PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Airborne transmission pathway for coastal water pollution
items: Estimation of the probability of daily fluctuations of incidence of COVID-19 according to official data
items: Development and validation of the Health Promoting Behaviour for Bloating (HPB-Bloat) scale
items: Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress
items: Spondias mombin as a reservoir of fruit fly parasitoid populations in the Eastern Amazon: an undervalued ecosystem service
items: Characteristics of the pediatric patients diagnosed with SARS-CoV-2 infection in a Romanian children’s hospital: a retrospective study
items: The m6A-related gene signature for predicting the prognosis of breast cancer
items: Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1
items: Response of the characteristics of organic carbon mineralization of soft rock and soil composed of sand to soil depth
items: Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Airborne transmission pathway for coastal water pollution
type: item
type: AcademicArticle
description: Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.
format: application/pdf
format: text/html
creator: Matthew A. Pendergraft
creator: Derek J. Grimes
creator: Sarah N. Giddings
creator: Falk Feddersen
creator: Charlotte M. Beall
creator: Christopher Lee
creator: Mitchell V. Santander
creator: Kimberly A. Prather
subject: Global Health
subject: Coupled Natural and Human Systems
subject: Atmospheric Chemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11358
publisher: PeerJ Inc.
rights: © 2021 Pendergraft et al.
abstract: Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.
bibliographic citation: Pendergraft et al. (2021) Airborne transmission pathway for coastal water pollution. PeerJ 9:e11358 https://doi.org/10.7717/peerj.11358
date submitted: 2020-12-22
date accepted: 2021-04-06
issued: 2021-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pendergraft
  given name: Matthew A.
author list: Agent
  family name: Grimes
  given name: Derek J.
author list: Agent
  family name: Giddings
  given name: Sarah N.
author list: Agent
  family name: Feddersen
  given name: Falk
author list: Agent
  family name: Beall
  given name: Charlotte M.
author list: Agent
  family name: Lee
  given name: Christopher
author list: Agent
  family name: Santander
  given name: Mitchell V.
author list: Agent
  family name: Prather
  given name: Kimberly A.
doi: 10.7717/peerj.11358
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-07
copyright: © 2021 Pendergraft et al.
attribution name: Pendergraft et al.

Estimation of the probability of daily fluctuations of incidence of COVID-19 according to official data
type: item
type: AcademicArticle
description: When studying the dynamics of morbidity and mortality, one should not limit ourselves to analyzing general trends. Interesting information can be obtained from the analysis of deviations in morbidity and mortality from the general dynamics. Comparison of the cases of morbidity or death for adjacent time intervals allows us to find out whether the changes in conditions were for short periods of time and whether the cases of morbidity or death were independent. The article consists of two parts: Study of the probability distribution (CDF) of the difference between two independent observations of the Poisson distribution; Application of the results to analyze the morbidity and mortality trends by day for the new coronavirus infection. For the distribution function of the module of difference between two independent observations of the Poisson distribution, an analytical expression has been obtained that allows to get an exact solution. A program has been created, whose software can be downloaded at http://1mgmu.com/nau/DeltaPoisson/DeltaPoisson.zip. An approximate solution that does not require complex calculations has also been obtained, which can be used for an average of more than 20. If real difference is greater than expected, it may be in the following cases: morbidity or mortality varies considerably during the day. That could happen, for example, if the registered number of morbidity on Saturday and Sunday is less than on weekdays due to the management model of the health system, or if the cases are not independent; for example, due to the active identification of infected people among those who have come into contact with the patient. If the difference is less than expected, it may be due to external limiting factors, such as a shortage of test systems for making a diagnosis, a limited number of pathologists to determine the cause of death, and so on. In the analysis of the actual data for COVID-19 it was found that for Poland and Russia, excluding Moscow, the…
format: application/pdf
format: text/html
creator: Andrey Gerasimov
creator: Elena Galkina
creator: Elena Danilova
creator: Irina Ikonnikova
creator: Tamara Novoselova
creator: Yuriy L. Orlov
creator: Irina Senenycheva
subject: Epidemiology
subject: Evidence Based Medicine
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11049
publisher: PeerJ Inc.
