PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Frequent, quantitative bone planar scintigraphy for determination of bone anabolism in growing mice
items: The phylogenetic nomenclature of ornithischian dinosaurs
items: Overexpression of fucosyltransferase 8 reverses the inhibitory effect of high-dose dexamethasone on osteogenic response of MC3T3-E1 preosteoblasts
items: A transcription factor signature predicts the survival of patients with adrenocortical carcinoma
items: Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)
items: Prognostic values of the core components of the mammalian circadian clock in prostate cancer
items: Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions
items: Preclinical models of acute liver failure: a comprehensive review
items: Change in alcohol consumption and physical activity during the COVID-19 pandemic amongst 76 medical students
items: The carbon and nitrogen budget of Desmophyllum dianthus—a voracious cold-water coral thriving in an acidified Patagonian fjord

Frequent, quantitative bone planar scintigraphy for determination of bone anabolism in growing mice
type: item
type: AcademicArticle
description: Background To provide insight into bone turnover, quantitative measurements of bone remodeling are required. Radionuclide studies are widely used in clinical care, but have been rarely used in the exploration of the bone in preclinical studies. We describe a bone planar scintigraphy method for frequent assessment of bone activity in mice across the growing period. Since repeated venous radiotracer injections are hardly feasible in mice, we investigated the subcutaneous route. Methods Repeated 99mTc-hydroxymethylene diphosphonate (HMDP) tracer bone planar scintigraphy studies of the knee region and µCT to measure femur growth rate were performed in eight mice between week 6 and week 27 of life, i.e., during their growth period. Three independent investigators assessed the regions of interest (ROI). An index was calculated based on the counts in knees ROI (normalized by pixels and seconds), corrected for the activity administered, the decay between administration and imaging, and individual weights. Results A total of 93 scintigraphy studies and 85 µCT were performed. Repeated subcutaneous tracer injections were well tolerated and allowed for adequate radionuclide studies. Mean scintigraphic indexes in the knees ROI decreased from 87.4 ± 2.6 × 10−6 counts s−1 pixel−1 MBq−1 g−1 at week 6 to 15.0 ± 3.3 × 10−6 counts s−1 pixel−1 MBq−1 g−1 at week 27. The time constant of the fitted exponential decay was equal to 23.5 days. As control mean femur length assessed by µCT increased from 12.2 ± 0.8 mm at week 6 to 15.8 ± 0.2 mm at week 22. The time constant of the fitted Gompertz law was equal to 26.7 days. A correlation index of −0.97 was found between femur growth and decrease of bone tracer activity count between week 6 and 24. Conclusion This methodological study demonstrates the potential of repeated bone planar scintigraphy in growing mice, with subcutaneous route for tracer administration, for quantitative assessment of bone remodeling.
format: application/pdf
format: text/html
creator: Ariane Zaloszyc
creator: Claus Peter Schmitt
creator: Amira Sayeh
creator: Laetitia Higel
creator: Catherine-Isabelle Gros
creator: Fabien Bornert
creator: Gaëlle Aubertin-Kirch
creator: Jean-Philippe Dillenseger
creator: Christian Goetz
creator: André Constantinesco
creator: Michel Fischbach
creator: Seiamak Bahram
creator: Philippe Choquet
subject: Biochemistry
subject: Developmental Biology
subject: Orthopedics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12355
publisher: PeerJ Inc.
rights: © 2021 Zaloszyc et al.
abstract: Background To provide insight into bone turnover, quantitative measurements of bone remodeling are required. Radionuclide studies are widely used in clinical care, but have been rarely used in the exploration of the bone in preclinical studies. We describe a bone planar scintigraphy method for frequent assessment of bone activity in mice across the growing period. Since repeated venous radiotracer injections are hardly feasible in mice, we investigated the subcutaneous route. Methods Repeated 99mTc-hydroxymethylene diphosphonate (HMDP) tracer bone planar scintigraphy studies of the knee region and µCT to measure femur growth rate were performed in eight mice between week 6 and week 27 of life, i.e., during their growth period. Three independent investigators assessed the regions of interest (ROI). An index was calculated based on the counts in knees ROI (normalized by pixels and seconds), corrected for the activity administered, the decay between administration and imaging, and individual weights. Results A total of 93 scintigraphy studies and 85 µCT were performed. Repeated subcutaneous tracer injections were well tolerated and allowed for adequate radionuclide studies. Mean scintigraphic indexes in the knees ROI decreased from 87.4 ± 2.6 × 10−6 counts s−1 pixel−1 MBq−1 g−1 at week 6 to 15.0 ± 3.3 × 10−6 counts s−1 pixel−1 MBq−1 g−1 at week 27. The time constant of the fitted exponential decay was equal to 23.5 days. As control mean femur length assessed by µCT increased from 12.2 ± 0.8 mm at week 6 to 15.8 ± 0.2 mm at week 22. The time constant of the fitted Gompertz law was equal to 26.7 days. A correlation index of −0.97 was found between femur growth and decrease of bone tracer activity count between week 6 and 24. Conclusion This methodological study demonstrates the potential of repeated bone planar scintigraphy in growing mice, with subcutaneous route for tracer administration, for quantitative assessment of bone remodeling.
