PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species
items: An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution
items: Experimental exposure to urban and pink noise affects brain development and song learning in zebra finches (Taenopygia guttata)
items: Effect of wetland management: are lentic wetlands refuges of plant-species diversity in the Andean–Orinoco Piedmont of Colombia?
items: https://peerj.com/articles/2233
items: Delivering a medical school elective with massive open online course (MOOC) technology
items: Prediction of pKa values using the PM6 semiempirical method
items: The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled
items: Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania
items: Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation

On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species
type: item
type: AcademicArticle
description: The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsae spec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented.
format: application/pdf
format: text/html
creator: Julio Parapar
creator: Juan Moreira
creator: Daniel Martin
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2313
publisher: PeerJ Inc.
rights: © 2016 Parapar et al.
abstract: The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsae spec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented.
bibliographic citation: Parapar et al. (2016) On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species. PeerJ 4:e2313 https://doi.org/10.7717/peerj.2313
date submitted: 2016-05-09
date accepted: 2016-07-11
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parapar
  given name: Julio
author list: Agent
  family name: Moreira
  given name: Juan
author list: Agent
  family name: Martin
  given name: Daniel
doi: 10.7717/peerj.2313
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Parapar et al.
attribution name: Parapar et al.

An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution
type: item
type: AcademicArticle
description: Estimating the exposure of honeybees to pesticides on a landscape scale requires models of their spatial foraging behaviour. For this purpose, we developed a mechanistic, energetics-based model for a single day of nectar foraging in complex landscape mosaics. Net energetic efficiency determined resource patch choice. In one version of the model a single optimal patch was selected each hour. In another version, recruitment of foragers was simulated and several patches could be exploited simultaneously. Resource availability changed during the day due to depletion and/or intrinsic properties of the resource (anthesis). The model accounted for the impact of patch distance and size, resource depletion and replenishment, competition with other nectar foragers, and seasonal and diurnal patterns in availability of nectar-providing crops and wild flowers. From the model we derived simple rules for resource patch selection, e.g., for landscapes with mass-flowering crops only, net energetic efficiency would be proportional to the ratio of the energetic content of the nectar divided by distance to the hive. We also determined maximum distances at which resources like oilseed rape and clover were still energetically attractive. We used the model to assess the potential for pesticide exposure dilution in landscapes of different composition and complexity. Dilution means a lower concentration in nectar arriving at the hive compared to the concentration in nectar at a treated field and can result from foraging effort being diverted away from treated fields. Applying the model for all possible hive locations over a large area, distributions of dilution factors were obtained that were characterised by their 90-percentile value. For an area for which detailed spatial data on crops and off-field semi-natural habitats were available, we tested three landscape management scenarios that were expected to lead to exposure dilution: providing alternative resources than the target crop (oils…
format: application/pdf
format: text/html
creator: Johannes M. Baveco
creator: Andreas Focks
creator: Dick Belgers
creator: Jozef J.M. van der Steen
creator: Jos J.T.I. Boesten
creator: Ivo Roessink
subject: Agricultural Science
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Environmental Sciences
description: doi:10.7717/peerj.2293
publisher: PeerJ Inc.
rights: © 2016 Baveco et al.
abstract: Estimating the exposure of honeybees to pesticides on a landscape scale requires models of their spatial foraging behaviour. For this purpose, we developed a mechanistic, energetics-based model for a single day of nectar foraging in complex landscape mosaics. Net energetic efficiency determined resource patch choice. In one version of the model a single optimal patch was selected each hour. In another version, recruitment of foragers was simulated and several patches could be exploited simultaneously. Resource availability changed during the day due to depletion and/or intrinsic properties of the resource (anthesis). The model accounted for the impact of patch distance and size, resource depletion and replenishment, competition with other nectar foragers, and seasonal and diurnal patterns in availability of nectar-providing crops and wild flowers. From the model we derived simple rules for resource patch selection, e.g., for landscapes with mass-flowering crops only, net energetic efficiency would be proportional to the ratio of the energetic content of the nectar divided by distance to the hive. We also determined maximum distances at which resources like oilseed rape and clover were still energetically attractive. We used the model to assess the potential for pesticide exposure dilution in landscapes of different composition and complexity. Dilution means a lower concentration in nectar arriving at the hive compared to the concentration in nectar at a treated field and can result from foraging effort being diverted away from treated fields. Applying the model for all possible hive locations over a large area, distributions of dilution factors were obtained that were characterised by their 90-percentile value. For an area for which detailed spatial data on crops and off-field semi-natural habitats were available, we tested three landscape management scenarios that were expected to lead to exposure dilution: providing alternative resources than the target crop (oils…
bibliographic citation: Baveco et al. (2016) An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution. PeerJ 4:e2293 https://doi.org/10.7717/peerj.2293
date submitted: 2015-11-19
date accepted: 2016-07-06
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baveco
  given name: Johannes M.
author list: Agent
  family name: Focks
  given name: Andreas
author list: Agent
  family name: Belgers
  given name: Dick
author list: Agent
  family name: van der Steen
  given name: Jozef J.M.
author list: Agent
  family name: Boesten
  given name: Jos J.T.I.
author list: Agent
  family name: Roessink
  given name: Ivo
doi: 10.7717/peerj.2293
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Baveco et al.
attribution name: Baveco et al.

