title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=489 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population link: https://peerj.com/articles/15617 last-modified: 2023-07-11 description: IntroductionThere are numerous reports of a higher prevalence of metabolic disorders in patients with schizophrenia and bipolar disorder (BD), yet its connections to diet and physical activity remain not fully explained. This article aimed to evaluate diet, physical activity and selected biochemical and anthropometric parameters associated with metabolism in patients with schizophrenia and BD and to analyse the relationships between these variables in the subjects.Materials and MethodsA total of 126 adults participated in the study: 47 patients with schizophrenia, 54 patients with BD and 25 patients in mental illness remission (reference group). Data were collected on the underlying illness and concomitant illnesses, and the severity of symptoms of the current episode was assessed using the following scales: PANSS, MADRS and YMRS. An assessment of the subjects’ diet (KomPAN questionnaire) and their physical activity (International Physical Activity Questionnaire) was carried out. Anthropometric and blood pressure measurements were taken and BMI and WHR were calculated. Serum concentrations of fasting glucose, TSH, total cholesterol, LDL and HDL fractions, triglycerides and leptin, ghrelin and resistin were determined. For statistical analysis, the significance level was set at 0.05. For multiple comparisons one way ANOVA or Kruskal Wallis were used with post hoc Tukey and Dunn tests, respectively. To determine correlation of variables, Pearson’s linear correlation coefficient or Spearman’s rank correlation coefficient were used.ResultsA total of 50.8% of the subjects had at least one metabolic disorder—most commonly excessive body weight (66.7%) and abdominal obesity (64.3%). Patients did not differ significantly in terms of physical activity, but they did differ in mean time spent sitting—with this being significantly longer for all groups than in the general population. The subjects differed in diet: patients with BD consumed less unhealthy foods than patients with schizophrenia. The highest correlations between physical activity, diet and variables defining metabolic disorders were found in patients with BD. Only in patients with schizophrenia were there significant correlations between the course of the disease and physical activity.DiscussionThe results suggest the existence of associations between diet, physical activity, and metabolic disorders in both BD and schizophrenia patients. They also suggest a tendency among those patients to spend long periods of time sitting. creator: Magdalena Głodek creator: Maria Skibinska creator: Aleksandra Suwalska uri: https://doi.org/10.7717/peerj.15617 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Głodek et al. title: Ecological indicators reveal historical regime shifts in the Black Sea ecosystem link: https://peerj.com/articles/15649 last-modified: 2023-07-11 description: BackgroundThe Black Sea is one of the most anthropogenically disturbed marine ecosystems in the world because of introduced species, fisheries overexploitation, nutrient enrichment via pollution through river discharge, and the impacts of climate change. It has undergone significant ecosystem transformations since the 1960s. The infamous anchovy and alien warty comb jelly Mnemiopsis leidyi shift that occurred in 1989 is the most well-known example of the drastic extent of anthropogenic disturbance in the Black Sea. Although a vast body of literature exists on the Black Sea ecosystem, a holistic look at the multidecadal changes in the Black Sea ecosystem using an ecosystem- and ecology-based approach is still lacking. Hence, this work is dedicated to filling this gap.MethodsFirst, a dynamic food web model of the Black Sea extending from 1960 to 1999 was established and validated against time-series data. Next, an ecological network analysis was performed to calculate the time series of synthetic ecological indicators, and a regime shift analysis was performed on the time series of indicators.ResultsThe model successfully replicated the regime shifts observed in the Black Sea. The results showed that the Black Sea ecosystem experienced four regime shifts and was reorganized due to effects instigated by overfishing in the 1960s, eutrophication and establishment of trophic dead-end organisms in the 1970s, and overfishing and intensifying interspecies trophic competition by the overpopulation of some r-selected organisms (i.e., jellyfish species) in the 1980s. Overall, these changes acted concomitantly to erode the structure and function of the ecosystem by manipulating the food web to reorganize itself through the introduction and selective removal of organisms and eutrophication. Basin-wide, cross-national management efforts, especially with regard to pollution and fisheries, could have prevented the undesirable changes observed in the Black Sea ecosystem and should be immediately