PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia
items: Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae)
items: Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines
items: Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia
items: On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton
items: Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma
items: Going rogue: what scientists can learn about Twitter communication from “alt” government accounts
items: Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery
items: Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea
items: Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics

Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia
type: item
type: AcademicArticle
description: Background Punicalagin is the major phenolic compound found in pomegranate peels. It has several reported medical benefits, including antioxidant, anti-inflammatory, and anticancer properties. The present study investigated the anti-leukemic effects and the molecular mechanism of punicalagin on NB4 and MOLT-4 leukemic cell lines. Methods Leukemic cells were treated with punicalagin and cell viability was determined using MTS assay. Apoptosis and autophagy were analyzed by flow cytometry using Annexin V-FITC/PI and anti-LC3/FITC antibodies staining, respectively. Apoptotic and autophagic mRNA expression were determined using reverse transcription-quantitative PCR. STITCH bioinformatics tools were used to predict the interaction between punicalagin and its proposed target proteins. Results Results indicated that punicalagin decreased NB4 and MOLT-4 cell viability in a dose-dependent manner. Punicalagin, in combination with daunorubicin, exhibited synergistic cytotoxic effects. Punicalagin induced apoptosis through the upregulation of caspase-3/-8/-9, Bax and the downregulation of Bcl-2 expression. Punicalagin also promoted autophagy via the downregulation of mTOR and the upregulation of ULK1 expression. Cyclooxygenase-2 and toll-like receptor 4 were found to be involved in punicalagin-induced cell death in punicalagin-targeted protein interactions. Conclusions These results suggest that punicalagin exerts cytotoxic activities by suppressing proliferation and promoting apoptosis and autophagy by activating the caspase cascade, altering Bax and Bcl-2, and regulating autophagy via mTOR/ULK1 signaling.
format: application/pdf
format: text/html
creator: Paweena Subkorn
creator: Chosita Norkaew
creator: Kamolchanok Deesrisak
creator: Dalina Tanyong
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.12303
publisher: PeerJ Inc.
rights: © 2021 Subkorn et al.
abstract: Background Punicalagin is the major phenolic compound found in pomegranate peels. It has several reported medical benefits, including antioxidant, anti-inflammatory, and anticancer properties. The present study investigated the anti-leukemic effects and the molecular mechanism of punicalagin on NB4 and MOLT-4 leukemic cell lines. Methods Leukemic cells were treated with punicalagin and cell viability was determined using MTS assay. Apoptosis and autophagy were analyzed by flow cytometry using Annexin V-FITC/PI and anti-LC3/FITC antibodies staining, respectively. Apoptotic and autophagic mRNA expression were determined using reverse transcription-quantitative PCR. STITCH bioinformatics tools were used to predict the interaction between punicalagin and its proposed target proteins. Results Results indicated that punicalagin decreased NB4 and MOLT-4 cell viability in a dose-dependent manner. Punicalagin, in combination with daunorubicin, exhibited synergistic cytotoxic effects. Punicalagin induced apoptosis through the upregulation of caspase-3/-8/-9, Bax and the downregulation of Bcl-2 expression. Punicalagin also promoted autophagy via the downregulation of mTOR and the upregulation of ULK1 expression. Cyclooxygenase-2 and toll-like receptor 4 were found to be involved in punicalagin-induced cell death in punicalagin-targeted protein interactions. Conclusions These results suggest that punicalagin exerts cytotoxic activities by suppressing proliferation and promoting apoptosis and autophagy by activating the caspase cascade, altering Bax and Bcl-2, and regulating autophagy via mTOR/ULK1 signaling.
bibliographic citation: Subkorn et al. (2021) Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia. PeerJ 9:e12303 https://doi.org/10.7717/peerj.12303
date submitted: 2021-03-22
date accepted: 2021-09-22
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Subkorn
  given name: Paweena
author list: Agent
  family name: Norkaew
  given name: Chosita
author list: Agent
  family name: Deesrisak
  given name: Kamolchanok
author list: Agent
  family name: Tanyong
  given name: Dalina
doi: 10.7717/peerj.12303
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Subkorn et al.
attribution name: Subkorn et al.

Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae)
type: item
type: AcademicArticle
description: Metrics to assess relative adult bee body size have included both mass and morphometrics, but these metrics may not equally or reliably estimate body size for all bee species and in all situations, due to bee age, diet, and/or environment. Understanding the relationships between different metrics and possible redundancies in the information they afford is important but not always known. Body size measurements provide valuable data for interpreting research outcomes for managed solitary bees, including Osmia lignaria Say and Megachile rotundata F. (Hymenoptera: Megachilidae). Applied studies of these important and readily available U.S. crop pollinators focus on refining commercial management practices, and basic empirical studies in various scientific disciplines (from genomics to ecology) employ them as model systems to study solitary bees. To examine common metrics of body size, we measured head capsule width (HCW), intertegular distance (ITD), and fresh and dry weights of newly emerged adults of both species. Using linear and exponential models, we determined relationships between these body size metrics. For M. rotundata, linear models best described relationships between ITD and all other metrics, and between HCW and fresh and dry weights. For O. lignaria, linear models best fit relationships between all metrics except for fresh weight with both ITD and HCW, which were fitted better with exponential models. For both species, model fits were strongest when males and females were pooled. Depending on the study question, knowing that only one metric may reliably measure body size can simplify evaluations of O. lignaria and M. rotundata responses to artificial or environmental variables.
format: application/pdf
format: text/html
creator: Lindsie M. McCabe
creator: Natalie K. Boyle
creator: Morgan B. Scalici
creator: Theresa L. Pitts-Singer
subject: Agricultural Science
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.12344
publisher: PeerJ Inc.
rights: © 2021
abstract: Metrics to assess relative adult bee body size have included both mass and morphometrics, but these metrics may not equally or reliably estimate body size for all bee species and in all situations, due to bee age, diet, and/or environment. Understanding the relationships between different metrics and possible redundancies in the information they afford is important but not always known. Body size measurements provide valuable data for interpreting research outcomes for managed solitary bees, including Osmia lignaria Say and Megachile rotundata F. (Hymenoptera: Megachilidae). Applied studies of these important and readily available U.S. crop pollinators focus on refining commercial management practices, and basic empirical studies in various scientific disciplines (from genomics to ecology) employ them as model systems to study solitary bees. To examine common metrics of body size, we measured head capsule width (HCW), intertegular distance (ITD), and fresh and dry weights of newly emerged adults of both species. Using linear and exponential models, we determined relationships between these body size metrics. For M. rotundata, linear models best described relationships between ITD and all other metrics, and between HCW and fresh and dry weights. For O. lignaria, linear models best fit relationships between all metrics except for fresh weight with both ITD and HCW, which were fitted better with exponential models. For both species, model fits were strongest when males and females were pooled. Depending on the study question, knowing that only one metric may reliably measure body size can simplify evaluations of O. lignaria and M. rotundata responses to artificial or environmental variables.
bibliographic citation: McCabe et al. (2021) Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae). PeerJ 9:e12344 https://doi.org/10.7717/peerj.12344
date submitted: 2021-06-21
date accepted: 2021-09-28
issued: 2021-11-02
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: McCabe
  given name: Lindsie M.
author list: Agent
  family name: Boyle
  given name: Natalie K.
author list: Agent
  family name: Scalici
  given name: Morgan B.
author list: Agent
  family name: Pitts-Singer
  given name: Theresa L.
doi: 10.7717/peerj.12344
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02

Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines
type: item
type: AcademicArticle
description: Background One of the most frequently deleted genes in cancer is CDKN2A encoding p16. This protein is often overexpressed in senescent cells, while its suppression can bypass the oncogene-induced senescence to enable transformation and tumorigenesis. The roles of the protein p16 are recently being expanded from the cell cycle progression regulator to the cellular regulator interacting in several different pathways. Yet data on its liver and liver cells’ expression are inconclusive. Methods The expression of the p16 gene in liver and liver cells was determined by RT-qPCR and compared to its protein amounts by western blotting. Results p16 is expressed at low levels in the liver and rat hepatocytes. Its expression varies from none to the considerable levels in the examined hepatocellular carcinoma cell lines (FaO and HepG2) and in immortalized mouse hepatocytes. Such significant expression differences of an important cellular regulator warrant the need to closely examine the differences in biochemical pathways correlated with the p16 expression when using hepatocytes and hepatoma liver models.
