PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus
items: Taxonomic and functional trait diversity of wild bees in different urban settings
items: Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida)
items: Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking
items: Survey of owner motivations and veterinary input of owners feeding diets containing raw animal products
items: New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples
items: The effects of elevated pain inhibition on endurance exercise performance
items: Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs
items: Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae)
items: Asymmetry of mandibular dentition is associated with dietary specialization in snail-eating snakes

A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus
type: item
type: AcademicArticle
description: Mourasuchus (Alligatoroidea, Caimaninae) is one of the most peculiar crocodyliforms due to the skull morphology consisting of a long, wide, dorsoventrally flat rostrum with long, slender mandibular rami. Despite these peculiarities, the systematics, phylogeny and feeding habits of this taxon have not been properly studied. In this paper, we describe a new species of the genus, Mourasuchus pattersoni sp. nov., from the late Miocene of the Urumaco Formation of Venezuela. The new species differs from the other Mourasuchus species in having a lateromedially wide, dorsoventrally high jugal bone and a circular incisive foramen, which both represent autapomorphies of the new taxon. Phylogenetically, M. pattersoni sp. nov. is more closely related to M. amazonensis and the specimen UFAC-1424 (formely attributed to M. nativus) than to M. arendsi or M. atopus, whilst Mourasuchus is recovered once more as a monophyletic group. Furthermore, the cladistic analysis performed in this contribution offers a new phylogenetic assessment of Caimaninae, including many taxa described recently for the group. In this study, we also discuss the crocodylian diversity of the Urumaco Formation as well as how paleoenvironment may have contributed toward its evolution. In addition, we provide a discussion of the potential feeding habits of Mourasuchus. In this contribution, Mourasuchus is regarded as a taxon that likely preferred to prey on small animals. The unusual skull morphology of this group may have evolved to cover a large area with the rostrum, allowing for a more efficient prey capture, while the prey may have consisted predominantly of large amounts of small animals.
format: application/pdf
format: text/html
creator: Giovanne M. Cidade
creator: Andrés Solórzano
creator: Ascanio Daniel Rincón
creator: Douglas Riff
creator: Annie Schmaltz Hsiou
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.3056
publisher: PeerJ Inc.
rights: © 2017 Cidade et al.
abstract: Mourasuchus (Alligatoroidea, Caimaninae) is one of the most peculiar crocodyliforms due to the skull morphology consisting of a long, wide, dorsoventrally flat rostrum with long, slender mandibular rami. Despite these peculiarities, the systematics, phylogeny and feeding habits of this taxon have not been properly studied. In this paper, we describe a new species of the genus, Mourasuchus pattersoni sp. nov., from the late Miocene of the Urumaco Formation of Venezuela. The new species differs from the other Mourasuchus species in having a lateromedially wide, dorsoventrally high jugal bone and a circular incisive foramen, which both represent autapomorphies of the new taxon. Phylogenetically, M. pattersoni sp. nov. is more closely related to M. amazonensis and the specimen UFAC-1424 (formely attributed to M. nativus) than to M. arendsi or M. atopus, whilst Mourasuchus is recovered once more as a monophyletic group. Furthermore, the cladistic analysis performed in this contribution offers a new phylogenetic assessment of Caimaninae, including many taxa described recently for the group. In this study, we also discuss the crocodylian diversity of the Urumaco Formation as well as how paleoenvironment may have contributed toward its evolution. In addition, we provide a discussion of the potential feeding habits of Mourasuchus. In this contribution, Mourasuchus is regarded as a taxon that likely preferred to prey on small animals. The unusual skull morphology of this group may have evolved to cover a large area with the rostrum, allowing for a more efficient prey capture, while the prey may have consisted predominantly of large amounts of small animals.
bibliographic citation: Cidade et al. (2017) A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus. PeerJ 5:e3056 https://doi.org/10.7717/peerj.3056
date submitted: 2016-10-05
date accepted: 2017-02-01
issued: 2017-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cidade
  given name: Giovanne M.
author list: Agent
  family name: Solórzano
  given name: Andrés
author list: Agent
  family name: Rincón
  given name: Ascanio Daniel
author list: Agent
  family name: Riff
  given name: Douglas
author list: Agent
  family name: Hsiou
  given name: Annie Schmaltz
doi: 10.7717/peerj.3056
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-07
copyright: ©2017 Cidade et al.
attribution name: Cidade et al.

