PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study
items: Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria
items: Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary
items: How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities
items: Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling
items: Monitoring monthly surface water dynamics of Dongting Lake using Sentinel-1 data at 10 m
items: Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
items: Cranial morphology of Sinovenator changii (Theropoda: Troodontidae) on the new material from the Yixian Formation of western Liaoning, China
items: Comparative health assessment of urban and non-urban free-ranging mule deer (Odocoileus hemionus) in southeastern British Columbia, Canada
items: GEsture: an online hand-drawing tool for gene expression pattern search

Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study
type: item
type: AcademicArticle
description: Many reports have mentioned the association between chronic periodontitis (CP) and primary Sjögren syndrome (pSS). However, no cohort study has been performed for the risk of pSS in patients with CP. In this study, we evaluated the risk of pSS from CP exposure in a nationwide population-based cohort study in Taiwan. We studied the claims data of Taiwanese population from 2001 to 2012. We identified 76,765 patients with CP from the National Health Insurance Database in Taiwan. We also selected 76,765 controls that were randomly frequency matched by age, sex, and index year from the general population. We analyzed the risk of pSS by using Cox proportional hazards regression models including sex, age, and comorbidities. In this study, 76,765 patients with CP (mean age: 40.8 years) and 76,765 controls (mean age: 41.0 years) were followed-up for 8.54 and 8.49 years, respectively. A total of 869 cases of pSS were identified in CP cohort and 483 cases in non-CP cohort. Multivariate Cox regression analysis indicated that the incidence rate of pSS was significantly higher in CP cohort than those who in non-CP cohort (adjusted HR: 1.79, 95% CI [1.60–2.00]). Taken together, this nationwide retrospective cohort study demonstrated that the risk of pSS was significantly higher in patients with CP than in the general population. The association between CP and pSS was significant in the female group.
format: application/pdf
format: text/html
creator: Tai-Chen Lin
creator: Chien-Fang Tseng
creator: Yu-Hsun Wang
creator: Hui-Chieh Yu
creator: Yu-Chao Chang
subject: Dentistry
subject: Epidemiology
subject: Immunology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.5109
publisher: PeerJ Inc.
rights: © 2018 Lin et al.
abstract: Many reports have mentioned the association between chronic periodontitis (CP) and primary Sjögren syndrome (pSS). However, no cohort study has been performed for the risk of pSS in patients with CP. In this study, we evaluated the risk of pSS from CP exposure in a nationwide population-based cohort study in Taiwan. We studied the claims data of Taiwanese population from 2001 to 2012. We identified 76,765 patients with CP from the National Health Insurance Database in Taiwan. We also selected 76,765 controls that were randomly frequency matched by age, sex, and index year from the general population. We analyzed the risk of pSS by using Cox proportional hazards regression models including sex, age, and comorbidities. In this study, 76,765 patients with CP (mean age: 40.8 years) and 76,765 controls (mean age: 41.0 years) were followed-up for 8.54 and 8.49 years, respectively. A total of 869 cases of pSS were identified in CP cohort and 483 cases in non-CP cohort. Multivariate Cox regression analysis indicated that the incidence rate of pSS was significantly higher in CP cohort than those who in non-CP cohort (adjusted HR: 1.79, 95% CI [1.60–2.00]). Taken together, this nationwide retrospective cohort study demonstrated that the risk of pSS was significantly higher in patients with CP than in the general population. The association between CP and pSS was significant in the female group.
bibliographic citation: Lin et al. (2018) Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study. PeerJ 6:e5109 https://doi.org/10.7717/peerj.5109
date submitted: 2018-03-29
date accepted: 2018-06-06
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Tai-Chen
author list: Agent
  family name: Tseng
  given name: Chien-Fang
author list: Agent
  family name: Wang
  given name: Yu-Hsun
author list: Agent
  family name: Yu
  given name: Hui-Chieh
author list: Agent
  family name: Chang
  given name: Yu-Chao
doi: 10.7717/peerj.5109
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Lin et al.
attribution name: Lin et al.

Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria
type: item
type: AcademicArticle
description: Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria.
format: application/pdf
format: text/html
creator: Rositsa Shumkova
creator: Boyko Neov
creator: Daniela Sirakova
creator: Ani Georgieva
creator: Dimitar Gadjev
creator: Denitsa Teofanova
creator: Georgi Radoslavov
creator: Maria Bouga
creator: Peter Hristov
subject: Biodiversity
subject: Entomology
subject: Genetics
subject: Virology
description: doi:10.7717/peerj.5077
publisher: PeerJ Inc.
rights: © 2018 Shumkova et al.
abstract: Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria.
bibliographic citation: Shumkova et al. (2018) Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria. PeerJ 6:e5077 https://doi.org/10.7717/peerj.5077
date submitted: 2018-02-28
date accepted: 2018-06-04
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shumkova
  given name: Rositsa
author list: Agent
  family name: Neov
  given name: Boyko
author list: Agent
  family name: Sirakova
  given name: Daniela
author list: Agent
  family name: Georgieva
  given name: Ani
author list: Agent
  family name: Gadjev
  given name: Dimitar
author list: Agent
  family name: Teofanova
  given name: Denitsa
author list: Agent
  family name: Radoslavov
  given name: Georgi
author list: Agent
  family name: Bouga
  given name: Maria
author list: Agent
  family name: Hristov
  given name: Peter
doi: 10.7717/peerj.5077
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: ©2018 Shumkova et al.
attribution name: Shumkova et al.

Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary
type: item
type: AcademicArticle
description: Plants and insects are constantly interacting in complex ways through forest communities since hundreds of millions of years. Those interactions are often related to variations in the climate. Climate change, due to human activities, may have disturbed these relationships in modern ecosystems. Fossil leaf assemblages are thus good opportunities to survey responses of plant–insect interactions to climate variations over the time. The goal of this study is to discuss the possible causes of the differences of plant–insect interactions’ patterns in European paleoforests from the Neogene–Quaternary transition. This was accomplished through three fossil leaf assemblages: Willershausen, Berga (both from the late Neogene of Germany) and Bernasso (from the early Quaternary of France). In Willershausen it has been measured that half of the leaves presented insect interactions, 35% of the fossil leaves were impacted by insects in Bernasso and only 25% in Berga. The largest proportion of these interactions in Bernasso were categorized as specialist (mainly due to galling) while in Willershausen and Berga those ones were significantly more generalist. Contrary to previous studies, this study did not support the hypothesis that the mean annual precipitation and temperature were the main factors that impacted the different plant–insect interactions’ patterns. However, for the first time, our results tend to support that the hydric seasonality and the mean temperature of the coolest months could be potential factors influencing fossil plant–insect interactions.
format: application/pdf
format: text/html
creator: Benjamin Adroit
creator: Vincent Girard
creator: Lutz Kunzmann
creator: Jean-Frédéric Terral
creator: Torsten Wappler
subject: Ecology
subject: Ecosystem Science
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.5075
publisher: PeerJ Inc.
rights: © 2018 Adroit et al.
abstract: Plants and insects are constantly interacting in complex ways through forest communities since hundreds of millions of years. Those interactions are often related to variations in the climate. Climate change, due to human activities, may have disturbed these relationships in modern ecosystems. Fossil leaf assemblages are thus good opportunities to survey responses of plant–insect interactions to climate variations over the time. The goal of this study is to discuss the possible causes of the differences of plant–insect interactions’ patterns in European paleoforests from the Neogene–Quaternary transition. This was accomplished through three fossil leaf assemblages: Willershausen, Berga (both from the late Neogene of Germany) and Bernasso (from the early Quaternary of France). In Willershausen it has been measured that half of the leaves presented insect interactions, 35% of the fossil leaves were impacted by insects in Bernasso and only 25% in Berga. The largest proportion of these interactions in Bernasso were categorized as specialist (mainly due to galling) while in Willershausen and Berga those ones were significantly more generalist. Contrary to previous studies, this study did not support the hypothesis that the mean annual precipitation and temperature were the main factors that impacted the different plant–insect interactions’ patterns. However, for the first time, our results tend to support that the hydric seasonality and the mean temperature of the coolest months could be potential factors influencing fossil plant–insect interactions.
