title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=862 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Towards an open and synergistic framework for mapping global land cover link: https://peerj.com/articles/11877 last-modified: 2021-08-04 description: Global land-cover datasets are key sources of information for understanding the complex inter-actions between human activities and global change. They are also among the most critical variables for climate change studies. Over time, the spatial resolution of land cover maps has increased from the kilometer scale to 10-m scale. Single-type historical land cover datasets, including for forests, water, and impervious surfaces, have also been developed in recent years. In this study, we present an open and synergy framework to produce a global land cover dataset that combines supervised land cover classification and aggregation of existing multiple thematic land cover maps with the Google Earth Engine (GEE) cloud computing platform. On the basis of this method of classification and mosaicking, we derived a global land cover dataset for 6 years over a time span of 25 years. The overall accuracies of the six maps were around 75% and the accuracy for change area detection was over 70%. Our product also showed good similarity with the FAO and existing land cover maps. creator: Jiyao Zhao creator: Le Yu creator: Han Liu creator: Huabing Huang creator: Jie Wang creator: Peng Gong uri: https://doi.org/10.7717/peerj.11877 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al. title: Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens link: https://peerj.com/articles/11918 last-modified: 2021-08-04 description: BackgroundNatural minerals have many beneficial properties in poultry production, taking into account production as well as hygiene, health, safety, and quality of broiler meat. The aim of the study was to evaluate the effect of aluminosilicates in feed and litter on the growth performance and meat quality in chickens. Aluminosilicates, including halloysite and zeolite, could be a good alternative for synthetics, as a good solution for the environment in line with the current trends.MethodsFive-hundred male Ross 308 chickens were managed in 5 groups (10 replicates/group): LITTER: 1, control; 2, 0.95 kg/m2 of halloysite; 3, 0.475 kg/m2 of halloysite and 0.475 zeolite; 4, 0.95 kg/m2 of zeolite; 5, 0.25 kg/m2of halloysite and 0.7 kg/m2 of zeolite. FEED: groups 2–5, halloysite and zeolite addition (25:75 ratio; 0.5–2%). Growth performance (body weight and feed indicators), carcass, and meat quality (pH, colour, water-holding capacity, chemical composition of muscles) were recorded. The experimental setup, where the aluminosilicate additives were applied simultaneously, was proposed and approved by experts after pilot testing and on the basis of extensive literature where feed or litter additives were tested.ResultsBody weight and its gain were higher in groups 3 and 4 than in 1, and feed intake was higher in 4. The weight of the carcass and some of its components, including muscles and skin with subcutaneous fat, were higher in 2–4. Water loss from leg muscles was lower in 4. The content of protein in muscles was significantly higher in 3. The addition of aluminosilicates in feed and litter had a positive effect on the growth performance and some traits of carcasses and meat quality, especially in group 3. Halloysite and zeolite can be used in feed and litter (especially 0.475 kg/m2 for each mineral in the wheat litter). creator: Mirosław Banaszak creator: Jakub Biesek creator: Marek Adamski uri: https://doi.org/10.7717/peerj.11918 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Banaszak et al. title: The effect of uncorrected ametropia on ocular torsion induced by changes in fixation link: https://peerj.com/articles/11932 last-modified: 2021-08-04 description: Background and ObjectiveOcular torsion, the eye movements to rotating around the line of sight, has not been well investigated regarding the influence of refractive errors. The purpose of this study was to investigate the effect of uncorrected ametropia on ocular torsion induced by fixation distances.MethodsSeventy-two subjects were classified according to the type of their refractive error, and ocular torsion of the uncorrected eye was compared based on changes induced by different fixation distances. Ocular torsion