PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: On the genus Mesopontonia Bruce, 1967 (Crustacea: Decapoda: Palaemonidae) in Korea, with the description of a new species
items: The past century of coral bleaching in the Saudi Arabian central Red Sea
items: Flower structure and development in Vietnamese Sciaphila (Triuridaceae: Pandanales): refined knowledge of the morphological misfit family and implications for taxonomy
items: Computerized monitoring of COVID-19 trials, studies and registries in ClinicalTrials.gov registry
items: Gene flow relates to evolutionary divergence among populations at the range margin
items: The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef
items: Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus
items: Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance
items: Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests
items: Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies

On the genus Mesopontonia Bruce, 1967 (Crustacea: Decapoda: Palaemonidae) in Korea, with the description of a new species
type: item
type: AcademicArticle
description: Mesopontonia verrucimanus and Mesopontonia kimwoni sp. nov. are recorded from high-latitude temperate waters in Munseom Islet, Jejudo Island, Republic of Korea, with both species collected on gorgonians and sponges by trimix diving between 50 and 75 m depth. Mesopontonia kimwoni sp. nov. is morphologically allied to M. brevicarpus, but can be distinguished by the cutting edges of the fingers of the first chela being entire. Significant morphological variation in the rostrum as well as the second pereiopods is documented in M. verrucimanus, although cytochrome c oxidase subunit I (COI) barcode analysis proves this to be infra-specific variation. A key to species of the genus Mesopontonia is provided.
format: application/pdf
format: text/html
creator: Jin-Ho Park
creator: Sammy De Grave
creator: Taeseo Park
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10190
publisher: PeerJ Inc.
rights: © 2020 Park et al.
abstract: Mesopontonia verrucimanus and Mesopontonia kimwoni sp. nov. are recorded from high-latitude temperate waters in Munseom Islet, Jejudo Island, Republic of Korea, with both species collected on gorgonians and sponges by trimix diving between 50 and 75 m depth. Mesopontonia kimwoni sp. nov. is morphologically allied to M. brevicarpus, but can be distinguished by the cutting edges of the fingers of the first chela being entire. Significant morphological variation in the rostrum as well as the second pereiopods is documented in M. verrucimanus, although cytochrome c oxidase subunit I (COI) barcode analysis proves this to be infra-specific variation. A key to species of the genus Mesopontonia is provided.
bibliographic citation: Park et al. (2020) On the genus Mesopontonia Bruce, 1967 (Crustacea: Decapoda: Palaemonidae) in Korea, with the description of a new species. PeerJ 8:e10190 https://doi.org/10.7717/peerj.10190
date submitted: 2020-06-25
date accepted: 2020-09-24
issued: 2020-10-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Park
  given name: Jin-Ho
author list: Agent
  family name: De Grave
  given name: Sammy
author list: Agent
  family name: Park
  given name: Taeseo
doi: 10.7717/peerj.10190
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-23
copyright: ©2020 Park et al.
attribution name: Park et al.

The past century of coral bleaching in the Saudi Arabian central Red Sea
type: item
type: AcademicArticle
description: Accurate knowledge of the spatial and temporal patterns of coral bleaching is essential both for understanding how coral reef ecosystems are changing today and forecasting their future states. Yet, in many regions of the world, the history of bleaching is poorly known, especially prior to the late 20th century. Here, I use the information preserved within skeleton cores of long-lived Porites corals to reconstruct the past century of bleaching events in the Saudi Arabian central Red Sea. In these cores, skeletal “stress bands”—indicative of past bleaching—captured known bleaching events that occurred in 1998 and 2010, but also revealed evidence of previously unknown bleaching events in 1931, 1978, and 1982. However, these earlier events affected a significantly lesser proportion of corals than 1998 and 2010. Therefore, coral bleaching may have occurred in the central Red Sea earlier than previously recognized, but the frequency and severity of bleaching events since 1998 on nearshore reefs is unprecedented over the past century. Conversely, corals living on mid- to outer-shelf reefs have not been equally susceptible to bleaching as their nearshore counterparts, which was evident in that stress bands were five times more prevalent nearshore. Whether this pattern of susceptible nearshore reefs and resistant outer-shelf reefs continues in the future remains a key question in forecasting coral reef futures in this region.
