PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Weather conditions associated with autumn migration by mule deer in Wyoming
items: A reappraisal of the Middle Triassic chirotheriid Chirotherium ibericus Navás, 1906 (Iberian Range NE Spain), with comments on the Triassic tetrapod track biochronology of the Iberian Peninsula
items: Life as a bachelor: quantifying the success of an alternative reproductive tactic in male blue monkeys
items: Sensitivity to the visual field origin of natural image patches in human low-level visual cortex
items: Primate tarsal bones from Egerkingen, Switzerland, attributable to the middle Eocene adapiform Caenopithecus lemuroides
items: Responses to simulated nitrogen deposition by the neotropical epiphytic orchid Laelia speciosa
items: Once bitten, twice shy: experienced regret and non-adaptive choice switching
items: The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?
items: Exploring the attitudes of medical faculty members and students in Pakistan towards plagiarism: a cross sectional survey
items: Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Weather conditions associated with autumn migration by mule deer in Wyoming
type: item
type: AcademicArticle
description: Maintaining ecological integrity necessitates a proactive approach of identifying and acquiring lands to conserve unfragmented landscapes, as well as evaluating existing mitigation strategies to increase connectivity in fragmented landscapes. The increased use of highway underpasses and overpasses to restore connectivity for wildlife species offers clear conservation benefits, yet also presents a unique opportunity to understand how weather conditions may impact movement of wildlife species. We used remote camera observations (19,480) from an existing wildlife highway underpass in Wyoming and daily meteorological observations to quantify weather conditions associated with autumn migration of mule deer in 2009 and 2010. We identified minimal daily temperature and snow depth as proximate cues associated with mule deer migration to winter range. These weather cues were consistent across does and bucks, but differed slightly by year. Additionally, extreme early season snow depth or cold temperature events appear to be associated with onset of migration. This information will assist wildlife managers and transportation officials as they plan future projects to maintain and enhance migration routes for mule deer.
format: application/pdf
format: text/html
creator: Chadwick D. Rittenhouse
creator: Tony W. Mong
creator: Thomas Hart
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.1045
publisher: PeerJ Inc.
rights: © 2015 Rittenhouse et al.
abstract: Maintaining ecological integrity necessitates a proactive approach of identifying and acquiring lands to conserve unfragmented landscapes, as well as evaluating existing mitigation strategies to increase connectivity in fragmented landscapes. The increased use of highway underpasses and overpasses to restore connectivity for wildlife species offers clear conservation benefits, yet also presents a unique opportunity to understand how weather conditions may impact movement of wildlife species. We used remote camera observations (19,480) from an existing wildlife highway underpass in Wyoming and daily meteorological observations to quantify weather conditions associated with autumn migration of mule deer in 2009 and 2010. We identified minimal daily temperature and snow depth as proximate cues associated with mule deer migration to winter range. These weather cues were consistent across does and bucks, but differed slightly by year. Additionally, extreme early season snow depth or cold temperature events appear to be associated with onset of migration. This information will assist wildlife managers and transportation officials as they plan future projects to maintain and enhance migration routes for mule deer.
bibliographic citation: Rittenhouse et al. (2015) Weather conditions associated with autumn migration by mule deer in Wyoming. PeerJ 3:e1045 https://doi.org/10.7717/peerj.1045
date submitted: 2015-03-31
date accepted: 2015-06-02
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rittenhouse
  given name: Chadwick D.
author list: Agent
  family name: Mong
  given name: Tony W.
author list: Agent
  family name: Hart
  given name: Thomas
doi: 10.7717/peerj.1045
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Rittenhouse et al.
attribution name: Rittenhouse et al.

