥ 2 or≤ 0.5) between buds at 30, 80, 100 days after SPD/water treatment or between buds under different treatment. Lipids, phenolic acids, amino acids, carbohydrates, and vitamins were among metabolites showing significant differences over time after SPD treatment. Here, 18 out of 20 lipids, including the lysophosphatidylethanolamine (12, LPE), lysophosphatidylcholine (7, LPC), and free fatty acids (1, FA), were significantly upregulated from 80 to 100 days after SPD treatment comared to water treatment. Meanwhile, the dormancy release of mango buds from 80 to 100 days after SPD treatment was accompanied by the accumulation of proline, ascorbic acid, carbohydrates, and tannins. In addition, metabolites, such as L-homocysteine, L-histidine, and L-homomethionine, showed more than a ten-fold difference in relative abundance from 30 to 100 days after SPD treatment, however, there were no significant changes after water treatment. The present study reveals novel metabolites involved in mango FI in response to SPD, which would provide a theoretical basis for utilizing SPD to induce mango flowering.
Liang et al. (2022) Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole. PeerJ 10:e14458 https://doi.org/10.7717/peerj.14458
An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients
Background The severe form of COVID-19 can cause a dysregulated host immune syndrome that might lead patients to death. To understand the underlying immune mechanisms that contribute to COVID-19 disease we have examined 28 different biomarkers in two cohorts of COVID-19 patients, aiming to systematically capture, quantify, and algorithmize how immune signals might be associated to the clinical outcome of COVID-19 patients. Methods The longitudinal concentration of 28 biomarkers of 95 COVID-19 patients was measured. We performed a dimensionality reduction analysis to determine meaningful biomarkers for explaining the data variability. The biomarkers were used as input of artificial neural network, random forest, classification and regression trees, k-nearest neighbors and support vector machines. Two different clinical cohorts were used to grant validity to the findings. Results We benchmarked the classification capacity of two COVID-19 clinicals studies with different models and found that artificial neural networks was the best classifier. From it, we could employ different sets of biomarkers to predict the clinical outcome of COVID-19 patients. First, all the biomarkers available yielded a satisfactory classification. Next, we assessed the prediction capacity of each protein separated. With a reduced set of biomarkers, our model presented 94% accuracy, 96.6% precision, 91.6% recall, and 95% of specificity upon the testing data. We used the same model to predict 83% and 87% (recovered and deceased) of unseen data, granting validity to the results obtained. Conclusions In this work, using state-of-the-art computational techniques, we systematically identified an optimal set of biomarkers that are related to a prediction capacity of COVID-19 patients. The screening of such biomarkers might assist in understanding the underlying immune response towards inflammatory diseases.
Martinez et al. (2022) An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients. PeerJ 10:e14487 https://doi.org/10.7717/peerj.14487
A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture
Cell density signaling drives tendon morphogenesis by regulating both procollagen production and cell proliferation. The signal is composed of a small, highly conserved protein (SNZR P) tightly bound to a tissue-specific, unique lipid (SNZR L). This allows the complex (SNZR PL) to bind to the membrane of the cell and locally diffuse over a radius of ~1 mm. The cell produces low levels of this signal but the binding to the membrane increases with the number of tendon cells in the local environment. In this article SNZR P was produced in E.coli and SNZR L was chemically synthesized. The two bind together when heated to 60 °C in the presence of Ca++ and Mg++ and the synthesized SNZR PL at ng/ml levels can replace serum. Adding SNZR PL to the medium was also tested on primary tendon cells from adult roosters. The older cells were in a maintenance state in vivo and in cell culture they proliferate more slowly than embryonic cells. Nevertheless, after reaching a moderately high cell density, they produced high levels of procollagen similar to the embryonic cells. This data was not expected from older cells but suggests that adult tendon cells can regenerate the tissue after injury when given the correct signals.
Schwarz (2022) A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture. PeerJ 10:e14533 https://doi.org/10.7717/peerj.14533
Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types
Background The dentoalveolar component of a Class II division 1 malocclusion can be orthodontically treated either with extractions or by distalization of the molars. This study aimed to compare skeletal, dentoalveolar and profile changes in normodivergent and hyperdivergent Class II Division I growing patients orthodontically treated with fixed appliances including maxillary first molar extraction. Methods Sixty-four patients treated orthodontically with full fixed appliances including maxillary first molar extractions were retrospectively analyzed. Patients were divided into a normodivergent group (Group N; 30° ≤ SN^GoGn < 36°) consisting of 38 patients (17M, 21F; mean age 13.2 ± 1.3 years) and a hyperdivergent (Group H; SN^GoGn ≥ 36°) including 26 patients (12M, 14F; mean age 13.7 ± 1.1 years). Lateral cephalograms were available before (T0) and after treatment (T1) and cephalometric changes were calculated for 10 linear and 13 angular variables. The Shapiro–Wilk test confirmed a normal distribution of data, hence parametric tests were employed. The Student t-test was used to compare groups at baseline. The paired t-test was used to analyze intragroup changes between timepoints, and the Student t-test for intergroup comparisons. The level of significance was set at 0.05. Results The Class II division 1 malocclusion was successfully corrected, and the facial profile improved both in normodivergent and hyperdivergent patients. Divergency increased by 0.76 ± 1.99° in Group N (p = 0.02) while it decreased −0.23 ± 2.25° (p = 0.60); These changes were not significant between groups after treatment (p = 0.680). Most dentoskeletal measurements changed significantly within groups but none of them showed statistically significant differences between groups after treatment. Dental and soft tissue changes were in accordance with the biomechanics used for this Class II orthodontic therapy. Discussion The effect of orthodontic treatment of Class II division 1 malocclusion including extraction of the maxillary first molars in growing patients can be considered clinically equivalent in normodivergent and hyperdivergent patients. For this reason, this orthodontic treatment can be considered a viable option in the armamentarium of the Class II Division I therapy for both facial types.
