title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=757 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift link: https://peerj.com/articles/13002 last-modified: 2022-02-23 description: Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP. creator: Lingxi Zeng creator: Gen Li creator: Maoting Zhang creator: Rui Zhu creator: Jingbo Chen creator: Mingyan Li creator: Shengtong Yin creator: Zelin Bai creator: Wei Zhuang creator: Jian Sun uri: https://doi.org/10.7717/peerj.13002 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zeng et al. title: Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum link: https://peerj.com/articles/12756 last-modified: 2022-02-22 description: Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease. creator: Junjun Huang creator: Dan Wang creator: Hong Li creator: Yanqiong Tang creator: Xiang Ma creator: Hongqian Tang creator: Min Lin creator: Zhu Liu uri: https://doi.org/10.7717/peerj.12756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huang et al. title: Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River link: https://peerj.com/articles/12817 last-modified: 2022-02-22 description: This study examined the age, growth, and maturation of 1,064 Coregonus ussuriensis individuals that were collected monthly from the middle section of the Amur River, China between 2016 and 2018. The fork length (FL) ranged from 14.9 to 49.1 cm for males and 21.5 to 58.8 cm for females, and the body weight (BW) ranged from 72.6 to 1,348.7 g for males and 107.9 to 2,854.9 g for females. The relationship of BW and FL was expressed as: BW♂ = 0.0324 × FL2.708; BW♀ = 0.014 × FL2.963. The sample ages ranged from 2 to 8 years for males and 2 to 9 years for females. We used the von Bertalanffy function based on otolith reading and observed FL data to simulate Coregonus ussuriensis growth, which has been suggested to be similar to that of other Salmonidae fishes. No significant difference in growth was determined between males and females. The monthly gonad somatic index (GSI) value ranged from 0.16% to 1.69% for males and from 0.73% to 16.15% for females, with a peak in November. Additionally, the reproductive staging suggested that the Coregonus ussuriensis spawning season was mainly in November and December. The size at maturity (FL50%) for males and females was 34.9 cm and 37.9 cm respectively, and the corresponding age (T50%) was 4.5 and 5.1, respectively. This study provides basic information for understanding the biological characteristics of Coregonus ussuriensis and should aid in the assessment and management of fishery resources. creator: Jilong Wang creator: Wei Liu creator: Peilun Li creator: Fujiang Tang creator: Wanqiao Lu uri: https://doi.org/10.7717/peerj.12817 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia link: https://peerj.com/articles/12830 last-modified: 2022-02-22 description: BackgroundCarbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards “last line” antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality.MethodsA total of 168 CRE strains isolated from a tertiary teaching hospital from 2014–2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically.ResultsThe predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality. creator: Zhi Xian Kong creator: Rina N. Karunakaran creator: Kartini Abdul Jabar creator: Sasheela Ponnampalavanar creator: Chun Wie Chong creator: Cindy Shuan Ju Teh uri: https://doi.org/10.7717/peerj.12830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kong et al. title: Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands link: https://peerj.com/articles/12885 last-modified: 2022-02-22 description: BackgroundUrbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination.MethodsIn this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants.ResultsThe heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of Cd was the industrial pollution, and Cr mainly originated from natural sources. Nutrients primarily came from the decomposition of aquatic animals, plants, and human-related activities. When the lake area was converted into farmland, the heavy metal concentrations in the soils increased and the TN and OM decreased. Based on the results, this study put forward key strategies including the adjustment of the land-use type and restriction of the entry of pollutants into the wetland ecosystems in the Zaozhadian Lake. More attention should be paid to the impact of land-use type change on pollutants in wetlands. creator: Yangyang Han creator: Hongjie Wang creator: Guangming Zhang creator: Shengqi Zhang creator: Xingchun Liu creator: Ling Liu uri: https://doi.org/10.7717/peerj.12885 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Han et al. title: Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia link: https://peerj.com/articles/12898 last-modified: 2022-02-22 description: BackgroundInvestigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia.MethodsLandsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis.ResultsIn total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that protecting and planting indigenous and multipurpose plant species is essential as restoration techniques for all degraded land-use types. Therefore, strengthening agroforestry practices and land-use planning is urgently needed for achieving multiple goals. creator: Misganaw Meragiaw creator: Zerihun Woldu creator: Bal Ram Singh uri: https://doi.org/10.7717/peerj.12898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Meragiaw et al. title: Methodological approaches for estimating populations of the endangered dhole Cuon alpinus link: https://peerj.com/articles/12905 last-modified: 2022-02-22 description: Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the species, and contribute towards conservation monitoring of this endangered carnivore. creator: Girish A. Punjabi creator: Linnea Worsøe Havmøller creator: Rasmus Worsøe Havmøller creator: Dusit Ngoprasert creator: Arjun Srivathsa uri: https://doi.org/10.7717/peerj.12905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Punjabi et al. title: SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. link: https://peerj.com/articles/12940 last-modified: 2022-02-22 description: BackgroundPogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil.MethodsTo better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads.ResultsIn this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” and “monoterpene biosynthesis”. Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in P. cablin. creator: Hongyi Zhang creator: Wenjing Deng creator: Changhua Lu creator: Mengling He creator: Hanjing Yan uri: https://doi.org/10.7717/peerj.12940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study link: https://peerj.com/articles/12973 last-modified: 2022-02-22 description: BackgroundIn the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida.MethodsVaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions.ResultsTotal exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high median income (p = 0.001), high percentage of Hispanic population (p = 0.046), and low percentage of population with a college education (p = 0.013). A predictor of high risk of non-medical vaccination exemptions was high percentage of White population (p = 0.045). However, predictors of low risks of non-medical exemptions were high percentages of population: living in rural areas (p = 0.023), with college education (p = 0.013), with high school education (p = 0.009), and with less than high school education (p < 0.001).ConclusionsThere is evidence of county-level geographic disparities in both total and non-medical vaccination exemption risks in Florida. These disparities are explained by differences in county-level socioeconomic and demographic factors. Study findings are important in guiding resource allocation for health planning aimed at improving vaccination rates and reducing incidence of vaccine-preventable diseases. creator: Corinne B. Tandy creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.12973 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tandy and Odoi title: Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition link: https://peerj.com/articles/12991 last-modified: 2022-02-22 description: BackgroundOral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism.MethodsTwo OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography.ResultsOur results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment.ConclusionsOur study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis. creator: Wenli Zang creator: Junchao Liu creator: Fengxue Geng creator: Dongjuan Liu creator: Shuwei Zhang creator: Yuchao Li creator: Yaping Pan uri: https://doi.org/10.7717/peerj.12991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zang et al.