PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Genetic structure of marine and lake forms of Pacific herring Clupea pallasii
items: Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum
items: Concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in adults with chronic heart failure
items: PLGA-PEG-PLGA hydrogel with NEP1-40 promotes the functional recovery of brachial plexus root avulsion in adult rats
items: Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes

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.

Genetic structure of marine and lake forms of Pacific herring Clupea pallasii
type: item
type: AcademicArticle
description: The Pacific herring (Clupea pallasii) is one of the most important species in the commercial fisheries distributed in the North Pacific Ocean and the northeastern European seas. This teleost has marine and lake ecological forms a long its distribution in the Holarctic. However, the level of genetic differentiation between these two forms is not well known. In the present study, we used ddRAD-sequencing to genotype 54 specimens from twelve wild Pacific herring populations from the Kara Sea and the Russian part of the northwestern Pacific Ocean for unveiling the genetic structure of Pacific herring. We found that the Kara Sea population is significantly distinct from Pacific Ocean populations. It was demonstrated that lake populations of Pacific herring differ from one another as well as from marine specimens. Our results show that fresh and brackish water Pacific herring, which inhabit lakes, can be distinguished as a separate lake ecological form. Moreover, we demonstrate that each observed lake Pacific herring population has its own and unique genetic legacy.
format: application/pdf
format: text/html
creator: Svetlana Yu. Orlova
creator: Sergey Rastorguev
creator: Tatyana Bagno
creator: Denis Kurnosov
creator: Artem Nedoluzhko
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Genomics
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.12444
publisher: PeerJ Inc.
rights: © 2021 Orlova et al.
abstract: The Pacific herring (Clupea pallasii) is one of the most important species in the commercial fisheries distributed in the North Pacific Ocean and the northeastern European seas. This teleost has marine and lake ecological forms a long its distribution in the Holarctic. However, the level of genetic differentiation between these two forms is not well known. In the present study, we used ddRAD-sequencing to genotype 54 specimens from twelve wild Pacific herring populations from the Kara Sea and the Russian part of the northwestern Pacific Ocean for unveiling the genetic structure of Pacific herring. We found that the Kara Sea population is significantly distinct from Pacific Ocean populations. It was demonstrated that lake populations of Pacific herring differ from one another as well as from marine specimens. Our results show that fresh and brackish water Pacific herring, which inhabit lakes, can be distinguished as a separate lake ecological form. Moreover, we demonstrate that each observed lake Pacific herring population has its own and unique genetic legacy.
bibliographic citation: Orlova et al. (2021) Genetic structure of marine and lake forms of Pacific herring Clupea pallasii. PeerJ 9:e12444 https://doi.org/10.7717/peerj.12444
date submitted: 2021-03-31
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: Orlova
  given name: Svetlana Yu.
author list: Agent
  family name: Rastorguev
  given name: Sergey
author list: Agent
  family name: Bagno
  given name: Tatyana
author list: Agent
  family name: Kurnosov
  given name: Denis
author list: Agent
  family name: Nedoluzhko
  given name: Artem
doi: 10.7717/peerj.12444
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Orlova et al.
attribution name: Orlova et al.

Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum
type: item
type: AcademicArticle
description: Background Malaria parasites reproduce asexually, leading to the production of large numbers of genetically identical parasites, here termed a clonal line or clone. Infected hosts may harbor one or more clones, and the number of clones in a host is termed multiplicity of infection (MOI). Understanding the distribution of parasite clones among hosts can shed light on the processes shaping this distribution and is important for modeling MOI. Here, I determine whether the distribution of clones of the lizard malaria parasite Plasmodium mexicanum differ significantly from statistical distributions commonly used to model MOI and logical extensions of these models. Methods The number of clones per infection was assessed using four microsatellite loci with the maximum number of alleles at any one locus used as a simple estimate of MOI for each infection. I fit statistical models (Poisson, negative binomial, zero-inflated models) to data from four individual sites to determine a best fit model. I also simulated the number of alleles per locus using an unbiased estimate of MOI to determine whether the simple (but potentially biased) method I used to estimate MOI influenced model fit. Results The distribution of clones among hosts at individual sites differed significantly from traditional Poisson and negative binomial distributions, but not from zero-inflated modifications of these distributions. A consistent excess of two-clone infections and shortage of one-clone infections relative to all fit distributions was also observed. Any bias introduced by the simple method for estimating of MOI did not appear to qualitatively alter the results. Conclusions The statistical distributions used to model MOI are typically zero-truncated; truncating the Poisson or zero-inflated Poisson yield the same distribution, so the reasonable fit of the zero-inflated Poisson to the data suggests that the use of the zero-truncated Poisson in modeling is adequate. The improved fit of zero-inflated …
format: application/pdf
format: text/html
creator: Allison T. Neal
subject: Ecology
subject: Mathematical Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.12448
publisher: PeerJ Inc.
rights: © 2021 Neal
abstract: Background Malaria parasites reproduce asexually, leading to the production of large numbers of genetically identical parasites, here termed a clonal line or clone. Infected hosts may harbor one or more clones, and the number of clones in a host is termed multiplicity of infection (MOI). Understanding the distribution of parasite clones among hosts can shed light on the processes shaping this distribution and is important for modeling MOI. Here, I determine whether the distribution of clones of the lizard malaria parasite Plasmodium mexicanum differ significantly from statistical distributions commonly used to model MOI and logical extensions of these models. Methods The number of clones per infection was assessed using four microsatellite loci with the maximum number of alleles at any one locus used as a simple estimate of MOI for each infection. I fit statistical models (Poisson, negative binomial, zero-inflated models) to data from four individual sites to determine a best fit model. I also simulated the number of alleles per locus using an unbiased estimate of MOI to determine whether the simple (but potentially biased) method I used to estimate MOI influenced model fit. Results The distribution of clones among hosts at individual sites differed significantly from traditional Poisson and negative binomial distributions, but not from zero-inflated modifications of these distributions. A consistent excess of two-clone infections and shortage of one-clone infections relative to all fit distributions was also observed. Any bias introduced by the simple method for estimating of MOI did not appear to qualitatively alter the results. Conclusions The statistical distributions used to model MOI are typically zero-truncated; truncating the Poisson or zero-inflated Poisson yield the same distribution, so the reasonable fit of the zero-inflated Poisson to the data suggests that the use of the zero-truncated Poisson in modeling is adequate. The improved fit of zero-inflated …
bibliographic citation: Neal (2021) Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum. PeerJ 9:e12448 https://doi.org/10.7717/peerj.12448
date submitted: 2021-01-28
date accepted: 2021-10-18
issued: 2021-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neal
  given name: Allison T.
doi: 10.7717/peerj.12448
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-02
copyright: ©2021 Neal
attribution name: Neal

Concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in adults with chronic heart failure
type: item
type: AcademicArticle
description: Background The study investigated the relationship between the concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in the blood serum of patients with heart failure (HF) and the potential influence on the development and progression of HF. Material & methods The study included 214 patients (155 men and 59 women), aged 40–87 years, presenting symptoms or signs typical of HF (according to the NYHA functional classification). Serum concentrations were determined for Mg, Ca, Fe, Cu, Zn, P, C-reactive protein (CRP), creatinine, urea, triglyceride levels (TG), total cholesterol (CH), high density protein (HDL), low density protein (LDL). The levels of macro-and microminerals were analysed using inductively coupled serum optical emission spectrometry (ICP-OES). Results Our study confirmed the role of known risk factors in the development of heart failure, including: overweight, diabetes, hypertension, high triglycerides (TG), high total cholesterol (CH), high levels of low density protein (LDL) and reduced levels of high density protein (HDL), high CRP, high creatinine. Moreover, deficient serum concentrations of Mg (47% of the studied men and 54% of the women) and Cu (in 44% of men and more than 30% of women) were observed, as well as subnormal serum Fe (2% of women) and Zn (1% of men). Elevated serum Ca was found in 50% of men and 49% of women. In 44% of the studied men and 52% of the studied women, P levels in serum were also above-average. The study revealed a significant positive correlation between serum levels of Ca and Mg, and also Ca and Cu in women. In men, serum Cu was positively correlated with Mg and Ca concentrations. In patients from group 1 (NYHA I–II), Mg content was positively correlated with Ca and Cu. In this patient group, Ca was also positively associated with Cu content in serum. In group 2 (NYHA III-IV), serum Mg concentration was significantly positively correlated with that of Cu and Ca. Conclusions Changes in the…
format: application/pdf
format: text/html
creator: Iwona Gorący
creator: Ewa Rębacz-Maron
creator: Jan Korbecki
creator: Jarosław Gorący
subject: Biochemistry
subject: Cardiology
subject: Epidemiology
subject: Hematology
description: doi:10.7717/peerj.12207
publisher: PeerJ Inc.
rights: © 2021 Gorący et al.
abstract: Background The study investigated the relationship between the concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in the blood serum of patients with heart failure (HF) and the potential influence on the development and progression of HF. Material & methods The study included 214 patients (155 men and 59 women), aged 40–87 years, presenting symptoms or signs typical of HF (according to the NYHA functional classification). Serum concentrations were determined for Mg, Ca, Fe, Cu, Zn, P, C-reactive protein (CRP), creatinine, urea, triglyceride levels (TG), total cholesterol (CH), high density protein (HDL), low density protein (LDL). The levels of macro-and microminerals were analysed using inductively coupled serum optical emission spectrometry (ICP-OES). Results Our study confirmed the role of known risk factors in the development of heart failure, including: overweight, diabetes, hypertension, high triglycerides (TG), high total cholesterol (CH), high levels of low density protein (LDL) and reduced levels of high density protein (HDL), high CRP, high creatinine. Moreover, deficient serum concentrations of Mg (47% of the studied men and 54% of the women) and Cu (in 44% of men and more than 30% of women) were observed, as well as subnormal serum Fe (2% of women) and Zn (1% of men). Elevated serum Ca was found in 50% of men and 49% of women. In 44% of the studied men and 52% of the studied women, P levels in serum were also above-average. The study revealed a significant positive correlation between serum levels of Ca and Mg, and also Ca and Cu in women. In men, serum Cu was positively correlated with Mg and Ca concentrations. In patients from group 1 (NYHA I–II), Mg content was positively correlated with Ca and Cu. In this patient group, Ca was also positively associated with Cu content in serum. In group 2 (NYHA III-IV), serum Mg concentration was significantly positively correlated with that of Cu and Ca. Conclusions Changes in the…
bibliographic citation: Gorący et al. (2021) Concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in adults with chronic heart failure. PeerJ 9:e12207 https://doi.org/10.7717/peerj.12207
date submitted: 2021-04-15
date accepted: 2021-09-03
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gorący
  given name: Iwona
author list: Agent
  family name: Rębacz-Maron
  given name: Ewa
author list: Agent
  family name: Korbecki
  given name: Jan
author list: Agent
  family name: Gorący
  given name: Jarosław
doi: 10.7717/peerj.12207
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: © 2021 Gorący et al.
attribution name: Gorący et al.

