title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1058
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept
link: https://peerj.com/articles/9750
last-modified: 2020-09-09
description: The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.
creator: Gaby Deckmyn
creator: Omar Flores
creator: Mathias Mayer
creator: Xavier Domene
creator: Andrea Schnepf
creator: Katrin Kuka
creator: Kris Van Looy
creator: Daniel P. Rasse
creator: Maria J.I. Briones
creator: Sébastien Barot
creator: Matty Berg
creator: Elena Vanguelova
creator: Ivika Ostonen
creator: Harry Vereecken
creator: Laura M. Suz
creator: Beat Frey
creator: Aline Frossard
creator: Alexei Tiunov
creator: Jan Frouz
creator: Tine Grebenc
creator: Maarja Öpik
creator: Mathieu Javaux
creator: Alexei Uvarov
creator: Olga Vindušková
creator: Paul Henning Krogh
creator: Oskar Franklin
creator: Juan Jiménez
creator: Jorge Curiel Yuste
uri: https://doi.org/10.7717/peerj.9750
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Deckmyn et al.

title: Omics approaches in Allium research: Progress and way ahead
link: https://peerj.com/articles/9824
last-modified: 2020-09-09
description: BackgroundThe genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.MethodIn the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.ResultsHere, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.ConclusionAll the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.
creator: Kiran Khandagale
creator: Ram Krishna
creator: Praveen Roylawar
creator: Avinash B. Ade
creator: Ashwini Benke
creator: Bharat Shinde
creator: Major Singh
creator: Suresh J. Gawande
creator: Ashutosh Rai
uri: https://doi.org/10.7717/peerj.9824
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Khandagale et al.

title: Assessment of postoperative health functioning after knee arthroplasty in relation to pain catastrophizing: a 6-month follow-up cohort study
link: https://peerj.com/articles/9903
last-modified: 2020-09-09
description: BackgroundKnee arthroplasty (KA) is a typically successful surgical procedure commonly performed to alleviate painin participants with end-stage knee osteoarthritis. Despite its beneficial effects, a significant proportion of individuals with KA continue experiencing persistent pain and functional limitations. The purpose of this study was to assess the postoperative outcomes after KA in relation to postoperative pain catastrophizing.MethodsParticipants were recruited at a domiciliary physiotherapy service, using a prospective, observational, hypothesis-generating cohort design. Participants were divided into two groups based on their Pain Catastrophizing Scale (PCS) total score (50th percentile), which resulted in high and low PCS groups. The primary outcome measure was the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). In addition, quality of life, walking speed, physical performance, range of motion, and pain were measured. Outcome measures were collected at baseline (1 week postoperatively) and at follow-up (1, 3, and 6 months postoperatively).ResultsA total of 60 participants (21 total KA and 39 unicompartmental KA) were recruited. Individuals with a higher degree of pain catastrophizing showed significantly higher WOMAC total scores at every follow-up, indicating poorer health functioning (p < 0.01). Similarly, the high PCS group showed higher WOMAC pain, stiffness and disability subscale scores (p < 0.05), poorer quality of life (p < 0.01), and poorer physical performance (p < 0.05) at every follow-up. In addition, the high PCS group achieved a slower walking speed at baseline and at 3 months follow-up (p < 0.05), and a higher degree of pain at rest, on walking and on knee flexion at every follow-up (p < 0.01, p < 0.05 and p < 0.05, respectively) except for walking pain at 3 months follow-up. No significant differences were observed between groups in range of motion, except for active knee extension at the 6-month follow-up (p < 0.05). Effect size was large at 1 month follow-up in WOMAC total score (r = 0.578) and pain intensity during knee flexion (r = 0.529). Longitudinal analyses revealed different improvement trends during the rehabilitation process between groups, with a lack of significant improvements in the high PCS group between the 3- and 6-month follow-up in WOMAC total score, WOMAC pain, WOMAC disability, quality of life, physical performance, active knee extension and resting pain (p > 0.05).ConclusionThe results of the present study suggest that participants with high postoperative pain catastrophizing might have poorer outcomes during the rehabilitation process after KA. Future work should seek to clarify if this relationship is causal.
creator: Marc Terradas-Monllor
creator: Mirari Ochandorena-Acha
creator: Julio Salinas-Chesa
creator: Sergi Ramírez
creator: Hector Beltran-Alacreu
uri: https://doi.org/10.7717/peerj.9903
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Terradas-Monllor et al.