bibliographic citation: Zaloszyc et al. (2021) Frequent, quantitative bone planar scintigraphy for determination of bone anabolism in growing mice. PeerJ 9:e12355 https://doi.org/10.7717/peerj.12355
date submitted: 2021-05-18
date accepted: 2021-09-30
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zaloszyc
  given name: Ariane
author list: Agent
  family name: Schmitt
  given name: Claus Peter
author list: Agent
  family name: Sayeh
  given name: Amira
author list: Agent
  family name: Higel
  given name: Laetitia
author list: Agent
  family name: Gros
  given name: Catherine-Isabelle
author list: Agent
  family name: Bornert
  given name: Fabien
author list: Agent
  family name: Aubertin-Kirch
  given name: Gaëlle
author list: Agent
  family name: Dillenseger
  given name: Jean-Philippe
author list: Agent
  family name: Goetz
  given name: Christian
author list: Agent
  family name: Constantinesco
  given name: André
author list: Agent
  family name: Fischbach
  given name: Michel
author list: Agent
  family name: Bahram
  given name: Seiamak
author list: Agent
  family name: Choquet
  given name: Philippe
doi: 10.7717/peerj.12355
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Zaloszyc et al.
attribution name: Zaloszyc et al.

The phylogenetic nomenclature of ornithischian dinosaurs
type: item
type: AcademicArticle
description: Ornithischians form a large clade of globally distributed Mesozoic dinosaurs, and represent one of their three major radiations. Throughout their evolutionary history, exceeding 134 million years, ornithischians evolved considerable morphological disparity, expressed especially through the cranial and osteodermal features of their most distinguishable representatives. The nearly two-century-long research history on ornithischians has resulted in the recognition of numerous diverse lineages, many of which have been named. Following the formative publications establishing the theoretical foundation of phylogenetic nomenclature throughout the 1980s and 1990s, many of the proposed names of ornithischian clades were provided with phylogenetic definitions. Some of these definitions have proven useful and have not been changed, beyond the way they were formulated, since their introduction. Some names, however, have multiple definitions, making their application ambiguous. Recent implementation of the International Code of Phylogenetic Nomenclature (ICPN, or PhyloCode) offers the opportunity to explore the utility of previously proposed definitions of established taxon names. Since the Articles of the ICPN are not to be applied retroactively, all phylogenetic definitions published prior to its implementation remain informal (and ineffective) in the light of the Code. Here, we revise the nomenclature of ornithischian dinosaur clades; we revisit 76 preexisting ornithischian clade names, review their recent and historical use, and formally establish their phylogenetic definitions. Additionally, we introduce five new clade names: two for robustly supported clades of later-diverging hadrosaurids and ceratopsians, one uniting heterodontosaurids and genasaurs, and two for clades of nodosaurids. Our study marks a key step towards a formal phylogenetic nomenclature of ornithischian dinosaurs.
format: application/pdf
format: text/html
creator: Daniel Madzia
creator: Victoria M. Arbour
creator: Clint A. Boyd
creator: Andrew A. Farke
creator: Penélope Cruzado-Caballero
creator: David C. Evans
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12362
publisher: PeerJ Inc.
rights: © 2021 Madzia et al.
