PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland
items: Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates
items: Autophagy-related prognostic signature for survival prediction of triple negative breast cancer
items: Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses
items: Cyber-victimization and its association with depression among Vietnamese adolescents
items: https://peerj.com/articles/12913
items: Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma
items: External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection
items: Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889
items: A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus

Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland
type: item
type: AcademicArticle
description: Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimii Steininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland.
format: application/pdf
format: text/html
creator: William I. Ausich
creator: Mariusz A. Salamon
creator: Bartosz J. Płachno
creator: Tomasz Brachaniec
creator: Wojciech Krawczyński
creator: Andrzej Boczarowski
creator: Karolina Paszcza
creator: Magdalena Łukowiak
creator: Przemysław Gorzelak
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.12842
publisher: PeerJ Inc.
rights: © 2022 Ausich et al.
abstract: Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimii Steininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland.
bibliographic citation: Ausich et al. (2022) Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland. PeerJ 10:e12842 https://doi.org/10.7717/peerj.12842
date submitted: 2021-12-13
date accepted: 2022-01-06
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ausich
  given name: William I.
author list: Agent
  family name: Salamon
  given name: Mariusz A.
author list: Agent
  family name: Płachno
  given name: Bartosz J.
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Krawczyński
  given name: Wojciech
author list: Agent
  family name: Boczarowski
  given name: Andrzej
author list: Agent
  family name: Paszcza
  given name: Karolina
author list: Agent
  family name: Łukowiak
  given name: Magdalena
author list: Agent
  family name: Gorzelak
  given name: Przemysław
doi: 10.7717/peerj.12842
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Ausich et al.
attribution name: Ausich et al.

Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates
type: item
type: AcademicArticle
description: Inhibitory control, the ability to override an inappropriate prepotent response, is crucial in many aspects of everyday life. However, the various paradigms designed to measure inhibitory control often suffer from a lack of systematic validation and have yielded mixed results. Thus the nature of this ability remains unclear, is it a general construct or a family of distinct sub-components? Therefore, the aim of this study was first to demonstrate the content validity and the temporal repeatability of a battery of inhibitory control tasks. Then we wanted to assess the contextual consistency of performances between these tasks to better understand the structure of inhibitory control. We tested 21 rhesus macaques (Macaca mulatta, 12 males, nine females) in a battery of touchscreen tasks assessing three main components of inhibitory control: inhibition of a distraction (using a Distraction task), inhibition of an impulsive action (using a Go/No-go task) and inhibition of a cognitive set (using a Reversal learning task). All tasks were reliable and effective at measuring the inhibition of a prepotent response. However, while there was consistency of performance between the inhibition of a distraction and the inhibition of an action, representing a response-driven basic form of inhibition, this was not found for the inhibition of a cognitive set. We argue that the inhibition of a cognitive set is a more cognitively demanding form of inhibition. This study gives a new insight in the multifaceted structure of inhibitory control and highlights the importance of a systematic validation of cognitive tasks in animal cognition.
format: application/pdf
format: text/html
creator: Louise Loyant
creator: Bridget M. Waller
creator: Jérôme Micheletta
creator: Marine Joly
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.12863
publisher: PeerJ Inc.
rights: © 2022 Loyant et al.
abstract: Inhibitory control, the ability to override an inappropriate prepotent response, is crucial in many aspects of everyday life. However, the various paradigms designed to measure inhibitory control often suffer from a lack of systematic validation and have yielded mixed results. Thus the nature of this ability remains unclear, is it a general construct or a family of distinct sub-components? Therefore, the aim of this study was first to demonstrate the content validity and the temporal repeatability of a battery of inhibitory control tasks. Then we wanted to assess the contextual consistency of performances between these tasks to better understand the structure of inhibitory control. We tested 21 rhesus macaques (Macaca mulatta, 12 males, nine females) in a battery of touchscreen tasks assessing three main components of inhibitory control: inhibition of a distraction (using a Distraction task), inhibition of an impulsive action (using a Go/No-go task) and inhibition of a cognitive set (using a Reversal learning task). All tasks were reliable and effective at measuring the inhibition of a prepotent response. However, while there was consistency of performance between the inhibition of a distraction and the inhibition of an action, representing a response-driven basic form of inhibition, this was not found for the inhibition of a cognitive set. We argue that the inhibition of a cognitive set is a more cognitively demanding form of inhibition. This study gives a new insight in the multifaceted structure of inhibitory control and highlights the importance of a systematic validation of cognitive tasks in animal cognition.
bibliographic citation: Loyant et al. (2022) Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates. PeerJ 10:e12863 https://doi.org/10.7717/peerj.12863
date submitted: 2021-09-28
date accepted: 2022-01-09
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loyant
  given name: Louise
author list: Agent
  family name: Waller
  given name: Bridget M.
author list: Agent
  family name: Micheletta
  given name: Jérôme
author list: Agent
  family name: Joly
  given name: Marine
doi: 10.7717/peerj.12863
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: © 2022 Loyant et al.
attribution name: Loyant et al.

