title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=415 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Seroprevalence of SARS-CoV-2 anti-spike IgG antibody among COVID-19 vaccinated individuals residing in Surabaya, East Java, Indonesia link: https://peerj.com/articles/16142 last-modified: 2023-09-25 description: BackgroundTo limit the SARS-CoV-2 transmission, the Indonesian government launched a COVID-19 vaccination program in January 2021. Studies on the clinical treatment and implementation of COVID-19 vaccination have shown promising results; however, it is necessary to estimate the effectiveness of the vaccines. With the ongoing COVID-19 pandemic, studies have highlighted the impact of COVID-19 vaccines, especially CoronaVac, on Indonesian healthcare workers. To get a better picture of how the vaccines work in Indonesia, it is necessary to estimate the prevalence of SARS-CoV-2 anti-S IgG antibody induced by the COVID-19 vaccine in individuals who have already received two-to-three doses of vaccines.Materials and MethodsFour-hundred and ninety-six whole-blood samples were collected from participants residing in Surabaya, East Java, Indonesia, who received a minimum of a two-dose COVID-19 vaccine. Serums were then isolated from the blood and subjected to detect SARS-CoV-2 anti-S IgG antibodies using a lateral flow immunochromatographic assay.ResultsThe prevalence of positive anti-S-IgG antibodies was 91.7% (455/496) in all participants receiving a minimum of a two-dose COVID-19 vaccine. As many as 209 (85.3%) and 141 (96.6%) participants were seropositive for receiving CoronaVac and AstraZeneca, respectively. Meanwhile, all participants receiving two-dose CoronaVac with one booster dose of Moderna (105/100%) were seropositive (p < 0.05). Age, comorbidity, and time after the last vaccine were significantly correlated with seropositivity (p < 0.05).ConclusionDifferent vaccines might produce different antibody responses. Adopting a stronger policy regarding the administration of booster doses might be beneficial to elicit positive anti-S-IgG antibodies, especially among older individuals, those with comorbid diseases, and those with a longer time after the second vaccination dose. creator: Ni Luh Ayu Megasari creator: Laura Navika Yamani creator: Juniastuti Juniastuti creator: Maria Inge Lusida creator: Yasuko Mori uri: https://doi.org/10.7717/peerj.16142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Megasari et al. title: Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis link: https://peerj.com/articles/16161 last-modified: 2023-09-25 description: The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity. creator: Li-Yan Zhang creator: Benshun Tian creator: Yuan-Hong Huang creator: Bin Gu creator: Pei Ju creator: Yanfei Luo creator: Jiawei Tang creator: Liang Wang uri: https://doi.org/10.7717/peerj.16161 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Systematic and meta-based evaluation of the relationship between the built environment and physical activity behaviors among older adults link: https://peerj.com/articles/16173 last-modified: 2023-09-25 description: ObjectivesExisting assertions about the relationship between various factors of the built environment and physical activity behaviors are inconsistent and warrant further exploration and analysis.MethodsThis study systematically searched PubMed, Embase, Web of Science, Scopus, the Cochrane Library and Google Scholar for the effect of the built environment on the physical activity behaviors of older adults. R software was used to calculate the meta-estimated odds ratio with a 95% confidence interval. Simultaneously, the quality of included studies was evaluated using an observational study quality evaluation standard recommended by American health care quality and research institutions.ResultsA total of 16 original researches were included in this meta-analysis and eight factors of the built environment were evaluated. These factors which ranked from high to low according to their impact were traffic safety (OR = 1.58, 95% CI [1.14–2.20]), destination accessibility (OR = 1.24, 95% CI [1.06–1.44]), aesthetics of sports venues (OR = 1.21, 95% CI [1.07–1.37]), virescence of sports venues (OR = 1.14, 95% CI [1.06–1.23]), building density (OR = 1.07, 95% CI [1.02–1.13]). Additionally, it seemed that there was no potential association between mixed land use (OR = 1.01, 95% CI [0.92–1.10]), the quality of pedestrian facilities (OR = 1.00, 95% CI [0.92–1.08]) or commercial facilities (OR = 0.94, 95% CI [0.88–1.00]) and physical activity behaviors of older adults.ConclusionsThe built environment has been found to exhibit a significant relationship with the physical activity behaviors of older adults. It is proposed that factors such as traffic safety, destination accessibility, aesthetics of sports venues, virescence of sports venues, and building density be given more consideration when aiming to promote physical activity levels among older adults. creator: Yanwei You creator: Yuquan Chen creator: Qi Zhang creator: Xiaojie Hu creator: Xingzhong Li creator: Ping Yang creator: Qun Zuo creator: Qiang Cao uri: https://doi.org/10.7717/peerj.16173 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 You et al. title: Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers link: https://peerj.com/articles/16183 last-modified: 2023-09-25 description: BackgroundThe non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations.MethodsBased on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree.ResultsA total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population.ConclusionsIn conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research. creator: Hongling Zhang creator: Xiaolan Huang creator: Xiaoye Jin creator: Zheng Ren creator: Qiyan Wang creator: Meiqing Yang creator: Ronglan Xu creator: Xiang Yuan creator: Daiquan Yang creator: Hongyan Liu creator: Wanyi