abstract: Ornithischians form a large clade of globally distributed Mesozoic dinosaurs, and represent one of their three major radiations. Throughout their evolutionary history, exceeding 134 million years, ornithischians evolved considerable morphological disparity, expressed especially through the cranial and osteodermal features of their most distinguishable representatives. The nearly two-century-long research history on ornithischians has resulted in the recognition of numerous diverse lineages, many of which have been named. Following the formative publications establishing the theoretical foundation of phylogenetic nomenclature throughout the 1980s and 1990s, many of the proposed names of ornithischian clades were provided with phylogenetic definitions. Some of these definitions have proven useful and have not been changed, beyond the way they were formulated, since their introduction. Some names, however, have multiple definitions, making their application ambiguous. Recent implementation of the International Code of Phylogenetic Nomenclature (ICPN, or PhyloCode) offers the opportunity to explore the utility of previously proposed definitions of established taxon names. Since the Articles of the ICPN are not to be applied retroactively, all phylogenetic definitions published prior to its implementation remain informal (and ineffective) in the light of the Code. Here, we revise the nomenclature of ornithischian dinosaur clades; we revisit 76 preexisting ornithischian clade names, review their recent and historical use, and formally establish their phylogenetic definitions. Additionally, we introduce five new clade names: two for robustly supported clades of later-diverging hadrosaurids and ceratopsians, one uniting heterodontosaurids and genasaurs, and two for clades of nodosaurids. Our study marks a key step towards a formal phylogenetic nomenclature of ornithischian dinosaurs.
bibliographic citation: Madzia et al. (2021) The phylogenetic nomenclature of ornithischian dinosaurs. PeerJ 9:e12362 https://doi.org/10.7717/peerj.12362
date submitted: 2021-05-04
date accepted: 2021-09-30
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Madzia
  given name: Daniel
author list: Agent
  family name: Arbour
  given name: Victoria M.
author list: Agent
  family name: Boyd
  given name: Clint A.
author list: Agent
  family name: Farke
  given name: Andrew A.
author list: Agent
  family name: Cruzado-Caballero
  given name: Penélope
author list: Agent
  family name: Evans
  given name: David C.
doi: 10.7717/peerj.12362
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Madzia et al.
attribution name: Madzia et al.

Overexpression of fucosyltransferase 8 reverses the inhibitory effect of high-dose dexamethasone on osteogenic response of MC3T3-E1 preosteoblasts
type: item
type: AcademicArticle
description: Background Core fucosylation catalyzed by FUT8 is essential for TGF-β binding to TGF-β receptors. Methods Indirect TGF-β1 binding assay was used to evaluate the ability of TGF-β1 to bind to TGFBRs, Alizarin red and alkaline phosphatase staining were used to detect osteogenic differentiation and mineralization ability , western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Plasmid-mediated gain-of-function study. The scale of core fucosylation modification was detected by Lectin-blot and LCA laser confocal. Results Our results showed that compared with vehicle treatment, high-dose (10−6 and 10−5 M) dexamethasone significantly inhibited cell proliferation, osteogenic differentiation, and FUT8 mRNA expression while promoting mRNA expression of adipogenesis-related genes in MC3T3-E1 cells, suggesting that downregulation of FUT8 is involved in the inhibitory effect of high-dose dexamethasone on osteogenesis. Overexpression of FUT8 significantly promoted osteogenic differentiation and activated TGF-β/Smad signaling in MC3T3-E1 cells in the presence of high-dose dexamethasone, suggesting that FUT8 reverses the inhibitory effect of high-dose dexamethasone on osteogenesis. In addition, lectin fluorescent staining and blotting showed that overexpression of FUT8 significantly reversed the inhibitory effects of high-dose dexamethasone on core fucosylation of TGFBR1 and TGFBR2. Furthermore, indirect TGF-β1 binding assay showed that overexpression of FUT8 remarkably promoted TGF-β1 binding to TGFBRs in MC3T3-E1 cells in the presence of high-dose dexamethasone. Conclusions Taken together, these results suggest that overexpression of FUT8 facilitates counteracting the inhibitory effect of dexamethasone on TGF-β signaling and osteogenesis.
format: application/pdf
format: text/html
creator: Zhiming Wu
creator: Tianye Lin
creator: Pan Kang
creator: Zhikun Zhuang
creator: Haibin Wang
creator: Wei He
creator: Qiushi Wei
creator: Ziqi Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Orthopedics
description: doi:10.7717/peerj.12380
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: Background Core fucosylation catalyzed by FUT8 is essential for TGF-β binding to TGF-β receptors. Methods Indirect TGF-β1 binding assay was used to evaluate the ability of TGF-β1 to bind to TGFBRs, Alizarin red and alkaline phosphatase staining were used to detect osteogenic differentiation and mineralization ability , western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Plasmid-mediated gain-of-function study. The scale of core fucosylation modification was detected by Lectin-blot and LCA laser confocal. Results Our results showed that compared with vehicle treatment, high-dose (10−6 and 10−5 M) dexamethasone significantly inhibited cell proliferation, osteogenic differentiation, and FUT8 mRNA expression while promoting mRNA expression of adipogenesis-related genes in MC3T3-E1 cells, suggesting that downregulation of FUT8 is involved in the inhibitory effect of high-dose dexamethasone on osteogenesis. Overexpression of FUT8 significantly promoted osteogenic differentiation and activated TGF-β/Smad signaling in MC3T3-E1 cells in the presence of high-dose dexamethasone, suggesting that FUT8 reverses the inhibitory effect of high-dose dexamethasone on osteogenesis. In addition, lectin fluorescent staining and blotting showed that overexpression of FUT8 significantly reversed the inhibitory effects of high-dose dexamethasone on core fucosylation of TGFBR1 and TGFBR2. Furthermore, indirect TGF-β1 binding assay showed that overexpression of FUT8 remarkably promoted TGF-β1 binding to TGFBRs in MC3T3-E1 cells in the presence of high-dose dexamethasone. Conclusions Taken together, these results suggest that overexpression of FUT8 facilitates counteracting the inhibitory effect of dexamethasone on TGF-β signaling and osteogenesis.