format: application/pdf
format: text/html
creator: Thomas M. DeCarlo
subject: Marine Biology
subject: Climate Change Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.10200
publisher: PeerJ Inc.
rights: © 2020 DeCarlo
abstract: Accurate knowledge of the spatial and temporal patterns of coral bleaching is essential both for understanding how coral reef ecosystems are changing today and forecasting their future states. Yet, in many regions of the world, the history of bleaching is poorly known, especially prior to the late 20th century. Here, I use the information preserved within skeleton cores of long-lived Porites corals to reconstruct the past century of bleaching events in the Saudi Arabian central Red Sea. In these cores, skeletal “stress bands”—indicative of past bleaching—captured known bleaching events that occurred in 1998 and 2010, but also revealed evidence of previously unknown bleaching events in 1931, 1978, and 1982. However, these earlier events affected a significantly lesser proportion of corals than 1998 and 2010. Therefore, coral bleaching may have occurred in the central Red Sea earlier than previously recognized, but the frequency and severity of bleaching events since 1998 on nearshore reefs is unprecedented over the past century. Conversely, corals living on mid- to outer-shelf reefs have not been equally susceptible to bleaching as their nearshore counterparts, which was evident in that stress bands were five times more prevalent nearshore. Whether this pattern of susceptible nearshore reefs and resistant outer-shelf reefs continues in the future remains a key question in forecasting coral reef futures in this region.
bibliographic citation: DeCarlo (2020) The past century of coral bleaching in the Saudi Arabian central Red Sea. PeerJ 8:e10200 https://doi.org/10.7717/peerj.10200
date submitted: 2020-07-14
date accepted: 2020-09-26
issued: 2020-10-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeCarlo
  given name: Thomas M.
doi: 10.7717/peerj.10200
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-23
copyright: ©2020 DeCarlo
attribution name: DeCarlo

Flower structure and development in Vietnamese Sciaphila (Triuridaceae: Pandanales): refined knowledge of the morphological misfit family and implications for taxonomy
type: item
type: AcademicArticle
description: The monocot family Triuridaceae is a morphological misfit with respect to several traits of floral morphology, including the uniformly apocarpous polymerous gynoecium and the famous inside-out flowers of Lacandonia. Although Triuridaceae are crucially important for understanding the floral evolution of Pandanales and angiosperms in general, significant knowledge gaps exist which hamper adequate morphological analysis of flowers in this family. The scarcity of morphological data is also reflected in numerous taxonomic inconsistencies. Here we provide a comprehensive study of reproductive organs of four species of Sciaphila occurring in Vietnam (S. arfakiana, S. densiflora, S. nana and S. stellata) including the first investigation of early floral development and gynoecium phyllotaxis. Our observations are mainly based on SEM images. We confirm the perianth (studied in male flowers) to be two-whorled and report a rare sequence of initiation of perianth parts: the outer tepals show a late congenital fusion, as their free lobes appear before the common perianth tube, whereas the inner tepals show an early congenital fusion, with their free lobes initiating on the tube rim. We interpret the stamen appendages as basal adaxial outgrowths of the stamen filaments. We discuss the number of thecae and locules in anthers of Sciaphila, and conclude that 3- and 4-, but not 2-locular anthers are characteristic of this genus. We describe the carpels as consisting of both ascidiate and plicate zones, the former being extremely short and completely obscured by anthesis. The single ovule is attached in the cross-zone. The style is non-plicate. We analyze gynoecium phyllotaxis by estimating its contact parastichies, and by investigating the number and arrangement of the outermost carpels. The carpel arrangement in a given gynoecium is a result of the balance between whorled and irregular (but not spiral) phyllotaxis. We recognize the following figures of gynoecium merism: 6, 9, 10, 10.…
format: application/pdf
format: text/html
creator: Maxim S. Nuraliev
creator: Margarita V. Remizowa
creator: Dmitry D. Sokoloff
subject: Evolutionary Studies
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.10205
publisher: PeerJ Inc.
rights: © 2020 Nuraliev et al.