Taxonomic and functional trait diversity of wild bees in different urban settings
type: item
type: AcademicArticle
description: Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.
format: application/pdf
format: text/html
creator: Étienne Normandin
creator: Nicolas J. Vereecken
creator: Christopher M. Buddle
creator: Valérie Fournier
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3051
publisher: PeerJ Inc.
rights: © 2017 Normandin et al.
abstract: Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.
bibliographic citation: Normandin et al. (2017) Taxonomic and functional trait diversity of wild bees in different urban settings. PeerJ 5:e3051 https://doi.org/10.7717/peerj.3051
date submitted: 2016-01-11
date accepted: 2017-01-31
issued: 2017-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Normandin
  given name: Étienne
author list: Agent
  family name: Vereecken
  given name: Nicolas J.
author list: Agent
  family name: Buddle
  given name: Christopher M.
author list: Agent
  family name: Fournier
  given name: Valérie
doi: 10.7717/peerj.3051
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-07
copyright: ©2017 Normandin et al.
attribution name: Normandin et al.

Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida)
type: item
type: AcademicArticle
description: Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean…
format: application/pdf
format: text/html
creator: Maria J. Uriz
creator: Leire Garate
creator: Gemma Agell
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2958
publisher: PeerJ Inc.
rights: © 2017 Uriz et al.
abstract: Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean…
bibliographic citation: Uriz et al. (2017) Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida). PeerJ 5:e2958 https://doi.org/10.7717/peerj.2958
date submitted: 2016-11-19
date accepted: 2017-01-04
issued: 2017-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uriz
  given name: Maria J.
author list: Agent
  family name: Garate
  given name: Leire
author list: Agent
  family name: Agell
  given name: Gemma
doi: 10.7717/peerj.2958
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-07
copyright: © 2017 Uriz et al.
attribution name: Uriz et al.

Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking
type: item
type: AcademicArticle
description: Head et al. (2015) provided a large collection of p-values that, from their perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05 than p-values reported to three decimal places, due to apparent tendencies to round p-values to two decimal places. Head et al. (2015) correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that eliminating p = .045 is a result of the need for symmetric bins and systematically more p-values are reported to two decimal places than to three decimal places, I did not exclude p = .045 and p = .05. I conducted Fisher’s method .04 < p < .05 and reanalyzed the data by adjusting the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we look at the entire range between .04 < p < .05 or when we inspect the second-decimal. Taking into account reporting tendencies when selecting the bins to compare is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, inspecting the bins that include two-decimal reported p-values potentially increases sensitivity if strategic rounding down of p-values as a form of p-hacking is widespread. Given the far-reaching implications of supposed widespread p-hacking throughout the sciences Head et al. (2015), it is important that these findings are robust to data analysis choices if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this reanalysis, this does not mean th…
format: application/pdf
format: text/html
creator: Chris H.J. Hartgerink
subject: Science Policy
subject: Statistics
description: doi:10.7717/peerj.3068
publisher: PeerJ Inc.
rights: © 2017
abstract: Head et al. (2015) provided a large collection of p-values that, from their perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05 than p-values reported to three decimal places, due to apparent tendencies to round p-values to two decimal places. Head et al. (2015) correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that eliminating p = .045 is a result of the need for symmetric bins and systematically more p-values are reported to two decimal places than to three decimal places, I did not exclude p = .045 and p = .05. I conducted Fisher’s method .04 < p < .05 and reanalyzed the data by adjusting the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we look at the entire range between .04 < p < .05 or when we inspect the second-decimal. Taking into account reporting tendencies when selecting the bins to compare is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, inspecting the bins that include two-decimal reported p-values potentially increases sensitivity if strategic rounding down of p-values as a form of p-hacking is widespread. Given the far-reaching implications of supposed widespread p-hacking throughout the sciences Head et al. (2015), it is important that these findings are robust to data analysis choices if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this reanalysis, this does not mean th…
bibliographic citation: Hartgerink (2017) Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking. PeerJ 5:e3068 https://doi.org/10.7717/peerj.3068
date submitted: 2016-09-10
date accepted: 2017-02-05
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Hartgerink
  given name: Chris H.J.
