PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The heart of a hibernator: EGFR and MAPK signaling in cardiac muscle during the hibernation of thirteen-lined ground squirrels, Ictidomys tridecemlineatus
items: The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae
items: Assessing blue orchard bee (Osmia lignaria) propagation and pollination services in the presence of honey bees (Apis mellifera) in Utah tart cherries
items: Pyriproxyfen, a juvenile hormone analog, damages midgut cells and interferes with behaviors of Aedes aegypti larvae
items: The number of nephrons in different glomerular diseases
items: Reduced gray matter volume in male adolescent violent offenders
items: Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy
items: https://peerj.com/articles/7551
items: Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem
items: Effects of reflective warning markers on wildlife

The heart of a hibernator: EGFR and MAPK signaling in cardiac muscle during the hibernation of thirteen-lined ground squirrels, Ictidomys tridecemlineatus
type: item
type: AcademicArticle
description: Background Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) experience dramatic changes in physiological and molecular parameters during winter hibernation. Notably, these animals experience reduced blood circulation during torpor, which can put numerous stresses on their hearts. The present study evaluates the role played by the epidermal growth factor receptor (EGFR) in signal transduction during hibernation at low body temperature to evaluate signaling mechanisms. By investigating the regulation of intracellular mitogen activated protein kinase (MAPK) pathway responses, anti-apoptosis signals, downstream transcription factors, and heat shock proteins in cardiac muscle we aim to determine the correlation between upstream tyrosine phosphorylation events and downstream outcomes. Methods Protein abundance of phosphorylated EGFR, MAPKs and downstream effector proteins were quantified using immunoblotting and Luminex® multiplex assays. Results Monitoring five time points over the torpor/arousal cycle, EGFR phosphorylation on T654, Y1068, Y1086 was found to increase significantly compared with euthermic control values particularly during the arousal process from torpor, whereas phosphorylation at Y1045 was reduced during torpor. Phosphorylation of intracellular MAPK targets (p-ERK 1/2, p-JNK, p-p38) also increased strongly during the early arousal stage with p-p38 levels also rising during prolonged torpor. However, of downstream MAPK effector kinases that were measured, only p-Elk-1 levels changed showing a decrease during interbout arousal (IA). Apoptosis markers revealed a strong reduction of the pro-apoptotic p-BAD protein during entrance into torpor that remained suppressed through torpor and IA. However, active caspase-9 protein rose strongly during IA. Levels of p-AKT were suppressed during the transition phases into and out of torpor. Of four heat shock proteins assessed, only HSP27 protein levels changed significantly (a 40% decrease) during torpor.…
format: application/pdf
format: text/html
creator: Christine L. Childers
creator: Shannon N. Tessier
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.7587
publisher: PeerJ Inc.
rights: © 2019 Childers et al.
abstract: Background Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) experience dramatic changes in physiological and molecular parameters during winter hibernation. Notably, these animals experience reduced blood circulation during torpor, which can put numerous stresses on their hearts. The present study evaluates the role played by the epidermal growth factor receptor (EGFR) in signal transduction during hibernation at low body temperature to evaluate signaling mechanisms. By investigating the regulation of intracellular mitogen activated protein kinase (MAPK) pathway responses, anti-apoptosis signals, downstream transcription factors, and heat shock proteins in cardiac muscle we aim to determine the correlation between upstream tyrosine phosphorylation events and downstream outcomes. Methods Protein abundance of phosphorylated EGFR, MAPKs and downstream effector proteins were quantified using immunoblotting and Luminex® multiplex assays. Results Monitoring five time points over the torpor/arousal cycle, EGFR phosphorylation on T654, Y1068, Y1086 was found to increase significantly compared with euthermic control values particularly during the arousal process from torpor, whereas phosphorylation at Y1045 was reduced during torpor. Phosphorylation of intracellular MAPK targets (p-ERK 1/2, p-JNK, p-p38) also increased strongly during the early arousal stage with p-p38 levels also rising during prolonged torpor. However, of downstream MAPK effector kinases that were measured, only p-Elk-1 levels changed showing a decrease during interbout arousal (IA). Apoptosis markers revealed a strong reduction of the pro-apoptotic p-BAD protein during entrance into torpor that remained suppressed through torpor and IA. However, active caspase-9 protein rose strongly during IA. Levels of p-AKT were suppressed during the transition phases into and out of torpor. Of four heat shock proteins assessed, only HSP27 protein levels changed significantly (a 40% decrease) during torpor.…
bibliographic citation: Childers et al. (2019) The heart of a hibernator: EGFR and MAPK signaling in cardiac muscle during the hibernation of thirteen-lined ground squirrels, Ictidomys tridecemlineatus. PeerJ 7:e7587 https://doi.org/10.7717/peerj.7587
date submitted: 2019-05-07
date accepted: 2019-07-30
issued: 2019-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Childers
  given name: Christine L.