bibliographic citation: Adroit et al. (2018) Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary. PeerJ 6:e5075 https://doi.org/10.7717/peerj.5075
date submitted: 2017-11-29
date accepted: 2018-06-04
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adroit
  given name: Benjamin
author list: Agent
  family name: Girard
  given name: Vincent
author list: Agent
  family name: Kunzmann
  given name: Lutz
author list: Agent
  family name: Terral
  given name: Jean-Frédéric
author list: Agent
  family name: Wappler
  given name: Torsten
doi: 10.7717/peerj.5075
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Adroit et al.
attribution name: Adroit et al.

How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities
type: item
type: AcademicArticle
description: Background Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. Methods The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. Results Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. Discussion Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility.
format: application/pdf
format: text/html
creator: Zoi Thanopoulou
creator: Maria Sini
creator: Konstantinos Vatikiotis
creator: Christos Katsoupis
creator: Panayiotis G. Dimitrakopoulos
creator: Stelios Katsanevakis
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5066
publisher: PeerJ Inc.
rights: © 2018 Thanopoulou et al.
abstract: Background Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. Methods The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. Results Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. Discussion Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility.
bibliographic citation: Thanopoulou et al. (2018) How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities. PeerJ 6:e5066 https://doi.org/10.7717/peerj.5066
date submitted: 2018-01-23
date accepted: 2018-06-03
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thanopoulou
  given name: Zoi
author list: Agent
  family name: Sini
  given name: Maria
author list: Agent
  family name: Vatikiotis
  given name: Konstantinos
author list: Agent
  family name: Katsoupis
  given name: Christos
author list: Agent
  family name: Dimitrakopoulos
  given name: Panayiotis G.
author list: Agent
  family name: Katsanevakis
  given name: Stelios
doi: 10.7717/peerj.5066
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Thanopoulou et al.
attribution name: Thanopoulou et al.

Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling
type: item
type: AcademicArticle
description: Background Biological interactions between varicella (chickenpox) and herpes zoster (shingles), two diseases caused by the varicella zoster virus (VZV), continue to be debated including the potential effect on shingles cases following the introduction of universal childhood chickenpox vaccination programs. We investigated how chickenpox vaccination in Alberta impacts the incidence and age-distribution of shingles over 75 years post-vaccination, taking into consideration a variety of plausible theories of waning and boosting of immunity. Methods We developed an agent-based model representing VZV disease, transmission, vaccination states and coverage, waning and boosting of immunity in a stylized geographic area, utilizing a distance-based network. We derived parameters from literature, including modeling, epidemiological, and immunology studies. We calibrated our model to the age-specific incidence of shingles and chickenpox prior to vaccination to derive optimal combinations of duration of boosting (DoB) and waning of immunity. We conducted paired simulations with and without implementing chickenpox vaccination. We computed the count and cumulative incidence rate of shingles cases at 10, 25, 50, and 75 years intervals, following introduction of vaccination, and compared the difference between runs with vaccination and without vaccination using the Mann–Whitney U-test to determine statistical significance. We carried out sensitivity analyses by increasing and lowering vaccination coverage and removing biological effect of boosting. Results Chickenpox vaccination led to a decrease in chickenpox cases. The cumulative incidence of chickenpox had dropped from 1,254 cases per 100,000 person-years pre chickenpox vaccination to 193 cases per 100,000 person-years 10 years after the vaccine implementation. We observed an increase in the all-ages shingles cumulative incidence at 10 and 25 years post chickenpox vaccination and mixed cumulative incidence change at 50 and 75 year…
format: application/pdf
format: text/html
creator: Ellen Rafferty
creator: Wade McDonald
creator: Weicheng Qian
creator: Nathaniel D. Osgood
creator: Alexander Doroshenko
subject: Computational Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.5012
publisher: PeerJ Inc.