bibliographic citation: Wu et al. (2021) Overexpression of fucosyltransferase 8 reverses the inhibitory effect of high-dose dexamethasone on osteogenic response of MC3T3-E1 preosteoblasts. PeerJ 9:e12380 https://doi.org/10.7717/peerj.12380
date submitted: 2021-07-22
date accepted: 2021-10-04
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Zhiming
author list: Agent
  family name: Lin
  given name: Tianye
author list: Agent
  family name: Kang
  given name: Pan
author list: Agent
  family name: Zhuang
  given name: Zhikun
author list: Agent
  family name: Wang
  given name: Haibin
author list: Agent
  family name: He
  given name: Wei
author list: Agent
  family name: Wei
  given name: Qiushi
author list: Agent
  family name: Li
  given name: Ziqi
doi: 10.7717/peerj.12380
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Wu et al.
attribution name: Wu et al.

A transcription factor signature predicts the survival of patients with adrenocortical carcinoma
type: item
type: AcademicArticle
description: Background Adrenocortical carcinoma (ACC) is a rare endocrine cancer that manifests as abdominal masses and excessive steroid hormone levels and is associated with poor clinical outcomes. Transcription factors (TFs) deregulation is found to be involved in adrenocortical tumorigenesis and cancer progression. This study aimed to construct a TF-based prognostic signature for the prediction of survival of ACC patients. Methods The gene expression profile and clinical information for ACC patients were downloaded from The Cancer Genome Atlas (TCGA, training set) and Gene Expression Omnibus (GEO, validation set) datasets after obtained 1,639 human TFs from a previously published study. The univariate Cox regression analysis was applied to identify the survival-related TFs and the LASSO Cox regression was conducted to construct the TF signature based on these survival-associated TFs candidates. Then, multivariate analysis was used to reveal the independent prognostic factors. Furthermore, Gene Set Enrichment Analysis (GSEA) was performed to analyze the significance of the TFs constituting the prognostic signature. Results LASSO Cox regression and multivariate Cox regression identified a 13-TF prognostic signature comprised of CREB3L3, NR0B1, CENPA, FOXM1, E2F2, MYBL2, HOXC11, ZIC2, ZNF282, DNMT1, TCF3, ELK4, and KLF6. The risk score based on the TF signature could classify patients into low- and high-risk groups. Kaplan-Meier analyses showed that patients in the high-risk group had significantly shorter overall survival (OS) compared to the low-risk patients. Receiver operating characteristic (ROC) curves showed that the prognostic signature predicted the OS of ACC patients with good sensitivity and specificity both in the training set (AUC > 0.9) and the validation set (AUC > 0.7). Furthermore, the TF-risk score was an independent prognostic factor. Conclusions Taken together, we identified a 13-TF prognostic marker to predict OS in ACC patients.
format: application/pdf
format: text/html
creator: Jianyu Zhao
creator: Bo Liu
creator: Xiaoping Li
subject: Bioinformatics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12433
publisher: PeerJ Inc.
rights: © 2021 Zhao et al.