format: application/pdf
format: text/html
creator: Barbara Kramar
creator: Dušan Šuput
creator: Irina Milisav
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12358
publisher: PeerJ Inc.
rights: © 2021 Kramar et al.
abstract: Background One of the most frequently deleted genes in cancer is CDKN2A encoding p16. This protein is often overexpressed in senescent cells, while its suppression can bypass the oncogene-induced senescence to enable transformation and tumorigenesis. The roles of the protein p16 are recently being expanded from the cell cycle progression regulator to the cellular regulator interacting in several different pathways. Yet data on its liver and liver cells’ expression are inconclusive. Methods The expression of the p16 gene in liver and liver cells was determined by RT-qPCR and compared to its protein amounts by western blotting. Results p16 is expressed at low levels in the liver and rat hepatocytes. Its expression varies from none to the considerable levels in the examined hepatocellular carcinoma cell lines (FaO and HepG2) and in immortalized mouse hepatocytes. Such significant expression differences of an important cellular regulator warrant the need to closely examine the differences in biochemical pathways correlated with the p16 expression when using hepatocytes and hepatoma liver models.
bibliographic citation: Kramar et al. (2021) Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines. PeerJ 9:e12358 https://doi.org/10.7717/peerj.12358
date submitted: 2021-07-13
date accepted: 2021-09-30
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kramar
  given name: Barbara
author list: Agent
  family name: Šuput
  given name: Dušan
author list: Agent
  family name: Milisav
  given name: Irina
doi: 10.7717/peerj.12358
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: © 2021 Kramar et al.
attribution name: Kramar et al.

Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia
type: item
type: AcademicArticle
description: In China, historical documents have recorded large quantities of information related to natural disasters, and these disasters have had long-lasting effects on economic and social activities. Understanding the occurrence of the natural disasters and their spatio-temporal variation characters is crucial for sustainable of our society. Therefore, based on the collection and collation of historical documents, and adopting mathematical statistics, Kriging interpolation, correlation analysis and other methods, we systematically explored the meteorological disasters in Henan Province during the past two millennia in analyzing their spatio-temporal distribution characters and driving forces. The results demonstrate that there were five major types of meteorological disasters in Henan Province, including drought, flood, hails, low temperature and frost and insect pests, which presented obvious spatio-temporal variations and have occurred frequently during the past two millennia. According to the historical documents, the major meteorological disasters occurred 1,929 times in Henan from 221 BCE to 2000 CE. On the whole, the disaster frequency show that the occurrence cycle of the meteorological disasters has obvious changes, which mainly occurred in the middle and late stages during the past two millennia, especially after 1300 CE. Furthermore, we also find that the variation of meteorological disaster events is consistent with the variation of temperature in eastern China and the frequency of meteorological disaster increases in the cold period, but decreases in the warm period. In addition, there are obvious differences in the spatial distribution of the major meteorological disaster, which were mainly distributed in the northwest and southern part region of the Henan Province before 1911 CE. While after 1911 CE, the northern and southeastern parts were the meteorological disaster-prone areas in this region during this period. Spatial correlation analysis of each meteorolo…
format: application/pdf
format: text/html
creator: Xiang Li
creator: Hui Lu
creator: Zhaokang Zhang
creator: Wei Xing
subject: Statistics
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12365
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: In China, historical documents have recorded large quantities of information related to natural disasters, and these disasters have had long-lasting effects on economic and social activities. Understanding the occurrence of the natural disasters and their spatio-temporal variation characters is crucial for sustainable of our society. Therefore, based on the collection and collation of historical documents, and adopting mathematical statistics, Kriging interpolation, correlation analysis and other methods, we systematically explored the meteorological disasters in Henan Province during the past two millennia in analyzing their spatio-temporal distribution characters and driving forces. The results demonstrate that there were five major types of meteorological disasters in Henan Province, including drought, flood, hails, low temperature