PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications
items: Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway
items: Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)
items: An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
items: Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)
items: To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis)
items: Rapid eye movement-sleep is reduced in patients with acute uncomplicated diverticulitis—an observational study
items: Seasonal variation in microhabitat of salamanders: environmental variation or shift of habitat selection?
items: Wireless laptop-based phonocardiograph and diagnosis
items: Enigmatic declines in bird numbers in lowland forest of eastern Ecuador may be a consequence of climate change

A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications
type: item
type: AcademicArticle
description: Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized au…
format: application/pdf
format: text/html
creator: Alejandro Blanco
creator: Josep Fortuny
creator: Alba Vicente
creator: Àngel H. Luján
creator: Jordi Alexis García-Marçà
creator: Albert G. Sellés
subject: Animal Behavior
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1171
publisher: PeerJ Inc.
rights: © 2015 Blanco et al.
abstract: Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high-specialized au…
bibliographic citation: Blanco et al. (2015) A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications. PeerJ 3:e1171 https://doi.org/10.7717/peerj.1171
date submitted: 2015-03-20
date accepted: 2015-07-20
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blanco
  given name: Alejandro
author list: Agent
  family name: Fortuny
  given name: Josep
author list: Agent
  family name: Vicente
  given name: Alba
author list: Agent
  family name: Luján
  given name: Àngel H.
author list: Agent
  family name: García-Marçà
  given name: Jordi Alexis
author list: Agent
  family name: Sellés
  given name: Albert G.
doi: 10.7717/peerj.1171
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Blanco et al.
attribution name: Blanco et al.

Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway
type: item
type: AcademicArticle
description: Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.
format: application/pdf
format: text/html
creator: Irene Pellegrino
creator: Marco Cucco
creator: Arne Follestad
creator: Mathieu Boos
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.1161
publisher: PeerJ Inc.
rights: © 2015 Pellegrino et al.
abstract: Greylag goose populations are steadily increasing in north-western Europe. Although individuals breeding in the Netherlands have been considered mainly sedentary birds, those from Scandinavia or northern Germany fly towards their winter quarters, namely over France as far as Spain. This study aimed to determine the genetic structure of these birds, and to evaluate how goose populations mix. We used mitochondrial DNA and microsatellites from individuals distributed throughout the European Atlantic flyway, from breeding sites in Norway and the Netherlands to stopover and wintering sites in northern and south-western France. The mtDNA marker (CR1 D-Loop, 288 bp sequence, 144 ind.) showed 23 different haplotypes. The genetic distances amongst individuals sampled in Norway, northern France and the Netherlands were low (range 0.012–0.013). Individuals in south-western France showed a slightly higher genetic distance compared to all other sampling areas (ranges 0.018–0.022). The NJ tree does not show evidence of any single clades grouping together all individuals from the same geographic area. Besides, individuals from each site are found in different branches. Bayesian clustering procedures on 14 microsatellites (169 individuals) did not detect any geographically distinct cluster, and a high genetic admixture was recorded in all studied areas except for the individuals from the breeding sites in Norway, which were genetically very close. Estimation of migration rates through Bayesian inference confirms the scenario for the current mixing of goose populations.
bibliographic citation: Pellegrino et al. (2015) Lack of genetic structure in greylag goose (Anser anser) populations along the European Atlantic flyway. PeerJ 3:e1161 https://doi.org/10.7717/peerj.1161
date submitted: 2015-04-07
date accepted: 2015-07-17
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pellegrino
  given name: Irene
author list: Agent
  family name: Cucco
  given name: Marco
author list: Agent
  family name: Follestad
  given name: Arne
author list: Agent
  family name: Boos
  given name: Mathieu
doi: 10.7717/peerj.1161
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Pellegrino et al.
attribution name: Pellegrino et al.

Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)
type: item
type: AcademicArticle
description: In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.
format: application/pdf
format: text/html
creator: Sammy De Grave
creator: Charles H.J.M. Fransen
creator: Timothy J. Page
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1167
publisher: PeerJ Inc.
rights: © 2015 De Grave et al.
abstract: In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.
bibliographic citation: De Grave et al. (2015) Let’s be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda). PeerJ 3:e1167 https://doi.org/10.7717/peerj.1167
date submitted: 2015-06-26
date accepted: 2015-07-18
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Grave
  given name: Sammy
author list: Agent
  family name: Fransen
  given name: Charles H.J.M.
author list: Agent
  family name: Page
  given name: Timothy J.
doi: 10.7717/peerj.1167
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 De Grave et al.
attribution name: De Grave et al.

