PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Diagnostic inertia in dyslipidaemia: results of a preventative programme in Spain
items: Using affective knowledge to generate and validate a set of emotion-related, action words
items: Klebsiella pneumoniae subsp. pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman
items: Early prediction of language and literacy problems: is 18 months too early?
items: A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef
items: All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality
items: Conducting perception research over the internet: a tutorial review
items: From promise to practice: pairing non-invasive sampling with genomics in conservation
items: A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution
items: Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus)

Diagnostic inertia in dyslipidaemia: results of a preventative programme in Spain
type: item
type: AcademicArticle
description: Others have analysed the relationship between inadequate behaviour by healthcare professionals in the diagnosis of dyslipidaemia (diagnostic inertia) and the history of cardiovascular risk factors. However, since no study has assessed cardiovascular risk scores as associated factors, we carried out a study to quantify diagnostic inertia in dyslipidaemia and to determine if cardiovascular risk scores are associated with this inertia. In the Valencian Community (Spain), a preventive programme (cardiovascular, gynaecologic and vaccination) was started in 2003 inviting persons aged ≥40 years to undergo a health check-up at their health centre. This cross-sectional study examined persons with no known dyslipidaemia seen during the first six months of the programme (n = 16, 905) but whose total cholesterol (TC) was ≥5.17 mmol/L. Diagnostic inertia was defined as lack of follow-up to confirm/discard the dyslipidaemia diagnosis. Other variables included in the analysis were gender, history of cardiovascular risk factors/cardiovascular disease, counselling (diet/exercise), body mass index (BMI), age, blood pressure, fasting blood glucose and lipids. TC was grouped as ≥/<6.20 mmol/L. In patients without cardiovascular disease and <75/≤65 years (n = 15, 778/13, 597), the REGICOR (REgistre GIroní del COr)/SCORE (Systematic COronary Risk Evaluation) cardiovascular risk functions were used to classify risk (high/low). Inertia was quantified and the adjusted odds ratios calculated from multivariate models. In the overall sample, the rate of diagnostic inertia was 52% (95% CI [51.2–52.7]); associated factors were TC ≥ 6.20 mmol/L, high or “not measured” BMI, hypertension, smoking and higher values of fasting blood glucose, systolic blood pressure and TC. In the REGICOR sample, the rate of diagnostic inertia was 51.9% (95% CI [51.1–52.7]); associated factors were REGICOR high and high or “not measured” BMI. In the SCORE sample the rate of diagnostic inertia was 51.7% (95% CI [50.9–5…
format: application/pdf
format: text/html
creator: Antonio Palazón-Bru
creator: Armina Sepehri
creator: Dolores Ramírez-Prado
creator: Felipe Navarro-Cremades
creator: Ernesto Cortés
creator: Mercedes Rizo-Baeza
creator: Vicente Francisco Gil-Guillén
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.1109
publisher: PeerJ Inc.
rights: © 2015 Palazón-Bru et al.