and frost and insect pests, which presented obvious spatio-temporal variations and have occurred frequently during the past two millennia. According to the historical documents, the major meteorological disasters occurred 1,929 times in Henan from 221 BCE to 2000 CE. On the whole, the disaster frequency show that the occurrence cycle of the meteorological disasters has obvious changes, which mainly occurred in the middle and late stages during the past two millennia, especially after 1300 CE. Furthermore, we also find that the variation of meteorological disaster events is consistent with the variation of temperature in eastern China and the frequency of meteorological disaster increases in the cold period, but decreases in the warm period. In addition, there are obvious differences in the spatial distribution of the major meteorological disaster, which were mainly distributed in the northwest and southern part region of the Henan Province before 1911 CE. While after 1911 CE, the northern and southeastern parts were the meteorological disaster-prone areas in this region during this period. Spatial correlation analysis of each meteorolo…
bibliographic citation: Li et al. (2021) Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia. PeerJ 9:e12365 https://doi.org/10.7717/peerj.12365
date submitted: 2021-06-07
date accepted: 2021-10-01
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xiang
author list: Agent
  family name: Lu
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Zhaokang
author list: Agent
  family name: Xing
  given name: Wei
doi: 10.7717/peerj.12365
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: © 2021 Li et al.
attribution name: Li et al.

On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton
type: item
type: AcademicArticle
description: Palaenigma wrangeli (Schmidt) is a finger-sized fossil with a tetraradiate conical skeleton; it occurs as a rare component in fossiliferous Upper Ordovician strata of the eastern Baltic Basin and is known exclusively from north Estonia. The systematic affinities and palaeoecology of P. wrangeli remained questionable. Here, the available specimens of P. wrangeli have been reexamined using scanning electron microscopy and x-ray computed tomography (microCT). Additionally, the elemental composition of the skeletal elements has been checked using energy dispersive X-ray spectroscopy. The resulting 2D-, and 3D-scans reveal that P. wrangeli consists of an alternation of distinct calcium phosphate (apatite) lamellae and originally organic-rich inter-layers. The lamellae form four semicircular marginal pillars, which are connected by irregularly spaced transverse diaphragms. Marginally, the diaphragms and pillar lamellae are not connected to each other and thus do not form a closed periderm structure. A non-mineralized or poorly mineralized external periderm existed originally in P. wrangeli but is only rarely and fragmentary preserved. P. wrangeli often co-occurs with conulariids in fossil-rich limestone with mudstone–wackestone lithologies. Based on the new data, P. wrangeli can be best interpreted as a poorly mineralized conulariinid from an original soft bottom habitat. Here the new conulariinid family Palaenigmaidae fam. nov. is proposed as the monotypic taxon for P. wrangeli.
format: application/pdf
format: text/html
creator: Björn Kröger
creator: Olev Vinn
creator: Ursula Toom
creator: Ian J. Corfe
creator: Jukka Kuva
creator: Michał Zatoń
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12374
publisher: PeerJ Inc.
rights: © 2021 Kröger et al.
abstract: Palaenigma wrangeli (Schmidt) is a finger-sized fossil with a tetraradiate conical skeleton; it occurs as a rare component in fossiliferous Upper Ordovician strata of the eastern Baltic Basin and is known exclusively from north Estonia. The systematic affinities and palaeoecology of P. wrangeli remained questionable. Here, the available specimens of P. wrangeli have been reexamined using scanning electron microscopy and x-ray computed tomography (microCT). Additionally, the elemental composition of the skeletal elements has been checked using energy dispersive X-ray spectroscopy. The resulting 2D-, and 3D-scans reveal that P. wrangeli consists of an alternation of distinct calcium phosphate (apatite) lamellae and originally organic-rich inter-layers. The lamellae form four semicircular marginal pillars, which are connected by irregularly spaced transverse diaphragms. Marginally, the diaphragms and pillar lamellae are not connected to each other and thus do not form a closed periderm structure. A non-mineralized or poorly mineralized external periderm existed originally in P. wrangeli but is only rarely and fragmentary preserved. P. wrangeli often co-occurs with conulariids in fossil-rich limestone with mudstone–wackestone lithologies. Based on the new data, P. wrangeli can be best interpreted as a poorly mineralized conulariinid from an original soft bottom habitat. Here the new conulariinid family Palaenigmaidae fam. nov. is proposed as the monotypic taxon for P. wrangeli.
