PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
items: Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
items: Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
items: Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
items: Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels
items: A newly recognized theropod assemblage from the Lewisville Formation (Woodbine Group; Cenomanian) and its implications for understanding Late Cretaceous Appalachian terrestrial ecosystems
items: Seasonal and diel variations in the vertical distribution, composition, abundance and biomass of zooplankton in a deep Chilean Patagonian Fjord
items: The relationship between endorsing reporting guidelines or trial registration and the impact factor or total citations in surgical journals
items: Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer
items: Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults

The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
type: item
type: AcademicArticle
description: Background Body composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women. Methods The sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated. Results The cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32). Conclusion BMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predictin…
format: application/pdf
format: text/html
creator: Jarosław Domaradzki
creator: Dawid Koźlenia
subject: Kinesiology
subject: Environmental Health
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12745
publisher: PeerJ Inc.
rights: © 2022 Domaradzki and Koźlenia
abstract: Background Body composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women. Methods The sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated. Results The cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32). Conclusion BMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predictin…
bibliographic citation: Domaradzki et al. (2022) The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women. PeerJ 10:e12745 https://doi.org/10.7717/peerj.12745
date submitted: 2021-10-04
date accepted: 2021-12-14
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Domaradzki
  given name: Jarosław
author list: Agent
  family name: Koźlenia
  given name: Dawid
doi: 10.7717/peerj.12745
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Domaradzki and Koźlenia
attribution name: Domaradzki and Koźlenia

Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
type: item
type: AcademicArticle
description: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, where…
format: application/pdf
format: text/html
creator: Jih-Terng Wang
creator: Chi-Wei Chu
creator: Keryea Soong
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.12840
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, where…
bibliographic citation: Wang et al. (2022) Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals. PeerJ 10:e12840 https://doi.org/10.7717/peerj.12840
date submitted: 2021-09-01
date accepted: 2022-01-06
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jih-Terng
author list: Agent
  family name: Chu
  given name: Chi-Wei
author list: Agent
  family name: Soong
  given name: Keryea
doi: 10.7717/peerj.12840
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
type: item
type: AcademicArticle
description: Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors fac…
format: application/pdf
format: text/html
creator: David M. Hudson
creator: Jason S. Krumholz
creator: Darby L. Pochtar
creator: Natasha C. Dickenson
creator: Georges Dossot
creator: Gillian Phillips
creator: Edward P. Baker
creator: Tara E. Moll
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.12841
publisher: PeerJ Inc.
rights: © 2022 Hudson et al.
abstract: Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors fac…
bibliographic citation: Hudson et al. (2022) Potential impacts from simulated vessel noise and sonar on commercially important invertebrates. PeerJ 10:e12841 https://doi.org/10.7717/peerj.12841
date submitted: 2021-02-04
date accepted: 2022-01-06
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hudson
  given name: David M.
author list: Agent
  family name: Krumholz
  given name: Jason S.
author list: Agent
  family name: Pochtar
  given name: Darby L.
author list: Agent
  family name: Dickenson
  given name: Natasha C.
author list: Agent
  family name: Dossot
  given name: Georges
author list: Agent
  family name: Phillips
  given name: Gillian
author list: Agent
  family name: Baker
  given name: Edward P.
author list: Agent
  family name: Moll
  given name: Tara E.
doi: 10.7717/peerj.12841
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Hudson et al.
attribution name: Hudson et al.

Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
type: item
type: AcademicArticle
description: Background Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
format: application/pdf
format: text/html
creator: Xiao Zhang
creator: Juanjuan Tong
creator: Mengmeng Dong
creator: Kashif Akhtar
creator: Bing He
subject: Agricultural Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12677
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
bibliographic citation: Zhang et al. (2022) Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production. PeerJ 10:e12677 https://doi.org/10.7717/peerj.12677
date submitted: 2021-09-06
date accepted: 2021-12-02
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiao
author list: Agent
  family name: Tong
  given name: Juanjuan
author list: Agent
  family name: Dong
  given name: Mengmeng
author list: Agent
  family name: Akhtar
  given name: Kashif
author list: Agent
  family name: He
  given name: Bing
doi: 10.7717/peerj.12677
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels
type: item
type: AcademicArticle
description: Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The …
format: application/pdf
format: text/html
creator: Ning Jiao
creator: Xiaoshuang Song
creator: Ruiqing Song
creator: Dachuan Yin
creator: Xun Deng
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.12778
publisher: PeerJ Inc.