Booij et al. (2022) Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types. PeerJ 10:e14537 https://doi.org/10.7717/peerj.14537
Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study
Background This study examined the association between type 2 diabetes mellitus (T2DM) and 5-year overall survival (OS) in patients with pancreatic cancer (PC). Methods This retrospective cohort study included patients diagnosed with stage I/II PC at Shengjing Hospital of China Medical University from January 2012 to December 2017. All patients had pancreatic ductal adenocarcinoma or its subtypes. The outcome was the 5-year OS rate based on data from the patient charts. Data analysis was performed using SPSS 22.0 Results A total of 238 patients were included: 72 with T2DM and 166 without T2DM. There were significant differences in blood glucose levels and OS between the two groups (all P < 0.05). The median OS was 11.4 (95% confidence interval CI [8.49–14.31]) months in the T2DM group and 16.3 (95% CI [12.44–20.16], P = 0.023) months in the non-T2DM group. After adjustment for confounders, T2DM was an independent factor affecting 5-year OS (P = 0.010). Compared with non-T2DM patients, T2DM patients had a higher risk of death (HR = 1.475, 95% CI [1.096–1.985]). Conclusions T2DM is associated with 5-year OS in patients with PC.
Tang et al. (2022) Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study. PeerJ 10:e14538 https://doi.org/10.7717/peerj.14538
Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture
The soil moisture daily diagnostic equation (SMDE) evaluates the relationship between the loss function coefficient and the summation of the weighted average of precipitation. The loss function coefficient uses the day of the year (DOY) to approximate the seasonal changes in soil moisture loss for a given location. Solar radiation is the source of the energy that drives the complex and intricates of the earth-atmospheric processes and biogeochemical cycles in the environment. Previous research assumed DOY is the approximation of other environmental factors (e.g., temperature, wind speed, solar radiation). In this article, two solar radiation parameters were introduced, i.e., the actual solar radiation and the clear sky solar radiation and were incorporated into the loss function coefficient to improve its estimation. This was applied to 2 years of continuous rainfall, soil moisture data from USDA soil climate network (SCAN) sites AL2053, GA2027 MS2025, and TN2076. It was observed that the correlation coefficient between the observed soil moisture and B values (which is the cumulated average of rainfall to soil moisture loss) increased on average by 2.3% and the root mean square errors (RMSEs) for estimating volumetric soil moisture at columns 0–5, 0–10, 0–20, 0–50, 0–100 cm reduced on average by 8.6% for all the study sites. The study has confirmed that using actual solar radiation data in the soil moisture daily diagnostic equation can improve its accuracy.
Spatial and Geographic Information Science
Omotere et al. (2022) Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture. PeerJ 10:e14561 https://doi.org/10.7717/peerj.14561
Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio
Background The migration of hoverflies (Diptera: Syrphidae) is a well-known phenomenon, with growing interest due to the ecosystem services provided by migrants. However, we still lack fundamental data on species composition, timing of migration, or sex ratio of migrants. To address this gap, we focused on the southward autumnal migration of hoverflies through central Europe. Methods To recognize migrating individuals from resident ones, we used a pair of one-side-blocked Malaise traps, exposed in a mountain pass in the Jeseníky mountains, Czech Republic, where a mass migration of hoverflies takes place annually. Traps were set for 4 years, from August to October. Results In total, we recorded 31 species of migrating hoverflies. The timing of migration differed between the years, taking place from the beginning of September to the end of October. Differences in phenology were observed in the four most common migrant species, where larger species seemed to migrate earlier or at the same time compared to the smaller ones. The sex ratio was strongly asymmetrical in most common species Episyrphus balteatus, Eupeodes corollae, and Sphaerophoria scripta, and varied between years for each species. Weather conditions strongly influenced the migration intensity at ground-level: hoverflies migrate mainly during days with south wind, high temperature, high atmospheric pressure, and low precipitation.
Hlaváček et al. (2022) Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio. PeerJ 10:e14393 https://doi.org/10.7717/peerj.14393