PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year
items: Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China
items: In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment
items: 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
items: Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland
items: Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction
items: Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma
items: The potential habitat of desert locusts is contracting: predictions under climate change scenarios
items: Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome
items: Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma

Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12296
publisher: PeerJ Inc.
rights: © 2021 Jedlicka et al.
abstract: 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.
bibliographic citation: Jedlicka et al. (2021) Differences in insectivore bird diets in coffee agroecosystems driven by obligate or generalist guild, shade management, season, and year. PeerJ 9:e12296 https://doi.org/10.7717/peerj.12296
date submitted: 2021-06-10
date accepted: 2021-09-21
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jedlicka
  given name: Julie A.
author list: Agent
  family name: Philpott
  given name: Stacy M.
author list: Agent
  family name: Baena
  given name: Martha L.
author list: Agent
  family name: Bichier
  given name: Peter
author list: Agent
  family name: Dietsch
  given name: Thomas V.
author list: Agent
  family name: Nute
  given name: Laney H.
author list: Agent
  family name: Langridge
  given name: Suzanne M.
author list: Agent
  family name: Perfecto
  given name: Ivette
author list: Agent
  family name: Greenberg
  given name: Russell
doi: 10.7717/peerj.12296
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: © 2021 Jedlicka et al.
attribution name: Jedlicka et al.

Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China
type: item
type: AcademicArticle
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).
format: application/pdf
format: text/html
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
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.12361
publisher: PeerJ Inc.
rights: © 2021 Chang et al.
abstract: 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).
bibliographic citation: Chang et al. (2021) Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China. PeerJ 9:e12361 https://doi.org/10.7717/peerj.12361
date submitted: 2021-06-08
date accepted: 2021-09-30
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Huali
author list: Agent
  family name: You
  given name: Hai-Lu
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Ma
  given name: Waisum
author list: Agent
  family name: Gao
  given name: Diansong
author list: Agent
  family name: Jia
  given name: Songhai
author list: Agent
  family name: Xia
  given name: Mengli
author list: Agent
  family name: Zhang
  given name: Jiming
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Wang
  given name: Xirui
author list: Agent
  family name: Liu
  given name: Di
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Jianhua
author list: Agent
  family name: Yang
  given name: Lili
author list: Agent
  family name: Wei
  given name: Xuefang
doi: 10.7717/peerj.12361
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Chang et al.
attribution name: Chang et al.

In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Wee Hiang Eng
creator: Wei Seng Ho
creator: Kwong Hung Ling
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.12399
publisher: PeerJ Inc.
rights: © 2021 Eng et al.
abstract: 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.
bibliographic citation: Eng et al. (2021) In vitro induction and identification of polyploid Neolamarckia cadamba plants by colchicine treatment. PeerJ 9:e12399 https://doi.org/10.7717/peerj.12399
date submitted: 2021-07-15
date accepted: 2021-10-06
issued: 2021-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eng
  given name: Wee Hiang
author list: Agent
  family name: Ho
  given name: Wei Seng
author list: Agent
  family name: Ling
  given name: Kwong Hung
doi: 10.7717/peerj.12399
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-27
copyright: ©2021 Eng et al.
attribution name: Eng et al.

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
type: item
type: AcademicArticle
description: Statement of problem It 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. Purpose To 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 Methods One 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. Results MAX 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 afte…
format: application/pdf
format: text/html
creator: Milad Hammal
creator: Zdeněk Chlup
creator: Tomáš Ingr
creator: Ján Staněk
creator: Radek Mounajjed
subject: Biochemistry
subject: Dentistry
description: doi:10.7717/peerj.11736
publisher: PeerJ Inc.
rights: © 2021 Hammal et al.
abstract: Statement of problem It 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. Purpose To 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 Methods One 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. Results MAX 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 afte…
bibliographic citation: Hammal et al. (2021) 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. PeerJ 9:e11736 https://doi.org/10.7717/peerj.11736
date submitted: 2021-04-22
date accepted: 2021-06-17
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hammal
  given name: Milad
author list: Agent
  family name: Chlup
  given name: Zdeněk
author list: Agent
  family name: Ingr
  given name: Tomáš
author list: Agent
  family name: Staněk
  given name: Ján
author list: Agent
  family name: Mounajjed
  given name: Radek
doi: 10.7717/peerj.11736
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Hammal et al.
attribution name: Hammal et al.

Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Arkadiusz Bartczak
creator: Halina Kaczmarek
creator: Michał Badocha
creator: Michał Krzemiński
creator: Sebastian Tyszkowski
subject: Coupled Natural and Human Systems
subject: Environmental Impacts
description: doi:10.7717/peerj.12153
publisher: PeerJ Inc.
rights: © 2021 Bartczak et al.
abstract: 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.
bibliographic citation: Bartczak et al. (2021) Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland. PeerJ 9:e12153 https://doi.org/10.7717/peerj.12153
date submitted: 2021-02-19
date accepted: 2021-08-22
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartczak
  given name: Arkadiusz
author list: Agent
  family name: Kaczmarek
  given name: Halina
author list: Agent
  family name: Badocha
  given name: Michał
author list: Agent
  family name: Krzemiński
  given name: Michał
author list: Agent
  family name: Tyszkowski
  given name: Sebastian
doi: 10.7717/peerj.12153
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Bartczak et al.
attribution name: Bartczak et al.

Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction
type: item
type: AcademicArticle
description: Background In 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. Methods We 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. Results Four 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.
format: application/pdf
format: text/html
creator: Chen Shuai
creator: Fengyan Yuan
creator: Yu Liu
creator: Chengchen Wang
creator: Jiansong Wang
creator: Hongye He
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.12202
publisher: PeerJ Inc.
rights: © 2021 Shuai et al.
abstract: Background In 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. Methods We 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. Results Four 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.
bibliographic citation: Shuai et al. (2021) Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction. PeerJ 9:e12202 https://doi.org/10.7717/peerj.12202
date submitted: 2021-02-25
date accepted: 2021-09-02
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shuai
  given name: Chen
author list: Agent
  family name: Yuan
  given name: Fengyan
author list: Agent
  family name: Liu
  given name: Yu
author list: Agent
  family name: Wang
  given name: Chengchen
author list: Agent
  family name: Wang
  given name: Jiansong
author list: Agent
  family name: He
  given name: Hongye
doi: 10.7717/peerj.12202
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Shuai et al.
attribution name: Shuai et al.

Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background The 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. Methods Direct 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. Results A 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 …
format: application/pdf
format: text/html
creator: Yuanyuan Zhao
creator: Jiahao Tao
creator: Zhuangzhong Chen
creator: Suihui Li
creator: Zeyu Liu
creator: Lizhu Lin
creator: Linzhu Zhai
subject: Bioinformatics
subject: Cell Biology
subject: Drugs and Devices
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.12339
publisher: PeerJ Inc.
rights: © 2021 Zhao et al.
abstract: Background The 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. Methods Direct 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. Results A 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 …
bibliographic citation: Zhao et al. (2021) Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma. PeerJ 9:e12339 https://doi.org/10.7717/peerj.12339
date submitted: 2021-06-02
date accepted: 2021-09-28
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yuanyuan
author list: Agent
  family name: Tao
  given name: Jiahao
author list: Agent
  family name: Chen
  given name: Zhuangzhong
author list: Agent
  family name: Li
  given name: Suihui
author list: Agent
  family name: Liu
  given name: Zeyu
author list: Agent
  family name: Lin
  given name: Lizhu
author list: Agent
  family name: Zhai
  given name: Linzhu
doi: 10.7717/peerj.12339
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Zhao et al.
attribution name: Zhao et al.