A reappraisal of the Middle Triassic chirotheriid Chirotherium ibericus Navás, 1906 (Iberian Range NE Spain), with comments on the Triassic tetrapod track biochronology of the Iberian Peninsula
type: item
type: AcademicArticle
description: Triassic vertebrate tracks are known from the beginning of the 19th century and have a worldwide distribution. Several Triassic track ichnoassemblages and ichnotaxa have a restricted stratigraphic range and are useful in biochronology and biostratigraphy. The record of Triassic tracks in the Iberian Peninsula has gone almost unnoticed although more than 25 localities have been described since 1897. In one of these localities, the naturalist Longinos Navás described the ichnotaxon Chirotherium ibericus in 1906.The vertebrate tracks are in two sandy slabs from the Anisian (Middle Triassic) of the Moncayo massif (Zaragoza, Spain). In a recent revision, new, previously undescribed vertebrate tracks have been identified. The tracks considered to be C. ibericus as well as other tracks with the same morphology from both slabs have been classified as Chirotherium barthii. The rest of the tracks have been assigned to Chirotheriidae indet., Rhynchosauroides isp. and undetermined material. This new identification of C. barthii at the Navás site adds new data to the Iberian record of this ichnotaxon, which is characterized by the small size of the tracks when compared with the main occurrences of this ichnotaxon elsewhere. As at the Navás tracksite, the Anisian C. barthii-Rhynchosauroides ichnoassemblage has been found in other coeval localities in Iberia and worldwide. This ichnoassemblage belongs to the upper Olenekian-lower Anisian interval according to previous biochronological proposals. Analysis of the Triassic Iberian record of tetrapod tracks is uneven in terms of abundance over time. From the earliest Triassic to the latest Lower Triassic the record is very scarce, with Rhynchosauroides being the only known ichnotaxon. Rhynchosauroides covers a wide temporal range and gives poor information for biochronology. The record from the uppermost Lower Triassic to the Middle Triassic is abundant. The highest ichnodiversity has been reported for the Anisian with an assemblage c…
format: application/pdf
format: text/html
creator: Ignacio Díaz-Martínez
creator: Diego Castanera
creator: José Manuel Gasca
creator: José Ignacio Canudo
subject: Biogeography
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.1044
publisher: PeerJ Inc.
rights: © 2015 Díaz-Martínez et al.
abstract: Triassic vertebrate tracks are known from the beginning of the 19th century and have a worldwide distribution. Several Triassic track ichnoassemblages and ichnotaxa have a restricted stratigraphic range and are useful in biochronology and biostratigraphy. The record of Triassic tracks in the Iberian Peninsula has gone almost unnoticed although more than 25 localities have been described since 1897. In one of these localities, the naturalist Longinos Navás described the ichnotaxon Chirotherium ibericus in 1906.The vertebrate tracks are in two sandy slabs from the Anisian (Middle Triassic) of the Moncayo massif (Zaragoza, Spain). In a recent revision, new, previously undescribed vertebrate tracks have been identified. The tracks considered to be C. ibericus as well as other tracks with the same morphology from both slabs have been classified as Chirotherium barthii. The rest of the tracks have been assigned to Chirotheriidae indet., Rhynchosauroides isp. and undetermined material. This new identification of C. barthii at the Navás site adds new data to the Iberian record of this ichnotaxon, which is characterized by the small size of the tracks when compared with the main occurrences of this ichnotaxon elsewhere. As at the Navás tracksite, the Anisian C. barthii-Rhynchosauroides ichnoassemblage has been found in other coeval localities in Iberia and worldwide. This ichnoassemblage belongs to the upper Olenekian-lower Anisian interval according to previous biochronological proposals. Analysis of the Triassic Iberian record of tetrapod tracks is uneven in terms of abundance over time. From the earliest Triassic to the latest Lower Triassic the record is very scarce, with Rhynchosauroides being the only known ichnotaxon. Rhynchosauroides covers a wide temporal range and gives poor information for biochronology. The record from the uppermost Lower Triassic to the Middle Triassic is abundant. The highest ichnodiversity has been reported for the Anisian with an assemblage c…
bibliographic citation: Díaz-Martínez et al. (2015) A reappraisal of the Middle Triassic chirotheriid Chirotherium ibericus Navás, 1906 (Iberian Range NE Spain), with comments on the Triassic tetrapod track biochronology of the Iberian Peninsula. PeerJ 3:e1044 https://doi.org/10.7717/peerj.1044
date submitted: 2015-03-25
date accepted: 2015-06-01
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díaz-Martínez
  given name: Ignacio
author list: Agent
  family name: Castanera
  given name: Diego
author list: Agent
  family name: Gasca
  given name: José Manuel
author list: Agent
  family name: Canudo
  given name: José Ignacio
doi: 10.7717/peerj.1044
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Díaz-Martínez et al.
attribution name: Díaz-Martínez et al.