rights: © 2022 Jiao et al.
abstract: Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The …
bibliographic citation: Jiao et al. (2022) Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels. PeerJ 10:e12778 https://doi.org/10.7717/peerj.12778
date submitted: 2021-08-17
date accepted: 2021-12-21
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Ning
author list: Agent
  family name: Song
  given name: Xiaoshuang
author list: Agent
  family name: Song
  given name: Ruiqing
author list: Agent
  family name: Yin
  given name: Dachuan
author list: Agent
  family name: Deng
  given name: Xun
doi: 10.7717/peerj.12778
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: ©2022 Jiao et al.
attribution name: Jiao et al.

A newly recognized theropod assemblage from the Lewisville Formation (Woodbine Group; Cenomanian) and its implications for understanding Late Cretaceous Appalachian terrestrial ecosystems
type: item
type: AcademicArticle
description: While the terrestrial fossil record of the mid-Cretaceous interval (Aptian to Cenomanian) in North America has been poorly studied, the recent focus on fossil localities from the western United States has offered a more detailed picture of vertebrate diversity, ecosystem dynamics and faunal turnover that took place on the western landmass of Laramidia. This is in stark contrast to the terrestrial record from the eastern landmass of Appalachia, where vertebrate fossils are rare and consist mostly of isolated and fragmentary remains. However, a detailed understanding of these fossil communities during this interval is necessary for comparison of the faunal patterns that developed during the opening of the Western Interior Seaway (WIS). The Woodbine Group of Texas is a Cenomanian age (95–100 mya) deposit consisting of shallow marine, deltaic, and terrestrial communities, which were only recently separated from their western counterparts. These deposits have yielded a wealth of vertebrate remains, yet non-avian theropods are still largely unknown. Recently, multiple localities in the Lewisville Formation of the Woodbine Group have yielded new non-avian theropod material, including numerous isolated teeth and postcranial remains. While largely fragmentary, this material is sufficiently diagnostic to identify the following taxa: a large-bodied carcharodontosaur, a mid-sized tyrannosauroid, a large ornithomimosaur, a large dromaeosaurine, a small dromaeosaurid, a small troodontid, and a small coelurosaur. Some of these groups represent the first occurrence for Appalachia and provide a broader understanding of a newly expanded faunal diversity for the Eastern landmass. The Lewisville Formation theropod fauna is similar in taxonomic composition to contemporaneous deposits in Laramidia, confirming that these groups were widespread across the continent prior to extension of the WIS. The Lewisville Formation documents the transitional nature of Cenomanian coastal ecosystems in …
format: application/pdf
format: text/html
creator: Christopher R. Noto
creator: Domenic C. D’Amore
creator: Stephanie K. Drumheller
creator: Thomas L. Adams
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.12782
publisher: PeerJ Inc.
rights: © 2022 Noto et al.
abstract: While the terrestrial fossil record of the mid-Cretaceous interval (Aptian to Cenomanian) in North America has been poorly studied, the recent focus on fossil localities from the western United States has offered a more detailed picture of vertebrate diversity, ecosystem dynamics and faunal turnover that took place on the western landmass of Laramidia. This is in stark contrast to the terrestrial record from the eastern landmass of Appalachia, where vertebrate fossils are rare and consist mostly of isolated and fragmentary remains. However, a detailed understanding of these fossil communities during this interval is necessary for comparison of the faunal patterns that developed during the opening of the Western Interior Seaway (WIS). The Woodbine Group of Texas is a Cenomanian age (95–100 mya) deposit consisting of shallow marine, deltaic, and terrestrial communities, which were only recently separated from their western counterparts. These deposits have yielded a wealth of vertebrate remains, yet non-avian theropods are still largely unknown. Recently, multiple localities in the Lewisville Formation of the Woodbine Group have yielded new non-avian theropod material, including numerous isolated teeth and postcranial remains. While largely fragmentary, this material is sufficiently diagnostic to identify the following taxa: a large-bodied carcharodontosaur, a mid-sized tyrannosauroid, a large ornithomimosaur, a large dromaeosaurine, a small dromaeosaurid, a small troodontid, and a small coelurosaur. Some of these groups represent the first occurrence for Appalachia and provide a broader understanding of a newly expanded faunal diversity for the Eastern landmass. The Lewisville Formation theropod fauna is similar in taxonomic composition to contemporaneous deposits in Laramidia, confirming that these groups were widespread across the continent prior to extension of the WIS. The Lewisville Formation documents the transitional nature of Cenomanian coastal ecosystems in …
bibliographic citation: Noto et al. (2022) A newly recognized theropod assemblage from the Lewisville Formation (Woodbine Group; Cenomanian) and its implications for understanding Late Cretaceous Appalachian terrestrial ecosystems. PeerJ 10:e12782 https://doi.org/10.7717/peerj.12782
date submitted: 2021-07-15
date accepted: 2021-12-21
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Noto
  given name: Christopher R.
