title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=703 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific link: https://peerj.com/articles/13451 last-modified: 2022-05-31 description: The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs. creator: Savanna Wenhua Chow creator: Shashank Keshavmurthy creator: James Davis Reimer creator: Nicole de Voogd creator: Hui Huang creator: Jih-Terng Wang creator: Sen-Lin Tang creator: Peter J. Schupp creator: Chun Hong Tan creator: Hock-Chark Liew creator: Keryea Soong creator: Beginer Subhan creator: Hawis Madduppa creator: Chaolun Allen Chen uri: https://doi.org/10.7717/peerj.13451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chow et al. title: Spain is not different: teaching quantitative courses can also be hazardous to one’s career (at least in undergraduate courses) link: https://peerj.com/articles/13456 last-modified: 2022-05-31 description: Student evaluations of teaching (SETs) have become a widely used tool for assessing teaching in higher education. However, numerous investigations have shown that SETs are subject to multiple biases, one of which is particularly relevant, namely, the area of knowledge to which the subject belongs. This article aims to replicate the article by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299) in a different educational context to verify whether the negative bias toward instructors who teach quantitative courses found by the authors in the US also appears in the Spanish university system. The study was conducted at the Business and Law School of the Universidad Pontificia Comillas, a private Spanish university, using two different samples. First, we analyzed undergraduate courses using a sample of 80,667 SETs in which 2,885 classes (defined as a single semester-long course taught by an individual instructor to a specific group of students), 488 instructors, and 322 different courses were evaluated over a time period of four academic years (2016/2017–2019/2020). Second, in the same period, 16,083 SETs corresponding to master’s degree courses were analyzed, which involved the study of 871 classes, 275 instructors, and 155 different courses. All the data included in the analysis were obtained from official university surveys developed by a team of professionals specialized in teaching quality responsible for ensuring the reliability of the information. At the degree level, the results show that despite the considerable cultural and temporal difference between the samples, the results are very similar to those obtained by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299); i.e., professors teaching quantitative courses are far more likely to obtain worse SETs than instructors in other areas. There are hardly any differences at the master’s degree level, regardless of whether nearly 75% of master’s degree instructors also teach at the undergraduate level. This leads us to three different conclusions. (1) Evidence suggests that the reason for these differences is not due to faculty teaching quantitative courses being less effective than faculty teaching in some other fields. Our results indicate that the same instructor is evaluated very differently depending on whether he or she teaches at the undergraduate or master’s level. (2) It is essential to avoid comparisons of SETs between different areas of knowledge, at least at the undergraduate level. (3) A significant change in the use and interpretation of SETs is imperative, or its replacement by other evaluation mechanisms should be considered. If this does not occur, it is possible that in the future, there will be an adverse selection effect among professors of quantitative methods; i.e., only the worst professionals in quantitative methods will opt for teaching since the good professionals will prefer other jobs. creator: Jose Luis Arroyo-Barrigüete creator: Antonio Obregón creator: José María Ortiz-Lozano creator: Antonio Rua-Vieites uri: https://doi.org/10.7717/peerj.13456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Arroyo-Barrigüete et al. title: Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae) link: https://peerj.com/articles/13464 last-modified: 2022-05-31 description: Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures. creator: Carmen Benítez-Benítez creator: María Sanz-Arnal creator: Malvina Urbani creator: Pedro Jiménez-Mejías creator: Santiago Martín-Bravo uri: https://doi.org/10.7717/peerj.13464 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Benítez-Benítez et al. title: A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors link: https://peerj.com/articles/13466 last-modified: 2022-05-31 description: The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK (‘Baidongkui’) and DK (‘Dongkui’), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry. creator: Qihua Lin creator: Qiuzhen Zhong creator: Zehuang Zhang uri: https://doi.org/10.7717/peerj.13466 