title: Effect of nest age and habitat variables on nest survival in Marsh Harrier (Circus aeruginosus) in a fishpond habitat
link: https://peerj.com/articles/9929
last-modified: 2020-09-09
description: BackgroundOne important anti‐predator strategy adopted by birds involves nest site selection and timing of breeding. Nest-site selection by marsh-nesting birds often involves nest concealment and water depth as key features influencing nest survival. Marsh Harrier (Circus aeruginosus) is an obligate ground nester, which sets it apart from other raptors. The aim of the present study was to identify for the first time possible temporal and habitat factors affecting nest survival in Marsh Harrier. Understanding features which affect nest survival are essential for assessing relevant conservation strategies.MethodsTo understand the relative contributions of different temporal and habitat variables to brood losses, it is useful to determine the daily survival rate (DSR). We examined 82 Marsh Harrier nests located on fishponds in eastern Poland, where predation is the main cause of nest loss. Six habitat variables were measured for each active nest. DSR was calculated using known-fate models with the RMark package.ResultsThe best-supported model predicted that DSR decreased with nest age and was positively affected by the water depth and the diameter of reed stems, but not by the height or density of vegetation at the nest site. The distances of nests to the fishpond dyke and to open water received no support in the models. The chances of nest survival were lower if a neighbouring nest had been depredated. This result suggests that the Marsh Harrier is more susceptible to mammalian than avian predation and confirms the high level of predator pressure in fishpond habitats.
creator: Urszula Zaremba
creator: Zbigniew Kasprzykowski
creator: Artur Golawski
uri: https://doi.org/10.7717/peerj.9929
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Zaremba et al.

title: A descriptive study of random forest algorithm for predicting COVID-19 patients outcome
link: https://peerj.com/articles/9945
last-modified: 2020-09-09
description: BackgroundThe outbreak of coronavirus disease 2019 (COVID-19) that occurred in Wuhan, China, has become a global public health threat. It is necessary to identify indicators that can be used as optimal predictors for clinical outcomes of COVID-19 patients.MethodsThe clinical information from 126 patients diagnosed with COVID-19 were collected from Wuhan Fourth Hospital. Specific clinical characteristics, laboratory findings, treatments and clinical outcomes were analyzed from patients hospitalized for treatment from 1 February to 15 March 2020, and subsequently died or were discharged. A random forest (RF) algorithm was used to predict the prognoses of COVID-19 patients and identify the optimal diagnostic predictors for patients’ clinical prognoses.ResultsSeven of the 126 patients were excluded for losing endpoints, 103 of the remaining 119 patients were discharged (alive) and 16 died in the hospital. A synthetic minority over-sampling technique (SMOTE) was used to correct the imbalanced distribution of clinical patients. Recursive feature elimination (RFE) was used to select the optimal subset for analysis. Eleven clinical parameters, Myo, CD8, age, LDH, LMR, CD45, Th/Ts, dyspnea, NLR, D-Dimer and CK were chosen with AUC approximately 0.9905. The RF algorithm was built to predict the prognoses of COVID-19 patients based on the best subset, and the area under the ROC curve (AUC) of the test data was 100%. Moreover, two optimal clinical risk predictors, lactate dehydrogenase (LDH) and Myoglobin (Myo), were selected based on the Gini index. The univariable logistic analysis revealed a substantial increase in the risk for in-hospital mortality when Myo was higher than 80 ng/ml (OR = 7.54, 95% CI [3.42–16.63]) and LDH was higher than 500 U/L (OR = 4.90, 95% CI [2.13–11.25]).ConclusionWe applied an RF algorithm to predict the mortality of COVID-19 patients with high accuracy and identified LDH higher than 500 U/L and Myo higher than 80 ng/ml to be potential risk factors for the prognoses of COVID-19 patients in the early stage of the disease.
creator: Jie Wang
creator: Heping Yu
creator: Qingquan Hua
creator: Shuili Jing
creator: Zhifen Liu
creator: Xiang Peng
creator: Cheng’an Cao
creator: Yongwen Luo
uri: https://doi.org/10.7717/peerj.9945
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Wang et al.

