PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study
items: Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players
items: Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis
items: Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux
items: Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands
items: Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept
items: Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata)
items: Montreal Cognitive Assessment (MoCA) performance in Huntington’s disease patients correlates with cortical and caudate atrophy
items: TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea
items: Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications

Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study
type: item
type: AcademicArticle
description: Background Most physical exercise programs for older people work the physical component in isolation, excluding cognitive aspects. Previous studies reported that both components (physical and cognitive) are necessary for correct functioning of older people in the society. Purpose To create and validate a dual-task exercise program (DualPro) to improve balance and gait speed in older people. Methods Expert consensus or the Delphi Method was used for validation. A group of 17 experts in neurorehabilitation and geriatrics was recruited to assess the proposed exercise program. They were selected taking into account their experience in clinical practice as well as their knowledge of the subject through the use of the expert competence coefficient (K). Online questionnaires were sent with a total of 11 exercises, which had to be rated using a “Likert” scale from 1 to 7. Results Two rounds were conducted to achieve 100% consensus in all exercises. The interquartile range of each exercise in both rounds was stable. During the second round, the relative interquartile range was less than 15% in all the questions, thus demonstrating consensus among the experts. Conclusion Experts in neurorehabilitation and geriatrics have concluded the validity of the progressive and systematized program of dual-task exercises focused on improving balance and gait speed for older people. This exercise program can help in the homogenization of the use of dual-task exercises in future studies and in professional practice.
format: application/pdf
format: text/html
creator: Luz Adriana Varela-Vásquez
creator: Montserrat Girabent-Farrés
creator: Almudena Medina-Rincón
creator: Sandra Rierola-Fochs
creator: Javier Jerez-Roig
creator: Eduard Minobes-Molina
subject: Geriatrics
subject: Kinesiology
subject: Rehabilitation
description: doi:10.7717/peerj.13204
publisher: PeerJ Inc.
rights: © 2022 Varela-Vásquez et al.
abstract: Background Most physical exercise programs for older people work the physical component in isolation, excluding cognitive aspects. Previous studies reported that both components (physical and cognitive) are necessary for correct functioning of older people in the society. Purpose To create and validate a dual-task exercise program (DualPro) to improve balance and gait speed in older people. Methods Expert consensus or the Delphi Method was used for validation. A group of 17 experts in neurorehabilitation and geriatrics was recruited to assess the proposed exercise program. They were selected taking into account their experience in clinical practice as well as their knowledge of the subject through the use of the expert competence coefficient (K). Online questionnaires were sent with a total of 11 exercises, which had to be rated using a “Likert” scale from 1 to 7. Results Two rounds were conducted to achieve 100% consensus in all exercises. The interquartile range of each exercise in both rounds was stable. During the second round, the relative interquartile range was less than 15% in all the questions, thus demonstrating consensus among the experts. Conclusion Experts in neurorehabilitation and geriatrics have concluded the validity of the progressive and systematized program of dual-task exercises focused on improving balance and gait speed for older people. This exercise program can help in the homogenization of the use of dual-task exercises in future studies and in professional practice.
bibliographic citation: Varela-Vásquez et al. (2022) Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study. PeerJ 10:e13204 https://doi.org/10.7717/peerj.13204
date submitted: 2021-09-16
date accepted: 2022-03-10
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Varela-Vásquez
  given name: Luz Adriana
author list: Agent
  family name: Girabent-Farrés
  given name: Montserrat
author list: Agent
  family name: Medina-Rincón
  given name: Almudena
author list: Agent
  family name: Rierola-Fochs
  given name: Sandra
author list: Agent
  family name: Jerez-Roig
  given name: Javier
author list: Agent
  family name: Minobes-Molina
  given name: Eduard
doi: 10.7717/peerj.13204
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Varela-Vásquez et al.
attribution name: Varela-Vásquez et al.

Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players
type: item
type: AcademicArticle
description: Background The identification of sport talent among adolescent athletes is a topic that in recent years has been a major focus of interest for both the scientific community and sport managers. Both anthropometry and physical performance through fitness tests have demonstrated to be key elements. Biological maturation, due to its influence on anthropometric variables and physical fitness, has also been studied in relation to sport talent identification. Objective To analyse differences according to biological maturation status in anthropometric characteristics and performance in physical fitness tests, and to determine which variables predict better performance in physical fitness tests in adolescent volleyball players. Methods A cross-sectional design was followed to collect the data. A total of 48 male sub-elite volleyball players (14.17 ± 0.73 years) completed a socio-demographic and sports ad hoc questionnaire. Anthropometric variables were measured following the guidelines of the International Society for the Advancement in Kinanthropometry (ISAK) including four basic measurements (body mass, height, sitting height and arm span); eight skinfolds (triceps, biceps, subscapular, iliac crest, supraspinale, abdominal, thigh and calf); four girths (arm relaxed, flexed and tensed arm, middle thigh and calf); five breadths (biacromial, biileocrestal, humerus, femur and bi-styloid); three lengths (acromiale-radiale, radiale-stylion and stylion-medio dactilion); and a height (ilioespinale). Physical fitness was assessed, including the sit-and-reach, back scratch, long jump, medicine ball throw, counter movement jump (CMJ), 20 meters sprint, and agility tests. Furthermore, maturity offset and age at peak height velocity (APHV) was calculated. Results Significant differences were found in the body mass (Mean Difference, MD = 20.86–30.75), height (MD = 11.72–19.09), sitting height (MD = 4.27–10.27), arm span (MD = 12.91–20.78), body mass index (MD = 3.72–5.63), upper limb le…
format: application/pdf
format: text/html
creator: Mario Albaladejo-Saura
creator: Raquel Vaquero-Cristóbal
creator: Juan A. García-Roca
creator: Francisco Esparza-Ros
subject: Anatomy and Physiology
subject: Kinesiology
subject: Pediatrics
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.13216
publisher: PeerJ Inc.
rights: © 2022 Albaladejo-Saura et al.
abstract: Background The identification of sport talent among adolescent athletes is a topic that in recent years has been a major focus of interest for both the scientific community and sport managers. Both anthropometry and physical performance through fitness tests have demonstrated to be key elements. Biological maturation, due to its influence on anthropometric variables and physical fitness, has also been studied in relation to sport talent identification. Objective To analyse differences according to biological maturation status in anthropometric characteristics and performance in physical fitness tests, and to determine which variables predict better performance in physical fitness tests in adolescent volleyball players. Methods A cross-sectional design was followed to collect the data. A total of 48 male sub-elite volleyball players (14.17 ± 0.73 years) completed a socio-demographic and sports ad hoc questionnaire. Anthropometric variables were measured following the guidelines of the International Society for the Advancement in Kinanthropometry (ISAK) including four basic measurements (body mass, height, sitting height and arm span); eight skinfolds (triceps, biceps, subscapular, iliac crest, supraspinale, abdominal, thigh and calf); four girths (arm relaxed, flexed and tensed arm, middle thigh and calf); five breadths (biacromial, biileocrestal, humerus, femur and bi-styloid); three lengths (acromiale-radiale, radiale-stylion and stylion-medio dactilion); and a height (ilioespinale). Physical fitness was assessed, including the sit-and-reach, back scratch, long jump, medicine ball throw, counter movement jump (CMJ), 20 meters sprint, and agility tests. Furthermore, maturity offset and age at peak height velocity (APHV) was calculated. Results Significant differences were found in the body mass (Mean Difference, MD = 20.86–30.75), height (MD = 11.72–19.09), sitting height (MD = 4.27–10.27), arm span (MD = 12.91–20.78), body mass index (MD = 3.72–5.63), upper limb le…
bibliographic citation: Albaladejo-Saura et al. (2022) Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players. PeerJ 10:e13216 https://doi.org/10.7717/peerj.13216
date submitted: 2022-01-20
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albaladejo-Saura
  given name: Mario
author list: Agent
  family name: Vaquero-Cristóbal
  given name: Raquel
author list: Agent
  family name: García-Roca
  given name: Juan A.
author list: Agent
  family name: Esparza-Ros
  given name: Francisco
doi: 10.7717/peerj.13216
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Albaladejo-Saura et al.
attribution name: Albaladejo-Saura et al.

Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis
type: item
type: AcademicArticle
description: Background Dendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated. Results In this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems’ transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages. Conclusion In general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis.
format: application/pdf
format: text/html
creator: Min Jiang
creator: Shangyun Li
creator: Changling Zhao
creator: Mingfu Zhao
creator: Shaozhong Xu
creator: Guosong Wen
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.13222
publisher: PeerJ Inc.
rights: © 2022 Jiang et al.
abstract: Background Dendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated. Results In this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems’ transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages. Conclusion In general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis.
bibliographic citation: Jiang et al. (2022) Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis. PeerJ 10:e13222 https://doi.org/10.7717/peerj.13222
date submitted: 2021-12-28
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Min
author list: Agent
  family name: Li
  given name: Shangyun
author list: Agent
  family name: Zhao
  given name: Changling
author list: Agent
  family name: Zhao
  given name: Mingfu
author list: Agent
  family name: Xu
  given name: Shaozhong
author list: Agent
  family name: Wen
  given name: Guosong
doi: 10.7717/peerj.13222
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Jiang et al.
attribution name: Jiang et al.

Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux
type: item
type: AcademicArticle
description: Coastal watershed are essential in transporting dissolved loads from terrestrial biogeochemical process of surface environment to the adjacent oceans. The solute chemistry of coastal river water contains significant information about environmental processes under the impact of both natural lithology and anthropogenic pressure. In this study, strontium (Sr) isotopes and water chemistry data of the Jiulongjiang (JLJ) river water were analyzed in detail to trace the contribution of bedrock weathering, and quantify Sr flux to the East China Sea (ECS). The dissolved Sr contents ranged 0.07–0.90 μmol L−1 and greatly fluctuated where tributaries encountered, and 87Sr/86Sr values relatively fluctuated between 0.7140 and 0.7514. Silicate weathering was identified to be the predominant contribution of riverine dissolved loads. Strontium flux to the ocean in dry season was estimated to be 689.2 tons per year, implying an essential influence on oceanic strontium evolution. In accordance with forward model, the silicate weathering rate and CO2 consumption rate were 55.7 tons km−2 per year and 16.9 × 105 mol km−2 per year, respectively, slightly higher than world average. Considering anthropogenic impacts alongside the river, the integrated effect of lower runoff and longer retention time of river water in dry season may aggravate weathering processes. Although CO2 sink by silicate weathering in JLJ seems less than the sink in world’s central reservoirs, it should still be taken into consideration for coastal carbon budget. These findings highlight the use of geochemical characteristics of strontium and its isotopes in identifying weathering process and output flux to the ocean, which provides basic data for sustainable coastal water resource management.
format: application/pdf
format: text/html
creator: Shitong Zhang
creator: Guilin Han
creator: Jie Zeng
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.13223
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Coastal watershed are essential in transporting dissolved loads from terrestrial biogeochemical process of surface environment to the adjacent oceans. The solute chemistry of coastal river water contains significant information about environmental processes under the impact of both natural lithology and anthropogenic pressure. In this study, strontium (Sr) isotopes and water chemistry data of the Jiulongjiang (JLJ) river water were analyzed in detail to trace the contribution of bedrock weathering, and quantify Sr flux to the East China Sea (ECS). The dissolved Sr contents ranged 0.07–0.90 μmol L−1 and greatly fluctuated where tributaries encountered, and 87Sr/86Sr values relatively fluctuated between 0.7140 and 0.7514. Silicate weathering was identified to be the predominant contribution of riverine dissolved loads. Strontium flux to the ocean in dry season was estimated to be 689.2 tons per year, implying an essential influence on oceanic strontium evolution. In accordance with forward model, the silicate weathering rate and CO2 consumption rate were 55.7 tons km−2 per year and 16.9 × 105 mol km−2 per year, respectively, slightly higher than world average. Considering anthropogenic impacts alongside the river, the integrated effect of lower runoff and longer retention time of river water in dry season may aggravate weathering processes. Although CO2 sink by silicate weathering in JLJ seems less than the sink in world’s central reservoirs, it should still be taken into consideration for coastal carbon budget. These findings highlight the use of geochemical characteristics of strontium and its isotopes in identifying weathering process and output flux to the ocean, which provides basic data for sustainable coastal water resource management.