abstract: Background Adrenocortical carcinoma (ACC) is a rare endocrine cancer that manifests as abdominal masses and excessive steroid hormone levels and is associated with poor clinical outcomes. Transcription factors (TFs) deregulation is found to be involved in adrenocortical tumorigenesis and cancer progression. This study aimed to construct a TF-based prognostic signature for the prediction of survival of ACC patients. Methods The gene expression profile and clinical information for ACC patients were downloaded from The Cancer Genome Atlas (TCGA, training set) and Gene Expression Omnibus (GEO, validation set) datasets after obtained 1,639 human TFs from a previously published study. The univariate Cox regression analysis was applied to identify the survival-related TFs and the LASSO Cox regression was conducted to construct the TF signature based on these survival-associated TFs candidates. Then, multivariate analysis was used to reveal the independent prognostic factors. Furthermore, Gene Set Enrichment Analysis (GSEA) was performed to analyze the significance of the TFs constituting the prognostic signature. Results LASSO Cox regression and multivariate Cox regression identified a 13-TF prognostic signature comprised of CREB3L3, NR0B1, CENPA, FOXM1, E2F2, MYBL2, HOXC11, ZIC2, ZNF282, DNMT1, TCF3, ELK4, and KLF6. The risk score based on the TF signature could classify patients into low- and high-risk groups. Kaplan-Meier analyses showed that patients in the high-risk group had significantly shorter overall survival (OS) compared to the low-risk patients. Receiver operating characteristic (ROC) curves showed that the prognostic signature predicted the OS of ACC patients with good sensitivity and specificity both in the training set (AUC > 0.9) and the validation set (AUC > 0.7). Furthermore, the TF-risk score was an independent prognostic factor. Conclusions Taken together, we identified a 13-TF prognostic marker to predict OS in ACC patients.
bibliographic citation: Zhao et al. (2021) A transcription factor signature predicts the survival of patients with adrenocortical carcinoma. PeerJ 9:e12433 https://doi.org/10.7717/peerj.12433
date submitted: 2021-06-10
date accepted: 2021-10-13
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Jianyu
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Li
  given name: Xiaoping
doi: 10.7717/peerj.12433
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Zhao et al.
attribution name: Zhao et al.

Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)
type: item
type: AcademicArticle
description: SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.
format: application/pdf
format: text/html
creator: Min Wang
creator: Zhenghai Mo
creator: Ruozhu Lin
creator: Cancan Zhu
subject: Agricultural Science
subject: Bioinformatics
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12490
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.
bibliographic citation: Wang et al. (2021) Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis). PeerJ 9:e12490 https://doi.org/10.7717/peerj.12490
date submitted: 2021-03-30
date accepted: 2021-10-25
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Mo
  given name: Zhenghai
author list: Agent
  family name: Lin
  given name: Ruozhu
author list: Agent
  family name: Zhu
  given name: Cancan
doi: 10.7717/peerj.12490
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Prognostic values of the core components of the mammalian circadian clock in prostate cancer
type: item
type: AcademicArticle
description: Background Prostate cancer (PC) is one of the most common malignancies in males. Extensive and complex connections between circadian rhythm and cancer were found. Nonetheless, in PC, the potential role of the core components of the mammalian circadian clock (CCMCCs) in prognosis prediction has not been fully clarified. Methods We firstly collected 605 patients with PC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Survival analysis was carried out for each CCMCC. Then, we investigated the prognostic ability of CCMCCs by Cox regression analysis. Independent prognostic signatures were extracted for the establishment of the circadian clock-based risk score model. We explored the predictive performance of the risk score model in the TCGA training cohort and the independent GEO dataset. Finally, the relationships between risk score and clinicopathological parameters, biological processes, and signaling pathways were evaluated. Results The expression levels of CCMCCs were widely correlated with age, tumor status, lymph node status, disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS). Nine circadian clock genes, including CSNK1D, BTRC, CLOCK, CSNK1E, FBXL3, PRKAA2, DBP, NR1D2, and RORB, were identified as vital prognostic factors in PC and were used to construct the circadian clock-based risk score model. For DFS, the area under the 3-year or 5-year receiver operating characteristic curves ranged from 0.728 to 0.821, suggesting better predictive performance. When compared with T3-4N1 stage, PC patients at T2N0 stage might be benefited more from the circadian clock-based risk score model. Furthermore, a high circadian clock-based risk score indicated shorter DFS (p < 0.0001), early progression (p < 0.0001), and higher 5-year death rate (p = 0.007) in PC. The risk score was related to tumor status (p < 0.001), lymph node status (p < 0.001), and ribosome-related biogenesis and pathways. Conclusions The …
format: application/pdf
format: text/html
creator: Wenchang Yue
creator: Xiao Du
creator: Xuhong Wang
creator: Niu Gui
creator: Weijie Zhang
creator: Jiale Sun
creator: Jiawei You
creator: Dong He
creator: Xinyu Geng
creator: Yuhua Huang
creator: Jianquan Hou
subject: Bioinformatics
subject: Andrology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12539
publisher: PeerJ Inc.
