title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=999 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Urinary MMP-9/UCr association with albumin concentration and albumin-creatinine-ratio in Mexican patients with type 2 diabetes mellitus link: https://peerj.com/articles/10474 last-modified: 2020-12-16 description: BackgroundChronic kidney disease is one of the most common complications of type 2 diabetes mellitus (T2DM), causing an increased risk of cardiovascular morbidity and mortality. Matrix metalloproteinase (MMP) activity has been proposed as useful biomarker for diabetic renal and vascular complications.MethodsA cross-sectional study was conducted among T2DM patients who attended a public secondary hospital in Mexico. We performed clinical, biochemical, and microbiological assessments, as well chronic kidney disease diagnosis according to the KDIGO guideline. Urinary MMP-9 was quantified by ELISA and adjusted using urinary creatinine (UCr).ResultsA total of 111 patients were included. Most participants were women (66%). Mean age was 61 ± 10 years and median T2DM duration was estimated at 11 years. Through multivariate analysis, MMP-9/UCr was found to be associated with albumin concentration and albumin to creatinine ratio.DiscussionValidation of non-invasive biomarkers of chronic kidney disease among T2DM patients is necessary. Here, we demonstrate MMP-9/UCr as a potential biomarker of albumin concentration and albumin to creatinine ratio in Mexican patients with T2DM. creator: Víctor Gildardo Arcos-Sacramento creator: Clara Luz Sampieri creator: Víctor Hugo Sandoval-Lozano creator: Rubén Arturo Orozco-Ortega creator: Mariel Alejandra Acuña-Hernández creator: Jaime Morales-Romero creator: Magda Elena Hernández-Hernández creator: Arturo Rodríguez-Hernández uri: https://doi.org/10.7717/peerj.10474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arcos-Sacramento et al. title: Combination of circulating miR-145-5p/miR-191-5p as biomarker for breast cancer detection link: https://peerj.com/articles/10494 last-modified: 2020-12-16 description: BackgroundBreast cancer (BC) is the most common cancer among women worldwide. At present, there is a need to search for new, accurate, reliable, minimally invasive and cheap biomarkers in addition to existing methods for the diagnosis and prognosis of BC. The main goal of this study was to test the diagnostic value of six circulating miRNAs in Kazakh women.Materials and methodsTaqMan-based miRNA profiling was conducted using plasma specimens from 35 BC women patients and 33 healthy women samples (control group).ResultsThe level of all seven miRNAs (including endogenous control) normalized by synthetic cel-miR-39 were significantly elevated in the group of BC patients. Normalization using miR-222-3p as endogenous control reduced differences in level of miRNAs between groups; as a result, only three miRNAs were significantly upregulated in the group of BC patients—miR-145-5p (P = 6.5e−12), miR-191-5p (P = 3.7e−10) and miR-21-5p (P = 0.0034). Moreover, ROC analysis showed that the use of miR-145-5p and miR-191-5p, both individually (AUC = 0.931 and 0.904, respectively) or in combination (AUC = 0.984), allows to accurately differentiate BC patients from healthy individuals.ConclusionsTwo plasma miRNAs—miR-145-5p and miR-191-5p—are potential biomarkers for diagnosis of BC in the Kazakh population. The findings need to be further substantiated using a more representative sample. creator: Yeldar Ashirbekov creator: Arman Abaildayev creator: Nazgul Omarbayeva creator: Dauren Botbayev creator: Ayaz Belkozhayev creator: Anel Askandirova creator: Alena Neupokoyeva creator: Gulzhakhan Utegenova creator: Kamalidin Sharipov creator: Nagima Aitkhozhina uri: https://doi.org/10.7717/peerj.10494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ashirbekov et al. title: Clinical features and prognostic factors of spinal fibroblastic/myofibroblastic tumors: a long-term, single-center, retrospective study link: https://peerj.com/articles/10530 last-modified: 2020-12-16 description: BackgroundSpinal fibroblastic and myofibroblastic tumors (FMTs) are extremely rare. Few studies have reported on the features and outcomes of this condition that affects the axial skeleton. We explored the clinical characteristics and factors affecting the prognosis of spinal FMTs.MethodsWe retroactively assessed the survival of 51 patients with spinal FMTs who underwent surgical and adjuvant treatments in our center between April 2006 and September 2018. Factors affecting disease-free survival (DFS) and overall survival (OS) were analyzed using the Kaplan–Meier method. Variables with p value ≤ 0.05 were subjected to multivariate analysis using the Cox proportional hazards regression model. A two-sided P value < 0.05 was considered statistically significant.ResultsThe mean follow-up period was 50.8 ± 35.6 months (Range 4.2–172.6). Kaplan–Meier survival curves showed that the 5-year DFS was 10% (95% CI [31.09-42.56]) and the 5-year OS was 53% (95% CI [61.28–97.20]). Multivariate analysis showed that en bloc excision was associated with better DFS (HR 0.214, 0.011) and OS (HR 0.273, 0.043), radiotherapy negatively affected OS (HR 0.353, 0.033), and the recurrence and Ki-67 index <5% significantly affected DFS (HR 3.008, 0.008 and 2.754, 0.029).ConclusionsSpinal FMTs are rare. Surgery is the treatment of choice and en bloc excision is strongly recommended to improve outcomes. Disease recurrence and the Ki-67 marker are correlated with the progression of these tumors. creator: Haitao Sun creator: Shaohui He creator: Yuechao Zhao creator: Chen Ye creator: Xinghai Yang creator: Wei Xu creator: Jianru Xiao uri: https://doi.org/10.7717/peerj.10530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: WeChat-based