Life as a bachelor: quantifying the success of an alternative reproductive tactic in male blue monkeys
type: item
type: AcademicArticle
description: In species that live in one-male groups, resident males monopolize access to a group of females and are assumed to have higher reproductive success than bachelors. We tested this assumption using genetic, demographic, and behavioral data from 8 groups of wild blue monkeys observed over 10 years to quantify reproduction by residents and bachelors and compare the success of the two tactics. We used maximum-likelihood methods to assign sires to 104 offspring born in the study groups, 36 of which were sired by extra-group males, i.e., residents of neighboring groups and bachelors. Among these extra-group males, high-ranking males (many of whom were neighboring residents) were more likely to sire offspring than low-ranking males, but the time these visiting males spent in the mother’s group when she conceived (male presence) did not predict their relative success. When bachelors competed for reproduction with other bachelors, neither rank nor male presence during the mother’s conceptive period affected the probability of siring an offspring, suggesting that highly opportunistic mating with conceptive females is important in bachelor reproduction. In a second analysis, we used long-term data to estimate resident and bachelor reproductive success over the long term, and particularly to determine if there are any circumstances in which a typical bachelor may sire as many offspring as a typical resident during one or two periods of residency. Our findings generally support the assumption of a resident reproductive advantage because in most circumstances, a lifelong bachelor would be unable to sire as many offspring as a resident. However, a bachelor who performs at the average rate in the average number of groups for several years may have similar lifetime reproductive success as a male whose reproduction is limited to one short period of residency, especially in a small group. Our findings suggest that one should not assume a resident reproductive advantage for males in one…
format: application/pdf
format: text/html
creator: Su-Jen Roberts
creator: Marina Cords
subject: Animal Behavior
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.1043
publisher: PeerJ Inc.
rights: © 2015 Roberts and Cords
abstract: In species that live in one-male groups, resident males monopolize access to a group of females and are assumed to have higher reproductive success than bachelors. We tested this assumption using genetic, demographic, and behavioral data from 8 groups of wild blue monkeys observed over 10 years to quantify reproduction by residents and bachelors and compare the success of the two tactics. We used maximum-likelihood methods to assign sires to 104 offspring born in the study groups, 36 of which were sired by extra-group males, i.e., residents of neighboring groups and bachelors. Among these extra-group males, high-ranking males (many of whom were neighboring residents) were more likely to sire offspring than low-ranking males, but the time these visiting males spent in the mother’s group when she conceived (male presence) did not predict their relative success. When bachelors competed for reproduction with other bachelors, neither rank nor male presence during the mother’s conceptive period affected the probability of siring an offspring, suggesting that highly opportunistic mating with conceptive females is important in bachelor reproduction. In a second analysis, we used long-term data to estimate resident and bachelor reproductive success over the long term, and particularly to determine if there are any circumstances in which a typical bachelor may sire as many offspring as a typical resident during one or two periods of residency. Our findings generally support the assumption of a resident reproductive advantage because in most circumstances, a lifelong bachelor would be unable to sire as many offspring as a resident. However, a bachelor who performs at the average rate in the average number of groups for several years may have similar lifetime reproductive success as a male whose reproduction is limited to one short period of residency, especially in a small group. Our findings suggest that one should not assume a resident reproductive advantage for males in one…
bibliographic citation: Roberts et al. (2015) Life as a bachelor: quantifying the success of an alternative reproductive tactic in male blue monkeys. PeerJ 3:e1043 https://doi.org/10.7717/peerj.1043
date submitted: 2015-04-17
date accepted: 2015-05-31
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roberts
  given name: Su-Jen
author list: Agent
  family name: Cords
  given name: Marina
doi: 10.7717/peerj.1043
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Roberts and Cords
attribution name: Roberts and Cords

Sensitivity to the visual field origin of natural image patches in human low-level visual cortex
type: item
type: AcademicArticle
description: Asymmetries in the response to visual patterns in the upper and lower visual fields (above and below the centre of gaze) have been associated with ecological factors relating to the structure of typical visual environments. Here, we investigated whether the content of the upper and lower visual field representations in low-level regions of human visual cortex are specialised for visual patterns that arise from the upper and lower visual fields in natural images. We presented image patches, drawn from above or below the centre of gaze of an observer navigating a natural environment, to either the upper or lower visual fields of human participants (n = 7) while we used functional magnetic resonance imaging (fMRI) to measure the magnitude of evoked activity in the visual areas V1, V2, and V3. We found a significant interaction between the presentation location (upper or lower visual field) and the image patch source location (above or below fixation); the responses to lower visual field presentation were significantly greater for image patches sourced from below than above fixation, while the responses in the upper visual field were not significantly different for image patches sourced from above and below fixation. This finding demonstrates an association between the representation of the lower visual field in human visual cortex and the structure of the visual input that is likely to be encountered below the centre of gaze.