bibliographic citation: Zhang et al. (2022) Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux. PeerJ 10:e13223 https://doi.org/10.7717/peerj.13223
date submitted: 2021-12-03
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shitong
author list: Agent
  family name: Han
  given name: Guilin
author list: Agent
  family name: Zeng
  given name: Jie
doi: 10.7717/peerj.13223
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands
type: item
type: AcademicArticle
description: Background Soil seed banks play a central role in vegetation dynamics and may be an important source of ecological restoration. However, the vast majority of seed bank studies examined only the uppermost soil layers (0–10 cm); hence, our knowledge on the depth distribution of seed bank and the ecological significance of deeply buried seeds is limited. The aim of our study was to examine the fine-scale vertical distribution of soil seed bank to a depth of 80 cm, which is one of the largest studied depth gradients so far. Our model systems were alkaline grasslands in East-Hungary, characterised by harsh environmental conditions, due to Solonetz soil reference group with Vertic horizon. We asked the following questions: (1) How do the seedling density and species richness of soil seed bank change along a vertical gradient and to what depth can germinable seeds be detected? (2) What is the relationship between the depth distribution of the germinable seeds and the species traits? Methods In each of the five study sites, four soil cores (4 cm diameter) of 80 cm depth were collected with an auger for soil seed bank analysis. Each sample was divided into sixteen 5-cm segments by depth (320 segments in total). Samples were concentrated by washing over sieves and then germinated in an unheated greenhouse. Soil penetration resistance was measured in situ next to each core location (0–80 cm depth, 1-cm resolution). We tested the number and species richness of seedlings observed in the soil segments (N = 320), using negative binomial generalized linear regression models, in which sampling layer and penetration resistance were the predictor variables. We ran the models for morphological groups (graminoids/forbs), ecological groups (grassland species/weeds) and life-form categories (short-lived/perennial). We also tested whether seed shape index, seed mass, water requirement or salt tolerance of the species influence the vertical distribution of their seed bank. Results Germinabl…
format: application/pdf
format: text/html
creator: Ágnes Tóth
creator: Balázs Deák
creator: Katalin Tóth
creator: Réka Kiss
creator: Katalin Lukács
creator: Zoltán Rádai
creator: Laura Godó
creator: Sándor Borza
creator: András Kelemen
creator: Tamás Miglécz
creator: Zoltán Bátori
creator: Tibor József Novák
creator: Orsolya Valkó
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13226
publisher: PeerJ Inc.
rights: © 2022 Tóth et al.
abstract: Background Soil seed banks play a central role in vegetation dynamics and may be an important source of ecological restoration. However, the vast majority of seed bank studies examined only the uppermost soil layers (0–10 cm); hence, our knowledge on the depth distribution of seed bank and the ecological significance of deeply buried seeds is limited. The aim of our study was to examine the fine-scale vertical distribution of soil seed bank to a depth of 80 cm, which is one of the largest studied depth gradients so far. Our model systems were alkaline grasslands in East-Hungary, characterised by harsh environmental conditions, due to Solonetz soil reference group with Vertic horizon. We asked the following questions: (1) How do the seedling density and species richness of soil seed bank change along a vertical gradient and to what depth can germinable seeds be detected? (2) What is the relationship between the depth distribution of the germinable seeds and the species traits? Methods In each of the five study sites, four soil cores (4 cm diameter) of 80 cm depth were collected with an auger for soil seed bank analysis. Each sample was divided into sixteen 5-cm segments by depth (320 segments in total). Samples were concentrated by washing over sieves and then germinated in an unheated greenhouse. Soil penetration resistance was measured in situ next to each core location (0–80 cm depth, 1-cm resolution). We tested the number and species richness of seedlings observed in the soil segments (N = 320), using negative binomial generalized linear regression models, in which sampling layer and penetration resistance were the predictor variables. We ran the models for morphological groups (graminoids/forbs), ecological groups (grassland species/weeds) and life-form categories (short-lived/perennial). We also tested whether seed shape index, seed mass, water requirement or salt tolerance of the species influence the vertical distribution of their seed bank. Results Germinabl…
bibliographic citation: Tóth et al. (2022) Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands. PeerJ 10:e13226 https://doi.org/10.7717/peerj.13226
date submitted: 2021-11-24
date accepted: 2022-03-15
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tóth
  given name: Ágnes
author list: Agent
  family name: Deák
  given name: Balázs
author list: Agent
  family name: Tóth
  given name: Katalin
author list: Agent
  family name: Kiss
  given name: Réka
author list: Agent
  family name: Lukács
  given name: Katalin
author list: Agent
  family name: Rádai
  given name: Zoltán
author list: Agent
  family name: Godó
  given name: Laura
author list: Agent
  family name: Borza
  given name: Sándor
author list: Agent
  family name: Kelemen
  given name: András
author list: Agent
  family name: Miglécz
  given name: Tamás
author list: Agent
  family name: Bátori
  given name: Zoltán
author list: Agent
  family name: Novák
  given name: Tibor József
author list: Agent
  family name: Valkó
  given name: Orsolya
doi: 10.7717/peerj.13226
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Tóth et al.