abstract: Others have analysed the relationship between inadequate behaviour by healthcare professionals in the diagnosis of dyslipidaemia (diagnostic inertia) and the history of cardiovascular risk factors. However, since no study has assessed cardiovascular risk scores as associated factors, we carried out a study to quantify diagnostic inertia in dyslipidaemia and to determine if cardiovascular risk scores are associated with this inertia. In the Valencian Community (Spain), a preventive programme (cardiovascular, gynaecologic and vaccination) was started in 2003 inviting persons aged ≥40 years to undergo a health check-up at their health centre. This cross-sectional study examined persons with no known dyslipidaemia seen during the first six months of the programme (n = 16, 905) but whose total cholesterol (TC) was ≥5.17 mmol/L. Diagnostic inertia was defined as lack of follow-up to confirm/discard the dyslipidaemia diagnosis. Other variables included in the analysis were gender, history of cardiovascular risk factors/cardiovascular disease, counselling (diet/exercise), body mass index (BMI), age, blood pressure, fasting blood glucose and lipids. TC was grouped as ≥/<6.20 mmol/L. In patients without cardiovascular disease and <75/≤65 years (n = 15, 778/13, 597), the REGICOR (REgistre GIroní del COr)/SCORE (Systematic COronary Risk Evaluation) cardiovascular risk functions were used to classify risk (high/low). Inertia was quantified and the adjusted odds ratios calculated from multivariate models. In the overall sample, the rate of diagnostic inertia was 52% (95% CI [51.2–52.7]); associated factors were TC ≥ 6.20 mmol/L, high or “not measured” BMI, hypertension, smoking and higher values of fasting blood glucose, systolic blood pressure and TC. In the REGICOR sample, the rate of diagnostic inertia was 51.9% (95% CI [51.1–52.7]); associated factors were REGICOR high and high or “not measured” BMI. In the SCORE sample the rate of diagnostic inertia was 51.7% (95% CI [50.9–5…
bibliographic citation: Palazón-Bru et al. (2015) Diagnostic inertia in dyslipidaemia: results of a preventative programme in Spain. PeerJ 3:e1109 https://doi.org/10.7717/peerj.1109
date submitted: 2015-04-21
date accepted: 2015-06-26
issued: 2015-07-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palazón-Bru
  given name: Antonio
author list: Agent
  family name: Sepehri
  given name: Armina
author list: Agent
  family name: Ramírez-Prado
  given name: Dolores
author list: Agent
  family name: Navarro-Cremades
  given name: Felipe
author list: Agent
  family name: Cortés
  given name: Ernesto
author list: Agent
  family name: Rizo-Baeza
  given name: Mercedes
author list: Agent
  family name: Gil-Guillén
  given name: Vicente Francisco
doi: 10.7717/peerj.1109
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-28
copyright: © 2015 Palazón-Bru et al.
attribution name: Palazón-Bru et al.

Using affective knowledge to generate and validate a set of emotion-related, action words
type: item
type: AcademicArticle
description: Emotion concepts are built through situated experience. Abstract word meaning is grounded in this affective knowledge, giving words the potential to evoke emotional feelings and reactions (e.g., Vigliocco et al., 2009). In the present work we explore whether words differ in the extent to which they evoke ‘specific’ emotional knowledge. Using a categorical approach, in which an affective ‘context’ is created, it is possible to assess whether words proportionally activate knowledge relevant to different emotional states (e.g., ‘sadness’, ‘anger’, Stevenson, Mikels & James, 2007a). We argue that this method may be particularly effective when assessing the emotional meaning of action words (e.g., Schacht & Sommer, 2009). In study 1 we use a constrained feature generation task to derive a set of action words that participants associated with six, basic emotional states (see full list in Appendix S1). Generation frequencies were taken to indicate the likelihood that the word would evoke emotional knowledge relevant to the state to which it had been paired. In study 2 a rating task was used to assess the strength of association between the six most frequently generated, or ‘typical’, action words and corresponding emotion labels. Participants were presented with a series of sentences, in which action words (typical and atypical) and labels were paired e.g., “If you are feeling ‘sad’ how likely would you be to act in the following way?” … ‘cry.’ Findings suggest that typical associations were robust. Participants always gave higher ratings to typical vs. atypical action word and label pairings, even when (a) rating direction was manipulated (the label or verb appeared first in the sentence), and (b) the typical behaviours were to be performed by the rater themselves, or others. Our findings suggest that emotion-related action words vary in the extent to which they evoke knowledge relevant for different emotional states. When measuring affective grounding, it may then be app…
format: application/pdf
format: text/html
creator: Emma Portch
creator: Jelena Havelka
creator: Charity Brown
creator: Roger Giner-Sorolla
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1100
publisher: PeerJ Inc.
rights: © 2015 Portch et al.
