PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata
items: Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman
items: Aetiology of livestock fetal mortality in Mazandaran province, Iran
items: A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay
items: Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)
items: Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model
items: Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample
items: Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
items: Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil
items: Evaluation of AAV-DJ vector for retinal gene therapy

Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata
type: item
type: AcademicArticle
description: Background Current regulatory pesticide risk assessments for bees are based primarily on the honey bee (Apis mellifera) and may not always be protective of solitary bees. To incorporate solitary bees into the risk assessment process, standardized methods to assess the hazard of pesticides under semi-field (Tier II) conditions will be needed. We conducted a series of experiments over 2 years to assess potential surrogate plants and adult release rates for use in semi-field experiments with the alfalfa leafcutting bee (ALB, Megachile rotundata). Methods We compared ALB foraging activity and reproduction on 12 m2 plots of flowering alfalfa (Medicago sativa) and buckwheat (Fagopyrum esculentum) at low (10♀/20♂) and high (20♀/40♂) adult release rates. The following year, we assessed the same endpoints on plots of purple tansy (Phacelia tanacetifolia) at a release rate of 10♀/15♂. Results Although ALB foraging activity was high on buckwheat plots, fewer adults were produced compared to alfalfa plots. On alfalfa, there were no differences in foraging activity, nesting, or reproduction between the low and high release rates. ALB readily foraged from purple tansy flowers, but females avoided purple tansy leaves for leaf cell construction. Discussion Our study suggests that buckwheat alone cannot support ALB during semi-field studies on small plots. For alfalfa, we recommend a maximum release rate of 10♀/20♂ in 12 m2 plots. Further study of higher ALB release rates on purple tansy is warranted. A mixed planting of purple tansy and a plant suitable for leaf piece collection (e.g., buckwheat) may provide favorable conditions for ALB activity and reproduction during semi-field testing.
format: application/pdf
format: text/html
creator: Andrew J. Frewin
creator: Angela E. Gradish
creator: Graham R. Ansell
creator: Cynthia D. Scott-Dupree
subject: Agricultural Science
subject: Entomology
subject: Toxicology
description: doi:10.7717/peerj.6278
publisher: PeerJ Inc.
rights: © 2019 Frewin et al.
abstract: Background Current regulatory pesticide risk assessments for bees are based primarily on the honey bee (Apis mellifera) and may not always be protective of solitary bees. To incorporate solitary bees into the risk assessment process, standardized methods to assess the hazard of pesticides under semi-field (Tier II) conditions will be needed. We conducted a series of experiments over 2 years to assess potential surrogate plants and adult release rates for use in semi-field experiments with the alfalfa leafcutting bee (ALB, Megachile rotundata). Methods We compared ALB foraging activity and reproduction on 12 m2 plots of flowering alfalfa (Medicago sativa) and buckwheat (Fagopyrum esculentum) at low (10♀/20♂) and high (20♀/40♂) adult release rates. The following year, we assessed the same endpoints on plots of purple tansy (Phacelia tanacetifolia) at a release rate of 10♀/15♂. Results Although ALB foraging activity was high on buckwheat plots, fewer adults were produced compared to alfalfa plots. On alfalfa, there were no differences in foraging activity, nesting, or reproduction between the low and high release rates. ALB readily foraged from purple tansy flowers, but females avoided purple tansy leaves for leaf cell construction. Discussion Our study suggests that buckwheat alone cannot support ALB during semi-field studies on small plots. For alfalfa, we recommend a maximum release rate of 10♀/20♂ in 12 m2 plots. Further study of higher ALB release rates on purple tansy is warranted. A mixed planting of purple tansy and a plant suitable for leaf piece collection (e.g., buckwheat) may provide favorable conditions for ALB activity and reproduction during semi-field testing.
bibliographic citation: Frewin et al. (2019) Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata. PeerJ 6:e6278 https://doi.org/10.7717/peerj.6278
date submitted: 2018-06-06
date accepted: 2018-12-12
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frewin
  given name: Andrew J.
author list: Agent
  family name: Gradish
  given name: Angela E.
author list: Agent
  family name: Ansell
  given name: Graham R.
author list: Agent
  family name: Scott-Dupree
  given name: Cynthia D.
doi: 10.7717/peerj.6278
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Frewin et al.
attribution name: Frewin et al.

Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman
type: item
type: AcademicArticle
description: The species of Meranoplus Smith, 1853 of the Arabian Peninsula are reviewed based on the worker caste. Two species are recognized, keyed, and illustrated by Scanning Electron Microscope images (SEM), Meranoplus mosalahi and M. pulcher, Sharaf, 2014. Meranoplus mosalahi sp. n. is described from the Dhofar Governorate, Oman based on the worker caste. The new species belongs to the M. magrettii-group and closely resembles M. pulcher Sharaf, 2014 from the Kingdom of Saudi Arabia (KSA), from which it can be distinguished by the bicolored body, the shallowly concave anterior clypeal margin, the absence of well-developed anterior clypeal teeth, the fewer irregular longitudinal cephalic rugae, and the feeble longitudinal rugae on posterior face of petiolar node.
format: application/pdf
format: text/html
creator: Mostafa R. Sharaf
creator: Abdulrahman S. Aldawood
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6287
publisher: PeerJ Inc.
rights: © 2019 Sharaf and Aldawood
abstract: The species of Meranoplus Smith, 1853 of the Arabian Peninsula are reviewed based on the worker caste. Two species are recognized, keyed, and illustrated by Scanning Electron Microscope images (SEM), Meranoplus mosalahi and M. pulcher, Sharaf, 2014. Meranoplus mosalahi sp. n. is described from the Dhofar Governorate, Oman based on the worker caste. The new species belongs to the M. magrettii-group and closely resembles M. pulcher Sharaf, 2014 from the Kingdom of Saudi Arabia (KSA), from which it can be distinguished by the bicolored body, the shallowly concave anterior clypeal margin, the absence of well-developed anterior clypeal teeth, the fewer irregular longitudinal cephalic rugae, and the feeble longitudinal rugae on posterior face of petiolar node.
bibliographic citation: Sharaf et al. (2019) Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman. PeerJ 7:e6287 https://doi.org/10.7717/peerj.6287
date submitted: 2018-11-11
date accepted: 2018-12-15
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharaf
  given name: Mostafa R.
author list: Agent
  family name: Aldawood
  given name: Abdulrahman S.
doi: 10.7717/peerj.6287
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Sharaf and Aldawood
attribution name: Sharaf and Aldawood

Aetiology of livestock fetal mortality in Mazandaran province, Iran
type: item
type: AcademicArticle
description: In the farming industry, the productivity of livestock herds depends on the fertility efficiency of animals. The accurate diagnosis of a broad range of aetiological agents causing fetal death is often difficult. Our aim was to assess the prevalence rates of Toxoplasma gondii, Neospora caninum, and Brucella spp. infections in ruminant abortion using bacteriological culture and molecular techniques in Mazandaran Province, northern Iran. Samples were collected from 70 aborted sheep, goat, and cattle fetuses between September 2014 and December 2015. Necropsy was performed on all the received samples, and brain tissue and abomasal content were obtained from the aborted fetuses. Protozoan infections were detected by specific polymerase chain reaction (PCR) and bacterial agents using bacteriological examinations and PCR assay. Infectious pathogens were detected in 22 out of 70 (31.4%) examined fetuses. Moreover, T. gondii, N. caninum, and B. melitensis were verified in 13 (18.6%), four (5.7%), and two (2.85%) samples, respectively. Our results showed that infection with the mentioned pathogenic agents may lead to fetal mortality, which can be a major cause of economic loss. The listed pathogens could be considered important etiological agents of fetal loss in Mazandaran Province, for which appropriate control measures such as vaccination and biosecurity can be implemented to prevent infection and reduce reproductive loss in livestock farms.