author list: Agent
  family name: Tessier
  given name: Shannon N.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.7587
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-05
copyright: © 2019 Childers et al.
attribution name: Childers et al.

The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae
type: item
type: AcademicArticle
description: Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.
format: application/pdf
format: text/html
creator: Jun Wang
creator: Xin-Yi Dai
creator: Xiao-Dong Xu
creator: Zi-Yi Zhang
creator: Dan-Na Yu
creator: Kenneth B. Storey
creator: Jia-Yong Zhang
subject: Bioinformatics
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.7633
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.
bibliographic citation: Wang et al. (2019) The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae. PeerJ 7:e7633 https://doi.org/10.7717/peerj.7633
date submitted: 2019-05-14
date accepted: 2019-08-06
issued: 2019-09-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jun
author list: Agent
  family name: Dai
  given name: Xin-Yi
author list: Agent
  family name: Xu
  given name: Xiao-Dong
author list: Agent
  family name: Zhang
  given name: Zi-Yi
author list: Agent
  family name: Yu
  given name: Dan-Na
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Zhang
  given name: Jia-Yong
doi: 10.7717/peerj.7633
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-05
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Assessing blue orchard bee (Osmia lignaria) propagation and pollination services in the presence of honey bees (Apis mellifera) in Utah tart cherries
type: item
type: AcademicArticle
description: Osmia lignaria is a commercially available, native solitary bee species recognized for its propensity to forage upon and pollinate tree fruit crops such as apple, almond and cherry. This study evaluated the implementation of O. lignaria co-pollination with honey bees in central Utah commercial tart cherry orchards during 2017 and 2018 bloom. Three paired 1.2 ha sites were selected for evaluation of cherry fruit set and yield with and without managed O. lignaria releases alongside the standard honey bee hive stocking rate of 2.5 hives/ha. Osmia lignaria supplementation did not measurably increase cherry fruit set, fruit per limb cross-sectional area or fruit weight. The lack of differences in yield is likely a consequence of local saturation of pollinator services supplied by managed honey bees throughout experimental orchards, such that no additive benefit of managed O. lignaria releases were measurable. An increase in managed O. lignaria populations was achieved in 2017 but not 2018, possibly due to unknown changes to orchard management or environmental factors. While flying O. lignaria in Utah tart cherries may support sustainable in-field bee propagation, their subsequent impacts on tart cherry yield were not detected when paired with standard stocking densities of honey bees.
format: application/pdf
format: text/html
creator: Natalie K. Boyle
creator: Theresa L. Pitts-Singer
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.7639
publisher: PeerJ Inc.
rights: ©
abstract: Osmia lignaria is a commercially available, native solitary bee species recognized for its propensity to forage upon and pollinate tree fruit crops such as apple, almond and cherry. This study evaluated the implementation of O. lignaria co-pollination with honey bees in central Utah commercial tart cherry orchards during 2017 and 2018 bloom. Three paired 1.2 ha sites were selected for evaluation of cherry fruit set and yield with and without managed O. lignaria releases alongside the standard honey bee hive stocking rate of 2.5 hives/ha. Osmia lignaria supplementation did not measurably increase cherry fruit set, fruit per limb cross-sectional area or fruit weight. The lack of differences in yield is likely a consequence of local saturation of pollinator services supplied by managed honey bees throughout experimental orchards, such that no additive benefit of managed O. lignaria releases were measurable. An increase in managed O. lignaria populations was achieved in 2017 but not 2018, possibly due to unknown changes to orchard management or environmental factors. While flying O. lignaria in Utah tart cherries may support sustainable in-field bee propagation, their subsequent impacts on tart cherry yield were not detected when paired with standard stocking densities of honey bees.
