title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=764 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support link: https://peerj.com/articles/12958 last-modified: 2022-02-17 description: BackgroundRecently, the concept of respiratory sarcopenia has been advocated, but evidence is lacking regarding which respiratory parameters are appropriate indicators. Therefore, we investigated the association between sarcopenia, respiratory function, and respiratory muscle strength to identify the most appropriate parameters for respiratory sarcopenia.MethodsWe included 124 older adults (67 men, 57 women; average age 77.2 ± 8.3 years) requiring long-term care/support who underwent Day Care for rehabilitation. Handgrip strength, usual gait speed, and skeletal muscle mass were measured using bioelectrical impedance analysis. Participants were then diagnosed with sarcopenia using the algorithm of the Asian Working Group for Sarcopenia 2019. Parameters of respiratory function (forced vital capacity, forced expiratory volume in one second [FEV1.0], FEV1.0%, and peak expiratory flow rate) and respiratory muscle strength (maximal expiratory pressure [MEP] and maximal inspiratory pressure) were also measured according to American Thoracic Society guidelines. Respiratory parameters significantly related to sarcopenia were identified using binomial logistic regression and receiver operating characteristic analyses.ResultsSeventy-seven participants were classified as having sarcopenia. Binomial logistic regression analysis showed that MEP was the only respiratory parameter significantly associated with sarcopenia. The cut-off MEP value for predicting sarcopenia was 47.0 cmH20 for men and 40.9 cmH20 for women.ConclusionsThe most appropriate parameter for assessing respiratory sarcopenia may be MEP, which is an indicator of expiratory muscle strength, rather than FVC, MIP, or PEFR, as suggested in previous studies. Measuring MEP is simpler than measuring respiratory function parameters. Moreover, it is expected to have clinical applications such as respiratory sarcopenia screening. creator: Yohei Sawaya creator: Takahiro Shiba creator: Masahiro Ishizaka creator: Tamaki Hirose creator: Ryo Sato creator: Akira Kubo creator: Tomohiko Urano uri: https://doi.org/10.7717/peerj.12958 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sawaya et al. title: Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis link: https://peerj.com/articles/12959 last-modified: 2022-02-17 description: BackgroundIron deficiency anemia (IDA) is among the most common micronutrient deficiencies in women of childbearing age and may affect children’s development. Brazil has several national programs to tackle this condition, such as food fortification and supplementation for pregnant women, but IDA prevalence in this population has not been systematically reviewed. We sought to determine the prevalence of IDA in Brazilian women of childbearing age through a systematic review with metanalysis.MethodologyA protocol was previously published on the PROSPERO platform under the code CRD42020200960. A panel of the National Council for Scientific and Technological Development (CNPq) approved the protocol of this study under the public call number 26/2019. The main databases searched were MEDLINE, Web of Science, Scopus, Lilacs, and SciELO. In gray literature, the Brazilian Digital Library of Theses and Dissertations and the annals of the Brazilian Congress of Epidemiology and the Brazilian Congress of Public Health were accessed. The search strategy involved terms related to the condition (IDA) and the age group of the population of interest (teenagers and adults). Studies that had assessed the prevalence of IDA in Brazilian women of childbearing age (10–49 years) were included. Three independent reviewers read all titles and abstracts and extracted data from the included studies. Random effects meta-analyses using the Freeman-Tukey arcsine transformation were carried out with prevalence data, and meta-regression was conducted to test for subgroup differences. The quality of the studies was assessed using the Newcastle-Ottawa Scale.ResultsFrom 21,210 unique records screened, 237 full-texts were retrieved, of which 91 were included in the qualitative synthesis, and 83 were included in the meta-analysis. The overall IDA prevalence was 25% (95% CI [23–28], 83 studies). The subgroup of studies that used random sampling showed a prevalence of 22% (95% CI [17–27], 22 studies), whereas in those with non-random sampling, the prevalence was 27% (95% CI [23–30], 61 studies), without significant differences between subgroups in the metaregression (P = 0.13). High prevalence of IDA were found in the subgroups of studies conducted in the North and