format: application/pdf
format: text/html
creator: Damien J. Mannion
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1038
publisher: PeerJ Inc.
rights: © 2015 Mannion
abstract: Asymmetries in the response to visual patterns in the upper and lower visual fields (above and below the centre of gaze) have been associated with ecological factors relating to the structure of typical visual environments. Here, we investigated whether the content of the upper and lower visual field representations in low-level regions of human visual cortex are specialised for visual patterns that arise from the upper and lower visual fields in natural images. We presented image patches, drawn from above or below the centre of gaze of an observer navigating a natural environment, to either the upper or lower visual fields of human participants (n = 7) while we used functional magnetic resonance imaging (fMRI) to measure the magnitude of evoked activity in the visual areas V1, V2, and V3. We found a significant interaction between the presentation location (upper or lower visual field) and the image patch source location (above or below fixation); the responses to lower visual field presentation were significantly greater for image patches sourced from below than above fixation, while the responses in the upper visual field were not significantly different for image patches sourced from above and below fixation. This finding demonstrates an association between the representation of the lower visual field in human visual cortex and the structure of the visual input that is likely to be encountered below the centre of gaze.
bibliographic citation: Mannion (2015) Sensitivity to the visual field origin of natural image patches in human low-level visual cortex. PeerJ 3:e1038 https://doi.org/10.7717/peerj.1038
date submitted: 2015-01-23
date accepted: 2015-05-30
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannion
  given name: Damien J.
doi: 10.7717/peerj.1038
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Mannion
attribution name: Mannion

Primate tarsal bones from Egerkingen, Switzerland, attributable to the middle Eocene adapiform Caenopithecus lemuroides
type: item
type: AcademicArticle
description: The middle Eocene species Caenopithecus lemuroides, known solely from the Egerkingen fissure fillings in Switzerland, was the first Paleogene fossil primate to be correctly identified as such (by Ludwig Rütimeyer in 1862), but has long been represented only by fragmentary mandibular and maxillary remains. More recent discoveries of adapiform fossils in other parts of the world have revealed Caenopithecus to be a biogeographic enigma, as it is potentially more closely related to Eocene adapiforms from Africa, Asia, and North America than it is to any known European forms. More anatomical evidence is needed, however, to provide robust tests of such phylogenetic hypotheses. Here we describe and analyze the first postcranial remains that can be attributed to C. lemuroides—an astragalus and three calcanei held in the collections of the Naturhistorisches Museum Basel that were likely recovered from Egerkingen over a century ago. Qualitative and multivariate morphometric analyses of these elements suggest that C. lemuroides was even more loris-like than European adapines such as Adapis and Leptadapis, and was not simply an adapine with an aberrant dentition. The astragalus of Caenopithecus is similar to that of younger Afradapis from the late Eocene of Egypt, and parsimony and Bayesian phylogenetic analyses that include the new tarsal data strongly support the placement of Afradapis and Caenopithecus as sister taxa to the exclusion of all other known adapiforms, thus implying that dispersal between Europe and Africa occurred during the middle Eocene. The new tarsal evidence, combined with previously known craniodental fossils, allows us to reconstruct C. lemuroides as having been an arboreal and highly folivorous 1.5–2.5 kg primate that likely moved slowly and deliberately with little or no capacity for acrobatic leaping, presumably maintaining consistent powerful grasps on branches in both above-branch and inverted postures.
format: application/pdf
format: text/html
creator: Erik R. Seiffert
creator: Loïc Costeur
creator: Doug M. Boyer
subject: Paleontology
description: doi:10.7717/peerj.1036
publisher: PeerJ Inc.
rights: © 2015 Seiffert et al.