Experimental exposure to urban and pink noise affects brain development and song learning in zebra finches (Taenopygia guttata)
type: item
type: AcademicArticle
description: Recently, numerous studies have observed changes in bird vocalizations—especially song—in urban habitats. These changes are often interpreted as adaptive, since they increase the active space of the signal in its environment. However, the proximate mechanisms driving cross-generational changes in song are still unknown. We performed a captive experiment to identify whether noise experienced during development affects song learning and the development of song-control brain regions. Zebra finches (Taeniopygia guttata) were bred while exposed, or not exposed, to recorded traffic urban noise (Study 1) or pink noise (Study 2). We recorded the songs of male offspring and compared these to fathers’ songs. We also measured baseline corticosterone and measured the size of song-control brain regions when the males reached adulthood (Study 1 only). While male zebra finches tended to copy syllables accurately from tutors regardless of noise environment, syntax (the ordering of syllables within songs) was incorrectly copied affected by juveniles exposed to noise. Noise did not affect baseline corticosterone, but did affect the size of brain regions associated with song learning: these regions were smaller in males that had been had been exposed to recorded traffic urban noise in early development. These findings provide a possible mechanism by which noise affects behaviour, leading to potential population differences between wild animals occupying noisier urban environments compared with those in quieter habitats.
format: application/pdf
format: text/html
creator: Dominique A. Potvin
creator: Michael T. Curcio
creator: John P. Swaddle
creator: Scott A. MacDougall-Shackleton
subject: Animal Behavior
subject: Ecology
subject: Neuroscience
subject: Zoology
description: doi:10.7717/peerj.2287
publisher: PeerJ Inc.
rights: © 2016 Potvin et al.
abstract: Recently, numerous studies have observed changes in bird vocalizations—especially song—in urban habitats. These changes are often interpreted as adaptive, since they increase the active space of the signal in its environment. However, the proximate mechanisms driving cross-generational changes in song are still unknown. We performed a captive experiment to identify whether noise experienced during development affects song learning and the development of song-control brain regions. Zebra finches (Taeniopygia guttata) were bred while exposed, or not exposed, to recorded traffic urban noise (Study 1) or pink noise (Study 2). We recorded the songs of male offspring and compared these to fathers’ songs. We also measured baseline corticosterone and measured the size of song-control brain regions when the males reached adulthood (Study 1 only). While male zebra finches tended to copy syllables accurately from tutors regardless of noise environment, syntax (the ordering of syllables within songs) was incorrectly copied affected by juveniles exposed to noise. Noise did not affect baseline corticosterone, but did affect the size of brain regions associated with song learning: these regions were smaller in males that had been had been exposed to recorded traffic urban noise in early development. These findings provide a possible mechanism by which noise affects behaviour, leading to potential population differences between wild animals occupying noisier urban environments compared with those in quieter habitats.
bibliographic citation: Potvin et al. (2016) Experimental exposure to urban and pink noise affects brain development and song learning in zebra finches (Taenopygia guttata). PeerJ 4:e2287 https://doi.org/10.7717/peerj.2287
date submitted: 2016-02-21
date accepted: 2016-07-04
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Potvin
  given name: Dominique A.
author list: Agent
  family name: Curcio
  given name: Michael T.
author list: Agent
  family name: Swaddle
  given name: John P.
author list: Agent
  family name: MacDougall-Shackleton
  given name: Scott A.
doi: 10.7717/peerj.2287
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Potvin et al.
attribution name: Potvin et al.

