title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=692 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Microplastics do not affect bleaching of Acropora cervicornis at ambient or elevated temperatures link: https://peerj.com/articles/13578 last-modified: 2022-06-17 description: Microplastic pollution can harm organisms and ecosystems such as coral reefs. Corals are important habitat-forming organisms that are sensitive to environmental conditions and have been declining due to stressors associated with climate change. Despite their ecological importance, it is unclear how corals may be affected by microplastics or if there are synergistic effects with rising ocean temperatures. To address this research gap, we experimentally examined the combined effects of environmentally relevant microplastic concentrations (i.e., the global average) and elevated temperatures on bleaching of the threatened Caribbean coral, Acropora cervicornis. In a controlled laboratory setting, we exposed coral fragments to orthogonally crossed treatment levels of low-density polyethylene microplastic beads (0 and 11.8 particles L−1) and water temperatures (ambient at 28 °C and elevated at 32 °C). Zooxanthellae densities were quantified after the 17-day experiment to measure the bleaching response. Regardless of microplastic treatment level, corals in the elevated temperature treatment were visibly bleached and necrotic (i.e., significant negative effect on zooxanthellae density) while those exposed to ambient temperature remained healthy. Thus, our study successfully elicited the expected bleaching response to a high-water temperature. However, we did not observe significant effects of microplastics at either individual (ambient temperature) or combined levels (elevated temperature). Although elevated temperatures remain a larger threat to corals, responses to microplastics are complex and may vary based on focal organisms or on plastic conditions (e.g., concentration, size, shape). Our findings add to a small but growing body of research on the effects of microplastics on corals, but further work is warranted in this emerging field to fully understand how sensitive ecosystems are affected by this pollutant. creator: Martina M. Plafcan creator: Christopher D. Stallings uri: https://doi.org/10.7717/peerj.13578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Plafcan and Stallings title: Composition and environmental interpretation of the weed communities in the main planting base of jujube (Ziziphus jujuba Mill. cv. ‘LingwuChangzao’), Ningxia province of China link: https://peerj.com/articles/13583 last-modified: 2022-06-17 description: BackgroundZiziphus jujuba Mill. cv. ‘LingwuChangzao’ is a traditional jujube cultivar in northwest China. It is of great significance to explore the weed community composition and environmental characterization for the ecological control and comprehensive management of weeds in jujube orchards. In this article, a total of 37 species were recorded in 40 sample plots (1 m × 1 m). Moreover, fourteen environmental indicators to characterize the spatial locations, climate and soil nutrient characteristics of the plant communities were adopted.MethodologyThrough the two-way indicator species analysis (TWINSPAN) quantity classification and canonical correspondence analysis (CCA) ranking methods, the types of weed communities in the main planting base of jujube ‘LingwuChangzao’ and the main environmental factors affecting the change and distribution of weed types were analyzed.ResultsThe weed communities within the study area were divided into 15 types by the TWINSPAN classification. There were significant differences in soil factors to the species diversity indices of the weed communities, the diversity of weed communities was negatively correlated with available potassium, whereas positively correlated with soil water content. The CCA results showed that community structure and spatial distribution of weed communities were affected by soil water content, total potassium, soil organic carbon, total phosphorus, total nitrogen. Our results can be used as a reference for orchard weed management and provide a theoretical basis for weed invasion control and creating a higher biodiversity in arable land under the background of environmental change. creator: Xiaojia Wang creator: Bing Cao creator: Jin Zou creator: Weijun Chen uri: https://doi.org/10.7717/peerj.13583 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Patient deaths during the period of prolonged stay in cases of delayed discharge for nonclinical reasons at a university hospital: a cross sectional study link: https://peerj.com/articles/13596 last-modified: 2022-06-17 description: BackgroundDelayed discharge for non-clinical reasons also affects patients in need of palliative care. Moreover, the number of people dying in hospitals has been increasing in recent years. Our aim was to describe characteristics of patients who died during prolonged stay, in comparison with the rest of patients