abstract: The middle Eocene species Caenopithecus lemuroides, known solely from the Egerkingen fissure fillings in Switzerland, was the first Paleogene fossil primate to be correctly identified as such (by Ludwig Rütimeyer in 1862), but has long been represented only by fragmentary mandibular and maxillary remains. More recent discoveries of adapiform fossils in other parts of the world have revealed Caenopithecus to be a biogeographic enigma, as it is potentially more closely related to Eocene adapiforms from Africa, Asia, and North America than it is to any known European forms. More anatomical evidence is needed, however, to provide robust tests of such phylogenetic hypotheses. Here we describe and analyze the first postcranial remains that can be attributed to C. lemuroides—an astragalus and three calcanei held in the collections of the Naturhistorisches Museum Basel that were likely recovered from Egerkingen over a century ago. Qualitative and multivariate morphometric analyses of these elements suggest that C. lemuroides was even more loris-like than European adapines such as Adapis and Leptadapis, and was not simply an adapine with an aberrant dentition. The astragalus of Caenopithecus is similar to that of younger Afradapis from the late Eocene of Egypt, and parsimony and Bayesian phylogenetic analyses that include the new tarsal data strongly support the placement of Afradapis and Caenopithecus as sister taxa to the exclusion of all other known adapiforms, thus implying that dispersal between Europe and Africa occurred during the middle Eocene. The new tarsal evidence, combined with previously known craniodental fossils, allows us to reconstruct C. lemuroides as having been an arboreal and highly folivorous 1.5–2.5 kg primate that likely moved slowly and deliberately with little or no capacity for acrobatic leaping, presumably maintaining consistent powerful grasps on branches in both above-branch and inverted postures.
bibliographic citation: Seiffert et al. (2015) Primate tarsal bones from Egerkingen, Switzerland, attributable to the middle Eocene adapiform Caenopithecus lemuroides. PeerJ 3:e1036 https://doi.org/10.7717/peerj.1036
date submitted: 2015-03-25
date accepted: 2015-05-29
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seiffert
  given name: Erik R.
author list: Agent
  family name: Costeur
  given name: Loïc
author list: Agent
  family name: Boyer
  given name: Doug M.
doi: 10.7717/peerj.1036
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Seiffert et al.
attribution name: Seiffert et al.

Responses to simulated nitrogen deposition by the neotropical epiphytic orchid Laelia speciosa
type: item
type: AcademicArticle
description: Potential ecophysiological responses to nitrogen deposition, which is considered to be one of the leading causes for global biodiversity loss, were studied for the endangered endemic Mexican epiphytic orchid, Laelia speciosa, via a shadehouse dose-response experiment (doses were 2.5, 5, 10, 20, 40, and 80 kg N ha−1 yr−1) in order to assess the potential risk facing this orchid given impending scenarios of nitrogen deposition. Lower doses of nitrogen of up to 20 kg N ha yr−1, the dose that led to optimal plant performance, acted as fertilizer. For instance, the production of leaves and pseudobulbs were respectively 35% and 36% greater for plants receiving 20 kg N ha yr−1 than under any other dose. Also, the chlorophyll content and quantum yield peaked at 0.66 ± 0.03 g m−2 and 0.85 ± 0.01, respectively, for plants growing under the optimum dose. In contrast, toxic effects were observed at the higher doses of 40 and 80 kg N ha yr−1. The δ13C for leaves averaged −14.7 ± 0.2‰ regardless of the nitrogen dose. In turn, δ15N decreased as the nitrogen dose increased from 0.9 ± 0.1‰ under 2.5 kg N ha−1yr−1 to −3.1 ± 0.2‰ under 80 kg N ha−1yr−1, indicating that orchids preferentially assimilate NH4+ rather than NO3− of the solution under higher doses of nitrogen. Laelia speciosa showed a clear response to inputs of nitrogen, thus, increasing rates of atmospheric nitrogen deposition can pose an important threat for this species.
format: application/pdf
format: text/html
creator: Edison A. Díaz-Álvarez
creator: Roberto Lindig-Cisneros
creator: Erick de la Barrera
subject: Ecology
subject: Environmental Sciences
subject: Plant Science
subject: Soil Science
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.1021
publisher: PeerJ Inc.
rights: © 2015 Díaz-Álvarez et al.