bibliographic citation: Boyle et al. (2019) Assessing blue orchard bee (Osmia lignaria) propagation and pollination services in the presence of honey bees (Apis mellifera) in Utah tart cherries. PeerJ 7:e7639 https://doi.org/10.7717/peerj.7639
date submitted: 2019-04-06
date accepted: 2019-08-06
issued: 2019-09-05
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Boyle
  given name: Natalie K.
author list: Agent
  family name: Pitts-Singer
  given name: Theresa L.
doi: 10.7717/peerj.7639
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-05

Pyriproxyfen, a juvenile hormone analog, damages midgut cells and interferes with behaviors of Aedes aegypti larvae
type: item
type: AcademicArticle
description: Juvenile hormone analogs (JHA) are known to interfere with growth and biosynthesis of insects with potential for insecticide action. However, there has been comparatively few data on morphological effects of JHA on insect organs. To determine pyriproxyfen effects on Aedes aegypti larvae, we conducted toxicity, behavioral bioassays and assessed ultrastructural effects of pyriproxyfen on midgut cells. A. aegypti larvae were exposed in aqueous solution of pyriproxyfen LC50 concentrations and evaluated for 24 h. This study fulfilled the toxic prevalence of pyriproxyfen to A. aegypti larvae (LC50 = 8.2 mg L−1). Behavioral observations confirmed that pyriproxyfen treatment significantly changes swimming behavior of larvae, limiting its displacement and speed. The pyriproxyfen causes remarkable histopathological and cytotoxic alterations in the midgut of larvae. Histopathological study reveals presence of cytoplasmic vacuolization and damage to brush border of the digestive cells. The main salient lesions of cytotoxic effects are occurrence of cell debris released into the midgut lumen, cytoplasm rich in lipid droplets, autophagosomes, disorganized microvilli and deformed mitochondria. Data suggest that pyriproxyfen can be used to help to control and eradicate this insect vector.
format: application/pdf
format: text/html
creator: Muhammad Fiaz
creator: Luis Carlos Martínez
creator: Angelica Plata-Rueda
creator: Wagner Gonzaga Gonçalves
creator: Debora Linhares Lino de Souza
creator: Jamile Fernanda Silva Cossolin
creator: Paulo Eduardo Gomes Rodrigues Carvalho
creator: Gustavo Ferreira Martins
creator: José Eduardo Serrão
subject: Agricultural Science
subject: Cell Biology
subject: Toxicology
subject: Histology
description: doi:10.7717/peerj.7489
publisher: PeerJ Inc.
rights: © 2019 Fiaz et al.
abstract: Juvenile hormone analogs (JHA) are known to interfere with growth and biosynthesis of insects with potential for insecticide action. However, there has been comparatively few data on morphological effects of JHA on insect organs. To determine pyriproxyfen effects on Aedes aegypti larvae, we conducted toxicity, behavioral bioassays and assessed ultrastructural effects of pyriproxyfen on midgut cells. A. aegypti larvae were exposed in aqueous solution of pyriproxyfen LC50 concentrations and evaluated for 24 h. This study fulfilled the toxic prevalence of pyriproxyfen to A. aegypti larvae (LC50 = 8.2 mg L−1). Behavioral observations confirmed that pyriproxyfen treatment significantly changes swimming behavior of larvae, limiting its displacement and speed. The pyriproxyfen causes remarkable histopathological and cytotoxic alterations in the midgut of larvae. Histopathological study reveals presence of cytoplasmic vacuolization and damage to brush border of the digestive cells. The main salient lesions of cytotoxic effects are occurrence of cell debris released into the midgut lumen, cytoplasm rich in lipid droplets, autophagosomes, disorganized microvilli and deformed mitochondria. Data suggest that pyriproxyfen can be used to help to control and eradicate this insect vector.
bibliographic citation: Fiaz et al. (2019) Pyriproxyfen, a juvenile hormone analog, damages midgut cells and interferes with behaviors of Aedes aegypti larvae. PeerJ 7:e7489 https://doi.org/10.7717/peerj.7489
date submitted: 2018-12-13
date accepted: 2019-07-16
issued: 2019-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fiaz
  given name: Muhammad
author list: Agent
  family name: Martínez
  given name: Luis Carlos
author list: Agent
  family name: Plata-Rueda
  given name: Angelica
author list: Agent
  family name: Gonçalves
  given name: Wagner Gonzaga
author list: Agent
  family name: de Souza
  given name: Debora Linhares Lino
author list: Agent
  family name: Cossolin
  given name: Jamile Fernanda Silva
author list: Agent
  family name: Carvalho
  given name: Paulo Eduardo Gomes Rodrigues
author list: Agent
  family name: Martins
  given name: Gustavo Ferreira
author list: Agent
  family name: Serrão
  given name: José Eduardo
doi: 10.7717/peerj.7489
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-04
copyright: © 2019 Fiaz et al.
attribution name: Fiaz et al.