with delayed discharge, in terms of length of hospital stay, patient characteristics and the context of care.MethodsA descriptive cross-sectional study at a high complexity public hospital in Northern Spain (2007–2015) was conducted. To compare the differential characteristics of the groups of patients died during delayed discharge with the rest, Student’s T test and Pearson’s chi-square test (χ2) were used.ResultsA total of 198 patients died (6.57% of the total), with a mean total stay of 27.45 days and a prolonged stay of 10.69 days. Mean age 77.27 years. These were highly complex cases, 77.79% resided in the urban area, were admitted urgently (95.45%), to internal medicine or oncology wards, and the most common diagnosis was pneumonia. In people with terminal illness, clinicians can better identify when therapeutic possibilities are exhausted and acute hospitalization is not an adequate resource for their needs. Living in an urban area with the availability of palliative care hospital beds is related to the decision to die in hospital. creator: Amada Pellico-López creator: Manuel Herrero-Montes creator: David Cantarero Prieto creator: Ana Fernández-Feito creator: Joaquin Cayon-De las Cuevas creator: Paula Parás-Bravo creator: María Paz-Zulueta uri: https://doi.org/10.7717/peerj.13596 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pellico-López et al. title: Rabbit hindlimb kinematics and ground contact kinetics during the stance phase of gait link: https://peerj.com/articles/13611 last-modified: 2022-06-17 description: Though the rabbit is a common animal model in musculoskeletal research, there are very limited data reported on healthy rabbit biomechanics. Our objective was to quantify the normative hindlimb biomechanics (kinematics and kinetics) of six New Zealand White rabbits (three male, three female) during the stance phase of gait. We measured biomechanics by synchronously recording sagittal plane motion and ground contact pressure using a video camera and pressure-sensitive mat, respectively. Both foot angle (i.e., angle between foot and ground) and ankle angle curves were unimodal. The maximum ankle dorsiflexion angle was 66.4 ± 13.4° (mean ± standard deviation across rabbits) and occurred at 38% stance, while the maximum ankle plantarflexion angle was 137.2 ± 4.8° at toe-off (neutral ankle angle = 90 degrees). Minimum and maximum foot angles were 17.2 ± 6.3° at 10% stance and 123.3 ± 3.6° at toe-off, respectively. The maximum peak plantar pressure and plantar contact area were 21.7 ± 4.6% BW/cm2 and 7.4 ± 0.8 cm2 respectively. The maximum net vertical ground reaction force and vertical impulse, averaged across rabbits, were 44.0 ± 10.6% BW and 10.9 ± 3.7% BW∙s, respectively. Stance duration (0.40 ± 0.15 s) was statistically significantly correlated (p < 0.05) with vertical impulse (Spearman’s ρ = 0.76), minimum foot angle (ρ = −0.58), plantar contact length (ρ = 0.52), maximum foot angle (ρ = 0.41), and minimum foot angle (ρ = −0.30). Our study confirmed that rabbits exhibit a digitigrade gait pattern during locomotion. Future studies can reference our data to quantify the extent to which clinical interventions affect rabbit biomechanics. creator: Patrick Hall creator: Caleb Stubbs creator: David E. Anderson creator: Cheryl Greenacre creator: Dustin L. Crouch uri: https://doi.org/10.7717/peerj.13611 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hall et al. title: PPBP gene as a biomarker for coronary heart disease risk in postmenopausal Thai women link: https://peerj.com/articles/13615 last-modified: 2022-06-17 description: BackgroundEstrogen is an important ovarian hormone with anti-atherogenic and cardioprotective effects. Postmenopausal women have lower estrogen levels, associated with significantly higher risks of coronary heart disease (CHD) and CHD-related death. Effective biomarkers for the diagnosis, prediction, and treatment of CHD are needed to address this problem and thus reduce the mortality due to CHD in postmenopausal women. We recently reported that the PPBP and DEFA1/DEFA3 genes may be feasible synergistic biomarkers for CHD risk in Thai men with hyperlipidemia. The PPBP gene encodes pro-platelet basic protein (PPBP) from activated platelets, and DEFA1/DEFA3 encodes human neutrophil peptides (HNP) 1–3, mainly produced by activated neutrophils. Both platelets and neutrophils are involved in chronic inflammation during the development of atherogenesis and CHD. This study investigated the potential roles of PPBP and DEFA1/DEFA3 and their proteins as biomarkers for CHD risk in postmenopausal Thai women.MethodsThis cross-sectional study enrolled 90 postmenopausal Thai women, including 12 healthy controls (N), 18 patients with hyperlipidemia (H), and 21 patients diagnosed with CHD. The remaining 39 women were receiving cholesterol-lowering drugs for hyperlipidemia (HD) were excluded from the study. All CHD patients underwent coronary bypass grafting or coronary angioplasty. PPBP and DEFA1/DEFA3 mRNA expression levels in peripheral