abstract: Potential ecophysiological responses to nitrogen deposition, which is considered to be one of the leading causes for global biodiversity loss, were studied for the endangered endemic Mexican epiphytic orchid, Laelia speciosa, via a shadehouse dose-response experiment (doses were 2.5, 5, 10, 20, 40, and 80 kg N ha−1 yr−1) in order to assess the potential risk facing this orchid given impending scenarios of nitrogen deposition. Lower doses of nitrogen of up to 20 kg N ha yr−1, the dose that led to optimal plant performance, acted as fertilizer. For instance, the production of leaves and pseudobulbs were respectively 35% and 36% greater for plants receiving 20 kg N ha yr−1 than under any other dose. Also, the chlorophyll content and quantum yield peaked at 0.66 ± 0.03 g m−2 and 0.85 ± 0.01, respectively, for plants growing under the optimum dose. In contrast, toxic effects were observed at the higher doses of 40 and 80 kg N ha yr−1. The δ13C for leaves averaged −14.7 ± 0.2‰ regardless of the nitrogen dose. In turn, δ15N decreased as the nitrogen dose increased from 0.9 ± 0.1‰ under 2.5 kg N ha−1yr−1 to −3.1 ± 0.2‰ under 80 kg N ha−1yr−1, indicating that orchids preferentially assimilate NH4+ rather than NO3− of the solution under higher doses of nitrogen. Laelia speciosa showed a clear response to inputs of nitrogen, thus, increasing rates of atmospheric nitrogen deposition can pose an important threat for this species.
bibliographic citation: Díaz-Álvarez et al. (2015) Responses to simulated nitrogen deposition by the neotropical epiphytic orchid Laelia speciosa. PeerJ 3:e1021 https://doi.org/10.7717/peerj.1021
date submitted: 2015-02-17
date accepted: 2015-05-24
issued: 2015-06-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díaz-Álvarez
  given name: Edison A.
author list: Agent
  family name: Lindig-Cisneros
  given name: Roberto
author list: Agent
  family name: de la Barrera
  given name: Erick
doi: 10.7717/peerj.1021
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-23
copyright: © 2015 Díaz-Álvarez et al.
attribution name: Díaz-Álvarez et al.

Once bitten, twice shy: experienced regret and non-adaptive choice switching
type: item
type: AcademicArticle
description: When a good decision leads to a bad outcome, the experience of regret can bias subsequent choices: people are less likely to select the regret-producing alternative a second time, even when it is still objectively the best alternative (non-adaptive choice switching). The first study presented herein showed that nearly half of participants experiencing regret rejected a previous alternative they had recognized as the best one, and chose a non-optimal alternative instead. The second study investigated the mechanism underlying this bias, and results supported the hypothesis that this non-adaptive choice switching is caused by inhibition of the previous decision (direct effect of experienced regret), rather than by increased sensitivity to anticipated regret in subsequent choices (indirect effect of experienced regret mediated by anticipated regret).
format: application/pdf
format: text/html
creator: Francesco Marcatto
creator: Anna Cosulich
creator: Donatella Ferrante
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1035
publisher: PeerJ Inc.
rights: © 2015 Marcatto et al.
abstract: When a good decision leads to a bad outcome, the experience of regret can bias subsequent choices: people are less likely to select the regret-producing alternative a second time, even when it is still objectively the best alternative (non-adaptive choice switching). The first study presented herein showed that nearly half of participants experiencing regret rejected a previous alternative they had recognized as the best one, and chose a non-optimal alternative instead. The second study investigated the mechanism underlying this bias, and results supported the hypothesis that this non-adaptive choice switching is caused by inhibition of the previous decision (direct effect of experienced regret), rather than by increased sensitivity to anticipated regret in subsequent choices (indirect effect of experienced regret mediated by anticipated regret).
bibliographic citation: Marcatto et al. (2015) Once bitten, twice shy: experienced regret and non-adaptive choice switching. PeerJ 3:e1035 https://doi.org/10.7717/peerj.1035
date submitted: 2015-04-10
date accepted: 2015-05-29
issued: 2015-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marcatto
  given name: Francesco
author list: Agent
  family name: Cosulich
  given name: Anna
author list: Agent
  family name: Ferrante
  given name: Donatella
doi: 10.7717/peerj.1035
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-18
copyright: © 2015 Marcatto et al.
attribution name: Marcatto et al.

The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?