abstract: The monocot family Triuridaceae is a morphological misfit with respect to several traits of floral morphology, including the uniformly apocarpous polymerous gynoecium and the famous inside-out flowers of Lacandonia. Although Triuridaceae are crucially important for understanding the floral evolution of Pandanales and angiosperms in general, significant knowledge gaps exist which hamper adequate morphological analysis of flowers in this family. The scarcity of morphological data is also reflected in numerous taxonomic inconsistencies. Here we provide a comprehensive study of reproductive organs of four species of Sciaphila occurring in Vietnam (S. arfakiana, S. densiflora, S. nana and S. stellata) including the first investigation of early floral development and gynoecium phyllotaxis. Our observations are mainly based on SEM images. We confirm the perianth (studied in male flowers) to be two-whorled and report a rare sequence of initiation of perianth parts: the outer tepals show a late congenital fusion, as their free lobes appear before the common perianth tube, whereas the inner tepals show an early congenital fusion, with their free lobes initiating on the tube rim. We interpret the stamen appendages as basal adaxial outgrowths of the stamen filaments. We discuss the number of thecae and locules in anthers of Sciaphila, and conclude that 3- and 4-, but not 2-locular anthers are characteristic of this genus. We describe the carpels as consisting of both ascidiate and plicate zones, the former being extremely short and completely obscured by anthesis. The single ovule is attached in the cross-zone. The style is non-plicate. We analyze gynoecium phyllotaxis by estimating its contact parastichies, and by investigating the number and arrangement of the outermost carpels. The carpel arrangement in a given gynoecium is a result of the balance between whorled and irregular (but not spiral) phyllotaxis. We recognize the following figures of gynoecium merism: 6, 9, 10, 10.…
bibliographic citation: Nuraliev et al. (2020) Flower structure and development in Vietnamese Sciaphila (Triuridaceae: Pandanales): refined knowledge of the morphological misfit family and implications for taxonomy. PeerJ 8:e10205 https://doi.org/10.7717/peerj.10205
date submitted: 2020-08-12
date accepted: 2020-09-28
issued: 2020-10-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nuraliev
  given name: Maxim S.
author list: Agent
  family name: Remizowa
  given name: Margarita V.
author list: Agent
  family name: Sokoloff
  given name: Dmitry D.
doi: 10.7717/peerj.10205
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-23
copyright: © 2020 Nuraliev et al.
attribution name: Nuraliev et al.

Computerized monitoring of COVID-19 trials, studies and registries in ClinicalTrials.gov registry
type: item
type: AcademicArticle
description: Clinical trial registries can provide important information about relevant studies for a given condition to other researchers and the public. We developed a computerized informatics based approach to provide an overview and analysis of COVID-19 studies registered on ClinicalTrials.gov registry. Using the perspective of analyzing active or completed COVID-19 studies, we identified 401 interventional clinical trials, 287 observational studies and 64 registries. We analyzed features of each study type separately such as location, design, interventions and update history. Our results show that the United States had the most COVID-19 interventional trials, France had the most COVID-19 observational studies and France and the United States tied for the most COVID-19 registries on ClinicalTrials.gov. The majority of studies in all three study types had a single study site. For update history “Study Status” is the most updated information and we found that studies located in Canada (2.70 updates per study) and the United States (1.76 updates per study) update their studies more often than studies in any other country. Using normalization and mapping techniques, we identified Hydroxychloroquine (92 studies) as the most common drug intervention, while convalescent plasma (20 studies) is the most common biological intervention. The primary purpose of most interventional trials is for treatment with 298 studies (74.3%). For COVID-19 registries we found the most common proposed follow-up time is 1 year (15 studies). Of specific importance and interest is COVID-19 vaccine trials, of which 12 were identified. Our informatics based approach allows for constant monitoring and updating as well as multiple applications to other conditions and interests.
format: application/pdf
format: text/html
creator: Craig S. Mayer
creator: Vojtech Huser
subject: Clinical Trials
subject: Drugs and Devices
subject: Global Health
subject: Infectious Diseases
subject: Data Science
description: doi:10.7717/peerj.10261
publisher: PeerJ Inc.