author list: Agent
  family name: D’Amore
  given name: Domenic C.
author list: Agent
  family name: Drumheller
  given name: Stephanie K.
author list: Agent
  family name: Adams
  given name: Thomas L.
doi: 10.7717/peerj.12782
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: © 2022 Noto et al.
attribution name: Noto et al.

Seasonal and diel variations in the vertical distribution, composition, abundance and biomass of zooplankton in a deep Chilean Patagonian Fjord
type: item
type: AcademicArticle
description: Comau Fjord is a stratified Chilean Patagonian Fjord characterized by a shallow brackish surface layer and a >400 m layer of aragonite-depleted subsurface waters. Despite the energetic burden of low aragonite saturation levels to calcification, Comau Fjord harbours dense populations of cold-water corals (CWC). While this paradox has been attributed to a rich supply of zooplankton, supporting abundance and biomass data are so far lacking. In this study, we investigated the seasonal and diel changes of the zooplankton community over the entire water column. We used a Nansen net (100 µm mesh) to take stratified vertical hauls between the surface and the bottom (0-50-100-200-300-400-450 m). Samples were scanned with a ZooScan, and abundance, biovolume and biomass were determined for 41 taxa identified on the web-based platform EcoTaxa 2.0. Zooplankton biomass was the highest in summer (209 g dry mass m−2) and the lowest in winter (61 g dry mass m−2). Abundance, however, peaked in spring, suggesting a close correspondence between reproduction and phytoplankton spring blooms (Chl a max. 50.86 mg m−3, 3 m depth). Overall, copepods were the most important group of the total zooplankton community, both in abundance (64–81%) and biovolume (20–70%) followed by mysids and chaetognaths (in terms of biovolume and biomass), and nauplii and Appendicularia (in terms of abundance). Throughout the year, diel changes in the vertical distribution of biomass were found with a daytime maximum in the 100–200 m depth layer and a nighttime maximum in surface waters (0–50 m), associated with the diel vertical migration of the calanoid copepod family Metridinidae. Diel differences in integrated zooplankton abundance, biovolume and biomass were probably due to a high zooplankton patchiness driven by biological processes (e.g., diel vertical migration or predation avoidance), and oceanographic processes (estuarine circulation, tidal mixing or water column stratification). Those factors are consi…
format: application/pdf
format: text/html
creator: Nur Garcia-Herrera
creator: Astrid Cornils
creator: Jürgen Laudien
creator: Barbara Niehoff
creator: Juan Höfer
creator: Günter Försterra
creator: Humberto E. González
creator: Claudio Richter
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12823
publisher: PeerJ Inc.
rights: © 2022 Garcia-Herrera et al.
