title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=346
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The contribution of estimated dead space fraction to mortality prediction in patients with chronic obstructive pulmonary disease—a new proposal
link: https://peerj.com/articles/17081
last-modified: 2024-03-27
description: BackgroundMortality due to chronic obstructive pulmonary disease (COPD) is increasing. However, dead space fractions at rest (VD/VTrest) and peak exercise (VD/VTpeak) and variables affecting survival have not been evaluated. This study aimed to investigate these issues.MethodsThis retrospective observational cohort study was conducted from 2010–2020. Patients with COPD who smoked, met the Global Initiatives for Chronic Lung Diseases (GOLD) criteria, had available demographic, complete lung function test (CLFT), medication, acute exacerbation of COPD (AECOPD), Charlson Comorbidity Index, and survival data were enrolled. VD/VTrest and VD/VTpeak were estimated (estVD/VTrest and estVD/VTpeak). Univariate and multivariable Cox regression with stepwise variable selection were performed to estimate hazard ratios of all-cause mortality.ResultsOverall, 14,910 patients with COPD were obtained from the hospital database, and 456 were analyzed after excluding those without CLFT or meeting the lung function criteria during the follow-up period (median (IQR) 597 (331–934.5) days). Of the 456 subjects, 81% had GOLD stages 2 and 3, highly elevated dead space fractions, mild air-trapping and diffusion impairment. The hospitalized AECOPD rate was 0.60 ± 2.84/person/year. Forty-eight subjects (10.5%) died, including 30 with advanced cancer. The incidence density of death was 6.03 per 100 person-years. The crude risk factors for mortality were elevated estVD/VTrest, estVD/VTpeak, ≥2 hospitalizations for AECOPD, advanced age, body mass index (BMI) <18.5 kg/m2, and cancer (hazard ratios (95% C.I.) from 1.03 [1.00–1.06] to 5.45 [3.04–9.79]). The protective factors were high peak expiratory flow%, adjusted diffusing capacity%, alveolar volume%, and BMI 24–26.9 kg/m2. In stepwise Cox regression analysis, after adjusting for all selected factors except cancer, estVD/VTrest and BMI <18.5 kg/m2 were risk factors, whereas BMI 24–26.9 kg/m2 was protective. Cancer was the main cause of all-cause mortality in this study; however, estVD/VTrest and BMI were independent prognostic factors for COPD after excluding cancer.ConclusionsThe predictive formula for dead space fraction enables the estimation of VD/VTrest, and the mortality probability formula facilitates the estimation of COPD mortality. However, the clinical implications should be approached with caution until these formulas have been validated.
creator: Ming-Lung Chuang
creator: Yu Hsun Wang
creator: I-Feng Lin
uri: https://doi.org/10.7717/peerj.17081
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2024 Chuang et al.

title: Buffalo-bur (Solanum rostratum Dunal) invasiveness, bioactivities, and utilization: a review
link: https://peerj.com/articles/17112
last-modified: 2024-03-27
description: Solanum rostratum Dunal, belongs to the Solanaceae family and has drawn attention for its intricate interplay of invasiveness, phytochemical composition, and potential bioactivities. Notably invasive, S. rostratum employs adaptive mechanisms during senescence, featuring thorn formation on leaves, fruits, and stems seed self-propulsion, and resistance to drought. This adaptability has led to its proliferation in countries such as China, Canada, and Australia, extending beyond its Mexican origin. Despite its invasive historical reputation, recent studies unveil a rich array of phytochemicals in S. rostratum, suggesting untapped economic potential due to under-exploration. This review delves into exploring the potential uses of S. rostratum while elucidating the bioactive compounds associated with diverse identified bioactivities. In terms of phytochemistry, S. rostratum reveals an abundance of various bioactive compounds, including alkaloids, flavonoids, phenols, saponins, and glycosides. These compounds confer a range of beneficial bioactivities, encompassing antioxidant, antifungal, anticarcinogenic, anti-inflammatory, phytotoxic, and pesticidal properties. This positions S. rostratum as a reservoir of valuable chemical constituents with potential applications, particularly in medicine and agriculture. The review provides comprehensive insights into the phytochemistry, bioactivities, and bioactivity-guided fractionation of S. rostratum. In this review, we focus on the potential utilization of S. rostratum by emphasizing its phytochemical profile, which holds promise for diverse applications. This review is the first that advocates for further exploration and research to unlock the plant’s full potential for both economic and environmental benefit.
creator: Sandra Amarachi Ozuzu
creator: Rizvi Syed Arif Hussain
creator: Nigora Kuchkarova
creator: Gift Donu Fidelis
creator: Shixing Zhou
creator: Théogène Habumugisha
creator: Hua Shao
uri: https://doi.org/10.7717/peerj.17112
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Ozuzu et al.