rights: © 2021 Yue et al.
abstract: Background Prostate cancer (PC) is one of the most common malignancies in males. Extensive and complex connections between circadian rhythm and cancer were found. Nonetheless, in PC, the potential role of the core components of the mammalian circadian clock (CCMCCs) in prognosis prediction has not been fully clarified. Methods We firstly collected 605 patients with PC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Survival analysis was carried out for each CCMCC. Then, we investigated the prognostic ability of CCMCCs by Cox regression analysis. Independent prognostic signatures were extracted for the establishment of the circadian clock-based risk score model. We explored the predictive performance of the risk score model in the TCGA training cohort and the independent GEO dataset. Finally, the relationships between risk score and clinicopathological parameters, biological processes, and signaling pathways were evaluated. Results The expression levels of CCMCCs were widely correlated with age, tumor status, lymph node status, disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS). Nine circadian clock genes, including CSNK1D, BTRC, CLOCK, CSNK1E, FBXL3, PRKAA2, DBP, NR1D2, and RORB, were identified as vital prognostic factors in PC and were used to construct the circadian clock-based risk score model. For DFS, the area under the 3-year or 5-year receiver operating characteristic curves ranged from 0.728 to 0.821, suggesting better predictive performance. When compared with T3-4N1 stage, PC patients at T2N0 stage might be benefited more from the circadian clock-based risk score model. Furthermore, a high circadian clock-based risk score indicated shorter DFS (p < 0.0001), early progression (p < 0.0001), and higher 5-year death rate (p = 0.007) in PC. The risk score was related to tumor status (p < 0.001), lymph node status (p < 0.001), and ribosome-related biogenesis and pathways. Conclusions The …
bibliographic citation: Yue et al. (2021) Prognostic values of the core components of the mammalian circadian clock in prostate cancer. PeerJ 9:e12539 https://doi.org/10.7717/peerj.12539
date submitted: 2021-07-07
date accepted: 2021-11-04
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Wenchang
author list: Agent
  family name: Du
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Xuhong
author list: Agent
  family name: Gui
  given name: Niu
author list: Agent
  family name: Zhang
  given name: Weijie
author list: Agent
  family name: Sun
  given name: Jiale
author list: Agent
  family name: You
  given name: Jiawei
author list: Agent
  family name: He
  given name: Dong
author list: Agent
  family name: Geng
  given name: Xinyu
author list: Agent
  family name: Huang
  given name: Yuhua
author list: Agent
  family name: Hou
  given name: Jianquan
doi: 10.7717/peerj.12539
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Yue et al.
attribution name: Yue et al.

Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions
type: item
type: AcademicArticle
description: Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.
format: application/pdf
format: text/html
creator: Gilles Didier
creator: Michel Laurin
subject: Evolutionary Studies
subject: Mathematical Biology
subject: Paleontology
description: doi:10.7717/peerj.12577
publisher: PeerJ Inc.
rights: © 2021 Didier and Laurin
abstract: Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.
bibliographic citation: Didier et al. (2021) Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions. PeerJ 9:e12577 https://doi.org/10.7717/peerj.12577
date submitted: 2021-06-14
date accepted: 2021-11-09
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Didier
  given name: Gilles
author list: Agent
  family name: Laurin
  given name: Michel
doi: 10.7717/peerj.12577
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Didier and Laurin
attribution name: Didier and Laurin

Preclinical models of acute liver failure: a comprehensive review
type: item
type: AcademicArticle
description: Acute liver failure is marked by the rapid deterioration of liver function in a previously well patient over period of days to weeks. Though relatively rare, it is associated with high morbidity and mortality. This makes it a challenging disease to study clinically, necessitating reliance on preclinical models as means to explore pathophysiology and novel therapies. Preclinical models of acute liver failure are artificial by nature, and generally fall into one of three categories: surgical, pharmacologic or immunogenic. This article reviews preclinical models of acute liver failure and considers their relevance in modeling clinical disease.
format: application/pdf
format: text/html
creator: Joshua Hefler
creator: Braulio A. Marfil-Garza
creator: Rena L. Pawlick
creator: Darren H. Freed
creator: Constantine J. Karvellas
creator: David L. Bigam
creator: A. M. James Shapiro
subject: Biochemistry
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.12579
publisher: PeerJ Inc.
rights: © 2021 Hefler et al.