rights: © 2021 Gerasimov et al.
abstract: When studying the dynamics of morbidity and mortality, one should not limit ourselves to analyzing general trends. Interesting information can be obtained from the analysis of deviations in morbidity and mortality from the general dynamics. Comparison of the cases of morbidity or death for adjacent time intervals allows us to find out whether the changes in conditions were for short periods of time and whether the cases of morbidity or death were independent. The article consists of two parts: Study of the probability distribution (CDF) of the difference between two independent observations of the Poisson distribution; Application of the results to analyze the morbidity and mortality trends by day for the new coronavirus infection. For the distribution function of the module of difference between two independent observations of the Poisson distribution, an analytical expression has been obtained that allows to get an exact solution. A program has been created, whose software can be downloaded at http://1mgmu.com/nau/DeltaPoisson/DeltaPoisson.zip. An approximate solution that does not require complex calculations has also been obtained, which can be used for an average of more than 20. If real difference is greater than expected, it may be in the following cases: morbidity or mortality varies considerably during the day. That could happen, for example, if the registered number of morbidity on Saturday and Sunday is less than on weekdays due to the management model of the health system, or if the cases are not independent; for example, due to the active identification of infected people among those who have come into contact with the patient. If the difference is less than expected, it may be due to external limiting factors, such as a shortage of test systems for making a diagnosis, a limited number of pathologists to determine the cause of death, and so on. In the analysis of the actual data for COVID-19 it was found that for Poland and Russia, excluding Moscow, the…
bibliographic citation: Gerasimov et al. (2021) Estimation of the probability of daily fluctuations of incidence of COVID-19 according to official data. PeerJ 9:e11049 https://doi.org/10.7717/peerj.11049
date submitted: 2020-09-14
date accepted: 2021-02-10
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gerasimov
  given name: Andrey
author list: Agent
  family name: Galkina
  given name: Elena
author list: Agent
  family name: Danilova
  given name: Elena
author list: Agent
  family name: Ikonnikova
  given name: Irina
author list: Agent
  family name: Novoselova
  given name: Tamara
author list: Agent
  family name: Orlov
  given name: Yuriy L.
author list: Agent
  family name: Senenycheva
  given name: Irina
doi: 10.7717/peerj.11049
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: © 2021 Gerasimov et al.
attribution name: Gerasimov et al.

Development and validation of the Health Promoting Behaviour for Bloating (HPB-Bloat) scale
type: item
type: AcademicArticle
description: Background Health management strategies may help patients with abdominal bloating (AB), but there are currently no tools that measure behaviour and awareness. This study aimed to validate and verify the dimensionality of the newly-developed Health Promoting Behaviour for Bloating (HPB-Bloat) scale. Methods Based on previous literature, expert input, and in-depth interviews, we generated new items for the HPB-Bloat. Its content validity was assessed by experts and pre-tested across 30 individuals with AB. Construct validity and dimensionality were first determined using exploratory factor analysis (EFA) and Promax rotation analysis, and then using confirmatory factor analysis (CFA). Results During the development stage, 35 items were generated for the HPB-Bloat, and were maintained following content validity assessment and pre-testing. One hundred and fifty-two participants (mean age of 31.27 years, 68.3% female) and 323 participants (mean age of 27.69 years, 59.4% male) completed the scale for EFA and CFA, respectively. Using EFA, we identified 20 items that we divided into five factors: diet (five items), health awareness (four items), physical activity (three items), stress management (four items), and treatment (four items). The total variance explained by the EFA model was 56.7%. The Cronbach alpha values of the five factors ranged between 0.52 and 0.81. In the CFA model, one problematic latent variable (treatment) was identified and three items were removed. In the final measurement model, four factors and 17 items fit the data well based on several fit indices (root mean square error of approximation (RMSEA) = 0.044 and standardized root mean squared residual (SRMR) = 0.052). The composite reliability of all factors in the final measurement model was above 0.60, indicating acceptable construct reliability. Conclusion The newly developed HPB-Bloat scale is valid and reliable when assessing the awareness of health-promoting behaviours across patients with AB. Fu…
format: application/pdf
format: text/html
creator: Nurzulaikha Abdullah
creator: Yee Cheng Kueh
creator: Garry Kuan
creator: Mung Seong Wong
creator: Fatan Hamamah Yahaya
creator: Nor Aslina Abd Samat
creator: Khairil Khuzaini Zulkifli
creator: Yeong Yeh Lee
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Nursing
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.11444
publisher: PeerJ Inc.