employed for management practices in the basin to prevent such drastic ecosystem fluctuations in the future. creator: Ekin Akoglu uri: https://doi.org/10.7717/peerj.15649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Akoglu title: Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields link: https://peerj.com/articles/15656 last-modified: 2023-07-11 description: Many factors influence selection of a target journal for publishing scientific papers, including “fit” within the journal’s scope, acceptance rate, readership, open access options, submission and publication costs, journal quality, and timeliness of publication. Timeliness of publication can be a critical factor affecting career development, but many journals are not transparent about turnaround times. Here we evaluated 49 journals publishing papers in zoological medicine and related fields between 2017 and 2022, and aggregated and examined distributions of turnaround time of journals that publicly provided the requisite data, in order to aid authors in selecting target journals that best meet their needs. Of 49 journals evaluated, 39 provided necessary dates for reconstructing turnaround times. Of these, median times to acceptance ranged from 37 to 338 days, and median times to publication ranged from 41 to 403.5 days. The percentage of papers published in greater than 1 year (“slow”) ranged from 0 to 57.1%, while the percentage of papers published in under 6 months (“timely”) ranged from 0.8 to 99.8%. Acceptance rates and times to first decision were available for only 22% and 20%, respectively, of journals evaluated. Results may prove useful for authors deciding where to submit their works, depending on how they prioritize the many factors involved. creator: Brendan Runde creator: Craig Harms uri: https://doi.org/10.7717/peerj.15656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Runde and Harms title: A retrospective study on expression and clinical significance of PHH3, Ki67 and P53 in bladder exophytic papillary urothelial neoplasms link: https://peerj.com/articles/15675 last-modified: 2023-07-11 description: BackgroundExophytic papillary urothelial neoplasms (EPUN) are difficult to diagnose pathologically and are well-known for their heterogeneous prognoses. Thus, searching for an objective and accurate diagnostic marker is of great clinical value in improving the outcomes of EPUN patients. PHH3 was reported to be expressed explicitly in the mitotic phase of the cell cycle, and recent studies have shown that PHH3 expression was associated with the differential diagnosis and prognosis of many tumors. However, its significance in EPUN remains unclear. This study aimed to determine the expression of PHH3 in different EPUN, compare its expression with cell-cycle related proteins Ki67 and P53, and analyze its significance in the differential diagnosis and prognostic value for high-grade papillary urothelial carcinoma (HGPUC), low-grade papillary urothelial carcinoma (LGPUC), papillary urothelial neoplasm of low malignant potential (PUNLMP) and urothelial papilloma (UP).MethodsWe retrospectively analyzed the pathological diagnosis and clinical features of 26 HGPUC cases, 43 LGPUC cases, 21 PUNLMP cases and 11 UP cases. PHH3, Ki67 and P53 were detected by immunohistochemistry in 101 EPUN cases samples. The cut-off values of PHH3 mitosis count (PHMC), HE mitosis count (HEMC), Ki67 and P53 in the different EPUN were determined using the ROC curve. The distribution of counts in each group and its relationship with clinical parameters and prognosis of EPUN patients were also analyzed.ResultsThe determination coefficient (R2 = 0.9980) of PHMC were more potent than those of HEMC (R2 = 0.9734) in the EPUN mitotic counts microscopically by both pathologists. Of the 101 EPUN cases investigated, significant positive linear correlations were found between PHMC and HEMC, PHMC and Ki67, and HEMC and Ki67 (P < 0.0001). In HGPUC, LGPUC, PUNLMP and UP, a decreasing trend was observed in the median and range of PHMC/10HPFs, HEMC/10HPFs, Ki67 (%) and P53 (%). PHMC, HEMC, Ki67 and P53 were associated with different clinical parameters of EPUN. PHMC, HEMC, Ki67 and P53 were found to exhibit substantial diagnostic values among different EPUN and tumor recurrence. Based on the ROC curve, when PHMC was >48.5/10HPFs, a diagnosis of HGPUC was more likely, and when PHMC was >13.5/10HPFs, LGPUC was more likely. In addition, when PHMC was >5.5/10HPFs, the possibility of non-infiltrating LGPUC was greater. Kaplan-Meier survival curve analysis showed that the median recurrence-free survival (RFS) for cases with PHMC > 13.5/10HPFs and HEMC > 14.5/10HPFs were 52.5 and 48 months, respectively, and their respective hazard ratio was significantly higher (Log-rank P < 0.05).ConclusionPHH3 exhibited high specificity and sensitivity in diagnosing EPUN. Combined with HEMC, Ki67 and P53, it can assist in the differential diagnosis of EPUN and estimate its clinical progression with high predictive value to a certain extent. creator: Gaoxiu Qi creator: Jinmeng