was measured using a slit-lamp biomicroscope equipped with an ophthalmic camera and a half-silvered mirror.ResultsIn all groups, excyclotorsion values increased as the fixation distance decreased, but the myopia and astigmatism groups had larger amounts of ocular torsion than the emmetropia group. In addition, as the amount of uncorrected myopia and astigmatism increased, the amount of ocular torsion increased.ConclusionSince the amount of ocular torsion caused by a change to a shorter fixation distance was larger when the refractive error was uncorrected, we suggest that ametropia should be fully corrected in patients frequently exposed to ocular torsion due to changes in fixation distance. creator: Kwang-Keun Oh creator: Byeong-Yeon Moon creator: Hyun Gug Cho creator: Sang-Yeob Kim creator: Dong-Sik Yu uri: https://doi.org/10.7717/peerj.11932 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Oh et al. title: Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking link: https://peerj.com/articles/11960 last-modified: 2021-08-04 description: Loss of a lower limb below the knee, i.e., transtibial limb loss, and subsequently walking with a prosthesis, is generally thought to increase the metabolic cost of walking vs. able-bodied controls. However, high-functioning individuals with limb loss such as military service members often walk with the same metabolic cost as controls. Here we used a 3-D computer model and optimal control simulation approach to test the hypothesis that transtibial limb loss in and of itself causes an increase in metabolic cost of walking. We first generated N = 36 simulations of walking at 1.45 m/s using a “pre-limb loss” model, with two intact biological legs, that minimized deviations from able-bodied experimental walking mechanics with minimum muscular effort. We then repeated these simulations using a “post-limb loss” model, with the right leg’s ankle muscles and joints replaced with a simple model of a passive transtibial prosthesis. No other changes were made to the post-limb loss model’s remaining muscles or musculoskeletal parameters compared to the pre-limb loss case. Post-limb loss, the gait deviations on average increased by only 0.17 standard deviations from the experimental means, and metabolic cost did not increase (3.58 ± 0.10 J/m/kg pre-limb loss vs. 3.59 ± 0.12 J/m/kg post-limb loss, p = 0.65). The results suggest that transtibial limb loss does not directly lead to an increase in metabolic cost, even when deviations from able-bodied gait mechanics are minimized. High metabolic costs observed in individuals with transtibial limb loss may be due to secondary changes in strength or general fitness after limb loss, modifiable prosthesis issues, or to prioritization of factors that affect locomotor control other than gait deviations and muscular effort. creator: Ross H. Miller creator: Elizabeth Russell Esposito uri: https://doi.org/10.7717/peerj.11960 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Miller and Russell Esposito title: Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models link: https://peerj.com/articles/11694 last-modified: 2021-08-03 description: BackgroundAccurate diagnosis of major depressive disorder (MDD) remains difficult, and one of the key challenges in diagnosing MDD is the lack of reliable diagnostic biomarkers. The objective of this study was to explore gene networks and identify potential biomarkers for MDD.MethodsIn the present study, we performed a comprehensive analysis of the mRNA expression profiles using blood samples of four patients with MDD and four controls by RNA sequencing. Differentially expressed genes (DEGs) were screened, and functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. All DEGs were inputted to the STRING database to build a PPI network, and the top 10 hub genes were screened using the cytoHubba plugin of the Cytoscape software. The relative expression of 10 key genes was identified by quantitative real-time polymerase chain reaction (qRT-PCR) of blood samples from 50 MDD patients and 50 controls. Plasma levels of SQSTM1 and TNFα were measured using an enzyme-linked immunosorbent assay in blood samples of 44 MDD patients and 44 controls. A sucrose preference test was used to evaluate depression-like behavior in chronic unpredictable mild stress (CUMS) model rats. Immunofluorescence assay and western blotting were performed to study the expression of proteins in the brain samples of CUMS model ratsResultsWe identified 247 DEGs that were closely associated with MDD. Gene ontology analyses suggested that the DEGs were mainly enriched in negative regulation of transcription by RNA polymerase II promoter, cytoplasm, and protein binding. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the DEGs were significantly enriched in the MAPK signaling pathway. Ten hub genes were screened through the PPI network, and qRT-PCR assay revealed that one and six genes were downregulated and upregulated, respectively; however, SMARCA2, PPP3CB, and RAB5C were not detected. Pathway enrichment analysis for the 10 genes showed that the mTOR signaling pathway was also enriched. A strong positive correlation was observed between SQSTM1 and TNFα protein levels in patients with MDD. LC3 II and SQSTM1 protein levels were increased in the CUMS rat model; however, p-mTOR protein levels were decreased. The sucrose preference values decreased in the CUMS rat model.ConclusionsWe identified 247 DEGs and constructed an MDD-specific network; thereafter, 10 hub genes were selected for further analysis. Our results provide novel insights into the pathogenesis of MDD. Moreover, SQSTM1, which is related to autophagy and inflammatory reactions, may play a key role in MDD. SQSTM1 may be used as a promising therapeutic target in MDD; additionally, more molecular mechanisms have been suggested that should be focused on in future in vivo and in vitro studies. creator: Jun He creator: Zhenkui Ren creator: Wansong Xia creator: Cao Zhou creator: Bin Bi creator: Wenfeng Yu creator: Li Zuo uri: https://doi.org/10.7717/peerj.11694 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 He et al. title: Cellulose aerogel composites as oil sorbents and their regeneration link: https://peerj.com/articles/11795 last-modified: 2021-08-03 description: BackgroundWith every oil tanker comes the risk of an accident and oil spill. Sorbents are the most suitable means to remove oil spills. Aerogels as sorbents have high porosity and can be made from cellulose from paper waste. The literature does not distinguish between paper and cardboard as sources of cellulose aerogels and little is known about composites of cellulose aerogels consisting of cellulose fibres and chemically untreated, unprocessed fibres or particles of straw, wool, macroalgae or cellulose acetate from cigarette butts. In this study, the sorption properties for marine diesel oil and biodiesel of such aerogels and their regenerative capacity with bioethanol were investigated.MethodsCellulose aerogels were prepared from office paper and cardboard waste without and with chemically untreated algae, straw, wool and cellulose acetate as a composite by freeze drying. All samples were hydrophobised with methylsilane. The density to calculate the porosity and the contact angle were determined. Then the sorption capacity was determined over five cycles of sorption of oil and regeneration with bioethanol.ResultsThe average contact angle of all samples was 125°, indicating hydrophobicity. Paper-based aerogels were found to consistently have higher sorption capacities for biodiesel, marine diesel oil and bioethanol than cardboard-based aerogels. In particular, the wool/cellulose aerogel composite was found to have better sorption capacity for biodiesel, marine diesel oil and bioethanol than all other samples. The cellulose acetate/cellulose aerogel composite showed significantly higher sorption capacities than the paper and cardboard control samples (highest value is 32.25 g g−1) only when first used as a sorbent for biodiesel, but with a rapid decrease in the following cycles. creator: Tatjana Paulauskiene creator: Jochen Uebe creator: Mindaugas Ziogas uri: https://doi.org/10.7717/peerj.11795 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Paulauskiene et al. title: Aberrant expression of PROS1 correlates with human papillary thyroid cancer progression link: https://peerj.com/articles/11813 last-modified: 2021-08-03 description: BackgroundPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Considering the important association between cellular immunity and PTC progression, it is worth exploring the biological significance of immune-related signaling in PTC.MethodsSeveral bioinformatics tools, such as R software, WEB-based Gene SeT AnaLysis Toolkit (WebGestalt), Database