rights: © 2021 Abdullah et al.
abstract: Background Health management strategies may help patients with abdominal bloating (AB), but there are currently no tools that measure behaviour and awareness. This study aimed to validate and verify the dimensionality of the newly-developed Health Promoting Behaviour for Bloating (HPB-Bloat) scale. Methods Based on previous literature, expert input, and in-depth interviews, we generated new items for the HPB-Bloat. Its content validity was assessed by experts and pre-tested across 30 individuals with AB. Construct validity and dimensionality were first determined using exploratory factor analysis (EFA) and Promax rotation analysis, and then using confirmatory factor analysis (CFA). Results During the development stage, 35 items were generated for the HPB-Bloat, and were maintained following content validity assessment and pre-testing. One hundred and fifty-two participants (mean age of 31.27 years, 68.3% female) and 323 participants (mean age of 27.69 years, 59.4% male) completed the scale for EFA and CFA, respectively. Using EFA, we identified 20 items that we divided into five factors: diet (five items), health awareness (four items), physical activity (three items), stress management (four items), and treatment (four items). The total variance explained by the EFA model was 56.7%. The Cronbach alpha values of the five factors ranged between 0.52 and 0.81. In the CFA model, one problematic latent variable (treatment) was identified and three items were removed. In the final measurement model, four factors and 17 items fit the data well based on several fit indices (root mean square error of approximation (RMSEA) = 0.044 and standardized root mean squared residual (SRMR) = 0.052). The composite reliability of all factors in the final measurement model was above 0.60, indicating acceptable construct reliability. Conclusion The newly developed HPB-Bloat scale is valid and reliable when assessing the awareness of health-promoting behaviours across patients with AB. Fu…
bibliographic citation: Abdullah et al. (2021) Development and validation of the Health Promoting Behaviour for Bloating (HPB-Bloat) scale. PeerJ 9:e11444 https://doi.org/10.7717/peerj.11444
date submitted: 2020-08-27
date accepted: 2021-04-21
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdullah
  given name: Nurzulaikha
author list: Agent
  family name: Kueh
  given name: Yee Cheng
author list: Agent
  family name: Kuan
  given name: Garry
author list: Agent
  family name: Wong
  given name: Mung Seong
author list: Agent
  family name: Yahaya
  given name: Fatan Hamamah
author list: Agent
  family name: Abd Samat
  given name: Nor Aslina
author list: Agent
  family name: Zulkifli
  given name: Khairil Khuzaini
author list: Agent
  family name: Lee
  given name: Yeong Yeh
doi: 10.7717/peerj.11444
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: © 2021 Abdullah et al.
attribution name: Abdullah et al.

Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress
type: item
type: AcademicArticle
description: Many agricultural regions in arid and semiarid climate zone need to deal with increased soil salinity. Legumes are classified as salt-sensitive crops. A field experiment was performed to examine the application of phosphorus (P) fertilizer source and rate on growth, chlorophylls and carotenoid content, DNA and RNA content and ion accumulation in common bean (Phaseolus vulgaris L.) cultivated under salinity stress. An experimental design was split-plot with three replicates. The main plots included two P sources, namely single superphosphate (SP) and urea phosphate (UP). The sub-plots covered four P rates, i.e., 0.0, 17.5, 35.0, and 52.5 kg P ha–1. All applied P fertilization rates, in both forms, increased plant height, leaf area, dry weight of shoots and roots per plant, and total dry weight (TDW) in t ha−1. The highest accumulation of N, P, K+, Mg2+, Mn2+, Zn2+, and Cu2+ was determined in the shoot and root of common bean, while 35 kg of P per ha−1 was used compared to the other levels of P fertilizer. The highest P rate (52.5 kg ha−1) resulted in a significant reduction in Na+ in shoot and root of common bean. The response curve of TDW (t ha–1) to different rates of P (kg ha–1) proved that the quadratic model fit better than the linear model for both P sources. Under SP, the expected TDW was 1.675 t ha–1 if P was applied at 51.5 kg ha–1, while under UP, the maximum expected TDW was 1.875 t ha–1 if P was supplied at 42.5 kg ha–1. In conclusion, the 35.0 kg P ha–1 could be considered the best effective P level imposed. The application of P fertilizer as urea phosphate is generally more effective than single superphosphate in enhancing plant growth and alleviating common bean plants against salinity stress.
format: application/pdf
format: text/html
creator: Heba I. Mohamed
creator: Adel A. El-Sayed
creator: Mostafa M. Rady
creator: Gianluca Caruso
creator: Agnieszka Sekara
creator: Magdi T. Abdelhamid
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11463
publisher: PeerJ Inc.
rights: © 2021 Mohamed et al.
abstract: Many agricultural regions in arid and semiarid climate zone need to deal with increased soil salinity. Legumes are classified as salt-sensitive crops. A field experiment was performed to examine the application of phosphorus (P) fertilizer source and rate on growth, chlorophylls and carotenoid content, DNA and RNA content and ion accumulation in common bean (Phaseolus vulgaris L.) cultivated under salinity stress. An experimental design was split-plot with three replicates. The main plots included two P sources, namely single superphosphate (SP) and urea phosphate (UP). The sub-plots covered four P rates, i.e., 0.0, 17.5, 35.0, and 52.5 kg P ha–1. All applied P fertilization rates, in both forms, increased plant height, leaf area, dry weight of shoots and roots per plant, and total dry weight (TDW) in t ha−1. The highest accumulation of N, P, K+, Mg2+, Mn2+, Zn2+, and Cu2+ was determined in the shoot and root of common bean, while 35 kg of P per ha−1 was used compared to the other levels of P fertilizer. The highest P rate (52.5 kg ha−1) resulted in a significant reduction in Na+ in shoot and root of common bean. The response curve of TDW (t ha–1) to different rates of P (kg ha–1) proved that the quadratic model fit better than the linear model for both P sources. Under SP, the expected TDW was 1.675 t ha–1 if P was applied at 51.5 kg ha–1, while under UP, the maximum expected TDW was 1.875 t ha–1 if P was supplied at 42.5 kg ha–1. In conclusion, the 35.0 kg P ha–1 could be considered the best effective P level imposed. The application of P fertilizer as urea phosphate is generally more effective than single superphosphate in enhancing plant growth and alleviating common bean plants against salinity stress.
bibliographic citation: Mohamed et al. (2021) Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress. PeerJ 9:e11463 https://doi.org/10.7717/peerj.11463
date submitted: 2020-11-20
date accepted: 2021-04-26
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohamed
  given name: Heba I.
author list: Agent
  family name: El-Sayed
  given name: Adel A.
author list: Agent
  family name: Rady
  given name: Mostafa M.
author list: Agent
  family name: Caruso
  given name: Gianluca
author list: Agent
  family name: Sekara
  given name: Agnieszka
author list: Agent
  family name: Abdelhamid
  given name: Magdi T.
doi: 10.7717/peerj.11463
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: © 2021 Mohamed et al.
attribution name: Mohamed et al.