An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
type: item
type: AcademicArticle
description: Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
format: application/pdf
format: text/html
creator: Attila Ősi
creator: Márton Rabi
creator: László Makádi
subject: Paleontology
description: doi:10.7717/peerj.1160
publisher: PeerJ Inc.
rights: © 2015 Ősi et al.
abstract: Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
bibliographic citation: Ősi et al. (2015) An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago. PeerJ 3:e1160 https://doi.org/10.7717/peerj.1160
date submitted: 2015-03-25
date accepted: 2015-07-17
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ősi
  given name: Attila
author list: Agent
  family name: Rabi
  given name: Márton
author list: Agent
  family name: Makádi
  given name: László
doi: 10.7717/peerj.1160
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Ősi et al.
attribution name: Ősi et al.

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)
type: item
type: AcademicArticle
description: The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.
format: application/pdf
format: text/html
creator: Lisa A. Beirn
creator: Ruying Wang
creator: Bruce B. Clarke
creator: Jo Anne Crouch
subject: Agricultural Science
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.1153
publisher: PeerJ Inc.
rights: © 2015
abstract: The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.
bibliographic citation: Beirn et al. (2015) Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua). PeerJ 3:e1153 https://doi.org/10.7717/peerj.1153
date submitted: 2015-04-14
date accepted: 2015-07-14
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Beirn
  given name: Lisa A.
author list: Agent
  family name: Wang
  given name: Ruying
author list: Agent
  family name: Clarke
  given name: Bruce B.
author list: Agent
  family name: Crouch
  given name: Jo Anne
doi: 10.7717/peerj.1153
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13

To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis)
type: item
type: AcademicArticle
description: Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens to humans, including bacteria, protozoa, and viruses. Their importance as a disease vector necessitates reliable and comparable methods for extracting microbial DNA from ticks. Furthermore, to explore the population genetics or genomics of this tick, appropriate DNA extraction techniques are needed for both the vector and its microbes. Although a few studies have investigated different methods of DNA isolation from ticks, they are limited in the number and types of DNA extraction and lack species-specific quantification of DNA yield. Methods. Here we determined the most efficient and consistent method of DNA extraction from two different developmental stages of I. scapularis—nymph and adult—that are the most important for disease transmission. We used various methods of physical disruption of the hard, chitinous exoskeleton, as well as commercial and non-commercial DNA isolation kits. To gauge the effectiveness of these methods, we quantified the DNA yield and confirmed the DNA quality via PCR of both tick and microbial genetic material. Results. DNA extraction using the Thermo GeneJET Genomic DNA Purification Kit resulted in the highest DNA yields and the most consistent PCR amplification when combined with either cutting or bead beating with select matrices across life stages. DNA isolation methods using ammonium hydroxide as well as the MoBio PowerSoil kit also produced strong and successful PCR amplification, but only for females. Discussion. We contrasted a variety of readily available methods of DNA extraction from single individual blacklegged ticks and presented the results through a quantitative and qualitative assessment.
format: application/pdf
format: text/html
creator: Alyssa D. Ammazzalorso
creator: Christine P. Zolnik
creator: Thomas J. Daniels
creator: Sergios-Orestis Kolokotronis
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.1147
publisher: PeerJ Inc.
rights: © 2015 Ammazzalorso et al.
abstract: Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens to humans, including bacteria, protozoa, and viruses. Their importance as a disease vector necessitates reliable and comparable methods for extracting microbial DNA from ticks. Furthermore, to explore the population genetics or genomics of this tick, appropriate DNA extraction techniques are needed for both the vector and its microbes. Although a few studies have investigated different methods of DNA isolation from ticks, they are limited in the number and types of DNA extraction and lack species-specific quantification of DNA yield. Methods. Here we determined the most efficient and consistent method of DNA extraction from two different developmental stages of I. scapularis—nymph and adult—that are the most important for disease transmission. We used various methods of physical disruption of the hard, chitinous exoskeleton, as well as commercial and non-commercial DNA isolation kits. To gauge the effectiveness of these methods, we quantified the DNA yield and confirmed the DNA quality via PCR of both tick and microbial genetic material. Results. DNA extraction using the Thermo GeneJET Genomic DNA Purification Kit resulted in the highest DNA yields and the most consistent PCR amplification when combined with either cutting or bead beating with select matrices across life stages. DNA isolation methods using ammonium hydroxide as well as the MoBio PowerSoil kit also produced strong and successful PCR amplification, but only for females. Discussion. We contrasted a variety of readily available methods of DNA extraction from single individual blacklegged ticks and presented the results through a quantitative and qualitative assessment.
bibliographic citation: Ammazzalorso et al. (2015) To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis). PeerJ 3:e1147 https://doi.org/10.7717/peerj.1147
date submitted: 2015-04-30
date accepted: 2015-07-12
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ammazzalorso
  given name: Alyssa D.
author list: Agent
  family name: Zolnik
  given name: Christine P.
author list: Agent
  family name: Daniels
  given name: Thomas J.
author list: Agent
  family name: Kolokotronis
  given name: Sergios-Orestis
doi: 10.7717/peerj.1147
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Ammazzalorso et al.
attribution name: Ammazzalorso et al.

