title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=814 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Land-use change influence soil quality parameters at an ecologically fragile area of YongDeng County of Gansu Province, China link: https://peerj.com/articles/12246 last-modified: 2021-10-27 description: Dry ecosystems, despite their relative levels of aridity, are very diverse, and play a vital role in the livelihoods of many dryland inhabitants. It is therefore critical to investigate the relationship between land-use change and soil quality parameters to offer a scientific basis for optimizing land-use planning and improving soil quality status in dry ecosystems and ecologically vulnerable areas. This study, therefore, analyzed the physicochemical properties of soils in five different land-use types namely farmland, abandoned farmland, natural grassland, artificial lemon forest, and poplar woodland at YongDeng County. The soil quality status of the aforementioned land-use types was also evaluated through Principal component analysis. The results revealed that abandoned farmland and natural grassland recorded the highest average values of soil coarse particles of 24.0% and 23.4% respectively compared to the other land-use types. The highest average value (46.1%) of fine soil particles was recorded in poplar woodland followed by natural grassland (36.6%) and the average value of very fine soil particles was higher in farmland (40.8%) and artificial lemon woodland (38.3%) than in the other land-use types. The average value of clayey particles was highest in farmland (11.1%), followed by artificial lemon woodland (9.3%), and abandoned farmland (6.5%), then poplar woodland which recorded an average value of (4.2%). The average values of Soil water content, soil pH, soil electrical conductivity, and soil total nitrogen content were significantly higher in farmland compared to the other land-use types. Soil organic carbon content was significantly higher in abandoned farmland at (P < 0.03) and lemon woodland at (P < 0.01) than in farmlands, natural grasslands, and poplar stands. The soil quality indicators of the different land-use types were significantly correlated with each other. Among them, the correlation coefficient of each evaluation index was highest in poplar woodland, followed by natural grassland, lower in farmland and artificial lemon woodland, and lowest in abandoned farmland. The overall soil quality scores were in the following order: farmland > abandoned farmland > 0 > grassland > lemon woodland > poplar woodland. In the study area, the soil quality of farmland that has been finely managed and naturally restored to grassland following abandonment is superior, whereas the soil quality of natural grassland, artificial lemon woodland, and poplar forest land is substandard. The comprehensive analysis of soil quality demonstrates that conservation tillage and fine management of water-irrigated farmland, as well as the natural conversion of abandoned farmland to grassland, can significantly improve the soil quality of sandy soils, reduce water and soil loss, increase fertility, and gradually improve regional ecological environmental conditions. creator: Samuel Adingo creator: Jie-Ru Yu creator: Liu Xuelu creator: Sun Jing creator: Xiaodan Li creator: Zhang Xiaoning uri: https://doi.org/10.7717/peerj.12246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Adingo et al. title: Hierarchical drift diffusion modeling uncovers multisensory benefit in numerosity discrimination tasks link: https://peerj.com/articles/12273 last-modified: 2021-10-27 description: Studies of accuracy and reaction time in decision making often observe a speed-accuracy tradeoff, where either accuracy or reaction time is sacrificed for the other. While this effect may mask certain multisensory benefits in performance when accuracy and reaction time are separately measured, drift diffusion models (DDMs) are able to consider both simultaneously. However, drift diffusion models are often limited by large sample size requirements for reliable parameter estimation. One solution to this restriction is the use of hierarchical Bayesian estimation for DDM parameters. Here, we utilize hierarchical drift diffusion models (HDDMs) to reveal a multisensory advantage in auditory-visual numerosity discrimination tasks. By fitting this model with a modestly sized dataset, we also demonstrate that large sample sizes are not necessary for reliable parameter estimation. creator: Edwin Chau creator: Carolyn A. Murray creator: Ladan Shams uri: https://doi.org/10.7717/peerj.12273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chau et al. title: Age and lunar cycle predict harbor porpoise bycatch in the south-western Baltic Sea link: https://peerj.com/articles/12284 last-modified: 2021-10-27 description: The harbor porpoise, Phocoena phocoena, is the only cetacean regularly occurring in the Baltic Sea. During the last decades, several anthropogenic activities have affected porpoises in the Baltic region. Most notably is bycatch in static fishing gear, such as gill nets, which is the main human-induced cause of death in odontocetes. There is still considerable uncertainty about which factors influence the amount of bycatch. In the present study, we reviewed bycatch data collected from 1987 to 2016 from the south-western Baltic Sea. There was a significant difference