rights: © 2020 Mayer and Huser
abstract: Clinical trial registries can provide important information about relevant studies for a given condition to other researchers and the public. We developed a computerized informatics based approach to provide an overview and analysis of COVID-19 studies registered on ClinicalTrials.gov registry. Using the perspective of analyzing active or completed COVID-19 studies, we identified 401 interventional clinical trials, 287 observational studies and 64 registries. We analyzed features of each study type separately such as location, design, interventions and update history. Our results show that the United States had the most COVID-19 interventional trials, France had the most COVID-19 observational studies and France and the United States tied for the most COVID-19 registries on ClinicalTrials.gov. The majority of studies in all three study types had a single study site. For update history “Study Status” is the most updated information and we found that studies located in Canada (2.70 updates per study) and the United States (1.76 updates per study) update their studies more often than studies in any other country. Using normalization and mapping techniques, we identified Hydroxychloroquine (92 studies) as the most common drug intervention, while convalescent plasma (20 studies) is the most common biological intervention. The primary purpose of most interventional trials is for treatment with 298 studies (74.3%). For COVID-19 registries we found the most common proposed follow-up time is 1 year (15 studies). Of specific importance and interest is COVID-19 vaccine trials, of which 12 were identified. Our informatics based approach allows for constant monitoring and updating as well as multiple applications to other conditions and interests.
bibliographic citation: Mayer et al. (2020) Computerized monitoring of COVID-19 trials, studies and registries in ClinicalTrials.gov registry. PeerJ 8:e10261 https://doi.org/10.7717/peerj.10261
date submitted: 2020-06-18
date accepted: 2020-10-07
issued: 2020-10-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mayer
  given name: Craig S.
author list: Agent
  family name: Huser
  given name: Vojtech
doi: 10.7717/peerj.10261
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-23
copyright: © 2020 Mayer and Huser
attribution name: Mayer and Huser

Gene flow relates to evolutionary divergence among populations at the range margin
type: item
type: AcademicArticle
description: Background Morphological differentiation between populations resulting from local adaptations to environmental conditions is likely to be more pronounced in populations with increasing genetic isolation. In a previous study a positive clinal variation in body size was observed in isolated Roesel’s bush-cricket, Metrioptera roeselii, populations, but were absent from populations within a continuous distribution at the same latitudinal range. This observational study inferred that there was a phenotypic effect of gene flow on climate-induced selection in this species. Methods To disentangle genetic versus environmental drivers of population differences in morphology, we measured the size of four different body traits in wild-caught individuals from the two most distinct latitudinally-matched pairs of populations occurring at about 60°N latitude in northern Europe, characterised by either restricted or continuous gene flow, and corresponding individuals raised under laboratory conditions. Results Individuals that originated from the genetically isolated populations were always bigger (femur, pronotum and genital appendages) when compared to individuals from latitudinally-matched areas characterised by continuous gene flow between populations. The magnitude of this effect was similar for wild-caught and laboratory-reared individuals. We found that previously observed size cline variation in both male and female crickets was likely to be the result of local genetic adaptation rather than phenotypic plasticity. Conclusions This strongly suggests that restricted gene flow is of major importance for frequencies of alleles that participate in climate-induced selection acting to favour larger phenotypes in isolated populations towards colder latitudes.
format: application/pdf
format: text/html
creator: Peter Kaňuch
creator: Berrit Kiehl
creator: Anna Cassel-Lundhagen
creator: Ane T. Laugen
creator: Matthew Low
creator: Åsa Berggren
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.10036
publisher: PeerJ Inc.
rights: © 2020 Kaňuch et al.
abstract: Background Morphological differentiation between populations resulting from local adaptations to environmental conditions is likely to be more pronounced in populations with increasing genetic isolation. In a previous study a positive clinal variation in body size was observed in isolated Roesel’s bush-cricket, Metrioptera roeselii, populations, but were absent from populations within a continuous distribution at the same latitudinal range. This observational study inferred that there was a phenotypic effect of gene flow on climate-induced selection in this species. Methods To disentangle genetic versus environmental drivers of population differences in morphology, we measured the size of four different body traits in wild-caught individuals from the two most distinct latitudinally-matched pairs of populations occurring at about 60°N latitude in northern Europe, characterised by either restricted or continuous gene flow, and corresponding individuals raised under laboratory conditions. Results Individuals that originated from the genetically isolated populations were always bigger (femur, pronotum and genital appendages) when compared to individuals from latitudinally-matched areas characterised by continuous gene flow between populations. The magnitude of this effect was similar for wild-caught and laboratory-reared individuals. We found that previously observed size cline variation in both male and female crickets was likely to be the result of local genetic adaptation rather than phenotypic plasticity. Conclusions This strongly suggests that restricted gene flow is of major importance for frequencies of alleles that participate in climate-induced selection acting to favour larger phenotypes in isolated populations towards colder latitudes.