Spondias mombin as a reservoir of fruit fly parasitoid populations in the Eastern Amazon: an undervalued ecosystem service
type: item
type: AcademicArticle
description: Fruit flies are economically important pests that infest a wide variety of host trees. The environmental damage caused by traditional pesticide-based control methods has prompted scientists to seek less damaging alternatives such as biological control by native species. Parasitoids, especially Braconidae species, have excellent potential as biological control agents for fruit flies, being both generalists and well distributed geographically. Native fruit trees that support medium or high levels of these parasitoids could therefore play an important role in biological control strategies. A good potential example is Spondias mombin L. in the Brazilian Amazon, which hosts several species of fruit flies and associated parasitoids. Here, we provide a unique synthesis of over nearly two decades of data from the east Amazon, clearly demonstrating the potential of S. mombin to act as a source and reservoir of fruit fly parasitoids. This important ecosystem service (biological control) provided by the parasitoids and supported by S. mombin could be further enhanced through conservation of this plant species in its natural environment.
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format: text/html
creator: Maria do Socorro Miranda de Sousa
creator: Ezequiel de Deus
creator: Adilson Lopes Lima
creator: Cristiane Ramos de Jesus
creator: Salustiano Vilar da Costa Neto
creator: Lailson do Nascimento Lemos
creator: Ana Claudia Mendes Malhado
creator: Richard J. Ladle
creator: Ricardo Adaime
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.11530
publisher: PeerJ Inc.
rights: © 2021 Sousa et al.
abstract: Fruit flies are economically important pests that infest a wide variety of host trees. The environmental damage caused by traditional pesticide-based control methods has prompted scientists to seek less damaging alternatives such as biological control by native species. Parasitoids, especially Braconidae species, have excellent potential as biological control agents for fruit flies, being both generalists and well distributed geographically. Native fruit trees that support medium or high levels of these parasitoids could therefore play an important role in biological control strategies. A good potential example is Spondias mombin L. in the Brazilian Amazon, which hosts several species of fruit flies and associated parasitoids. Here, we provide a unique synthesis of over nearly two decades of data from the east Amazon, clearly demonstrating the potential of S. mombin to act as a source and reservoir of fruit fly parasitoids. This important ecosystem service (biological control) provided by the parasitoids and supported by S. mombin could be further enhanced through conservation of this plant species in its natural environment.
bibliographic citation: Miranda de Sousa et al. (2021) Spondias mombin as a reservoir of fruit fly parasitoid populations in the Eastern Amazon: an undervalued ecosystem service. PeerJ 9:e11530 https://doi.org/10.7717/peerj.11530
date submitted: 2020-12-29
date accepted: 2021-05-06
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miranda de Sousa
  given name: Maria do Socorro
author list: Agent
  family name: de Deus
  given name: Ezequiel
author list: Agent
  family name: Lima
  given name: Adilson Lopes
author list: Agent
  family name: Ramos de Jesus
  given name: Cristiane
author list: Agent
  family name: Vilar da Costa Neto
  given name: Salustiano
author list: Agent
  family name: do Nascimento Lemos
  given name: Lailson
author list: Agent
  family name: Mendes Malhado
  given name: Ana Claudia
author list: Agent
  family name: Ladle
  given name: Richard J.
author list: Agent
  family name: Adaime
  given name: Ricardo
doi: 10.7717/peerj.11530
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: ©2021 Sousa et al.
attribution name: Sousa et al.