Rapid eye movement-sleep is reduced in patients with acute uncomplicated diverticulitis—an observational study
type: item
type: AcademicArticle
description: Introduction. Sleep disturbances are commonly found in patients in the postoperative period. Sleep disturbances may give rise to several complications including cardiopulmonary instability, transient cognitive dysfunction and prolonged convalescence. Many factors including host inflammatory responses are believed to cause postoperative sleep disturbances, as inflammatory responses can alter sleep architecture through cytokine-brain interactions. Our aim was to investigate alteration of sleep architecture during acute infection and its relationships to inflammation and clinical symptoms. Materials & Methods. In this observational study, we included patients with acute uncomplicated diverticulitis as a model to investigate the isolated effects of inflammatory responses on sleep. Eleven patients completed the study. Patients were admitted and treated with antibiotics for two nights, during which study endpoints were measured by polysomnography recordings, self-reported discomfort scores and blood samples of cytokines. One month later, the patients, who now were in complete remission, were readmitted and the endpoints were re-measured (the baseline values). Results. Total sleep time was reduced 4% and 7% the first (p = 0.006) and second (p = 0.014) nights of diverticulitis, compared to baseline, respectively. The rapid eye movement sleep was reduced 33% the first night (p = 0.016), compared to baseline. Moreover, plasma IL-6 levels were correlated to non-rapid eye movement sleep, rapid eye movement sleep and fatigue. Conclusion. Total sleep time and rapid eye movement sleep were reduced during nights with active diverticulitis and correlated with markers of inflammation.
format: application/pdf
format: text/html
creator: Chenxi Huang
creator: Mahdi Alamili
creator: Claus Henrik Nielsen
creator: Jacob Rosenberg
creator: Ismail Gögenur
subject: Anesthesiology and Pain Management
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Neurology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1146
publisher: PeerJ Inc.
rights: © 2015 Huang et al.
abstract: Introduction. Sleep disturbances are commonly found in patients in the postoperative period. Sleep disturbances may give rise to several complications including cardiopulmonary instability, transient cognitive dysfunction and prolonged convalescence. Many factors including host inflammatory responses are believed to cause postoperative sleep disturbances, as inflammatory responses can alter sleep architecture through cytokine-brain interactions. Our aim was to investigate alteration of sleep architecture during acute infection and its relationships to inflammation and clinical symptoms. Materials & Methods. In this observational study, we included patients with acute uncomplicated diverticulitis as a model to investigate the isolated effects of inflammatory responses on sleep. Eleven patients completed the study. Patients were admitted and treated with antibiotics for two nights, during which study endpoints were measured by polysomnography recordings, self-reported discomfort scores and blood samples of cytokines. One month later, the patients, who now were in complete remission, were readmitted and the endpoints were re-measured (the baseline values). Results. Total sleep time was reduced 4% and 7% the first (p = 0.006) and second (p = 0.014) nights of diverticulitis, compared to baseline, respectively. The rapid eye movement sleep was reduced 33% the first night (p = 0.016), compared to baseline. Moreover, plasma IL-6 levels were correlated to non-rapid eye movement sleep, rapid eye movement sleep and fatigue. Conclusion. Total sleep time and rapid eye movement sleep were reduced during nights with active diverticulitis and correlated with markers of inflammation.
bibliographic citation: Huang et al. (2015) Rapid eye movement-sleep is reduced in patients with acute uncomplicated diverticulitis—an observational study. PeerJ 3:e1146 https://doi.org/10.7717/peerj.1146
date submitted: 2015-05-12
date accepted: 2015-07-11
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Chenxi
author list: Agent
  family name: Alamili
  given name: Mahdi
author list: Agent
  family name: Nielsen
  given name: Claus Henrik
author list: Agent
  family name: Rosenberg
  given name: Jacob
author list: Agent
  family name: Gögenur
  given name: Ismail
doi: 10.7717/peerj.1146
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Huang et al.
attribution name: Huang et al.