bibliographic citation: Kaňuch et al. (2020) Gene flow relates to evolutionary divergence among populations at the range margin. PeerJ 8:e10036 https://doi.org/10.7717/peerj.10036
date submitted: 2020-06-10
date accepted: 2020-09-03
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaňuch
  given name: Peter
author list: Agent
  family name: Kiehl
  given name: Berrit
author list: Agent
  family name: Cassel-Lundhagen
  given name: Anna
author list: Agent
  family name: Laugen
  given name: Ane T.
author list: Agent
  family name: Low
  given name: Matthew
author list: Agent
  family name: Berggren
  given name: Åsa
doi: 10.7717/peerj.10036
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: © 2020 Kaňuch et al.
attribution name: Kaňuch et al.

The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef
type: item
type: AcademicArticle
description: Ecological processes on coral reefs commonly have limited spatial and temporal scales and may not be recorded in their long-term geological history. The widespread degradation of Caribbean coral reefs over the last 40 years therefore provides an opportunity to assess the impact of more significant ecological changes on the geological and geomorphic structure of reefs. Here, we document the changing ecology of communities in a coral reef seascape within the context of its geomorphic zonation. By comparing basic ecological indices between historical and modern data we show that in 35 years the reef-front zone was transformed from a complex coral assemblage with a three-dimensional structure, to a size-homogenized and flattened one that is quasi indistinguishable from the adjacent non-accretional coral-ground zone. Today coral assemblages at Punta Maroma are characterized by the dominance of opportunistic species which are either tolerant to adverse environmental conditions, including sedimentation, or are known to be the first scleractinian species to recruit on disturbed reefs, implying they reflect a post-hurricane stage of adjustment. Despite an increase in similarity in ecological indices, the reef-front and coral-ground geomorphic zones still retain significant differences in coral assemblages and benthic habitat and are not homogeneous. The partial convergence of coral assemblages certainly has important consequences for the ecology and geological viability of the reef and its role in coastal protection, but environmental physical drivers continue to exert a fundamental role in the character and zonation of benthic communities of this reef seascape.
format: application/pdf
format: text/html
creator: Alexis Enrique Medina-Valmaseda
creator: Rosa E. Rodríguez-Martínez
creator: Lorenzo Alvarez-Filip
creator: Eric Jordan-Dahlgren
creator: Paul Blanchon
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.10103
publisher: PeerJ Inc.
rights: © 2020 Medina-Valmaseda et al.
abstract: Ecological processes on coral reefs commonly have limited spatial and temporal scales and may not be recorded in their long-term geological history. The widespread degradation of Caribbean coral reefs over the last 40 years therefore provides an opportunity to assess the impact of more significant ecological changes on the geological and geomorphic structure of reefs. Here, we document the changing ecology of communities in a coral reef seascape within the context of its geomorphic zonation. By comparing basic ecological indices between historical and modern data we show that in 35 years the reef-front zone was transformed from a complex coral assemblage with a three-dimensional structure, to a size-homogenized and flattened one that is quasi indistinguishable from the adjacent non-accretional coral-ground zone. Today coral assemblages at Punta Maroma are characterized by the dominance of opportunistic species which are either tolerant to adverse environmental conditions, including sedimentation, or are known to be the first scleractinian species to recruit on disturbed reefs, implying they reflect a post-hurricane stage of adjustment. Despite an increase in similarity in ecological indices, the reef-front and coral-ground geomorphic zones still retain significant differences in coral assemblages and benthic habitat and are not homogeneous. The partial convergence of coral assemblages certainly has important consequences for the ecology and geological viability of the reef and its role in coastal protection, but environmental physical drivers continue to exert a fundamental role in the character and zonation of benthic communities of this reef seascape.
bibliographic citation: Medina-Valmaseda et al. (2020) The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef. PeerJ 8:e10103 https://doi.org/10.7717/peerj.10103
date submitted: 2020-04-28
date accepted: 2020-09-14
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medina-Valmaseda
  given name: Alexis Enrique
author list: Agent
  family name: Rodríguez-Martínez
  given name: Rosa E.
author list: Agent
  family name: Alvarez-Filip
  given name: Lorenzo
author list: Agent
  family name: Jordan-Dahlgren
  given name: Eric
author list: Agent
  family name: Blanchon
  given name: Paul
doi: 10.7717/peerj.10103
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: © 2020 Medina-Valmaseda et al.
attribution name: Medina-Valmaseda et al.

Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus
type: item
type: AcademicArticle
description: Background Type 2 diabetes mellitus (T2DM) is a metabolic disease affecting a huge population worldwide. Teucrium polium L. has been used as a folk medicine for the treatment of T2DM in Anatolia, Turkey. The antihyperglycemic effect of the plant was reported previously. However, there was no detailed study on the underlying molecular mechanisms. In this study, we generated a research plan to clarify the active constituents of the extract and uncover the molecular mechanisms using network pharmacology analysis. Methods For this purpose, we composed a dataset of 126 compounds for the phytochemical profile of the aerial parts of T. polium. Drug-likeness of the compounds was evaluated, and 52 compounds were selected for further investigation. A total of 252 T2DM related targets hit by selected compounds were subjected to DAVID database. Results The KEGG pathway analysis showed enrichment for the TNF signaling pathway, insulin resistance, the HIF-1 signaling pathway, apoptosis, the PI3K-AKT signaling pathway, the FOXO signaling pathway, the insulin signaling pathway, and type 2 diabetes mellitus which are related to T2DM . AKT1, IL6, STAT3, TP53, INS, and VEGFA were found to be key targets in protein-protein interaction. Besides these key targets, with this study the role of GSK3β, GLUT4, and PDX1 were also discussed through literature and considered as important targets in the antidiabetic effect of T. polium. Various compounds of T. polium were shown to interact with the key targets activating PI3K-AKT and insulin signaling pathways. Conclusions According to these findings, mainly phenolic compounds were identified as the active components and IRS1/PI3K/AKT signaling and insulin resistance were identified as the main pathways regulated by T. polium. This study reveals the relationship of the compounds in T. polium with the targets of T2DM in human. Our findings suggested the use of T. polium as an effective herbal drug in the treatment of T2DM and provides new insights…
format: application/pdf
format: text/html
creator: Vahap Murat Kutluay
creator: Neziha Yagmur Diker
subject: Bioinformatics
subject: Plant Science
subject: Diabetes and Endocrinology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.10111
publisher: PeerJ Inc.
rights: © 2020 Kutluay and Diker
abstract: Background Type 2 diabetes mellitus (T2DM) is a metabolic disease affecting a huge population worldwide. Teucrium polium L. has been used as a folk medicine for the treatment of T2DM in Anatolia, Turkey. The antihyperglycemic effect of the plant was reported previously. However, there was no detailed study on the underlying molecular mechanisms. In this study, we generated a research plan to clarify the active constituents of the extract and uncover the molecular mechanisms using network pharmacology analysis. Methods For this purpose, we composed a dataset of 126 compounds for the phytochemical profile of the aerial parts of T. polium. Drug-likeness of the compounds was evaluated, and 52 compounds were selected for further investigation. A total of 252 T2DM related targets hit by selected compounds were subjected to DAVID database. Results The KEGG pathway analysis showed enrichment for the TNF signaling pathway, insulin resistance, the HIF-1 signaling pathway, apoptosis, the PI3K-AKT signaling pathway, the FOXO signaling pathway, the insulin signaling pathway, and type 2 diabetes mellitus which are related to T2DM . AKT1, IL6, STAT3, TP53, INS, and VEGFA were found to be key targets in protein-protein interaction. Besides these key targets, with this study the role of GSK3β, GLUT4, and PDX1 were also discussed through literature and considered as important targets in the antidiabetic effect of T. polium. Various compounds of T. polium were shown to interact with the key targets activating PI3K-AKT and insulin signaling pathways. Conclusions According to these findings, mainly phenolic compounds were identified as the active components and IRS1/PI3K/AKT signaling and insulin resistance were identified as the main pathways regulated by T. polium. This study reveals the relationship of the compounds in T. polium with the targets of T2DM in human. Our findings suggested the use of T. polium as an effective herbal drug in the treatment of T2DM and provides new insights…
bibliographic citation: Kutluay et al. (2020) Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PeerJ 8:e10111 https://doi.org/10.7717/peerj.10111
date submitted: 2020-07-08
date accepted: 2020-09-16
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kutluay
  given name: Vahap Murat
author list: Agent
  family name: Diker
  given name: Neziha Yagmur
doi: 10.7717/peerj.10111
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: ©2020 Kutluay and Diker
attribution name: Kutluay and Diker

Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance
type: item
type: AcademicArticle
description: Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
format: application/pdf
format: text/html
creator: Alexandra Gubanova
creator: Inna Drapun
creator: Oksana Garbazey
creator: Olga Krivenko
creator: Ekaterina Vodiasova
subject: Ecology
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10153
publisher: PeerJ Inc.
