title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=513 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A systematic review of informal supporters of intimate partner violence survivors: the intimate partner violence model of informal supporter readiness link: https://peerj.com/articles/15160 last-modified: 2023-05-09 description: BackgroundIntimate partner violence (IPV) is a serious public health issue that consists of physical, sexual, and psychological violence perpetrated by a current or former partner. Informal supporters (e.g., family and friends) of survivors are more often witness to IPV or are the first people a survivor will disclose abuse to and are more able to provide consistent ongoing support than professional services. Therefore, greater understanding of informal supporters is warranted to aid in reducing the risks experienced by survivors. This systematic review aimed to: (1) identify factors associated with either an increase or decrease in helping behaviour toward a survivor, (2), identify the most effective self-care strategies employed by informal supporters, and (3) consider the current theoretical approaches used to understand informal supporters help-giving behavioural intention.MethodsA systematic literature search was conducted following the PRISMA guidelines. The search included English language articles published between 2005 and 2021 in the databases Psych Articles, Scopus, Proquest Social Services Abstracts, and Ebscohost. Studies were included if the primary research aims explored the motivators and inhibitors of helping intention or self-care strategies of adult social network members of adult IPV survivors. Two reviewers independently screened all identified articles for inclusion suitability.ResultsOne hundred and twenty articles were subjected to full text screening resulting in 31 articles being identified as meeting inclusion criteria. Synthesis of the findings identified the following three key areas associated with help-giving behavioural intentions: normative factors, individual factors, and situational factors. There were no articles identified that considered self-care of informal supporters. Of the 31 articles, 22 had a theoretical underpinning. None of the utilised theories explained all three of the identified factors of help-giving behavioural intention.ConclusionThese results are integrated into a proposed Intimate Partner Violence Model of Informal Supporter Readiness (IPV-MISR), incorporating the identified factors associated with help-giving behavioural intention. This model provides a framework for conceptualising the readiness of an informal supporter to provide adequate support to IPV survivors. The model extends existing theoretical standpoints and has utility in both practice and research. creator: Ryan L. Davies creator: Kylie Rice creator: Adam J. Rock uri: https://doi.org/10.7717/peerj.15160 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Davies et al. title: Two new syntopic species of glassfrogs (Amphibia, Centrolenidae, Centrolene) from the southwestern Andes of Ecuador link: https://peerj.com/articles/15195 last-modified: 2023-05-09 description: We describe two new species of glassfrogs of the genus Centrolene living in syntopy at La Enramada, province of Azuay, southwestern Ecuador. They were found in a small creek in montane evergreen forests at 2,900 m elevation. The first new species is distinguished from all other members of the genus Centrolene by having the following combination of characters: dentigerous process of vomer absent; sloping snout in lateral view; thick, white labial stripe and a faint white line between the lip and anterior ¼ of body; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); ulnar and tarsal ornamentation; dorsal skin shagreen with dispersed warts; uniform green dorsum with light yellowish green warts; and green bones. The new species is remarkable by being sister to a species from the opposite Andean versant, C. condor. The second new species is distinguished from all other Centrolene by having the following combination of characters: dentigerous process of vomer absent; round snout in lateral view; thin, yellowish labial stripe with a row of white tubercles between the lip and arm insertion, and a yellowish line between arm insertion and groin; uniform green dorsum; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); dorsal skin shagreen with dispersed spicules; ulnar and tarsal ornamentation; and green bones. The second new species is sister to C. sabini and an undescribed species of Centrolene from southeastern Ecuador. Based on nuclear and mitochondrial DNA sequences, we present a new phylogeny for Centrolene and comment on the phylogenetic relationships inside the genus. creator: Diego F. Cisneros-Heredia creator: Mario H. Yánez-Muñoz creator: Juan C. Sánchez-Nivicela creator: Santiago R. Ron uri: https://doi.org/10.7717/peerj.15195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cisneros-Heredia et al. title: Epithelial to mesenchymal transition in mammary gland tissue fibrosis and insights