The number of nephrons in different glomerular diseases
type: item
type: AcademicArticle
description: Background The total number of nephrons has been measured mainly from post-mortem studies and only in selected populations. Data from living subjects are scanty, and direct comparisons among different glomerular diseases are lacking. The present work exploits modern methodology to estimate the total nephron number in glomerulopathies with prevalent proteinuria/nephrotic syndrome versus glomerulopathies with nephritic syndrome (IgA nephropathy (IgAN), lupus nephritis), thus extending previous observations about the number and function of glomeruli in different physiological and pathological states. Methods This is a retrospective study based on one hundred and seven patients who have undergone renal biopsy. The glomerular density has been estimated from the biopsy specimens and the total cortical volume has been obtained from ultrasound recordings. Stereological methods have been applied to calculate the total number of nephrons and their volume. The correlation between clinical parameters and quantitative morphological data have studied using the Pearson correlation coefficient (r). Results The total number of nephrons inversely correlated with the systolic blood pressure (r = −0.4, p < 0.05). In proteinuric diseases, such as focal segmental glomerulo-sclerosis (FSGS), membranous nephropathy (MN) and diabetes, the change in estimated GFR (eGFR) directly correlated with the total number of non-sclerotic glomeruli (NSG) (r = 0.62, p < 0.01), whereas in nephritic syndrome no significant correlation was observed. The alterations in eGFR occurring in nephritic syndromes such as IgAN cannot be explained on the basis of the number of NSG. Discussion The fusion of the podocyte foot-processes that typically occurs in purely proteinuric diseases does not modify the glomerular filtration rate: therefore in these situations, the change in eGFR depends mainly on the number of available glomeruli. On the other side, the eGFR decrease occurring in nephritic syndromes, such as IgAN…
format: application/pdf
format: text/html
creator: Davide Viggiano
creator: Michelangelo Nigro
creator: Francesco Sessa
creator: Graziano Vignolini
creator: Riccardo Campi
creator: Sergio Serni
creator: Rosa Maria Pollastro
creator: Gianfranco Vallone
creator: Giuseppe Gigliotti
creator: Giovambattista Capasso
subject: Nephrology
subject: Pathology
description: doi:10.7717/peerj.7640
publisher: PeerJ Inc.
rights: © 2019 Viggiano et al.
abstract: Background The total number of nephrons has been measured mainly from post-mortem studies and only in selected populations. Data from living subjects are scanty, and direct comparisons among different glomerular diseases are lacking. The present work exploits modern methodology to estimate the total nephron number in glomerulopathies with prevalent proteinuria/nephrotic syndrome versus glomerulopathies with nephritic syndrome (IgA nephropathy (IgAN), lupus nephritis), thus extending previous observations about the number and function of glomeruli in different physiological and pathological states. Methods This is a retrospective study based on one hundred and seven patients who have undergone renal biopsy. The glomerular density has been estimated from the biopsy specimens and the total cortical volume has been obtained from ultrasound recordings. Stereological methods have been applied to calculate the total number of nephrons and their volume. The correlation between clinical parameters and quantitative morphological data have studied using the Pearson correlation coefficient (r). Results The total number of nephrons inversely correlated with the systolic blood pressure (r = −0.4, p < 0.05). In proteinuric diseases, such as focal segmental glomerulo-sclerosis (FSGS), membranous nephropathy (MN) and diabetes, the change in estimated GFR (eGFR) directly correlated with the total number of non-sclerotic glomeruli (NSG) (r = 0.62, p < 0.01), whereas in nephritic syndrome no significant correlation was observed. The alterations in eGFR occurring in nephritic syndromes such as IgAN cannot be explained on the basis of the number of NSG. Discussion The fusion of the podocyte foot-processes that typically occurs in purely proteinuric diseases does not modify the glomerular filtration rate: therefore in these situations, the change in eGFR depends mainly on the number of available glomeruli. On the other side, the eGFR decrease occurring in nephritic syndromes, such as IgAN…