abstract: Emotion concepts are built through situated experience. Abstract word meaning is grounded in this affective knowledge, giving words the potential to evoke emotional feelings and reactions (e.g., Vigliocco et al., 2009). In the present work we explore whether words differ in the extent to which they evoke ‘specific’ emotional knowledge. Using a categorical approach, in which an affective ‘context’ is created, it is possible to assess whether words proportionally activate knowledge relevant to different emotional states (e.g., ‘sadness’, ‘anger’, Stevenson, Mikels & James, 2007a). We argue that this method may be particularly effective when assessing the emotional meaning of action words (e.g., Schacht & Sommer, 2009). In study 1 we use a constrained feature generation task to derive a set of action words that participants associated with six, basic emotional states (see full list in Appendix S1). Generation frequencies were taken to indicate the likelihood that the word would evoke emotional knowledge relevant to the state to which it had been paired. In study 2 a rating task was used to assess the strength of association between the six most frequently generated, or ‘typical’, action words and corresponding emotion labels. Participants were presented with a series of sentences, in which action words (typical and atypical) and labels were paired e.g., “If you are feeling ‘sad’ how likely would you be to act in the following way?” … ‘cry.’ Findings suggest that typical associations were robust. Participants always gave higher ratings to typical vs. atypical action word and label pairings, even when (a) rating direction was manipulated (the label or verb appeared first in the sentence), and (b) the typical behaviours were to be performed by the rater themselves, or others. Our findings suggest that emotion-related action words vary in the extent to which they evoke knowledge relevant for different emotional states. When measuring affective grounding, it may then be app…
bibliographic citation: Portch et al. (2015) Using affective knowledge to generate and validate a set of emotion-related, action words. PeerJ 3:e1100 https://doi.org/10.7717/peerj.1100
date submitted: 2015-03-17
date accepted: 2015-06-22
issued: 2015-07-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Portch
  given name: Emma
author list: Agent
  family name: Havelka
  given name: Jelena
author list: Agent
  family name: Brown
  given name: Charity
author list: Agent
  family name: Giner-Sorolla
  given name: Roger
doi: 10.7717/peerj.1100
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-28
copyright: © 2015 Portch et al.
attribution name: Portch et al.

Klebsiella pneumoniae subsp. pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman
type: item
type: AcademicArticle
description: A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages (phages). A lytic phage, named KLPN1, was isolated on a strain identified as Klebsiella pneumoniae subsp. pneumoniae (capsular type K2, rmpA+). This Siphoviridae phage presents a rosette-like tail tip and exhibits depolymerase activity, as demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of clinical isolates of K. pneumoniae subsp. pneumoniae, phage KLPN1 was shown to infect and lyse capsular type K2 strains, though it did not exhibit depolymerase activity on such hosts. The genome of KLPN1 was determined to be 49,037 bp (50.53 %GC) in length, encompassing 73 predicted ORFs, of which 23 represented genes associated with structure, host recognition, packaging, DNA replication and cell lysis. On the basis of sequence analyses, phages KLPN1 (GenBank: KR262148) and 1513 (a member of the family Siphoviridae, GenBank: KP658157) were found to be two new members of the genus “Kp36likevirus.”
format: application/pdf
format: text/html
creator: Lesley Hoyles
creator: James Murphy
creator: Horst Neve
creator: Knut J. Heller
creator: Jane F. Turton
creator: Jennifer Mahony
creator: Jeremy D. Sanderson
creator: Barry Hudspith
creator: Glenn R. Gibson
creator: Anne L. McCartney
creator: Douwe van Sinderen
subject: Biodiversity
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.1061
publisher: PeerJ Inc.
rights: ©
abstract: A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages (phages). A lytic phage, named KLPN1, was isolated on a strain identified as Klebsiella pneumoniae subsp. pneumoniae (capsular type K2, rmpA+). This Siphoviridae phage presents a rosette-like tail tip and exhibits depolymerase activity, as demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of clinical isolates of K. pneumoniae subsp. pneumoniae, phage KLPN1 was shown to infect and lyse capsular type K2 strains, though it did not exhibit depolymerase activity on such hosts. The genome of KLPN1 was determined to be 49,037 bp (50.53 %GC) in length, encompassing 73 predicted ORFs, of which 23 represented genes associated with structure, host recognition, packaging, DNA replication and cell lysis. On the basis of sequence analyses, phages KLPN1 (GenBank: KR262148) and 1513 (a member of the family Siphoviridae, GenBank: KP658157) were found to be two new members of the genus “Kp36likevirus.”
