State-space modeling of the dynamics of temporal plant cover using visually determined class data
A lot of vegetation-related data have been collected as an ordered plant cover class that can be determined visually. However, they are difficult to analyze numerically as they are in an ordinal scale and have uncertainty in their classification. Here, I constructed a state-space model to estimate unobserved plant cover proportions (ranging from zero to one) from such cover class data. The model assumed that the data were measured longitudinally, so that the autocorrelations in the time-series could be utilized to estimate the unobserved cover proportion. The model also assumed that the quadrats where the data were collected were arranged sequentially, so that the spatial autocorrelations also could be utilized to estimate the proportion. Assuming a beta distribution as the probability distribution of the cover proportion, the model was implemented with a regularized incomplete beta function, which is the cumulative density function of the beta distribution. A simulated dataset and real datasets, with one-dimensional spatial structure and longitudinal survey, were fit to the model, and the parameters were estimated using the Markov chain Monte Carlo method. Then, the validity was examined using posterior predictive checks. As a result of the fitting, the Markov chain successfully converged to the stationary distribution, and the posterior predictive checks did not show large discrepancies. For the simulated dataset, the estimated values were close to the values used for the data generation. The estimated values for the real datasets also seemed to be reasonable. These results suggest that the proposed state-space model was able to successfully estimate the unobserved cover proportion. The present model is applicable to similar types of plant cover class data, and has the possibility to be expanded, for example, to incorporate a two-dimensional spatial structure and/or zero-inflation.
Itô (2020) State-space modeling of the dynamics of temporal plant cover using visually determined class data. PeerJ 8:e9383 https://doi.org/10.7717/peerj.9383
Smoking cessation interventions on health-care workers: a systematic review and meta-analysis
Objective The authors carried out a systematic review and a meta-analysis on smoking cessation interventions on health -care workers to clarify the state of the art interventions and to identify the best one. Materials and Methods This review was registered with PROSPERO: CRD42019130117. The databases PubMed, Scopus, Web of Science and CINAHL were searched until December 2018. Quality of all studies included in the systematic review was assessed according to the Newcastle-Ottawa Scale (NOS) on cohort or cross-sectional studies and to the Cochrane Risk of Bias Tool for Randomized Controlled Trials. Meta-analysis and meta-regression analyses were also carried out for cohort studies (quasi-experimental or a before-after studies design) and clinical trials. Results Twenty–four studies have been included in the analysis: four before-after, 13 cross-sectional, three quasi-experimental studies and four clinical trials. Articles were heterogeneous (P for homogeneity <0.01), but they have all shown positive results since they reached the goal of smoking cessation among health-care workers, even if with different proportions. Meta-analysis was performed on 10 studies (six cohort studies and four clinical trials), showing a 21% of success rate from the application of smoking cessation interventions, either pharmacological or behavioral ones. The resulted pooled RR (Risk Ratio) was 1.21 (95% CI [1.06–1.38]), being 24% of success rate from clinical trials (pooled RR 1.244; 95% CI [1.099–1.407]) and 19% of success rate from cohort studies (pooled RR 1.192; 0.996–1.426). However, two studies have confidence intervals which include unity and one study has a wide confidence interval; as a consequence, the meta-analysis for its results depends heavily on one single study. Meta-regression analysis revealed that results were influenced by the number of participants. Conclusion Both policy and pharmaceutical interventions can obtain positive results in quitting smoking among health-care workers. However, as shown by our review, combination approaches can produce better results in terms of cessation percentages and smoking abstinence.
