Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata
Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution. Due to ocean warming and eutrophication, the ocean is deoxygenating. In the Eastern Tropical Pacific (ETP), deep waters with low DO (<1 mg L−1) may reach coral reefs, because upwelling will likely intensify due to climate change. To understand oxygen variability and its effects on corals, we characterize the Spatio-temporal changes of DO in coral reefs of Gorgona Island and calculate the critical oxygen tension (Pcrit) to identify the DO concentration that could represent a hypoxic condition for Pocillopora capitata, one of the main reef-building species in the ETP. The mean (±SD) DO concentration in the coral reefs of Gorgona Island was 4.6 ± 0.89 mg L−1. Low DO conditions were due to upwelling, but hypoxia (<3.71 mg L−1, defined as a DO value 1 SD lower than the Mean) down to 3.0 mg O2 L−1 sporadically occurred at 10 m depth. The Pcrit of P. capitata was 3.7 mg L−1 and lies close to the hypoxic condition recorded on coral reefs during the upwelling season at 10 m depth. At Gorgona Island oxygen conditions lower than 2.3 mg L−1 occur at >20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora. Because DO concentrations in coral reefs of Gorgona Island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.
Castrillón-Cifuentes et al. (2023) Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata. PeerJ 11:e14586 https://doi.org/10.7717/peerj.14586
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples
Background The accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (e.g., air or wastewater) is imperative for successful surveillance of community level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja). Methods We simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators. Results Based on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (e.g., Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants). Conclusion This work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (e.g., wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions.
Kayikcioglu et al. (2023) Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples. PeerJ 11:e14596 https://doi.org/10.7717/peerj.14596
Emotional Appetite Questionnaire: psychometric properties in Brazilian adult samples before and after the COVID-19 pandemic onset
Background Appetite represents a desire of a person to eat specific food in order to reach satisfaction and pleasure states. This desire may be associated with the experience of negative or positive emotions (emotional appetite). Emotional appetite can influence eating behavior, and its investigation is relevant to avoid possible damage to health resulting from a disordered eating. Objectives To adapt the Emotional Appetite Questionnaire (EMAQ) to the Portuguese language; to assess the validity and reliability of the data; and to assess emotional appetite in three samples of adults collected before and after the outbreak of the COVID-19 pandemic. Methods This is a cross-sectional study with non-probabilistic convenience sampling. The Portuguese version of the EMAQ was presented after translation, back-translation, and content analysis. Two studies were conducted, the first before and the second after the pandemic onset. Three samples were formed (2019: Sample 1 (age = 19.7 ± 1.5 years) n = 323; 2020: Sample 2 (age = 21.3 ± 1.8 years) n = 1,011; and Sample 3 (age = 28.9 ± 3.1 years) n = 909). An exploratory strategy with parallel analysis was performed. The analyses were conducted in FACTOR and R (lavaan and semTools packages) software. After determining the best-fit model for the data, emotional appetite was examined considering decrease, non-alteration, and increase in appetite in the face of positive and negative emotions/situations. The profile of emotional appetite was determined using a circumplex model. Results The two-factor model described by the valence of emotions/situations fitted the samples (Comparative Fit Indexminimum-maximum = 0.95–0.98; Tucker-Lewis Index = 0.94–0.98; Root Mean Square Error of Approximation = 0.03–0.08; αord = 0.78–0.88). Increases in appetite were more frequent for positive emotions/situations (52.0–57.5%), and both decreases (35.4–44.5%) and increases (50.0–56.2%) in appetite were observed for negative emotions/situations. Emotions with negative valence and activation were more relevant to appetite reduction, while a significant increase in appetite was observed with anxiety (negative valence and positive activation). Conclusion Different emotions and situations may influence appetite in people, and such an investigation may be useful in preparing eating protocols.