abstract: Comau Fjord is a stratified Chilean Patagonian Fjord characterized by a shallow brackish surface layer and a >400 m layer of aragonite-depleted subsurface waters. Despite the energetic burden of low aragonite saturation levels to calcification, Comau Fjord harbours dense populations of cold-water corals (CWC). While this paradox has been attributed to a rich supply of zooplankton, supporting abundance and biomass data are so far lacking. In this study, we investigated the seasonal and diel changes of the zooplankton community over the entire water column. We used a Nansen net (100 µm mesh) to take stratified vertical hauls between the surface and the bottom (0-50-100-200-300-400-450 m). Samples were scanned with a ZooScan, and abundance, biovolume and biomass were determined for 41 taxa identified on the web-based platform EcoTaxa 2.0. Zooplankton biomass was the highest in summer (209 g dry mass m−2) and the lowest in winter (61 g dry mass m−2). Abundance, however, peaked in spring, suggesting a close correspondence between reproduction and phytoplankton spring blooms (Chl a max. 50.86 mg m−3, 3 m depth). Overall, copepods were the most important group of the total zooplankton community, both in abundance (64–81%) and biovolume (20–70%) followed by mysids and chaetognaths (in terms of biovolume and biomass), and nauplii and Appendicularia (in terms of abundance). Throughout the year, diel changes in the vertical distribution of biomass were found with a daytime maximum in the 100–200 m depth layer and a nighttime maximum in surface waters (0–50 m), associated with the diel vertical migration of the calanoid copepod family Metridinidae. Diel differences in integrated zooplankton abundance, biovolume and biomass were probably due to a high zooplankton patchiness driven by biological processes (e.g., diel vertical migration or predation avoidance), and oceanographic processes (estuarine circulation, tidal mixing or water column stratification). Those factors are consi…
bibliographic citation: Garcia-Herrera et al. (2022) Seasonal and diel variations in the vertical distribution, composition, abundance and biomass of zooplankton in a deep Chilean Patagonian Fjord. PeerJ 10:e12823 https://doi.org/10.7717/peerj.12823
date submitted: 2021-08-20
date accepted: 2021-12-31
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia-Herrera
  given name: Nur
author list: Agent
  family name: Cornils
  given name: Astrid
author list: Agent
  family name: Laudien
  given name: Jürgen
author list: Agent
  family name: Niehoff
  given name: Barbara
author list: Agent
  family name: Höfer
  given name: Juan
author list: Agent
  family name: Försterra
  given name: Günter
author list: Agent
  family name: González
  given name: Humberto E.
author list: Agent
  family name: Richter
  given name: Claudio
doi: 10.7717/peerj.12823
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: ©2022 Garcia-Herrera et al.
attribution name: Garcia-Herrera et al.

The relationship between endorsing reporting guidelines or trial registration and the impact factor or total citations in surgical journals
type: item
type: AcademicArticle
description: Background A journal’s impact factor (IF) and total citations are often used as indicators of its publication quality. Furthermore, journals that require authors to abide by reporting guidelines or conduct trial registration generally have a higher quality of reporting. In this study, we sought to explore the potential associations between the enforcement of reporting guidelines or trial registration and a surgical journal’s IF or total citations in order to find new approaches and ideas to improve journal publication quality. Methods We examined surgical journals from the 2018 Journal Citation Report’s Expanded Scientific Citation Index to quantify the use of reporting guidelines or study registration. We reviewed the “instructions for authors” from each journal and used multivariable linear regression analysis to determine which guidelines were associated with the journal IF and total citations. The dependent variable was the logarithm base 10 of the IF in 2018 or the logarithm base 10 of total citations in 2018 (the results were presented as geometric means, specifically the ratio of the “endorsed group” results to “not endorsed group” results). The independent variable was one of the requirements (endorsed and not endorsed). Models adjust for the publication region, language, start year, publisher and journal size (only used to adjust total citations). Results We included 188 surgical journals in our study. The results of multivariable linear regression analysis showed that journal IF was associated (P < 0.01) with the following requirements: randomized controlled trial (RCT) registration (geometric means ratio (GR) = 1.422, 95% CI [1.197–1.694]), Consolidated Standards of Reporting Trials (CONSORT) statement (1.318, [1.104–1.578]), Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) statement (1.390, [1.148–1.683]), Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement (1.556, [1.262–1.919]), Standards for R…
format: application/pdf
format: text/html
creator: Jing Zhou
creator: Jianqiang Li
creator: Jingao Zhang
creator: Bo Geng
creator: Yao Chen
creator: Xiaobin Zhou
subject: Surgery and Surgical Specialties
subject: Statistics
description: doi:10.7717/peerj.12837
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background A journal’s impact factor (IF) and total citations are often used as indicators of its publication quality. Furthermore, journals that require authors to abide by reporting guidelines or conduct trial registration generally have a higher quality of reporting. In this study, we sought to explore the potential associations between the enforcement of reporting guidelines or trial registration and a surgical journal’s IF or total citations in order to find new approaches and ideas to improve journal publication quality. Methods We examined surgical journals from the 2018 Journal Citation Report’s Expanded Scientific Citation Index to quantify the use of reporting guidelines or study registration. We reviewed the “instructions for authors” from each journal and used multivariable linear regression analysis to determine which guidelines were associated with the journal IF and total citations. The dependent variable was the logarithm base 10 of the IF in 2018 or the logarithm base 10 of total citations in 2018 (the results were presented as geometric means, specifically the ratio of the “endorsed group” results to “not endorsed group” results). The independent variable was one of the requirements (endorsed and not endorsed). Models adjust for the publication region, language, start year, publisher and journal size (only used to adjust total citations). Results We included 188 surgical journals in our study. The results of multivariable linear regression analysis showed that journal IF was associated (P < 0.01) with the following requirements: randomized controlled trial (RCT) registration (geometric means ratio (GR) = 1.422, 95% CI [1.197–1.694]), Consolidated Standards of Reporting Trials (CONSORT) statement (1.318, [1.104–1.578]), Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) statement (1.390, [1.148–1.683]), Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement (1.556, [1.262–1.919]), Standards for R…
bibliographic citation: Zhou et al. (2022) The relationship between endorsing reporting guidelines or trial registration and the impact factor or total citations in surgical journals. PeerJ 10:e12837 https://doi.org/10.7717/peerj.12837
date submitted: 2020-11-18
date accepted: 2022-01-05
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Jing
author list: Agent
  family name: Li
  given name: Jianqiang
author list: Agent
  family name: Zhang
  given name: Jingao
author list: Agent
  family name: Geng
  given name: Bo
author list: Agent
  family name: Chen
  given name: Yao
author list: Agent
  family name: Zhou
  given name: Xiaobin
doi: 10.7717/peerj.12837
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: © 2022 Zhou et al.