doi: 10.7717/peerj.3068
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02

Survey of owner motivations and veterinary input of owners feeding diets containing raw animal products
type: item
type: AcademicArticle
description: Background The practice of feeding of diets containing raw animal products (RAP) to pets (dogs and cats) is discouraged by veterinary organizations and governmental public health organizations. Nevertheless, the practice of feeding RAP to pets is increasing in popularity. Pet owner motivations for feeding RAP diets to pets have not been explored and the benefits of RAP diets remain largely anecdotal. We hypothesized that pet owners feeding RAP diets would not rely on veterinary advice in choosing their pet’s diet. We also hypothesized that these owners would have lower levels of trust in veterinary advice with respect to nutrition relative to pet owners not feeding RAP. Methods An anonymous web-based survey was developed to identify pet owner motivations for feeding RAP diets, and to characterize the veterinarian-client relationships of individuals feeding RAP diets. Results There were 2,337 respondents and 2,171 completed surveys. Of survey respondents, 804 reported feeding RAP at the time of the survey. While 20% of pet owners feeding RAP relied on online resources to determine what or how much RAP to feed, only 9% reported consulting with a veterinarian in making decisions about feeding RAP. Pet owners feeding RAP reported lower levels of trust in veterinary advice both ‘in general’ and ‘with respect to nutrition’ than pet owners not feeding RAP. Most pet owners reported that a discussion regarding their pet’s nutrition does not occur at every veterinary appointment. Discussion Pet owners feeding a RAP diet have lower trust in veterinary advice than pet owners not feeding a RAP diet. Owners feeding RAP are more reliant on online resources than their own veterinarian in deciding what and how much RAP to feed. Pet owners perceive that nutrition is not discussed at most veterinary appointments. Therefore, there is room for improvement in the veterinarian-client communication with regards to nutrition.
format: application/pdf
format: text/html
creator: Stewart K. Morgan
creator: Susan Willis
creator: Megan L. Shepherd
subject: Veterinary Medicine
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.3031
publisher: PeerJ Inc.
rights: © 2017 Morgan et al.
abstract: Background The practice of feeding of diets containing raw animal products (RAP) to pets (dogs and cats) is discouraged by veterinary organizations and governmental public health organizations. Nevertheless, the practice of feeding RAP to pets is increasing in popularity. Pet owner motivations for feeding RAP diets to pets have not been explored and the benefits of RAP diets remain largely anecdotal. We hypothesized that pet owners feeding RAP diets would not rely on veterinary advice in choosing their pet’s diet. We also hypothesized that these owners would have lower levels of trust in veterinary advice with respect to nutrition relative to pet owners not feeding RAP. Methods An anonymous web-based survey was developed to identify pet owner motivations for feeding RAP diets, and to characterize the veterinarian-client relationships of individuals feeding RAP diets. Results There were 2,337 respondents and 2,171 completed surveys. Of survey respondents, 804 reported feeding RAP at the time of the survey. While 20% of pet owners feeding RAP relied on online resources to determine what or how much RAP to feed, only 9% reported consulting with a veterinarian in making decisions about feeding RAP. Pet owners feeding RAP reported lower levels of trust in veterinary advice both ‘in general’ and ‘with respect to nutrition’ than pet owners not feeding RAP. Most pet owners reported that a discussion regarding their pet’s nutrition does not occur at every veterinary appointment. Discussion Pet owners feeding a RAP diet have lower trust in veterinary advice than pet owners not feeding a RAP diet. Owners feeding RAP are more reliant on online resources than their own veterinarian in deciding what and how much RAP to feed. Pet owners perceive that nutrition is not discussed at most veterinary appointments. Therefore, there is room for improvement in the veterinarian-client communication with regards to nutrition.
bibliographic citation: Morgan et al. (2017) Survey of owner motivations and veterinary input of owners feeding diets containing raw animal products. PeerJ 5:e3031 https://doi.org/10.7717/peerj.3031
date submitted: 2016-10-25
date accepted: 2017-01-25
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morgan
  given name: Stewart K.
author list: Agent
  family name: Willis
  given name: Susan
author list: Agent
  family name: Shepherd
  given name: Megan L.
doi: 10.7717/peerj.3031
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Morgan et al.
attribution name: Morgan et al.