type: item
type: AcademicArticle
description: The exceptionally well-preserved Romanian dinosaur Balaur bondoc is the most complete theropod known to date from the Upper Cretaceous of Europe. Previous studies of this remarkable taxon have included its phylogenetic interpretation as an aberrant dromaeosaurid with velociraptorine affinities. However, Balaur displays a combination of both apparently plesiomorphic and derived bird-like characters. Here, we analyse those features in a phylogenetic revision and show how they challenge its referral to Dromaeosauridae. Our reanalysis of two distinct phylogenetic datasets focusing on basal paravian taxa supports the reinterpretation of Balaur as an avialan more crownward than Archaeopteryx but outside of Pygostylia, and as a flightless taxon within a paraphyletic assemblage of long-tailed birds. Our placement of Balaur within Avialae is not biased by character weighting. The placement among dromaeosaurids resulted in a suboptimal alternative that cannot be rejected based on the data to hand. Interpreted as a dromaeosaurid, Balaur has been assumed to be hypercarnivorous and predatory, exhibiting a peculiar morphology influenced by island endemism. However, a dromaeosaurid-like ecology is contradicted by several details of Balaur’s morphology, including the loss of a third functional manual digit, the non-ginglymoid distal end of metatarsal II, and a non-falciform ungual on the second pedal digit that lacks a prominent flexor tubercle. Conversely, an omnivorous ecology is better supported by Balaur’s morphology and is consistent with its phylogenetic placement within Avialae. Our reinterpretation of Balaur implies that a superficially dromaeosaurid-like taxon represents the enlarged, terrestrialised descendant of smaller and probably volant ancestors.
format: application/pdf
format: text/html
creator: Andrea Cau
creator: Sienna A Birch
creator: Darren Naish
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.1032
publisher: PeerJ Inc.
rights: © 2015 Cau et al.
abstract: The exceptionally well-preserved Romanian dinosaur Balaur bondoc is the most complete theropod known to date from the Upper Cretaceous of Europe. Previous studies of this remarkable taxon have included its phylogenetic interpretation as an aberrant dromaeosaurid with velociraptorine affinities. However, Balaur displays a combination of both apparently plesiomorphic and derived bird-like characters. Here, we analyse those features in a phylogenetic revision and show how they challenge its referral to Dromaeosauridae. Our reanalysis of two distinct phylogenetic datasets focusing on basal paravian taxa supports the reinterpretation of Balaur as an avialan more crownward than Archaeopteryx but outside of Pygostylia, and as a flightless taxon within a paraphyletic assemblage of long-tailed birds. Our placement of Balaur within Avialae is not biased by character weighting. The placement among dromaeosaurids resulted in a suboptimal alternative that cannot be rejected based on the data to hand. Interpreted as a dromaeosaurid, Balaur has been assumed to be hypercarnivorous and predatory, exhibiting a peculiar morphology influenced by island endemism. However, a dromaeosaurid-like ecology is contradicted by several details of Balaur’s morphology, including the loss of a third functional manual digit, the non-ginglymoid distal end of metatarsal II, and a non-falciform ungual on the second pedal digit that lacks a prominent flexor tubercle. Conversely, an omnivorous ecology is better supported by Balaur’s morphology and is consistent with its phylogenetic placement within Avialae. Our reinterpretation of Balaur implies that a superficially dromaeosaurid-like taxon represents the enlarged, terrestrialised descendant of smaller and probably volant ancestors.
bibliographic citation: Cau et al. (2015) The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?. PeerJ 3:e1032 https://doi.org/10.7717/peerj.1032
date submitted: 2015-04-13
date accepted: 2015-05-27
issued: 2015-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cau
  given name: Andrea
author list: Agent
  family name: Birch
  given name: Sienna A
author list: Agent
  family name: Naish
  given name: Darren
doi: 10.7717/peerj.1032
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-18
copyright: © 2015 Cau et al.
attribution name: Cau et al.

Exploring the attitudes of medical faculty members and students in Pakistan towards plagiarism: a cross sectional survey
type: item
type: AcademicArticle
description: Objective. The objective of this survey was to explore the attitudes towards plagiarism of faculty members and medical students in Pakistan. Methods. The Attitudes Toward Plagiarism questionnaire (ATP) was modified and distributed among 550 medical students and 130 faculty members in 7 medical colleges of Lahore and Rawalpindi. Data was entered in the SPSS v.20 and descriptive statistics were analyzed. The questionnaire was validated by principal axis factoring analysis. Results. Response rate was 93% and 73%, respectively. Principal axis factoring analysis confirmed one factor structure of ATP in the present sample. It had an acceptable Cronbach’s alpha value of 0.73. There were 421 medical students (218 (52%) female, 46% 3rd year MBBS students, mean age of 20.93 ± 1.4 years) and 95 faculty members (54.7% female, mean age 34.5 ± 8.9 years). One fifth of the students (19.7%) trained in medical writing (19.7%), research ethics (25.2%) or were currently involved in medical writing (17.6%). Most of the faculty members were demonstrators (66) or assistant professors (20) with work experience between 1 and 10 years. Most of them had trained in medical writing (68), research ethics (64) and were currently involved in medical writing (64). Medical students and faculty members had a mean score of 43.21 (7.1) and 48.4 (5.9) respectively on ATP. Most of the respondents did not consider that they worked in a plagiarism free environment and reported that self-plagiarism should not be punishable in the same way as plagiarism. Opinion regarding leniency in punishment of younger researchers who were just learning medical writing was divided. Conclusions. The general attitudes of Pakistani medical faculty members and medical students as assessed by ATP were positive. We propose training in medical writing and research ethics as part of the under and post graduate medical curriculum.