bibliographic citation: Viggiano et al. (2019) The number of nephrons in different glomerular diseases. PeerJ 7:e7640 https://doi.org/10.7717/peerj.7640
date submitted: 2019-04-01
date accepted: 2019-08-07
issued: 2019-09-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Viggiano
  given name: Davide
author list: Agent
  family name: Nigro
  given name: Michelangelo
author list: Agent
  family name: Sessa
  given name: Francesco
author list: Agent
  family name: Vignolini
  given name: Graziano
author list: Agent
  family name: Campi
  given name: Riccardo
author list: Agent
  family name: Serni
  given name: Sergio
author list: Agent
  family name: Pollastro
  given name: Rosa Maria
author list: Agent
  family name: Vallone
  given name: Gianfranco
author list: Agent
  family name: Gigliotti
  given name: Giuseppe
author list: Agent
  family name: Capasso
  given name: Giovambattista
doi: 10.7717/peerj.7640
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-04
copyright: © 2019 Viggiano et al.
attribution name: Viggiano et al.

Reduced gray matter volume in male adolescent violent offenders
type: item
type: AcademicArticle
description: Background Previous studies reported that reduced gray matter volume (GMV) was associated with violent-related behaviors. However, the previous studies were conducted on adults and no study has studied the association between GMV and violent behaviors on adolescents. The purpose of the study was to investigate GMV’s effects in adolescent violent offenders based on a Chinese Han population, which can address the problem of possible confounding factors in adult studies. Methods We recruited 30 male adolescent violent offenders and 29 age- and sex-matched healthy controls (HCs). Differences in both whole-brain and GMV were evaluated using voxel-based morphometry (VBM). We assessed the accuracy of VBM using the receiver operating characteristic curve (ROC) and discriminant analysis. Results Compared with HCs, the male adolescent offenders showed significantly reduced GMV in five cortical and subcortical brain regions, including the olfactory cortex, amygdala, middle temporal gyrus and inferior parietal lobe in the left hemisphere, as well as the right superior temporal gyrus. Both ROC curve and discriminate analyses showed that these regions had relatively high sensitivities (58.6%–89.7%) and specificities (58.1%–74.2%) with 76.7% classification accuracy. Conclusions Our results indicated that reduced volume in the frontal-temporal-parietal-subcortical circuit may be closely related to violent behaviors in male adolescents, which might be an important biomarker for detecting violent behaviors in male adolescents.
format: application/pdf
format: text/html
creator: Ying-Dong Zhang
creator: Jian-Song Zhou
creator: Feng-Mei Lu
creator: Xiao-Ping Wang
subject: Neuroscience
subject: Population Biology
description: doi:10.7717/peerj.7349
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Previous studies reported that reduced gray matter volume (GMV) was associated with violent-related behaviors. However, the previous studies were conducted on adults and no study has studied the association between GMV and violent behaviors on adolescents. The purpose of the study was to investigate GMV’s effects in adolescent violent offenders based on a Chinese Han population, which can address the problem of possible confounding factors in adult studies. Methods We recruited 30 male adolescent violent offenders and 29 age- and sex-matched healthy controls (HCs). Differences in both whole-brain and GMV were evaluated using voxel-based morphometry (VBM). We assessed the accuracy of VBM using the receiver operating characteristic curve (ROC) and discriminant analysis. Results Compared with HCs, the male adolescent offenders showed significantly reduced GMV in five cortical and subcortical brain regions, including the olfactory cortex, amygdala, middle temporal gyrus and inferior parietal lobe in the left hemisphere, as well as the right superior temporal gyrus. Both ROC curve and discriminate analyses showed that these regions had relatively high sensitivities (58.6%–89.7%) and specificities (58.1%–74.2%) with 76.7% classification accuracy. Conclusions Our results indicated that reduced volume in the frontal-temporal-parietal-subcortical circuit may be closely related to violent behaviors in male adolescents, which might be an important biomarker for detecting violent behaviors in male adolescents.