rights: © 2020 Gubanova et al.
abstract: Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
bibliographic citation: Gubanova et al. (2020) Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance. PeerJ 8:e10153 https://doi.org/10.7717/peerj.10153
date submitted: 2020-01-16
date accepted: 2020-09-21
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gubanova
  given name: Alexandra
author list: Agent
  family name: Drapun
  given name: Inna
author list: Agent
  family name: Garbazey
  given name: Oksana
author list: Agent
  family name: Krivenko
  given name: Olga
author list: Agent
  family name: Vodiasova
  given name: Ekaterina
doi: 10.7717/peerj.10153
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: ©2020 Gubanova et al.
attribution name: Gubanova et al.

Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests
type: item
type: AcademicArticle
description: In this study we combine information from aerial LIDAR and hemispherical images taken in the field with ForeStereo—a forest inventory device—to assess the vulnerability and to design conservation strategies for endangered Mediterranean fir forests based on the mapping of fire risk and canopy structure spatial variability. We focused on the largest continuous remnant population of the endangered tree species Abies pinsapo Boiss. spanning 252 ha in Sierra de las Nieves National Park (South Andalusia, Spain). We established 49 sampling plots over the study area. Stand structure variables were derived from ForeStereo device, a proximal sensing technology for tree diameter, height and crown dimensions and stand crown cover and basal area retrieval from stereoscopic hemispherical images photogrammetry. With this information, we developed regression models with airborne LIDAR data (spatial resolution of 0.5 points∙m−2). Thereafter, six fuel models were fitted to the plots according to the UCO40 classification criteria, and then the entire area was classified using the Nearest Neighbor algorithm on Sentinel imagery (overall accuracy of 0.56 and a KIA-Kappa Coefficient of 0.46). FlamMap software was used for fire simulation scenarios based on fuel models, stand structure, and terrain data. Besides the fire simulation, we analyzed canopy structure to assess the status and vulnerability of this fir population. The assessment shows a secondary growth forest that has an increasing presence of fuel models with the potential for high fire spread rate fire and burn probability. Our methodological approach has the potential to be integrated as a support tool for the adaptive management and conservation of A. pinsapo across its whole distribution area (<4,000 ha), as well as for other endangered circum-Mediterranean fir forests, as A. numidica de Lannoy and A. pinsapo marocana Trab. in North Africa.
format: application/pdf
format: text/html
creator: Álvaro Cortés-Molino
creator: Isabel Aulló-Maestro
creator: Ismael Fernandez-Luque
creator: Antonio Flores-Moya
creator: José A. Carreira
creator: A. Enrique Salvo
subject: Ecosystem Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.10158
publisher: PeerJ Inc.
rights: © 2020 Cortés-Molino et al.
abstract: In this study we combine information from aerial LIDAR and hemispherical images taken in the field with ForeStereo—a forest inventory device—to assess the vulnerability and to design conservation strategies for endangered Mediterranean fir forests based on the mapping of fire risk and canopy structure spatial variability. We focused on the largest continuous remnant population of the endangered tree species Abies pinsapo Boiss. spanning 252 ha in Sierra de las Nieves National Park (South Andalusia, Spain). We established 49 sampling plots over the study area. Stand structure variables were derived from ForeStereo device, a proximal sensing technology for tree diameter, height and crown dimensions and stand crown cover and basal area retrieval from stereoscopic hemispherical images photogrammetry. With this information, we developed regression models with airborne LIDAR data (spatial resolution of 0.5 points∙m−2). Thereafter, six fuel models were fitted to the plots according to the UCO40 classification criteria, and then the entire area was classified using the Nearest Neighbor algorithm on Sentinel imagery (overall accuracy of 0.56 and a KIA-Kappa Coefficient of 0.46). FlamMap software was used for fire simulation scenarios based on fuel models, stand structure, and terrain data. Besides the fire simulation, we analyzed canopy structure to assess the status and vulnerability of this fir population. The assessment shows a secondary growth forest that has an increasing presence of fuel models with the potential for high fire spread rate fire and burn probability. Our methodological approach has the potential to be integrated as a support tool for the adaptive management and conservation of A. pinsapo across its whole distribution area (<4,000 ha), as well as for other endangered circum-Mediterranean fir forests, as A. numidica de Lannoy and A. pinsapo marocana Trab. in North Africa.