title: Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study
link: https://peerj.com/articles/9675
last-modified: 2020-09-08
description: ObjectiveTo explore the relationship between body mass index (BMI) and clinicopathological characteristics in patients with papillary thyroid carcinoma (PTC).MethodsThe clinical data of 1,579 patients with PTC, admitted to our hospital from May 2016 to March 2017, were retrospectively analyzed. According to the different BMI of patients, it can be divided into underweight recombination (BMI < 18.5 kg/m), normal body recombination (18.5 ≤ BMI < 24.0 kg/m2), overweight recombination (24.0 ≤ BMI < 28.0 kg/m2) and obesity group (BMI ≥ 28.0 kg/m2). The clinicopathological characteristics of PTC in patients with different BMIs group were compared.ResultsIn our study, the risk for extrathyroidal extension (ETE), advanced T stage (T III/IV), and advanced tumor-node-metastasis stage (TNM III/IV) in the overweight group were higher, with OR (odds ratio) = 1.99(1.41–2.81), OR = 2.01(1.43–2.84), OR = 2.94(1.42–6.07), respectively, relative to the normal weight group. The risk for ETE and T III/IV stage in the obese group were higher, with OR = 1.82(1.23–2.71) and OR = 1.82(1.23–2.70), respectively, relative to the normal weight group.ConclusionBMI is associated with the invasiveness of PTC. There is a higher risk for ETE and TNM III/IV stage among patients with PTC in the overweight group and for ETE among patients with PTC in the obese group.
creator: Huijuan Wang
creator: Pingping Wang
creator: Yu Wu
creator: Xiukun Hou
creator: Zechun Peng
creator: Weiwei Yang
creator: Lizhao Guan
creator: Linfei Hu
creator: Jingtai Zhi
creator: Ming Gao
creator: Xiangqian Zheng
uri: https://doi.org/10.7717/peerj.9675
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Wang et al.

title: Advances and complications of regenerative medicine in diabetes therapy
link: https://peerj.com/articles/9746
last-modified: 2020-09-08
description: The rapid development of technologies in regenerative medicine indicates clearly that their common application is not a matter of if, but of when. However, the regeneration of beta-cells for diabetes patients remains a complex challenge due to the plurality of related problems. Indeed, the generation of beta-cells masses expressing marker genes is only a first step, with maintaining permanent insulin secretion, their protection from the immune system and avoiding pathological modifications in the genome being the necessary next developments. The prospects of regenerative medicine in diabetes therapy were promoted by the emergence of promising results with embryonic stem cells (ESCs). Their pluripotency and proliferation in an undifferentiated state during culture have ensured the success of ESCs in regenerative medicine. The discovery of induced pluripotent stem cells (iPSCs) derived from the patients’ own mesenchymal cells has provided further hope for diabetes treatment. Nonetheless, the use of stem cells has significant limitations related to the pluripotent stage, such as the risk of development of teratomas. Thus, the direct conversion of mature cells into beta-cells could address this issue. Recent studies have shown the possibility of such transdifferentiation and have set trends for regeneration medicine, directed at minimizing genome modifications and invasive procedures. In this review, we will discuss the published results of beta-cell regeneration and the advantages and disadvantages illustrated by these experiments.
creator: Olga Brovkina
creator: Erdem Dashinimaev
uri: https://doi.org/10.7717/peerj.9746
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Brovkina and Dashinimaev