attribution name: Tóth et al.

Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept
type: item
type: AcademicArticle
description: The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequ…
format: application/pdf
format: text/html
creator: Joanna Pakulnicka
creator: Paweł Buczyński
creator: Edyta Buczyńska
creator: Edyta Stępień
creator: Agnieszka Szlauer-Łukaszewska
creator: Robert Stryjecki
creator: Aleksandra Bańkowska
creator: Vladimir Pešić
creator: Ewa Filip
creator: Andrzej Zawal
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13232
publisher: PeerJ Inc.
rights: © 2022 Pakulnicka et al.
abstract: The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequ…
bibliographic citation: Pakulnicka et al. (2022) Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept. PeerJ 10:e13232 https://doi.org/10.7717/peerj.13232
date submitted: 2021-10-04
date accepted: 2022-03-16
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pakulnicka
  given name: Joanna
author list: Agent
  family name: Buczyński
  given name: Paweł
author list: Agent
  family name: Buczyńska
  given name: Edyta
author list: Agent
  family name: Stępień
  given name: Edyta
author list: Agent
  family name: Szlauer-Łukaszewska
  given name: Agnieszka
author list: Agent
  family name: Stryjecki
  given name: Robert
author list: Agent
  family name: Bańkowska
  given name: Aleksandra
author list: Agent
  family name: Pešić
  given name: Vladimir
author list: Agent
  family name: Filip
  given name: Ewa
author list: Agent
  family name: Zawal
  given name: Andrzej
doi: 10.7717/peerj.13232
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Pakulnicka et al.
attribution name: Pakulnicka et al.

Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata)
type: item
type: AcademicArticle
description: Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
format: application/pdf
format: text/html
creator: Zihao Zhou
creator: Hongying Wu
creator: Dinghong Li
creator: Wenlong Zeng
creator: Jinlong Huang
creator: Zhengjun Wu
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.13245
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
bibliographic citation: Zhou et al. (2022) Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata). PeerJ 10:e13245 https://doi.org/10.7717/peerj.13245
date submitted: 2021-12-10
date accepted: 2022-03-18
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zihao
author list: Agent
  family name: Wu
  given name: Hongying
author list: Agent
  family name: Li
  given name: Dinghong
author list: Agent
  family name: Zeng
  given name: Wenlong
author list: Agent
  family name: Huang
  given name: Jinlong
author list: Agent
  family name: Wu
  given name: Zhengjun
doi: 10.7717/peerj.13245
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

Montreal Cognitive Assessment (MoCA) performance in Huntington’s disease patients correlates with cortical and caudate atrophy
type: item
type: AcademicArticle
description: Huntington’s Disease (HD) is an autosomal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. Cognitive impairment develops gradually in HD patients, progressing later into a severe cognitive dysfunction. The Montreal Cognitive Assessment (MoCA) is a brief screening test commonly employed to detect mild cognitive impairment, which has also been useful to assess cognitive decline in HD patients. However, the relationship between MoCA performance and brain structural integrity in HD patients remains unclear. Therefore, to explore this relationship we analyzed if cortical thinning and subcortical nuclei volume differences correlated with HD patients’ MoCA performance. Twenty-two HD patients and twenty-two healthy subjects participated in this study. T1-weighted images were acquired to analyze cortical thickness and subcortical nuclei volumes. Group comparison analysis showed a significantly lower score in the MoCA global performance of HD patients. Also, the MoCA total score correlated with cortical thinning of fronto-parietal and temporo-occipital cortices, as well as with bilateral caudate volume differences in HD patients. These results provide new insights into the effectiveness of using the MoCA test to detect cognitive impairment and the brain atrophy pattern associated with the cognitive status of prodromal/early HD patients.