bibliographic citation: Cortés-Molino et al. (2020) Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests. PeerJ 8:e10158 https://doi.org/10.7717/peerj.10158
date submitted: 2020-03-03
date accepted: 2020-09-21
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortés-Molino
  given name: Álvaro
author list: Agent
  family name: Aulló-Maestro
  given name: Isabel
author list: Agent
  family name: Fernandez-Luque
  given name: Ismael
author list: Agent
  family name: Flores-Moya
  given name: Antonio
author list: Agent
  family name: Carreira
  given name: José A.
author list: Agent
  family name: Salvo
  given name: A. Enrique
doi: 10.7717/peerj.10158
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: © 2020 Cortés-Molino et al.
attribution name: Cortés-Molino et al.

Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies
type: item
type: AcademicArticle
description: There is an increasing prevalence of human immunodeficiency virus (HIV) infection in older adults in China, but the findings across prevalence studies have been mixed. This is the first meta-analysis of the prevalence of HIV infection and its moderating factors in older adults in China. Two investigators systematically and independently searched both international (PubMed, PsycINFO, Web of Sciences and EMBASE) and Chinese (WanFang, CNKI, and CQVIP) databases. HIV infection rates in older adults were analyzed using the random-effects model. Altogether 46 studies were included in the analysis. The pooled prevalence of HIV infection in older adults was 2.1% (95% CI [1.9%–2.3%], I2 = 99.4%). Subgroup analyses revealed that men who have sex with men (MSM), hospital population samples, publications after 2014, studies conducted in the western region of China, and higher study quality were significantly associated with higher HIV infection rate. This meta-analysis found that the HIV infection prevalence in older adults is significantly higher than the general population in China. Attention should be given to this urgent public health issue, and effective HIV/AIDS preventive, screening and treatment measures are warranted in this population. PROSPERO: CRD42019124286.
format: application/pdf
format: text/html
creator: Yuan Yuan Wang
creator: Yuan Yang
creator: Chang Chen
creator: Ling Zhang
creator: Chee H. Ng
creator: Gabor S. Ungvari
creator: Xiaohua Douglas Zhang
creator: Yu-Tao Xiang
subject: HIV
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9731
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: There is an increasing prevalence of human immunodeficiency virus (HIV) infection in older adults in China, but the findings across prevalence studies have been mixed. This is the first meta-analysis of the prevalence of HIV infection and its moderating factors in older adults in China. Two investigators systematically and independently searched both international (PubMed, PsycINFO, Web of Sciences and EMBASE) and Chinese (WanFang, CNKI, and CQVIP) databases. HIV infection rates in older adults were analyzed using the random-effects model. Altogether 46 studies were included in the analysis. The pooled prevalence of HIV infection in older adults was 2.1% (95% CI [1.9%–2.3%], I2 = 99.4%). Subgroup analyses revealed that men who have sex with men (MSM), hospital population samples, publications after 2014, studies conducted in the western region of China, and higher study quality were significantly associated with higher HIV infection rate. This meta-analysis found that the HIV infection prevalence in older adults is significantly higher than the general population in China. Attention should be given to this urgent public health issue, and effective HIV/AIDS preventive, screening and treatment measures are warranted in this population. PROSPERO: CRD42019124286.
bibliographic citation: Wang et al. (2020) Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies. PeerJ 8:e9731 https://doi.org/10.7717/peerj.9731
date submitted: 2020-02-05
date accepted: 2020-07-24
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yuan Yuan
author list: Agent
  family name: Yang
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Chang
author list: Agent
  family name: Zhang
  given name: Ling
author list: Agent
  family name: Ng
  given name: Chee H.
author list: Agent
  family name: Ungvari
  given name: Gabor S.
author list: Agent
  family name: Zhang
  given name: Xiaohua Douglas
author list: Agent
  family name: Xiang
  given name: Yu-Tao
doi: 10.7717/peerj.9731
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

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