Autophagy-related prognostic signature for survival prediction of triple negative breast cancer
type: item
type: AcademicArticle
description: Background Triple-negative breast cancer (TNBC) is a highly aggressive type of cancer with few available treatment methods. The aim of the current study was to provide a prognostic autophagy-related gene (ARG) model to predict the outcomes for TNBC patients using bioinformatic analysis. Methods mRNA expression data and its clinical information for TNBC samples obtained from The Cancer Genome Atlas (TCGA) and Metabric databases were extracted for bioinformatic analysis. Differentially expressed autophagy genes were identified using the Wilcoxon rank sum test in R software. ARGs were downloaded from the Human Autophagy Database. The Kaplan–Meier plotter was employed to determine the prognostic significance of the ARGs. The sample splitting method and Cox regression analysis were employed to establish the risk model and to demonstrate the association between the ARGs and the survival duration. The corresponding ARG-transcription factor interaction network was visualized using the Cytoscape software. Results A signature-based risk score model was established for eight genes (ITGA3, HSPA8, CTSD, ATG12, CLN3, ATG7, MAP1LC3C, and WIPI1) using the TCGA data and the model was validated with the GSE38959 and Metabric datasets, respectively. Patients with high risk scores had worse survival outcomes than those with low risk scores. Of note, amplification of ATG12 and reduction of WIPI were confirmed to be significantly correlated with the clinical stage of TNBC. Conclusion An eight-gene autophagic signature model was developed in this study to predict the survival risk for TNBC. The genes identified in the study may favor the design of target agents for autophagy control in advanced TNBC.
format: application/pdf
format: text/html
creator: Qiong Yang
creator: Kewang Sun
creator: Wenjie Xia
creator: Ying Li
creator: Miaochun Zhong
creator: Kefeng Lei
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.12878
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background Triple-negative breast cancer (TNBC) is a highly aggressive type of cancer with few available treatment methods. The aim of the current study was to provide a prognostic autophagy-related gene (ARG) model to predict the outcomes for TNBC patients using bioinformatic analysis. Methods mRNA expression data and its clinical information for TNBC samples obtained from The Cancer Genome Atlas (TCGA) and Metabric databases were extracted for bioinformatic analysis. Differentially expressed autophagy genes were identified using the Wilcoxon rank sum test in R software. ARGs were downloaded from the Human Autophagy Database. The Kaplan–Meier plotter was employed to determine the prognostic significance of the ARGs. The sample splitting method and Cox regression analysis were employed to establish the risk model and to demonstrate the association between the ARGs and the survival duration. The corresponding ARG-transcription factor interaction network was visualized using the Cytoscape software. Results A signature-based risk score model was established for eight genes (ITGA3, HSPA8, CTSD, ATG12, CLN3, ATG7, MAP1LC3C, and WIPI1) using the TCGA data and the model was validated with the GSE38959 and Metabric datasets, respectively. Patients with high risk scores had worse survival outcomes than those with low risk scores. Of note, amplification of ATG12 and reduction of WIPI were confirmed to be significantly correlated with the clinical stage of TNBC. Conclusion An eight-gene autophagic signature model was developed in this study to predict the survival risk for TNBC. The genes identified in the study may favor the design of target agents for autophagy control in advanced TNBC.