bibliographic citation: Kröger et al. (2021) On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton. PeerJ 9:e12374 https://doi.org/10.7717/peerj.12374
date submitted: 2021-04-19
date accepted: 2021-10-03
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kröger
  given name: Björn
author list: Agent
  family name: Vinn
  given name: Olev
author list: Agent
  family name: Toom
  given name: Ursula
author list: Agent
  family name: Corfe
  given name: Ian J.
author list: Agent
  family name: Kuva
  given name: Jukka
author list: Agent
  family name: Zatoń
  given name: Michał
doi: 10.7717/peerj.12374
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Kröger et al.
attribution name: Kröger et al.

Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma
type: item
type: AcademicArticle
description: Background Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous malignancy with varied outcomes. However, the fundamental mechanisms remain to be fully defined. Aim We aimed to identify core differentially co-expressed hub genes and perturbed pathways relevant to the pathogenesis and prognosis of DLBCL. Methods We retrieved the raw gene expression profile and clinical information of GSE12453 from the Gene Expression Omnibus (GEO) database. We used integrated bioinformatics analysis to identify differentially co-expressed genes. The CIBERSORT analysis was also applied to predict tumor-infiltrating immune cells (TIICs) in the GSE12453 dataset. We performed survival and ssGSEA (single-sample Gene Set Enrichment Analysis) (for TIICs) analyses and validated the hub genes using GEPIA2 and an independent GSE31312 dataset. Results We identified 46 differentially co-expressed hub genes in the GSE12453 dataset. Gene expression levels and survival analysis found 15 differentially co-expressed core hub genes. The core genes prognostic values and expression levels were further validated in the GEPIA2 database and GSE31312 dataset to be reliable (p < 0.01). The core genes’ main KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichments were Ribosome and Coronavirus disease-COVID-19. High expressions of the 15 core hub genes had prognostic value in DLBCL. The core genes showed significant predictive accuracy in distinguishing DLBCL cases from non-tumor controls, with the area under the curve (AUC) ranging from 0.992 to 1.00. Finally, CIBERSORT analysis on GSE12453 revealed immune cells, including activated memory CD4+ T cells and M0, M1, and M2-macrophages as the infiltrates in the DLBCL microenvironment. Conclusion Our study found differentially co-expressed core hub genes and relevant pathways involved in ribosome and COVID-19 disease that may be potential targets for prognosis and novel therapeutic intervention in DLBCL.
format: application/pdf
format: text/html
creator: Alice Charwudzi
creator: Ye Meng
creator: Linhui Hu
creator: Chen Ding
creator: Lianfang Pu
creator: Qian Li
creator: Mengling Xu
creator: Zhimin Zhai
creator: Shudao Xiong
subject: Bioinformatics
subject: Hematology
subject: Oncology
subject: Medical Genetics
subject: COVID-19
description: doi:10.7717/peerj.12394
publisher: PeerJ Inc.
rights: © 2021 Charwudzi et al.