Martins et al. (2023) Emotional Appetite Questionnaire: psychometric properties in Brazilian adult samples before and after the COVID-19 pandemic onset. PeerJ 11:e14597 https://doi.org/10.7717/peerj.14597
Next-generation sequencing shows the genomic features of ovarian clear cell cancer and compares the genetic architectures of high-grade serous ovarian cancer and clear cell carcinoma in ovarian and endometrial tissues
Ovarian clear cell carcinoma (OCCC) is a special histological type of epithelial ovarian cancer (EOC) that is not derived from epithelial cells of the ovarian or fallopian tube as the most common type of ovarian cancer, high-grade serous ovarian carcinoma (HGSOC), but is closely related to endometriosis and similar to endometrial clear cell carcinoma (ECCC) at morphologic and phenotypic features. However, limited data was shown in OCCC genomic features and compared with that in OCCC, HGSOC and ECCC. Herein, we utilized next-generation sequencing analysis of a panel of 1,021 genes to profile the mutational alterations in 34 OCCC and compared them to those from HGSOC (402 cases) and ECCC (30 cases). In result, the ARID1A and PIK3CA are high-frequency mutations of OCCC. Clonal architectures showed that all the mutations of genes occur in the later stage in the OCCC progress, whereas KRAS mutation is the earlier event compared with mutation of ARID1A or PIK3CA, which usually occurs in a group of ARID1A or PIK3CA mutations. The mutation frequency of main driver genes is similar between OCCC and ECCC, while TP53 is the main mutation in HGSOC and ECCC. Shared mutational signatures between OCCC and ECCC tissues with commonly observed a C>T change indicated a common carcinogens-exposed between these two carcinomas, but HGSOC and ECCC have common and distinct mutational signatures across cohorts respectively. In addition, we identified some novel CNV gains in NF1, ASXL1, TCF7L2, CREBBP and LRP1B and loss in ATM, FANCM, RB1 and FLT in OCCC. Our study offered a new perspective for OCCC tumorigenesis from two organs, the ovary and uterus, at genomic architectures and revealed novel CNV events for helping to provide theoretical support for OCCC treatment.
Gan et al. (2023) Next-generation sequencing shows the genomic features of ovarian clear cell cancer and compares the genetic architectures of high-grade serous ovarian cancer and clear cell carcinoma in ovarian and endometrial tissues. PeerJ 11:e14653 https://doi.org/10.7717/peerj.14653
Applicability of VGGish embedding in bee colony monitoring: comparison with MFCC in colony sound classification
Background Bee colony sound is a continuous, low-frequency buzzing sound that varies with the environment or the colony’s behavior and is considered meaningful. Bees use sounds to communicate within the hive, and bee colony sounds investigation can reveal helpful information about the circumstances in the colony. Therefore, one crucial step in analyzing bee colony sounds is to extract appropriate acoustic feature. Methods This article uses VGGish (a visual geometry group—like audio classification model) embedding and Mel-frequency Cepstral Coefficient (MFCC) generated from three bee colony sound datasets, to train four machine learning algorithms to determine which acoustic feature performs better in bee colony sound recognition. Results The results showed that VGGish embedding performs better than or on par with MFCC in all three datasets.
Di et al. (2023) Applicability of VGGish embedding in bee colony monitoring: comparison with MFCC in colony sound classification. PeerJ 11:e14696 https://doi.org/10.7717/peerj.14696
Detection of fungicide resistance to fludioxonil and tebuconazole in Fusarium pseudograminearum, the causal agent of Fusarium crown rot in wheat
Fusarium crown rot (FCR) on wheat is a soil-borne disease that affects the yield and quality of the produce. In 2020, 297 Fusarium pseudograminearum isolates were isolated from diseased FCR wheat samples from eight regional areas across Hebei Province in China. Baseline sensitivity of F. pseudograminearum to fludioxonil (0.0613 ± 0.0347 μg/mL) and tebuconazole (0.2328 ± 0.0840 μg/mL) were constructed based on the in vitro tests of 71 and 83 isolates, respectively. The resistance index analysis showed no resistance isolate to fludioxonil but two low-resistance isolates to tebuconazole in 2020. There was an increased frequency of resistant isolates from 2021 to 2022 based on the baseline sensitivity for tebuconazole. There was no cross-resistance between fludioxonil and tebuconazole. This study provides a significant theoretical and practical basis for monitoring the resistance of F. pseudograminearum to fungicides, especially the control of FCR.