rights: © 2018 Rafferty et al.
abstract: Background Biological interactions between varicella (chickenpox) and herpes zoster (shingles), two diseases caused by the varicella zoster virus (VZV), continue to be debated including the potential effect on shingles cases following the introduction of universal childhood chickenpox vaccination programs. We investigated how chickenpox vaccination in Alberta impacts the incidence and age-distribution of shingles over 75 years post-vaccination, taking into consideration a variety of plausible theories of waning and boosting of immunity. Methods We developed an agent-based model representing VZV disease, transmission, vaccination states and coverage, waning and boosting of immunity in a stylized geographic area, utilizing a distance-based network. We derived parameters from literature, including modeling, epidemiological, and immunology studies. We calibrated our model to the age-specific incidence of shingles and chickenpox prior to vaccination to derive optimal combinations of duration of boosting (DoB) and waning of immunity. We conducted paired simulations with and without implementing chickenpox vaccination. We computed the count and cumulative incidence rate of shingles cases at 10, 25, 50, and 75 years intervals, following introduction of vaccination, and compared the difference between runs with vaccination and without vaccination using the Mann–Whitney U-test to determine statistical significance. We carried out sensitivity analyses by increasing and lowering vaccination coverage and removing biological effect of boosting. Results Chickenpox vaccination led to a decrease in chickenpox cases. The cumulative incidence of chickenpox had dropped from 1,254 cases per 100,000 person-years pre chickenpox vaccination to 193 cases per 100,000 person-years 10 years after the vaccine implementation. We observed an increase in the all-ages shingles cumulative incidence at 10 and 25 years post chickenpox vaccination and mixed cumulative incidence change at 50 and 75 year…
bibliographic citation: Rafferty et al. (2018) Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling. PeerJ 6:e5012 https://doi.org/10.7717/peerj.5012
date submitted: 2017-08-15
date accepted: 2018-05-30
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rafferty
  given name: Ellen
author list: Agent
  family name: McDonald
  given name: Wade
author list: Agent
  family name: Qian
  given name: Weicheng
author list: Agent
  family name: Osgood
  given name: Nathaniel D.
author list: Agent
  family name: Doroshenko
  given name: Alexander
doi: 10.7717/peerj.5012
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Rafferty et al.
attribution name: Rafferty et al.

Monitoring monthly surface water dynamics of Dongting Lake using Sentinel-1 data at 10 m
type: item
type: AcademicArticle
description: High temporal resolution water distribution maps are essential for surface water monitoring because surface water exhibits significant inner-annual variation. Therefore, high-frequency remote sensing data are needed for surface water mapping. Dongting Lake, the second-largest freshwater lake in China, is famous for the seasonal fluctuations of its inundation extents in the middle reaches of the Yangtze River. It is also greatly affected by the Three Gorges Project. In this study, we used Sentinel-1 data to generate surface water maps of Dongting Lake at 10 m resolution. First, we generated the Sentinel-1 time series backscattering coefficient for VH and VV polarizations at 10 m resolution by using a monthly composition method. Second, we generated the thresholds for mapping surface water at 10 m resolution with monthly frequencies using Sentinel-1 data. Then, we derived the monthly surface water distribution product of Dongting Lake in 2016, and finally, we analyzed the inner-annual surface water dynamics. The results showed that: (1) The thresholds were −21.56 and −15.82 dB for the backscattering coefficients for VH and VV, respectively, and the overall accuracy and Kappa coefficients were above 95.50% and 0.90, respectively, for the VH backscattering coefficient, and above 94.50% and 0.88, respectively, for the VV backscattering coefficient. The VV backscattering coefficient achieved lower accuracy due to the effect of the wind causing roughness on the surface of the water. (2) The maximum and minimum areas of surface water were 2040.33 km2 in July, and 738.89 km2 in December. The surface water area of Dongting Lake varied most significantly in April and August. The permanent water acreage in 2016 was 556.35 km2, accounting for 19.65% of the total area of Dongting Lake, and the acreage of seasonal water was 1525.21 km2. This study proposed a method to automatically generate monthly surface water at 10 m resolution, which may contribute to monitoring surface water …
format: application/pdf
format: text/html
creator: Liwei Xing
creator: Xinming Tang
creator: Huabin Wang
creator: Wenfeng Fan
creator: Guanghui Wang
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4992
publisher: PeerJ Inc.