bibliographic citation: Hoyles et al. (2015) Klebsiella pneumoniae subsp. pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman. PeerJ 3:e1061 https://doi.org/10.7717/peerj.1061
date submitted: 2015-05-03
date accepted: 2015-06-06
issued: 2015-07-28
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Hoyles
  given name: Lesley
author list: Agent
  family name: Murphy
  given name: James
author list: Agent
  family name: Neve
  given name: Horst
author list: Agent
  family name: Heller
  given name: Knut J.
author list: Agent
  family name: Turton
  given name: Jane F.
author list: Agent
  family name: Mahony
  given name: Jennifer
author list: Agent
  family name: Sanderson
  given name: Jeremy D.
author list: Agent
  family name: Hudspith
  given name: Barry
author list: Agent
  family name: Gibson
  given name: Glenn R.
author list: Agent
  family name: McCartney
  given name: Anne L.
author list: Agent
  family name: van Sinderen
  given name: Douwe
doi: 10.7717/peerj.1061
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-28

Early prediction of language and literacy problems: is 18 months too early?
type: item
type: AcademicArticle
description: There is a lack of stability in language difficulties across early childhood: most late talkers (LTs) resolve their difficulties by pre-school; and a significant number of children who were not LTs subsequently manifest language difficulties. Greater reliability in predicting individual outcomes is needed, which might be achieved by waiting until later in development when language is more stable. At 18 months, productive vocabulary scores on the Oxford Communicative Developmental Inventory were used to classify children as LTs or average talkers (ATs). Thirty matched-pairs of LTs and ATs were followed up at school-age (average age 7 years), when language and literacy outcomes were assessed. For 18 children, intermediate testing at age 4 had classified them as showing typical development (TD) or specific language impairment (SLI). After correcting for multiple comparisons, there were no significant differences between the LTs and ATs on any outcome measure, and the LTs were performing in the average range. However, there were large-sized effects on all outcomes when comparing the TD and SLI groups. LT status on its own is not determinative of language and literacy difficulties. It would therefore not be appropriate to use expressive vocabulary measures alone to screen for language difficulties at 18 months. However, children with language impairment at age 4 are at risk of enduring difficulties.
format: application/pdf
format: text/html
creator: Fiona J. Duff
creator: Kate Nation
creator: Kim Plunkett
creator: DVM Bishop
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1098
publisher: PeerJ Inc.
rights: © 2015 Duff et al.
abstract: There is a lack of stability in language difficulties across early childhood: most late talkers (LTs) resolve their difficulties by pre-school; and a significant number of children who were not LTs subsequently manifest language difficulties. Greater reliability in predicting individual outcomes is needed, which might be achieved by waiting until later in development when language is more stable. At 18 months, productive vocabulary scores on the Oxford Communicative Developmental Inventory were used to classify children as LTs or average talkers (ATs). Thirty matched-pairs of LTs and ATs were followed up at school-age (average age 7 years), when language and literacy outcomes were assessed. For 18 children, intermediate testing at age 4 had classified them as showing typical development (TD) or specific language impairment (SLI). After correcting for multiple comparisons, there were no significant differences between the LTs and ATs on any outcome measure, and the LTs were performing in the average range. However, there were large-sized effects on all outcomes when comparing the TD and SLI groups. LT status on its own is not determinative of language and literacy difficulties. It would therefore not be appropriate to use expressive vocabulary measures alone to screen for language difficulties at 18 months. However, children with language impairment at age 4 are at risk of enduring difficulties.
bibliographic citation: Duff et al. (2015) Early prediction of language and literacy problems: is 18 months too early?. PeerJ 3:e1098 https://doi.org/10.7717/peerj.1098
date submitted: 2014-12-18
date accepted: 2015-06-19
issued: 2015-07-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duff
  given name: Fiona J.
author list: Agent
  family name: Nation
  given name: Kate
author list: Agent
  family name: Plunkett
  given name: Kim
author list: Agent
  family name: Bishop
  given name: DVM
doi: 10.7717/peerj.1098
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-23
copyright: © 2015 Duff et al.
attribution name: Duff et al.