title: Erythropoietin alleviates lung ischemia-reperfusion injury by activating the FGF23/FGFR4/ERK signaling pathway
link: https://peerj.com/articles/17123
last-modified: 2024-03-27
description: BackgroundThe purpose of the present study was to investigate the effect of erythropoietin (EPO) on lung ischemia-reperfusion injury (LIRI).MethodsSprague Dawley rats and BEAS-2B cells were employed to construct an ischemia-reperfusion (I/R)-induced model in vivo and in vitro, respectively. Afterward, I/R rats and tert-butyl hydroperoxide (TBHP)-induced cells were treated with different concentrations of EPO. Furthermore, 40 patients with LIRI and healthy controls were enrolled in the study.ResultsIt was observed that lung tissue damage, cell apoptosis and the expression of BAX and caspase-3 were higher in the LIRI model in vivo and in vitro than in the control group, nevertheless, the Bcl-2, FGF23 and FGFR4 expression level was lower than in the control group. EPO administration significantly reduced lung tissue damage and cell apoptosis while also up-regulating the expression of FGF23 and FGFR4. Rescue experiments indicated that EPO exerted a protective role associated with the FGF23/FGFR4/p-ERK1/2 signal pathway. Notably, the expression of serum EPO, FGF23, FGFR4 and Bcl-2 was decreased in patients with LIRI, while the expression of caspase-3 and BAX was higher.ConclusionEPO could effectively improve LIRI, which might be related to the activation of the FGF23/FGFR4/p-ERK1/2 signaling pathway.
creator: Xiaosheng Jin
creator: Weijing Jin
creator: Guoping Li
creator: Jisheng Zheng
creator: Xianrong Xu
uri: https://doi.org/10.7717/peerj.17123
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Jin et al.

title: Comprehensive analysis of the microbiome in Apis cerana honey highlights honey as a potential source for the isolation of beneficial bacterial strains
link: https://peerj.com/articles/17157
last-modified: 2024-03-27
description: BackgroundHoney is a nutritious food made by bees from nectar and sweet deposits of flowering plants and has been used for centuries as a natural remedy for wound healing and other bacterial infections due to its antibacterial properties. Honey contains a diverse community of bacteria, especially probiotic bacteria, that greatly affect the health of bees and their consumers. Therefore, understanding the microorganisms in honey can help to ensure the quality of honey and lead to the identification of potential probiotic bacteria.MethodsHerein, the bacteria community in honey produced by Apis cerana was investigated by applying the next-generation sequencing (NGS) method for the V3–V4 hypervariable regions of the bacterial 16S rRNA gene. In addition, lactic acid bacteria (LAB) in the honey sample were also isolated and screened for in vitro antimicrobial activity.ResultsThe results showed that the microbiota of A. cerana honey consisted of two major bacterial phyla, Firmicutes (50%; Clostridia, 48.2%) and Proteobacteria (49%; Gammaproteobacteria, 47.7%). Among the 67 identified bacterial genera, the three most predominant genera were beneficial obligate anaerobic bacteria, Lachnospiraceae (48.14%), followed by Gilliamella (26.80%), and Enterobacter (10.16%). Remarkably, among the identified LAB, Lactobacillus kunkeei was found to be the most abundant species. Interestingly, the isolated L. kunkeei strains exhibited antimicrobial activity against some pathogenic bacteria in honeybees, including Klebsiella spp., Escherichia coli, Enterococcus faecalis, Pseudomonas aeruginosa and Staphylococcus aureus. This underscores the potential candidacy of L. kunkeei for developing probiotics for medical use. Taken together, our results provided new insights into the microbiota community in the A. cerana honey in Hanoi, Vietnam, highlighting evidence that honey can be an unexplored source for isolating bacterial strains with potential probiotic applications in honeybees and humans.
creator: Pham T. Lanh
creator: Bui T.T. Duong
creator: Ha T. Thu
creator: Nguyen T. Hoa
creator: Dong Van Quyen
uri: https://doi.org/10.7717/peerj.17157
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Lanh et al.

