title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1287 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices link: https://peerj.com/articles/7599 last-modified: 2019-08-28 description: BackgroundWrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices.MethodsA total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension.ResultsAll of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other four indices). However, the odd ratios (OR) of WrC was the smallest, while BMI was the largest. Consistently, the AUC of BMI was the largest and statistically larger than that observed for WrC (P-value <0.001).ConclusionsWrC was associated with hypertension among northeastern Chinese populations. However, the association was not stronger than the other generally used indices, particularly BMI. creator: Yongfang Li creator: Yuyan Liu creator: Jing He creator: Ping Ma creator: Luyang Yu creator: Guifan Sun uri: https://doi.org/10.7717/peerj.7599 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling link: https://peerj.com/articles/7600 last-modified: 2019-08-28 description: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS. creator: Ming-Hsin Tsai creator: Yen-Yi Liu creator: Chih-Chieh Chen uri: https://doi.org/10.7717/peerj.7600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tsai et al. title: Healthy eating promoting in a Brazilian sports-oriented school: a pilot study link: https://peerj.com/articles/7601 last-modified: 2019-08-28 description: BackgroundAdolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation.MethodsOur pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57).ResultsIn 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating.ConclusionOur results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency of their consumption of unprocessed foods. This pilot study’s results inspired us to implement an expanded project at the municipal level. Since 2018, teachers who participated in this program are working with Rio de Janeiro’s Municipal Secretary of Education for Coordination of Curricular Projects. Some learnings from this pilot study on implementing the garden/experimental kitchen project in this school are being applied in 65 schools of the municipal network: joint activities must be fostered among students, teachers, and parents; healthy eating needs to be a respected value among adolescent athletes and become an example for parents and teachers. creator: Fábia Albernaz Massarani creator: Marta Citelli creator: Daniela Silva Canella creator: Josely Correa Koury uri: https://doi.org/10.7717/peerj.7601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Massarani et al. title: Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement link: https://peerj.com/articles/7628 last-modified: 2019-08-28 description: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL. creator: Hao Zhang creator: Juan Cheng creator: Zijian Li creator: Yaming Xi uri: https://doi.org/10.7717/peerj.7628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies link: https://peerj.com/articles/7386 last-modified: 2019-08-27 description: Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively. creator: Leidys Murillo-Ramos creator: Gunnar Brehm creator: Pasi Sihvonen creator: Axel Hausmann creator: Sille Holm creator: Hamid Reza Ghanavi creator: Erki Õunap creator: Andro Truuverk creator: Hermann Staude creator: Egbert Friedrich creator: Toomas Tammaru creator: Niklas Wahlberg uri: https://doi.org/10.7717/peerj.7386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Murillo-Ramos et al. title: Effect of adjuvant radioactive iodine therapy on survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma) link: https://peerj.com/articles/7458 last-modified: 2019-08-27 description: PurposeRadioactive iodine (RAI) is widely used for adjuvant therapy after thyroidectomy, while its value for thyroid cancer has been controversial recently. The primary objectives of this study were to clarify the influence of Radioactive iodine (RAI) on the survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma, HCC).MethodsPatients diagnosed with oxyphilic thyroid carcinoma from 2004 to 2015 were extracted from the Surveillance, Epidemiology, and End Results Program database. The Kaplan-Meier method was used to compare overall survival (OS) and cancer-specific survival (CSS) among patients who had adjuvant RAI use or not. Univariate and multivariate Cox proportional hazard models were performed for survival analysis, and subsequently visualized by nomogram.ResultsIn all, 2,799 patients were identified, of which 1529 patients had adjuvant RAI use while 1,270 patients had not. Based on multivariate Cox analysis, the RAI therapy confers an improved OS for HCC patients (HR = 0.57, 95% CI [0.44–0.72], P < 0.001), whereas it has no significant benefit in the survival analysis regarding CSS (HR = 0.79, 95% CI [[0.47–1.34], P = 0.382). In a subgroup analysis, the same survival benefit of RAI treatment on OS, but not CSS was observed among patients stratified by AJCC stage and tumor extension. Nevertheless, patients with regional lymph node metastasis benefited from RAI therapy both in OS and CSS (P < 0.001, respectively). Furthermore, nomograms used for predicting long term survival of HCC patients exhibited a better prediction power for OS compared with traditional tumor, nodal and metastatic (TNM) stage made by American Joint Committee on Cancer (AJCC) (C-index = 0.833 of the