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lin et al. title: Prospective quantitative gene expression analysis of kallikrein-related peptidase KLK10 as a diagnostic biomarker for childhood acute lymphoblastic leukemia link: https://peerj.com/articles/13489 last-modified: 2022-05-31 description: BackgroundThe most common malignancy in children is acute lymphoblastic leukemia (ALL). This study aimed to explore KLK10 mRNA expression as a potential diagnostic biomarker for ALL in children and to examine the effect of chemotherapy on KLK10 mRNA expression following the induction and after three months of receiving chemotherapy.MethodsIn this prospective study, total RNA was extracted from blood samples of 23 pediatric ALL patients on diagnosis, after one month and three months of receiving chemotherapy. Healthy pediatric volunteers (n = 12) were selected as control individuals. After cDNA synthesis, KLK10 mRNA gene expression levels were quantified using quantitative real-time PCR (qRT-PCR).ResultsKLK10 mRNA expression levels were significantly decreased in leukemic cells compared to their levels in cells of normal blood samples (p = 0.0001). KLK10 expression levels in ALL patients after one month and three months of receiving chemotherapy decreased compared to normal blood samples (p < 0.0001 and p = 0.0175 respectively). The expression level of KLK10 mRNA in ALL patients after one month of chemotherapy was decreased compared to their level on diagnosis (p = 0.4413). KLK10 mRNA expression levels in ALL patients after three months of chemotherapy were increased compared to their level on diagnosis (p = 0.0602). The ROC curve illustrated that KLK10 mRNA expression could very efficiently discriminate ALL patients from normal counterparts (AUC=0.886, 95% CI [0.7720–1.000], SE = 0.0582, p = 0.0004).ConclusionKLK10 mRNA expression could serve as a potential diagnostic molecular biomarker for ALL in children. creator: Shwan Majid Ahmad creator: Basima Sadq Ahmed creator: Karzan Ghafur Khidhir creator: Heshu Sulaiman Rahman uri: https://doi.org/10.7717/peerj.13489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ahmad et al. title: Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3 link: https://peerj.com/articles/13529 last-modified: 2022-05-31 description: BackgroundPrimary dental caries is the most prevalent oral disease among preschool children, which can cause severe damage to teeth and even affect the mental well-being of children. Various studies have demonstrated that the oral microbiome plays a pivotal role in the onset and development of dental caries. However, it remains uncertain about the key microbial markers associated with caries, owing to the limited evidence.MethodsFifteen S-ECC children and fifteen healthy controls were selected from three-year-old children in this study. Their clinical data and oral saliva samples were collected. Shotgun sequencing was conducted to investigate the microbial differences and the relevant functions between the two groups.ResultsWe observed no apparent difference in oral microbial community diversity between the two groups. Still, at the genus/species levels, several characteristic genera/species such as Propionibacterium, Propionibacterium acidifaciens, Prevotella denticola, Streptococcus mutans and Actinomyces sp. oral taxon 448/414 increased significantly in S-ECC children, compared with the oral health group. Furthermore, we found that functional pathways involving glycolysis and acid production, such as starch and sucrose metabolism, fructose and mannose metabolism, glycolysis/gluconeogenesis, were prominently up-regulated in the high-caries group.ConclusionsOur study showed that dental caries in children were associated with the alterations in the oral microbiota at the composition and functional levels, which may potentially inspire the exploration of microbial diagnosis or therapeutic treatments. creator: Zhe Tang creator: Wenyi Xu creator: Zhifang Zhou creator: Yanchun Qiao creator: Shuguo Zheng creator: Wensheng Rong uri: https://doi.org/10.7717/peerj.13529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tang et al. title: Goal adjustment and well-being after an acquired brain injury: the role of cognitive flexibility and personality traits link: https://peerj.com/articles/13531 last-modified: 2022-05-31 description: ObjectiveThe tendency to flexibly adjust goals that are hindered by chronic illness is related to indicators of wellbeing. However, cognitive flexibility is often impaired in persons with an acquired brain injury (ABI), possibly affecting the ability to flexibly adjust goals. In this study we examined whether cognitive flexibility is positively related with the ability to disengage from goals to reengage with goals in persons with ABI. Second, we explored whether goal adjustment abilities are predictive of a unique proportion of the variance inabilities are predictive of quality of life