bibliographic citation: Yang et al. (2022) Autophagy-related prognostic signature for survival prediction of triple negative breast cancer. PeerJ 10:e12878 https://doi.org/10.7717/peerj.12878
date submitted: 2020-05-14
date accepted: 2022-01-12
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Qiong
author list: Agent
  family name: Sun
  given name: Kewang
author list: Agent
  family name: Xia
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Zhong
  given name: Miaochun
author list: Agent
  family name: Lei
  given name: Kefeng
doi: 10.7717/peerj.12878
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses
type: item
type: AcademicArticle
description: Background The ability to maintain sufficient oxygen levels in the belowground tissues and the rhizosphere is crucial for the growth and survival of seagrasses in habitats with highly reduced sediment. Such ability varies depending on plant anatomical features and environmental conditions. Methods In the present study, we compared anatomical structures of roots, rhizomes and leaves of the tropical intertidal seagrasses, Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis, followed by an investigation of their gas exchange both in the belowground and aboveground tissues and photosynthetic electron transport rates (ETR) in response to experimental manipulations of O2 level (normoxia and root hypoxia) and temperature (30 °C and 40 °C). Results We found that C. rotundata and T. hemprichii displayed mostly comparable anatomical structures, whereas H. ovalis displayed various distinctive features, including leaf porosity, number and size of lacunae in roots and rhizomes and structure of radial O2 loss (ROL) barrier. H. ovalis also showed unique responses to root hypoxia and heat stress. Root hypoxia increased O2 release from belowground tissues and overall photosynthetic activity of H. ovalis but did not affect the other two seagrasses. More pronounced warming effects were detected in H. ovalis, measured as lower O2 release in the belowground tissues and overall photosynthetic capacity (O2 release and dissolved inorganic carbon uptake in the light and ETR). High temperature inhibited photosynthesis of C. rotundata and T. hemprichii but did not affect their O2 release in belowground tissues. Our data show that seagrasses inhabiting the same area respond differently to root hypoxia and temperature, possibly due to their differences in anatomical and physiological attributes. Halophila ovalis is highly dependent on photosynthesis and appears to be the most sensitive species with the highest tendency of O2 loss in hypoxic sediment. At the same time, its root oxidat…
format: application/pdf
format: text/html
creator: Sutthinut Soonthornkalump
creator: Yan Xiang Ow
creator: Chanida Saewong
creator: Pimchanok Buapet
subject: Marine Biology
subject: Plant Science
subject: Histology
subject: Biological Oceanography
description: doi:10.7717/peerj.12899
publisher: PeerJ Inc.
rights: © 2022 Soonthornkalump et al.
abstract: Background The ability to maintain sufficient oxygen levels in the belowground tissues and the rhizosphere is crucial for the growth and survival of seagrasses in habitats with highly reduced sediment. Such ability varies depending on plant anatomical features and environmental conditions. Methods In the present study, we compared anatomical structures of roots, rhizomes and leaves of the tropical intertidal seagrasses, Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis, followed by an investigation of their gas exchange both in the belowground and aboveground tissues and photosynthetic electron transport rates (ETR) in response to experimental manipulations of O2 level (normoxia and root hypoxia) and temperature (30 °C and 40 °C). Results We found that C. rotundata and T. hemprichii displayed mostly comparable anatomical structures, whereas H. ovalis displayed various distinctive features, including leaf porosity, number and size of lacunae in roots and rhizomes and structure of radial O2 loss (ROL) barrier. H. ovalis also showed unique responses to root hypoxia and heat stress. Root hypoxia increased O2 release from belowground tissues and overall photosynthetic activity of H. ovalis but did not affect the other two seagrasses. More pronounced warming effects were detected in H. ovalis, measured as lower O2 release in the belowground tissues and overall photosynthetic capacity (O2 release and dissolved inorganic carbon uptake in the light and ETR). High temperature inhibited photosynthesis of C. rotundata and T. hemprichii but did not affect their O2 release in belowground tissues. Our data show that seagrasses inhabiting the same area respond differently to root hypoxia and temperature, possibly due to their differences in anatomical and physiological attributes. Halophila ovalis is highly dependent on photosynthesis and appears to be the most sensitive species with the highest tendency of O2 loss in hypoxic sediment. At the same time, its root oxidat…
bibliographic citation: Soonthornkalump et al. (2022) Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses. PeerJ 10:e12899 https://doi.org/10.7717/peerj.12899
date submitted: 2021-10-01
date accepted: 2022-01-17
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soonthornkalump
  given name: Sutthinut
author list: Agent
  family name: Ow
  given name: Yan Xiang
author list: Agent
  family name: Saewong
  given name: Chanida
author list: Agent
  family name: Buapet
  given name: Pimchanok
doi: 10.7717/peerj.12899
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: © 2022 Soonthornkalump et al.
attribution name: Soonthornkalump et al.