bibliographic citation: Zhang et al. (2019) Reduced gray matter volume in male adolescent violent offenders. PeerJ 7:e7349 https://doi.org/10.7717/peerj.7349
date submitted: 2019-05-07
date accepted: 2019-06-25
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ying-Dong
author list: Agent
  family name: Zhou
  given name: Jian-Song
author list: Agent
  family name: Lu
  given name: Feng-Mei
author list: Agent
  family name: Wang
  given name: Xiao-Ping
doi: 10.7717/peerj.7349
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy
type: item
type: AcademicArticle
description: Objective This study aims to identify effective gene networks and biomarkers to predict response and prognosis for HER2-negative breast cancer patients who received sequential taxane-anthracycline neoadjuvant chemotherapy. Materials and Methods Transcriptome data of training dataset including 310 HER2-negative breast cancer who received taxane-anthracycline treatment and an independent validation set with 198 samples were analyzed by weighted gene co-expression network analysis (WGCNA) approach in R language. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed for the selected genes. Module-clinical trait relationships were analyzed to explore the genes and pathways that associated with clinicopathological parameters. Log-rank tests and COX regression were used to identify the prognosis-related genes. Results We found a significant correlation of an expression module with distant relapse–free survival (HR = 0.213, 95% CI [0.131–0.347], P = 4.80E−9). This blue module contained genes enriched in biological process of hormone levels regulation, reproductive system, response to estradiol, cell growth and mammary gland development as well as pathways including estrogen, apelin, cAMP, the PPAR signaling pathway and fatty acid metabolism. From this module, we further screened and validated six hub genes (CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2), the expression of which were significantly associated with both better chemotherapeutic response and favorable survival for BC patients. Conclusion We used WGCNA approach to reveal a gene network that regulate HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy, which enriched in pathways of estrogen signaling, apelin signaling, cAMP signaling, the PPAR signaling pathway and fatty acid metabolism. In addition, genes of CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2 might serve as novel biomarkers predicting chemotherapeutic response and progn…
format: application/pdf
format: text/html
creator: Cui Jiang
creator: Shuo Wu
creator: Lei Jiang
creator: Zhichao Gao
creator: Xiaorui Li
creator: Yangyang Duan
creator: Na Li
creator: Tao Sun
subject: Cell Biology
subject: Genetics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.7515
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Objective This study aims to identify effective gene networks and biomarkers to predict response and prognosis for HER2-negative breast cancer patients who received sequential taxane-anthracycline neoadjuvant chemotherapy. Materials and Methods Transcriptome data of training dataset including 310 HER2-negative breast cancer who received taxane-anthracycline treatment and an independent validation set with 198 samples were analyzed by weighted gene co-expression network analysis (WGCNA) approach in R language. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed for the selected genes. Module-clinical trait relationships were analyzed to explore the genes and pathways that associated with clinicopathological parameters. Log-rank tests and COX regression were used to identify the prognosis-related genes. Results We found a significant correlation of an expression module with distant relapse–free survival (HR = 0.213, 95% CI [0.131–0.347], P = 4.80E−9). This blue module contained genes enriched in biological process of hormone levels regulation, reproductive system, response to estradiol, cell growth and mammary gland development as well as pathways including estrogen, apelin, cAMP, the PPAR signaling pathway and fatty acid metabolism. From this module, we further screened and validated six hub genes (CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2), the expression of which were significantly associated with both better chemotherapeutic response and favorable survival for BC patients. Conclusion We used WGCNA approach to reveal a gene network that regulate HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy, which enriched in pathways of estrogen signaling, apelin signaling, cAMP signaling, the PPAR signaling pathway and fatty acid metabolism. In addition, genes of CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2 might serve as novel biomarkers predicting chemotherapeutic response and progn…
bibliographic citation: Jiang et al. (2019) Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy. PeerJ 7:e7515 https://doi.org/10.7717/peerj.7515
date submitted: 2019-01-15
date accepted: 2019-07-18
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Cui
author list: Agent
  family name: Wu
  given name: Shuo
author list: Agent
  family name: Jiang
  given name: Lei
author list: Agent
  family name: Gao
  given name: Zhichao
author list: Agent
  family name: Li
  given name: Xiaorui
author list: Agent
  family name: Duan
  given name: Yangyang
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Sun
  given name: Tao
doi: 10.7717/peerj.7515
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: ©2019 Jiang et al.
attribution name: Jiang et al.