rights: © 2018 Xing et al.
abstract: High temporal resolution water distribution maps are essential for surface water monitoring because surface water exhibits significant inner-annual variation. Therefore, high-frequency remote sensing data are needed for surface water mapping. Dongting Lake, the second-largest freshwater lake in China, is famous for the seasonal fluctuations of its inundation extents in the middle reaches of the Yangtze River. It is also greatly affected by the Three Gorges Project. In this study, we used Sentinel-1 data to generate surface water maps of Dongting Lake at 10 m resolution. First, we generated the Sentinel-1 time series backscattering coefficient for VH and VV polarizations at 10 m resolution by using a monthly composition method. Second, we generated the thresholds for mapping surface water at 10 m resolution with monthly frequencies using Sentinel-1 data. Then, we derived the monthly surface water distribution product of Dongting Lake in 2016, and finally, we analyzed the inner-annual surface water dynamics. The results showed that: (1) The thresholds were −21.56 and −15.82 dB for the backscattering coefficients for VH and VV, respectively, and the overall accuracy and Kappa coefficients were above 95.50% and 0.90, respectively, for the VH backscattering coefficient, and above 94.50% and 0.88, respectively, for the VV backscattering coefficient. The VV backscattering coefficient achieved lower accuracy due to the effect of the wind causing roughness on the surface of the water. (2) The maximum and minimum areas of surface water were 2040.33 km2 in July, and 738.89 km2 in December. The surface water area of Dongting Lake varied most significantly in April and August. The permanent water acreage in 2016 was 556.35 km2, accounting for 19.65% of the total area of Dongting Lake, and the acreage of seasonal water was 1525.21 km2. This study proposed a method to automatically generate monthly surface water at 10 m resolution, which may contribute to monitoring surface water …
bibliographic citation: Xing et al. (2018) Monitoring monthly surface water dynamics of Dongting Lake using Sentinel-1 data at 10 m. PeerJ 6:e4992 https://doi.org/10.7717/peerj.4992
date submitted: 2018-01-02
date accepted: 2018-05-26
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Liwei
author list: Agent
  family name: Tang
  given name: Xinming
author list: Agent
  family name: Wang
  given name: Huabin
author list: Agent
  family name: Fan
  given name: Wenfeng
author list: Agent
  family name: Wang
  given name: Guanghui
doi: 10.7717/peerj.4992
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Xing et al.
attribution name: Xing et al.

Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
type: item
type: AcademicArticle
description: Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of the bacterial community withstanding a harsh extraction treatment eliminating the easily lysed fraction of the total bacterial community. The sporobiota has been identified as a critical component of the human microbiome, and therefore potentially a key element in the dissemination of ARG in human-impacted environments. A region of Lake Geneva in which the accumulation of ARG in the sediments has been previously linked to the deposition of treated wastewater was selected to investigate the dissemination of tet(W) and sul1, two genes conferring resistance to tetracycline and sulfonamide, respectively. Analysis of the abundance of these ARG within the sporobiome (collection of genes of the sporobiota) and correlation with community composition and environmental parameters demonstrated that ARG can spread across the environment with the sporobiota being the dispersal vector. A highly abundant OTU affiliated with the genus Clostridium was identified as a potential specific vector for the dissemination of tet(W), due to a strong correlation with tet(W) frequency (ARG copy numbers/ng DNA). The high dispersal rate, long-term survival, and potential reactivation of the sporobiota constitute a serious concern in terms of dissemination and persistence of ARG in the environment.
format: application/pdf
format: text/html
creator: Christophe Paul
creator: Zhanna Bayrychenko
creator: Thomas Junier
creator: Sevasti Filippidou
creator: Karin Beck
creator: Matthieu Bueche
creator: Gilbert Greub
creator: Helmut Bürgmann
creator: Pilar Junier
subject: Microbiology
subject: Public Health
subject: Ecotoxicology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.4989
publisher: PeerJ Inc.
