title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=997 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets link: https://peerj.com/articles/10383 last-modified: 2020-12-08 description: BackgroundThe practice of feeding a raw meat-based diet (RMBD) to dogs is a topic of increasing interest to owners and veterinary professionals alike. Despite the research around the practice, particularly about the risk of nutritional imbalances and microbial contamination, an increasing number of dog owners are adopting a raw diet for their dogs. This study expands the research into owner motivations for feeding RMBDs and cooked diets and asks them their opinions about risk and nutritional value.MethodsAn anonymized, online, internationally accessible questionnaire was developed to ascertain owner perspectives on the risks, benefits, and nutritional value of commercially prepared and homemade RMBDs as compared with commercially prepared cooked diets (CCDs).ResultsThe questionnaire was completed by 419 dog owners of diverse backgrounds across the world. Of the participants, 25.3% fed RMBDs. Just over 70.0% of all participants had spoken to their veterinarian about their dog’s nutrition. Owners who fed RMBDs ranked their veterinarian’s knowledge lower and their own knowledge of canine nutrition higher than owners who fed CCDs. They rated commercial and homemade RMBDs as highly nutritious 83.5% and 73.6% of the time, respectively, while only 12.5% rated CCDs as highly nutritious. Owners who fed CCDs ranked RMBDs as highly nutritious less often, but also only ranked CCDs as highly nutritious 52.7% of the time. All participants agreed that CCDs were low risk to human health. Owners who fed RMBDs ranked raw diets as highly risky to human or dog health under 20.0% of the time but deemed CCDs risky to animal health over 65.0% of the time. When asked about benefits of raw diets, the most repeated words offered by owners were “health”, “better”, “coat” and “teeth”. The most repeated risks presented were “bacteria”, “nutrition”, “risk” and “Salmonella”. Owners who fed RMBDs tended to use vague terminology like “health” and “better” when asked why they fed a raw diet. Owners who did not feed RMBDs used more specific terminology like “expensive”, “time” and “risk” when asked why they did not feed a raw diet. Overall, the two groups differed in their perceptions around RMBD and CCD feeding, which highlights the need for a better line of communication and education between veterinarians and owners. creator: Alysia Empert-Gallegos creator: Sally Hill creator: Philippa S. Yam uri: https://doi.org/10.7717/peerj.10383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Empert-Gallegos et al. title: Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods link: https://peerj.com/articles/10458 last-modified: 2020-12-08 description: BackgroundExisting studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer.MethodsA total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays.ResultsA total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.94, AUC = 0.92). Kaplan-Meier survival curves showed that the event-free survival rate of cervical cancer patients with higher expression of PLK1 was shorter than that of patients with lower PLK1 (HR = 2.020, P = 0.0197). Genetic alteration of PLK1 including missense mutation and mRNA low occurred in 6% of cervical cancer samples profiled in mRNA expression. Genes positively or negatively correlated with PLK1 were mainly assembled in pathways such as DNA replication, cell cycle, mismatch repair, Ras signaling pathway, melanoma, EGFR tyrosine kinase inhibitor resistance and homologous recombination (P < 0.05).ConclusionsHere, we provided sufficient evidence of PLK1 overexpression in cervical cancer. The overexpression of PLK1 in cervical cancer and the contributory effect of it on clinical progression indicated the hopeful prospect of PLK1 as a biomarker for cervical cancer. creator: Li Gao creator: Yu-Yan Pang creator: Xian-Yu Guo creator: Jing-Jing Zeng creator: Zhong-Qing Tang creator: Dan-Dan Xiong creator: Xia Yang creator: Ying Li creator: Fu-Chao Ma creator: Lin-Jiang Pan creator: Zhen-Bo Feng creator: Gang Chen uri: https://doi.org/10.7717/peerj.10458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gao et al. title: Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers link: https://peerj.com/articles/10485 last-modified: 2020-12-08 description: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro. creator: Zhixin Wang creator: Yalin Sun creator: Xinfang Huang creator: Feng Li creator: Yuping Liu creator: Honglian Zhu creator: Zhengwei Liu creator: Weidong Ke uri: https://doi.org/10.7717/peerj.10485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot link: https://peerj.com/articles/10492 last-modified: 2020-12-08 description: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants. creator: Ahmed Khadr creator: Guang-Long Wang creator: Ya-Hui Wang creator: Rong-Rong Zhang creator: Xin-Rui Wang creator: Zhi-Sheng Xu creator: Yong-Sheng Tian creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.10492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khadr et al. title: Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet link: https://peerj.com/articles/10496 last-modified: 2020-12-08 description: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and interspecific competition for food items is surmised to occur, predominantly within seagrass beds near the tidal inlet. However, this hypothesis needs to be tested in future studies. creator: Zeferino Blanco-Martínez creator: Roberto Pérez-Castañeda creator: Jesús Genaro Sánchez-Martínez creator: Flaviano Benavides-González creator: Jaime Luis Rábago-Castro creator: María de la Luz Vázquez-Sauceda creator: Lorena Garrido-Olvera uri: https://doi.org/10.7717/peerj.10496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Blanco-Martínez et al. title: Pro-inflammatory effect of obesity on rats with burn wounds link: https://peerj.com/articles/10499 last-modified: 