abstract: Background Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous malignancy with varied outcomes. However, the fundamental mechanisms remain to be fully defined. Aim We aimed to identify core differentially co-expressed hub genes and perturbed pathways relevant to the pathogenesis and prognosis of DLBCL. Methods We retrieved the raw gene expression profile and clinical information of GSE12453 from the Gene Expression Omnibus (GEO) database. We used integrated bioinformatics analysis to identify differentially co-expressed genes. The CIBERSORT analysis was also applied to predict tumor-infiltrating immune cells (TIICs) in the GSE12453 dataset. We performed survival and ssGSEA (single-sample Gene Set Enrichment Analysis) (for TIICs) analyses and validated the hub genes using GEPIA2 and an independent GSE31312 dataset. Results We identified 46 differentially co-expressed hub genes in the GSE12453 dataset. Gene expression levels and survival analysis found 15 differentially co-expressed core hub genes. The core genes prognostic values and expression levels were further validated in the GEPIA2 database and GSE31312 dataset to be reliable (p < 0.01). The core genes’ main KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichments were Ribosome and Coronavirus disease-COVID-19. High expressions of the 15 core hub genes had prognostic value in DLBCL. The core genes showed significant predictive accuracy in distinguishing DLBCL cases from non-tumor controls, with the area under the curve (AUC) ranging from 0.992 to 1.00. Finally, CIBERSORT analysis on GSE12453 revealed immune cells, including activated memory CD4+ T cells and M0, M1, and M2-macrophages as the infiltrates in the DLBCL microenvironment. Conclusion Our study found differentially co-expressed core hub genes and relevant pathways involved in ribosome and COVID-19 disease that may be potential targets for prognosis and novel therapeutic intervention in DLBCL.
bibliographic citation: Charwudzi et al. (2021) Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma. PeerJ 9:e12394 https://doi.org/10.7717/peerj.12394
date submitted: 2021-06-28
date accepted: 2021-10-05
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charwudzi
  given name: Alice
author list: Agent
  family name: Meng
  given name: Ye
author list: Agent
  family name: Hu
  given name: Linhui
author list: Agent
  family name: Ding
  given name: Chen
author list: Agent
  family name: Pu
  given name: Lianfang
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Xu
  given name: Mengling
author list: Agent
  family name: Zhai
  given name: Zhimin
author list: Agent
  family name: Xiong
  given name: Shudao
doi: 10.7717/peerj.12394
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: © 2021 Charwudzi et al.
attribution name: Charwudzi et al.

Going rogue: what scientists can learn about Twitter communication from “alt” government accounts
type: item
type: AcademicArticle
description: The inauguration of President Trump in the United States led to the active restriction of science communication from federal agencies, resulting in the creation of many unofficial “alt” Twitter accounts to maintain communication. Alt accounts had many followers (e.g., 15 accounts had > 100,000) and received a large amount of media attention, making them ideal for better understanding how differences in messaging can affect public engagement with science on microblogging platforms. We analyzed tweets produced by alt and corresponding official agency accounts to compare the two groups and determine if specific features of a tweet made them more likely to be retweeted or liked to help the average scientist potentially reach a broader audience on Twitter. We found adding links, images, hashtags, and mentions, as well as expressing angry and annoying sentiments all increased retweets and likes. Evidence-based terms such as “peer-review” had high retweet rates but linking directly to peer-reviewed publications decreased attention compared to popular science websites. Word choice and attention did not reflect official or alt account types, indicating topic is more important than source. The number of tweets generated and attention received by alt accounts has decreased since their creation, demonstrating the importance of timeliness in science communication on social media. Together our results show potential pathways for scientists to increase efficacy in Twitter communications.
format: application/pdf
format: text/html
creator: Matthew J. Wilson
creator: Elizabeth K. Perkin
subject: Conservation Biology
subject: Computational Science
subject: Coupled Natural and Human Systems
subject: Data Science
description: doi:10.7717/peerj.12407
publisher: PeerJ Inc.
rights: © 2021 Wilson and Perkin
abstract: The inauguration of President Trump in the United States led to the active restriction of science communication from federal agencies, resulting in the creation of many unofficial “alt” Twitter accounts to maintain communication. Alt accounts had many followers (e.g., 15 accounts had > 100,000) and received a large amount of media attention, making them ideal for better understanding how differences in messaging can affect public engagement with science on microblogging platforms. We analyzed tweets produced by alt and corresponding official agency accounts to compare the two groups and determine if specific features of a tweet made them more likely to be retweeted or liked to help the average scientist potentially reach a broader audience on Twitter. We found adding links, images, hashtags, and mentions, as well as expressing angry and annoying sentiments all increased retweets and likes. Evidence-based terms such as “peer-review” had high retweet rates but linking directly to peer-reviewed publications decreased attention compared to popular science websites. Word choice and attention did not reflect official or alt account types, indicating topic is more important than source. The number of tweets generated and attention received by alt accounts has decreased since their creation, demonstrating the importance of timeliness in science communication on social media. Together our results show potential pathways for scientists to increase efficacy in Twitter communications.