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format: text/html
creator: Afsaneh Amouei
creator: Mehdi Sharif
creator: Shahabeddin Sarvi
creator: Ramin Bagheri Nejad
creator: Sargis A. Aghayan
creator: Mohammad Bagher Hashemi-Soteh
creator: Azadeh Mizani
creator: Seyed Abdollah Hosseini
creator: Sara Gholami
creator: Alireza Sadeghi
creator: Mohammad Sarafrazi
creator: Ahmad Daryani
subject: Agricultural Science
subject: Microbiology
subject: Parasitology
subject: Veterinary Medicine
description: doi:10.7717/peerj.5920
publisher: PeerJ Inc.
rights: © 2019 Amouei et al.
abstract: In the farming industry, the productivity of livestock herds depends on the fertility efficiency of animals. The accurate diagnosis of a broad range of aetiological agents causing fetal death is often difficult. Our aim was to assess the prevalence rates of Toxoplasma gondii, Neospora caninum, and Brucella spp. infections in ruminant abortion using bacteriological culture and molecular techniques in Mazandaran Province, northern Iran. Samples were collected from 70 aborted sheep, goat, and cattle fetuses between September 2014 and December 2015. Necropsy was performed on all the received samples, and brain tissue and abomasal content were obtained from the aborted fetuses. Protozoan infections were detected by specific polymerase chain reaction (PCR) and bacterial agents using bacteriological examinations and PCR assay. Infectious pathogens were detected in 22 out of 70 (31.4%) examined fetuses. Moreover, T. gondii, N. caninum, and B. melitensis were verified in 13 (18.6%), four (5.7%), and two (2.85%) samples, respectively. Our results showed that infection with the mentioned pathogenic agents may lead to fetal mortality, which can be a major cause of economic loss. The listed pathogens could be considered important etiological agents of fetal loss in Mazandaran Province, for which appropriate control measures such as vaccination and biosecurity can be implemented to prevent infection and reduce reproductive loss in livestock farms.
bibliographic citation: Amouei et al. (2019) Aetiology of livestock fetal mortality in Mazandaran province, Iran. PeerJ 6:e5920 https://doi.org/10.7717/peerj.5920
date submitted: 2017-10-12
date accepted: 2018-10-03
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amouei
  given name: Afsaneh
author list: Agent
  family name: Sharif
  given name: Mehdi
author list: Agent
  family name: Sarvi
  given name: Shahabeddin
author list: Agent
  family name: Bagheri Nejad
  given name: Ramin
author list: Agent
  family name: Aghayan
  given name: Sargis A.
author list: Agent
  family name: Hashemi-Soteh
  given name: Mohammad Bagher
author list: Agent
  family name: Mizani
  given name: Azadeh
author list: Agent
  family name: Hosseini
  given name: Seyed Abdollah
author list: Agent
  family name: Gholami
  given name: Sara
author list: Agent
  family name: Sadeghi
  given name: Alireza
author list: Agent
  family name: Sarafrazi
  given name: Mohammad
author list: Agent
  family name: Daryani
  given name: Ahmad
doi: 10.7717/peerj.5920
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Amouei et al.
attribution name: Amouei et al.