A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef
type: item
type: AcademicArticle
description: Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes …
format: application/pdf
format: text/html
creator: Madeleine J.H. van Oppen
creator: Vimoksalehi Lukoschek
creator: Ray Berkelmans
creator: Lesa M. Peplow
creator: Alison M. Jones
subject: Ecology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.1092
publisher: PeerJ Inc.
rights: © 2015 van Oppen et al.
abstract: Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes …
bibliographic citation: van Oppen et al. (2015) A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef. PeerJ 3:e1092 https://doi.org/10.7717/peerj.1092
date submitted: 2015-05-29
date accepted: 2015-06-18
issued: 2015-07-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Oppen
  given name: Madeleine J.H.
author list: Agent
  family name: Lukoschek
  given name: Vimoksalehi
author list: Agent
  family name: Berkelmans
  given name: Ray
author list: Agent
  family name: Peplow
  given name: Lesa M.
author list: Agent
  family name: Jones
  given name: Alison M.
doi: 10.7717/peerj.1092
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-23
copyright: © 2015 van Oppen et al.
attribution name: van Oppen et al.

All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality
type: item
type: AcademicArticle
description: More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.
format: application/pdf
format: text/html
creator: JinHee Choi
creator: HyeJi Lee
creator: Alexey Shipunov
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.1087
publisher: PeerJ Inc.
rights: © 2015 Choi et al.
abstract: More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.
bibliographic citation: Choi et al. (2015) All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality. PeerJ 3:e1087 https://doi.org/10.7717/peerj.1087
date submitted: 2015-03-04
date accepted: 2015-06-16
issued: 2015-07-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: JinHee
author list: Agent
  family name: Lee
  given name: HyeJi
author list: Agent
  family name: Shipunov
  given name: Alexey
doi: 10.7717/peerj.1087
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-23
copyright: © 2015 Choi et al.
attribution name: Choi et al.

Conducting perception research over the internet: a tutorial review
type: item
type: AcademicArticle
description: This article provides an overview of the recent literature on the use of internet-based testing to address important questions in perception research. Our goal is to provide a starting point for the perception researcher who is keen on assessing this tool for their own research goals. Internet-based testing has several advantages over in-lab research, including the ability to reach a relatively broad set of participants and to quickly and inexpensively collect large amounts of empirical data, via services such as Amazon’s Mechanical Turk or Prolific Academic. In many cases, the quality of online data appears to match that collected in lab research. Generally-speaking, online participants tend to be more representative of the population at large than those recruited for lab based research. There are, though, some important caveats, when it comes to collecting data online. It is obviously much more difficult to control the exact parameters of stimulus presentation (such as display characteristics) with online research. There are also some thorny ethical elements that need to be considered by experimenters. Strengths and weaknesses of the online approach, relative to others, are highlighted, and recommendations made for those researchers who might be thinking about conducting their own studies using this increasingly-popular approach to research in the psychological sciences.
format: application/pdf
format: text/html
creator: Andy T. Woods
creator: Carlos Velasco
creator: Carmel A. Levitan
creator: Xiaoang Wan
creator: Charles Spence
subject: Psychiatry and Psychology
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.1058
publisher: PeerJ Inc.
rights: © 2015 Woods et al.
abstract: This article provides an overview of the recent literature on the use of internet-based testing to address important questions in perception research. Our goal is to provide a starting point for the perception researcher who is keen on assessing this tool for their own research goals. Internet-based testing has several advantages over in-lab research, including the ability to reach a relatively broad set of participants and to quickly and inexpensively collect large amounts of empirical data, via services such as Amazon’s Mechanical Turk or Prolific Academic. In many cases, the quality of online data appears to match that collected in lab research. Generally-speaking, online participants tend to be more representative of the population at large than those recruited for lab based research. There are, though, some important caveats, when it comes to collecting data online. It is obviously much more difficult to control the exact parameters of stimulus presentation (such as display characteristics) with online research. There are also some thorny ethical elements that need to be considered by experimenters. Strengths and weaknesses of the online approach, relative to others, are highlighted, and recommendations made for those researchers who might be thinking about conducting their own studies using this increasingly-popular approach to research in the psychological sciences.