attribution name: Zhou et al.

Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer
type: item
type: AcademicArticle
description: Background Bladder cancer (BC) is a common urinary tract system tumor with high recurrence rate and different populations show distinct response to immunotherapy. Novel biomarkers that can accurately predict prognosis and therapeutic responses are urgently needed. Here, we aim to identify a novel prognostic and therapeutic responses immune-related gene signature of BC through a comprehensive bioinformatics analysis. Methods The robust rank aggregation was conducted to integrate differently expressed genes (DEGs) in datasets of the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO). Lasso and Cox regression analyses were performed to formulate a novel mRNA signature that could predict prognosis of BC patients. Subsequently, the prognostic value and predictive value of the signature was validated with two independent cohorts GSE13507 and IMvigor210. Finally, quantitative Real-time PCR (qRT-PCR) analysis was conducted to determine the expression of mRNAs in BC cell lines (UM-UC-3, EJ-1, SW780 and T24). Results We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1. Our prognostic signature could be used to stratify BC population into two risk groups with distinct immune profile and responsiveness to immunotherapy. The results of qRT-PCR demonstrated that the eight mRNAs exhibited different expression levels in BC cell lines. Conclusion Our study constructed a convenient and reliable 8-mRNA gene signature, which might provide prognostic prediction and aid treatment decision making of BC patients in clinical practice.
format: application/pdf
format: text/html
creator: Yichi Zhang
creator: Yifeng Lin
creator: Daojun Lv
creator: Xiangkun Wu
creator: Wenjie Li
creator: Xueqing Wang
creator: Dongmei Jiang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.12843
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Bladder cancer (BC) is a common urinary tract system tumor with high recurrence rate and different populations show distinct response to immunotherapy. Novel biomarkers that can accurately predict prognosis and therapeutic responses are urgently needed. Here, we aim to identify a novel prognostic and therapeutic responses immune-related gene signature of BC through a comprehensive bioinformatics analysis. Methods The robust rank aggregation was conducted to integrate differently expressed genes (DEGs) in datasets of the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO). Lasso and Cox regression analyses were performed to formulate a novel mRNA signature that could predict prognosis of BC patients. Subsequently, the prognostic value and predictive value of the signature was validated with two independent cohorts GSE13507 and IMvigor210. Finally, quantitative Real-time PCR (qRT-PCR) analysis was conducted to determine the expression of mRNAs in BC cell lines (UM-UC-3, EJ-1, SW780 and T24). Results We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1. Our prognostic signature could be used to stratify BC population into two risk groups with distinct immune profile and responsiveness to immunotherapy. The results of qRT-PCR demonstrated that the eight mRNAs exhibited different expression levels in BC cell lines. Conclusion Our study constructed a convenient and reliable 8-mRNA gene signature, which might provide prognostic prediction and aid treatment decision making of BC patients in clinical practice.