Effect of wetland management: are lentic wetlands refuges of plant-species diversity in the Andean–Orinoco Piedmont of Colombia?
type: item
type: AcademicArticle
description: Accelerated degradation of the wetlands and fragmentation of surrounding vegetation in the Andean–Orinoco Piedmont are the main threats to diversity and ecological integrity of these ecosystems; however, information on this topic is of limited availability. In this region, we evaluated the value of 37 lentic wetlands as reservoirs of woody and aquatic plants and analyzed diversity and changes in species composition within and among groups defined according to management given by: (1) type (swamps, heronries, rice fields, semi-natural lakes, constructed lakes and fish farms) and (2) origins (natural, mixed and artificial). A total of 506 plant species were recorded: 80% woody and 20% aquatic. Of these, 411 species (81%) were considered species typical of the area (Meta Piedmont distribution). Diversity patterns seem to be driven by high landscape heterogeneity and wetland management. The fish farms presented the highest diversity of woody plants, while swamps ranked highest for aquatic plant diversity. Regarding wetland origin, the artificial systems were the most diverse, but natural wetlands presented the highest diversity of typical species and can therefore be considered representative ecosystems at the regional scale. Our results suggest that lentic wetlands act as refuges for native vegetation of Meta Piedmont forest, hosting 55% of the woody of Piedmont species and 29% of the aquatic species of Orinoco basin. The wetlands showed a high species turnover and the results indicated that small wetlands (mean ± SD: size = 11 ± 18.7 ha), with a small area of surrounding forest (10 ± 8.6 ha) supported high local and regional plant diversity. To ensure long-term conservation of lentic wetlands, it is necessary to develop management and conservation strategies that take both natural and created wetlands into account.
format: application/pdf
format: text/html
creator: Johanna I. Murillo-Pacheco
creator: Matthias Rös
creator: Federico Escobar
creator: Francisco Castro-Lima
creator: José R. Verdú
creator: Germán M. López-Iborra
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.2267
publisher: PeerJ Inc.
rights: © 2016 Murillo-Pacheco et al.
abstract: Accelerated degradation of the wetlands and fragmentation of surrounding vegetation in the Andean–Orinoco Piedmont are the main threats to diversity and ecological integrity of these ecosystems; however, information on this topic is of limited availability. In this region, we evaluated the value of 37 lentic wetlands as reservoirs of woody and aquatic plants and analyzed diversity and changes in species composition within and among groups defined according to management given by: (1) type (swamps, heronries, rice fields, semi-natural lakes, constructed lakes and fish farms) and (2) origins (natural, mixed and artificial). A total of 506 plant species were recorded: 80% woody and 20% aquatic. Of these, 411 species (81%) were considered species typical of the area (Meta Piedmont distribution). Diversity patterns seem to be driven by high landscape heterogeneity and wetland management. The fish farms presented the highest diversity of woody plants, while swamps ranked highest for aquatic plant diversity. Regarding wetland origin, the artificial systems were the most diverse, but natural wetlands presented the highest diversity of typical species and can therefore be considered representative ecosystems at the regional scale. Our results suggest that lentic wetlands act as refuges for native vegetation of Meta Piedmont forest, hosting 55% of the woody of Piedmont species and 29% of the aquatic species of Orinoco basin. The wetlands showed a high species turnover and the results indicated that small wetlands (mean ± SD: size = 11 ± 18.7 ha), with a small area of surrounding forest (10 ± 8.6 ha) supported high local and regional plant diversity. To ensure long-term conservation of lentic wetlands, it is necessary to develop management and conservation strategies that take both natural and created wetlands into account.
bibliographic citation: Murillo-Pacheco et al. (2016) Effect of wetland management: are lentic wetlands refuges of plant-species diversity in the Andean–Orinoco Piedmont of Colombia?. PeerJ 4:e2267 https://doi.org/10.7717/peerj.2267
date submitted: 2016-04-20
date accepted: 2016-06-28
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murillo-Pacheco
  given name: Johanna I.
author list: Agent
  family name: Rös
  given name: Matthias
author list: Agent
  family name: Escobar
  given name: Federico
author list: Agent
  family name: Castro-Lima
  given name: Francisco
author list: Agent
  family name: Verdú
  given name: José R.
author list: Agent
  family name: López-Iborra
  given name: Germán M.
doi: 10.7717/peerj.2267
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Murillo-Pacheco et al.
attribution name: Murillo-Pacheco et al.