format: application/pdf
format: text/html
creator: Gabriel Ramirez-Garcia
creator: Victor Galvez
creator: Rosalinda Diaz
creator: Aurelio Campos-Romo
creator: Juan Fernandez-Ruiz
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.12917
publisher: PeerJ Inc.
rights: © 2022 Ramirez-Garcia et al.
abstract: Huntington’s Disease (HD) is an autosomal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. Cognitive impairment develops gradually in HD patients, progressing later into a severe cognitive dysfunction. The Montreal Cognitive Assessment (MoCA) is a brief screening test commonly employed to detect mild cognitive impairment, which has also been useful to assess cognitive decline in HD patients. However, the relationship between MoCA performance and brain structural integrity in HD patients remains unclear. Therefore, to explore this relationship we analyzed if cortical thinning and subcortical nuclei volume differences correlated with HD patients’ MoCA performance. Twenty-two HD patients and twenty-two healthy subjects participated in this study. T1-weighted images were acquired to analyze cortical thickness and subcortical nuclei volumes. Group comparison analysis showed a significantly lower score in the MoCA global performance of HD patients. Also, the MoCA total score correlated with cortical thinning of fronto-parietal and temporo-occipital cortices, as well as with bilateral caudate volume differences in HD patients. These results provide new insights into the effectiveness of using the MoCA test to detect cognitive impairment and the brain atrophy pattern associated with the cognitive status of prodromal/early HD patients.
bibliographic citation: Ramirez-Garcia et al. (2022) Montreal Cognitive Assessment (MoCA) performance in Huntington’s disease patients correlates with cortical and caudate atrophy. PeerJ 10:e12917 https://doi.org/10.7717/peerj.12917
date submitted: 2021-09-03
date accepted: 2022-01-20
issued: 2022-04-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramirez-Garcia
  given name: Gabriel
author list: Agent
  family name: Galvez
  given name: Victor
author list: Agent
  family name: Diaz
  given name: Rosalinda
author list: Agent
  family name: Campos-Romo
  given name: Aurelio
author list: Agent
  family name: Fernandez-Ruiz
  given name: Juan
doi: 10.7717/peerj.12917
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-04
copyright: © 2022 Ramirez-Garcia et al.
attribution name: Ramirez-Garcia et al.

TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea
type: item
type: AcademicArticle
description: Background Clostridium perfringens (C. perfringens) type C is the principal pathogenic clostridia of swine, frequently causing hemorrhagic diarrhea, even necrotic enteritis in piglets, leading to severe economic loss for swine industr ies worldwide. However, there are no specific and effective prevention measures. Therefore, clarifying the molecular mechanisms of hosts against pathogenesis infection is very important to reduce the incidence of C. perfringens type C infected piglet diarrhea disease. Methods We performed an TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection. Results In this study, a total of 115, 176 and 83 DEPs were identified in SR vs SC, SS vs SC, and SR vs SC, respectively, which may play the important regulatory roles in the process of piglet spleens in response toC. perfringens type C-infected diarrhea diseases. GO enrichment analysis revealed that the DEPs were mostly significantly enriched in acute inflammatory response, defense response, antimicrobial response, transporter activity, cellular metabolic process and so on, and KEGG pathway enrichment analysis showed that the significantly enriched immune related pathways of the PPAR signaling pathway, IL-17 signaling pathway, antigen processing and presentation, which hints at the immune defense process of piglet spleen against C. perfringens infection. This study helps to elucidate the protein expressional pattern of piglet spleen against C. perfringens type C-infected diarrhea disease, which can contribute to the prevention and control for pig diarrhea disease and the further development of diarrhea resistant pig breeding.
