PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost
items: Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults
items: Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia
items: Catalases in the pathogenesis of Sporothrix schenckii research
items: Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions
items: Symbiotic association of microalgae and plants in a deep water culture system
items: N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India
items: Hypoxia-induced factor and its role in liver fibrosis
items: Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers
items: Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction

Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost
type: item
type: AcademicArticle
description: Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.
format: application/pdf
format: text/html
creator: Wanqiu Chang
creator: Weilin Feng
creator: Yang Yang
creator: Yingyue Shen
creator: Tingting Song
creator: Yu Li
creator: Weiming Cai
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.14426
publisher: PeerJ Inc.
rights: © 2022 Chang et al.
abstract: Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.
bibliographic citation: Chang et al. (2022) Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost. PeerJ 10:e14426 https://doi.org/10.7717/peerj.14426
date submitted: 2022-08-10
date accepted: 2022-10-30
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Wanqiu
author list: Agent
  family name: Feng
  given name: Weilin
author list: Agent
  family name: Yang
  given name: Yang
author list: Agent
  family name: Shen
  given name: Yingyue
author list: Agent
  family name: Song
  given name: Tingting
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Cai
  given name: Weiming
doi: 10.7717/peerj.14426
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: ©2022 Chang et al.
attribution name: Chang et al.

Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults
type: item
type: AcademicArticle
description: Background Adequate trunk muscle endurance is considered to be an important indicator of good low back stability; therefore, its assessment is needed when determining an individual’s risk for back pain. Optimal tests to assess each trunk muscle group separately are difficult to find. The objective of this study was to verify if two groups of trunk muscle endurance tests (standard and alternative) show comparable results in terms of muscle endurance ratios, holding times and rated perceived effort to perform each test. Methods The study was designed as a quasi-experimental repeated-measures design. There was a single group of participants who took part in two different trunk muscle endurance testing. Sixty-eight healthy adult volunteers, aged 20–45 years (31.9 ± 7.2 years), without recent musculoskeletal injury or disorder participated in the study. All participants finished the study. Trunk muscle endurance tests as tested on the Roman chair (B tests) were compared with standard tests as suggested by McGill (A tests). Each group of tests consisted of an endurance test for trunk extensors, trunk flexors, and lateral trunk muscles for left and right side. The order of tests’ performances was randomly assigned to each participant, whereby a participant did perform A and B tests in the same order. In each test of A and B the holding time was recorded and a perceived effort in each test performance was also assessed by participants. Post testing performance the four ratios of trunk muscles endurance comparison were calculated for each group of tests to determine if there is a good or poor ratio between muscles. Results of each participant were compared for trunk muscle endurance ratio calculations, holding times and rated perceived effort for A and B tests. Results Results showed comparable trunk muscle endurance ratios in the three ratios observed, except for the flexors:extensors ratio (AFL:EX: 1.2 (IQR: 0.7–1.6) vs. BFL:EX: 0.6 (IQR: 0.3–0.8); p < 0.001). As compared …
format: application/pdf
format: text/html
creator: Maja Petrič
creator: Lijana Zaletel-Kragelj
creator: Renata Vauhnik
subject: Anatomy and Physiology
subject: Kinesiology
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.14469
publisher: PeerJ Inc.
rights: © 2022 Petrič et al.
abstract: Background Adequate trunk muscle endurance is considered to be an important indicator of good low back stability; therefore, its assessment is needed when determining an individual’s risk for back pain. Optimal tests to assess each trunk muscle group separately are difficult to find. The objective of this study was to verify if two groups of trunk muscle endurance tests (standard and alternative) show comparable results in terms of muscle endurance ratios, holding times and rated perceived effort to perform each test. Methods The study was designed as a quasi-experimental repeated-measures design. There was a single group of participants who took part in two different trunk muscle endurance testing. Sixty-eight healthy adult volunteers, aged 20–45 years (31.9 ± 7.2 years), without recent musculoskeletal injury or disorder participated in the study. All participants finished the study. Trunk muscle endurance tests as tested on the Roman chair (B tests) were compared with standard tests as suggested by McGill (A tests). Each group of tests consisted of an endurance test for trunk extensors, trunk flexors, and lateral trunk muscles for left and right side. The order of tests’ performances was randomly assigned to each participant, whereby a participant did perform A and B tests in the same order. In each test of A and B the holding time was recorded and a perceived effort in each test performance was also assessed by participants. Post testing performance the four ratios of trunk muscles endurance comparison were calculated for each group of tests to determine if there is a good or poor ratio between muscles. Results of each participant were compared for trunk muscle endurance ratio calculations, holding times and rated perceived effort for A and B tests. Results Results showed comparable trunk muscle endurance ratios in the three ratios observed, except for the flexors:extensors ratio (AFL:EX: 1.2 (IQR: 0.7–1.6) vs. BFL:EX: 0.6 (IQR: 0.3–0.8); p < 0.001). As compared …
bibliographic citation: Petrič et al. (2022) Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults. PeerJ 10:e14469 https://doi.org/10.7717/peerj.14469
date submitted: 2022-07-13
date accepted: 2022-11-06
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petrič
  given name: Maja
author list: Agent
  family name: Zaletel-Kragelj
  given name: Lijana
author list: Agent
  family name: Vauhnik
  given name: Renata
doi: 10.7717/peerj.14469
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: © 2022 Petrič et al.
attribution name: Petrič et al.

Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia
type: item
type: AcademicArticle
description: Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013–2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn’t demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source p…
format: application/pdf
format: text/html
creator: Slobodan Davidović
creator: Saša Marinković
creator: Irena Hribšek
creator: Aleksandra Patenković
creator: Marina Stamenković-Radak
creator: Marija Tanasković
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.14477
publisher: PeerJ Inc.
rights: © 2022 Davidović et al.
abstract: Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013–2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn’t demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source p…
bibliographic citation: Davidović et al. (2022) Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia. PeerJ 10:e14477 https://doi.org/10.7717/peerj.14477
date submitted: 2022-07-13
date accepted: 2022-11-07
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davidović
  given name: Slobodan
author list: Agent
  family name: Marinković
  given name: Saša
author list: Agent
  family name: Hribšek
  given name: Irena
author list: Agent
  family name: Patenković
  given name: Aleksandra
author list: Agent
  family name: Stamenković-Radak
  given name: Marina
author list: Agent
  family name: Tanasković
  given name: Marija
doi: 10.7717/peerj.14477
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: © 2022 Davidović et al.
attribution name: Davidović et al.

Catalases in the pathogenesis of Sporothrix schenckii research
type: item
type: AcademicArticle
description: Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enz…
format: application/pdf
format: text/html
creator: Naurú Idalia Vargas-Maya
creator: Vianey Olmedo-Monfil
creator: Jorge Humberto Ramírez-Prado
creator: Ruth Reyes-Cortés
creator: Felipe Padilla-Vaca
creator: Bernardo Franco
subject: Biochemistry
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.14478
publisher: PeerJ Inc.
rights: © 2022 Vargas-Maya et al.
abstract: Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enz…
bibliographic citation: Vargas-Maya et al. (2022) Catalases in the pathogenesis of Sporothrix schenckii research. PeerJ 10:e14478 https://doi.org/10.7717/peerj.14478
date submitted: 2022-09-08
date accepted: 2022-11-07
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vargas-Maya
  given name: Naurú Idalia
author list: Agent
  family name: Olmedo-Monfil
  given name: Vianey
author list: Agent
  family name: Ramírez-Prado
  given name: Jorge Humberto
author list: Agent
  family name: Reyes-Cortés
  given name: Ruth
author list: Agent
  family name: Padilla-Vaca
  given name: Felipe
author list: Agent
  family name: Franco
  given name: Bernardo
doi: 10.7717/peerj.14478
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: ©2022 Vargas-Maya et al.
attribution name: Vargas-Maya et al.

Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions
type: item
type: AcademicArticle
description: Weighted percentiles in many areas can be used to investigate the overall trend in a particular context. In this article, the confidence intervals for the common percentile are constructed to estimate rainfall in Thailand. The confidence interval for the common percentile help to indicate intensity of rainfall. Herein, four new approaches for estimating confidence intervals for the common percentile of several delta-lognormal distributions are presented: the fiducial generalized confidence interval, the adjusted method of variance estimates recovery, and two Bayesian approaches using fiducial quantity and approximate fiducial distribution. The Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths via the R statistical program. The proposed confidence intervals are compared in terms of their coverage probabilities and average lengths, and the results of a comparative study based on these metrics indicate that one of the Bayesian confidence intervals is better than the others. The efficacies of the approaches are also illustrated by applying them to daily rainfall datasets from various regions in Thailand.
format: application/pdf
format: text/html
creator: Warisa Thangjai
creator: Sa-Aat Niwitpong
creator: Suparat Niwitpong
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Environmental Impacts
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.14498
publisher: PeerJ Inc.
rights: © 2022 Thangjai et al.
abstract: Weighted percentiles in many areas can be used to investigate the overall trend in a particular context. In this article, the confidence intervals for the common percentile are constructed to estimate rainfall in Thailand. The confidence interval for the common percentile help to indicate intensity of rainfall. Herein, four new approaches for estimating confidence intervals for the common percentile of several delta-lognormal distributions are presented: the fiducial generalized confidence interval, the adjusted method of variance estimates recovery, and two Bayesian approaches using fiducial quantity and approximate fiducial distribution. The Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths via the R statistical program. The proposed confidence intervals are compared in terms of their coverage probabilities and average lengths, and the results of a comparative study based on these metrics indicate that one of the Bayesian confidence intervals is better than the others. The efficacies of the approaches are also illustrated by applying them to daily rainfall datasets from various regions in Thailand.
bibliographic citation: Thangjai et al. (2022) Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions. PeerJ 10:e14498 https://doi.org/10.7717/peerj.14498
date submitted: 2022-09-06
date accepted: 2022-11-10
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thangjai
  given name: Warisa
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
author list: Agent
  family name: Niwitpong
  given name: Suparat
doi: 10.7717/peerj.14498
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: © 2022 Thangjai et al.
attribution name: Thangjai et al.

Symbiotic association of microalgae and plants in a deep water culture system
type: item
type: AcademicArticle
description: In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow.
format: application/pdf
format: text/html
creator: Gülsüm Ebru Özer Uyar
creator: Nurdan Mısmıl
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.14536
publisher: PeerJ Inc.
rights: © 2022 Özer Uyar and Mısmıl
abstract: In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow.
bibliographic citation: Özer Uyar et al. (2022) Symbiotic association of microalgae and plants in a deep water culture system. PeerJ 10:e14536 https://doi.org/10.7717/peerj.14536
date submitted: 2022-09-11
date accepted: 2022-11-17
issued: 2022-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Özer Uyar
  given name: Gülsüm Ebru
author list: Agent
  family name: Mısmıl
  given name: Nurdan
doi: 10.7717/peerj.14536
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-07
copyright: © 2022 Özer Uyar and Mısmıl
attribution name: Özer Uyar and Mısmıl

N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India
type: item
type: AcademicArticle
description: Reliable estimation of abundance is a prerequisite for a species’ conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides bett…
format: application/pdf
format: text/html
creator: Sankarshan Chaudhuri
creator: Rajasekar Rajaraman
creator: Sankar Kalyanasundaram
creator: Sambandam Sathyakumar
creator: Ramesh Krishnamurthy
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.13649
publisher: PeerJ Inc.
rights: © 2022 Chaudhuri et al.
abstract: Reliable estimation of abundance is a prerequisite for a species’ conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides bett…
bibliographic citation: Chaudhuri et al. (2022) N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India. PeerJ 10:e13649 https://doi.org/10.7717/peerj.13649
date submitted: 2021-09-27
date accepted: 2022-06-07
issued: 2022-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chaudhuri
  given name: Sankarshan
author list: Agent
  family name: Rajaraman
  given name: Rajasekar
author list: Agent
  family name: Kalyanasundaram
  given name: Sankar
author list: Agent
  family name: Sathyakumar
  given name: Sambandam
author list: Agent
  family name: Krishnamurthy
  given name: Ramesh
doi: 10.7717/peerj.13649
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-06
copyright: © 2022 Chaudhuri et al.
attribution name: Chaudhuri et al.