Cyber-victimization and its association with depression among Vietnamese adolescents
type: item
type: AcademicArticle
description: Background Cyberbullying has become an alarming social issue, but little is known about its prevalence and consequences in many countries. This study investigated the prevalence of cyber-victimization and its association with depression among students in Ho Chi Minh City, Vietnam. Methods A cross-sectional study was conducted in 1,492 students from eight secondary schools and high schools in four urban and suburban areas. Multi-stage cluster sampling approach was used to recruit participants. Students participated in this study on a voluntary basis and completed a self-report questionnaire that included validated scales to measure their experience of cyber-bullying (Cyber Bullying Scale) and symptoms of depression (Center for Epidemiologic Studies–Depression Scale). Weighted logistic regression analysis was used to adjust for the cluster effect and sampling probability. Results Almost all (92.4%) students reported using the internet everyday and nearly 40% used internet for more than four hours per day. Cyber-victimization was identified in 36.5% of students and almost 25% experienced multiple types of cyber-victimization. Nearly half of students reported symptoms of depression. After adjusting for other covariates, students who experienced cyber-victimization were found to have 1.81 times (95% CI [1.42–2.30]) higher in odds of having symptoms of depression. Conclusions Cyber victimization and depression are both common in Vietnamese adolescents. Those who experienced cyber bullying have a higher likelihood of having symptoms of depression. These findings indicate an urgent need for interventions and policies targeting this emerging type of bullying in Vietnam and similar settings due to its potential harmful effects on adolescents’ health.
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creator: Truc Thanh Thai
creator: Mai Huynh Thi Duong
creator: Duy Kim Vo
creator: Ngan Thien Thi Dang
creator: Quynh Ngoc Ho Huynh
creator: Huong Giang Nguyen Tran
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12907
publisher: PeerJ Inc.
rights: © 2022 Thai et al.
abstract: Background Cyberbullying has become an alarming social issue, but little is known about its prevalence and consequences in many countries. This study investigated the prevalence of cyber-victimization and its association with depression among students in Ho Chi Minh City, Vietnam. Methods A cross-sectional study was conducted in 1,492 students from eight secondary schools and high schools in four urban and suburban areas. Multi-stage cluster sampling approach was used to recruit participants. Students participated in this study on a voluntary basis and completed a self-report questionnaire that included validated scales to measure their experience of cyber-bullying (Cyber Bullying Scale) and symptoms of depression (Center for Epidemiologic Studies–Depression Scale). Weighted logistic regression analysis was used to adjust for the cluster effect and sampling probability. Results Almost all (92.4%) students reported using the internet everyday and nearly 40% used internet for more than four hours per day. Cyber-victimization was identified in 36.5% of students and almost 25% experienced multiple types of cyber-victimization. Nearly half of students reported symptoms of depression. After adjusting for other covariates, students who experienced cyber-victimization were found to have 1.81 times (95% CI [1.42–2.30]) higher in odds of having symptoms of depression. Conclusions Cyber victimization and depression are both common in Vietnamese adolescents. Those who experienced cyber bullying have a higher likelihood of having symptoms of depression. These findings indicate an urgent need for interventions and policies targeting this emerging type of bullying in Vietnam and similar settings due to its potential harmful effects on adolescents’ health.
bibliographic citation: Thai et al. (2022) Cyber-victimization and its association with depression among Vietnamese adolescents. PeerJ 10:e12907 https://doi.org/10.7717/peerj.12907
date submitted: 2021-09-10
date accepted: 2022-01-18
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thai
  given name: Truc Thanh
author list: Agent
  family name: Duong
  given name: Mai Huynh Thi
author list: Agent
  family name: Vo
  given name: Duy Kim
author list: Agent
  family name: Dang
  given name: Ngan Thien Thi
author list: Agent
  family name: Huynh
  given name: Quynh Ngoc Ho
author list: Agent
  family name: Tran
  given name: Huong Giang Nguyen
doi: 10.7717/peerj.12907
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Thai et al.
attribution name: Thai et al.