https://peerj.com/articles/7551
type: item
type: AcademicArticle
title: Non-dinosaurian dinosauromorphs from the Chinle Formation (Upper Triassic) of the Eagle Basin, northern Colorado: Dromomeron romeri (Lagerpetidae) and a new taxon, Kwanasaurus williamparkeri (Silesauridae)
description: The “red siltstone” member of the Upper Triassic Chinle Formation in the Eagle Basin of Colorado contains a diverse assemblage of dinosauromorphs falling outside of Dinosauria. This assemblage is the northernmost known occurrence of non-dinosaurian dinosauromorphs in North America, and probably falls within the Revueltian land vertebrate estimated biochronozone (215–207 Ma, middle to late Norian). Lagerpetids are represented by proximal femora and a humerus referable to Dromomeron romeri. Silesaurids (non-dinosaurian dinosauriforms) are the most commonly recovered dinosauromorph elements, consisting of dentaries, maxillae, isolated teeth, humeri, illia, femora, and possibly a scapula and tibiae. These elements represent a new silesaurid, Kwanasaurus williamparkeri, gen. et sp. nov., which possesses several autapomorphies: a short, very robust maxilla with a broad ascending process, a massive ventromedial process, a complex articular surface for the lacrimal and jugal, and 12 teeth; 14 dentary teeth; an ilium with an elongate and blade-like preacetabular process and concave acetabular margin; a femur with an extremely thin medial distal condyle and a depression on the distal end anterior to the crista tibiofibularis. The recognition of K. williamparkeri further demonstrates the predominantly Late Triassic diversity and widespread geographic distribution across Pangea of the sister clade to Asilisaurus, here named Sulcimentisauria. Silesaurid dentition suggests a variety of dietary specializations from faunivory and omnivory in the Middle Triassic and early Late Triassic (Carnian), to herbivory in the Late Triassic (Carnian and Norian), with the latter specialization possibly coinciding with the radiation of Sulcimentisauria across Pangea. The extremely robust maxilla and folidont teeth of K. williamparkei may represent a strong herbivorous dietary specialization among silesaurids.
format: application/pdf
format: text/html
creator: Jeffrey W. Martz
creator: Bryan J. Small
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7551
publisher: PeerJ Inc.
rights: © 2019 Martz and Small
abstract: The “red siltstone” member of the Upper Triassic Chinle Formation in the Eagle Basin of Colorado contains a diverse assemblage of dinosauromorphs falling outside of Dinosauria. This assemblage is the northernmost known occurrence of non-dinosaurian dinosauromorphs in North America, and probably falls within the Revueltian land vertebrate estimated biochronozone (215–207 Ma, middle to late Norian). Lagerpetids are represented by proximal femora and a humerus referable to Dromomeron romeri. Silesaurids (non-dinosaurian dinosauriforms) are the most commonly recovered dinosauromorph elements, consisting of dentaries, maxillae, isolated teeth, humeri, illia, femora, and possibly a scapula and tibiae. These elements represent a new silesaurid, Kwanasaurus williamparkeri, gen. et sp. nov., which possesses several autapomorphies: a short, very robust maxilla with a broad ascending process, a massive ventromedial process, a complex articular surface for the lacrimal and jugal, and 12 teeth; 14 dentary teeth; an ilium with an elongate and blade-like preacetabular process and concave acetabular margin; a femur with an extremely thin medial distal condyle and a depression on the distal end anterior to the crista tibiofibularis. The recognition of K. williamparkeri further demonstrates the predominantly Late Triassic diversity and widespread geographic distribution across Pangea of the sister clade to Asilisaurus, here named Sulcimentisauria. Silesaurid dentition suggests a variety of dietary specializations from faunivory and omnivory in the Middle Triassic and early Late Triassic (Carnian), to herbivory in the Late Triassic (Carnian and Norian), with the latter specialization possibly coinciding with the radiation of Sulcimentisauria across Pangea. The extremely robust maxilla and folidont teeth of K. williamparkei may represent a strong herbivorous dietary specialization among silesaurids.