Characteristics of the pediatric patients diagnosed with SARS-CoV-2 infection in a Romanian children’s hospital: a retrospective study
type: item
type: AcademicArticle
description: Background To date, information on COVID-19 pediatric patients is still sparse. We aimed to highlight the epidemiological and clinical data regarding SARS-CoV-2 infection in children and adolescents to improve the understanding of the disease in this age group and inform physicians during the ongoing COVID-19 pandemic. Methods We conducted a retrospective, observational study in “Marie Curie” Emergency Children’s Hospital from Bucharest, Romania. We analyzed clinical and epidemiological characteristics of the patients confirmed with SARS-CoV-2 infection, between April 1, 2020–October 31, 2020. Results A total of 172 patients aged 0–18 years were included, 79 (45.93%) female and 93 (54.07%) male patients. 28 (16.28%) patients had co-morbidities (more often identified in asymptomatic group; p < 0.0001). 47 (27.32%) had exposure to an identified source. 30 (17.44%) patients were asymptomatic; 142 (85.56%) had mild or moderate disease. The most frequent symptoms were: pyrexia (78.87%), digestive symptoms (50%), cough (40.14%). Chest X-ray was performed in 50 patients and it was abnormal in half of them, all being symptomatic. About 2/3 of the evaluated patients had normal leukocytes. The most common hematological change was lymphopenia; monocytes tended to be higher in symptomatic patients. About 40% of the patients were admitted; none required admission to ICU. No significant differences were found between symptomatic and asymptomatic patients regarding gender, age distribution, and exposure to a source. Conclusions All the patients had asymptomatic, mild or moderate disease. Patients with comorbidities, classically considered high risk patients, presented the same pattern of disease.
format: application/pdf
format: text/html
creator: Liana-Cătălina Gavriliu
creator: Carmen Murariu
creator: Vladimir Potop
creator: Radu Spătaru
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.11560
publisher: PeerJ Inc.
rights: © 2021 Gavriliu et al.
abstract: Background To date, information on COVID-19 pediatric patients is still sparse. We aimed to highlight the epidemiological and clinical data regarding SARS-CoV-2 infection in children and adolescents to improve the understanding of the disease in this age group and inform physicians during the ongoing COVID-19 pandemic. Methods We conducted a retrospective, observational study in “Marie Curie” Emergency Children’s Hospital from Bucharest, Romania. We analyzed clinical and epidemiological characteristics of the patients confirmed with SARS-CoV-2 infection, between April 1, 2020–October 31, 2020. Results A total of 172 patients aged 0–18 years were included, 79 (45.93%) female and 93 (54.07%) male patients. 28 (16.28%) patients had co-morbidities (more often identified in asymptomatic group; p < 0.0001). 47 (27.32%) had exposure to an identified source. 30 (17.44%) patients were asymptomatic; 142 (85.56%) had mild or moderate disease. The most frequent symptoms were: pyrexia (78.87%), digestive symptoms (50%), cough (40.14%). Chest X-ray was performed in 50 patients and it was abnormal in half of them, all being symptomatic. About 2/3 of the evaluated patients had normal leukocytes. The most common hematological change was lymphopenia; monocytes tended to be higher in symptomatic patients. About 40% of the patients were admitted; none required admission to ICU. No significant differences were found between symptomatic and asymptomatic patients regarding gender, age distribution, and exposure to a source. Conclusions All the patients had asymptomatic, mild or moderate disease. Patients with comorbidities, classically considered high risk patients, presented the same pattern of disease.
bibliographic citation: Gavriliu et al. (2021) Characteristics of the pediatric patients diagnosed with SARS-CoV-2 infection in a Romanian children’s hospital: a retrospective study. PeerJ 9:e11560 https://doi.org/10.7717/peerj.11560
date submitted: 2021-03-02
date accepted: 2021-05-13
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gavriliu
  given name: Liana-Cătălina
author list: Agent
  family name: Murariu
  given name: Carmen
author list: Agent
  family name: Potop
  given name: Vladimir
author list: Agent
  family name: Spătaru
  given name: Radu
doi: 10.7717/peerj.11560
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: © 2021 Gavriliu et al.
attribution name: Gavriliu et al.

The m6A-related gene signature for predicting the prognosis of breast cancer
type: item
type: AcademicArticle
description: N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A RNA methylation regulators. The signature divided patients into low- and high-risk group. High-risk patients had a worse prognosis than the low-risk group. Further analyses indicated that IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. Survival analysis showed that IGF2BP1 is an independent prognostic factor of breast cancer, and higher expression level of IGF2BP1 is associated with shorter overall survival of breast cancer patients. In conclusion, we identified a 10 m6A-related gene signature associated with overall survival of breast cancer. IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer.