format: application/pdf
format: text/html
creator: Xiaoli Wang
creator: Xiaoyu Huang
creator: Qiaoli Yang
creator: Zunqiang Yan
creator: Pengfei Wang
creator: Xiaoli Gao
creator: Ruirui Luo
creator: Shuangbao Gun
subject: Agricultural Science
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13006
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Clostridium perfringens (C. perfringens) type C is the principal pathogenic clostridia of swine, frequently causing hemorrhagic diarrhea, even necrotic enteritis in piglets, leading to severe economic loss for swine industr ies worldwide. However, there are no specific and effective prevention measures. Therefore, clarifying the molecular mechanisms of hosts against pathogenesis infection is very important to reduce the incidence of C. perfringens type C infected piglet diarrhea disease. Methods We performed an TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection. Results In this study, a total of 115, 176 and 83 DEPs were identified in SR vs SC, SS vs SC, and SR vs SC, respectively, which may play the important regulatory roles in the process of piglet spleens in response toC. perfringens type C-infected diarrhea diseases. GO enrichment analysis revealed that the DEPs were mostly significantly enriched in acute inflammatory response, defense response, antimicrobial response, transporter activity, cellular metabolic process and so on, and KEGG pathway enrichment analysis showed that the significantly enriched immune related pathways of the PPAR signaling pathway, IL-17 signaling pathway, antigen processing and presentation, which hints at the immune defense process of piglet spleen against C. perfringens infection. This study helps to elucidate the protein expressional pattern of piglet spleen against C. perfringens type C-infected diarrhea disease, which can contribute to the prevention and control for pig diarrhea disease and the further development of diarrhea resistant pig breeding.
bibliographic citation: Wang et al. (2022) TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea. PeerJ 10:e13006 https://doi.org/10.7717/peerj.13006
date submitted: 2021-02-08
date accepted: 2022-02-03
issued: 2022-04-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoli
author list: Agent
  family name: Huang
  given name: Xiaoyu
author list: Agent
  family name: Yang
  given name: Qiaoli
author list: Agent
  family name: Yan
  given name: Zunqiang
author list: Agent
  family name: Wang
  given name: Pengfei
author list: Agent
  family name: Gao
  given name: Xiaoli
author list: Agent
  family name: Luo
  given name: Ruirui
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.13006
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-04
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
type: item
type: AcademicArticle
description: Biomedical knowledge is represented in structured databases and published in biomedical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that combines information from literature and databases to predict drug targets and indications. To effectively utilize information in published literature, we integrate knowledge graphs and published literature using named entity recognition and normalization before applying a machine learning model that utilizes the combination of graph and literature. We then use supervised machine learning to show the effects of combining features from biomedical knowledge and published literature on the prediction of drug targets and drug indications. We demonstrate that our approach using datasets for drug-target interactions and drug indications is scalable to large graphs and can be used to improve the ranking of targets and indications by exploiting features from either structure or unstructured information alone.
format: application/pdf
format: text/html
creator: Mona Alshahrani
creator: Abdullah Almansour
creator: Asma Alkhaldi
creator: Maha A. Thafar
creator: Mahmut Uludag
creator: Magbubah Essack
creator: Robert Hoehndorf
subject: Computational Biology
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.13061
publisher: PeerJ Inc.
rights: © 2022 Alshahrani et al.
abstract: Biomedical knowledge is represented in structured databases and published in biomedical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that combines information from literature and databases to predict drug targets and indications. To effectively utilize information in published literature, we integrate knowledge graphs and published literature using named entity recognition and normalization before applying a machine learning model that utilizes the combination of graph and literature. We then use supervised machine learning to show the effects of combining features from biomedical knowledge and published literature on the prediction of drug targets and drug indications. We demonstrate that our approach using datasets for drug-target interactions and drug indications is scalable to large graphs and can be used to improve the ranking of targets and indications by exploiting features from either structure or unstructured information alone.
bibliographic citation: Alshahrani et al. (2022) Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PeerJ 10:e13061 https://doi.org/10.7717/peerj.13061
date submitted: 2020-08-28
date accepted: 2022-02-13
issued: 2022-04-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alshahrani
  given name: Mona
author list: Agent
  family name: Almansour
  given name: Abdullah
author list: Agent
  family name: Alkhaldi
  given name: Asma
author list: Agent
  family name: Thafar
  given name: Maha A.
author list: Agent
  family name: Uludag
  given name: Mahmut
author list: Agent
  family name: Essack
  given name: Magbubah
author list: Agent
  family name: Hoehndorf
  given name: Robert
doi: 10.7717/peerj.13061
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-04
copyright: ©2022 Alshahrani et al.
attribution name: Alshahrani et al.

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