La Torre et al. (2020) Smoking cessation interventions on health-care workers: a systematic review and meta-analysis. PeerJ 8:e9396 https://doi.org/10.7717/peerj.9396
Prevalence and correlates of depressive symptoms among Chinese patients with cataracts treated in tertiary general hospitals
Background Previous studies recruited unrepresentative samples of Chinese patients with cataract and reported a wide range of prevalence of depressive symptoms in this patient population (18.0–89.7%). The present study determined the prevalence and correlates of depressive symptoms among a consecutive sample of Chinese patients with cataract treated in tertiary general hospitals. Methods A total of 339 patients with cataract were consecutively selected from ophthalmology departments of two large general hospitals in Wuhan, China. Depressive symptoms were assessed with the Chinese Hospital Anxiety and Depression Scale. Logistic regression was used to identify factors that were associated with depression. Results The prevalence of depressive symptoms was 23.9% (95% CI [19.4–28.4]%) among patients with cataract. Correlates for depressive symptoms include an education level of primary school and below (OR = 1.93, P = 0.038), marital status of “others” (OR =3.15, P < 0.001), poor family economic status (OR = 2.26, P = 0.010), nuclear cataract (OR =4.32, P < 0.001), and mixed cataract (OR = 2.76, P = 0.017). Conclusions Depressive symptoms are common among Chinese patients with cataract treated in large general hospitals. Patients who are poorly educated, have a marital status other than “married”, have poor family economic status, and suffer from nuclear and mixed cataracts are at greater risk for depressive symptoms.
Liu et al. (2020) Prevalence and correlates of depressive symptoms among Chinese patients with cataracts treated in tertiary general hospitals. PeerJ 8:e9397 https://doi.org/10.7717/peerj.9397
Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017
The urbanization growth in the 20th and 21st centuries has led to a series of unprecedented problems in the ecological environment. Based on constructing an integrated urbanization-ecological environment index system, this article conducts a comprehensive evaluation of the coupling coordination degree between urbanization and the ecological environment and uncovers its spatiotemporal variation characteristics in the Siberian and Far East Federal Districts, Russia from 2005 to 2017. The coupling coordination of urbanization and the ecological environment in the Siberian and Far East Federal Districts improve from slightly unbalanced development stage to barely balanced development stage from 2005 to 2017. In 2017, more than half regions achieved the barely balanced development of urbanization and the ecological environment. However, the most desirable development stage, the superior balanced development stage, is never achieved in the Siberian and Far East Federal Districts during the study period. The spatial pattern of the coupling coordination degree of urbanization and the ecological environment in the Siberian and Far East Federal District gradually changes from “dumbbell” to “high-north low-south”. The south part of the Siberian and Far East Federal Districts should be paid more attention in the future urban development process. This research will provide support in the future coordination of urban development in the Siberian and Far East Federal Districts.
Zheng et al. (2020) Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017. PeerJ 8:e9125 https://doi.org/10.7717/peerj.9125
Physiological and anatomical differentiation of two sympatric weed populations
In the vineyards of Rhineland-Palatinate (Germany), two different types of Shepherd’s Purse (Capsella bursa-pastoris) coexist: (1) the common type called ‘wild type’, and (2) the decandric type called Capsella apetala or ‘Spe’ with four stamens in place of the four petals. In this study, we compare the anatomical and physiological characters of rosette leaves of the respective types. Progeny of individual plants was cultivated in growth chambers under low- and high-light conditions. Under low-light conditions, the stomata densities of the adaxial and abaxial epidermis did not differ between the two types. When grown under high-light conditions, wild type and Spe, both exhibited increased stomata densities compared to low-light conditions, but Spe to a lesser extent than the wild type. The maximal photosynthetic capacity of Spe was lower in both, low-light and high-light conditions compared to wild-type plants. Under all CO2 concentrations, Spe seemed to be less productive. The less effective CO2 assimilation of the Spe mutant C. apetala was accompanied by later flowering. This fact prolonged the vegetative phase of Spe by about two weeks and was sufficient for the maintenance of both populations stably over years.