bibliographic citation: Zhang et al. (2022) Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer. PeerJ 10:e12843 https://doi.org/10.7717/peerj.12843
date submitted: 2021-09-29
date accepted: 2022-01-06
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yichi
author list: Agent
  family name: Lin
  given name: Yifeng
author list: Agent
  family name: Lv
  given name: Daojun
author list: Agent
  family name: Wu
  given name: Xiangkun
author list: Agent
  family name: Li
  given name: Wenjie
author list: Agent
  family name: Wang
  given name: Xueqing
author list: Agent
  family name: Jiang
  given name: Dongmei
doi: 10.7717/peerj.12843
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults
type: item
type: AcademicArticle
description: Background Lockdowns amid the COVID-19 pandemic drastically reduced the possibility of undertaking physical activity (PA) in gyms, swimming pools, or work-related PA, e.g., active commuting. However, the stay-at-home order could have reduced PA the most, i.e., the ban of unnecessary outdoor activities. It affected free walking, running, skiing, active tourism, etc. It is, therefore, crucial to estimate how the stay-at-home order affected PA. We estimated how the stay-at-home order affected perceived PA and sedentary behavior compared to the pre-pandemic time in Poland. Methods We used a self-reported International Physical Activity Questionnaire—Long Form (IPAQ-LF) to estimate the time (minutes per day) of vigorous and moderate PA and walking and sitting time. Results We gathered data from 320 Polish participants. Bayesian approaches, including t-test and Bayesian correlations, were used to find differences and correlations between PA before and during the stay-at-home lockdown. Our data supported the hypotheses that vigorous PA, as well as walking, declined during the lockdown. Surprisingly, our data did not support the hypothesis that moderate physical activity was reduced. We found that moderate PA during lockdown increased compared to the pre-lockdown PA. As hypothesized, our data strongly evinced that sitting time inclined during the lockdown. PA decline was not correlated with the available living space. People who had access to gardens did not demonstrate a higher PA level than those without. Discussion Walking and sitting time have drastically changed during the stay-at-home lockdown, decreasing and increasing, respectively. Given results from studies focusing on lockdowns without the stay-at-home restriction, it may be assumed that letting people go outside is crucial in keeping them more active and less sedentary. Authorities should take into account the effect the stay-at-home order may have on PA and sedentary behavior and as a result, on health. Stay-at…
format: application/pdf
format: text/html
creator: Stanisław H. Czyż
creator: Wojciech Starościak
subject: Global Health
subject: Kinesiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12779
publisher: PeerJ Inc.
rights: © 2022 Czyż and Starościak
abstract: Background Lockdowns amid the COVID-19 pandemic drastically reduced the possibility of undertaking physical activity (PA) in gyms, swimming pools, or work-related PA, e.g., active commuting. However, the stay-at-home order could have reduced PA the most, i.e., the ban of unnecessary outdoor activities. It affected free walking, running, skiing, active tourism, etc. It is, therefore, crucial to estimate how the stay-at-home order affected PA. We estimated how the stay-at-home order affected perceived PA and sedentary behavior compared to the pre-pandemic time in Poland. Methods We used a self-reported International Physical Activity Questionnaire—Long Form (IPAQ-LF) to estimate the time (minutes per day) of vigorous and moderate PA and walking and sitting time. Results We gathered data from 320 Polish participants. Bayesian approaches, including t-test and Bayesian correlations, were used to find differences and correlations between PA before and during the stay-at-home lockdown. Our data supported the hypotheses that vigorous PA, as well as walking, declined during the lockdown. Surprisingly, our data did not support the hypothesis that moderate physical activity was reduced. We found that moderate PA during lockdown increased compared to the pre-lockdown PA. As hypothesized, our data strongly evinced that sitting time inclined during the lockdown. PA decline was not correlated with the available living space. People who had access to gardens did not demonstrate a higher PA level than those without. Discussion Walking and sitting time have drastically changed during the stay-at-home lockdown, decreasing and increasing, respectively. Given results from studies focusing on lockdowns without the stay-at-home restriction, it may be assumed that letting people go outside is crucial in keeping them more active and less sedentary. Authorities should take into account the effect the stay-at-home order may have on PA and sedentary behavior and as a result, on health. Stay-at…
bibliographic citation: Czyż et al. (2022) Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults. PeerJ 10:e12779 https://doi.org/10.7717/peerj.12779
date submitted: 2021-10-08
date accepted: 2021-12-21
issued: 2022-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Czyż
  given name: Stanisław H.
author list: Agent
  family name: Starościak
  given name: Wojciech
doi: 10.7717/peerj.12779
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-24
copyright: © 2022 Czyż and Starościak
attribution name: Czyż and Starościak

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