bibliographic citation: Wilson et al. (2021) Going rogue: what scientists can learn about Twitter communication from “alt” government accounts. PeerJ 9:e12407 https://doi.org/10.7717/peerj.12407
date submitted: 2021-05-13
date accepted: 2021-10-08
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilson
  given name: Matthew J.
author list: Agent
  family name: Perkin
  given name: Elizabeth K.
doi: 10.7717/peerj.12407
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Wilson and Perkin
attribution name: Wilson and Perkin

Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery
type: item
type: AcademicArticle
description: This study aims to understand the spatial distribution of coral reefs in the central region of Viet Nam. We classified live coral cover in Son Tra Peninsula (ST) and Cu Lao Cham Island (CLC) in the South-Central Coast Region of Viet Nam using the Maximum Likelihood Classifier on 3 m Planetscope imagery. Confusion matrices and the accuracy of the classifier were assessed using field data (1,543 and 1,560 photographs in ST and CLC, respectively). The results showed that the reef’s width ranged from 30 to 300 m across the study site, and we were able to detect live coral cover across a depth gradient of 2 to 6 m below the sea surface. The overall accuracies of the classifier (the Kappa coefficient) were 76.78% (0.76) and 78.08% (0.78) for ST and CLC, respectively. We found that 60.25% of coral reefs in ST were unhealthy and the live coral cover was less than 50%, while 25.75% and 11.46% of those in CLC were in good and excellent conditions, respectively. This study demonstrates the feasibility of utilizing Planetscope imagery to monitor shallow coral reefs of small islands at a high spatial resolution of 3 m. The results of this study provide valuable information for coral reef protection and conservation.
format: application/pdf
format: text/html
creator: Khanh V. Nguyen
creator: Vinh C. Duong
creator: Kinh T. Kieu
creator: Thuong V. Tran
creator: Cho-ying Huang
creator: Ruth Reef
creator: Thien M. Hoang
subject: Biogeography
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12413
publisher: PeerJ Inc.
rights: © 2021 Nguyen et al.
abstract: This study aims to understand the spatial distribution of coral reefs in the central region of Viet Nam. We classified live coral cover in Son Tra Peninsula (ST) and Cu Lao Cham Island (CLC) in the South-Central Coast Region of Viet Nam using the Maximum Likelihood Classifier on 3 m Planetscope imagery. Confusion matrices and the accuracy of the classifier were assessed using field data (1,543 and 1,560 photographs in ST and CLC, respectively). The results showed that the reef’s width ranged from 30 to 300 m across the study site, and we were able to detect live coral cover across a depth gradient of 2 to 6 m below the sea surface. The overall accuracies of the classifier (the Kappa coefficient) were 76.78% (0.76) and 78.08% (0.78) for ST and CLC, respectively. We found that 60.25% of coral reefs in ST were unhealthy and the live coral cover was less than 50%, while 25.75% and 11.46% of those in CLC were in good and excellent conditions, respectively. This study demonstrates the feasibility of utilizing Planetscope imagery to monitor shallow coral reefs of small islands at a high spatial resolution of 3 m. The results of this study provide valuable information for coral reef protection and conservation.
bibliographic citation: Nguyen et al. (2021) Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery. PeerJ 9:e12413 https://doi.org/10.7717/peerj.12413
date submitted: 2021-06-14
date accepted: 2021-10-08
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Khanh V.
author list: Agent
  family name: Duong
  given name: Vinh C.
author list: Agent
  family name: Kieu
  given name: Kinh T.
author list: Agent
  family name: Tran
  given name: Thuong V.
author list: Agent
  family name: Huang
  given name: Cho-ying
author list: Agent
  family name: Reef
  given name: Ruth
author list: Agent
  family name: Hoang
  given name: Thien M.
doi: 10.7717/peerj.12413
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Nguyen et al.
attribution name: Nguyen et al.

Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea
type: item
type: AcademicArticle
description: In this study, size selectivity and exploitation pattern of six diamond-mesh codends with different mesh sizes, ranging from 25 to 54 mm, for Southern velvet shrimp (Metapenaeopsis palmensis) were tested and compared in a shrimp trawl fishery of the South China Sea (SCS). We used a codend with a mesh size of 25 mm (D25) as a starting point, which is the minimum mesh size (MMS) currently regulated in the studied area. Four different fishing population scenarios were applied to quantify and compare how mesh sizes of codends used would impact the size selectivity and exploitation pattern for the target shrimp species. The results demonstrated that the D25 codend was not proper for protecting juvenile shrimp at the studied area. By applying this legal codend, L50 (50% retention length) of the target shrimp species was below its minimum conservation reference size (MCRS, 7.0 cm total length), the retention probability of shrimp with a length of MCRS was above 95% CI [91–99] and more than 43% of undersized shrimp was retained. To mitigate the bycatch issue of undersized shrimp, increasing the mesh size in the diamond mesh codend is a simple and effective option. However, the loss of catch efficiency for marketable shrimp is a major concern while increasing the mesh size. A good compromise between releasing undersized shrimp and maintaining the legal individuals is manifested by using the codend with 35 mm mesh size (D35). Our study will be beneficial for the management of shrimp trawl fisheries in the SCS.
format: application/pdf
format: text/html
creator: Bingzhong Yang
creator: Bent Herrmann
creator: Lei Yan
creator: Jie Li
creator: Teng Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.12436
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: In this study, size selectivity and exploitation pattern of six diamond-mesh codends with different mesh sizes, ranging from 25 to 54 mm, for Southern velvet shrimp (Metapenaeopsis palmensis) were tested and compared in a shrimp trawl fishery of the South China Sea (SCS). We used a codend with a mesh size of 25 mm (D25) as a starting point, which is the minimum mesh size (MMS) currently regulated in the studied area. Four different fishing population scenarios were applied to quantify and compare how mesh sizes of codends used would impact the size selectivity and exploitation pattern for the target shrimp species. The results demonstrated that the D25 codend was not proper for protecting juvenile shrimp at the studied area. By applying this legal codend, L50 (50% retention length) of the target shrimp species was below its minimum conservation reference size (MCRS, 7.0 cm total length), the retention probability of shrimp with a length of MCRS was above 95% CI [91–99] and more than 43% of undersized shrimp was retained. To mitigate the bycatch issue of undersized shrimp, increasing the mesh size in the diamond mesh codend is a simple and effective option. However, the loss of catch efficiency for marketable shrimp is a major concern while increasing the mesh size. A good compromise between releasing undersized shrimp and maintaining the legal individuals is manifested by using the codend with 35 mm mesh size (D35). Our study will be beneficial for the management of shrimp trawl fisheries in the SCS.
bibliographic citation: Yang et al. (2021) Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea. PeerJ 9:e12436 https://doi.org/10.7717/peerj.12436
date submitted: 2021-06-23
date accepted: 2021-10-14
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Bingzhong
author list: Agent
  family name: Herrmann
  given name: Bent
author list: Agent
  family name: Yan
  given name: Lei
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Wang
  given name: Teng
doi: 10.7717/peerj.12436
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: © 2021 Yang et al.
attribution name: Yang et al.

Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics
type: item
type: AcademicArticle
description: In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.
format: application/pdf
format: text/html
creator: Sebastian Höhna
creator: Michael J. Landis
creator: John P. Huelsenbeck
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Statistics
description: doi:10.7717/peerj.12438
publisher: PeerJ Inc.
rights: © 2021 Höhna et al.
abstract: In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.
bibliographic citation: Höhna et al. (2021) Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics. PeerJ 9:e12438 https://doi.org/10.7717/peerj.12438
date submitted: 2021-05-27
date accepted: 2021-10-15
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Höhna
  given name: Sebastian
author list: Agent
  family name: Landis
  given name: Michael J.
author list: Agent
  family name: Huelsenbeck
  given name: John P.
doi: 10.7717/peerj.12438
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Höhna et al.
attribution name: Höhna et al.

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