format: application/pdf
format: text/html
creator: Shanliang Zhong
creator: Zhenzhong Lin
creator: Huanwen Chen
creator: Ling Mao
creator: Jifeng Feng
creator: Siying Zhou
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
subject: Computational Science
description: doi:10.7717/peerj.11561
publisher: PeerJ Inc.
rights: © 2021 Zhong et al.
abstract: N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A RNA methylation regulators. The signature divided patients into low- and high-risk group. High-risk patients had a worse prognosis than the low-risk group. Further analyses indicated that IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. Survival analysis showed that IGF2BP1 is an independent prognostic factor of breast cancer, and higher expression level of IGF2BP1 is associated with shorter overall survival of breast cancer patients. In conclusion, we identified a 10 m6A-related gene signature associated with overall survival of breast cancer. IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer.
bibliographic citation: Zhong et al. (2021) The m6A-related gene signature for predicting the prognosis of breast cancer. PeerJ 9:e11561 https://doi.org/10.7717/peerj.11561
date submitted: 2021-01-26
date accepted: 2021-05-13
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Shanliang
author list: Agent
  family name: Lin
  given name: Zhenzhong
author list: Agent
  family name: Chen
  given name: Huanwen
author list: Agent
  family name: Mao
  given name: Ling
author list: Agent
  family name: Feng
  given name: Jifeng
author list: Agent
  family name: Zhou
  given name: Siying
doi: 10.7717/peerj.11561
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: ©2021 Zhong et al.
attribution name: Zhong et al.

Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1
type: item
type: AcademicArticle
description: Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests t…
format: application/pdf
format: text/html
creator: Chhavi Sharma
creator: Arti Nigam
creator: Rajni Singh
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11570
publisher: PeerJ Inc.
rights: © 2021 Sharma et al.
abstract: Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests t…
bibliographic citation: Sharma et al. (2021) Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1. PeerJ 9:e11570 https://doi.org/10.7717/peerj.11570
date submitted: 2020-11-24
date accepted: 2021-05-17
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharma
  given name: Chhavi
author list: Agent
  family name: Nigam
  given name: Arti
author list: Agent
  family name: Singh
  given name: Rajni
doi: 10.7717/peerj.11570
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: ©2021 Sharma et al.
attribution name: Sharma et al.

Response of the characteristics of organic carbon mineralization of soft rock and soil composed of sand to soil depth
type: item
type: AcademicArticle
description: The addition of soft rock to aeolian sandy soil can improve the level of fertility and ability of the soil to sequester carbon, which is of substantial significance to improve the ecological environment of the Mu Us sandy land and supplement newly added cultivated land. S oft rock and sand were combined using the ratio (v/v) of 0:1 (CK), 1:5 (S1), 1:2 (S2), and 1:1 (S3). The process of mineralization of organic carbon at different depths (0–10 cm, 10–20 cm, and 20–30 cm) in the combined soil was studied by 58 days of incubation indoors at a constant temperature. The content of soil nutrient s increased significantly under the S2 and S3 treatments and was higher in the 0–10 cm soil depth. The mineralization of rate of soil organic carbon (SOC) of different combination ratios can be divided into three time periods: the stress mineralization stage (1–7 d), the rapid mineralization stage (7–9 d) and the slow mineralization stage (9–58 d). At the end of incubation, the rates of mineralization of SOC and accumulated mineralization amount (Ct) were relatively large in the 0–10 cm soil depth, followed by the 10–20 cm and 20–30 cm soil layers , indicating that the stability of SOC in the surface layer was poor, which is not conducive to the storage of carbon. The content of potentially mineralizable organic carbon (C0) in the soil was consistent with the trend of change of Ct. Compared with the CK treatment, the cumulative organic carbon mineralization rate (Cr) of the S2 and S3 treatment s decreased by 7.77% and 6.05%, respectively; and the C0/SOC decreased by 22.84% and 15.55%, respectively. Moreover, the Cr and C0/SOC values in the 10–20 cm soil depth were small, which indirectly promoted the storage of organic carbon. With the process of SOC mineralization, the contents of soil microbial biomass carbon (SMBC) and dissolved organic carbon (DOC) tended to decrease compared with the initial contents, with larger amplitudes in the 20–30 cm and 10–20 cm soil depth s, respecti…