2020-12-08 description: ObjectiveA burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study.Materials and methodsDifferent degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted.ResultsThe ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14.ConclusionBurn injury and obesity have a mutually synergistic effect on the body’s inflammatory response. creator: Chan Nie creator: Huiting Yu creator: Xue Wang creator: Xiahong Li creator: Zairong Wei creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.10499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nie et al. title: Self-reports vs. physical measures of spinal stiffness link: https://peerj.com/articles/9598 last-modified: 2020-12-07 description: BackgroundObjectively measured reduction in lumbar posterior-to-anterior (PA) stiffness is associated with pain relief in some, but not all persons with low back pain. Unfortunately, these measurements can be time consuming to perform. In comparison, the Lumbar Spine Instability Questionnaire (LSIQ) is intended to measure spinal instability and the Lumbar Spine Disability Index (LSDI) is created for self-reporting functional disability due to increased spinal stiffness. Given the above, the aim of this study is to compare measures of the LSIQ and LSDI with objective measures of lumbar PA stiffness as measured by a mechanical device, Vertetrack (VT), in patients with persistent non-specific low back pain (nsLBP).MethodsTwenty-nine patients with nsLBP completed the LSIQ and LSDI at baseline and after two weeks. On these same occasions, PA spinal stiffness was measured using the VT. Between measurements, patients received four sessions of spinal manipulation. The resulting data was analyzed to determine the correlation between the self-report and objective measures of stiffness at both time points. Further, the patients were categorized into responders and non-responders based on pre-established cut points depending on values from the VT and compared those to self-report measures in order to determine whether the LSIQ and the LSDI were sensitive to change.ResultsTwenty-nine participants completed the study. Measures from the LSIQ and LSDI correlated poorly with objectively measured lumbar PA stiffness at baseline and also with the change scores. The change in objectively measured lumbar PA stiffness following spinal manipulation did not differ between those who improved, and those who did not improve according to the pre-specified cut-points. Finally, a reduction in lumbar PA stiffness following intervention was not associated with improvement in LSIQ and LSDI outcomes.ConclusionsThe current data indicate that the LSIQ and LSDI questionnaires do not correlate with measures obtained objectively by VT. Our results suggest that these objective and self- reported measures represent different domains and as such, cannot stand in place of one another. creator: Jonas Nielsen creator: Casper Glissmann Nim creator: Søren O’Neill creator: Eleanor Boyle creator: Jan Hartvigsen creator: Gregory N. Kawchuk uri: https://doi.org/10.7717/peerj.9598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nielsen et al. title: Identification of key genes and pathways in endometriosis by integrated expression profiles analysis link: https://peerj.com/articles/10171 last-modified: 2020-12-07 description: The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis. creator: Ding Cui creator: Yang Liu creator: Junyan Ma creator: Kaiqing Lin creator: Kaihong Xu creator: Jun Lin uri: https://doi.org/10.7717/peerj.10171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cui et al. title: Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies link: https://peerj.com/articles/10370 last-modified: 2020-12-07 description: BackgroundBlow flies are a family of dipterans of medical, veterinary and sanitary importance. We aim to predict the current geographical distribution of six neotropical blowfly species with different altitudinal ranges of distribution (high, medium, and lowlands) and degree of synanthropy (eusynanthropic, hemisynanthropic and asynanthropic) based on their existing fundamental niche (EA) in Northwestern South America.MethodsGeographical records were compiled based on data from museum specimens and literature. The accessible area hypothesis (M) was calculated based on three criteria: (1) Altitudinal range, (2) Synanthropy values deducted based on the Human Influence Index (HII) raster dataset, and (3). The mean dispersal capability of flies. The modeling was performed using the Maxent entropy modeling software. The selection of parameters was made with the R Program ENMeval package.ResultsThe models were assessed using the area under the operator-partial receiver curve (ROCp). The high statistical performance was evidenced in every modeling prediction. The modeling allowed identifying possible taxonomic inaccuracies and the lack of exhaustive collection in the field, especially for lowlands species. Geographical distribution predicted by the modeling and empirical data was remarkably coherent in montane species.DiscussionThe data obtained evidence that montane elevational ranges affect the performance of the distribution models. These models will allow a more precise predicting of medium and high elevation blow flies than lowlands species. Montane species modeling will accurately predict the fly occurrence to use such biological information for medical, legal, veterinary, and conservation purposes. creator: Mariano Altamiranda-Saavedra creator: Eduardo Amat creator: Luz Miryam Gómez-P uri: https://doi.org/10.7717/peerj.10370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Altamiranda-Saavedra et al. title: Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery link: https://peerj.com/articles/10381 last-modified: 2020-12-07 description: Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored. creator: Rohit Nandakumar creator: Valentin Dinu uri: https://doi.org/10.7717/peerj.10381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nandakumar and Dinu