title: Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system
link: https://peerj.com/articles/9794
last-modified: 2020-09-08
description: The digestive system and metabolism of the cannonball jellyfish Stomolophus sp. 2 are not well-known. The digestion study was critical to explain its ecology and bloom success. Different enzymes are involved in food digestion, which hydrolyze carbohydrates, proteins, and lipids. This study detected lipolytic activity in enzymatic extracts from gastric pouches of Stomolophus sp. 2 collected in the summer of 2013 at Bahía de Kino, Sonora, México (28°47′47″N 111°57′25″W). Lipase/esterase activity showed optimal pH at 11.0 and 50–60 °C with a half-life (t1/2) of 33 min at 55 °C, whereas halotolerance of this activity was recorded from 0-4 M NaCl. Metal ions Ca2+ and Mn2+ did not affect the activity, but Mg2+ decreased it 14.2% ± 3.15, while chelating agents as ethylenediaminetetraacetic acid reduced the activity 8.55% ± 2.13. Inhibition of lipase/esterase activity with tetrahydrolipstatin and paraoxon-ethyl decreased the activity 18.2% ± 2.3, and 62.80% ± 0.74, respectively, whereas phenylmethanesulfonyl fluoride (a protease inhibitor) did not affect it. The enzyme displayed a higher specificity for short-chain triglycerides, but triolein, coconut oil, olive oil, and fish oil were hydrolyzed. For the first time, phospholipase activity from the gastric pouch of Stomolophus sp. 2 was detected using L-α-phosphatidylethanolamine from chicken egg yolk as a substrate. These results suggest that Stomolophus sp. 2 hydrolyze several kinds of lipids, and lipolytic enzymes are active at alkaline pH under different saline conditions, which may be essential to digest different preys.
creator: Raul B.  Martínez-Pérez
creator: Jorge A. Rodríguez
creator: Luis Alonso Leyva Soto
creator: Pablo Gortáres-Moroyoqui
creator: Lourdes M. Diaz-Tenorio
uri: https://doi.org/10.7717/peerj.9794
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Martínez-Pérez et al.

title: Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment
link: https://peerj.com/articles/9800
last-modified: 2020-09-08
description: BackgroundAbundant studies have identified the association between childhood maltreatment and self-harm (SH), but little has been discussed with regard to the role of resilience in SH behaviors of adolescents who had experienced childhood maltreatment. In this study, we investigated if resilience, as well as its five dimensions, could present negative associations with presence, repetition, and severity of SH among maltreated and neglected adolescents in China.MethodsA cross-sectional survey including 2,084 maltreated teenagers aged from 10 to 17 years was conducted in southwest China Yunnan province. The Childhood Trauma Questionnaire (CTQ), The Resilience Scale for Chinese Adolescents (RSCA), and the Modified version of Adolescents Self-Harm Scale (MASHS) were adopted to measure childhood maltreatment experiences, psychological resilience, and SH behaviors of the respondents, respectively. Binary univariate and multivariate logistic regression models were employed to discuss the associations between resilience and occurrence, repetition, severity of SH.ResultsAmong the participants who met the criteria of CTQ, the prevalence rates of SH were 63.83%, 73.94%, 71.50%, 55.53%, and 58.21% for physical abuse (PA), emotional abuse (EA), sexual abuse (SA), physical neglect (PN), and emotional neglect (EN). Final regression model demonstrated that resilience was in general inversely associated with SH, repeated SH, and severe SH for all types of childhood maltreatment, with adjusted odds ratios (aORs) ranging from 0.29 (95% CI: 0.19-0.44) to 0.46 (95% CI: 0.26-0.81). Of the five dimensions of resilience, emotion regulation served as the strongest associated factor of SH among abused youths, regardless of maltreatment types. Besides, compared with those who had lower level of goal concentration and interpersonal assistance, subjects with higher resilience level reported significantly decreased risks of SH occurrence, SH repetition, and more severe SH, in adolescents who had experienced EA and PN.ConclusionsResilience showed inverse association with childhood maltreatment related SH in Chinese adolescents. These findings preliminarily indicated that interventions targeting on building up resilience, especially enhancing emotion regulation ability, improving goal concentration, and consolidating interpersonal assistance, could be effective in reducing SH risk, repetition, and severity in maltreated Chinese teenagers.
creator: Xin Tian
creator: Guangya Yang
creator: Linling Jiang
creator: Runxu Yang
creator: Hailiang Ran
creator: Fujia Xie
creator: Xiufeng Xu
creator: Jin Lu
creator: Yuanyuan Xiao
uri: https://doi.org/10.7717/peerj.9800
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Tian et al.

title: A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering
link: https://peerj.com/articles/9805
last-modified: 2020-09-08
description: BackgroundSub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering.MethodsTo this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC.ResultsThe biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering.
creator: Herbert M. Huttanus
creator: Ryan S. Senger
uri: https://doi.org/10.7717/peerj.9805
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Huttanus and Senger