https://peerj.com/articles/12913
type: item
type: AcademicArticle
title: On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum
description: The weevil genus Leschenius del Río (Curculionidae: Entiminae: Naupactini) is distributed in the northern Andes, in Colombia and Ecuador. Among its species, L. vulcanorum stands out as an important pest of potatoes in its parthenogenetic form, which is known as “tiroteador de la papa”. In this study, the adult male and the larval stage (first and mature larvae) of L. vulcanorun are described and illustrated for the first time. A description of the male of Leschenius bifurcatus is also provided. A new bisexual species was discovered, Leschenius ventrilingulatus sp. nov., and is described from Ecuador. An updated phylogenetic analysis was performed, including the new species, with results indicating a sister group relationship between L. ventrilingulatus and L. vulcanorum. They can be distinguished because the former is usually of smaller size and is covered by denser and thicker setae, has shorter antennae, a subcylindrical shape of the pronotum, shorter elytra (about 1.5×longer than wide at base), the female has ventrite 4 with a posterior rounded projection, and posterior margin of ventrite 5 subacute, not excavated. This paper also includes lectotype designations, a revised key to all known species of Leschenius, habitus photos of males and females, illustrations of genitalia, and a distribution map.
format: application/pdf
format: text/html
creator: María Guadalupe del Río
creator: Adriana E. Marvaldi
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12913
publisher: PeerJ Inc.
rights: © 2022 del Río and Marvaldi
abstract: The weevil genus Leschenius del Río (Curculionidae: Entiminae: Naupactini) is distributed in the northern Andes, in Colombia and Ecuador. Among its species, L. vulcanorum stands out as an important pest of potatoes in its parthenogenetic form, which is known as “tiroteador de la papa”. In this study, the adult male and the larval stage (first and mature larvae) of L. vulcanorun are described and illustrated for the first time. A description of the male of Leschenius bifurcatus is also provided. A new bisexual species was discovered, Leschenius ventrilingulatus sp. nov., and is described from Ecuador. An updated phylogenetic analysis was performed, including the new species, with results indicating a sister group relationship between L. ventrilingulatus and L. vulcanorum. They can be distinguished because the former is usually of smaller size and is covered by denser and thicker setae, has shorter antennae, a subcylindrical shape of the pronotum, shorter elytra (about 1.5×longer than wide at base), the female has ventrite 4 with a posterior rounded projection, and posterior margin of ventrite 5 subacute, not excavated. This paper also includes lectotype designations, a revised key to all known species of Leschenius, habitus photos of males and females, illustrations of genitalia, and a distribution map.
bibliographic citation: del Río et al. (2022) On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum. PeerJ 10:e12913 https://doi.org/10.7717/peerj.12913
date submitted: 2021-11-26
date accepted: 2022-01-19
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: del Río
  given name: María Guadalupe
author list: Agent
  family name: Marvaldi
  given name: Adriana E.
doi: 10.7717/peerj.12913
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 del Río and Marvaldi
attribution name: del Río and Marvaldi

Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma
type: item
type: AcademicArticle
description: Purpose Multiple myeloma (MM), a kind of malignant neoplasm of clonal plasma cells in the bone marrow, is a refractory disease. Understanding the metabolism disorders and identification of metabolomics pathways as well as key metabolites will provide new insights for exploring diagnosis and therapeutic targets of MM. Methods We conducted nontargeted metabolomics analysis of MM patients and normal controls (NC) using ultra-high-performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF-MS) in 40 cases of cohort 1 subjects. The targeted metabolomics analysis of amino acids using multiple reaction monitoring-mass spectrometry (MRM-MS) was also performed in 30 cases of cohort 1 and 30 cases of cohort 2 participants, to comprehensively investigate the metabolomics disorders of MM. Results The nontargeted metabolomics analysis in cohort 1 indicated that there was a significant metabolic signature change between MM patients and NC. The differential metabolites were mainly enriched in metabolic pathways related to amino acid metabolism, such as protein digestion and absorption, and biosynthesis of amino acids. Further, the targeted metabolomics analysis of amino acids in both cohort 1 and cohort 2 revealed differential metabolic profiling between MM patients and NC. We identified 12 and 14 amino acid metabolites with altered abundance in MM patients compared to NC subjects, in cohort 1 and cohort 2, respectively. Besides, key differential amino acid metabolites, such as choline, creatinine, leucine, tryptophan, and valine, may discriminate MM patients from NC. Moreover, the differential amino acid metabolites were associated with clinical indicators of MM patients. Conclusions Our findings indicate that amino acid metabolism disorders are involved in MM. The differential profiles reveal the potential utility of key amino acid metabolites as diagnostic biomarkers of MM. The alterations in metabolome, especially the amino acid m…
format: application/pdf
format: text/html
creator: Lingling Yue
creator: Pengyun Zeng
creator: Yanhong Li
creator: Ye Chai
creator: Chongyang Wu
creator: Bingren Gao
subject: Molecular Biology
subject: Oncology
subject: Orthopedics
subject: Pathology
subject: Metabolic Sciences
description: doi:10.7717/peerj.12918
publisher: PeerJ Inc.