Neuffer et al. (2020) Physiological and anatomical differentiation of two sympatric weed populations. PeerJ 8:e9226 https://doi.org/10.7717/peerj.9226
Optimizing a reliable ex vivo human blood model to analyze expression of Staphylococcus epidermidis genes
Human blood is often used as an ex vivo model to mimic the environment encountered by pathogens inside the host. A significant variety of experimental conditions has been reported. However, optimization strategies are often not described. This study aimed to evaluate key parameters that are expected to influence Staphylococcus epidermidis gene expression when using human blood ex vivo models. Our data confirmed that blood antimicrobial activity was dependent on initial bacterial concentration. Furthermore, blood degradation over time resulted in lower antimicrobial activity, with a 2% loss of leukocytes viability correlating with a 5-fold loss of antimicrobial activity against S. epidermidis. We further demonstrated that the volume of human blood could be reduced to as little as 0.18 mL without affecting the stability of gene expression of the tested genes. Overall, the data described herein highlight experimental parameters that should be considered when using a human blood ex vivo model for S. epidermidis gene expression analysis.
Brás et al. (2020) Optimizing a reliable ex vivo human blood model to analyze expression of Staphylococcus epidermidis genes. PeerJ 8:e9295 https://doi.org/10.7717/peerj.9295
Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis
Background Pancreatic cancer is one of the most common malignant cancers worldwide. Currently, the pathogenesis of pancreatic cancer remains unclear; thus, it is necessary to explore its precise molecular mechanisms. Methods To identify candidate genes involved in the tumorigenesis and proliferation of pancreatic cancer, the microarray datasets GSE32676, GSE15471 and GSE71989 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between Pancreatic ductal adenocarcinoma (PDAC) and nonmalignant samples were screened by GEO2R. The Database for Annotation Visualization and Integrated Discovery (DAVID) online tool was used to obtain a synthetic set of functional annotation information for the DEGs. A PPI network of the DEGs was established using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and a combination of more than 0.4 was considered statistically significant for the PPI. Subsequently, we visualized the PPI network using Cytoscape. Functional module analysis was then performed using Molecular Complex Detection (MCODE). Genes with a degree ≥10 were chosen as hub genes, and pathways of the hub genes were visualized using ClueGO and CluePedia. Additionally, GenCLiP 2.0 was used to explore interactions of hub genes. The Literature Mining Gene Networks module was applied to explore the cocitation of hub genes. The Cytoscape plugin iRegulon was employed to analyze transcription factors regulating the hub genes. Furthermore, the expression levels of the 13 hub genes in pancreatic cancer tissues and normal samples were validated using the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Moreover, overall survival and disease-free survival analyses according to the expression of hub genes were performed using Kaplan-Meier curve analysis in the cBioPortal online platform. The relationship between expression level and tumor grade was analyzed using the online database Oncomine. Lastly, the eight snap-frozen tumorous and adjacent noncancerous adjacent tissues of pancreatic cancer patients used to detect the CDK1 and CEP55 protein levels by western blot. Conclusions Altogether, the DEGs and hub genes identified in this work can help uncover the molecular mechanisms underlying the tumorigenesis of pancreatic cancer and provide potential targets for the diagnosis and treatment of this disease.