abstract: Acute liver failure is marked by the rapid deterioration of liver function in a previously well patient over period of days to weeks. Though relatively rare, it is associated with high morbidity and mortality. This makes it a challenging disease to study clinically, necessitating reliance on preclinical models as means to explore pathophysiology and novel therapies. Preclinical models of acute liver failure are artificial by nature, and generally fall into one of three categories: surgical, pharmacologic or immunogenic. This article reviews preclinical models of acute liver failure and considers their relevance in modeling clinical disease.
bibliographic citation: Hefler et al. (2021) Preclinical models of acute liver failure: a comprehensive review. PeerJ 9:e12579 https://doi.org/10.7717/peerj.12579
date submitted: 2021-09-10
date accepted: 2021-11-10
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hefler
  given name: Joshua
author list: Agent
  family name: Marfil-Garza
  given name: Braulio A.
author list: Agent
  family name: Pawlick
  given name: Rena L.
author list: Agent
  family name: Freed
  given name: Darren H.
author list: Agent
  family name: Karvellas
  given name: Constantine J.
author list: Agent
  family name: Bigam
  given name: David L.
author list: Agent
  family name: Shapiro
  given name: A. M. James
doi: 10.7717/peerj.12579
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Hefler et al.
attribution name: Hefler et al.

Change in alcohol consumption and physical activity during the COVID-19 pandemic amongst 76 medical students
type: item
type: AcademicArticle
description: Objective To investigate whether the COVID-19 pandemic has affected physical activity and alcohol consumption among medical students. Methods Cross-sectional survey study among 76 students in their second year of medical school. The Wilcoxon sign-rank test and Kruskal-Wallis H test were used to assess the difference between groups. Results Of 76 respondents, 68% were women, 66% were single and 34% were co-habiting. The median age was 21 years. Overall alcohol consumption decreased during the pandemic year by 12 g/week. Overall physical activity did not significantly change. The decrease in alcohol consumption was mostly caused by a change seen in a high tertile, change was −96 g/week. Alcohol consumption decreased more in women than in men, p = 0.0001. Conclusions It seems that alcohol consumption among medical students has decreased during the COVID-19 pandemic probably due to reduced social contacts and negative effect of social isolation. This decrease was seen especially among women and among students with higher alcohol consumption before the pandemic. Also, it seems that students had found their ways to remain active during the pandemic since the amount of leisure-time physical activity had not changed significantly.
format: application/pdf
format: text/html
creator: Christina Sandell
creator: Mikhail Saltychev
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12580
publisher: PeerJ Inc.
rights: © 2021 Sandell and Saltychev
abstract: Objective To investigate whether the COVID-19 pandemic has affected physical activity and alcohol consumption among medical students. Methods Cross-sectional survey study among 76 students in their second year of medical school. The Wilcoxon sign-rank test and Kruskal-Wallis H test were used to assess the difference between groups. Results Of 76 respondents, 68% were women, 66% were single and 34% were co-habiting. The median age was 21 years. Overall alcohol consumption decreased during the pandemic year by 12 g/week. Overall physical activity did not significantly change. The decrease in alcohol consumption was mostly caused by a change seen in a high tertile, change was −96 g/week. Alcohol consumption decreased more in women than in men, p = 0.0001. Conclusions It seems that alcohol consumption among medical students has decreased during the COVID-19 pandemic probably due to reduced social contacts and negative effect of social isolation. This decrease was seen especially among women and among students with higher alcohol consumption before the pandemic. Also, it seems that students had found their ways to remain active during the pandemic since the amount of leisure-time physical activity had not changed significantly.
