Exploring abnormal Cambrian-aged trilobites in the Smithsonian collection
Biomineralised trilobite exoskeletons provide a 250 million year record of abnormalities in one of the most diverse arthropod groups in history. One type of abnormality—repaired injuries—have allowed palaeobiologists to document records of Paleozoic predation, accidental damage, and complications in moulting experienced by the group. Although Cambrian trilobite injuries are fairly well documented, the illustration of new injured specimens will produce a more complete understanding of Cambrian prey items. To align with this perspective, nine new abnormal specimens displaying healed injuries from the Smithsonian National Museum of Natural History collection are documented. The injury pattern conforms to the suggestion of lateralised prey defence or predator preference, but it is highlighted that the root cause for such patterns is obscured by the lumping of data across different palaeoecological and environmental conditions. Further studies of Cambrian trilobites with injuries represent a key direction for uncovering evidence for the Cambrian escalation event.
Bicknell et al. (2020) Exploring abnormal Cambrian-aged trilobites in the Smithsonian collection. PeerJ 8:e8453 https://doi.org/10.7717/peerj.8453
Key genes and co-expression modules involved in asthma pathogenesis
Machine learning and weighted gene co-expression network analysis (WGCNA) have been widely used due to its well-known accuracy in the biological field. However, due to the nature of a gene’s multiple functions, it is challenging to locate the exact genes involved in complex diseases such as asthma. In this study, we combined machine learning and WGCNA in order to analyze the gene expression data of asthma for better understanding of associated pathogenesis. Specifically, the role of machine learning is assigned to screen out the key genes in the asthma development, while the role of WGCNA is to set up gene co-expression network. Our results indicated that hormone secretion regulation, airway remodeling, and negative immune regulation, were all regulated by critical gene modules associated with pathogenesis of asthma progression. Overall, the method employed in this study helped identify key genes in asthma and their roles in the asthma pathogenesis.
Huang et al. (2020) Key genes and co-expression modules involved in asthma pathogenesis. PeerJ 8:e8456 https://doi.org/10.7717/peerj.8456
Larger contactor area increases low-frequency vibratory sensitivity in hairy skin
Background In research, assessing vibratory cutaneous sensitivity is an important research branch to quantify various diseases or to develop devices for pattern recognition. The measured vibration perception thresholds (VPTs), however, are subjective and usually result in a large data variability. This might induce difficulties to detect differences, for example, when comparing different anatomical locations. Hence, a higher ability to detect changes is desirable. Another feature of VPTs is spatial summation, but in the literature it is controversially discussed whether or not this phenomenon is also present in the lower frequency range. For these reasons, the present study aimed to investigate whether an enlarged matrix contactor area (measured at the hairy skin) induces improvements in subjective sensitivity using high and low frequencies, and whether a large contactor area is better able to identify changes of VPTs than a small contactor area of a single contactor. For each frequency, we hypothesized an increased sensitivity for the matrix compared to the single contactor. We also hypothesized that changes can be better-detected between the anatomical locations when using the matrix than the single contactor. Methods Twenty healthy and young participants voluntarily took part in this study. Three anatomical locations at the torso were measured at the middle aspect of the lower back, middle lateral aspect of the upper arm, and the region just below the armpit. At each location, two frequencies (30, 200 Hz) and two contactor conditions (single contactor: 0.48 cm2 , contactor matrix: 9 × 0.48 cm2 = 4.32 cm2) were tested in a randomized order. Results Supporting our hypothesis, we found that improved cutaneous sensitivity after increasing the contactor size occurs not only at high, but also at low frequencies at all anatomical locations. Large contactor sizes resulted in higher sensitivity and in a superior ability to detect changes. The superior behavior of the matrix to exhibit a lower variability could not always be proven. This work may be relevant for future studies aiming to identify changes of VPTs in various patient groups, for example.