in bycatch due to seasonality and region, and there was a higher bycatch rate in juveniles than in adults. The only abiotic factor associated with bycatch was the lunar cycle, with more animals bycaught during a full moon. These results improve our understanding of which biotic and abiotic factors are associated with bycatch of Baltic harbor porpoises, which can be used to strengthen conservation endeavors such as managing fishing efforts. creator: Dennis Brennecke creator: Magnus Wahlberg creator: Anita Gilles creator: Ursula Siebert uri: https://doi.org/10.7717/peerj.12284 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Brennecke et al. title: Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year link: https://peerj.com/articles/12296 last-modified: 2021-10-27 description: Neotropical shade-grown coffee systems are renowned for their potential to conserve avian biodiversity. Yet, little is known about food resources consumed by insectivorous birds in these systems, the extent of resource competition between resident and migratory birds, or how management of shade trees might influence diet selection. We identified arthropods in stomach contents from obligate and generalist insectivorous birds captured in mist-nets at five coffee farms in Chiapas, Mexico between 2001–2003. Overall stomach contents from 938 individuals revealed dietary differences resulting from changes in seasons, years, and foraging guilds. Of four species sampled across all management systems, Yellow-green Vireo (Vireo flavoviridis) prey differed depending on coffee shade management, consuming more ants in shaded monoculture than polyculture systems. Diets of obligate and generalist resident insectivores were 72% dissimilar with obligate insectivores consuming more Coleoptera and Araneae, and generalist insectivores consuming more Formicidae and other Hymenoptera. This suggests that obligate insectivores target more specialized prey whereas generalist insectivores rely on less favorable, chemically-defended prey found in clumped distributions. Our dataset provides important natural history data for many Nearctic-Neotropical migrants such as Tennessee Warbler (Leiothlypis peregrina; N = 163), Nashville Warbler (Leiothlypis ruficapilla; N = 69), and Swainson’s Thrush (Catharus ustulatus; N = 68) and tropical residents including Red-legged Honeycreepers (Cyanerpes cyaneus; N = 70) and Rufous-capped Warblers (Basileuterus rufifrons; N = 56). With declining arthropod populations worldwide, understanding the ecological interactions between obligate and generalist avian insectivores gives researchers the tools to evaluate community stability and inform conservation efforts. creator: Julie A. Jedlicka creator: Stacy M. Philpott creator: Martha L. Baena creator: Peter Bichier creator: Thomas V. Dietsch creator: Laney H. Nute creator: Suzanne M. Langridge creator: Ivette Perfecto creator: Russell Greenberg uri: https://doi.org/10.7717/peerj.12296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jedlicka et al. title: Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China link: https://peerj.com/articles/12361 last-modified: 2021-10-27 description: Tooth replacement rate is an important feature related to feeding mechanics and food choices for dinosaurs. However, only a few data points are available for sauropod dinosaurs, partially due to rarity of relevant fossil material. Four somphospondylan sauropod species have been recovered from the Lower Cretaceous Aptian–Albian Haoling Formation in the Ruyang Basin, Henan Province of central China, but no cranial material has been reported except for a single crown. Here we report the discovery of the rostral portion of a left dentary with replacement teeth in its first five alveoli. Comparative anatomical study shows the partial dentary can be assigned to a member of early diverging somphospondylans. The non-destructive tooth length-based approach to estimating tooth formation time and replacement rate is adopted here. The estimated tooth replacement rate is 76 days, faster than that of Brachiosaurus (83 days) and much lower than typical late diverging lithostrotian titanosaurians (20 days). Thus, this discovery adds an intermediate tooth replacement rate in the evolution of titanosauriform sauropods and supports the idea that evolution of tooth replacement rate is clade-specific. This discovery also provides more information to understand the Ruyang sauropod assemblage, which includes one of the most giant dinosaurs to have walked our Earth (Ruyangosaurus giganteus). creator: Huali Chang creator: Hai-Lu You creator: Li Xu creator: Waisum Ma creator: Diansong Gao creator: Songhai Jia creator: Mengli Xia creator: Jiming Zhang creator: Yu Li creator: Xirui Wang creator: Di Liu creator: Jie Li creator: Jianhua Zhang creator: Lili Yang creator: Xuefang Wei uri: https://doi.org/10.7717/peerj.12361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chang et al. title: In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment link: https://peerj.com/articles/12399 last-modified: 2021-10-27 description: Polyploidization has played a crucial role in plant breeding and crop improvement. However, studies on the polyploidization of tropical tree species are still very scarce in this region. This paper described the in vitro induction and identification of polyploid plants of Neolamarckia cadamba by colchicine treatment. N. cadamba