Liu creator: Shuqi Tao creator: Wenyuan Fan creator: Haoning Zheng creator: Meihong Wang creator: Hanchao Yang creator: Yongting Liu creator: Huancai Liu creator: Fenghua Zhou uri: https://doi.org/10.7717/peerj.15675 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Qi et al. title: In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants link: https://peerj.com/articles/15696 last-modified: 2023-07-11 description: Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants. creator: So Youn Won creator: Prabhakaran Soundararajan creator: Vadivelmurugan Irulappan creator: Jung Sun Kim uri: https://doi.org/10.7717/peerj.15696 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Won et al. title: Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China link: https://peerj.com/articles/15462 last-modified: 2023-07-10 description: The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases. creator: Yaru Zhao creator: Dulan Bao creator: Ying Sun creator: Yajie Meng creator: Ziteng Li creator: Rui Liu creator: Jiwei Lang creator: Li Liu creator: Li Gao uri: https://doi.org/10.7717/peerj.15462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Is retroflexion a stable cue for distributional learning for speech sounds across languages? Learning for some bilingual adults, but not generalisable to a wider population in a well powered pre-registered study link: https://peerj.com/articles/15467 last-modified: 2023-07-10 description: Bilinguals are widely reported to have certain kinds of cognitive advantages, including language learning advantages. One possible pathway is a language-specific transfer effect, whereby sensitivity to structural regularities in known languages can be brought to to-be-acquired languages that share particular features. Here we tested for transfer of a specific linguistic property, sensitivity to retroflexion as contrastive phonemic feature. We designed a task for bilinguals with homogeneous language exposure (i.e., bilingual in the same languages) and heterogeneous feature representation (i.e., differing levels of proficiency). Hindi and Mandarin Chinese both have retroflexion in phoneme contrasts (Hindi: stop consonants, Mandarin: sibilants). In a preregistered study, we conducted a statistical learning task for the Hindi dental-retroflex stop contrast with a group of early parallel English-Mandarin bilinguals, who varied in their Mandarin understanding levels. We based the target sample size on power analysis of a pilot study with a Bayesian stop-rule after minimum threshold. Contrary to the pilot study (N = 15), the main study (N = 50) did not find evidence for a learning effect, nor language-experience variance within the group. This finding suggests that statistical effects for the feature in question may be more fragile than commonly assumed, and may be evident in only a small subsample of the general population (as in our pilot). These stimuli have previously shown learning effects in children, so an additional possibility is that neural commitment to adults’ languages prevents learning of the fine-grained stimulus contrast in question for this adult population. creator: Hannah L. Goh creator: Luca Onnis creator: Suzy J. Styles uri: https://doi.org/10.7717/peerj.15467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Goh et al. title: Perceptions of the impact of COVID-19 in Tennessee, USA: a retrospective study link: https://peerj.com/articles/15473 last-modified: 2023-07-10 description: BackgroundDespite high incidence and mortality risks associated with COVID-19 during the pandemic, stay-at-home orders and vaccination recommendations were met with varying levels of acceptance in Tennessee. Understanding perceptions of individuals regarding the health and economic impacts of COVID-19 is necessary to address public concerns while ensuring appropriate public health response. Therefore, the objectives of this study were to (a) investigate differences in opinions among residents of Tennessee regarding the impacts of COVID-19; and (b) identify socioeconomic and demographic predictors/determinants of these opinions.MethodsThis retrospective cross-sectional study was conducted using survey data collected in nine waves during 2020. Distributions of survey-weighted sociodemographic characteristics and respondent perceptions of the impact of COVID-19 were computed. Weighted logistic models were used to investigate predictors of a number of perceptions: whether the health or economic impact was greater, concern for respondent’s health, concern for family’s health, and willingness to accept COVID-19 vaccine.ResultsThe study included a total of 9,754 survey respondents. Approximately equal percentages considered COVID-19 to have a greater economic (48.4%) versus health impact (51.6%). Just 40.1% of the respondents reported that they would definitely accept a COVID-19 vaccine. Age group, race, educational attainment, and household composition were significant (p < 0.05) predictors of all investigated perceptions regarding COVID-19. Lack of prior infection was the strongest