Schmidt et al. (2020) Larger contactor area increases low-frequency vibratory sensitivity in hairy skin. PeerJ 8:e8479 https://doi.org/10.7717/peerj.8479
EMT-related gene expression is positively correlated with immunity and may be derived from stromal cells in osteosarcoma
Background Osteosarcoma is the most common type of bone cancer in children and young adults. Recent studies have shown a correlation between epithelial–mesenchymal transition (EMT)-related gene expression and immunity in human cancers. Here, we investigated the relationship among EMT, immune activity, stromal activity and tumor purity in osteosarcoma. Methods We defined EMT gene signatures and evaluated immune activity and stromal activity based on the gene expression and clinical data from three independent microarray datasets. These factors were evaluated by single sample Gene Set Enrichment Analyses and the ESTIMATE tool. Finally, we analyzed the key source of EMT gene expression in osteosarcoma using microarray datasets from the Gene Expression Omnibus and human samples that we collected. Results EMT-related gene expression was positively correlated with immune and stromal activity in osteosarcoma. Tumor purity was negatively correlated with EMT, immune activity and stromal cells. We further demonstrated that high EMT gene expression could significantly predict poor overall survival (OS) and recurrence-free survival (RFS) in osteosarcoma patients, while high immune activity cannot. However, combining these factors could have further prognostic value for osteosarcoma patients in terms of OS and RFS. Finally, we found that stromal cells may serve as a key source of EMT gene expression in osteosarcoma. Conclusion The results of this study reveal that the expression of EMT genes and immunity are positively correlated, but these signatures convey disparate prognostic information. Furthermore, the results indicate that EMT-related gene expression may be derived from stromal rather than epithelial cancer cells.
Peng et al. (2020) EMT-related gene expression is positively correlated with immunity and may be derived from stromal cells in osteosarcoma. PeerJ 8:e8489 https://doi.org/10.7717/peerj.8489
Radiotherapy after mastectomy has significant survival benefits for inflammatory breast cancer: a SEER population-based retrospective study
Objectives The survival benefit of postmastectomy radiotherapy (PMRT) has not been fully proven in inflammatory breast cancer (IBC). Thus, in the present research, we aimed at elucidating the effects of PMRT on the survival of IBC patients. Methods Eligible patients were collected from the Surveillance, Epidemiology, and End Results (SEER) dataset between 2010 and 2013. The Kaplan-Meier method along with the log-rank test was utilized for the comparison of both the overall survival (OS) andthe cancer-specific survival (CSS) in patients undergoing PMRT or not. Additionally, multivariate survival analysis of CSS and OS were performed using the Cox proportional hazard model. Results In total, 293 eligible cases were identified, with the median follow-up time of 27 months (range: 5–59 months). After propensity score matching (PSM), 188 patients (94 for each) were classified intothe No-PMRT and the PMRT group. Consequently, significantly higher OS rates were detected in the PMRT group compared with the No-PMRT group prior to PSM (P = 0.034), and significantly higher CSS (P = 0.013) and OS (P = 0.0063) rates were observed following PSM. Furthermore, multivariate analysis revealed thatPMRT [CSS (HR: 0.519, 95% CI [0.287–0.939], P = 0.030); OS (HR: 0.480, 95% CI [0.269–0.859], P = 0.013)], as well as Her2+/HR+ subtype, was independent favorable prognostic factors.Besides, black ethnicity, AJCC stage IV and triple-negative subtype were independent unfavorable prognostic factors. Further subgroup analysis revealed that most of the study population could benefit from PMRT, no matter OS or CSS. Conclusions Our findings support that PMRT could improve the survival of IBC patients.