Northeast regions (30%; 95% CI [24–37]; seven studies, and 30%; 95% CI [26–34]; 27 studies, respectively), in studies conducted with indigenous population (53%; 95% CI [27–78], four studies), and with studies that had their collections after 2015 (28%; 95% CI [23–34], nine studies).ConclusionsIDA in women of childbearing age remains a public health problem in Brazil, especially in the North and Northeast region. The national programs should be strengthened and more thoroughly supervised to decrease this condition nationally. creator: Mateus Macena creator: Dafiny Praxedes creator: Ana Debora De Oliveira creator: Déborah Paula creator: Maykon Barros creator: André Silva Júnior creator: Witiane Araújo creator: Isabele Pureza creator: Ingrid Sofia de Melo creator: Nassib Bueno uri: https://doi.org/10.7717/peerj.12959 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Macena et al. title: PCAtest: testing the statistical significance of Principal Component Analysis in R link: https://peerj.com/articles/12967 last-modified: 2022-02-17 description: Principal Component Analysis (PCA) is one of the most broadly used statistical methods for the ordination and dimensionality-reduction of multivariate datasets across many scientific disciplines. Trivial PCs can be estimated from data sets without any correlational structure among the original variables, and traditional criteria for selecting non-trivial PC axes are difficult to implement, partially subjective or based on ad hoc thresholds. PCAtest is an R package that implements permutation-based statistical tests to evaluate the overall significance of a PCA, the significance of each PC axis, and of contributions of each observed variable to the significant axes. Based on simulation and empirical results, I encourage R users to routinely apply PCAtest to test the significance of their PCA before proceeding with the direct interpretation of PC axes and/or the utilization of PC scores in subsequent evolutionary and ecological analyses. creator: Arley Camargo uri: https://doi.org/10.7717/peerj.12967 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Camargo title: Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon link: https://peerj.com/articles/12980 last-modified: 2022-02-17 description: Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were detected in various tissues including nervous tissue, gill, heart, hepatopancreas, gut, and gonads. Interestingly, the sexually dimorphic expression of PmOvtra 2, Pmfru-1, and Pmfru-2 was demonstrated in fully developed gonads in which the ovary showed significantly higher expressions than the testis. The great difference in the expression pattern of PmOvtra 2, Pmfru-1, and Pmfru-2 in the ovary and testis suggested their roles in the female sex determination in P. monodon. creator: Prawporn Thaijongrak creator: Charoonroj Chotwiwatthanakun creator: Phaivit Laphyai creator: Anuphap Prachumwat creator: Thanapong Kruangkum creator: Prasert Sobhon creator: Rapeepun Vanichviriyakit uri: https://doi.org/10.7717/peerj.12980 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Thaijongrak et al. title: The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure link: https://peerj.com/articles/12985 last-modified: 2022-02-17 description: BackgroundAnimal behaviour is under strong selection. Selection on behaviour, however, might not act in isolation from other fitness-related traits. Since predators represent outstanding selective forces, animal behaviour could covary with antipredator defences, such that individuals better suited against predators could afford facing the costs of riskier behaviours. Moreover, not all individuals undergo equivalent degrees of predation pressure, which can vary across sexes or habitats. Individuals under lower predation pressure might also exhibit riskier behaviours.MethodsIn this work, I tested these hypotheses on natterjack toads (Epidalea calamita). Specifically, I gauged activity time, exploratory behaviour and boldness in standard laboratory conditions, and assessed whether they correlated with body size and antipredator strategies, namely sprint speed, parotoid gland area and parotoid gland colour contrast. Additionally, I compared these traits between sexes and individuals from an agrosystem and pine grove, since there is evidence that males and agrosystem individuals are subjected to greater predation pressure.ResultsSprint speed as well as parotoid gland contrast and size appeared unrelated to the behavioural traits studied. In turn, body mass was negatively related to activity time, boldness and exploration. This trend is consistent with the fact that larger toads could be more detectable to their predators, which are mostly gape unconstrained and could easily consume