Hypoxia-induced factor and its role in liver fibrosis
type: item
type: AcademicArticle
description: Liver fibrosis develops as a result of severe liver damage and is considered a major clinical concern throughout the world. Many factors are crucial for liver fibrosis progression. While advancements have been made to understand this disease, no effective pharmacological drug and treatment strategies have been established that can effectively prevent liver fibrosis or even could halt the fibrotic process. Most of those advances in curing liver fibrosis have been aimed towards mitigating the causes of fibrosis, including the development of potent antivirals to inhibit the hepatitis virus. It is not practicable for many individuals; however, a liver transplant becomes the only suitable alternative. A liver transplant is an expensive procedure. Thus, there is a significant need to identify potential targets of liver fibrosis and the development of such agents that can effectively treat or reverse liver fibrosis by targeting them. Researchers have identified hypoxia-inducible factors (HIFs) in the last 16 years as important transcription factors driving several facets of liver fibrosis, making them possible therapeutic targets. The latest knowledge on HIFs and their possible role in liver fibrosis, along with the cell-specific activities of such transcription factors that how they play role in liver fibrosis progression, is discussed in this review.
format: application/pdf
format: text/html
creator: Jan Mohammad Omar
creator: Yang Hai
creator: Shizhu Jin
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.14299
publisher: PeerJ Inc.
rights: © 2022 Mohammad Omar et al.
abstract: Liver fibrosis develops as a result of severe liver damage and is considered a major clinical concern throughout the world. Many factors are crucial for liver fibrosis progression. While advancements have been made to understand this disease, no effective pharmacological drug and treatment strategies have been established that can effectively prevent liver fibrosis or even could halt the fibrotic process. Most of those advances in curing liver fibrosis have been aimed towards mitigating the causes of fibrosis, including the development of potent antivirals to inhibit the hepatitis virus. It is not practicable for many individuals; however, a liver transplant becomes the only suitable alternative. A liver transplant is an expensive procedure. Thus, there is a significant need to identify potential targets of liver fibrosis and the development of such agents that can effectively treat or reverse liver fibrosis by targeting them. Researchers have identified hypoxia-inducible factors (HIFs) in the last 16 years as important transcription factors driving several facets of liver fibrosis, making them possible therapeutic targets. The latest knowledge on HIFs and their possible role in liver fibrosis, along with the cell-specific activities of such transcription factors that how they play role in liver fibrosis progression, is discussed in this review.
bibliographic citation: Mohammad Omar et al. (2022) Hypoxia-induced factor and its role in liver fibrosis. PeerJ 10:e14299 https://doi.org/10.7717/peerj.14299
date submitted: 2022-05-16
date accepted: 2022-10-04
issued: 2022-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohammad Omar
  given name: Jan
author list: Agent
  family name: Hai
  given name: Yang
author list: Agent
  family name: Jin
  given name: Shizhu
doi: 10.7717/peerj.14299
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-06
copyright: ©2022 Mohammad Omar et al.
attribution name: Mohammad Omar et al.

Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers
type: item
type: AcademicArticle
description: Background Indoor climbing involves overloading the shoulder girdle, including the rotator cuff and upper trapezius muscles. This on the field study aimed to investigate the effects of repeated climbing bouts on morphological and mechanical measures of the upper trapezius muscle. Materials and Methods Fifteen experienced male climbers participated in the study. Rate of perceived exertion (RPE), blood lactate concentration ([La−]b), and stiffness and thickness over four points of the upper trapezius were assessed before and after a repeated climbing exercise. The procedure for the climbing exercise consisted of five climbs for a total time of 5-minutes per climb, followed by a 5-minute rest. Results The analysis showed an increase from baseline to after the 3rd climb (p ≤ 0.01) for RPE and after the 5th climb for [La−]b (p ≤ 0.001). Muscle stiffness and thickness increased at all points (1–2–3–4) after the 5th climb (p ≤ 0.01). We found spatial heterogeneity in muscle stiffness and thickness; muscle stiffness was the highest at Point 4 (p ≤ 0.01), while muscle thickness reached the highest values at points 1–2 (both p ≤ 0.01). Moreover, the analysis between the dominant and non-dominant shoulder showed greater stiffness after the 1st climb at Point 1 (p = 0.004) and after the 5th climb at Point 4 (p ≤ 0.001). Conclusions For muscle thickness, the analysis showed significant changes in time and location between the dominant and the non-dominant shoulder. Bilateral increases in upper trapezius muscle stiffness and thickness, with simultaneous increases in RPE and blood lactate in response to consecutive climbs eliciting fatigue.
format: application/pdf
format: text/html
creator: Sebastian Klich
creator: Adam Kawczyński
creator: Klaudia Sommer
creator: Natalia Danek
creator: César Fernández-de-las-Peñas
creator: Lori A. Michener
creator: Pascal Madeleine
subject: Anatomy and Physiology
subject: Kinesiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.14409
publisher: PeerJ Inc.
rights: © 2022 Klich et al.
abstract: Background Indoor climbing involves overloading the shoulder girdle, including the rotator cuff and upper trapezius muscles. This on the field study aimed to investigate the effects of repeated climbing bouts on morphological and mechanical measures of the upper trapezius muscle. Materials and Methods Fifteen experienced male climbers participated in the study. Rate of perceived exertion (RPE), blood lactate concentration ([La−]b), and stiffness and thickness over four points of the upper trapezius were assessed before and after a repeated climbing exercise. The procedure for the climbing exercise consisted of five climbs for a total time of 5-minutes per climb, followed by a 5-minute rest. Results The analysis showed an increase from baseline to after the 3rd climb (p ≤ 0.01) for RPE and after the 5th climb for [La−]b (p ≤ 0.001). Muscle stiffness and thickness increased at all points (1–2–3–4) after the 5th climb (p ≤ 0.01). We found spatial heterogeneity in muscle stiffness and thickness; muscle stiffness was the highest at Point 4 (p ≤ 0.01), while muscle thickness reached the highest values at points 1–2 (both p ≤ 0.01). Moreover, the analysis between the dominant and non-dominant shoulder showed greater stiffness after the 1st climb at Point 1 (p = 0.004) and after the 5th climb at Point 4 (p ≤ 0.001). Conclusions For muscle thickness, the analysis showed significant changes in time and location between the dominant and the non-dominant shoulder. Bilateral increases in upper trapezius muscle stiffness and thickness, with simultaneous increases in RPE and blood lactate in response to consecutive climbs eliciting fatigue.
bibliographic citation: Klich et al. (2022) Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers. PeerJ 10:e14409 https://doi.org/10.7717/peerj.14409
date submitted: 2022-09-27
date accepted: 2022-10-27
issued: 2022-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klich
  given name: Sebastian
author list: Agent
  family name: Kawczyński
  given name: Adam
author list: Agent
  family name: Sommer
  given name: Klaudia
author list: Agent
  family name: Danek
  given name: Natalia
author list: Agent
  family name: Fernández-de-las-Peñas
  given name: César
author list: Agent
  family name: Michener
  given name: Lori A.
author list: Agent
  family name: Madeleine
  given name: Pascal
doi: 10.7717/peerj.14409
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-06
copyright: ©2022 Klich et al.
attribution name: Klich et al.

Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction
type: item
type: AcademicArticle
description: Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational methods for ubiquitination site prediction in recent years. However, traditional machine learning methods focus on feature engineering and are not suitable for large-scale proteomic data. In addition, deep learning methods are mostly based on convolutional neural networks and fuse multiple coding approaches to achieve classification prediction. This cannot effectively identify potential fine-grained features of the input data and has limitations in the representation of dependencies between low-level features and high-level features. A multi-dimensional feature recognition model based on a capsule network (MDCapsUbi) was proposed to predict protein ubiquitination sites. The proposed module consisting of convolution operations and channel attention was used to recognize coarse-grained features in the sequence dimension and the feature map dimension. The capsule network module consisting of capsule vectors was used to identify fine-grained features and classify ubiquitinated sites. With ten-fold cross-validation, the MDCapsUbi achieved 91.82% accuracy, 91.39% sensitivity, 92.24% specificity, 0.837 MCC, 0.918 F-Score and 0.97 AUC. Experimental results indicated that the proposed method outperformed other ubiquitination site prediction technologies.
format: application/pdf
format: text/html
creator: Weimin Li
creator: Jie Wang
creator: Yin Luo
creator: Tsigabu Teame Bezabih
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.14427
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational methods for ubiquitination site prediction in recent years. However, traditional machine learning methods focus on feature engineering and are not suitable for large-scale proteomic data. In addition, deep learning methods are mostly based on convolutional neural networks and fuse multiple coding approaches to achieve classification prediction. This cannot effectively identify potential fine-grained features of the input data and has limitations in the representation of dependencies between low-level features and high-level features. A multi-dimensional feature recognition model based on a capsule network (MDCapsUbi) was proposed to predict protein ubiquitination sites. The proposed module consisting of convolution operations and channel attention was used to recognize coarse-grained features in the sequence dimension and the feature map dimension. The capsule network module consisting of capsule vectors was used to identify fine-grained features and classify ubiquitinated sites. With ten-fold cross-validation, the MDCapsUbi achieved 91.82% accuracy, 91.39% sensitivity, 92.24% specificity, 0.837 MCC, 0.918 F-Score and 0.97 AUC. Experimental results indicated that the proposed method outperformed other ubiquitination site prediction technologies.
bibliographic citation: Li et al. (2022) Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction. PeerJ 10:e14427 https://doi.org/10.7717/peerj.14427
date submitted: 2022-06-23
date accepted: 2022-10-30
issued: 2022-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Weimin
author list: Agent
  family name: Wang
  given name: Jie
author list: Agent
  family name: Luo
  given name: Yin
author list: Agent
  family name: Bezabih
  given name: Tsigabu Teame
doi: 10.7717/peerj.14427
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-06
copyright: ©2022 Li et al.
attribution name: Li et al.

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