for Annotation, Visualization and Integrated Discovery (DAVID), Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape were used to identify the immune-related hub genes in PTC. Furthermore, in vitro experiments were adopted to identify the proliferation and migration ability of PROS1 knockdown groups and control groups in PTC cells.ResultsThe differentially expressed genes (DEGs) of five datasets from Gene Expression Omnibus (GEO) contained 154 upregulated genes and 193 downregulated genes, with Protein S (PROS1) being the only immune-related hub gene. Quantitative real-time polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) have been conducted to prove the high expression of PROS1 in PTC. Moreover, PROS1 expression was significantly correlated with lymph nodes classification. Furthermore, knockdown of PROS1 by shRNAs inhibited the cell proliferation and cell migration in PTC cells.ConclusionsThe findings unveiled the clinical relevance and significance of PROS1 in PTC and provided potential immune-related biomarkers for PTC development and prognosis. creator: Jing Wang creator: Minxiang Lei creator: Zhijie Xu uri: https://doi.org/10.7717/peerj.11813 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: A comparative study on knowledge towards COVID-19 prevention among undergraduate students in Macao and Zhuhai, China link: https://peerj.com/articles/11833 last-modified: 2021-08-03 description: In order to develop the strategy more suitable campus-based coronavirus disease 2019 (COVID-19) prevention programs for undergraduate students, it is critical to identify discrepancies in knowledge of COVID-19 prevention among students from different campuses in China. The present study examined the difference in preventive knowledge about COVID-19 pandemic in undergraduate students from two cities of Guangdong-Hong Kong-Macao Greater Bay Area (GBA), Macao Special Administrative Region (SAR), which had very few cases of COVID-19 patients, and Zhuhai, which is borders Macao SAR. In August 2020, two cohorts of undergraduate students from universities in Macao (n = 977) and Zhuhai (n = 2,818) were recruited for online. The self-rating questionnaire was used to gain information about their knowledge in COVID-19 prevention. Macao and Zhuhai students had similar correct rates in terms of heat inactivation conditions of SARS-CoV-2, (76.8% vs. 76.9%, P = 0.950), etiquette when coughing and sneezing (75.9% vs. 75.0%, P = 0.562), and use of disposable masks (92.2% vs. 90.6%, P = 0.126). However, students from Macao had significantly higher rates in correct use of disinfectants against SARS-CoV-2 (24.6% vs. 17.5%, P < 0.001) and in the route of transmission of SARS-CoV-2 (84.5% vs. 79.6%, P < 0.001) than those from Zhuhai. In conclusion, the knowledge level of COVID-19 prevention differs among undergraduate students from Macao and Zhuhai, which warrants an appropriate region-specific health education strategie for COVID-19 prevention. creator: Xiaoyu Tao creator: Dong Chen creator: Rining Liang creator: Xiaoyu Zhang creator: Xi Yu creator: Sookja Chung creator: Yaqin Yu creator: Ying Xiao uri: https://doi.org/10.7717/peerj.11833 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tao et al. title: Influenza A virus infects pulmonary microvascular endothelial cells leading to microvascular leakage and release of pro-inflammatory cytokines link: https://peerj.com/articles/11892 last-modified: 2021-08-03 description: ObjectiveTo investigate the replication of influenza A virus A/Puerto Rico/8/34 (H1N1) in pulmonary microvascular endothelial cells and its effect on endothelial barrier function.MethodsHuman pulmonary microvascular endothelial cells were infected with influenza A/Puerto Rico/8/34 (H1N1) virus. Plaque reduction assay, real-time quantitative PCR, immunofluorescence staining, and western blot were used to elucidate the replication process of virus-infected endothelial cells. In addition, real-time quantitative PCR was used to detect the relative expression levels of mRNA of some inflammatory factors. The endothelial resistance assay was used to determine the permeability of the endothelial monolayer. Excavation and analysis of data from open databases, such as the GeneCards database, DAVID Bioinformatics Resources, STRING search tool, and DGIdb database determined the genes, proteins, and signal pathways related to microvascular