into drug therapeutics link: https://peerj.com/articles/15207 last-modified: 2023-05-09 description: BackgroundThe epithelial-mesenchymal transition (EMT) is a multi-step morphogenetic process in which epithelial cells lose their epithelial properties and gain mesenchymal characteristics. The process of EMT has been shown to mediate mammary gland fibrosis. Understanding how mesenchymal cells emerge from an epithelial default state will aid in unravelling the mechanisms that control fibrosis and, ultimately, in identifying therapeutic targets to alleviate fibrosis.MethodsThe effects of EGF and high glucose (HG) on EMT in mammary epithelial cells, MCF10A and GMECs, as well as their pathogenic role, were studied. In-silico analysis was used to find interacting partners and protein-chemical/drug molecule interactions.ResultsOn treatment with EGF and/or HG, qPCR analysis showed a significant increase in the gene expression of EMT markers and downstream signalling genes. The expression of these genes was reduced on treatment with EGF+HG combination in both cell lines. The protein expression of COL1A1 increased as compared to the control in cells treated with EGF or HG alone, but when the cells were treated with EGF and HG together, the protein expression of COL1A1 decreased. ROS levels and cell death increased in cells treated with EGF and HG alone, whereas cells treated with EGF and HG together showed a decrease in ROS production and apoptosis. In-silico analysis of protein-protein interactions suggest the possible role of MAPK1, actin alpha 2 (ACTA2), COL1A1, and NFκB1 in regulating TGFβ1, ubiquitin C (UBC), specificity protein 1 (SP1) and E1A binding protein P300 (EP300). Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment suggests advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signalling pathway, relaxin signalling pathway and extra cellular matrix (ECM) receptor interactions underlying fibrosis mechanism.ConclusionThis study demonstrates that EGF and HG induce EMT in mammary epithelial cells and may also have a role in fibrosis. creator: Mudasir Ahmad Syed creator: Basharat Bhat creator: Abiza Wali creator: Afnan Saleem creator: Lateef Ahmad Dar creator: Mudasir Bashir Gugjoo creator: Shakil Bhat creator: Sahar Saleem Bhat uri: https://doi.org/10.7717/peerj.15207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Syed et al. title: Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration link: https://peerj.com/articles/15238 last-modified: 2023-05-09 description: ObjectiveThrough analyzing the SH2D5 expression profiles, clinical features, and immune infiltration in lung adenocarcinoma (LUAD), the study was intended to discuss the correlations of SH2D5 with prognosis and immune infiltration in LUAD.MethodsWe downloaded transcriptome and clinical data of LUAD patients from TCGA, GEO, and CCLE databases. Sangerbox, R language, GEPIA, UALCAN, and Kaplan-Meier Plotter were adopted to analyze the SH2D5 expression patterns, prognosis, and clinical features. Spearman correlation analysis was performed to determine the association between SH2D5 expression and immune cell infiltration and immune checkpoint genes. The miRNA-SH2D5 relations were predicted by miRDB and starbase. Lastly, quantitative PCR, IHC and Western blot were implemented for validation.ResultsA prominent up-regulation of SH2D5 was noted in the LUAD group relative to the normal group, which was validated by quantitative PCR, IHC and Western blot. SH2D5 expression was inversely related to overall survival (OS) of LUAD patients as well as B cell immune infiltration. Additionally, SH2D5 expression was negatively correlated with dendritic cells resting (p < 0.001), plasma cells (p < 0.001), mast cells resting (p = 0.031) and T cells CD4 memory resting (p = 0.036) in LUAD patients with abundant SH2D5 expression correlated with poor prognosis. Furthermore, enrichment analysis suggested that SH2D5 was associated with lung cancer and immunity. Lastly, we investigated the relationship between the expression of SH2D5 and the use of antitumor drugs.ConclusionHigh SH2D5 expression shares an association with unfavorable prognosis in LUAD, and SH2D5 may also provide new ideas for immunotherapy as a potential therapeutic target. creator: Hao Zhou creator: Shengjun Li creator: Yuansheng Lin uri: https://doi.org/10.7717/peerj.15238 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al. title: A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress link: https://peerj.com/articles/15243 last-modified: 2023-05-09 description: Phyllostachys edulis (moso bamboo) is China’s most widespread bamboo species, with significant economic and ecological values. Long non-coding RNA (lncRNA) is a type of regulatory RNA that is longer than 200 nucleotides and incapable of encoding proteins, and is frequently involved in regulating biotic and abiotic stress and plant development. However, the biological functions of lncRNA in moso bamboo are unknown. In this study, a lncRNA (named PelncRNA1) differentially expressed following UV-B treatment was discovered in the whole transcriptome