title: Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species
link: https://peerj.com/articles/17175
last-modified: 2024-03-27
description: BackgroundGeographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex.MethodsWe analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time.ResultsThe results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensissp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.
creator: Qianru Liang
creator: Lei Shi
uri: https://doi.org/10.7717/peerj.17175
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2024 Liang and Shi

title: Physiological and biochemical effects of 24-Epibrassinolide on drought stress adaptation in maize (Zea mays L.)
link: https://peerj.com/articles/17190
last-modified: 2024-03-27
description: Maize production and productivity are affected by drought stress in tropical and subtropical ecologies, as the majority of the area under maize cultivation in these ecologies is rain-fed. The present investigation was conducted to study the physiological and biochemical effects of 24-Epibrassinolide (EBR) as a plant hormone on drought tolerance in maize. Two maize hybrids, Vivek hybrid 9 and Bio 9637, were grown under three different conditions: (i) irrigated, (ii) drought, and (iii) drought+EBR. A total of 2 weeks before the anthesis, irrigation was discontinued to produce a drought-like condition. In the drought+EBR treatment group, irrigation was also stopped, and in addition, EBR was applied as a foliar spray on the same day in the drought plots. It was observed that drought had a major influence on the photosynthesis rate, membrane stability index, leaf area index, relative water content, and leaf water potential; this effect was more pronounced in Bio 9637. Conversely, the activities of antioxidant enzymes such as catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) increased in both hybrids under drought conditions. Specifically, Vivek hybrid 9 showed 74% higher CAT activity under drought conditions as compared to the control. Additionally, EBR application further enhanced the activity of this enzyme by 23% compared to plants under drought conditions. Both hybrids experienced a significant reduction in plant girth due to drought stress. However, it was found that exogenously applying EBR reduced the detrimental effects of drought stress on the plant, and this effect was more pronounced in Bio 9637. In fact, Bio 9637 treated with EBR showed an 86% increase in proline content and a 70% increase in glycine betaine content compared to untreated plants under drought conditions. Taken together, our results suggested EBR enhanced tolerance to drought in maize hybrids. Hence, pre-anthesis foliar application of EBR might partly overcome the adverse effects of flowering stage drought in maize.
creator: Bicky Kumar
creator: Madan Pal
creator: Pranjal Yadava
creator: Krishan Kumar
creator: Sapna Langyan
creator: Abhishek Kumar Jha
creator: Ishwar Singh
uri: https://doi.org/10.7717/peerj.17190
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2024 Kumar et al.

title: Geographic patterns of distribution and ecological niche of the snake-necked turtle genus Hydromedusa
link: https://peerj.com/articles/16712
last-modified: 2024-03-26
description: Biotic and abiotic factors play a crucial role in determining the distribution of species. These factors dictate the conditions that must be met for a species to thrive in a particular area. Sister species that present some degree of niche overlap can shed light on how they are distributed and coexist in their environment. This study aims to investigate the geographical distribution and ecological niche of the sister species of snake-necked turtles Hydromedusa maximiliani and H. tectifera. By analyzing their niche overlap, we aim to obtain a better understanding of how these two species coexist and which variables are determining their occurences. We applied species distribution modeling and compared the niches using the niche equivalence and similarity tests. Our findings show that the distribution of H. maximiliani is most influenced by temperature seasonality and isothermality, while H. tectifera is most affected by the temperature seasonality, precipitation of warmest quarter and mean diurnal range. In addition, our results suggest that the niche expressed by H. maximiliani retained ecological characteristics that can accurately predict the H. tectifera distribution, but the inverse is not true. In this sense, differences are not solely due to the geographic availability of environmental conditions but can reflect niche restrictions, such as competition.
creator: Márcia M.P. Muller
creator: Diego J. Santana
creator: Henrique C. Costa
creator: Karoline Ceron
uri: https://doi.org/10.7717/peerj.16712
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Muller et al.