Zhang et al. (2023) Detection of fungicide resistance to fludioxonil and tebuconazole in Fusarium pseudograminearum, the causal agent of Fusarium crown rot in wheat. PeerJ 11:e14705 https://doi.org/10.7717/peerj.14705
Comprehensive profile and contrastive analysis of circular RNA expression in cervical squamous carcinoma and adenocarcinoma
Background Numerous studies have shown circular RNA (circRNA) dysregulation is associated with the pathogenesis of cervical cancer,particularly in individual carcinoma variants. The aim of this study is to investigate and contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma and adenocarcinoma mediated by human papillomavirus type 16 (HPV-16). Methods The expression of circRNAs in cervical squamous carcinoma (SCC), adenocarcinoma (ADC) and adenosquamous carcinoma (ASC) tissues, together with the adjacent normal tissues (ANT), was profiled by high-throughput RNA sequencing (RNA-seq). Bioinformatics analysis and quantitative real time polymerase chain reaction (qRT-PCR) validation of the sequencing data were performed. A network of circRNA-miRNA (microRNA)-mRNA was then constructed according to predicted targets and function of candidate circRNAs. Results A total of 11,685 annotated circRNAs were identified in six cervical samples. There were 42 up-regulated and 98 down-regulated circRNAs. 215 circRNAs were up-regulated in SCC but down-regulated circRNAs in ADC, while 50 circRNAs displayed the opposite trend. Function enrichment analysis based on different expressions of circRNAs found that the most enriched pathway in all the three pathologic variants of cervical cancer was the “ubiquitin mediated proteolysis” pathway. Eight key candidate circRNAs derived from this pathway were further validated, and we noticed that several target miRNAs of candidate circRNAs could target the source genes. Based on this we constructed a related competing endogenous RNA (ceRNA) network. Conclusion Through a comprehensive interpretation of differentially expressed circRNAs in different pathologic variants of cervical cancer, this study provides new insights into the process of tumor differentiation mediated by HPV. Our results may help to complement the molecular typing and stem cell theory of cervical cancer.
Luo et al. (2023) Comprehensive profile and contrastive analysis of circular RNA expression in cervical squamous carcinoma and adenocarcinoma. PeerJ 11:e14759 https://doi.org/10.7717/peerj.14759
Effects of six weeks of sub-plateau cold environment training on physical functioning and athletic ability in elite parallel giant slalom snowboard athletes
Background Hypoxic and cold environments have been shown to improve the function and performance of athletes. However, it is unclear whether the combination of subalpine conditions and cold temperatures may have a greater effect. The present study aims to investigate the effects of 6 weeks of training in a sub-plateau cold environment on the physical function and athletic ability of elite parallel giant slalom snowboard athletes. Methods Nine elite athletes (four males and five females) participated in the study. The athletes underwent 6 weeks of high intensity ski-specific technical training (150 min/session, six times/week) and medium-intensity physical training (120 min/session, six times/week) prior to the Beijing 2021 Winter Olympic Games test competition. The physiological and biochemical parameters were collected from elbow venous blood samples after each 2-week session to assess the athletes’ physical functional status. The athletes’ athletic ability was evaluated by measuring their maximal oxygen uptake, Wingate 30 s anaerobic capacity, 30 m sprint run, and race performance. Measurements were taken before and after participating in the training program for six weeks. The repeated measure ANOVA was used to test the overall differences of blood physiological and biochemical indicators. For indicators with significant time main effects, post-hoc tests were conducted using the least significant difference (LSD) method. The paired-samples t-test was used to analyze changes in athletic ability indicators before and after training. Results (1) There was a significant overall time effect for red blood cells (RBC) and white blood cells (WBC) in males; there was also a significant effect on the percentage of lymphocytes (LY%), serum testosterone (T), and testosterone to cortisol ratio (T/C) in females (p < 0.001 − 0.015, ${\eta }_{p}^{2}=0.81-0.99$ η p 2 = 0 . 81 − 0 . 99 ). In addition, a significant time effect was also found for blood urea(BU), serum creatine kinase (CK), and serum cortisol levels in both male and female athletes (p = 0.001 − 0.029, ${\eta }_{p}^{2}=0.52-0.95$ η p 2 = 0 . 52 − 0 . 95 ). (2) BU and CK levels in males and LY% in females were all significantly higher at week 6 (p = 0.001 − 0.038), while WBC in males was significantly lower (p = 0.030). T and T/C were significantly lower in females at week 2 compared to pre-training (p = 0.007, 0.008, respectively), while cortisol (C) was significantly higher in males and females at weeks 2 and 4 (p(male) = 0.015, 0.004, respectively; p(female) = 0.024, 0.030, respectively). (3) There was a noticeable increase in relative maximal oxygen uptake, Wingate 30 s relative average anaerobic power, 30 m sprint run performance, and race performance in comparison to the pre-training measurements (p < 0.001 − 0.027). Conclusions Six weeks of sub-plateau cold environment training may improve physical functioning and promote aerobic and anaerobic capacity for parallel giant slalom snowboard athletes. Furthermore, male athletes had a greater improvement of physical functioning and athletic ability when trained in sub-plateau cold environments.