them. As predicted, females exhibited riskier behaviours. Nonetheless, agrosystem toads did not differ from pine grove toads in the behavioural traits measured, despite being under stronger predation pressure. creator: Francisco Javier Zamora-Camacho uri: https://doi.org/10.7717/peerj.12985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zamora-Camacho title: Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution link: https://peerj.com/articles/12988 last-modified: 2022-02-17 description: Air pollution is a growing concern for the general public in Thailand with PM 2.5 (particulate matter ≤ 2.5 µm) having the greatest impact on health. The inverse Gaussian (IG) distribution is used for examining the frequency of high concentration events and has often been applied to analyze pollution data, with the coefficient of variation (CV) being used to calculate the quantitative difference in PM 2.5 concentrations. Herein, we propose confidence intervals for the CV of an IG distribution based on the generalized confidence interval (GCI), the adjusted generalized confidence interval (AGCI), the bootstrap percentile confidence interval (BPCI), the fiducial confidence interval (FCI), and the fiducial highest posterior density confidence interval (F-HPDCI). The performance of the proposed confidence intervals was evaluated by using their coverage probabilities and average lengths from various scenarios via Monte Carlo simulations. The simulation results indicate that the coverage probabilities of the AGCI and FCI methods were higher than or close to the nominal level in all of test case scenarios. Moreover, FCI outperformed the others for small sample sizes by achieving the shortest average length. The efficacies of the confidence intervals were demonstrated by using PM 2.5 data from the Din Daeng and Bang Khun Thian districts in Bangkok, Thailand. creator: Wasana Chankham creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.12988 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chankham et al. title: Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe link: https://peerj.com/articles/12507 last-modified: 2022-02-16 description: BackgroundAfter implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear.MethodWe selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured.ResultsResults shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe. creator: Qi Lu creator: Hongbin Ma creator: Yao Zhou creator: Roberto Calvelo-Pereira creator: Yan Shen uri: https://doi.org/10.7717/peerj.12507 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lu et al. title: Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets link: https://peerj.com/articles/12662 last-modified: 2022-02-16 description: BackgroundWithin the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets.MethodsForty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets.ResultsNineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria. creator: Marcus Vinicius Canário Viana creator: Rodrigo Profeta creator: Janaína Canário Cerqueira creator: Alice Rebecca Wattam creator: Debmalya Barh creator: Artur Silva creator: Vasco Azevedo uri: https://doi.org/10.7717/peerj.12662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Canário Viana et al. title: Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs link: https://peerj.com/articles/12695 last-modified: 2022-02-16 description: Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome. creator: Pamela Thomson creator: Rodrigo Santibáñez creator: Camila Rodríguez-Salas creator: Carla Flores-Yañez creator: Daniel Garrido uri: https://doi.org/10.7717/peerj.12695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Thomson et al. title: Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey link: https://peerj.com/articles/12887 last-modified: 2022-02-16 description: To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38). creator: Alexandria Caple creator: Arnie Dimaano creator: Marc Martin Sagolili creator: April Anne Uy creator: Panjee Mariel Aguirre creator: Dean Lotus Alano creator: Giselle Sophia Camaya creator: Brent John Ciriaco creator: Princess Jerah Mae Clavo creator: Dominic Cuyugan creator: Cleinne Florence Geeseler Fermo creator: Paul Jeremy Lanete creator: Ardwayne Jurel La Torre creator: Thomas Loteyro creator: Raisa Mikaela Lua creator: Nicole Gayle Manansala creator: Raphael Willard Mosquito creator: Alexa Octaviano creator: Alexandra Erika Orfanel creator: Gheyanna Merly Pascual creator: Aubrey Joy Sale creator: Sophia Lorraine Tendenilla creator: Maria Sofia Lauren Trinidad creator: Nicole Jan Trinidad creator: Daphne Louise Verano creator: Nicanor Austriaco uri: https://doi.org/10.7717/peerj.12887 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Caple et al.