belongs to the Rubiaceae family is a natural tetraploid plant with 44 chromosomes (2n = 4x = 44). Nodal segments were treated with colchicine (0.1%, 0.3% and 0.5%) for 24 h and 48 h before transferring to shoot regeneration medium. Flow cytometry (FCM) and chromosome count were employed to determine the ploidy level and chromosome number of the regenerants, respectively. Of 180 colchicine-treated nodal segments, 39, 14 and 22 were tetraploids, mixoploids and octoploids, respectively. The highest percentage of polyploidization (20% octoploids; 6.7% mixoploids) was observed after treated with 0.3% colchicine for 48 h. The DNA content of tetraploid (4C) and octoploid (8C) was 2.59 ± 0.09 pg and 5.35 ± 0.24 pg, respectively. Mixoploid plants are made up of mixed tetraploid and octoploid cells. Chromosome count confirmed that tetraploid cell has 44 chromosomes and colchicine-induced octoploid cell has 88 chromosomes. Both octoploids and mixoploids grew slower than tetraploids under in vitro conditions. Morphological characterizations showed that mixoploid and octoploid leaves had thicker leaf blades, thicker midrib, bigger stomata size, lower stomata density, higher SPAD value and smaller pith layer than tetraploids. This indicates that polyploidization has changed and resulted in traits that are predicted to increase photosynthetic capacity of N. cadamba. These novel polyploid plants could be valuable resources for advanced N. cadamba breeding programs to produce improved clones for planted forest development. creator: Wee Hiang Eng creator: Wei Seng Ho creator: Kwong Hung Ling uri: https://doi.org/10.7717/peerj.12399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Eng et al. title: Effectiveness of dentin pre-treatment on bond strength of two self-adhesive resin cements compared to an etch-and-rinse system: an in vitro study link: https://peerj.com/articles/11736 last-modified: 2021-10-26 description: Statement of problemIt has been shown that selective etching improves the bond strength of some self-adhesive resin cements to enamel. The same has yet to be determined with dentin pre-treatment.PurposeTo evaluate the tensile bond strength of two self-adhesive resin cements after two dentin surface pre-treatments, and also to analyze the cement/dentin interface.Material and MethodsOne hundred and twelve human third molars were extracted. The teeth were distributed into seven groups (n = 16). Maxcem Elite Chroma (MAX) (Kerr, Scafati, Italy) and Relyx U200 (RLX) (3M ESPE, Neuss, Germany) were used without pre-treatment or with two dentin pre-treatments (polyacrylic acid or phosphoric acid). A conventional etch-and-rinse (EAR) luting cement, NX3 Nexus (NX3) (Kerr, Scafati, Italy), was used as an external control group. Before testing, all specimens were stored in distilled water for 24 hours. Three specimens from each group were prepared for scanning electron microscopy observation (SEM). A tensile bond strength test (TBS) was performed for the remaining samples. The data were statistically analyzed using the Kruskal–Wallis test and Pairwise comparisons using the Wilcoxon rank sum test.ResultsMAX without pre-treatment and with phosphoric acid etching attained statistically similar bond strengths to NX3 (P > 0.05). There was a statistical difference (P = 0.00488) between RLX without pre-treatment (5.62 MPa) and NX3 (10.88 MPa). Phosphoric acid pre-treatment increases the bond strength values of RLX to a strength that is comparable to NX3 (P > 0.05). The lowest tensile bond strength (TBS) was attained after the application of polyacrylic acid with MAX (1.98 MPa). No statistical differences were found between the RLX bond strength values after polyacrylic acid treatment and RLX without pre-treatment or NX3 (P > 0.05). SEM observations disclosed an enhanced potential of the self-adhesive cements to infiltrate into dentin tubules and form resin tags when applied after phosphoric acid pre-treatment. The failure mode was dominantly adhesive.ConclusionsOn dentin, the self-adhesive resin cement MAX might be an effective alternative to conventional resin cement. Etching the dentin with phosphoric acid does not have a negative effect on the bond strength of MAX to dentin. On the other hand, phosphoric acid improved the bond strength of RLX when compared to EAR cement. creator: Milad Hammal creator: Zdeněk Chlup creator: Tomáš Ingr creator: Ján Staněk creator: Radek Mounajjed uri: https://doi.org/10.7717/peerj.11736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hammal et al. title: Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland link: https://peerj.com/articles/12153 last-modified: 2021-10-26 description: The rate of progression of geomorphological phenomena is greatly influenced by freeze-thaw processes. In the face of air temperature increasing over the past few decades, a question of the future impact of these processes arises, notably in the temperate and cold climate zones. Using the mean, maximum and minimum daily air temperature data in the period 1951–2018 obtained from three weather stations located in the vicinity of Jeziorsko reservoir (central Poland), we have determined the mathematical correlation, described with a polynomial function, between the mean monthly air temperature and the monthly number of freeze-thaw days (FTD). A freeze-thaw day is a day when the maximum air temperature is above 0 °C while the minimum air temperature