New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples
type: item
type: AcademicArticle
description: Background To find the best individual chemotherapy for cancer patients, the efficacy of different chemotherapeutic drugs can be predicted by pretesting tumor samples in vitro via the chemotherapy-resistance (CTR)-Test®. Although drug combinations are widely used among cancer therapy, so far only single drugs are tested by this and other tests. However, several first line chemotherapies are combining two or more chemotherapeutics, leading to the necessity of drug combination testing methods. Methods We established a system to measure and predict the efficacy of chemotherapeutic drug combinations with the help of the Loewe additivity concept in combination with the CTR-test. A combination is measured by using half of the monotherapy’s concentration of both drugs simultaneously. With this method, the efficacy of a combination can also be calculated based on single drug measurements. Results The established system was tested on a data set of ovarian carcinoma samples using the combination carboplatin and paclitaxel and confirmed by using other tumor species and chemotherapeutics. Comparing the measured and the calculated values of the combination testings revealed a high correlation. Additionally, in 70% of the cases the measured and the calculated values lead to the same chemotherapeutic resistance category of the tumor. Conclusion Our data suggest that the best drug combination consists of the most efficient single drugs and the worst drug combination of the least efficient single drugs. Our results showed that single measurements are sufficient to predict combinations in specific cases but there are exceptions in which it is necessary to measure combinations, which is possible with the presented system.
format: application/pdf
format: text/html
creator: Frank Christian Kischkel
creator: Julia Eich
creator: Carina I. Meyer
creator: Paula Weidemüller
creator: Jens Krapfl
creator: Rauaa Yassin-Kelepir
creator: Laura Job
creator: Marius Fraefel
creator: Ioana Braicu
creator: Annette Kopp-Schneider
creator: Jalid Sehouli
creator: Rudy Leon De Wilde
subject: Gynecology and Obstetrics
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.3030
publisher: PeerJ Inc.
rights: © 2017 Kischkel et al.
abstract: Background To find the best individual chemotherapy for cancer patients, the efficacy of different chemotherapeutic drugs can be predicted by pretesting tumor samples in vitro via the chemotherapy-resistance (CTR)-Test®. Although drug combinations are widely used among cancer therapy, so far only single drugs are tested by this and other tests. However, several first line chemotherapies are combining two or more chemotherapeutics, leading to the necessity of drug combination testing methods. Methods We established a system to measure and predict the efficacy of chemotherapeutic drug combinations with the help of the Loewe additivity concept in combination with the CTR-test. A combination is measured by using half of the monotherapy’s concentration of both drugs simultaneously. With this method, the efficacy of a combination can also be calculated based on single drug measurements. Results The established system was tested on a data set of ovarian carcinoma samples using the combination carboplatin and paclitaxel and confirmed by using other tumor species and chemotherapeutics. Comparing the measured and the calculated values of the combination testings revealed a high correlation. Additionally, in 70% of the cases the measured and the calculated values lead to the same chemotherapeutic resistance category of the tumor. Conclusion Our data suggest that the best drug combination consists of the most efficient single drugs and the worst drug combination of the least efficient single drugs. Our results showed that single measurements are sufficient to predict combinations in specific cases but there are exceptions in which it is necessary to measure combinations, which is possible with the presented system.
bibliographic citation: Kischkel et al. (2017) New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples. PeerJ 5:e3030 https://doi.org/10.7717/peerj.3030
date submitted: 2016-11-03
date accepted: 2017-01-25
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kischkel
  given name: Frank Christian
author list: Agent
  family name: Eich
  given name: Julia
author list: Agent
  family name: Meyer
  given name: Carina I.
author list: Agent
  family name: Weidemüller
  given name: Paula
author list: Agent
  family name: Krapfl
  given name: Jens
author list: Agent
  family name: Yassin-Kelepir
  given name: Rauaa
author list: Agent
  family name: Job
  given name: Laura
author list: Agent
  family name: Fraefel
  given name: Marius
author list: Agent
  family name: Braicu
  given name: Ioana
author list: Agent
  family name: Kopp-Schneider
  given name: Annette
author list: Agent
  family name: Sehouli
  given name: Jalid
author list: Agent
  family name: De Wilde
  given name: Rudy Leon
doi: 10.7717/peerj.3030
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Kischkel et al.
attribution name: Kischkel et al.