rights: © 2018 Paul et al.
abstract: Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of the bacterial community withstanding a harsh extraction treatment eliminating the easily lysed fraction of the total bacterial community. The sporobiota has been identified as a critical component of the human microbiome, and therefore potentially a key element in the dissemination of ARG in human-impacted environments. A region of Lake Geneva in which the accumulation of ARG in the sediments has been previously linked to the deposition of treated wastewater was selected to investigate the dissemination of tet(W) and sul1, two genes conferring resistance to tetracycline and sulfonamide, respectively. Analysis of the abundance of these ARG within the sporobiome (collection of genes of the sporobiota) and correlation with community composition and environmental parameters demonstrated that ARG can spread across the environment with the sporobiota being the dispersal vector. A highly abundant OTU affiliated with the genus Clostridium was identified as a potential specific vector for the dissemination of tet(W), due to a strong correlation with tet(W) frequency (ARG copy numbers/ng DNA). The high dispersal rate, long-term survival, and potential reactivation of the sporobiota constitute a serious concern in terms of dissemination and persistence of ARG in the environment.
bibliographic citation: Paul et al. (2018) Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PeerJ 6:e4989 https://doi.org/10.7717/peerj.4989
date submitted: 2018-03-02
date accepted: 2018-05-27
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paul
  given name: Christophe
author list: Agent
  family name: Bayrychenko
  given name: Zhanna
author list: Agent
  family name: Junier
  given name: Thomas
author list: Agent
  family name: Filippidou
  given name: Sevasti
author list: Agent
  family name: Beck
  given name: Karin
author list: Agent
  family name: Bueche
  given name: Matthieu
author list: Agent
  family name: Greub
  given name: Gilbert
author list: Agent
  family name: Bürgmann
  given name: Helmut
author list: Agent
  family name: Junier
  given name: Pilar
doi: 10.7717/peerj.4989
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: ©2018 Paul et al.
attribution name: Paul et al.

Cranial morphology of Sinovenator changii (Theropoda: Troodontidae) on the new material from the Yixian Formation of western Liaoning, China
type: item
type: AcademicArticle
description: A new three-dimensionally preserved troodontid specimen consisting of most of the skull, partial mandibles and six articulated cervical vertebrae (PMOL-AD00102) from the Early Cretaceous Yixian Formation of Beipiao, western Liaoning, China is identified as Sinovenator changii on the basis of a surangular with a “T”-shaped cross-section. High-resolution computed tomographic data for the skull of this new specimen facilitated a detailed description of the cranial anatomy of S. changii. New diagnostic features of S. changii include a well-developed medial shelf on the jugal, a slender bar in the parasphenoid recess, a lateral groove on the pterygoid flange of the ectopterygoid, and the lateral surface of the anterior cervical vertebrae bearing two pneumatic foramina. Our new observation confirms that the braincase of Sinovenator is not as primitive as previously suggested, although it still shows an intermediate state between derived troodontids and non-troodontid paravians in having an initial stage of the subotic recess and the otosphenoidal crest. Additionally, this new specimen reveals some novel and valuable anatomical information of troodontids regarding the quadrate-quadratojugal articulation, the stapes, the epipterygoid and the atlantal ribs.
format: application/pdf
format: text/html
creator: Ya-Lei Yin
creator: Rui Pei
creator: Chang-Fu Zhou
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4977
publisher: PeerJ Inc.
rights: © 2018 Yin et al.