blood mononuclear cells isolated from heparinized blood were determined by quantitative reverse-transcription polymerase chain reaction. Levels of PPBP and HNP-1–3 proteins in corresponding plasma samples were assessed by enzyme-linked immunosorbent assay. Differences in parameters were compared among groups and correlations between parameters and clinical manifestations were analyzed.ResultsPPBP mRNA and protein levels were significantly increased in the CHD group compared with the N and H groups. In contrast, DEFA1/DEFA3 mRNA and HNP-1–3 protein levels did not differ significantly among the groups. None of the levels were associated with any of the clinical parameters analyzed in this study.ConclusionThe results indicate that gene and protein expression levels of PPBP, but not DEFA1/DEFA3, and HNP-1–3, may be feasible biomarkers for assessing CHD risk in postmenopausal Thai women with hyperlipidemia. creator: Chayasin Mansanguan creator: Yaowapa Maneerat uri: https://doi.org/10.7717/peerj.13615 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mansanguan and Maneerat title: An efficient numerical representation of genome sequence: natural vector with covariance component link: https://peerj.com/articles/13544 last-modified: 2022-06-16 description: BackgroundThe characterization and comparison of microbial sequences, including archaea, bacteria, viruses and fungi, are very important to understand their evolutionary origin and the population relationship. Most methods are limited by the sequence length and lack of generality. The purpose of this study is to propose a general characterization method, and to study the classification and phylogeny of the existing datasets.MethodsWe present a new alignment-free method to represent and compare biological sequences. By adding the covariance between each two nucleotides, the new 18-dimensional natural vector successfully describes 24,250 genomic sequences and 95,542 DNA barcode sequences. The new numerical representation is used to study the classification and phylogenetic relationship of microbial sequences.ResultsFirst, the classification results validate that the six-dimensional covariance vector is necessary to characterize sequences. Then, the 18-dimensional natural vector is further used to conduct the similarity relationship between giant virus and archaea, bacteria, other viruses. The nearest distance calculation results reflect that the giant viruses are closer to bacteria in distribution of four nucleotides. The phylogenetic relationships of the three representative families, Mimiviridae, Pandoraviridae and Marsellieviridae from giant viruses are analyzed. The trees show that ten sequences of Mimiviridae are clustered with Pandoraviridae, and Mimiviridae is closer to the root of the tree than Marsellieviridae. The new developed alignment-free method can be computed very fast, which provides an effective numerical representation for the sequence of microorganisms. creator: Nan Sun creator: Xin Zhao creator: Stephen S.-T. Yau uri: https://doi.org/10.7717/peerj.13544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al. title: Population structure in Quercus suber L. revealed by nuclear microsatellite markers link: https://peerj.com/articles/13565 last-modified: 2022-06-16 description: Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure. creator: Filipe Sousa creator: Joana Costa creator: Carla Ribeiro creator: Marta Varandas creator: Francisco Pina-Martins creator: Fernanda Simões creator: José Matos creator: Maria Glushkova creator: Célia Miguel creator: Maria Manuela Veloso creator: Margarida Oliveira creator: Cândido Pinto Ricardo creator: Dora Batista creator: Octávio S. Paulo uri: https://doi.org/10.7717/peerj.13565 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sousa et al. title: Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida’s Coral Reef link: https://peerj.com/articles/13574 last-modified: 2022-06-16 description: Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont—the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals’ health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida’s Coral Reef and sampled after residing within Mote Marine Laboratory’s in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management. creator: Sara D. Williams creator: J. Grace Klinges creator: Samara Zinman creator: Abigail S. Clark creator: Erich Bartels creator: Marina Villoch Diaz Maurino creator: Erinn M. Muller uri: https://doi.org/10.7717/peerj.13574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Williams et al. title: Effect of plyometric training and neuromuscular electrical stimulation assisted strength training on muscular, sprint, and functional performances in collegiate male football players link: https://peerj.com/articles/13588 last-modified: 2022-06-16 description: BackgroundThe study’s objective was to analyze the influence of an 8-week neuromuscular electrical stimulation (NMES) with a plyometric (PT) and strength training (ST) program on muscular, sprint, and