Ma et al. (2023) Effects of six weeks of sub-plateau cold environment training on physical functioning and athletic ability in elite parallel giant slalom snowboard athletes. PeerJ 11:e14770 https://doi.org/10.7717/peerj.14770
Energy conservation prospects in water intensive Paddy-Wheat cropping system for groundwater pumping in the semi-arid region of Haryana
The study was aimed at identifying the potential energy saving for groundwater pumping through enhanced efficiency of the pump sets. A total of 65 electrically powered tube wells were selected in the Sonipat district of the north Indian State of Haryana to study the energy use efficiency for groundwater pumping. The existing efficiency as well as the minimum expected overall efficiency of the tubewells were determined based on field survey, measurements, and applicable standard code of the Bureau of India Standards. The overall efficiencies of selected tube wells, computed based on actual measured power consumption, varied from 10.1% to 56.6% in the Sonipat block and 15.3% to 52.8% in the Rai block. The average energy requirement, for the selected tube wells, at the current efficiency level was 4,364.0 and 13,100.4 kWh for wheat and paddy crops, respectively, in the Sonipat block, while it was 3,424.8 and 10,280.9 kWh for wheat and paddy crops, respectively, in the Rai block. Analysis revealed that improving overall efficiency from the current level to the minimum expected level can lead to energy savings of 48.3% and 35.9% for tube wells in the Sonipat and Rai block, respectively. In the Rai block, where the groundwater level has declined significantly, the replacement of inefficient pumps should be done in tandem with crop diversification, improving water application efficiency and groundwater status by employing improved irrigation management practices and adopting groundwater recharge techniques.
Singh et al. (2023) Energy conservation prospects in water intensive Paddy-Wheat cropping system for groundwater pumping in the semi-arid region of Haryana. PeerJ 11:e14815 https://doi.org/10.7717/peerj.14815
Change in eating habits during the Spanish COVID-19 pandemic lockdown: evidence for a sample of university community
Background The stress and anxiety caused by COVID-19 lockdown may have changed the eating habits of the population. Our aim is to assess the eating changes that have taken place due to the pandemic. Methods Data were collected through an electronic survey created by the Health Economics Research Group of the University of Cantabria and IDIVAL and conducted between 14/01/2021 and 19/02/2021. A total of 1,417 responses were recorded, but only 507 complete observations were considered. We carried out a cross-sectional analysis through ordered probit regressions. Results The improvement in post-confinement eating habits is associated with higher income level, better self-assessed health status and more physical activity. The worsening of eating habits is associated with having a certain level of nomophobia or the fear of contagion. Conclusions Our analysis can be used for designing and implementing new strategies to overcome the negative spill overs of the COVID-19 pandemic and improve the dietary patterns.
Cantarero Prieto et al. (2023) Change in eating habits during the Spanish COVID-19 pandemic lockdown: evidence for a sample of university community. PeerJ 11:e14244 https://doi.org/10.7717/peerj.14244