abstract: A new three-dimensionally preserved troodontid specimen consisting of most of the skull, partial mandibles and six articulated cervical vertebrae (PMOL-AD00102) from the Early Cretaceous Yixian Formation of Beipiao, western Liaoning, China is identified as Sinovenator changii on the basis of a surangular with a “T”-shaped cross-section. High-resolution computed tomographic data for the skull of this new specimen facilitated a detailed description of the cranial anatomy of S. changii. New diagnostic features of S. changii include a well-developed medial shelf on the jugal, a slender bar in the parasphenoid recess, a lateral groove on the pterygoid flange of the ectopterygoid, and the lateral surface of the anterior cervical vertebrae bearing two pneumatic foramina. Our new observation confirms that the braincase of Sinovenator is not as primitive as previously suggested, although it still shows an intermediate state between derived troodontids and non-troodontid paravians in having an initial stage of the subotic recess and the otosphenoidal crest. Additionally, this new specimen reveals some novel and valuable anatomical information of troodontids regarding the quadrate-quadratojugal articulation, the stapes, the epipterygoid and the atlantal ribs.
bibliographic citation: Yin et al. (2018) Cranial morphology of Sinovenator changii (Theropoda: Troodontidae) on the new material from the Yixian Formation of western Liaoning, China. PeerJ 6:e4977 https://doi.org/10.7717/peerj.4977
date submitted: 2018-03-26
date accepted: 2018-05-24
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Ya-Lei
author list: Agent
  family name: Pei
  given name: Rui
author list: Agent
  family name: Zhou
  given name: Chang-Fu
doi: 10.7717/peerj.4977
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Yin et al.
attribution name: Yin et al.

Comparative health assessment of urban and non-urban free-ranging mule deer (Odocoileus hemionus) in southeastern British Columbia, Canada
type: item
type: AcademicArticle
description: Background The provincial wildlife management agency, British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, performed a translocation to control the urban mule deer (Odocoileus hemionus; uMD) overpopulation and supplement the declining non-urban mule deer (nuMD) population in the Kootenay region, British Columbia, Canada. The objectives of this cross-sectional study were to evaluate the health of the urban and nuMD populations by comparing pathogen exposure, body condition scores (BCS) and pregnancy rates, to characterize the health risks associated with the translocation and to investigate the role of infectious diseases in the decline of the nuMD deer population. Methods Two hundred free-ranging mule deer were captured in urban and non-urban environments in the Kootenay region from 2014 to 2017. BCS and morphometric examinations were performed for each deer. Blood samples collected from each deer were tested for exposure to selected pathogens and pregnancy status. Results Body condition scores averaged 3.4 on a five-point scale, was greater in nuMD, and significantly differed between years. Antibodies were detected for adenovirus hemorrhagic disease virus (38.4% (uMD 43.7%, nuMD 33.3%)), bluetongue virus (0.6% (uMD 1.2%, nuMD 0%)), bovine respiratory syncytial virus (8.4% (uMD 4.6%, nuMD 12.1%)), bovine viral diarrhea virus (1.1% (uMD 0%, nuMD 2.2%)), bovine parainfluenza-3 virus (27.0% (uMD 27.6%, nuMD 26.4%)), Neospora caninum (22.1% (uMD 24.4%, nuMD 19.7%)) and Toxoplasma gondii (8.2% (uMD 12.3%, nuMD 3.9%)). No antibodies against epizootic hemorrhagic disease virus were detected. Pregnancy rates did not differ between the two deer populations (90.7% (uMD 90.6%, nuMD 90.9%)). Exposure to N. caninum was associated with a reduced probability of being pregnant. uMD were more likely to be exposed to T. gondii than nuMD. Discussion Comparison of BCS, pregnancy rates and pathogen exposure of uMD and nuMD showed that the healt…
format: application/pdf
format: text/html
creator: Amélie Mathieu
creator: Mark Flint
creator: Patrick M. Stent
creator: Helen M. Schwantje
creator: Thomas E. Wittum
subject: Conservation Biology
subject: Veterinary Medicine
subject: Zoology
subject: Infectious Diseases
description: doi:10.7717/peerj.4968
publisher: PeerJ Inc.
rights: © 2018 Mathieu et al.