Seasonal variation in microhabitat of salamanders: environmental variation or shift of habitat selection?
type: item
type: AcademicArticle
description: Relationships between species and their habitats are not always constant. Different processes may determine changes in species-habitat association: individuals may prefer different habitat typologies in different periods, or they may be forced to occupy a different habitat in order to follow the changing environment. The aim of our study was to assess whether cave salamanders change their habitat association pattern through the year, and to test whether such changes are determined by environmental changes or by changes in preferences. We monitored multiple caves in Central Italy through one year, and monthly measured biotic and abiotic features of microhabitat and recorded Italian cave salamanders distribution. We used mixed models and niche similarity tests to assess whether species-habitat relationships remain constant through the year. Microhabitat showed strong seasonal variation, with the highest variability in the superficial sectors. Salamanders were associated to relatively cold and humid sectors in summer, but not during winter. Such apparent shift in habitat preferences mostly occurred because the environmental gradient changed through the year, while individuals generally selected similar conditions. Nevertheless, juveniles were more tolerant to dry sectors during late winter, when food demand was highest. This suggests that tolerance for suboptimal abiotic conditions may change through time, depending on the required resources. Differences in habitat use are jointly determined by environmental variation through time, and by changes in the preferred habitat. The trade-offs between tolerance and resources requirement are major determinant of such variation.
format: application/pdf
format: text/html
creator: Enrico Lunghi
creator: Raoul Manenti
creator: Gentile Francesco Ficetola
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.1122
publisher: PeerJ Inc.
rights: © 2015 Lunghi et al.
abstract: Relationships between species and their habitats are not always constant. Different processes may determine changes in species-habitat association: individuals may prefer different habitat typologies in different periods, or they may be forced to occupy a different habitat in order to follow the changing environment. The aim of our study was to assess whether cave salamanders change their habitat association pattern through the year, and to test whether such changes are determined by environmental changes or by changes in preferences. We monitored multiple caves in Central Italy through one year, and monthly measured biotic and abiotic features of microhabitat and recorded Italian cave salamanders distribution. We used mixed models and niche similarity tests to assess whether species-habitat relationships remain constant through the year. Microhabitat showed strong seasonal variation, with the highest variability in the superficial sectors. Salamanders were associated to relatively cold and humid sectors in summer, but not during winter. Such apparent shift in habitat preferences mostly occurred because the environmental gradient changed through the year, while individuals generally selected similar conditions. Nevertheless, juveniles were more tolerant to dry sectors during late winter, when food demand was highest. This suggests that tolerance for suboptimal abiotic conditions may change through time, depending on the required resources. Differences in habitat use are jointly determined by environmental variation through time, and by changes in the preferred habitat. The trade-offs between tolerance and resources requirement are major determinant of such variation.
bibliographic citation: Lunghi et al. (2015) Seasonal variation in microhabitat of salamanders: environmental variation or shift of habitat selection?. PeerJ 3:e1122 https://doi.org/10.7717/peerj.1122
date submitted: 2015-04-15
date accepted: 2015-07-03
issued: 2015-08-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lunghi
  given name: Enrico
author list: Agent
  family name: Manenti
  given name: Raoul
author list: Agent
  family name: Ficetola
  given name: Gentile Francesco
doi: 10.7717/peerj.1122
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-13
copyright: © 2015 Lunghi et al.
attribution name: Lunghi et al.

