Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study
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.
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
Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria
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.
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
Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary
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.
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
How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities
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.
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
Evaluation of the effect of chickenpox vaccination on shingles epidemiology using agent-based modeling
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 years post-vaccination. The magnitude of change was sensitive to DoB and ranged from an increase of 22–100 per 100,000 person-years at 10 years post-vaccination for two and seven years of boosting respectively (p < 0.001). At 75 years post-vaccination, cumulative incidence ranged from a decline of 70 to an increase of 71 per 100,000 person-years for two and seven years of boosting respectively (p < 0.001). Sensitivity analyses had a minimal impact on our inferences except for removing the effect of boosting. Discussion Our model demonstrates that over the longer time period, there will be a reduction in shingles incidence driven by the depletion of the source of shingles reactivation; however in the short to medium term some age cohorts may experience an increase in shingles incidence. Our model offers a platform to further explore the relationship between chickenpox and shingles, including analyzing the impact of different chickenpox vaccination schedules and cost-effectiveness studies.
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
Monitoring monthly surface water dynamics of Dongting Lake using Sentinel-1 data at 10 m
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 in a timely manner.
Spatial and Geographic Information Science
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
Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater
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.
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
Cranial morphology of Sinovenator changii (Theropoda: Troodontidae) on the new material from the Yixian Formation of western Liaoning, China
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.
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
Comparative health assessment of urban and non-urban free-ranging mule deer (Odocoileus hemionus) in southeastern British Columbia, Canada
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 health of the two populations did not significantly differ, suggesting uMD translocations do not pose a severe risk of pathogen transmission between mule deer populations and that these selected pathogens do not factor in the decline of the nuMD population. However, inclusion of additional health indicators and creation of a robust predictive disease model are warranted to further characterize the health of mule deer and the health risks associated with uMD translocations. These results should be considered as part of a formal risk assessment for future uMD translocations in southeastern British Columbia.
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
GEsture: an online hand-drawing tool for gene expression pattern search
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.
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