rights: © 2022 Yue et al.
abstract: Purpose Multiple myeloma (MM), a kind of malignant neoplasm of clonal plasma cells in the bone marrow, is a refractory disease. Understanding the metabolism disorders and identification of metabolomics pathways as well as key metabolites will provide new insights for exploring diagnosis and therapeutic targets of MM. Methods We conducted nontargeted metabolomics analysis of MM patients and normal controls (NC) using ultra-high-performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF-MS) in 40 cases of cohort 1 subjects. The targeted metabolomics analysis of amino acids using multiple reaction monitoring-mass spectrometry (MRM-MS) was also performed in 30 cases of cohort 1 and 30 cases of cohort 2 participants, to comprehensively investigate the metabolomics disorders of MM. Results The nontargeted metabolomics analysis in cohort 1 indicated that there was a significant metabolic signature change between MM patients and NC. The differential metabolites were mainly enriched in metabolic pathways related to amino acid metabolism, such as protein digestion and absorption, and biosynthesis of amino acids. Further, the targeted metabolomics analysis of amino acids in both cohort 1 and cohort 2 revealed differential metabolic profiling between MM patients and NC. We identified 12 and 14 amino acid metabolites with altered abundance in MM patients compared to NC subjects, in cohort 1 and cohort 2, respectively. Besides, key differential amino acid metabolites, such as choline, creatinine, leucine, tryptophan, and valine, may discriminate MM patients from NC. Moreover, the differential amino acid metabolites were associated with clinical indicators of MM patients. Conclusions Our findings indicate that amino acid metabolism disorders are involved in MM. The differential profiles reveal the potential utility of key amino acid metabolites as diagnostic biomarkers of MM. The alterations in metabolome, especially the amino acid m…
bibliographic citation: Yue et al. (2022) Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma. PeerJ 10:e12918 https://doi.org/10.7717/peerj.12918
date submitted: 2021-07-05
date accepted: 2022-01-20
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Lingling
author list: Agent
  family name: Zeng
  given name: Pengyun
author list: Agent
  family name: Li
  given name: Yanhong
author list: Agent
  family name: Chai
  given name: Ye
author list: Agent
  family name: Wu
  given name: Chongyang
author list: Agent
  family name: Gao
  given name: Bingren
doi: 10.7717/peerj.12918
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Yue et al.
attribution name: Yue et al.

External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection
type: item
type: AcademicArticle
description: Background No postoperative cardiopulmonary morbidity models have been developed or validated in Chinese patients with lung resection. This study aims to externally validate five predictive models, including Eurolung models, the Brunelli model and the Age-adjusted Charlson Comorbidity Index, in a Chinese population. Methods Patients with lung cancer who underwent anatomic lung resection between 2018/09/01 and 2019/08/31 in our center were involved. Model discrimination was assessed by the area under the receiver operating characteristic curve. Model calibration was evaluated by the Hosmer–Lemeshow test. Calibration curves were plotted. Specificity, sensitivity, negative predictive value, positive predictive value and accuracy were calculated. Model updating was achieved by re-estimating the intercept and/or the slope of the linear predictor and re-estimating all coefficients. Results Among 1085 patients, 91 patients had postoperative cardiopulmonary complications defined by the European Society of Thoracic Surgeons. For original models, only parsimonious Eurolung1 had acceptable discrimination (area under the receiver operating characteristic curve = 0.688, 95% confidence interval 0.630–0.745) and calibration (p = 0.23 > 0.05) abilities simultaneously. Its sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 0.700, 0.649, 0.153, 0.960 and 0.653, respectively. In the secondary analysis, increased pleural effusion (n = 94), which was nonchylous and nonpurulent, was labeled as a kind of postoperative complication. The area under the receiver operating characteristic curve of the models increased slightly, but all models were miscalibrated. The original Eurolung1 model had the highest discrimination ability but poor calibration, and thus it was updated by three methods. After model updating, new models showed good calibration and small improvements in discrimination. The discrimination ability was still merely acceptable. Conc…
format: application/pdf
format: text/html
creator: Guanghua Huang
creator: Lei Liu
creator: Luyi Wang
creator: Zhile Wang
creator: Zhaojian Wang
creator: Shanqing Li
subject: Oncology
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12936
publisher: PeerJ Inc.