Shen creator: Huiying Zhang creator: Yangjie Que creator: Jiang Huang uri: https://doi.org/10.7717/peerj.16183 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Age and socio-economic status affect dengue and COVID-19 incidence: spatio-temporal analysis of the 2020 syndemic in Buenos Aires City link: https://peerj.com/articles/14735 last-modified: 2023-09-22 description: In early 2020, Argentina experienced the worst dengue outbreak in its history, concomitant with first-to-date increasing COVID-19 cases. Dengue epidemics in temperate Argentina have already been described as spatially heterogeneous; in the previous 2016 outbreak, transmission occurred 7.3 times more frequently in slums compared to the rest of Buenos Aires City (CABA). These informal settlements have deficient sanitary conditions, precarious housing and high incidence of social vulnerabilities. The purpose of this work was to study the spatio-temporal patterns of the 2020 dengue epidemic in CABA in relation to socio-economic living conditions of its inhabitants and its interaction with the onset of COVID-19. The study considered the period between Jan 1st and May 30th 2020. Dengue and COVID-19 databases were obtained from the National Health Surveillance System; each record was anonymized and geo-localized. The city was divided according to census tracts and grouped in four socio-economic strata: slums, high, mid and low residential. An aligned-rank transform ANOVA was performed to test for differences in the incidence of dengue and COVID-19, and age at death due to COVID-19, among socio-economic strata, four age categories and their interaction. The incidence by cluster was calculated with a distance matrix up to 600 m from the centroid. Spatial joint dengue and COVID-19 risk was estimated by multiplying the nominal risk for each disease, defined from 1 (low) to 5 (high) according to their quantiles. During the study period, 7,175 dengue cases were registered in CABA (incidence rate 23.3 cases per 10,000 inh), 29.2% of which occurred in slums. During the same period, 8,809 cases of COVID-19 were registered (28.6 cases per 10,000 inh); over half (51.4%) occurred in slums, where the median age of cases (29 years old) was lower than in residential areas (42 years old). The mean age of the deceased was 58 years old in slums compared to 79 years old outside. The percentage of deaths in patients under 60 years old was 56% in slums compared to 8% in the rest of the city. The incidence of both diseases was higher in slums than in residential areas for most age categories. Spatial patterns were heterogeneous: dengue presented higher incidence values in the southern sector of the city and the west, and low values in highly urbanized quarters, whereas COVID-19 presented higher values in the east, south, high populated areas and slums. The lowest joint risk clusters were located mainly in high residential areas, whereas high joint risk was observed mainly in the south, some western clusters, the historical part of the city and center north. The social epidemiological perspective of dengue and COVID-19 differed, given that socio environmental heterogeneity influenced the burden of both viruses in a different manner. Despite the overwhelming effect of the COVID-19 pandemic, health care towards other diseases, especially in territories with pre-existing vulnerabilities, should not be unattended. creator: Aníbal E. Carbajo creator: María V. Cardo creator: Martina Pesce creator: Luciana E. Iummato creator: Pilar Bárcena Barbeira creator: María Soledad Santini creator: María Eugenia Utgés uri: https://doi.org/10.7717/peerj.14735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Carbajo et al. title: Research on the coupling coordination and driving role of urbanization and ecological resilience in the middle and lower reaches of the Yangtze River link: https://peerj.com/articles/15869 last-modified: 2023-09-22 description: BackgroundThe growth of urbanization in the 20th and 21st centuries has resulted in unprecedented ecological security issues. The imbalance between urban development and internal ecological security is a growing concern.MethodsBased on the urban development process and the characteristics of ecosystem resilience, the corresponding urbanization evaluation system (“scale-structure-benefit”) and ecosystem resilience assessment model (“resistance-adaptability-restoring”) were constructed to explore the changes in each dimension as well as to analyze the spatial and temporal changes and driving effects of the coupled coordination level of urbanization and ecological resilience using the coupled coordination degree (CCD) model and geographically and temporally weighted regression (GTWR).Results(1) From 2005 to 2020, urbanization levels increased (from 0.204 to 0.264, respectively), whereas the level of ecological resilience gradually decreased (from 0.435 to 0.421, respectively). The spatial distribution of urbanization is rather steady, with a “high-northeast low-southwest” pattern of regional distribution; however, the spatial distribution pattern of ecological resilience is essentially the reverse. (2) During the study period, there was an improvement in the level of coordination between urbanization and ecological resilience, with an increase from 0.524 to 0.540. However, the main coordination type remained the same, with over 46% being at the basic coordination stage. The relative development type was dominated by the lagging urbanization stage, with the lagging ecological resilience and synchronous development stages accounting for a smaller proportion, and the space was distributed in a block-like cluster. (3) The running results of the GTWR show that the core dimensions of the whole region are scale, benefit, and structure, and the impact of each dimension shows obvious spatial heterogeneity. Cities with different levels of relative development also have different central