format: application/pdf
format: text/html
creator: Wanying Li
creator: Zhen Guo
creator: Juan Li
creator: Jichang Han
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.11572
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: The addition of soft rock to aeolian sandy soil can improve the level of fertility and ability of the soil to sequester carbon, which is of substantial significance to improve the ecological environment of the Mu Us sandy land and supplement newly added cultivated land. S oft rock and sand were combined using the ratio (v/v) of 0:1 (CK), 1:5 (S1), 1:2 (S2), and 1:1 (S3). The process of mineralization of organic carbon at different depths (0–10 cm, 10–20 cm, and 20–30 cm) in the combined soil was studied by 58 days of incubation indoors at a constant temperature. The content of soil nutrient s increased significantly under the S2 and S3 treatments and was higher in the 0–10 cm soil depth. The mineralization of rate of soil organic carbon (SOC) of different combination ratios can be divided into three time periods: the stress mineralization stage (1–7 d), the rapid mineralization stage (7–9 d) and the slow mineralization stage (9–58 d). At the end of incubation, the rates of mineralization of SOC and accumulated mineralization amount (Ct) were relatively large in the 0–10 cm soil depth, followed by the 10–20 cm and 20–30 cm soil layers , indicating that the stability of SOC in the surface layer was poor, which is not conducive to the storage of carbon. The content of potentially mineralizable organic carbon (C0) in the soil was consistent with the trend of change of Ct. Compared with the CK treatment, the cumulative organic carbon mineralization rate (Cr) of the S2 and S3 treatment s decreased by 7.77% and 6.05%, respectively; and the C0/SOC decreased by 22.84% and 15.55%, respectively. Moreover, the Cr and C0/SOC values in the 10–20 cm soil depth were small, which indirectly promoted the storage of organic carbon. With the process of SOC mineralization, the contents of soil microbial biomass carbon (SMBC) and dissolved organic carbon (DOC) tended to decrease compared with the initial contents, with larger amplitudes in the 20–30 cm and 10–20 cm soil depth s, respecti…
bibliographic citation: Li et al. (2021) Response of the characteristics of organic carbon mineralization of soft rock and soil composed of sand to soil depth. PeerJ 9:e11572 https://doi.org/10.7717/peerj.11572
date submitted: 2021-01-21
date accepted: 2021-05-18
issued: 2021-06-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wanying
author list: Agent
  family name: Guo
  given name: Zhen
author list: Agent
  family name: Li
  given name: Juan
author list: Agent
  family name: Han
  given name: Jichang
doi: 10.7717/peerj.11572
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-04
copyright: ©2021 Li et al.
attribution name: Li et al.

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats
type: item
type: AcademicArticle
description: Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.
format: application/pdf
format: text/html
creator: Imogene A. Cancellare
creator: Elizabeth M. Kierepka
creator: Jan Janecka
creator: Byron Weckworth
creator: Richard T. Kazmaier
creator: Rocky Ward
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.11498
publisher: PeerJ Inc.
rights: © 2021 Cancellare et al.
abstract: Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.
bibliographic citation: Cancellare et al. (2021) Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats. PeerJ 9:e11498 https://doi.org/10.7717/peerj.11498
date submitted: 2020-10-02
date accepted: 2021-05-01
issued: 2021-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cancellare
  given name: Imogene A.
author list: Agent
  family name: Kierepka
  given name: Elizabeth M.
author list: Agent
  family name: Janecka
  given name: Jan
author list: Agent
  family name: Weckworth
  given name: Byron
author list: Agent
  family name: Kazmaier
  given name: Richard T.
author list: Agent
  family name: Ward
  given name: Rocky
doi: 10.7717/peerj.11498
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-06-03
copyright: © 2021 Cancellare et al.
attribution name: Cancellare et al.

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