format: application/pdf
format: text/html
creator: Farooq Azam Rathore
creator: Ahmed Waqas
creator: Ahmad Marjan Zia
creator: Martina Mavrinac
creator: Fareeha Farooq
subject: Ethical Issues
subject: Science and Medical Education
description: doi:10.7717/peerj.1031
publisher: PeerJ Inc.
rights: © 2015 Rathore et al.
abstract: Objective. The objective of this survey was to explore the attitudes towards plagiarism of faculty members and medical students in Pakistan. Methods. The Attitudes Toward Plagiarism questionnaire (ATP) was modified and distributed among 550 medical students and 130 faculty members in 7 medical colleges of Lahore and Rawalpindi. Data was entered in the SPSS v.20 and descriptive statistics were analyzed. The questionnaire was validated by principal axis factoring analysis. Results. Response rate was 93% and 73%, respectively. Principal axis factoring analysis confirmed one factor structure of ATP in the present sample. It had an acceptable Cronbach’s alpha value of 0.73. There were 421 medical students (218 (52%) female, 46% 3rd year MBBS students, mean age of 20.93 ± 1.4 years) and 95 faculty members (54.7% female, mean age 34.5 ± 8.9 years). One fifth of the students (19.7%) trained in medical writing (19.7%), research ethics (25.2%) or were currently involved in medical writing (17.6%). Most of the faculty members were demonstrators (66) or assistant professors (20) with work experience between 1 and 10 years. Most of them had trained in medical writing (68), research ethics (64) and were currently involved in medical writing (64). Medical students and faculty members had a mean score of 43.21 (7.1) and 48.4 (5.9) respectively on ATP. Most of the respondents did not consider that they worked in a plagiarism free environment and reported that self-plagiarism should not be punishable in the same way as plagiarism. Opinion regarding leniency in punishment of younger researchers who were just learning medical writing was divided. Conclusions. The general attitudes of Pakistani medical faculty members and medical students as assessed by ATP were positive. We propose training in medical writing and research ethics as part of the under and post graduate medical curriculum.
bibliographic citation: Rathore et al. (2015) Exploring the attitudes of medical faculty members and students in Pakistan towards plagiarism: a cross sectional survey. PeerJ 3:e1031 https://doi.org/10.7717/peerj.1031
date submitted: 2015-01-05
date accepted: 2015-05-26
issued: 2015-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rathore
  given name: Farooq Azam
author list: Agent
  family name: Waqas
  given name: Ahmed
author list: Agent
  family name: Zia
  given name: Ahmad Marjan
author list: Agent
  family name: Mavrinac
  given name: Martina
author list: Agent
  family name: Farooq
  given name: Fareeha
doi: 10.7717/peerj.1031
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-18
copyright: © 2015 Rathore et al.
attribution name: Rathore et al.

Compact graphical representation of phylogenetic data and metadata with GraPhlAn
type: item
type: AcademicArticle
description: The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.
format: application/pdf
format: text/html
creator: Francesco Asnicar
creator: George Weingart
creator: Timothy L. Tickle
creator: Curtis Huttenhower
creator: Nicola Segata
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.1029
publisher: PeerJ Inc.
rights: © 2015 Asnicar et al.
abstract: The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.
bibliographic citation: Asnicar et al. (2015) Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3:e1029 https://doi.org/10.7717/peerj.1029
date submitted: 2015-04-10
date accepted: 2015-05-26
issued: 2015-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Asnicar
  given name: Francesco
author list: Agent
  family name: Weingart
  given name: George
author list: Agent
  family name: Tickle
  given name: Timothy L.
author list: Agent
  family name: Huttenhower
  given name: Curtis
author list: Agent
  family name: Segata
  given name: Nicola
doi: 10.7717/peerj.1029
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-18
copyright: © 2015 Asnicar et al.
attribution name: Asnicar et al.

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