rights: © 2022 Huang et al.
abstract: Background No postoperative cardiopulmonary morbidity models have been developed or validated in Chinese patients with lung resection. This study aims to externally validate five predictive models, including Eurolung models, the Brunelli model and the Age-adjusted Charlson Comorbidity Index, in a Chinese population. Methods Patients with lung cancer who underwent anatomic lung resection between 2018/09/01 and 2019/08/31 in our center were involved. Model discrimination was assessed by the area under the receiver operating characteristic curve. Model calibration was evaluated by the Hosmer–Lemeshow test. Calibration curves were plotted. Specificity, sensitivity, negative predictive value, positive predictive value and accuracy were calculated. Model updating was achieved by re-estimating the intercept and/or the slope of the linear predictor and re-estimating all coefficients. Results Among 1085 patients, 91 patients had postoperative cardiopulmonary complications defined by the European Society of Thoracic Surgeons. For original models, only parsimonious Eurolung1 had acceptable discrimination (area under the receiver operating characteristic curve = 0.688, 95% confidence interval 0.630–0.745) and calibration (p = 0.23 > 0.05) abilities simultaneously. Its sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 0.700, 0.649, 0.153, 0.960 and 0.653, respectively. In the secondary analysis, increased pleural effusion (n = 94), which was nonchylous and nonpurulent, was labeled as a kind of postoperative complication. The area under the receiver operating characteristic curve of the models increased slightly, but all models were miscalibrated. The original Eurolung1 model had the highest discrimination ability but poor calibration, and thus it was updated by three methods. After model updating, new models showed good calibration and small improvements in discrimination. The discrimination ability was still merely acceptable. Conc…
bibliographic citation: Huang et al. (2022) External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection. PeerJ 10:e12936 https://doi.org/10.7717/peerj.12936
date submitted: 2021-12-17
date accepted: 2022-01-23
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Guanghua
author list: Agent
  family name: Liu
  given name: Lei
author list: Agent
  family name: Wang
  given name: Luyi
author list: Agent
  family name: Wang
  given name: Zhile
author list: Agent
  family name: Wang
  given name: Zhaojian
author list: Agent
  family name: Li
  given name: Shanqing
doi: 10.7717/peerj.12936
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Huang et al.
attribution name: Huang et al.

Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889
type: item
type: AcademicArticle
description: For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the …
format: application/pdf
format: text/html
creator: Tina N. Molodtsova
creator: Dennis M. Opresko
creator: Daniel Wagner
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
subject: Taxonomy
subject: Biological Oceanography
description: doi:10.7717/peerj.12638
publisher: PeerJ Inc.
rights: © 2022 Molodtsova et al.
abstract: For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the …
bibliographic citation: Molodtsova et al. (2022) Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889. PeerJ 10:e12638 https://doi.org/10.7717/peerj.12638
date submitted: 2021-03-25
date accepted: 2021-11-24
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Molodtsova
  given name: Tina N.
author list: Agent
  family name: Opresko
  given name: Dennis M.
author list: Agent
  family name: Wagner
  given name: Daniel
doi: 10.7717/peerj.12638
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: © 2022 Molodtsova et al.
attribution name: Molodtsova et al.

A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus
type: item
type: AcademicArticle
description: A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus—Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
format: application/pdf
format: text/html
creator: Jhon Jairo Ospina Sarria
creator: David Andrés Velásquez Trujillo
creator: Christian Oswaldo Castaño Saavedra
creator: Luis Fernando Castillo
creator: Wilmar Bolívar-García
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12765
publisher: PeerJ Inc.
rights: © 2022 Ospina Sarria et al.
abstract: A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus—Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
bibliographic citation: Ospina Sarria et al. (2022) A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus. PeerJ 10:e12765 https://doi.org/10.7717/peerj.12765
date submitted: 2021-08-25
date accepted: 2021-12-17
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ospina Sarria
  given name: Jhon Jairo
author list: Agent
  family name: Velásquez Trujillo
  given name: David Andrés
author list: Agent
  family name: Castaño Saavedra
  given name: Christian Oswaldo
author list: Agent
  family name: Castillo
  given name: Luis Fernando
author list: Agent
  family name: Bolívar-García
  given name: Wilmar
doi: 10.7717/peerj.12765
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Ospina Sarria et al.
attribution name: Ospina Sarria et al.

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