and life satisfaction after controlling for personality traits.MethodSeventy-eight persons with an ABI completed a set of questionnaires. Goal disengagement and goal reengagement were assessed using the Wrosch Goal Adjustment Scale (GAS). Indicators of wellbeing were measured with the European Brain Injury Questionnaire (EBIQ) and the Satisfaction with Life Scale (SWLS). The percentage of perseverative errors on the Wisconsin Card Sorting Test (WCST) was used as an indicator of cognitive inflexibility. Big Five personality traits were assessed via the NEO Five Factor Inventory (NEO-FFI). Four hierarchical multiple regression analyses were then conducted. The first two analyses tested the effect of cognitive flexibility on goal adjustment tendencies. The second two analyses tested whether goal adjustment has a predictive value for life satisfaction and QOL beyond personality.ResultsCognitive flexibility was positively related to goal reengagement, but not to goal disengagement. Goal reengagement was positively associated with both quality of life and life satisfaction after controlling for demographic, illness characteristics and personality factors. Goal disengagement was negatively related to life satisfaction.ConclusionFlexible goal adjustment abilities have a unique explanatory value for indicators of wellbeing, beyond personality traits. The findings indicate that in persons with lower cognitive flexibility, goal reengagement ability might be negatively affected, and should be taking into account during rehabilitation. creator: Gunther Van Bost creator: Stefaan Van Damme creator: Geert Crombez uri: https://doi.org/10.7717/peerj.13531 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Van Bost et al. title: Seamens’ Sign: a novel electrocardiogram prediction tool for left ventricular hypertrophy link: https://peerj.com/articles/13548 last-modified: 2022-05-31 description: IntroductionPatients with left ventricular hypertrophy (LVH) diagnosed by electrocardiogram (ECG) have increased mortality and higher risk for life-threatening cardiovascular disease. ECGs offer an opportunity to identify patients with increased risk for potential risk-modifying therapy. We developed a novel, quick, easy to use ECG screening criterion (Seamens’ Sign) for LVH. This new criterion was defined as the presence of QRS complexes touching or overlapping in two contiguous precordial leads.MethodsThis study was a retrospective chart review of 2,184 patient records of patients who had an ECG performed in the emergency department and a transthoracic echocardiogram performed within 90 days. The primary outcome was whether Seamens’ Sign was noninferior in confirming LVH compared to other common diagnostic criteria. Test characteristics were calculated for each of the LVH criteria. Inter-rater agreement was assessed on a random sample using Cohen’s Kappa.ResultsMedian age was 63, 52% of patients were male and there was a 35% prevalence of LVH by transthoracic echocardiogram (TTE). Nine percent were positive for LVH on ECG based on Seamens’ Sign. Seamens’ Sign had a specificity of 0.92. Tests assessing noninferiority indicated Seamens’ Sign was non-inferior to all criteria (p < 0.001) except for Cornell criterion for women (p = 0.98). Seamens’ Sign had 90% (0.81–1.00) inter-rater agreement, the highest of all criteria in this study.ConclusionWhen compared to both the Sokolow-Lyon criteria and the Cornell criterion for men, Seamens’ Sign is noninferior in ruling in LVH on ECG. Additionally, Seamens’ Sign has higher inter-rater agreement compared to both Sokolow-Lyon criteria as well as the Cornell criteria for men and women, perhaps related to its ease of use. creator: Philip Walker creator: Cathy A. Jenkins creator: Jeremy Hatcher creator: Clifford Freeman creator: Nickolas Srica creator: Bryant Rosell creator: Eriny Hanna creator: Cooper March creator: Charles Seamens creator: Alan Storrow creator: Nicole McCoin uri: https://doi.org/10.7717/peerj.13548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Walker et al. title: Glomerular filtration rate correlation and agreement between common predictive equations and standard 24-hour urinary creatinine clearance in medical critically ill patients link: https://peerj.com/articles/13556 last-modified: 2022-05-31 description: BackgroundDetermining kidney function in critically ill patients is paramount for the dose adjustment of several medications. When assessing kidney function, the glomerular filtration rate (GFR) is generally estimated either by calculating urine creatinine clearance (UCrCl) or using a predictive equation. Unfortunately, all predictive equations have been derived for medical outpatients. Therefore, the validity of predictive equations is of concern when compared with that of the UCrCl method, particularly in medical critically ill patients. Therefore, we conducted this study to assess the agreement of the estimated GFR (eGFR) using common predictive equations and UCrCl in medical critical care setting.MethodsThis was the secondary analysis of a nutrition therapy study. Urine was collected from participating patients over 24 h for urine creatinine, urine nitrogen, urine volume, and serum creatinine measurements on days 1, 3, 5, and 14 of the study. Subsequently, we calculated UCrCl and eGFR using four predictive equations, the Cockcroft–Gault (CG) formula, the four and six-variable Modification of Diet in Renal Disease Study (MDRD-4 and MDRD-6) equations, and the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. The correlation and agreement between eGFR and UCrCl were determined using the Spearman rank correlation coefficient and Bland–Altman plot with multiple measurements per subject, respectively. The performance of each predictive equation for estimating GFR was reported as bias, precision, and absolute percentage error (APE).ResultsA total of 49 patients with 170 urine samples were included in the final analysis. Of 49 patients, the median age was 74 (21–92) years-old and 49% was male. All patients were hemodynamically stable with mean arterial blood pressure of 82 (65–108) mmHg. Baseline serum creatinine was 0.93 (0.3–4.84) mg/dL and baseline UCrCl was 46.69 (3.40–165.53) mL/min. The eGFR from all the predictive equations showed modest correlation with UCrCl (r: 0.692 to 0.759). However, the performance of all the predictive equations in estimating GFR compared to that of UCrCl was poor, demonstrating bias ranged from −8.36 to −31.95 mL/min, precision ranged from 92.02 to 166.43 mL/min, and an unacceptable APE (23.01% to 47.18%). Nevertheless, the CG formula showed the best performance in estimating GFR, with a small bias (−2.30 (−9.46 to 4.86) mL/min) and an acceptable APE (14.72% (10.87% to 23.80%)), especially in patients with normal UCrCl.ConclusionFrom our finding, CG formula was the best eGFR formula in the medical critically ill patients, which demonstrated the least bias and acceptable APE, especially in normal UCrCl patients. However, the predictive equation commonly used to estimate GFR in critically ill patients must be cautiously applied due to its large bias, wide precision, and unacceptable error, particularly in renal function impairment. creator: Suwikran Wongpraphairot creator: Attamon Thongrueang creator: Rungsun Bhurayanontachai uri: https://doi.org/10.7717/peerj.13556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wongpraphairot et al. title: Quality assessment of a serum and xenofree medium for the expansion of human GMP-grade mesenchymal stromal cells link: https://peerj.com/articles/13391 last-modified: 2022-05-30 description: BackgroundCell-based therapies are emerging as a viable modality to treat challenging diseases, resulting in an increasing demand for their large-scale, high-quality production. Production facilities face the issue of batch-to-batch consistency while producing a safe and efficient cell-based product. Controlling culture conditions and particularly media composition is a key factor of success in this challenge. Serum and Xeno-Free Media (SXFM) represent an interesting option to achieve this goal. By reducing batch to batch variability, they increase Good Manufacturing Practices (GMP)-compliance and safety regarding xenogenic transmission, as compared to fetal bovine serum (FBS) supplemented-media or human platelet lysate supplemented medium.MethodsIn this study, the isolation, expansion and characteristics including the anti-inflammatory function of human mesenchymal stromal cells (MSC) are compared after culture in MEMα supplemented with human Concentrate Platelet Lysate (hCPL, reference medium) or in MSC-Brew GMP Medium. The latter is a GMP SXFM manufactured in bags under strictly controlled conditions in volumes suitable for expansion to a clinical scale and does not require neither pre-coating of the cell culture units nor the addition of blood derivatives at the isolation step.ResultsWe showed that MSC derived from human bone-marrow and adipose tissue can be successfully isolated and expanded in this SXFM. Number and size of Colony-Forming Unit fibroblast (CFU-F) is increased compared to cells cultivated in hCPL medium. All cells retained a CD90+, CD73+, CD105+, HLADR−, CD34−, CD45− phenotype. Furthermore, the osteogenic and adipocyte potentials as well as the anti-inflammatory activity were comparable between culture conditions. All cells reached the release criteria established in our production facility to treat inflammatory pathologies.ConclusionsThe use of MSC-Brew GMP Medium can therefore be considered for clinical bioprocesses as a safe and efficient substitute for hCPL media. creator: Clotilde Aussel creator: Elodie Busson creator: Helene Vantomme creator: Juliette Peltzer creator: Christophe Martinaud uri: https://doi.org/10.7717/peerj.13391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aussel et al.