https://peerj.com/articles/2233
type: item
type: AcademicArticle
title: Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic
description: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions a…
format: application/pdf
format: text/html
creator: Amira Chaabane
creator: Jean-Lou Justine
creator: Delphine Gey
creator: Micah D. Bakenhaster
creator: Lassad Neifar
subject: Biodiversity
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2233
publisher: PeerJ Inc.
rights: © 2016 Chaabane et al.
abstract: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions a…
bibliographic citation: Chaabane et al. (2016) Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic. PeerJ 4:e2233 https://doi.org/10.7717/peerj.2233
date submitted: 2016-04-12
date accepted: 2016-06-17
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chaabane
  given name: Amira
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Bakenhaster
  given name: Micah D.
author list: Agent
  family name: Neifar
  given name: Lassad
doi: 10.7717/peerj.2233
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Chaabane et al.
attribution name: Chaabane et al.

Delivering a medical school elective with massive open online course (MOOC) technology
type: item
type: AcademicArticle
description: Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery. Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth-year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012–2015 academic years was conducted. This course was delivered by small group flipped classroom discussions for 2012–2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations. Results: Course enrollment has ranged from 6–19 students per year in the 2012–2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5-point Likert scale. The majority of all student ratings (76–95%) of this elective course are for the highest possible choice (Strongly agree or Excellent) for any criteria, regardless if the course was delivered via a traditional or MOOC format. Statistical analysis of these ratings suggests that the Effective Teacher and Overall Evaluations did not statistically differ between the two delivery formats. Discussion: Student ratings of this elective course were highly similar when delivered in a flipped classroom format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations suggest this is a change that is acceptable to the …
format: application/pdf
format: text/html
creator: Robert Robinson
subject: Science and Medical Education
subject: Human-Computer Interaction
description: doi:10.7717/peerj.2343
publisher: PeerJ Inc.
rights: © 2016 Robinson
abstract: Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery. Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth-year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012–2015 academic years was conducted. This course was delivered by small group flipped classroom discussions for 2012–2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations. Results: Course enrollment has ranged from 6–19 students per year in the 2012–2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5-point Likert scale. The majority of all student ratings (76–95%) of this elective course are for the highest possible choice (Strongly agree or Excellent) for any criteria, regardless if the course was delivered via a traditional or MOOC format. Statistical analysis of these ratings suggests that the Effective Teacher and Overall Evaluations did not statistically differ between the two delivery formats. Discussion: Student ratings of this elective course were highly similar when delivered in a flipped classroom format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations suggest this is a change that is acceptable to the …
bibliographic citation: Robinson (2016) Delivering a medical school elective with massive open online course (MOOC) technology. PeerJ 4:e2343 https://doi.org/10.7717/peerj.2343
date submitted: 2016-04-14
date accepted: 2016-07-19
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robinson
  given name: Robert
doi: 10.7717/peerj.2343
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Robinson
attribution name: Robinson

Prediction of pKa values using the PM6 semiempirical method
type: item
type: AcademicArticle
description: The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
format: application/pdf
format: text/html
creator: Jimmy C. Kromann
creator: Frej Larsen
creator: Hadeel Moustafa
creator: Jan H. Jensen
subject: Biophysics
subject: Computational Biology
description: doi:10.7717/peerj.2335
publisher: PeerJ Inc.
rights: © 2016 Kromann et al.
abstract: The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
bibliographic citation: Kromann et al. (2016) Prediction of pKa values using the PM6 semiempirical method. PeerJ 4:e2335 https://doi.org/10.7717/peerj.2335
date submitted: 2016-06-01
date accepted: 2016-07-16
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kromann
  given name: Jimmy C.
author list: Agent
  family name: Larsen
  given name: Frej
author list: Agent
  family name: Moustafa
  given name: Hadeel
author list: Agent
  family name: Jensen
  given name: Jan H.
doi: 10.7717/peerj.2335
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Kromann et al.
attribution name: Kromann et al.