PLGA-PEG-PLGA hydrogel with NEP1-40 promotes the functional recovery of brachial plexus root avulsion in adult rats
type: item
type: AcademicArticle
description: Adult brachial plexus root avulsion can cause serious damage to nerve tissue and impair axonal regeneration, making the recovery of nerve function difficult. Nogo-A extracellular peptide residues 1-40 (NEP1-40) promote axonal regeneration by inhibiting the Nogo-66 receptor (NgR1), and poly (D, L-lactide-co-glycolide)-poly (ethylene glycol)-poly (D, L-lactide-co-glycolide) (PLGA-PEG-PLGA) hydrogel can be used to fill in tissue defects and concurrently function to sustain the release of NEP1-40. In this study, we established an adult rat model of brachial plexus nerve root avulsion injury and conducted nerve root replantation. PLGA-PEG-PLGA hydrogel combined with NEP1-40 was used to promote nerve regeneration and functional recovery in this rat model. Our results demonstrated that functional recovery was enhanced, and the survival rate of spinal anterior horn motoneurons was higher in rats that received a combination of PLGA-PEG-PLGA hydrogel and NEP1-40 than in those receiving other treatments. The combined therapy also significantly increased the number of fluorescent retrogradely labeled neurons, muscle fiber diameter, and motor endplate area of the biceps brachii. In conclusion, this study demonstrates that the effects of PLGA-PEG-PLGA hydrogel combined with NEP1-40 are superior to those of other therapies used to treat brachial plexus nerve root avulsion injury. Therefore, future studies should investigate the potential of PLGA-PEG-PLGA hydrogel as a primary treatment for brachial plexus root avulsion.
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creator: Wenlai Guo
creator: Bingbing Pei
creator: Zehui Li
creator: Xiao Lan Ou
creator: Tianwen Sun
creator: Zhe Zhu
subject: Biochemistry
subject: Neuroscience
subject: Neurology
subject: Histology
description: doi:10.7717/peerj.12269
publisher: PeerJ Inc.
rights: © 2021 Guo et al.
abstract: Adult brachial plexus root avulsion can cause serious damage to nerve tissue and impair axonal regeneration, making the recovery of nerve function difficult. Nogo-A extracellular peptide residues 1-40 (NEP1-40) promote axonal regeneration by inhibiting the Nogo-66 receptor (NgR1), and poly (D, L-lactide-co-glycolide)-poly (ethylene glycol)-poly (D, L-lactide-co-glycolide) (PLGA-PEG-PLGA) hydrogel can be used to fill in tissue defects and concurrently function to sustain the release of NEP1-40. In this study, we established an adult rat model of brachial plexus nerve root avulsion injury and conducted nerve root replantation. PLGA-PEG-PLGA hydrogel combined with NEP1-40 was used to promote nerve regeneration and functional recovery in this rat model. Our results demonstrated that functional recovery was enhanced, and the survival rate of spinal anterior horn motoneurons was higher in rats that received a combination of PLGA-PEG-PLGA hydrogel and NEP1-40 than in those receiving other treatments. The combined therapy also significantly increased the number of fluorescent retrogradely labeled neurons, muscle fiber diameter, and motor endplate area of the biceps brachii. In conclusion, this study demonstrates that the effects of PLGA-PEG-PLGA hydrogel combined with NEP1-40 are superior to those of other therapies used to treat brachial plexus nerve root avulsion injury. Therefore, future studies should investigate the potential of PLGA-PEG-PLGA hydrogel as a primary treatment for brachial plexus root avulsion.
bibliographic citation: Guo et al. (2021) PLGA-PEG-PLGA hydrogel with NEP1-40 promotes the functional recovery of brachial plexus root avulsion in adult rats. PeerJ 9:e12269 https://doi.org/10.7717/peerj.12269
date submitted: 2021-03-23
date accepted: 2021-09-17
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Wenlai
author list: Agent
  family name: Pei
  given name: Bingbing
author list: Agent
  family name: Li
  given name: Zehui
author list: Agent
  family name: Ou
  given name: Xiao Lan
author list: Agent
  family name: Sun
  given name: Tianwen
author list: Agent
  family name: Zhu
  given name: Zhe
doi: 10.7717/peerj.12269
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: © 2021 Guo et al.
attribution name: Guo et al.

Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes
type: item
type: AcademicArticle
description: Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
format: application/pdf
format: text/html
creator: Hilda A. Valdez-Salazar
creator: Miguel A. Ares
creator: Francisco J. Fernández
creator: J Antonio Ibarra
creator: Javier Torres
creator: Víctor H. Bustamante
creator: Miguel A. De la Cruz
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12270
publisher: PeerJ Inc.
rights: © 2021 Valdez-Salazar et al.
abstract: Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
bibliographic citation: Valdez-Salazar et al. (2021) Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes. PeerJ 9:e12270 https://doi.org/10.7717/peerj.12270
date submitted: 2020-06-26
date accepted: 2021-09-17
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valdez-Salazar
  given name: Hilda A.
author list: Agent
  family name: Ares
  given name: Miguel A.
author list: Agent
  family name: Fernández
  given name: Francisco J.
author list: Agent
  family name: Ibarra
  given name: J Antonio
author list: Agent
  family name: Torres
  given name: Javier
author list: Agent
  family name: Bustamante
  given name: Víctor H.
author list: Agent
  family name: De la Cruz
  given name: Miguel A.
doi: 10.7717/peerj.12270
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: ©2021 Valdez-Salazar et al.
attribution name: Valdez-Salazar et al.

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