leakage caused by the H1N1 virus, and predicted the drugs that could be effective for treatment.ResultsIn vitro experiments showed that the influenza virus can infect endothelial cells, leading to a significant increase in the permeability of pulmonary microvascular endothelial cells and the release of pro-inflammatory cytokines, but does not efficiently replicate in endothelial cells. A total of 107 disease-related target genes were obtained from the Gene-cards database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these genes mainly affected the pathways related to “Inflammatory bowel disease” (IBD), “Chagas disease” (American trypanosomiasis), “Influenza A”, and also played a key role in anti-inflammation and regulation of immunity. After enrichment analysis, 46 hub genes were screened. A total of 42 FDA-approved drugs corresponding to the hub genes were screened from the DGIdb database, and these could be formulated for topical application. In addition, these drugs can be used to treat other diseases, including cancer, inflammatory diseases, immune system disorders, and cardiovascular diseases.ConclusionH1N1 influenza virus affects the barrier function of endothelial cells indirectly. Combined with bioinformatics tools, we can better understand the possible mechanism of action of influenza A (H1N1) virus causing pulmonary microvascular leakage and provide new clues for the treatment of pulmonary microvascular leakage. creator: Tiantian Han creator: Yanni Lai creator: Yong Jiang creator: Xiaohong Liu creator: Danhua Li uri: https://doi.org/10.7717/peerj.11892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Han et al. title: DOG1 is commonly expressed in pancreatic adenocarcinoma but unrelated to cancer aggressiveness link: https://peerj.com/articles/11905 last-modified: 2021-08-03 description: BackgroundDOG1 (ANO1; TMEM16A) is a voltage-gated calcium-activated chloride and bicarbonate channel. DOG1 is physiologically expressed in Cajal cells, where it plays an important role in regulating intestinal motility and its expression is a diagnostic hallmark of gastrointestinal stromal tumors (GIST). Data on a possible role of DOG1 in pancreatic cancer are rare and controversial. The aim of our study was to clarify the prevalence of DOG1 expression in pancreatic cancer and to study its association with parameters of cancer aggressiveness.MethodsDOG1 expression was analyzed by immunohistochemistry in 599 pancreatic cancers in a tissue microarray format and in 12 cases of pancreatitis on large tissue sections.ResultsDOG1 expression was always absent in normal pancreas but a focal weak expression was seen in four of 12 cases of pancreatitis. DOG1 expression was, however, common in pancreatic cancer. Membranous and cytoplasmic DOG1 expression in tumor cells was highest in pancreatic ductal adenocarcinomas (61% of 444 interpretable cases), followed by cancers of the ampulla Vateri (43% of 51 interpretable cases), and absent in 6 acinus cell carcinomas. DOG1 expression in tumor associated stroma cells was seen in 76 of 444 (17%) pancreatic ductal adenocarcinomas and in seven of 51 (14%) cancers of the ampulla Vateri. Both tumoral and stromal DOG1 expression were unrelated to tumor stage, grade, lymph node and distant metastasis, mismatch repair protein deficiency and the density of CD8 positive cytotoxic T-lymphocytes in the subgroups of ductal adenocarcinomas and cancers of ampulla Vateri. Overall, the results of our study indicate that DOG1 may represent a potential biomarker for pancreatic cancer diagnosis and a putative therapeutic target in pancreatic cancer. However, DOG1 expression is unrelated to pancreatic cancer aggressiveness. creator: Kristina Jansen creator: Franziska Büscheck creator: Katharina Moeller creator: Martina Kluth creator: Claudia Hube-Magg creator: Niclas Christian Blessin creator: Daniel Perez creator: Jakob Izbicki creator: Michael Neipp creator: Hamid Mofid creator: Thies Daniels creator: Ulf Nahrstedt creator: Christoph Fraune creator: Frank Jacobsen creator: Christian Bernreuther creator: Patrick Lebok creator: Guido Sauter creator: Ria Uhlig creator: Waldemar Wilczak creator: Ronald Simon creator: Stefan Steurer creator: Eike Burandt creator: Andreas Marx creator: Till Krech creator: Till Clauditz uri: https://doi.org/10.7717/peerj.11905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jansen et al.