PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
items: Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
items: Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
items: Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
items: An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients
items: 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
items: Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types
items: Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study
items: Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture
items: Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio

Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
type: item
type: AcademicArticle
description: 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…
format: application/pdf
format: text/html
creator: Alexandrea M. Rice
creator: Mariann T. Garrison-Johnston
creator: Arianna J. Libenson
creator: Ruth D. Yanai
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.14410
publisher: PeerJ Inc.
rights: © 2022 Rice et al.
abstract: 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…
bibliographic citation: 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
date submitted: 2021-03-24
date accepted: 2022-10-27
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rice
  given name: Alexandrea M.
author list: Agent
  family name: Garrison-Johnston
  given name: Mariann T.
author list: Agent
  family name: Libenson
  given name: Arianna J.
author list: Agent
  family name: Yanai
  given name: Ruth D.
doi: 10.7717/peerj.14410
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Rice et al.
attribution name: Rice et al.

Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Can Chen
creator: Xi Xia
creator: Dawei Wang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14441
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-02-21
date accepted: 2022-11-01
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Can
author list: Agent
  family name: Xia
  given name: Xi
author list: Agent
  family name: Wang
  given name: Dawei
doi: 10.7717/peerj.14441
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Jocelyn R. Holt
creator: Antonino Malacrinò
creator: Raul F. Medina
subject: Agricultural Science
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.14448
publisher: PeerJ Inc.
rights: © 2022 Holt et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-05-16
date accepted: 2022-11-01
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holt
  given name: Jocelyn R.
author list: Agent
  family name: Malacrinò
  given name: Antonino
author list: Agent
  family name: Medina
  given name: Raul F.
doi: 10.7717/peerj.14448
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Holt et al.
attribution name: Holt et al.

Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
type: item
type: AcademicArticle
description: 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 stu…
format: application/pdf
format: text/html
creator: Fei Liang
creator: Wentian Xu
creator: Hongxia Wu
creator: Bin Zheng
creator: Qingzhi Liang
creator: Yingzhi Li
creator: Songbiao Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.14458
publisher: PeerJ Inc.
rights: © 2022 Liang et al.
abstract: 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 stu…
bibliographic citation: 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
date submitted: 2022-05-04
date accepted: 2022-11-02
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Fei
author list: Agent
  family name: Xu
  given name: Wentian
author list: Agent
  family name: Wu
  given name: Hongxia
author list: Agent
  family name: Zheng
  given name: Bin
author list: Agent
  family name: Liang
  given name: Qingzhi
author list: Agent
  family name: Li
  given name: Yingzhi
author list: Agent
  family name: Wang
  given name: Songbiao
doi: 10.7717/peerj.14458
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Liang et al.
attribution name: Liang et al.

An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Gustavo Martinez
creator: Alexis Garduno
creator: Abdullah Mahmud-Al-Rafat
creator: Ali Toloue Ostadgavahi
creator: Ann Avery
creator: Scheila de Avila e Silva
creator: Rachael Cusack
creator: Cheryl Cameron
creator: Mark Cameron
creator: Ignacio Martin-Loeches
creator: David Kelvin
subject: Bioinformatics
subject: Immunology
subject: Data Mining and Machine Learning
subject: COVID-19
description: doi:10.7717/peerj.14487
publisher: PeerJ Inc.
rights: © 2022 Martinez et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-07-25
date accepted: 2022-11-08
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez
  given name: Gustavo
author list: Agent
  family name: Garduno
  given name: Alexis
author list: Agent
  family name: Mahmud-Al-Rafat
  given name: Abdullah
author list: Agent
  family name: Ostadgavahi
  given name: Ali Toloue
author list: Agent
  family name: Avery
  given name: Ann
author list: Agent
  family name: de Avila e Silva
  given name: Scheila
author list: Agent
  family name: Cusack
  given name: Rachael
author list: Agent
  family name: Cameron
  given name: Cheryl
author list: Agent
  family name: Cameron
  given name: Mark
author list: Agent
  family name: Martin-Loeches
  given name: Ignacio
author list: Agent
  family name: Kelvin
  given name: David
doi: 10.7717/peerj.14487
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Martinez et al.
attribution name: Martinez et al.

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
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Richard I. Schwarz
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.14533
publisher: PeerJ Inc.
rights: © 2022 Schwarz
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-03
date accepted: 2022-11-16
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schwarz
  given name: Richard I.
doi: 10.7717/peerj.14533
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Schwarz
attribution name: Schwarz

Treatment outcome of class II malocclusion therapy including extraction of maxillary first molars: a cephalometric comparison between normodivergent and hyperdivergent facial types
type: item
type: AcademicArticle
description: 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 incl…
format: application/pdf
format: text/html
creator: Johan Willem Booij
creator: Marta Fontana
creator: Marco Serafin
creator: Rosamaria Fastuca
creator: Anne Marie Kuijpers-Jagtman
creator: Alberto Caprioglio
subject: Anatomy and Physiology
subject: Dentistry
subject: Drugs and Devices
subject: Biomechanics
description: doi:10.7717/peerj.14537
publisher: PeerJ Inc.
rights: © 2022 Booij et al.
abstract: 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 incl…
bibliographic citation: 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
date submitted: 2022-08-15
date accepted: 2022-11-17
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Booij
  given name: Johan Willem
author list: Agent
  family name: Fontana
  given name: Marta
author list: Agent
  family name: Serafin
  given name: Marco
author list: Agent
  family name: Fastuca
  given name: Rosamaria
author list: Agent
  family name: Kuijpers-Jagtman
  given name: Anne Marie
author list: Agent
  family name: Caprioglio
  given name: Alberto
doi: 10.7717/peerj.14537
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Booij et al.
attribution name: Booij et al.

Association between type 2 diabetes and 5-year overall survival in early-stage pancreatic cancer: a retrospective cohort study
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Zhiyin Tang
creator: Wanfeng Xu
creator: Mingming Zhang
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Oncology
description: doi:10.7717/peerj.14538
publisher: PeerJ Inc.
rights: © 2022 Tang et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-08-01
date accepted: 2022-11-17
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Zhiyin
author list: Agent
  family name: Xu
  given name: Wanfeng
author list: Agent
  family name: Zhang
  given name: Mingming
doi: 10.7717/peerj.14538
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Tang et al.
attribution name: Tang et al.

Using solar radiation data in soil moisture diagnostic equation for estimating root-zone soil moisture
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Olumide Omotere
creator: Feifei Pan
creator: Lei Wang
subject: Soil Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14561
publisher: PeerJ Inc.
rights: © 2022 Omotere et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-25
date accepted: 2022-11-22
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Omotere
  given name: Olumide
author list: Agent
  family name: Pan
  given name: Feifei
author list: Agent
  family name: Wang
  given name: Lei
doi: 10.7717/peerj.14561
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Omotere et al.
attribution name: Omotere et al.

Autumnal migration patterns of hoverflies (Diptera: Syrphidae): interannual variability in timing and sex ratio
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Antonín Hlaváček
creator: Radek K. Lučan
creator: Jiří Hadrava
subject: Animal Behavior
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.14393
publisher: PeerJ Inc.
rights: © 2022 Hlaváček et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-06-20
date accepted: 2022-10-24
issued: 2022-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hlaváček
  given name: Antonín
author list: Agent
  family name: Lučan
  given name: Radek K.
author list: Agent
  family name: Hadrava
  given name: Jiří
doi: 10.7717/peerj.14393
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-09
copyright: © 2022 Hlaváček et al.
attribution name: Hlaváček et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359