Wireless laptop-based phonocardiograph and diagnosis
type: item
type: AcademicArticle
description: Auscultation is used to evaluate heart health, and can indicate when it’s needed to refer a patient to a cardiologist. Advanced phonocardiograph (PCG) signal processing algorithms are developed to assist the physician in the initial diagnosis but they are primarily designed and demonstrated with research quality equipment. Therefore, there is a need to demonstrate the applicability of those techniques with consumer grade instrument. Furthermore, routine monitoring would benefit from a wireless PCG sensor that allows continuous monitoring of cardiac signals of patients in physical activity, e.g., treadmill or weight exercise. In this work, a low-cost portable and wireless healthcare monitoring system based on PCG signal is implemented to validate and evaluate the most advanced algorithms. Off-the-shelf electronics and a notebook PC are used with MATLAB codes to record and analyze PCG signals which are collected with a notebook computer in tethered and wireless mode. Physiological parameters based on the S1 and S2 signals and MATLAB codes are demonstrated. While the prototype is based on MATLAB, the later is not an absolute requirement.
format: application/pdf
format: text/html
creator: Amy T. Dao
subject: Bioengineering
subject: Cardiology
description: doi:10.7717/peerj.1178
publisher: PeerJ Inc.
rights: © 2015 Dao
abstract: Auscultation is used to evaluate heart health, and can indicate when it’s needed to refer a patient to a cardiologist. Advanced phonocardiograph (PCG) signal processing algorithms are developed to assist the physician in the initial diagnosis but they are primarily designed and demonstrated with research quality equipment. Therefore, there is a need to demonstrate the applicability of those techniques with consumer grade instrument. Furthermore, routine monitoring would benefit from a wireless PCG sensor that allows continuous monitoring of cardiac signals of patients in physical activity, e.g., treadmill or weight exercise. In this work, a low-cost portable and wireless healthcare monitoring system based on PCG signal is implemented to validate and evaluate the most advanced algorithms. Off-the-shelf electronics and a notebook PC are used with MATLAB codes to record and analyze PCG signals which are collected with a notebook computer in tethered and wireless mode. Physiological parameters based on the S1 and S2 signals and MATLAB codes are demonstrated. While the prototype is based on MATLAB, the later is not an absolute requirement.
bibliographic citation: Dao (2015) Wireless laptop-based phonocardiograph and diagnosis. PeerJ 3:e1178 https://doi.org/10.7717/peerj.1178
date submitted: 2015-04-20
date accepted: 2015-07-21
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dao
  given name: Amy T.
doi: 10.7717/peerj.1178
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Dao
attribution name: Dao

Enigmatic declines in bird numbers in lowland forest of eastern Ecuador may be a consequence of climate change
type: item
type: AcademicArticle
description: Bird populations have declined in many parts of the world but most of those declines can be attributed to effects of human activities (e.g., habitat fragmentation); declines in areas unaffected by human activities are not common. We have been sampling bird populations at an undisturbed site in lowland forest of eastern Ecuador annually since 2001 using a combination of mist nets and direct observations on two 100-ha plots. Bird numbers fluctuated on both plots during the first 8 years but did not show a consistent pattern of change. Since about 2008, numbers of birds on both plots have declined; capture rates in 2014 were ∼40% less than at the start of the study and observation rates were ∼50% less. Both understory and canopy species declined in abundance. Overall, insectivores showed the most pronounced declines but declines varied among trophic groups. The period from 2008 onward also was a period of stronger La Niña events which, at this study site, are associated with increased rainfall. The mechanism for the declines is not known but likely reflects a combination of reduced reproductive success coupled with reduced survival associated with changing climate.
format: application/pdf
format: text/html
creator: John G. Blake
creator: Bette A. Loiselle
subject: Biodiversity
subject: Climate Change Biology
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.1177
publisher: PeerJ Inc.
rights: © 2015 Blake and Loiselle
abstract: Bird populations have declined in many parts of the world but most of those declines can be attributed to effects of human activities (e.g., habitat fragmentation); declines in areas unaffected by human activities are not common. We have been sampling bird populations at an undisturbed site in lowland forest of eastern Ecuador annually since 2001 using a combination of mist nets and direct observations on two 100-ha plots. Bird numbers fluctuated on both plots during the first 8 years but did not show a consistent pattern of change. Since about 2008, numbers of birds on both plots have declined; capture rates in 2014 were ∼40% less than at the start of the study and observation rates were ∼50% less. Both understory and canopy species declined in abundance. Overall, insectivores showed the most pronounced declines but declines varied among trophic groups. The period from 2008 onward also was a period of stronger La Niña events which, at this study site, are associated with increased rainfall. The mechanism for the declines is not known but likely reflects a combination of reduced reproductive success coupled with reduced survival associated with changing climate.
bibliographic citation: Blake et al. (2015) Enigmatic declines in bird numbers in lowland forest of eastern Ecuador may be a consequence of climate change. PeerJ 3:e1177 https://doi.org/10.7717/peerj.1177
date submitted: 2015-06-26
date accepted: 2015-07-21
issued: 2015-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blake
  given name: John G.
author list: Agent
  family name: Loiselle
  given name: Bette A.
doi: 10.7717/peerj.1177
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-11
copyright: © 2015 Blake and Loiselle
attribution name: Blake and Loiselle

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