nomogram model vs. 0.696 of the AJCC system).ConclusionsThis study suggests that RAI therapy is significantly associated with improved OS in patients with Hürthle cell carcinoma. However, there was no association between treatment with radioiodine and CSS, possibly due to small number of deaths that were related to HCC. creator: Qiong Yang creator: Zhongsheng Zhao creator: Guansheng Zhong creator: Aixiang Jin creator: Kun Yu uri: https://doi.org/10.7717/peerj.7458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells link: https://peerj.com/articles/7524 last-modified: 2019-08-27 description: BackgroundAluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity.MethodsMTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes.ResultsAl inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings.ConclusionThe metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism. creator: Leilei Yu creator: Jiangping Wu creator: Qixiao Zhai creator: Fengwei Tian creator: Jianxin Zhao creator: Hao Zhang creator: Wei Chen uri: https://doi.org/10.7717/peerj.7524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yu et al. title: Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing link: https://peerj.com/articles/7527 last-modified: 2019-08-27 description: BackgroundThe degradation of nucleotides and their enzymes had been widely used to evaluate fish freshness. Immediately after fish death, adenosine triphosphate (ATP) degrades into inosine-5-monophosphate (IMP) via adenosine-5-diphosphate (ADP) and adenosine-5-monophosphate (AMP). IMP degradation continues to produce inosine (ino) and hypoxanthine (Hx) and further deteriorates the fish by producing xanthine and uric acid. The dephosphorylation of IMP to Ino is carried out by the enzyme 5′-nucleotidase (5′-NT), whereas the degradation of Ino to Hx is carried out by the enzyme nucleoside phosphorylase (NP). This study assesses the application of high pressure processing (HPP) in two species of fishes; haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) as a means to extend the shelf-life by slowing down the rate of nucleotides degradation.MethodsHaddock (Melanogrammus aeglefinus) and herring (Clupea harengus) fillets were subjected to HPP at 200, 250 and 300 MPa for 1 and 3 min before being stored for 14 days. In addition, 5′-NT and NP enzyme activities were determined on both fish species that were subjected to 100–600 MPa for 1 and 3 min.ResultsAdenosine triphosphate, ADP and AMP in both haddock and herring were lower at higher pressure levels. Inosine (Ino) increased (p < 0.05) after treatment at higher pressures in both species. Hx in herring decreased significantly (p < 0.05) at higher pressures but not in haddock. K values are the ratio of Ino and Hx to all nucleotides. K values in haddock were not significantly (p > 0.05) affected by the pressure treatment. H values are ratio of Hx to the sum of IMP, Ino and Hx. H values in haddock were significantly decreased (p < 0.05) with increasing pressure level. F values are ratio of IMP to the sum of IMP, Ino and Hx. F values showed no significant effects (p > 0.05) after pressure treatment. Furthermore, K values in control herring were significantly higher (p < 0.05) than those of the pressure-treated samples. H values in herring decreased significantly (p < 0.05) with increasing pressure level. F values in herring showed no significant effects (p > 0.05) after pressure treatment. Pressure treatment brought a significant decrease (p < 0.05) in protein content in both haddock and herring. 5′-NT activity was 20–35 fold higher compared to NP activity in haddock and 15–44 fold higher than NP activity in herring. 5′-NT and NP activities decreased significantly with increasing pressure level in both species.DiscussionHigh pressure processing effectively slows down the conversion of Ino to Hx, delaying the undesirable flavour that develops in spoiling fish. The autolytic conversion of IMP to Ino by endogenous 5′-NT predominates in the earliest stages of storage is an autolytic process. However, both bacterial and endogenous NP enzymes are probably responsible for the gradual accumulation of Hx in fish. K values are recommended as a useful measurement of fish freshness. creator: Nurul Ulfah Karim creator: James Terence Kennedy creator: Mark Linton creator: Margaret Patterson creator: Sally Watson creator: Norman Gault uri: https://doi.org/10.7717/peerj.7527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Karim et al. title: Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus) link: https://peerj.com/articles/7548 last-modified: 2019-08-27 description: Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies. creator: Carl J. Yeoman creator: Laura M. Brutscher creator: Özcan C. Esen creator: Furkan Ibaoglu creator: Curtis Fowler creator: A. Murat Eren creator: Kevin Wanner creator: David K. Weaver uri: https://doi.org/10.7717/peerj.7548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yeoman et al. title: Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum link: https://peerj.com/articles/7553 last-modified: 2019-08-27 description: This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture. creator: Md Javed Foysal creator: Thi Thu Thuy Nguyen creator: Md Reaz Chaklader creator: Muhammad A.B. Siddik creator: Chin-Yen Tay creator: Ravi Fotedar creator: Sanjay Kumar Gupta uri: https://doi.org/10.7717/peerj.7553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Foysal et al.