The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled
type: item
type: AcademicArticle
description: The modified Thomas test was developed to assess the presence of hip flexion contracture and to measure hip extensibility. Despite its widespread use, to the authors’ knowledge, its criterion reference validity has not yet been investigated. The purpose of this study was to assess the criterion reference validity of the modified Thomas test for measuring peak hip extension angle and hip extension deficits, as defined by the hip not being able to extend to 0º, or neutral. Twenty-nine healthy college students (age = 22.00 ± 3.80 years; height = 1.71 ± 0.09 m; body mass = 70.00 ± 15.60 kg) were recruited for this study. Bland–Altman plots revealed poor validity for the modified Thomas test’s ability to measure hip extension, which could not be explained by differences in hip flexion ability alone. The modified Thomas test displayed a sensitivity of 31.82% (95% CI [13.86–54.87]) and a specificity of 57.14% (95% CI [18.41–90.10]) for testing hip extension deficits. It appears, however, that by controlling pelvic tilt, much of this variance can be accounted for (r = 0.98). When pelvic tilt is not controlled, the modified Thomas test displays poor criterion reference validity and, as per previous studies, poor reliability. However, when pelvic tilt is controlled, the modified Thomas test appears to be a valid test for evaluating peak hip extension angle.
format: application/pdf
format: text/html
creator: Andrew D. Vigotsky
creator: Gregory J. Lehman
creator: Chris Beardsley
creator: Bret Contreras
creator: Bryan Chung
creator: Erin H. Feser
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.2325
publisher: PeerJ Inc.
rights: © 2016 Vigotsky et al.
abstract: The modified Thomas test was developed to assess the presence of hip flexion contracture and to measure hip extensibility. Despite its widespread use, to the authors’ knowledge, its criterion reference validity has not yet been investigated. The purpose of this study was to assess the criterion reference validity of the modified Thomas test for measuring peak hip extension angle and hip extension deficits, as defined by the hip not being able to extend to 0º, or neutral. Twenty-nine healthy college students (age = 22.00 ± 3.80 years; height = 1.71 ± 0.09 m; body mass = 70.00 ± 15.60 kg) were recruited for this study. Bland–Altman plots revealed poor validity for the modified Thomas test’s ability to measure hip extension, which could not be explained by differences in hip flexion ability alone. The modified Thomas test displayed a sensitivity of 31.82% (95% CI [13.86–54.87]) and a specificity of 57.14% (95% CI [18.41–90.10]) for testing hip extension deficits. It appears, however, that by controlling pelvic tilt, much of this variance can be accounted for (r = 0.98). When pelvic tilt is not controlled, the modified Thomas test displays poor criterion reference validity and, as per previous studies, poor reliability. However, when pelvic tilt is controlled, the modified Thomas test appears to be a valid test for evaluating peak hip extension angle.
bibliographic citation: Vigotsky et al. (2016) The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled. PeerJ 4:e2325 https://doi.org/10.7717/peerj.2325
date submitted: 2016-05-24
date accepted: 2016-07-14
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vigotsky
  given name: Andrew D.
author list: Agent
  family name: Lehman
  given name: Gregory J.
author list: Agent
  family name: Beardsley
  given name: Chris
author list: Agent
  family name: Contreras
  given name: Bret
author list: Agent
  family name: Chung
  given name: Bryan
author list: Agent
  family name: Feser
  given name: Erin H.
doi: 10.7717/peerj.2325
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Vigotsky et al.
attribution name: Vigotsky et al.

Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania
type: item
type: AcademicArticle
description: The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens.
format: application/pdf
format: text/html
creator: Joyce M. Sakamoto
creator: Terry Fei Fan Ng
creator: Yasutsugu Suzuki
creator: Hitoshi Tsujimoto
creator: Xutao Deng
creator: Eric Delwart
creator: Jason L. Rasgon
subject: Ecology
subject: Entomology
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.2324
publisher: PeerJ Inc.
rights: © 2016 Sakamoto et al.
abstract: The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens.
bibliographic citation: Sakamoto et al. (2016) Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania. PeerJ 4:e2324 https://doi.org/10.7717/peerj.2324
date submitted: 2016-06-14
date accepted: 2016-07-13
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakamoto
  given name: Joyce M.
author list: Agent
  family name: Ng
  given name: Terry Fei Fan
author list: Agent
  family name: Suzuki
  given name: Yasutsugu
author list: Agent
  family name: Tsujimoto
  given name: Hitoshi
author list: Agent
  family name: Deng
  given name: Xutao
author list: Agent
  family name: Delwart
  given name: Eric
author list: Agent
  family name: Rasgon
  given name: Jason L.
doi: 10.7717/peerj.2324
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Sakamoto et al.
attribution name: Sakamoto et al.

Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation
type: item
type: AcademicArticle
description: Background. Mammalian hibernation in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) is characterized by dramatic changes on a physiological and molecular level. During hibernation, mammalian hearts show a propensity to hypertrophy due to the need for increasing contractility to pump colder and more viscous blood. While cardiac hypertrophy is quite often a process characterized by decompensation, the ground squirrel studied is an excellent model of cardiac plasticity and cardioprotection under conditions of hypothermia and ischemia. The forkhead box O (Foxo) family of proteins and myogenin (MyoG) are transcription factors that control protein degradation and muscle atrophy by regulating the expression of the E3 ubiquitin ligases, MAFbx and MuRF1. These ligases are part of the ubiquitin proteasome system by transferring ubiquitin to proteins and targeting these proteins for degradation. Regulation of Foxo1 and 3a occurs through phosphorylation at different residues. The threonine-24 (Thr-24) and serine-319 (Ser-319) residues on Foxo1, and the Thr-32 residue on Foxo3a are phosphorylated by Akt, leading to cytoplasmic localization of Foxo. We propose that the described mechanism contributes to the changes taking place in cardiac muscle throughout hibernation. Methods. Total and phosphorylated protein levels of Foxo1 and Foxo3a, as well as total protein levels of MyoG, MAFbx, and MuRF1, were studied using immunoblotting. Results. Immunoblotting results demonstrated upregulations in Foxo1 and Foxo3a total protein levels (1.3- and 4.5-fold increases relative to euthermic control, for Foxo1 and 3a respectively) during late torpor, and protein levels remained elevated throughout the rest of torpor and at interbout arousal. We also observed decreases in inactive, phosphorylated Foxo1 and 3a proteins during throughout torpor, where levels of p-Foxo1 Ser319 and Thr24, as well as p-Foxo3a Thr32 decreased by at least 45% throughout torpor. MyoG was upregulated only …
format: application/pdf
format: text/html
creator: Yichi Zhang
creator: Oscar A. Aguilar
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Cardiology
description: doi:10.7717/peerj.2317
publisher: PeerJ Inc.
rights: © 2016 Zhang et al.
abstract: Background. Mammalian hibernation in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) is characterized by dramatic changes on a physiological and molecular level. During hibernation, mammalian hearts show a propensity to hypertrophy due to the need for increasing contractility to pump colder and more viscous blood. While cardiac hypertrophy is quite often a process characterized by decompensation, the ground squirrel studied is an excellent model of cardiac plasticity and cardioprotection under conditions of hypothermia and ischemia. The forkhead box O (Foxo) family of proteins and myogenin (MyoG) are transcription factors that control protein degradation and muscle atrophy by regulating the expression of the E3 ubiquitin ligases, MAFbx and MuRF1. These ligases are part of the ubiquitin proteasome system by transferring ubiquitin to proteins and targeting these proteins for degradation. Regulation of Foxo1 and 3a occurs through phosphorylation at different residues. The threonine-24 (Thr-24) and serine-319 (Ser-319) residues on Foxo1, and the Thr-32 residue on Foxo3a are phosphorylated by Akt, leading to cytoplasmic localization of Foxo. We propose that the described mechanism contributes to the changes taking place in cardiac muscle throughout hibernation. Methods. Total and phosphorylated protein levels of Foxo1 and Foxo3a, as well as total protein levels of MyoG, MAFbx, and MuRF1, were studied using immunoblotting. Results. Immunoblotting results demonstrated upregulations in Foxo1 and Foxo3a total protein levels (1.3- and 4.5-fold increases relative to euthermic control, for Foxo1 and 3a respectively) during late torpor, and protein levels remained elevated throughout the rest of torpor and at interbout arousal. We also observed decreases in inactive, phosphorylated Foxo1 and 3a proteins during throughout torpor, where levels of p-Foxo1 Ser319 and Thr24, as well as p-Foxo3a Thr32 decreased by at least 45% throughout torpor. MyoG was upregulated only …
bibliographic citation: Zhang et al. (2016) Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation. PeerJ 4:e2317 https://doi.org/10.7717/peerj.2317
date submitted: 2016-05-26
date accepted: 2016-07-12
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yichi
author list: Agent
  family name: Aguilar
  given name: Oscar A.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.2317
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Zhang et al.
attribution name: Zhang et al.

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