bibliographic citation: Sandell et al. (2021) Change in alcohol consumption and physical activity during the COVID-19 pandemic amongst 76 medical students. PeerJ 9:e12580 https://doi.org/10.7717/peerj.12580
date submitted: 2021-08-30
date accepted: 2021-11-10
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sandell
  given name: Christina
author list: Agent
  family name: Saltychev
  given name: Mikhail
doi: 10.7717/peerj.12580
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Sandell and Saltychev
attribution name: Sandell and Saltychev

The carbon and nitrogen budget of Desmophyllum dianthus—a voracious cold-water coral thriving in an acidified Patagonian fjord
type: item
type: AcademicArticle
description: In the North Patagonian fjord region, the cold-water coral (CWC) Desmophyllum dianthus occurs in high densities, in spite of low pH and aragonite saturation. If and how these conditions affect the energy demand of the corals is so far unknown. In a laboratory experiment, we investigated the carbon and nitrogen (C, N) budget of D. dianthus from Comau Fjord under three feeding scenarios: (1) live fjord zooplankton (100–2,300 µm), (2) live fjord zooplankton plus krill (>7 mm), and (3) four-day food deprivation. In closed incubations, C and N budgets were derived from the difference between C and N uptake during feeding and subsequent C and N loss through respiration, ammonium excretion, release of particulate organic carbon and nitrogen (POC, PON). Additional feeding with krill significantly increased coral respiration (35%), excretion (131%), and POC release (67%) compared to feeding on zooplankton only. Nevertheless, the higher C and N losses were overcompensated by the threefold higher C and N uptake, indicating a high assimilation and growth efficiency for the krill plus zooplankton diet. In contrast, short food deprivation caused a substantial reduction in respiration (59%), excretion (54%), release of POC (73%) and PON (87%) compared to feeding on zooplankton, suggesting a high potential to acclimatize to food scarcity (e.g., in winter). Notwithstanding, unfed corals ‘lost’ 2% of their tissue-C and 1.2% of their tissue-N per day in terms of metabolism and released particulate organic matter (likely mucus). To balance the C (N) losses, each D. dianthus polyp has to consume around 700 (400) zooplankters per day. The capture of a single, large krill individual, however, provides enough C and N to compensate daily C and N losses and grow tissue reserves, suggesting that krill plays an important nutritional role for the fjord corals. Efficient krill and zooplankton capture, as well as dietary and metabolic flexibility, may enable D. dianthus to thrive under adverse en…
format: application/pdf
format: text/html
creator: Sandra R. Maier
creator: Carin Jantzen
creator: Jürgen Laudien
creator: Verena Häussermann
creator: Günter Försterra
creator: Astrid Cornils
creator: Jutta Niggemann
creator: Thorsten Dittmar
creator: Claudio Richter
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
description: doi:10.7717/peerj.12609
publisher: PeerJ Inc.
rights: © 2021 Maier et al.
abstract: In the North Patagonian fjord region, the cold-water coral (CWC) Desmophyllum dianthus occurs in high densities, in spite of low pH and aragonite saturation. If and how these conditions affect the energy demand of the corals is so far unknown. In a laboratory experiment, we investigated the carbon and nitrogen (C, N) budget of D. dianthus from Comau Fjord under three feeding scenarios: (1) live fjord zooplankton (100–2,300 µm), (2) live fjord zooplankton plus krill (>7 mm), and (3) four-day food deprivation. In closed incubations, C and N budgets were derived from the difference between C and N uptake during feeding and subsequent C and N loss through respiration, ammonium excretion, release of particulate organic carbon and nitrogen (POC, PON). Additional feeding with krill significantly increased coral respiration (35%), excretion (131%), and POC release (67%) compared to feeding on zooplankton only. Nevertheless, the higher C and N losses were overcompensated by the threefold higher C and N uptake, indicating a high assimilation and growth efficiency for the krill plus zooplankton diet. In contrast, short food deprivation caused a substantial reduction in respiration (59%), excretion (54%), release of POC (73%) and PON (87%) compared to feeding on zooplankton, suggesting a high potential to acclimatize to food scarcity (e.g., in winter). Notwithstanding, unfed corals ‘lost’ 2% of their tissue-C and 1.2% of their tissue-N per day in terms of metabolism and released particulate organic matter (likely mucus). To balance the C (N) losses, each D. dianthus polyp has to consume around 700 (400) zooplankters per day. The capture of a single, large krill individual, however, provides enough C and N to compensate daily C and N losses and grow tissue reserves, suggesting that krill plays an important nutritional role for the fjord corals. Efficient krill and zooplankton capture, as well as dietary and metabolic flexibility, may enable D. dianthus to thrive under adverse en…
bibliographic citation: Maier et al. (2021) The carbon and nitrogen budget of Desmophyllum dianthus—a voracious cold-water coral thriving in an acidified Patagonian fjord. PeerJ 9:e12609 https://doi.org/10.7717/peerj.12609
date submitted: 2021-07-23
date accepted: 2021-11-17
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maier
  given name: Sandra R.
author list: Agent
  family name: Jantzen
  given name: Carin
author list: Agent
  family name: Laudien
  given name: Jürgen
author list: Agent
  family name: Häussermann
  given name: Verena
author list: Agent
  family name: Försterra
  given name: Günter
author list: Agent
  family name: Cornils
  given name: Astrid
author list: Agent
  family name: Niggemann
  given name: Jutta
author list: Agent
  family name: Dittmar
  given name: Thorsten
author list: Agent
  family name: Richter
  given name: Claudio
doi: 10.7717/peerj.12609
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Maier et al.
attribution name: Maier et al.

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