The potential habitat of desert locusts is contracting: predictions under climate change scenarios
type: item
type: AcademicArticle
description: Desert locusts are notorious for their widespread distribution and strong destructive power. Their influence extends from the vast arid and semiarid regions of western Africa to northwestern India. Large-scale locust outbreaks can have devastating consequences for food security, and their social impact may be long-lasting. Climate change has increased the uncertainty of desert locust outbreaks, and predicting suitable habitats for this species under climate change scenarios will help humans deal with the potential threat of locust outbreaks. By comprehensively considering climate, soil, and terrain variables, the maximum entropy (MaxEnt) model was used to predict the potential habitats of solitary desert locusts in the 2050s and 2070s under the four shared socioeconomic pathways (SSP126, SSP245, SSP370, and SSP585) in the CMIP6 model. The modeling results show that the average area under the curve (AUC) and true skill statistic (TSS) reached 0.908 ± 0.002 and 0.701, respectively, indicating that the MaxEnt model performed extremely well and provided outstanding prediction results. The prediction results indicate that climate change will have an impact on the distribution of the potential habitat of solitary desert locusts. With the increase in radiative forcing overtime, the suitable areas for desert locusts will continue to contract, especially in the 2070s under the SSP585 scenario, and the moderately and highly suitable areas will decrease by 0.88 × 106 km2 and 1.55 × 106 km2, respectively. Although the potentially suitable area for desert locusts is contracting, the future threat posed by the desert locust to agricultural production and food security cannot be underestimated, given the combination of maintained breeding areas, frequent extreme weather events, pressure from population growth, and volatile sociopolitical environments. In conclusion, methods such as monitoring and early warning, financial support, regional cooperation, and scientific prevention and…
format: application/pdf
format: text/html
creator: Jingyun Guan
creator: Moyan Li
creator: Xifeng Ju
creator: Jun Lin
creator: Jianguo Wu
creator: Jianghua Zheng
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.12311
publisher: PeerJ Inc.
rights: © 2021 Guan et al.
abstract: Desert locusts are notorious for their widespread distribution and strong destructive power. Their influence extends from the vast arid and semiarid regions of western Africa to northwestern India. Large-scale locust outbreaks can have devastating consequences for food security, and their social impact may be long-lasting. Climate change has increased the uncertainty of desert locust outbreaks, and predicting suitable habitats for this species under climate change scenarios will help humans deal with the potential threat of locust outbreaks. By comprehensively considering climate, soil, and terrain variables, the maximum entropy (MaxEnt) model was used to predict the potential habitats of solitary desert locusts in the 2050s and 2070s under the four shared socioeconomic pathways (SSP126, SSP245, SSP370, and SSP585) in the CMIP6 model. The modeling results show that the average area under the curve (AUC) and true skill statistic (TSS) reached 0.908 ± 0.002 and 0.701, respectively, indicating that the MaxEnt model performed extremely well and provided outstanding prediction results. The prediction results indicate that climate change will have an impact on the distribution of the potential habitat of solitary desert locusts. With the increase in radiative forcing overtime, the suitable areas for desert locusts will continue to contract, especially in the 2070s under the SSP585 scenario, and the moderately and highly suitable areas will decrease by 0.88 × 106 km2 and 1.55 × 106 km2, respectively. Although the potentially suitable area for desert locusts is contracting, the future threat posed by the desert locust to agricultural production and food security cannot be underestimated, given the combination of maintained breeding areas, frequent extreme weather events, pressure from population growth, and volatile sociopolitical environments. In conclusion, methods such as monitoring and early warning, financial support, regional cooperation, and scientific prevention and…
bibliographic citation: Guan et al. (2021) The potential habitat of desert locusts is contracting: predictions under climate change scenarios. PeerJ 9:e12311 https://doi.org/10.7717/peerj.12311
date submitted: 2021-06-15
date accepted: 2021-09-23
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Jingyun
author list: Agent
  family name: Li
  given name: Moyan
author list: Agent
  family name: Ju
  given name: Xifeng
author list: Agent
  family name: Lin
  given name: Jun
author list: Agent
  family name: Wu
  given name: Jianguo
author list: Agent
  family name: Zheng
  given name: Jianghua
doi: 10.7717/peerj.12311
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Guan et al.
attribution name: Guan et al.

Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome
type: item
type: AcademicArticle
description: Background Acute respiratory distress syndrome (ARDS) is a common cause of death in ICU patients and its underlying mechanism remains unclear, which leads to its high mortality rate. This study aimed to identify candidate genes potentially implicating in the pathogenesis of ARDS and provide novel therapeutic targets. Methods Using bioinformatics tools, we searched for differentially expressed genes (DEGs) in an ARDS microarray dataset downloaded from the Gene Expression Omnibus (GEO) database. Afterwards, functional enrichment analysis of GO, KEGG, GSEA and WGCNA were carried out to investigate the potential involvement of these DEGs. Moreover, the Protein–protein interaction (PPI) network was constructed and molecular complexes and hub genes were identified, followed by prognosis analysis of the hub genes. Further, we performed qRT-PCR, Western Blot and flow cytometry analysis to detect candidate genes of CCR2 and FPR3 in macrophage model of LPS-induced ARDS and primary alveolar macrophages(AMs). Macrophage chemotaxis was evaluated using Transwell assay. Results DEGs mainly involved in myeloid leukocyte activation, cell chemotaxis, adenylate cyclase-modulating G protein-coupled receptor signaling pathway and cytokine-cytokine receptor interaction. Basing on the constructed PPI network, we identified five molecular complexes and 10 hub genes potentially participating in the pathogenesis of ARDS. It was observed that candidate genes of CCR2 and FPR3 were significantly over-expressed in primary alveolar macrophages from ARDS patients and macrophgae model of LPS-induced ARDS. Moreover, in vitro transwell assay demonstrated that CCR2 and FPR3 down-regulation, respectively, inhibited LPS-triggered macrophage chemotaxis toward CCL2. Finally, a positive correlation between FPR3 and CCR2 expression was confirmed using pearson correlation analysis and Western Blot assay. Conclusions Our study identified CCR2 and FPR3 as the candidate genes which can promote macrophage chemot…
format: application/pdf
format: text/html
creator: Yong Mao
creator: Xin Lv
creator: Wei Xu
creator: Youguo Ying
creator: Zonghe Qin
creator: Handi Liao
creator: Li Chen
creator: Ya Liu
subject: Bioinformatics
subject: Cell Biology
subject: Emergency and Critical Care
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12312
publisher: PeerJ Inc.
rights: © 2021 Mao et al.
abstract: Background Acute respiratory distress syndrome (ARDS) is a common cause of death in ICU patients and its underlying mechanism remains unclear, which leads to its high mortality rate. This study aimed to identify candidate genes potentially implicating in the pathogenesis of ARDS and provide novel therapeutic targets. Methods Using bioinformatics tools, we searched for differentially expressed genes (DEGs) in an ARDS microarray dataset downloaded from the Gene Expression Omnibus (GEO) database. Afterwards, functional enrichment analysis of GO, KEGG, GSEA and WGCNA were carried out to investigate the potential involvement of these DEGs. Moreover, the Protein–protein interaction (PPI) network was constructed and molecular complexes and hub genes were identified, followed by prognosis analysis of the hub genes. Further, we performed qRT-PCR, Western Blot and flow cytometry analysis to detect candidate genes of CCR2 and FPR3 in macrophage model of LPS-induced ARDS and primary alveolar macrophages(AMs). Macrophage chemotaxis was evaluated using Transwell assay. Results DEGs mainly involved in myeloid leukocyte activation, cell chemotaxis, adenylate cyclase-modulating G protein-coupled receptor signaling pathway and cytokine-cytokine receptor interaction. Basing on the constructed PPI network, we identified five molecular complexes and 10 hub genes potentially participating in the pathogenesis of ARDS. It was observed that candidate genes of CCR2 and FPR3 were significantly over-expressed in primary alveolar macrophages from ARDS patients and macrophgae model of LPS-induced ARDS. Moreover, in vitro transwell assay demonstrated that CCR2 and FPR3 down-regulation, respectively, inhibited LPS-triggered macrophage chemotaxis toward CCL2. Finally, a positive correlation between FPR3 and CCR2 expression was confirmed using pearson correlation analysis and Western Blot assay. Conclusions Our study identified CCR2 and FPR3 as the candidate genes which can promote macrophage chemot…
bibliographic citation: Mao et al. (2021) Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome. PeerJ 9:e12312 https://doi.org/10.7717/peerj.12312
date submitted: 2021-05-31
date accepted: 2021-09-24
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Yong
author list: Agent
  family name: Lv
  given name: Xin
author list: Agent
  family name: Xu
  given name: Wei
author list: Agent
  family name: Ying
  given name: Youguo
author list: Agent
  family name: Qin
  given name: Zonghe
author list: Agent
  family name: Liao
  given name: Handi
author list: Agent
  family name: Chen
  given name: Li
author list: Agent
  family name: Liu
  given name: Ya
doi: 10.7717/peerj.12312
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Mao et al.
attribution name: Mao et al.

Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was …
format: application/pdf
format: text/html
creator: Bing-Bing Shang
creator: Jun Chen
creator: Zhi-Guo Wang
creator: Hui Liu
subject: Bioinformatics
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.12315
publisher: PeerJ Inc.
rights: © 2021 Shang et al.
abstract: Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was …
bibliographic citation: Shang et al. (2021) Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma. PeerJ 9:e12315 https://doi.org/10.7717/peerj.12315
date submitted: 2021-06-25
date accepted: 2021-09-24
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Bing-Bing
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Wang
  given name: Zhi-Guo
author list: Agent
  family name: Liu
  given name: Hui
doi: 10.7717/peerj.12315
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Shang et al.
attribution name: Shang et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359