mHealth intention and preferences among people living with schizophrenia link: https://peerj.com/articles/10550 last-modified: 2020-12-16 description: BackgroundThe past few decades have seen a rapid expansion of mHealth programs among people with serious mental illness, yet mHealth for schizophrenia is in a much earlier stage of development. This study examined the intention of WeChat-based mHealth programs among people living with schizophrenia (PLS) and evaluated correlates of the intention.MethodsA total of 400 PLS aged 18–77 completed a cross-sectional survey by face-to-face interviews. The survey included a general question asking about participants’ willingness to attend WeChat-based mHealth programs, followed by preferences of three specific WeChat-based programs: psychoeducation, peer support, and professional support. PLS symptoms, functioning and disability were measured using the 18-item Brief Psychiatric Rating Scale (BPRS-18), the Global Assessment of Functioning (GAF), and the 12-item World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0), respectively. A multivariate logistic regression was used to determine correlates of program participation intention.ResultsOver forty percent (43%, n = 172) of participants were willing to participate in WeChat-based mHealth programs, among whom preferences for each specific program were shown in descending order: psychoeducation (68.60%), professional support (60.47%), and peer support (52.33%). A multivariate analysis revealed that younger age (OR: 0.13–0.20, 95% CI [0.05–0.43]), higher education (OR: 3.48–6.84, 95% CI [1.69–18.21]), and lower disability (OR: 0.97, 95% CI [0.94–0.99]) were all independently associated with WeChat-based mHealth program participation intention.ConclusionThe findings provide guidance for further development of WeChat-based mHealth programs among PLS in China, and targeted at those who are younger, well-educated and with lower disability. creator: Shuiyuan Xiao creator: Tongxin Li creator: Wei Zhou creator: Minxue Shen creator: Yu Yu uri: https://doi.org/10.7717/peerj.10550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xiao et al. title: Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus) link: https://peerj.com/articles/10240 last-modified: 2020-12-15 description: Skin mucus in fish is the first barrier between the organism and the environment but the role of skin mucus in protecting fish against pathogens is not well understood. During copulation in sharks, the male bites the female generating wounds, which are then highly likely to become infected by opportunistic bacteria from the water or from the male shark’s mouth. Describing the microbial component of epithelial mucus may allow future understanding of this first line of defense in sharks. In this study, we analyzed mucus and skin samples obtained from 19 individuals of two shark species and a stingray: the nurse shark (Ginglymostoma cirratum), the lemon shark (Negaprion brevirostris) and the southern stingray (Hypanus americanus). Total DNA was extracted from all samples, and the bacterial 16S rRNA gene (region V3-V4) was amplified and sequenced on the Ion Torrent Platform. Bacterial diversity (order) was higher in skin and mucus than in water. Order composition was more similar between the two shark species. Alpha-diversities (Shannon and Simpson) for OTUs (clusters of sequences defined by a 97% identity threshold for the16S rRNA gene) were high and there were non-significant differences between elasmobranch species or types of samples. We found orders of potentially pathogenic bacteria in water samples collected from the area where the animals were found, such as Pasteurellales (i.e., genus Pasteurella spp. and Haemophilus spp.) and Oceanospirillales (i.e., genus Halomonas spp.) but these were not found in the skin or mucus samples from any species. Some bacterial orders, such as Flavobacteriales, Vibrionales (i.e., genus Pseudoalteromonas), Lactobacillales and Bacillales were found only in mucus and skin samples. However, in a co-occurrence analyses, no significant relationship was found among these orders (strength less than 0.6, p-value > 0.01) but significant relationships were found among the order Trembayales, Fusobacteriales, and some previously described marine environmental Bacteria and Archaea, including Elusimicrobiales, Thermoproteales, Deinococcales and Desulfarculales. This is the first study focusing on elasmobranch microbial communities. The functional role and the benefits of these bacteria still needs understanding as well as the potential changes to microbial communities as a result of changing environmental conditions. creator: Susana Caballero creator: Ana Maria Galeano creator: Juan Diego Lozano creator: Martha Vives uri: https://doi.org/10.7717/peerj.10240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Caballero et al. title: Fungal survival under temperature stress: a proteomic perspective link: https://peerj.com/articles/10423 last-modified: 2020-12-15 description: BackgroundIncreases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role in soil ecosystems as the primary agent of decomposition, recycling of organic nutrients. Fungi also include important pathogens of plants, insects, bacteria, domestic animals and humans, thus highlighting their importance in many contexts. Temperature directly affects fungal growth and protein dynamics, which ultimately will cascade through to affect crop performance. To study changes in the global protein complement of fungi, proteomic approaches have been used to examine links between temperature stress and fungal proteomic profiles.Survey methodology and objectivesA traditional rather than a systematic review approach was taken to focus on fungal responses to temperature stress elucidated