sequencing database of moso bamboo. The target genes were filtered and defined by correlation analysis of PelncRNA1 and gene expression pattern. The expression levels of PelncRNA1 and its target genes were verified using qRT-PCR. The results demonstrated that the expression levels of PelncRNA1 and its target genes increased during UV-B treatment. In Arabidopsis transgenic seedlings and moso bamboo protoplasts, PelncRNA1 was discovered to influence the expression of its target genes when overexpressed. In addition, transgenic Arabidopsis showed higher tolerance to UV-B stress. These results suggest that PelncRNA1 and its target genes are involved in the response of moso bamboo to UV-B stress. The novel findings would contribute to our understanding of how lncRNAs regulate the response to abiotic stresses in moso bamboo. creator: Lu Yu creator: Yiqian Ding creator: Mingbing Zhou uri: https://doi.org/10.7717/peerj.15243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yu et al. title: Topological feature generation for link prediction in biological networks link: https://peerj.com/articles/15313 last-modified: 2023-05-09 description: Graph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions in a graph with low-dimensional vectors, which facilitates research to predict potential interactions in networks. However, most graph embedding methods suffer from high computational costs in the form of high computational complexity of the embedding methods and learning times of the classifier, as well as the high dimensionality of complex biological networks. To address these challenges, in this study, we use the Chopper algorithm as an alternative approach to graph embedding, which accelerates the iterative processes and thus reduces the running time of the iterative algorithms for three different (nervous system, blood, heart) undirected protein-protein interaction (PPI) networks. Due to the high dimensionality of the matrix obtained after the embedding process, the data are transformed into a smaller representation by applying feature regularization techniques. We evaluated the performance of the proposed method by comparing it with state-of-the-art methods. Extensive experiments demonstrate that the proposed approach reduces the learning time of the classifier and performs better in link prediction. We have also shown that the proposed embedding method is faster than state-of-the-art methods on three different PPI datasets. creator: Mustafa Temiz creator: Burcu Bakir-Gungor creator: Pınar Güner Şahan creator: Mustafa Coskun uri: https://doi.org/10.7717/peerj.15313 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Temiz et al. title: Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae link: https://peerj.com/articles/15322 last-modified: 2023-05-09 description: BackgroundElaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking.MethodsTo understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software.ResultsThe results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic analysis revealed that the genus Elaeocarpus is closely related to Crinodendron patagua on an independent branch and Aristotelia fruticosa is closely related to Vallea stipularis, forming a clade with the genus Sloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus Elaeocarpus diverged 53 Mya and that the genus Sloanea diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae. creator: Yihui Wang creator: Yifei Xie creator: Jiayi Jin creator: Jinyue Li creator: Xiangdong Qiu creator: Yang Tong creator: Zhongyang Li creator: Zhixiang Zhang creator: Wenling Lai uri: https://doi.org/10.7717/peerj.15322 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Botanical characteristics, chemical components, biological activity, and potential applications of mangosteen link: https://peerj.com/articles/15329 last-modified: 2023-05-09 description: Garcinia mangostana L. (Mangosteen), a functional food, belongs to the Garcinaceae family and has various pharmacological effects, including anti-oxidative, anti-inflammatory, anticancer, antidiabetic, and neuroprotective effects. Mangosteen has abundant chemical constituents with powerful pharmacological effects. After searching scientific literature databases, including PubMed, Science Direct, Research Gate, Web of Science, VIP, Wanfang, and CNKI, we summarized the traditional applications, botanical features, chemical composition, and pharmacological effects of mangosteen. Further, we revealed the mechanism by which it improves health and treats disease. These findings provide a theoretical basis for mangosteen’s future clinical use and will aid doctors and researchers who investigate the biological activity and functions of food. creator: Chenchen Bi creator: Hang Xu creator: Jingru Yu creator: Zhinan Ding creator: Zheng Liu uri: https://doi.org/10.7717/peerj.15329 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Bi et al. title: 24-Epibrassinolide confers zinc stress tolerance in watermelon seedlings through modulating antioxidative capacities and lignin accumulation link: https://peerj.com/articles/15330 last-modified: 2023-05-09 description: Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. It is well-known that brassinolide (BR) plays a key role in the regulation of abiotic stress responses in plants. However, the effects of brassinolide on alleviating Zn phytotoxicity in watermelon (Citrullus lanatus L.) seedlings are not clear. The purpose of this study was to study the effect of 24-epibrassinolide (EBR, one of the bioactive BRs) on Zn tolerance of watermelon seedlings and its potential resistance mechanism. Exposure to excessive Zn significantly inhibited shoot and root fresh weight of watermelon, but this could be significantly alleviated by the optimum 0.05 μM EBR. Exogenous spraying EBR increased the pigments and alleviated oxidative damage caused by Zn through reducing Zn accumulation and the levels of reactive oxygen species (ROS) and malonaldehyde (MDA) and increasing the activities of antioxidant enzymes and contents of ascorbic acid (AsA) and glutathione (GSH). Importantly, the relative mRNA levels of antioxidant genesincluding Cu/Zn-superoxidedismutase (Cu-Zn SOD), catalase (CAT), ascorbic acid peroxidase (APX), and glutathione reductase (GR) were significantly induced after EBR treatment. In addition, EBR pre-treatment induced lignin accumulation under Zn stress, and the activity of phenylalanine ammonia-lyase (PAL) and 4-coumaric ligase (4CL), two key enzymes regulating lignin synthesis, also tended to be consistent. Collectively, the present research proves the beneficial effects of EBR in response to Zn stress through enhancing antioxidant defense and lignin accumulation and provides a new insight into the mechanism of BR-enhancing heavy metal tolerance. creator: Xuefang Liu creator: Quanwen Zhu creator: Wentao Liu creator: Jun Zhang uri: https://doi.org/10.7717/peerj.15330 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Molecular analysis of the 14-3-3 genes in Panax ginseng and their responses to heat stress link: https://peerj.com/articles/15331 last-modified: 2023-05-09 description: BackgroundPanax Ginseng is a perennial and semi-shady herb with tremendous medicinal value. Due to its unique botanical characteristics, ginseng is vulnerable to various abiotic factors during its growth and development, especially in high temperatures. Proteins encoded by 14-3-3 genes form a highly conserved protein family that widely exists in eukaryotes. The 14-3-3 family regulates the vital movement of cells and plays an essential role in the response of plants to abiotic stresses, including high temperatures. Currently, there is no relevant research on the 14-3-3 genes of ginseng.MethodsThe identification of the ginseng 14-3-3 gene family was mainly based on ginseng genomic data and Hidden Markov Models (HMM). We used bioinformatics-related databases and tools to analyze the gene structure, physicochemical properties, cis-acting elements, gene ontology (GO), phylogenetic tree, interacting proteins, and transcription factor regulatory networks. We analyzed the transcriptome data of different ginseng tissues to clarify the expression pattern of the 14-3-3 gene family in ginseng. The expression level and modes of 14-3-3 genes under heat stress were analyzed by quantitative real-time PCR (qRT-PCR) technology to determine the genes in the 14-3-3 gene family responding to high-temperature stress.ResultsIn this study, 42 14-3-3 genes were identified from the ginseng genome and renamed PgGF14-1 to PgGF14-42. Gene structure and evolutionary relationship research divided PgGF14s into epsilon (ε) and non-epsilon (non-ε) groups, mainly located in four evolutionary branches. The gene structure and motif remained highly consistent within a subgroup. The physicochemical properties and structure of the predicted PgGF14 proteins conformed to the essential characteristics of 14-3-3 proteins. RNA-seq results indicated that the detected PgGF14s existed in different organs and tissues but differed in abundance; their expression was higher in roots, stems, leaves, and fruits but lower in seeds. The analysis of GO, cis-acting elements, interacting proteins, and regulatory networks of transcription factors indicated that PgGF14s might participate in physiological processes, such as response to stress, signal transduction, material synthesis-metabolism, and cell development. The qRT-PCR results indicated PgGF14s had multiple expression patterns under high-temperature stress with different change trends in several treatment times, and 38 of them had an apparent response to high-temperature stress. Furthermore, PgGF14-5 was significantly upregulated, and PgGF14-4 was significantly downregulated in all treatment times. This research lays a foundation for further study on the function of 14-3-3 genes and provides theoretical guidance for investigating abiotic stresses in ginseng. creator: Qi Wang creator: Wenyue Peng creator: Junbo Rong creator: Mengyang Zhang creator: Wenhao Jia creator: Xiujuan Lei creator: Yingping Wang uri: https://doi.org/10.7717/peerj.15331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al.