A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay
type: item
type: AcademicArticle
description: Barona arcuata, n.gen et n.sp., a left forewing of a relatively large cockroach of the Order Blattaria, is described from mesosaur-bearing lagoonal shales of the Mangrullo Formation (north-eastern Uruguay). While most of the insect remains recovered from the Mangrullo Formation come from sandy limestones, associated to scarce isolated mesosaur bones and pygocephalomorph crustaceans, the cockroach wing here described was found in the overlaying green to brownish, gray and dark black shales associated to intercalated bentonites and evaporitic gypsum crystals. Barona arcuata shares some features with typical Late Carboniferous taxa such as its general venation pattern and outline of the wing, four main and powerful veins arising close together from near the base of the wing, Sc simple forked, pectinate, reaching the costal border through a long fork, R and M bifurcating and terminating in the wing margin above and below the apex respectively, short and narrow CuA, and the presence of a broad interspace between CuP and AA. Cross venation seems to be absent or it was not preserved. Some characters might relate Barona arcuata to the Late Carboniferous-Early Permian Neothroblattinidae such as the presence of sigmoidal veins in the anal area, a condition not found in any of the remaining representatives of the Palaeozoic Blattaria. Intriguingly, the Uruguayan blattarian also presents a strong similarity with Qilianiblatta namurensis Zhang, Schneider & Hong, 2012 from the Westphalian of China, clearly a smaller taxon that is also difficult to relate to any of the preexistent families. The apparent plesiomorphic venation pattern of the new species which is reminiscent of that present in the oldest known blattarians, is in agreement with a Permo-Carboniferous (Gzhelian-Asselian) age for the Mangrullo Formation also supported by the presence of a macrofloral assemblage dominated by arborescent lepidondendrids and other lycopsids and the pygocephalid-like morphology of the pygoc…
format: application/pdf
format: text/html
creator: Viviana Calisto
creator: Graciela Piñeiro
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6289
publisher: PeerJ Inc.
rights: © 2019 Calisto et al.
abstract: Barona arcuata, n.gen et n.sp., a left forewing of a relatively large cockroach of the Order Blattaria, is described from mesosaur-bearing lagoonal shales of the Mangrullo Formation (north-eastern Uruguay). While most of the insect remains recovered from the Mangrullo Formation come from sandy limestones, associated to scarce isolated mesosaur bones and pygocephalomorph crustaceans, the cockroach wing here described was found in the overlaying green to brownish, gray and dark black shales associated to intercalated bentonites and evaporitic gypsum crystals. Barona arcuata shares some features with typical Late Carboniferous taxa such as its general venation pattern and outline of the wing, four main and powerful veins arising close together from near the base of the wing, Sc simple forked, pectinate, reaching the costal border through a long fork, R and M bifurcating and terminating in the wing margin above and below the apex respectively, short and narrow CuA, and the presence of a broad interspace between CuP and AA. Cross venation seems to be absent or it was not preserved. Some characters might relate Barona arcuata to the Late Carboniferous-Early Permian Neothroblattinidae such as the presence of sigmoidal veins in the anal area, a condition not found in any of the remaining representatives of the Palaeozoic Blattaria. Intriguingly, the Uruguayan blattarian also presents a strong similarity with Qilianiblatta namurensis Zhang, Schneider & Hong, 2012 from the Westphalian of China, clearly a smaller taxon that is also difficult to relate to any of the preexistent families. The apparent plesiomorphic venation pattern of the new species which is reminiscent of that present in the oldest known blattarians, is in agreement with a Permo-Carboniferous (Gzhelian-Asselian) age for the Mangrullo Formation also supported by the presence of a macrofloral assemblage dominated by arborescent lepidondendrids and other lycopsids and the pygocephalid-like morphology of the pygoc…
bibliographic citation: Calisto et al. (2019) A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay. PeerJ 7:e6289 https://doi.org/10.7717/peerj.6289
date submitted: 2018-08-06
date accepted: 2018-12-16
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calisto
  given name: Viviana
author list: Agent
  family name: Piñeiro
  given name: Graciela
doi: 10.7717/peerj.6289
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Calisto and Piñeiro
attribution name: Calisto et al.

Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)
type: item
type: AcademicArticle
description: Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
format: application/pdf
format: text/html
creator: Andrinajoro R. Rakotoarivelo
creator: Steven M. Goodman
creator: M. Corrie Schoeman
creator: Sandi Willows-Munro
subject: Biogeography
subject: Evolutionary Studies
description: doi:10.7717/peerj.5866
publisher: PeerJ Inc.
rights: © 2019 Rakotoarivelo et al.
abstract: Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
bibliographic citation: Rakotoarivelo et al. (2019) Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 7:e5866 https://doi.org/10.7717/peerj.5866
date submitted: 2018-08-13
date accepted: 2018-10-03
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rakotoarivelo
  given name: Andrinajoro R.
author list: Agent
  family name: Goodman
  given name: Steven M.
author list: Agent
  family name: Schoeman
  given name: M. Corrie
author list: Agent
  family name: Willows-Munro
  given name: Sandi
doi: 10.7717/peerj.5866
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Rakotoarivelo et al.
attribution name: Rakotoarivelo et al.

Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model
type: item
type: AcademicArticle
description: Background Scarlet fever is recognized as being a major public health issue owing to its increase in notifications in mainland China, and an advanced response based on forecasting techniques is being adopted to tackle this. Here, we construct a new hybrid method incorporating seasonal autoregressive integrated moving average (SARIMA) with a nonlinear autoregressive with external input(NARX) to analyze its seasonality and trend in order to efficiently prevent and control this re-emerging disease. Methods Four statistical models, including a basic SARIMA, basic nonlinear autoregressive (NAR) method, traditional SARIMA-NAR and new SARIMA-NARX hybrid approaches, were developed based on scarlet fever incidence data between January 2004 and July 2018 to evaluate its temporal patterns, and their mimic and predictive capacities were compared to discover the optimal using the mean absolute percentage error, root mean square error, mean error rate, and root mean square percentage error. Results The four preferred models identified were comprised of the SARIMA(0,1,0)(0,1,1)12, NAR with 14 hidden neurons and five delays, SARIMA-NAR with 33 hidden neurons and five delays, and SARIMA-NARX with 16 hidden neurons and 4 delays. Among which presenting the lowest values of the aforementioned indices in both simulation and prediction horizons is the SARIMA-NARX method. Analyses from the data suggested that scarlet fever was a seasonal disease with predominant peaks of summer and winter and a substantial rising trend in the scarlet fever notifications was observed with an acceleration of 9.641% annually, particularly since 2011 with 12.869%, and moreover such a trend will be projected to continue in the coming year. Conclusions The SARIMA-NARX technique has the promising ability to better consider both linearity and non-linearity behind scarlet fever data than the others, which significantly facilitates its prevention and intervention of scarlet fever. Besides, under current trend of on…
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format: text/html
creator: Yongbin Wang
creator: Chunjie Xu
creator: Zhende Wang
creator: Juxiang Yuan
subject: Mathematical Biology
subject: Epidemiology
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6165
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Scarlet fever is recognized as being a major public health issue owing to its increase in notifications in mainland China, and an advanced response based on forecasting techniques is being adopted to tackle this. Here, we construct a new hybrid method incorporating seasonal autoregressive integrated moving average (SARIMA) with a nonlinear autoregressive with external input(NARX) to analyze its seasonality and trend in order to efficiently prevent and control this re-emerging disease. Methods Four statistical models, including a basic SARIMA, basic nonlinear autoregressive (NAR) method, traditional SARIMA-NAR and new SARIMA-NARX hybrid