KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept
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.
Deckmyn et al. (2020) KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept. PeerJ 8:e9750 https://doi.org/10.7717/peerj.9750
Omics approaches in Allium research: Progress and way ahead
Background The 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. Method In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. Results Here, 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. Conclusion All 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.
Khandagale et al. (2020) Omics approaches in Allium research: Progress and way ahead. PeerJ 8:e9824 https://doi.org/10.7717/peerj.9824
Assessment of postoperative health functioning after knee arthroplasty in relation to pain catastrophizing: a 6-month follow-up cohort study
Background Knee 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. Methods Participants 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). Results A 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). Conclusion The 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.
Terradas-Monllor et al. (2020) Assessment of postoperative health functioning after knee arthroplasty in relation to pain catastrophizing: a 6-month follow-up cohort study. PeerJ 8:e9903 https://doi.org/10.7717/peerj.9903
Effect of nest age and habitat variables on nest survival in Marsh Harrier (Circus aeruginosus) in a fishpond habitat
Background One 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. Methods To 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. Results The 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.
Zaremba et al. (2020) Effect of nest age and habitat variables on nest survival in Marsh Harrier (Circus aeruginosus) in a fishpond habitat. PeerJ 8:e9929 https://doi.org/10.7717/peerj.9929
A descriptive study of random forest algorithm for predicting COVID-19 patients outcome
Background The 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. Methods The 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. Results Seven 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]). Conclusion We 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.
Wang et al. (2020) A descriptive study of random forest algorithm for predicting COVID-19 patients outcome. PeerJ 8:e9945 https://doi.org/10.7717/peerj.9945
Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study
Objective To explore the relationship between body mass index (BMI) and clinicopathological characteristics in patients with papillary thyroid carcinoma (PTC). Methods The 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. Results In 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. Conclusion BMI 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.
Wang et al. (2020) Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study. PeerJ 8:e9675 https://doi.org/10.7717/peerj.9675
Advances and complications of regenerative medicine in diabetes therapy
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.
Brovkina et al. (2020) Advances and complications of regenerative medicine in diabetes therapy. PeerJ 8:e9746 https://doi.org/10.7717/peerj.9746
Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system
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.
Martínez-Pérez et al. (2020) Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system. PeerJ 8:e9794 https://doi.org/10.7717/peerj.9794
Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment
Background Abundant 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. Methods A 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. Results Among 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. Conclusions Resilience 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.
Tian et al. (2020) Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment. PeerJ 8:e9800 https://doi.org/10.7717/peerj.9800
A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering
Background Sub-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. Methods To 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. Results The 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.
Huttanus et al. (2020) A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering. PeerJ 8:e9805 https://doi.org/10.7717/peerj.9805