Li et al. (2020) Radiotherapy after mastectomy has significant survival benefits for inflammatory breast cancer: a SEER population-based retrospective study. PeerJ 8:e8512 https://doi.org/10.7717/peerj.8512
Glycyrrhizin suppresses epithelial-mesenchymal transition by inhibiting high-mobility group box1 via the TGF-β1/Smad2/3 pathway in lung epithelial cells
Background Epithelial-mesenchymal transition (EMT) plays an important role in fibrosis, chronic inflammation, tumor metastasis, etc. Glycyrrhizin, an active component extracted from licorice plant, has been reported to treat a variety of inflammatory reactions through inhibiting high-mobility group box1 (HMGB1), which has been suggested to be a significant mediator in EMT process. However, whether glycyrrhizin affects the EMT process or not remains unclear. Methods Human alveolar epithelial cell line A549 and normal human bronchial epithelial cell line BEAS-2B were treated with extrinsic TGF-β1 to induce EMT. Elisa was used to detect HMGB1 concentrations in cell supernatant. RNA interference and lentivirus infection experiments were performed to investigate the involvement of HMGB1 in EMT process. Cell Counting Kit-8 (CCK-8) was used to detect the viability of A549 and BEAS-2B cells treated with glycyrrhizin. Finally, the effects of glycyrrhizin on EMT changes, as well as the underlying mechanisms, were evaluated via Western blot, immunofluorescence and transwell assays. Results Our results showed that HMGB1 expression was increased by TGF-β1, and knockdown of HMGB1 expression reversed TGF-β1-induced EMT in A549 and BEAS-2B cells. Ectopic HMGB1 expression or TGF-β1 treatment caused a significant increase in HMGB1 release. Notably, we found that glycyrrhizin treatment effectively suppressed TGF-β1-induced EMT process by inhibiting HMGB1. Also, glycyrrhizin significantly inhibited the migration of both A549 and BEAS-2B cells promoted by TGF-β1. Mechanistically, HMGB1 overexpression could activate Smad2/3 signaling in A549 and BEAS-2B cells. Glycyrrhizin significantly blocked the phosphorylation of Smad2/3 stimulated either by TGF-β1 or by ectopic HMGB1 in A549 and BEAS-2B cells. Conclusions HMGB1 is a vital mediator of EMT changes induced by TGF-β1 in lung epithelial cells. Importantly, glycyrrhizin can effectively block Smad2/3 signaling pathway through inhibiting HMGB1, thereby suppressing the EMT progress.
Gui et al. (2020) Glycyrrhizin suppresses epithelial-mesenchymal transition by inhibiting high-mobility group box1 via the TGF-β1/Smad2/3 pathway in lung epithelial cells. PeerJ 8:e8514 https://doi.org/10.7717/peerj.8514
Epidemiological scenario of dengue in the state of Manipur during the last 3 years
Background The study of disease transmission of dengue fever (DF) is perplexing in the Indian subcontinent as all the four serotypes are circling. Also, there is no efficient epidemiological examination done on dengue cases in Manipur, a north-eastern territory of India. Method We utilized the dengue information extricated from the lab register of Viral Research and Diagnostic Laboratory (VRDL) from 2016 to 2018. All presumed outpatient and inpatients dengue cases from open and private health-care facilities are incorporated into the VRDL database whose informed consent were gotten. Results A sum of 1689 instances of associated patients with dengue infection was tried for dengue ELISA test and 272 (16.10%) samples were seen as seropositive. The month-wise conveyance of dengue cases is very intriguing as the three years of study demonstrates a variation design in perception. In all the three years dengue seropositive cases were seen higher in the male populace. Be that as it may, there is no noteworthy incentive to the inspiration of dengue seropositive towards male than female. Conclusion Our examination exhibits a comparative epidemiological investigation on seroprevelance of dengue in the province of Manipur for three years. This is an endeavour to show epidemiological dengue seroprevelance in the territory of Manipur which in future would be a reference from general wellbeing worries for making up essential move intend to shorten the spread of dengue.
Singh et al. (2020) Epidemiological scenario of dengue in the state of Manipur during the last 3 years. PeerJ 8:e8518 https://doi.org/10.7717/peerj.8518
Protein expression profile changes of lung tissue in patients with pulmonary hypertension
Background Pulmonary hypertension occurs in approximately 1% of the global population, and the prognosis for such patients may be poor. However, the mechanisms underlying the development of this disease remain unclear. Thus, understanding the development of pulmonary hypertension and finding new therapeutic targets and approaches are important for improved clinical outcomes. Methods Lung tissue specimens were collected from six patients with atrial septal defect and pulmonary hypertension (all women, with a mean age of 46.5 ± 4.7 years, and their condition could not be corrected with an internal medical occlusion device) and from nine control patients with lung cancer who underwent lobectomy (six men and three women, with a mean age of 56.7 ± 1.7 years). Isobaric tags for relative and absolute quantitation and liquid chromatography tandem mass spectrometry analyses were used to detect protein expression levels. Results We found 74 significantly upregulated and 88 significantly downregulated differentially expressed proteins between control and pulmonary hypertensive lung tissue specimens. Gene ontology analyses identified the top 20 terms in all three categories, that is, biological process, cellular component, and molecular function. Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction analyses determined the top 10 signaling pathways and found that the six hub proteins associated with the differentially expressed upregulated proteins (PRKAA1, DHPR, ACTB, desmin, ACTG1, and ITGA1) were all involved in hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, and dilated cardiomyopathy. Conclusion Our results identified protein expression profile changes in lung tissue derived from patients with pulmonary hypertension, providing potential new biomarkers for clinical diagnosis and prognosis for patients with pulmonary hypertension and offering candidate protein targets for future therapeutic drug development.