approaches, were developed based on scarlet fever incidence data between January 2004 and July 2018 to evaluate its temporal patterns, and their mimic and predictive capacities were compared to discover the optimal using the mean absolute percentage error, root mean square error, mean error rate, and root mean square percentage error. Results The four preferred models identified were comprised of the SARIMA(0,1,0)(0,1,1)12, NAR with 14 hidden neurons and five delays, SARIMA-NAR with 33 hidden neurons and five delays, and SARIMA-NARX with 16 hidden neurons and 4 delays. Among which presenting the lowest values of the aforementioned indices in both simulation and prediction horizons is the SARIMA-NARX method. Analyses from the data suggested that scarlet fever was a seasonal disease with predominant peaks of summer and winter and a substantial rising trend in the scarlet fever notifications was observed with an acceleration of 9.641% annually, particularly since 2011 with 12.869%, and moreover such a trend will be projected to continue in the coming year. Conclusions The SARIMA-NARX technique has the promising ability to better consider both linearity and non-linearity behind scarlet fever data than the others, which significantly facilitates its prevention and intervention of scarlet fever. Besides, under current trend of on…
bibliographic citation: Wang et al. (2019) Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model. PeerJ 7:e6165 https://doi.org/10.7717/peerj.6165
date submitted: 2018-09-19
date accepted: 2018-11-27
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yongbin
author list: Agent
  family name: Xu
  given name: Chunjie
author list: Agent
  family name: Wang
  given name: Zhende
author list: Agent
  family name: Yuan
  given name: Juxiang
doi: 10.7717/peerj.6165
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample
type: item
type: AcademicArticle
description: Background Patients with atrial fibrillation-flutter (AF) admitted on the weekends were initially reported to have poor outcomes. The primary purpose of this study is to re-evaluate the outcomes for weekend versus weekday AF hospitalization using the 2014 Nationwide Inpatient Sample (NIS). Methods Included hospitalizations were aged above 18 years. The hospitalizations with AF were identified using the international classification of diseases 9 (ICD-9) codes (427.31, 427.32). In-hospital mortality, length of stay (LOS), other co-morbidities, cardioversion procedures, and time to cardioversion were recorded. All analysis was performed using SAS 9.4 statistical software (Cary, North Carolina). Results A total of 453,505 hospitalizations with atrial fibrillation and flutter as primary discharge diagnosis were identified. Among the total hospitalizations with a primary diagnosis of AF, 20.3% were admitted on the weekend. Among the weekend hospitalizations, 0.19% died in hospital compared to 0.74% among those admitted during the week. After adjusting for patient characteristics, hospital characteristics and disease severity, the adjusted odds for in-hospital mortality were not significantly different for weekend vs. weekday hospitalizations (OR = 0.91, 95% CI [0.77–1.11]; p = 0.33). The weekend admissions were associated with significantly lower odds of cardioversion procedures (OR = 0.72, 95% CI [0.69–0.76], P < 0.0001), lower cost of hospitalization (USD 8265.8 on weekends vs. USD 8966.5 on the weekdays, P < 0.001), slightly lower rate of anticoagulation (17.09% on the weekends vs. 18.73% on the weekdays. P < 0.0001), and slightly increased time to cardioversion (1.94 days on the weekend vs. 1.73 days on weekdays, P < 0.0005). The mean length of hospital stay (LOS) was statistically not different in both groups: (3.49 days ± 3.70 (SD) in the weekend group vs. 3.47 days ± 3.50 (SD) in the weekday group, P = 0.42) Discussion The weekend AF hospitalizations did not have a…
format: application/pdf
format: text/html
creator: Dinesh C. Voruganti
creator: Ghanshyam Palamaner Subash Shantha
creator: Abhishek Deshmukh
creator: Michael C. Giudici
subject: Cardiology
subject: Global Health
subject: Health Policy
description: doi:10.7717/peerj.6211
publisher: PeerJ Inc.
rights: © 2019 Voruganti et al.