equals or is below this threshold. The number of FTDs within the study area averaged 64–71 and demonstrated a downward trend of 2–4 FTDs/10 years. The study period (1951–2018), includes a clearly marked distinct sub-period (1991–2018), when the reservoir was in operation, which experienced 58–68 FTDs. Considering the assumed rise in temperature, one should expect a further, though slightly slower, decline in the future number of FTDs. Depending on the accepted model of the temperature increase, which for the area of Poland (Central Europe) in the perspective of 30 years oscillates between +1.1 to +1.3 °C, the number of FTDs within the study area is expected to decline by −4.5 to −5.3 FTD, i.e. 6–7% and 5.4–5.5 FTD i.e. 8–9% respectively. creator: Arkadiusz Bartczak creator: Halina Kaczmarek creator: Michał Badocha creator: Michał Krzemiński creator: Sebastian Tyszkowski uri: https://doi.org/10.7717/peerj.12153 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bartczak et al. title: Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction link: https://peerj.com/articles/12202 last-modified: 2021-10-26 description: BackgroundIn recent years, ER+ and HER2- breast cancer of adjuvant therapy has made great progress, including chemotherapy and endocrine therapy. We found that the responsiveness of breast cancer treatment was related to the prognosis of patients. However, reliable prognostic signatures based on ER+ and HER2- breast cancer and drug resistance-related prognostic markers have not been well confirmed, This study in amied to establish a drug resistance-related gene signature for risk stratification in ER+ and HER2- breast cancer.MethodsWe used the data from The Cancer Genoma Atlas (TCGA) breast cancer dataset and gene expression database (Gene Expression Omnibus, GEO), constructed a risk profile based on four drug resistance-related genes, and developed a nomogram to predict the survival of patients with I-III ER+ and HER2- breast cancer. At the same time, we analyzed the relationship between immune infiltration and the expression of these four genes or risk groups.ResultsFour drug resistance genes (AMIGO2, LGALS3BP, SCUBE2 and WLS) were found to be promising tools for ER+ and HER2- breast cancer risk stratification. Then, the nomogram, which combines genetic characteristics with known risk factors, produced better performance and net benefits in calibration and decision curve analysis. Similar results were validated in three separate GEO cohorts. All of these results showed that the model can be used as a prognostic classifier for clinical decision-making, individual prediction and treatment, as well as follow-up. creator: Chen Shuai creator: Fengyan Yuan creator: Yu Liu creator: Chengchen Wang creator: Jiansong Wang creator: Hongye He uri: https://doi.org/10.7717/peerj.12202 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shuai et al. title: Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma link: https://peerj.com/articles/12339 last-modified: 2021-10-26 description: BackgroundThe anti-tumor properties of curcumin have been demonstrated for many types of cancer. However, a systematic functional and biological analysis of its target proteins has yet to be fully documented. The aim of this study was to explore the underlying mechanisms of curcumin and broaden the perspective of targeted therapies.MethodsDirect protein targets (DPTs) of curcumin were searched in the DrugBank database. Using the STRING database, the interactions between curcumin and DPTs and indirect protein targets (IPTs) weres documented. The protein–protein interaction (PPI) network of curcumin-mediated proteins was visualized using Cytoscape. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed for all curcumin-mediated proteins. Furthermore, the cancer targets were searched in the Comparative Toxicogenomics Database (CTD). The overlapping targets were studied using Kaplan–Meier analysis to evaluate cancer survival. Further genomic analysis of overlapping genes was conducted using the cBioPortal database. Lastly, MTT, quantitative polymerase chain reaction (qPCR), and western blot (WB) analysis were used to validate the predicted results on hepatocellular carcinoma (HCC) cells.ResultsA total of five DPTs and 199 IPTs were found. These protein targets were found in 121 molecular pathways analyzed via KEGG enrichment. Based on the anti-tumor properties of curcumin, two pathways were selected, including pathways in cancer (36 genes) and HCC (22 genes). Overlapping with 505 HCC-related gene sets identified in CTD, five genes (TP53, RB1, TGFB1, GSTP1, and GSTM1) were finally identified. High mRNA levels of TP53, RB1, and GSTM1 indicated a prolonged overall survival (OS) in HCC, whereas elevated mRNA levels of TGFB1 were correlated with poor prognosis. The viability of both HepG2 cells and Hep3B cells was significantly reduced by curcumin at concentrations of 20 or 30 μM after 48 or 72 h of culture. At a concentration of 20 μM curcumin cultured for 48 h, the expression of TGFB1 and GSTP1 in Hep3B cells was reduced significantly in qPCR analysis, and reduced TGFB1 protein expression was also found in Hep3B cells. creator: Yuanyuan Zhao creator: Jiahao Tao creator: Zhuangzhong Chen creator: Suihui Li creator: Zeyu Liu creator: Lizhu Lin creator: Linzhu Zhai uri: https://doi.org/10.7717/peerj.12339 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al.