abstract: Background The provincial wildlife management agency, British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, performed a translocation to control the urban mule deer (Odocoileus hemionus; uMD) overpopulation and supplement the declining non-urban mule deer (nuMD) population in the Kootenay region, British Columbia, Canada. The objectives of this cross-sectional study were to evaluate the health of the urban and nuMD populations by comparing pathogen exposure, body condition scores (BCS) and pregnancy rates, to characterize the health risks associated with the translocation and to investigate the role of infectious diseases in the decline of the nuMD deer population. Methods Two hundred free-ranging mule deer were captured in urban and non-urban environments in the Kootenay region from 2014 to 2017. BCS and morphometric examinations were performed for each deer. Blood samples collected from each deer were tested for exposure to selected pathogens and pregnancy status. Results Body condition scores averaged 3.4 on a five-point scale, was greater in nuMD, and significantly differed between years. Antibodies were detected for adenovirus hemorrhagic disease virus (38.4% (uMD 43.7%, nuMD 33.3%)), bluetongue virus (0.6% (uMD 1.2%, nuMD 0%)), bovine respiratory syncytial virus (8.4% (uMD 4.6%, nuMD 12.1%)), bovine viral diarrhea virus (1.1% (uMD 0%, nuMD 2.2%)), bovine parainfluenza-3 virus (27.0% (uMD 27.6%, nuMD 26.4%)), Neospora caninum (22.1% (uMD 24.4%, nuMD 19.7%)) and Toxoplasma gondii (8.2% (uMD 12.3%, nuMD 3.9%)). No antibodies against epizootic hemorrhagic disease virus were detected. Pregnancy rates did not differ between the two deer populations (90.7% (uMD 90.6%, nuMD 90.9%)). Exposure to N. caninum was associated with a reduced probability of being pregnant. uMD were more likely to be exposed to T. gondii than nuMD. Discussion Comparison of BCS, pregnancy rates and pathogen exposure of uMD and nuMD showed that the healt…
bibliographic citation: Mathieu et al. (2018) Comparative health assessment of urban and non-urban free-ranging mule deer (Odocoileus hemionus) in southeastern British Columbia, Canada. PeerJ 6:e4968 https://doi.org/10.7717/peerj.4968
date submitted: 2018-01-25
date accepted: 2018-05-23
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mathieu
  given name: Amélie
author list: Agent
  family name: Flint
  given name: Mark
author list: Agent
  family name: Stent
  given name: Patrick M.
author list: Agent
  family name: Schwantje
  given name: Helen M.
author list: Agent
  family name: Wittum
  given name: Thomas E.
doi: 10.7717/peerj.4968
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Mathieu et al.
attribution name: Mathieu et al.

GEsture: an online hand-drawing tool for gene expression pattern search
type: item
type: AcademicArticle
description: Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.
format: application/pdf
format: text/html
creator: Chunyan Wang
creator: Yiqing Xu
creator: Xuelin Wang
creator: Li Zhang
creator: Suyun Wei
creator: Qiaolin Ye
creator: Youxiang Zhu
creator: Hengfu Yin
creator: Manoj Nainwal
creator: Luis Tanon-Reyes
creator: Feng Cheng
creator: Tongming Yin
creator: Ning Ye
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.4927
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.
bibliographic citation: Wang et al. (2018) GEsture: an online hand-drawing tool for gene expression pattern search. PeerJ 6:e4927 https://doi.org/10.7717/peerj.4927
date submitted: 2018-02-19
date accepted: 2018-05-18
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chunyan
author list: Agent
  family name: Xu
  given name: Yiqing
author list: Agent
  family name: Wang
  given name: Xuelin
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Wei
  given name: Suyun
author list: Agent
  family name: Ye
  given name: Qiaolin
author list: Agent
  family name: Zhu
  given name: Youxiang
author list: Agent
  family name: Yin
  given name: Hengfu
author list: Agent
  family name: Nainwal
  given name: Manoj
author list: Agent
  family name: Tanon-Reyes
  given name: Luis
author list: Agent
  family name: Cheng
  given name: Feng
author list: Agent
  family name: Yin
  given name: Tongming
author list: Agent
  family name: Ye
  given name: Ning
doi: 10.7717/peerj.4927
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: ©2018 Wang et al.
attribution name: Wang et al.

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