Jin et al. (2020) Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis. PeerJ 8:e9301 https://doi.org/10.7717/peerj.9301
Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb
Morphological shifts observed in the fossil record of a lineage potentially indicate concomitant shifts in ecology of that lineage. Mekosuchine crocodiles of Cenozoic Australia display departures from the typical eusuchian body-plan both in the cranium and postcranium. Previous qualitative studies have suggested that these crocodiles had a more terrestrial habitus than extant crocodylians, yet the capacity of mekosuchine locomotion remains to be tested. Limb bone shape, such as diaphyseal cross-section and curvature, has been related to habitual use and locomotory function across a wide variety of taxa. Available specimens of mekosuchine limbs, primarily humeri, are distinctly columnar compared with those of extant crocodylians. Here we apply a quantitative approach to biomechanics in mekosuchine taxa using both geomorphic morphometric and finite element methods to measure bone shape and estimate locomotory stresses in a comparative context. Our results show mekosuchines appear to diverge from extant semi-aquatic saltwater and freshwater crocodiles in cross-sectional geometry of the diaphysis and generate different structural stresses between models that simulate sprawling and high-walk gaits. The extant crocodylians display generally rounded cross-sectional diaphyseal outlines, which may provide preliminary indication of resistance to torsional loads that predominate during sprawling gait, whereas mekosuchine humeri appear to vary between a series of elliptical outlines. Mekosuchine structural stresses are comparatively lower than those of the extant crocodylians and reduce under high-walk gait in some instances. This appears to be a function of bending moments induced by differing configurations of diaphyseal curvature. Additionally, the neutral axis of structural stresses is differently oriented in mekosuchines. This suggests a shift in the focus of biomechanical optimisation, from torsional to axial loadings. Our results lend quantitative support to the terrestrial habitus hypothesis in so far as they suggest that mekosuchine humeri occupied a different morphospace than that associated with the semi-aquatic habit. The exact adaptational trajectory of mekosuchines, however, remains to be fully quantified. Novel forms appear to emerge among mekosuchines during the late Cenozoic. Their adaptational function is considered here; possible applications include navigation of uneven terrain and burrowing.
Stein et al. (2020) Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb. PeerJ 8:e9349 https://doi.org/10.7717/peerj.9349
A potential role for Galectin-3 inhibitors in the treatment of COVID-19
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), has been declared a global pandemic by the World Health Organization. With no standard of care for the treatment of COVID-19, there is an urgent need to identify therapies that may be effective in treatment. Recent evidence has implicated the development of cytokine release syndrome as the major cause of fatality in COVID-19 patients, with elevated levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) observed in patients. Galectin-3 (Gal-3) is an animal lectin that has been implicated in the disease process of a variety of inflammatory conditions. Inhibitors of the small molecule Gal-3 have been shown to reduce the levels of both IL-6 and TNF-α in vitro and have shown anti-inflammatory effects in vivo. Additionally, a key domain in the spike protein of β-coronaviridae, a genus which includes SARS-CoV2, is nearly identical in morphology to human Gal-3. These spike proteins are critical for the virus’ entry into host cells. Here we provide a systematic review of the available literature and an impetus for further research on the use of Gal-3 inhibitors in the treatment of COVID-19. Further, we propose a dual mechanism by which Gal-3 inhibition may be beneficial in the treatment of COVID-19, both suppressing the host inflammatory response and impeding viral attachment to host cells.
Caniglia et al. (2020) A potential role for Galectin-3 inhibitors in the treatment of COVID-19. PeerJ 8:e9392 https://doi.org/10.7717/peerj.9392
Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods
Cataract formation is a slow accumulative process due to protein aggregates promoted by different factors over time. Zinc and copper ions have been reported to induce the formation of aggregates opaque to light in the human gamma D crystallin (HγD) in a concentration and temperature dependent manner. In order to gain insight into the mechanism of metal-induced aggregation of HγD under conditions that mimic more closely the slow, accumulative process of the disease, we have studied the non-equilibrium process with the minimal metal dose that triggers HγD aggregation. Using a wide variety of biophysics techniques such as turbidimetry, dynamic light scattering, fluorescence, nuclear magnetic resonance and computational methods, we obtained information on the molecular mechanisms for the formation of aggregates. Zn(II) ions bind to different regions at the protein, probably with similar affinities. This binding induces a small conformational rearrangement within and between domains and aggregates via the formation of metal bridges without any detectable unfolded intermediates. In contrast, Cu(II)-induced aggregation includes a lag time, in which the N-terminal domain partially unfolds while the C-terminal domain and parts of the N-terminal domain remain in a native-like conformation. This partially unfolded intermediate is prone to form the high-molecular weight aggregates. Our results clearly show that different external factors can promote protein aggregation following different pathways.
Fernández-Silva et al. (2020) Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods. PeerJ 8:e9178 https://doi.org/10.7717/peerj.9178