dimensions. This research will provide support for the coordination of urban development in areas where economic construction and ecological resilience are not coordinated, and will contribute to the sustainable development of urban areas. creator: Sheng Xiao creator: Linghua Duo creator: Xiaofei Guo creator: Zili Zou creator: Yanan Li creator: Dongxue Zhao uri: https://doi.org/10.7717/peerj.15869 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xiao et al. title: Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium link: https://peerj.com/articles/15929 last-modified: 2023-09-22 description: The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response. creator: Lulu Li creator: Yiqian Ju creator: Cuiping Zhang creator: Boqiang Tong creator: Yizeng Lu creator: Xiaoman Xie creator: Wei Li uri: https://doi.org/10.7717/peerj.15929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Immunosuppressive effect of Plantago major on the innate immunity of Galleria mellonella link: https://peerj.com/articles/15982 last-modified: 2023-09-22 description: Greater plantain (Plantago major), a medicinal plant species, is used in folk medicine for the treatment of various diseases in many countries of the world. Different studies have shown that the bioactive components contained in the plant have a dual effect. It was also reported that in vivo and in vitro studies showed different results. The aim of the study was to determine the effects of P. major extract on the hemocyte-mediated and humoral immune responses of the invertebrate model organism Galleria mellonella, which is widely used in immune studies. In the evaluation of these effects, total hemocyte count, encapsulation, melanization, phenoloxidase, superoxide dismutase, catalase, malondialdehyde and total protein parameters were evaluated. The results of the study showed that the total hemocyte count did not change, that the encapsulation responses decreased, that the melanization responses and phenoloxidase activity increased and that the superoxide dismutase activity decreased. As a result, it was determined that high doses of P. major had negative effects on cell-mediated immunity and antioxidant defence and positive effects on melanization. High doses and continuous use of P. major may have negative effects on living things. creator: Serhat Kaya uri: https://doi.org/10.7717/peerj.15982 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kaya title: Urine proteomic analysis of the rat e-cigarette model link: https://peerj.com/articles/16041 last-modified: 2023-09-22 description: BackgroundWe were curious if the urinary proteome could reflect the effects of e-cigarettes on the organism.MethodsUrine samples were collected from a rat e-cigarette model before, during, and after two weeks of e-cigarette smoking. Urine proteomes before and after smoking of each rat were compared individually, while the control group was set up to rule out differences caused by rat growth and development.ResultsFetuin-B, a biomarker of chronic obstructive pulmonary disease (COPD), and annexin A2, which is recognized as a multiple tumour marker, were identified as differential proteins in five out of six smoking rats on day 3. To our surprise, odourant-binding proteins expressed in the olfactory epithelium were also found and were significantly upregulated. Pathways enriched by the differential proteins include the apelin signalling pathway, folate biosynthesis pathway, arachidonic acid metabolism, chemical carcinogenesis-DNA adducts and chemical carcinogenesis-reactive oxygen species. They have been reported to be associated with immune system, cardiovascular system, respiratory system, etc.ConclusionsUrinary proteome could reflect the effects of e-cigarettes in rats. creator: Yuqing Liu creator: Ziyun Shen creator: Chenyang Zhao creator: Youhe Gao uri: https://doi.org/10.7717/peerj.16041 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Trophic assessment of three sympatric batoid species in the Southern Gulf of California link: https://peerj.com/articles/16117 last-modified: 2023-09-22 description: The competitive exclusion principle establishes that the coexistence of closely related species requires a certain degree of resource partitioning. However, populations have individuals with different morphological or behavioral traits (e.g., maturity stages, sexes, temporal or spatial segregation). This interaction often results in a multi-level differentiation in food preferences and habits. We explored such resource partitioning between and within three batoid species: Hypanus dipterurus, Narcine entemedor, and Rhinoptera steindachneri in the southern Gulf of California, Mexico, using a combination of stomach content (excluding R. steindachneri) and stable isotope analyses. We found a clear differentiation between H. dipterurus and N. entemedor, where the latter exhibited more benthic habitats, supported by a greater association to infaunal prey and higher δ13C values. Though the degree and patterns of intra-specific segregation varied among species, there was a notable differentiation in both sex and stage of maturity, corresponding to changes in specialization (i.e., isotopic niche breadth) or trophic spectrum (varying prey importance and isotopic values per group). This work is a promising step towards understanding the dietary niche dynamics of these species in a potentially important feeding area within the southern Gulf of California, as well as the biological and ecological mechanisms that facilitate their coexistence. creator: Arturo Bell Enríquez-García creator: Víctor Hugo Cruz-Escalona creator: José D. Carriquiry creator: Nicolás R. Ehemann creator: Paola A. Mejía-Falla creator: Emigdio Marín-Enríquez creator: Christina Treinen-Crespo creator: José R. Vélez-Tacuri creator: Andrés F. Navia uri: https://doi.org/10.7717/peerj.16117 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Enríquez-García et al.