abstract: Background Patients with atrial fibrillation-flutter (AF) admitted on the weekends were initially reported to have poor outcomes. The primary purpose of this study is to re-evaluate the outcomes for weekend versus weekday AF hospitalization using the 2014 Nationwide Inpatient Sample (NIS). Methods Included hospitalizations were aged above 18 years. The hospitalizations with AF were identified using the international classification of diseases 9 (ICD-9) codes (427.31, 427.32). In-hospital mortality, length of stay (LOS), other co-morbidities, cardioversion procedures, and time to cardioversion were recorded. All analysis was performed using SAS 9.4 statistical software (Cary, North Carolina). Results A total of 453,505 hospitalizations with atrial fibrillation and flutter as primary discharge diagnosis were identified. Among the total hospitalizations with a primary diagnosis of AF, 20.3% were admitted on the weekend. Among the weekend hospitalizations, 0.19% died in hospital compared to 0.74% among those admitted during the week. After adjusting for patient characteristics, hospital characteristics and disease severity, the adjusted odds for in-hospital mortality were not significantly different for weekend vs. weekday hospitalizations (OR = 0.91, 95% CI [0.77–1.11]; p = 0.33). The weekend admissions were associated with significantly lower odds of cardioversion procedures (OR = 0.72, 95% CI [0.69–0.76], P < 0.0001), lower cost of hospitalization (USD 8265.8 on weekends vs. USD 8966.5 on the weekdays, P < 0.001), slightly lower rate of anticoagulation (17.09% on the weekends vs. 18.73% on the weekdays. P < 0.0001), and slightly increased time to cardioversion (1.94 days on the weekend vs. 1.73 days on weekdays, P < 0.0005). The mean length of hospital stay (LOS) was statistically not different in both groups: (3.49 days ± 3.70 (SD) in the weekend group vs. 3.47 days ± 3.50 (SD) in the weekday group, P = 0.42) Discussion The weekend AF hospitalizations did not have a…
bibliographic citation: Voruganti et al. (2019) Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample. PeerJ 7:e6211 https://doi.org/10.7717/peerj.6211
date submitted: 2018-08-14
date accepted: 2018-12-04
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Voruganti
  given name: Dinesh C.
author list: Agent
  family name: Subash Shantha
  given name: Ghanshyam Palamaner
author list: Agent
  family name: Deshmukh
  given name: Abhishek
author list: Agent
  family name: Giudici
  given name: Michael C.
doi: 10.7717/peerj.6211
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Voruganti et al.
attribution name: Voruganti et al.

Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
type: item
type: AcademicArticle
description: Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
format: application/pdf
format: text/html
creator: Simon Pfanzelt
creator: Dirk C. Albach
creator: K. Bernhard von Hagen
subject: Biogeography
subject: Plant Science
description: doi:10.7717/peerj.6244
publisher: PeerJ Inc.
rights: © 2019 Pfanzelt et al.
abstract: Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
bibliographic citation: Pfanzelt et al. (2019) Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ 7:e6244 https://doi.org/10.7717/peerj.6244
date submitted: 2018-08-28
date accepted: 2018-12-08
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pfanzelt
  given name: Simon
author list: Agent
  family name: Albach
  given name: Dirk C.
author list: Agent
  family name: von Hagen
  given name: K. Bernhard
doi: 10.7717/peerj.6244
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Pfanzelt et al.
attribution name: Pfanzelt et al.

Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil
type: item
type: AcademicArticle
description: Background Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively. Results The highest methane production rate was 561 mg CH4 kg−1 dry soil d−1 with the addition of 50 mg kg−1 Ni and 684 mg CH4 kg−1 dry soil d−1 with the addition of 25 mg kg−1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg−1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g−1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg−1 Co addition (9.2× 105 ± 0.4 × 105 copies g−1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg−1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%). Discussion Our results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, whil…
format: application/pdf
format: text/html
creator: Tianwei Wang
creator: Zhaoxia Li
creator: Xueping Chen
creator: Xi-En Long
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6274
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively. Results The highest methane production rate was 561 mg CH4 kg−1 dry soil d−1 with the addition of 50 mg kg−1 Ni and 684 mg CH4 kg−1 dry soil d−1 with the addition of 25 mg kg−1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg−1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g−1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg−1 Co addition (9.2× 105 ± 0.4 × 105 copies g−1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg−1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%). Discussion Our results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, whil…
bibliographic citation: Wang et al. (2019) Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil. PeerJ 7:e6274 https://doi.org/10.7717/peerj.6274
date submitted: 2018-05-30
date accepted: 2018-12-07
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Tianwei
author list: Agent
  family name: Li
  given name: Zhaoxia
author list: Agent
  family name: Chen
  given name: Xueping
author list: Agent
  family name: Long
  given name: Xi-En
doi: 10.7717/peerj.6274
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Evaluation of AAV-DJ vector for retinal gene therapy
type: item
type: AcademicArticle
description: Purpose The most common virus vector used in gene therapy research for ophthalmologic diseases is the adeno-associated virus (AAV) vector, which has been used successfully in a number of preclinical and clinical studies. It is important to evaluate novel AAV vectors in animal models for application of clinical gene therapy. The AAV-DJ (type 2/type 8/type 9 chimera) was engineered from shuffling eight different wild-type native viruses. In this study, we investigated the efficiency of gene transfer by AAV-DJ injections into the retina. Methods One microliter of AAV-2-CAGGS-EGFP or AAV-DJ-CAGGS-EGFP vector at a titer of 1.4 × 10e12 vg/ml was injected intravitreally or subretinally in each eye of C57BL/6 mice. We evaluated the transduction characteristics of AAV-2 and -DJ vectors using fluorescence microscopy and electroretinography. Results The results confirmed that AAV-DJ could deeply transfer gene to photoreceptor layer with intravitreal injection and has an efficient gene transfer to various cell types especially the Mueller cells in the retina. Retinal function was not affected by AAV-DJ infection or ectopic EGFP expression. Conclusions The AAV-DJ vector efficiently induces the reporter gene in both the inner and outer murine retina without functional toxicity. These data indicated that the AAV-DJ vector is a useful tool for the gene therapy research targeting retinal disorders.
format: application/pdf
format: text/html
creator: Yusaku Katada
creator: Kenta Kobayashi
creator: Kazuo Tsubota
creator: Toshihide Kurihara
subject: Virology
subject: Ophthalmology
description: doi:10.7717/peerj.6317
publisher: PeerJ Inc.
rights: © 2019 Katada et al.
abstract: Purpose The most common virus vector used in gene therapy research for ophthalmologic diseases is the adeno-associated virus (AAV) vector, which has been used successfully in a number of preclinical and clinical studies. It is important to evaluate novel AAV vectors in animal models for application of clinical gene therapy. The AAV-DJ (type 2/type 8/type 9 chimera) was engineered from shuffling eight different wild-type native viruses. In this study, we investigated the efficiency of gene transfer by AAV-DJ injections into the retina. Methods One microliter of AAV-2-CAGGS-EGFP or AAV-DJ-CAGGS-EGFP vector at a titer of 1.4 × 10e12 vg/ml was injected intravitreally or subretinally in each eye of C57BL/6 mice. We evaluated the transduction characteristics of AAV-2 and -DJ vectors using fluorescence microscopy and electroretinography. Results The results confirmed that AAV-DJ could deeply transfer gene to photoreceptor layer with intravitreal injection and has an efficient gene transfer to various cell types especially the Mueller cells in the retina. Retinal function was not affected by AAV-DJ infection or ectopic EGFP expression. Conclusions The AAV-DJ vector efficiently induces the reporter gene in both the inner and outer murine retina without functional toxicity. These data indicated that the AAV-DJ vector is a useful tool for the gene therapy research targeting retinal disorders.
bibliographic citation: Katada et al. (2019) Evaluation of AAV-DJ vector for retinal gene therapy. PeerJ 7:e6317 https://doi.org/10.7717/peerj.6317
date submitted: 2018-10-15
date accepted: 2018-12-19
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katada
  given name: Yusaku
author list: Agent
  family name: Kobayashi
  given name: Kenta
author list: Agent
  family name: Tsubota
  given name: Kazuo
author list: Agent
  family name: Kurihara
  given name: Toshihide
doi: 10.7717/peerj.6317
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Katada et al.
attribution name: Katada et al.

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