title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=533 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Plain set and stirred yogurt with different additives: implementation of food safety system as quality checkpoints link: https://peerj.com/articles/14648 last-modified: 2023-01-27 description: Hazard Analysis Critical Control Point (HACCP) is a risk management protocol developed to ensure food safety through a precautionary approach that is believed to offer assurances in producing safe food for customers. Yogurt is made in a number of phases, commencing with the collection of raw milk and ending with consumer consumption. While this is happening, major economic and health issues might arise from exposing the manufacturing line to biological, chemical, and/or physical contaminations. As a result, the decision tree approach was used to determine the CCPs during the production of yogurt. Additionally, biological dangers are incorporated as a by-product of the system’s implementation performance. In particular, the plain set and nut puree-honey-fortified stirred yogurt manufacturing techniques are highlighted for the first time in this study. The potential manufacturing risks are described for the first time, together with information on how HACCP plans may guard against major risks that could result in the production of yogurt that is not in compliance with established standards. creator: Aya Allam creator: Noha Shafik creator: Ahmed Zayed creator: Ibrahim Khalifa creator: Ibrahim A. Bakry creator: Mohamed A. Farag uri: https://doi.org/10.7717/peerj.14648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Allam et al. title: Novel genetic variants in long non-coding RNA MEG3 are associated with the risk of asthma link: https://peerj.com/articles/14760 last-modified: 2023-01-27 description: BackgroundAsthma is the most common chronic inflammatory airway disease worldwide. Asthma is a complex disease whose exact etiologic mechanisms remain elusive; however, it is increasingly evident that genetic factors play essential roles in the development of asthma. The purpose of this study is to identify novel genetic susceptibility loci for asthma in Taiwanese. We selected a well-studied long non-coding RNA (lncRNA), MEG3, which is involved in multiple cellular functions and whose expression has been associated with asthma. We hypothesize that genetic variants in MEG3 may influence the risk of asthma.MethodsWe genotyped four single nucleotide polymorphisms (SNPs) in MEG3, rs7158663, rs3087918, rs11160608, and rs4081134, in 198 patients with asthma and 453 healthy controls and measured serum MEG3 expression level in a subset of controls.ResultsThe variant AG and AA genotypes of MEG3rs7158663 were significantly over-represented in the patients compared to the controls (P = 0.0024). In logistic regression analyses, compared with the wild-type GG genotype, the heterozygous variant genotype (AG) was associated with a 1.62-fold [95% confidence interval (CI) [1.18–2.32], P = 0.0093] increased risk and the homozygous variant genotype (AA) conferred a 2.68-fold (95% CI [1.52–4.83], P = 0.003) increased risk of asthma. The allelic test showed the A allele was associated with a 1.63-fold increased risk of asthma (95% CI [1.25–2.07], P = 0.0004). The AG plus AA genotypes were also associated with severe symptoms (P = 0.0148). Furthermore, the AG and AA genotype carriers had lower serum MEG3 expression level than the GG genotype carriers, consistent with the reported downregulation of MEG3 in asthma patients.ConclusionMEG3 SNP rs7158663 is a genetic susceptibility locus for asthma in Taiwanese. Individuals carrying the variant genotypes have lower serum MEG3 level and are at increased risks of asthma and severe symptoms. creator: Kuo-Liang Chiu creator: Wen-Shin Chang creator: Chia-Wen Tsai creator: Mei-Chin Mong creator: Te-Chun Hsia creator: Da-Tian Bau uri: https://doi.org/10.7717/peerj.14760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chiu et al. title: Targeting super enhancers for liver disease: a review link: https://peerj.com/articles/14780 last-modified: 2023-01-27 description: BackgroundSuper enhancers (SEs) refer to the ultralong regions of a gene accompanied by multiple transcription factors and cofactors and strongly drive the expression of cell-type-related genes. Recent studies have demonstrated that SEs play crucial roles in regulating gene expression related to cell cycle progression and transcription. Aberrant activation of SEs is closely related to the occurrence and development of liver disease. Liver disease, especially liver failure and hepatocellular carcinoma (HCC), constitutes a major class of diseases that seriously endanger human health. Currently, therapeutic strategies targeting SEs can dramatically prevent disease progression and improve the prognosis of animal models. The associated new approaches to the treatment of related liver disease are relatively new and need systematic elaboration.ObjectivesIn this review, we elaborate on the features of SEs and discuss their function in liver disease. Additionally, we review their application prospects in clinical practice in the future. The article would be of interest to hepatologists, molecular biologists, clinicians, and all those concerned with targeted therapy and prognosis of liver disease.MethodologyWe searched three bibliographic databases (Web of Science Core Collection, Embase, PubMed) from 01/1981 to 06/2022 for peer-reviewed scientific publications focused on (1) gene treatment of liver disease; (2) current status of SE research; and (3) targeting SEs for liver disease. We included English language original studies only.ResultsThe number of published studies considering the role of enhancers in liver disease is considerable. Since SEs were just defined in 2013, the corresponding data on SEs are scarce: approximately 50 papers found in bibliographic databases on the correlation between enhancers (or SEs) and liver disease. Remarkably, half of these papers were published in the past three years, indicating the growing interest of the scientific community in this issue. Studies have shown that treatments targeting components of SEs can improve outcomes in liver disease in animal and clinical trials.ConclusionsThe treatment of liver disease is facing a bottleneck, and new treatments are needed. Therapeutic regimens targeting SEs have an important role in the treatment of liver disease. However, given