using proteomic approaches. The effects of temperature stress on fungal metabolic pathways and, in particular, heat shock proteins (HSPs) are discussed. The objective of this review is to provide an overview of the effects of temperature stress on fungal proteomes.Concluding remarksElucidating fungal proteomic response under temperature stress is useful in the context of increasing understanding of fungal sensitivity and resilience to the challenges posed by contemporary climate change processes. Although useful, a more thorough work is needed such as combining data from multiple -omics platforms in order to develop deeper understanding of the factor influencing and controlling cell physiology. This information can be beneficial to identify potential biomarkers for monitoring environmental changes in soil, including the agricultural ecosystems vital to human society and economy. creator: Nurlizah Abu Bakar creator: Saiful Anuar Karsani creator: Siti Aisyah Alias uri: https://doi.org/10.7717/peerj.10423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abu Bakar et al. title: The performance of a modified EWMA control chart for monitoring autocorrelated PM2.5 and carbon monoxide air pollution data link: https://peerj.com/articles/10467 last-modified: 2020-12-15 description: PM2.5 (particulate matter less than or equal to 2.5 micron) is found in the air and comprises dust, dirt, soot, smoke, and liquid droplets. PM2.5 and carbon monoxide emissions can have a negative impact on humans and animals throughout the world. In this paper, we present the performance of a modified exponentially weighted moving average (modified EWMA) control chart to detect small changes when the observations are autocorrelated with exponential white noise through the average run length evaluated (ARLs) by explicit formulas. The accuracy of the solution was verified with a numerical integral equation method. The efficacy of the modified EWMA control chart to monitor PM2.5 and carbon monoxide air pollution data and compare its performance with the standard EWMA control chart. The results suggest that the modified EWMA control chart is far superior to the standard one. creator: Yadpirun Supharakonsakun creator: Yupaporn Areepong creator: Saowanit Sukparungsee uri: https://doi.org/10.7717/peerj.10467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Supharakonsakun et al. title: Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments link: https://peerj.com/articles/10482 last-modified: 2020-12-15 description: The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes. creator: Mingze Zhang creator: Jaime A. Teixeira da Silva creator: Zhenming Yu creator: Haobin Wang creator: Can Si creator: Conghui Zhao creator: Chunmei He creator: Jun Duan uri: https://doi.org/10.7717/peerj.10482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors link: https://peerj.com/articles/10483 last-modified: 2020-12-15 description: The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions. creator: Lei Dong creator: Yue Lu creator: Shubing Liu uri: https://doi.org/10.7717/peerj.10483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dong et al. title: Polyester or epoxy: assessing embedding product efficacy in paleohistological methods link: https://peerj.com/articles/10495 last-modified: 2020-12-15 description: Histological examination of bone microstructure provides insight into extant and extinct vertebrate physiology. Fossil specimens sampled for histological examination are typically first embedded in an inexpensive polyester resin and then cut into thin sections, mounted on slides, and polished for viewing. Modern undecalcified bone is chemically processed prior to embedding in plastic resin, sectioning, mounting, and polishing. Conversely, small fossil material and modern undecalcified bone are typically embedded in higher priced epoxy resin because these specimen types require final sections near or below 100 µm thick. Anecdotal evidence suggests thin sections made of polyester resin embedded material polished thinner than 100 µm increases likelihood of sample peeling, material loss, and is unsuitable for modern tissue and small fossil material. To test this assertion, a sample of modern bones and fossil bones, teeth, and scales were embedded in either polyester resin or epoxy resin. Embedded specimens were sectioned and mounted following standard published protocol. Thin sections were ground on a lapidary wheel using decreasing grit sizes until tissue microstructure was completely discernible when viewed under a polarizing light microscope. Additionally, eight prepared thin sections (four from polyester resin embedded specimens and four from epoxy resin embedded specimens) were continuously ground on a lapidary wheel using 600 grit carbide paper until peeling occurred or material integrity was lost. Slide thickness when peeling occurred was measured for comparing slide thickness when specimen integrity was lost between the two resin types. Final slide thickness ranged from 38 µm to 247 µm when tissue was identifiable using a polarizing microscope. Finished slide thickness varied between resin types despite similar tissue visibility. However, finished slide thickness appears more dependent on hard tissue composition than resin type. Additionally, we did not find a difference of slide thickness when material was lost between resin types. The results of this preliminary study suggest that polyester resins can be used for embedding undecalcified modern hard tissues and fossilized hard tissues without loss of tissue visibility or material integrity, at least in the short term. creator: Christian T. Heck creator: Gwyneth Volkmann creator: Holly N. Woodward uri: https://doi.org/10.7717/peerj.10495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Heck et al.