Wu et al. (2020) Protein expression profile changes of lung tissue in patients with pulmonary hypertension. PeerJ 8:e8153 https://doi.org/10.7717/peerj.8153
Spatial analysis, local people’s perception and economic valuation of wetland ecosystem services in the Usumacinta floodplain, Southern Mexico
The Usumacinta floodplain is an exceptional area for biodiversity with important ecosystem services for local people. The main objective of this paper was to estimate reference values and define local perceptions of ecosystem services provided by wetlands and overlapping them with spatially explicit socioeconomic and biodiversity indicators. We used the Usumacinta floodplain as an example of a territory where high dependence of rural people on ecosystem services is confronted with development projects that threat the flow of ecosystem services, thus affecting rural people well-being. With a combination of data from remote sensing, global databases of ecosystem service values, local perception of ecosystem services and socioeconomic and biodiversity richness indicators in a spatially explicit framework, we develop a policy-oriented approach for rapid assessment to manage wetlands and maintain people’s livelihoods. Regulating and provisioning services are identified as the most relevant ecosystem services in terms of their monetary value and local perceived importance. In a spatially explicit manner, this approach highlights the most valuable wetlands and identifies rural societies that are highly dependent on ecosystem services. Our approach can be replicated elsewhere and could provide valuable information for policymakers to design policies that can contribute to conserve wetland ecosystems where under threat of development.
Spatial and Geographic Information Science
Camacho-Valdez et al. (2020) Spatial analysis, local people’s perception and economic valuation of wetland ecosystem services in the Usumacinta floodplain, Southern Mexico. PeerJ 8:e8395 https://doi.org/10.7717/peerj.8395
Novel insights into the effect of drought stress on the development of root and caryopsis in barley
Drought is a common natural disaster in barley production, which restricts the growth and development of barley roots and caryopses seriously, thereby decreasing yield and debasing grain quality. However, mechanisms for how drought stress affects barley caryopses and roots development under drought stress are unclear. In this paper, Suluomai1 was treated with drought from flowering to caryopses mature stage. The morphological and structural changes in roots growth and caryopses development of barley were investigated. Drought stress increased root/shoot ratio and eventually led to the 20.16% reduction of ear weight and 7.75% reduction of 1,000-grain weight by affecting the biomass accumulation of roots and caryopses. The barley roots under drought had more lateral roots while the vessel number and volume of roots decreased. Meanwhile, drought stress accelerated the maturation of caryopses, resulting in a decrease in the accumulation of starch but a significant increase of protein accumulation in barley endosperm. There was a significantly positive correlation (0.76) between the area of root vessel and the relative area of protein in endosperm cells under normal condition and drought increased the correlation coefficient (0.81). Transcriptome analysis indicated that drought induced differential expressions of genes in caryopses were mainly involved in encoding storage proteins and protein synthesis pathways. In general, drought caused changes in the morphology and structure of barley roots, and the roots conveyed stress signals to caryopses, inducing differential expression of genes related to protein biosynthesis, ultimately leading to the increase in the accumulation of endosperm protein. The results not only deepen the study on drought mechanism of barley, but also provide theoretical basis for molecular breeding, high-yield cultivation and quality improvement in barley.
Li et al. (2020) Novel insights into the effect of drought stress on the development of root and caryopsis in barley. PeerJ 8:e8469 https://doi.org/10.7717/peerj.8469