predictor of the perception of COVID-19 having a greater impact on health (OR = 2.40, p < 0.001), concern for respondent’s health (OR = 1.86, p = 0.002), and concern for family members’ health (OR = 1.90, p = 0.001). Compared to males, females had higher odds of identifying the health impact of COVID-19 as greater (OR = 1.09, p = 0.041) and reporting concern for family health (OR = 1.14, p = 0.003). However, they had lower odds (OR = 0.63, p < 0.001) of willingness to accept vaccine than males.ConclusionThese findings improve our understanding of the drivers of health behaviors, including vaccine hesitancy, and are useful for guiding public health outreach/education programs. creator: Tamara L. Chavez-Lindell creator: Katie A. Cahill creator: Kristina W. Kintziger creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.15473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chavez-Lindell et al. title: Psychological flexibility, cognitive emotion regulation and mental health outcomes among patients with asthma in Pakistan link: https://peerj.com/articles/15506 last-modified: 2023-07-10 description: Background/ObjectiveAdults with asthma who experience difficulties in emotion regulation are prone to developing psychopathological symptoms that may affect their self-management activities and symptom control. The current research investigated the role of psychological flexibility and cognitive emotion regulation strategies in relation to mental health outcomes (psychological distress and quality of life) among patients with asthma in Pakistan.MethodA sample of 200 adults, diagnosed with asthma (32% men, 68% women; Mage = 42.32, SDage = 16.99), completed the acceptance and action questionnaire (AAQ-II) cognitive emotion regulation questionnaire (CERQ), depression, anxiety, stress scale-21 (DASS-21), asthma-related quality of life questionnaire (AQLQ) and a self-structured demographic sheet.ResultsResults of Pearson product moment correlation showed that most of the adaptive cognitive emotion regulation strategies (positive refocusing, refocus on planning, and positive reappraisal) were positively correlated with psychological flexibility and quality of life, whereas negatively correlated with psychological distress. All the maladaptive strategies of cognitive emotion regulation had a significant inverse relationship with psychological flexibility and quality of life, while positively correlated with psychological distress. Results of serial mediation analysis through PROCESS MACRO showed that catastrophising and anxiety fully mediated the relationship between psychological flexibility and asthma-related quality of life.ConclusionEvidence-based interventions should focus on developing psychological flexibility and identifying maladaptive patterns of cognitive emotion regulation strategies for improved mental health and quality of life outcomes for adults with asthma. creator: Samavia Hussain creator: Rabia Khawar creator: Rizwana Amin creator: Asma Hamdani creator: Asma Majeed uri: https://doi.org/10.7717/peerj.15506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hussain et al. title: A comparison of survey method efficiencies for estimating densities of zebra mussels (Dreissena polymorpha) link: https://peerj.com/articles/15528 last-modified: 2023-07-10 description: Abundance surveys are commonly used to estimate plant or animal densities and frequently require estimating detection probabilities to account for imperfect detection. The estimation of detection probabilities requires additional measurements that take time, potentially reducing the efficiency of the survey when applied to high-density populations. We conducted quadrat, removal, and distance surveys of zebra mussels (Dreissena polymorpha) in three central Minnesota lakes and determined how much survey effort would be required to achieve a pre-specified level of precision for each abundance estimator, allowing us to directly compare survey design efficiencies across a range of conditions. We found that the required sampling effort needed to achieve our precision goal depended on both the survey design and population density. At low densities, survey designs that could cover large areas but with lower detection probabilities, such as distance surveys, were more efficient (i.e., required less sampling effort to achieve the same level of precision). However, at high densities, quadrat surveys, which tend to cover less area but with high detection rates, were more efficient. These results demonstrate that the best survey design is likely to be context-specific, requiring some prior knowledge of the underlying population density and the cost/time needed to collect additional information for estimating detection probabilities. creator: Jake M. Ferguson creator: Laura Jiménez creator: Aislyn A. Keyes creator: Austen Hilding creator: Michael A. McCartney creator: Katherine St. Clair creator: Douglas H. Johnson creator: John R. Fieberg uri: https://doi.org/10.7717/peerj.15528 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ferguson et al.