The effects of elevated pain inhibition on endurance exercise performance
type: item
type: AcademicArticle
description: Background The ergogenic effects of analgesic substances suggest that pain perception is an important regulator of work-rate during fatiguing exercise. Recent research has shown that endogenous inhibitory responses, which act to attenuate nociceptive input and reduce perceived pain, can be increased following transcranial direct current stimulation of the hand motor cortex. Using high-definition transcranial direct current stimulation (HD-tDCS; 2 mA, 20 min), the current study aimed to examine the effects of elevated pain inhibitory capacity on endurance exercise performance. It was hypothesised that HD-tDCS would enhance the efficiency of the endogenous pain inhibitory response and improve endurance exercise performance. Methods Twelve healthy males between 18 and 40 years of age (M = 24.42 ± 3.85) were recruited for participation. Endogenous pain inhibitory capacity and exercise performance were assessed before and after both active and sham (placebo) stimulation. The conditioned pain modulation protocol was used for the measurement of pain inhibition. Exercise performance assessment consisted of both maximal voluntary contraction (MVC) and submaximal muscular endurance performance trials using isometric contractions of the non-dominant leg extensors. Results Active HD-tDCS (pre-tDCS, −.32 ± 1.33 kg; post-tDCS, −1.23 ± 1.21 kg) significantly increased pain inhibitory responses relative to the effects of sham HD-tDCS (pre-tDCS, −.91 ± .92 kg; post-tDCS, −.26 ± .92 kg; p = .046). Irrespective of condition, peak MVC force and muscular endurance was reduced from pre- to post-stimulation. HD-tDCS did not significantly influence this reduction in maximal force (active: pre-tDCS, 264.89 ± 66.87 Nm; post-tDCS, 236.33 ± 66.51 Nm; sham: pre-tDCS, 249.25 ± 88.56 Nm; post-tDCS, 239.63 ± 67.53 Nm) or muscular endurance (active: pre-tDCS, 104.65 ± 42.36 s; post-tDCS, 93.07 ± 33.73 s; sham: pre-tDCS, 123.42 ± 72.48 s; post-tDCS, 100.27 ± 44.25 s). Discussion Despite increasing p…
format: application/pdf
format: text/html
creator: Andrew Flood
creator: Gordon Waddington
creator: Richard J. Keegan
creator: Kevin G. Thompson
creator: Stuart Cathcart
subject: Anesthesiology and Pain Management
subject: Neurology
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3028
publisher: PeerJ Inc.
rights: © 2017 Flood et al.
abstract: Background The ergogenic effects of analgesic substances suggest that pain perception is an important regulator of work-rate during fatiguing exercise. Recent research has shown that endogenous inhibitory responses, which act to attenuate nociceptive input and reduce perceived pain, can be increased following transcranial direct current stimulation of the hand motor cortex. Using high-definition transcranial direct current stimulation (HD-tDCS; 2 mA, 20 min), the current study aimed to examine the effects of elevated pain inhibitory capacity on endurance exercise performance. It was hypothesised that HD-tDCS would enhance the efficiency of the endogenous pain inhibitory response and improve endurance exercise performance. Methods Twelve healthy males between 18 and 40 years of age (M = 24.42 ± 3.85) were recruited for participation. Endogenous pain inhibitory capacity and exercise performance were assessed before and after both active and sham (placebo) stimulation. The conditioned pain modulation protocol was used for the measurement of pain inhibition. Exercise performance assessment consisted of both maximal voluntary contraction (MVC) and submaximal muscular endurance performance trials using isometric contractions of the non-dominant leg extensors. Results Active HD-tDCS (pre-tDCS, −.32 ± 1.33 kg; post-tDCS, −1.23 ± 1.21 kg) significantly increased pain inhibitory responses relative to the effects of sham HD-tDCS (pre-tDCS, −.91 ± .92 kg; post-tDCS, −.26 ± .92 kg; p = .046). Irrespective of condition, peak MVC force and muscular endurance was reduced from pre- to post-stimulation. HD-tDCS did not significantly influence this reduction in maximal force (active: pre-tDCS, 264.89 ± 66.87 Nm; post-tDCS, 236.33 ± 66.51 Nm; sham: pre-tDCS, 249.25 ± 88.56 Nm; post-tDCS, 239.63 ± 67.53 Nm) or muscular endurance (active: pre-tDCS, 104.65 ± 42.36 s; post-tDCS, 93.07 ± 33.73 s; sham: pre-tDCS, 123.42 ± 72.48 s; post-tDCS, 100.27 ± 44.25 s). Discussion Despite increasing p…
bibliographic citation: Flood et al. (2017) The effects of elevated pain inhibition on endurance exercise performance. PeerJ 5:e3028 https://doi.org/10.7717/peerj.3028
date submitted: 2016-10-03
date accepted: 2017-01-25
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flood
  given name: Andrew
author list: Agent
  family name: Waddington
  given name: Gordon
author list: Agent
  family name: Keegan
  given name: Richard J.
author list: Agent
  family name: Thompson
  given name: Kevin G.
author list: Agent
  family name: Cathcart
  given name: Stuart
doi: 10.7717/peerj.3028
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Flood et al.
attribution name: Flood et al.

Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs
type: item
type: AcademicArticle
description: Background Much of the recent research in companion animal nutrition has focussed on understanding the role of diet on faecal microbiota composition. To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to pets in spite of their very different dietary and metabolic requirements. This lack of direct evidence means that the mechanisms by which microbiota influences health in dogs are poorly understood. We hypothesised that changes in faecal microbiota correlate with physiological parameters including apparent macronutrient digestibility. Methods Fifteen adult dogs were assigned to two diet groups, exclusively fed either a premium kibbled diet (kibble; K; n = 8) or a raw red meat diet (meat; M; n = 7) for nine weeks. Apparent digestibility of macronutrients (protein, fat, gross energy and dry matter), faecal weight, faecal health scores, faecal VFA concentrations and faecal microbial composition were determined. Datasets were integrated using mixOmics in R. Results Faecal weight and VFA levels were lower and the apparent digestibility of protein and energy were higher in dogs on the meat diet. Diet significantly affected 27 microbial families and 53 genera in the faeces. In particular, the abundances of Bacteriodes, Prevotella, Peptostreptococcus and Faecalibacterium were lower in dogs fed the meat diet, whereas Fusobacterium, Lactobacillus and Clostridium were all more abundant. Discussion Our results show clear associations of specific microbial taxa with diet composition. For example, Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae were highly correlated to parameters such as protein and fat digestibility in the dog. By understanding the relationship between faecal microbiota and physiological parameters we will gain better insights into the effects of diet on the nutrition of our pets.
format: application/pdf
format: text/html
creator: Emma N. Bermingham
creator: Paul Maclean
creator: David G. Thomas
creator: Nicholas J. Cave
creator: Wayne Young
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.3019
publisher: PeerJ Inc.
rights: © 2017 Bermingham et al.
abstract: Background Much of the recent research in companion animal nutrition has focussed on understanding the role of diet on faecal microbiota composition. To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to pets in spite of their very different dietary and metabolic requirements. This lack of direct evidence means that the mechanisms by which microbiota influences health in dogs are poorly understood. We hypothesised that changes in faecal microbiota correlate with physiological parameters including apparent macronutrient digestibility. Methods Fifteen adult dogs were assigned to two diet groups, exclusively fed either a premium kibbled diet (kibble; K; n = 8) or a raw red meat diet (meat; M; n = 7) for nine weeks. Apparent digestibility of macronutrients (protein, fat, gross energy and dry matter), faecal weight, faecal health scores, faecal VFA concentrations and faecal microbial composition were determined. Datasets were integrated using mixOmics in R. Results Faecal weight and VFA levels were lower and the apparent digestibility of protein and energy were higher in dogs on the meat diet. Diet significantly affected 27 microbial families and 53 genera in the faeces. In particular, the abundances of Bacteriodes, Prevotella, Peptostreptococcus and Faecalibacterium were lower in dogs fed the meat diet, whereas Fusobacterium, Lactobacillus and Clostridium were all more abundant. Discussion Our results show clear associations of specific microbial taxa with diet composition. For example, Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae were highly correlated to parameters such as protein and fat digestibility in the dog. By understanding the relationship between faecal microbiota and physiological parameters we will gain better insights into the effects of diet on the nutrition of our pets.
bibliographic citation: Bermingham et al. (2017) Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ 5:e3019 https://doi.org/10.7717/peerj.3019
date submitted: 2016-09-07
date accepted: 2017-01-23
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bermingham
  given name: Emma N.
author list: Agent
  family name: Maclean
  given name: Paul
author list: Agent
  family name: Thomas
  given name: David G.
author list: Agent
  family name: Cave
  given name: Nicholas J.
author list: Agent
  family name: Young
  given name: Wayne
doi: 10.7717/peerj.3019
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Bermingham et al.
attribution name: Bermingham et al.

Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae)
type: item
type: AcademicArticle
description: The iconic gastropod genus Cyphoma is commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genus Cyphoma has a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisability Cyphoma gibbosum has been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S) for three Cyphoma species (C. gibbosum, C. mcgintyi, C. signatum) and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a result C. mcgintyi and C. signatum are synonymised with C. gibbosum, which is a key result for future work using C. gibbosum as a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism), or incipient speciation.
format: application/pdf
format: text/html
creator: Bastian T. Reijnen
creator: Sancia E.T. van der Meij
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.3018
publisher: PeerJ Inc.
rights: © 2017 Reijnen and Van der Meij
abstract: The iconic gastropod genus Cyphoma is commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genus Cyphoma has a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisability Cyphoma gibbosum has been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S) for three Cyphoma species (C. gibbosum, C. mcgintyi, C. signatum) and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a result C. mcgintyi and C. signatum are synonymised with C. gibbosum, which is a key result for future work using C. gibbosum as a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism), or incipient speciation.
bibliographic citation: Reijnen et al. (2017) Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae). PeerJ 5:e3018 https://doi.org/10.7717/peerj.3018
date submitted: 2016-03-25
date accepted: 2017-01-23
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reijnen
  given name: Bastian T.
author list: Agent
  family name: van der Meij
  given name: Sancia E.T.
doi: 10.7717/peerj.3018
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Reijnen and Van der Meij
attribution name: Reijnen and Van der Meij

Asymmetry of mandibular dentition is associated with dietary specialization in snail-eating snakes
type: item
type: AcademicArticle
description: Background In vertebrates, the left-and-right pairs of homologous organs are generally present in equal numbers. A remarkable exception is known in the snail-eating snakes of the family Pareidae: almost all the pareid snakes have much more teeth on the right mandible than on the left for functional specialization in feeding on the dextral majority of land snails. Because the only exceptional species with symmetric dentition has been regarded as a slug-eater, the extent of dietary specialization on slugs could shape the degree of the lateral asymmetry of mandibular dentition (dentition asymmetry) even among snail eaters. Methods To test this, I compared the morphology and behavior of two sympatric species of Taiwanese snail-eating snakes, Pareas atayal and P. formosensis. Results Specimens collected in the same locality showed that the dentition asymmetry of P. formosensis was significantly smaller than that of P. atayal. Congruent to its weak asymmetry, P. formosensis showed a strong preference of slugs to snails in the feeding experiment. Discussion The dietary specialization of P. formosensis on slugs would contribute to niche partitioning from the sympatric congener P. atayal. This study suggests that the diverse variation in the dentition asymmetry of pareid snakes is the result of their dietary specialization and divergence.
format: application/pdf
format: text/html
creator: Masaki Hoso
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3011
publisher: PeerJ Inc.
rights: © 2017 Hoso
abstract: Background In vertebrates, the left-and-right pairs of homologous organs are generally present in equal numbers. A remarkable exception is known in the snail-eating snakes of the family Pareidae: almost all the pareid snakes have much more teeth on the right mandible than on the left for functional specialization in feeding on the dextral majority of land snails. Because the only exceptional species with symmetric dentition has been regarded as a slug-eater, the extent of dietary specialization on slugs could shape the degree of the lateral asymmetry of mandibular dentition (dentition asymmetry) even among snail eaters. Methods To test this, I compared the morphology and behavior of two sympatric species of Taiwanese snail-eating snakes, Pareas atayal and P. formosensis. Results Specimens collected in the same locality showed that the dentition asymmetry of P. formosensis was significantly smaller than that of P. atayal. Congruent to its weak asymmetry, P. formosensis showed a strong preference of slugs to snails in the feeding experiment. Discussion The dietary specialization of P. formosensis on slugs would contribute to niche partitioning from the sympatric congener P. atayal. This study suggests that the diverse variation in the dentition asymmetry of pareid snakes is the result of their dietary specialization and divergence.
bibliographic citation: Hoso (2017) Asymmetry of mandibular dentition is associated with dietary specialization in snail-eating snakes. PeerJ 5:e3011 https://doi.org/10.7717/peerj.3011
date submitted: 2016-12-07
date accepted: 2017-01-21
issued: 2017-03-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoso
  given name: Masaki
doi: 10.7717/peerj.3011
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-02
copyright: ©2017 Hoso
attribution name: Hoso

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