bibliographic citation: Woods et al. (2015) Conducting perception research over the internet: a tutorial review. PeerJ 3:e1058 https://doi.org/10.7717/peerj.1058
date submitted: 2015-03-26
date accepted: 2015-06-07
issued: 2015-07-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woods
  given name: Andy T.
author list: Agent
  family name: Velasco
  given name: Carlos
author list: Agent
  family name: Levitan
  given name: Carmel A.
author list: Agent
  family name: Wan
  given name: Xiaoang
author list: Agent
  family name: Spence
  given name: Charles
doi: 10.7717/peerj.1058
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-23
copyright: © 2015 Woods et al.
attribution name: Woods et al.

From promise to practice: pairing non-invasive sampling with genomics in conservation
type: item
type: AcademicArticle
description: Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 ng. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.
format: application/pdf
format: text/html
creator: Michael A. Russello
creator: Matthew D. Waterhouse
creator: Paul D. Etter
creator: Eric A. Johnson
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.1106
publisher: PeerJ Inc.
rights: © 2015 Russello et al.
abstract: Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 ng. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.
bibliographic citation: Russello et al. (2015) From promise to practice: pairing non-invasive sampling with genomics in conservation. PeerJ 3:e1106 https://doi.org/10.7717/peerj.1106
date submitted: 2015-04-20
date accepted: 2015-06-25
issued: 2015-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Russello
  given name: Michael A.
author list: Agent
  family name: Waterhouse
  given name: Matthew D.
author list: Agent
  family name: Etter
  given name: Paul D.
author list: Agent
  family name: Johnson
  given name: Eric A.
doi: 10.7717/peerj.1106
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-21
copyright: © 2015 Russello et al.
attribution name: Russello et al.

A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution
type: item
type: AcademicArticle
description: Overdispersion is a common feature of models of biological data, but researchers often fail to model the excess variation driving the overdispersion, resulting in biased parameter estimates and standard errors. Quantifying and modeling overdispersion when it is present is therefore critical for robust biological inference. One means to account for overdispersion is to add an observation-level random effect (OLRE) to a model, where each data point receives a unique level of a random effect that can absorb the extra-parametric variation in the data. Although some studies have investigated the utility of OLRE to model overdispersion in Poisson count data, studies doing so for Binomial proportion data are scarce. Here I use a simulation approach to investigate the ability of both OLRE models and Beta-Binomial models to recover unbiased parameter estimates in mixed effects models of Binomial data under various degrees of overdispersion. In addition, as ecologists often fit random intercept terms to models when the random effect sample size is low (<5 levels), I investigate the performance of both model types under a range of random effect sample sizes when overdispersion is present. Simulation results revealed that the efficacy of OLRE depends on the process that generated the overdispersion; OLRE failed to cope with overdispersion generated from a Beta-Binomial mixture model, leading to biased slope and intercept estimates, but performed well for overdispersion generated by adding random noise to the linear predictor. Comparison of parameter estimates from an OLRE model with those from its corresponding Beta-Binomial model readily identified when OLRE were performing poorly due to disagreement between effect sizes, and this strategy should be employed whenever OLRE are used for Binomial data to assess their reliability. Beta-Binomial models performed well across all contexts, but showed a tendency to underestimate effect sizes when modelling non-Beta-Binomial data. Fina…
format: application/pdf
format: text/html
creator: Xavier A. Harrison
subject: Ecology
subject: Evolutionary Studies
subject: Statistics
description: doi:10.7717/peerj.1114
publisher: PeerJ Inc.