title: Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis
link: https://peerj.com/articles/16973
last-modified: 2024-03-26
description: The discovery of plant-derived compounds that are able to combat antibiotic-resistant pathogens is an urgent demand. Over years, Centaurea hyalolepis attracted considerable attention because of its beneficial medical properties. Phytochemical analyses revealed that Centaurea plant species contain several metabolites, such as sesquiterpene lactones (STLs), essential oils, flavonoids, alkaloids, and lignans.The organic extract of C. hyalolepis plant, collected in Palestine, showed significant antimicrobial properties towards a panel of Gram-negative and Gram-positive bacterial strains when the Minimal Inhibitory Concentration (MIC) values were evaluated by broth microdilution assays. A bio-guided fractionation of the active extract via multiple steps of column and thin layer chromatography allowed us to obtain three main compounds. The isolated metabolites were identified as the STLs cnicin, 11β,13-dihydrosalonitenolide and salonitenolide by spectroscopic and spectrometric analyses. Cnicin conferred the strongest antimicrobial activity among the identified compounds. Moreover, the evaluation of its antibiofilm activity by biomass assays through crystal violet staining revealed almost 30% inhibition of biofilm formation in the case of A. baumannii ATCC 17878 strain. Furthermore, the quantification of carbohydrates and proteins present in the extracellular polymeric substance (EPS) revealed the ability of cnicin to significantly perturb biofilm structure. Based on these promising results, further investigations might open interesting perspectives to its applicability in biomedical field to counteract multidrug resistant infections.
creator: Shurooq Ismail
creator: Marco Masi
creator: Rosa Gaglione
creator: Angela Arciello
creator: Alessio Cimmino
uri: https://doi.org/10.7717/peerj.16973
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Ismail et al.

title: Similarities and differences: species and diet impact gut microbiota of captive pheasants
link: https://peerj.com/articles/16979
last-modified: 2024-03-26
description: The fecal microbiota plays an important role in maintaining animal health and is closely related to host life activities. In recent years, there have been an increasing number of studies on the fecal microbiota from birds. An exploration of the effects of species and living environments on the composition of gut microbiota will provide better protection for wildlife. In this study, non-injury sampling and 16S rDNA high-throughput sequencing were used to investigate the bacterial composition and diversity of the fecal microbiota in silver pheasants (Lophura nycthemera) and golden pheasants (Chrysolophus pictus) from Tianjin Zoo and Beijing Wildlife Park. The results showed that the abundance of Firmicutes was the highest in all fecal samples. At the genus level, Bacteroides was the common dominant bacteria, while there were some differences in other dominant bacteria genera. There were significant differences in fecal microbial composition between the golden pheasants from Tianjin Zoo and Beijing Wildlife Park. The metabolic analysis and functional prediction suggested that the gut microbiota composition and host metabolism were influenced by dietary interventions and living conditions. The results of this study provide the basis for further research of intestinal microbial of L. nycthemera and C. pictus, and valuable insights for conservation of related species.
creator: Yushuo Zhang
creator: Xin He
creator: Xiuhong Mo
creator: Hong Wu
creator: Dapeng Zhao
uri: https://doi.org/10.7717/peerj.16979
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2024 Zhang et al.

title: Plasticity-led and mutation-led evolutions are different modes of the same developmental gene regulatory network
link: https://peerj.com/articles/17102
last-modified: 2024-03-26
description: The standard theory of evolution proposes that mutations cause heritable variations, which are naturally selected, leading to evolution. However, this mutation-led evolution (MLE) is being questioned by an alternative theory called plasticity-led evolution (PLE). PLE suggests that an environmental change induces adaptive phenotypes, which are later genetically accommodated. According to PLE, developmental systems should be able to respond to environmental changes adaptively. However, developmental systems are known to be robust against environmental and mutational perturbations. Thus, we expect a transition from a robust state to a plastic one. To test this hypothesis, we constructed a gene regulatory network (GRN) model that integrates developmental processes, hierarchical regulation, and environmental cues. We then simulated its evolution over different magnitudes of environmental changes. Our findings indicate that this GRN model exhibits PLE under large environmental changes and MLE under small environmental changes. Furthermore, we observed that the GRN model is susceptible to environmental or genetic fluctuations under large environmental changes but is robust under small environmental changes. This indicates a breakdown of robustness due to large environmental changes. Before the breakdown of robustness, the distribution of phenotypes is biased and aligned to the environmental changes, which would facilitate rapid adaptation should a large environmental change occur. These observations suggest that the evolutionary transition from mutation-led to plasticity-led evolution is due to a developmental transition from robust to susceptible regimes over increasing magnitudes of environmental change. Thus, the GRN model can reconcile these conflicting theories of evolution.
creator: Eden T.H. Ng
creator: Akira R. Kinjo
uri: https://doi.org/10.7717/peerj.17102
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Ng and Kinjo