bibliographic citation: Martz et al. (2019) Non-dinosaurian dinosauromorphs from the Chinle Formation (Upper Triassic) of the Eagle Basin, northern Colorado: Dromomeron romeri (Lagerpetidae) and a new taxon, Kwanasaurus williamparkeri (Silesauridae). PeerJ 7:e7551 https://doi.org/10.7717/peerj.7551
date submitted: 2019-04-24
date accepted: 2019-07-25
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martz
  given name: Jeffrey W.
author list: Agent
  family name: Small
  given name: Bryan J.
doi: 10.7717/peerj.7551
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: © 2019 Martz and Small
attribution name: Martz and Small

Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem
type: item
type: AcademicArticle
description: Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.
format: application/pdf
format: text/html
creator: Alexander May
creator: Shrinath Narayanan
creator: Joe Alcock
creator: Arvind Varsani
creator: Carlo Maley
creator: Athena Aktipis
subject: Evolutionary Studies
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.7565
publisher: PeerJ Inc.
rights: © 2019 May et al.
abstract: Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.
bibliographic citation: May et al. (2019) Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 7:e7565 https://doi.org/10.7717/peerj.7565
date submitted: 2019-03-13
date accepted: 2019-07-29
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: May
  given name: Alexander
author list: Agent
  family name: Narayanan
  given name: Shrinath
author list: Agent
  family name: Alcock
  given name: Joe
author list: Agent
  family name: Varsani
  given name: Arvind
author list: Agent
  family name: Maley
  given name: Carlo
author list: Agent
  family name: Aktipis
  given name: Athena
doi: 10.7717/peerj.7565
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: © 2019 May et al.
attribution name: May et al.

Effects of reflective warning markers on wildlife
type: item
type: AcademicArticle
description: Light pollution has become one of the top issues in environmental pollution, especially concerning how secondary light pollution, such as from traffic reflective materials, influences animal distribution and behavior. In this study, 15 camera traps were set up at sites with or without reflective warning markers (RWM) in coniferous forests on Cangshan Mountain located in Dali Prefecture, China. The results showed that the number of independent photographs and species at sites without RWMs were significantly higher than those at sites with RWMs. Significant differences were found between daytime and nighttime composition of bird species and non-flying mammals between two sites. This study found that RWMs had negative effects on wildlife, with the avoidance response of birds to RWMs being more obvious than that of animals at daytime. It is recommended that the use of reflective materials be carefully considered, especially in protected areas.
format: application/pdf
format: text/html
creator: Yi-Hao Fang
creator: Ying Gao
creator: Yin Yang
creator: Kun Tan
creator: Yan-Peng Li
creator: Guo-Peng Ren
creator: Zhi-Pang Huang
creator: Liang-Wei Cui
creator: Wen Xiao
subject: Biodiversity
subject: Conservation Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.7614
publisher: PeerJ Inc.
rights: © 2019 Fang et al.
abstract: Light pollution has become one of the top issues in environmental pollution, especially concerning how secondary light pollution, such as from traffic reflective materials, influences animal distribution and behavior. In this study, 15 camera traps were set up at sites with or without reflective warning markers (RWM) in coniferous forests on Cangshan Mountain located in Dali Prefecture, China. The results showed that the number of independent photographs and species at sites without RWMs were significantly higher than those at sites with RWMs. Significant differences were found between daytime and nighttime composition of bird species and non-flying mammals between two sites. This study found that RWMs had negative effects on wildlife, with the avoidance response of birds to RWMs being more obvious than that of animals at daytime. It is recommended that the use of reflective materials be carefully considered, especially in protected areas.
bibliographic citation: Fang et al. (2019) Effects of reflective warning markers on wildlife. PeerJ 7:e7614 https://doi.org/10.7717/peerj.7614
date submitted: 2019-03-22
date accepted: 2019-08-05
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Yi-Hao
author list: Agent
  family name: Gao
  given name: Ying
author list: Agent
  family name: Yang
  given name: Yin
author list: Agent
  family name: Tan
  given name: Kun
author list: Agent
  family name: Li
  given name: Yan-Peng
author list: Agent
  family name: Ren
  given name: Guo-Peng
author list: Agent
  family name: Huang
  given name: Zhi-Pang
author list: Agent
  family name: Cui
  given name: Liang-Wei
author list: Agent
  family name: Xiao
  given name: Wen
doi: 10.7717/peerj.7614
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: ©2019 Fang et al.
attribution name: Fang et al.

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