rights: © 2015 Harrison
abstract: Overdispersion is a common feature of models of biological data, but researchers often fail to model the excess variation driving the overdispersion, resulting in biased parameter estimates and standard errors. Quantifying and modeling overdispersion when it is present is therefore critical for robust biological inference. One means to account for overdispersion is to add an observation-level random effect (OLRE) to a model, where each data point receives a unique level of a random effect that can absorb the extra-parametric variation in the data. Although some studies have investigated the utility of OLRE to model overdispersion in Poisson count data, studies doing so for Binomial proportion data are scarce. Here I use a simulation approach to investigate the ability of both OLRE models and Beta-Binomial models to recover unbiased parameter estimates in mixed effects models of Binomial data under various degrees of overdispersion. In addition, as ecologists often fit random intercept terms to models when the random effect sample size is low (<5 levels), I investigate the performance of both model types under a range of random effect sample sizes when overdispersion is present. Simulation results revealed that the efficacy of OLRE depends on the process that generated the overdispersion; OLRE failed to cope with overdispersion generated from a Beta-Binomial mixture model, leading to biased slope and intercept estimates, but performed well for overdispersion generated by adding random noise to the linear predictor. Comparison of parameter estimates from an OLRE model with those from its corresponding Beta-Binomial model readily identified when OLRE were performing poorly due to disagreement between effect sizes, and this strategy should be employed whenever OLRE are used for Binomial data to assess their reliability. Beta-Binomial models performed well across all contexts, but showed a tendency to underestimate effect sizes when modelling non-Beta-Binomial data. Fina…
bibliographic citation: Harrison (2015) A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution. PeerJ 3:e1114 https://doi.org/10.7717/peerj.1114
date submitted: 2015-03-26
date accepted: 2015-06-29
issued: 2015-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harrison
  given name: Xavier A.
doi: 10.7717/peerj.1114
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-21
copyright: © 2015 Harrison
attribution name: Harrison

Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus)
type: item
type: AcademicArticle
description: Many decapod crustaceans perform escape tailflips with a neural circuit involving giant interneurons, a specialized fast flexor motor giant (MoG) neuron, populations of larger, less specialized fast flexor motor neurons, and fast extensor motor neurons. These escape-related neurons are well described in crayfish (Reptantia), but not in more basal decapod groups. To clarify the evolution of the escape circuit, I examined the fast flexor and fast extensor motor neurons of white shrimp (Litopenaeus setiferus; Dendrobranchiata) using backfilling. In crayfish, the MoGs in each abdominal ganglion are a bilateral pair of separate neurons. In L. setiferus, the MoGs have massive, possibly syncytial, cell bodies and fused axons. The non-MoG fast flexor motor neurons and fast extensor motor neurons are generally found in similar locations to where they are found in crayfish, but the number of motor neurons in both the flexor and extensor pools is smaller than in crayfish. The loss of fusion in the MoGs and increased number of fast motor neurons in reptantian decapods may be correlated with an increased reliance on non-giant mediated tailflipping.
format: application/pdf
format: text/html
creator: Zen Faulkes
subject: Neuroscience
subject: Zoology
description: doi:10.7717/peerj.1112
publisher: PeerJ Inc.
rights: © 2015 Faulkes
abstract: Many decapod crustaceans perform escape tailflips with a neural circuit involving giant interneurons, a specialized fast flexor motor giant (MoG) neuron, populations of larger, less specialized fast flexor motor neurons, and fast extensor motor neurons. These escape-related neurons are well described in crayfish (Reptantia), but not in more basal decapod groups. To clarify the evolution of the escape circuit, I examined the fast flexor and fast extensor motor neurons of white shrimp (Litopenaeus setiferus; Dendrobranchiata) using backfilling. In crayfish, the MoGs in each abdominal ganglion are a bilateral pair of separate neurons. In L. setiferus, the MoGs have massive, possibly syncytial, cell bodies and fused axons. The non-MoG fast flexor motor neurons and fast extensor motor neurons are generally found in similar locations to where they are found in crayfish, but the number of motor neurons in both the flexor and extensor pools is smaller than in crayfish. The loss of fusion in the MoGs and increased number of fast motor neurons in reptantian decapods may be correlated with an increased reliance on non-giant mediated tailflipping.
bibliographic citation: Faulkes (2015) Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3:e1112 https://doi.org/10.7717/peerj.1112
date submitted: 2015-03-22
date accepted: 2015-06-29
issued: 2015-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Faulkes
  given name: Zen
doi: 10.7717/peerj.1112
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-21
copyright: © 2015 Faulkes
attribution name: Faulkes

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