the off-target effect of gene therapy and the lack of clinical trials, the available experimental data are still fragmented and controversial. creator: Zhongyuan Yang creator: Yunhui Liu creator: Qiuyu Cheng creator: Tao Chen uri: https://doi.org/10.7717/peerj.14780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Alterations of ecosystem nitrogen status following agricultural land abandonment in the Karst Critical Zone Observatory (KCZO), Southwest China link: https://peerj.com/articles/14790 last-modified: 2023-01-27 description: BackgroundSecondary succession after agricultural land abandonment generally affects nitrogen (N) cycle processes and ecosystem N status. However, changes in soil N availability and NO3– loss potential following secondary succession are not well understood in karst ecosystems.MethodsIn the Karst Critical Zone Observatory (KCZO) of Southwest China, croplands, shrub-grass lands, and secondary forest lands were selected to represent the three stages of secondary succession after agricultural land abandonment by using a space-for-time substitution approach. The contents and 15N natural abundance (δ15N) of leaves, soils, and different-sized aggregates at the three stages of secondary succession were analyzed. The δ15N compositions of soil organic nitrogen (SON) in aggregates and soil to plant 15N enrichment factor (EF = δ15Nleaf −δ15Nsoil), combined with soil inorganic N contents and δ15N compositions were used to indicate the alterations of soil N availability and NO3–loss potential following secondary succession.ResultsLeaf N content and SON content significantly increased following secondary succession, indicating N accumulation in the soil and plant. The δ15N values of SON also significantly decreased, mainly affected by plant δ15N composition and N mineralization. SON content in macro-aggregates and soil NH4+ content significantly increased while δ15N values of NH4+ decreased, implying increases in SON stabilization and improved soil N availability following secondary succession. Leaf δ15N values, the EF values, and the (NO3–-N)/(NH4+-N) ratio gradually decreased, indicating reduced NO3– loss following secondary succession.ConclusionsSoil N availability improves and NO3– leaching loss reduces following secondary succession after agricultural land abandonment in the KCZO. creator: Man Liu creator: Guilin Han uri: https://doi.org/10.7717/peerj.14790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu and Han title: Relationship between the roots of Hippophae rhamnoides at different stump heights and the root microenvironment in feldspathic sandstone areas link: https://peerj.com/articles/14819 last-modified: 2023-01-27 description: BackgroundTo solve the withering of Hippophae rhamnoides plantation in the feldspathic sandstone areas of Inner Mongolia and to promote the regeneration, rejuvenation, and sustainability of H. rhamnoides forests.MethodsWe stumped aging H. rhamnoides trees at the ground heights of 0, 10, 15, and 20 cm (S1, S2, S3, and S4, respectively) and utilized unstumped trees as the control (CK). We then analyzed the effects of the different stump heights on the roots and the root microenvironment of H. rhamnoides and the relationship between the roots and the root microenvironment in the stumped H. rhamnoides.ResultsThe root fractal features, root branching rate, root length, root soluble proteins, soil moisture content, and soil nutrients among the different treatments were ranked as S3>S2>S1>S4>CK (P < 0.05). The root topological index, root proline, and malondialdehyde among the different treatments were ranked as S320 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. creator: Ana Lucia Castrillón-Cifuentes creator: Fernando A. Zapata creator: Alan Giraldo creator: Christian Wild uri: https://doi.org/10.7717/peerj.14586 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Castrillon-Cifuentes et al. title: Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples link: https://peerj.com/articles/14596 last-modified: 2023-01-26 description: BackgroundThe 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).MethodsWe 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.ResultsBased 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).ConclusionThis 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. creator: Tunc Kayikcioglu creator: Jasmine Amirzadegan creator: Hugh Rand creator: Bereket Tesfaldet creator: Ruth E. Timme creator: James B. Pettengill uri: https://doi.org/10.7717/peerj.14596 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Emotional Appetite Questionnaire: psychometric properties in Brazilian adult samples before and after the COVID-19 pandemic onset link: https://peerj.com/articles/14597 last-modified: 2023-01-26 description: BackgroundAppetite 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.ObjectivesTo 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.MethodsThis 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.ResultsThe 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).ConclusionDifferent emotions and situations may influence appetite in people, and such an investigation may be useful in preparing eating protocols. creator: Bianca G. Martins creator: Nadine V. Vanini creator: Lucas A. Campos creator: Juliana ADB Campos uri: https://doi.org/10.7717/peerj.14597 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martins et al. title: 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 link: https://peerj.com/articles/14653 last-modified: 2023-01-26 description: 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. creator: Meifu Gan creator: Zaixian Tai creator: Yijian Yu creator: Chao Zhang creator: Juan Xu uri: https://doi.org/10.7717/peerj.14653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gan et al. title: Applicability of VGGish embedding in bee colony monitoring: comparison with MFCC in colony sound classification link: https://peerj.com/articles/14696 last-modified: 2023-01-26 description: BackgroundBee 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.MethodsThis 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.ResultsThe results showed that VGGish embedding performs better than or on par with MFCC in all three datasets. creator: Nayan Di creator: Muhammad Zahid Sharif creator: Zongwen Hu creator: Renjie Xue creator: Baizhong Yu uri: https://doi.org/10.7717/peerj.14696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Di et al.