functional performances in collegiate male football players.MethodsSixty collegiate male football players participated in this randomized controlled trial single-blind study. All the participants were randomly divided into two groups: (1) NMES group (Experimental, n = 30) who received NMES assisted ST and (2) sham NMES group (Control, n = 30) who received sham NMES assisted ST. In addition, participants from both groups received a PT program; both groups received intervention on three days a week for 8-weeks. The study’s outcomes, such as muscular, sprint, and functional performances, were assessed using a strength test (STN) for quadriceps muscle, sprint test (ST), and single-leg triple hop test (SLTHT), respectively, at baseline pre-intervention and 8-week post-intervention. The interaction between group and time was identified using a mixed design (2 × 2) ANOVA.ResultsSignificant difference found across the two time points for the scores of STN: F (1.58) = 5,479.70, p < 0.05; SLTHT: F (1.58) = 118.17, p < 0.05; and ST: F (1.58) = 201.63, p < 0.05. Similarly, the significant differences were found between groups averaged across time for the scores of STN: F (1.58) = 759.62, p < 0.05 and ST: F (1.58) = 10.08, p < 0.05. In addition, after 8-week of training, Cohen’s d observed between two groups a large to medium treatment’s effect size for the outcome STN (d = 10.84) and ST (d = 1.31). However, a small effect size was observed only for the SLTHT (d = 0.613).ConclusionsFindings suggest that the effect of PT and ST with either NMES or sham NMES are equally capable of enhancing muscular, sprint, and functional performances in collegiate male football players. However, PT and ST with NMES have shown an advantage over PT and ST with sham NMES in improving muscular performance and sprint performance among the same participants. creator: Shahnaz Hasan creator: Gokulakannan Kandasamy creator: Danah Alyahya creator: Asma Alonazi creator: Azfar Jamal creator: Amir Iqbal creator: Radhakrishnan Unnikrishnan creator: Hariraja Muthusamy uri: https://doi.org/10.7717/peerj.13588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hasan et al. title: Reliability and accuracy of ultrasound image analyses completed manually versus an automated tool link: https://peerj.com/articles/13609 last-modified: 2022-06-16 description: Analysis of Brightness-mode ultrasound-captured fascicle angle (FA) and fascicle length (FL) can be completed manually with computer-based programs or by automated programs. Insufficient data exists regarding reliability and accuracy of automated tools. Therefore, the purpose of this study was to determine the test-retest reliability of automatic and manual ultrasound analyses, while determining accuracy of the automatic tool against the manual equivalent. Twenty-three participants (mean ± SD; age = 24 ± 4 years; height = 172.2 ± 10.5 cm; body mass = 73.1 ± 16.1 kg) completed one laboratory visit consisting of two trials where vastus lateralis muscle architecture was assessed with ultrasound. Images were taken at both lower (10 MHz) and higher frequency (12 MHz). Images were analyzed manually in an open-source imaging program and automatically using a separate open-source macro function. Test-retest reliability statistics were calculated for automatic and manual analyses. Accuracy was determined with validity statistics and were calculated for automatic analyses. The results show that manual ultrasound analyses for FA and FL for both lower and higher frequency displayed good reliability (ICC2,1 = 0.75–0.86). However, automatic ultrasound analyses for FA and FL revealed moderate reliability (ICC2,1 = 0.61–0.72) for the lower frequency images and poor reliability (ICC2,1 = 0.16–0.27) for higher frequency images. When assessed against manual techniques, automatic analyses presented greater total error (TE) and standard error of the estimate (SEE) for FA at lower frequency (constant error (CE) = −3.91°, TE = 5.57°, SEE = 3.45°) than higher (CE = −2.78°, TE = −4.54°, SEE = 2.45°). For FL, the higher frequency error (CE = 0.92 cm, TE = 2.12 cm, SEE = 1.15 cm) was similar to lower frequency error (CE = 1.98 cm, TE = 3.66 cm, SEE = 1.57 cm). The findings overall show that manual analyses had good reliability and low absolute error, while demonstrating the automated counterpart had poor to moderate reliability and large errors in analyses. These findings may be impactful as they highlight the good reliability and low error associated with manually analyzed ultrasound images and validate a novel automatic tool for analyzing ultrasound images. Future work should focus on improving reliability and decreasing error in automated image analysis tools. Automated tools are promising for the field as they eliminate biases between analysts and may be more time efficient than manual techniques. creator: Kealey J. Wohlgemuth creator: Malia N.M Blue creator: Jacob A. Mota uri: https://doi.org/10.7717/peerj.13609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wohlgemuth et al.