PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mutational spectra of SARS-CoV-2 isolated from animals
items: Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians
items: Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island
items: A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment
items: The effect of decay and lexical uncertainty on processing long-distance dependencies in reading
items: Digitizing abdominal palpation with a pressure measurement and positioning device
items: Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea
items: Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
items: bmd: an R package for benchmark dose estimation
items: Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas

Mutational spectra of SARS-CoV-2 isolated from animals
type: item
type: AcademicArticle
description: Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.
format: application/pdf
format: text/html
creator: Ahmed Elaswad
creator: Mohamed Fawzy
creator: Shereen Basiouni
creator: Awad A. Shehata
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.10609
publisher: PeerJ Inc.
rights: © 2020 Elaswad et al.
abstract: Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.
bibliographic citation: Elaswad et al. (2020) Mutational spectra of SARS-CoV-2 isolated from animals. PeerJ 8:e10609 https://doi.org/10.7717/peerj.10609
date submitted: 2020-07-31
date accepted: 2020-11-29
issued: 2020-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elaswad
  given name: Ahmed
author list: Agent
  family name: Fawzy
  given name: Mohamed
author list: Agent
  family name: Basiouni
  given name: Shereen
author list: Agent
  family name: Shehata
  given name: Awad A.
doi: 10.7717/peerj.10609
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-18
copyright: © 2020 Elaswad et al.
attribution name: Elaswad et al.

Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians
type: item
type: AcademicArticle
description: Background In 2020, to limit the spread of Coronavirus (COVID-19), many countries, including Italy, have issued a lengthy quarantine period for the entire population. For this reason lifestyle has changed, bringing inevitable repercussions to the Quality of Life (QoL). The present study aims to identify which psychosocial variables predict behaviors capable of affecting the QoL during the lockdown period, potentially highlighting factors that might promote well-being and health in the Italian population during the epidemic. Methods Between 27 April 2020 and 11 May 2020, we administered a web-survey to a sample of young Italian people (age M = 21.2; SD = 3.5; female = 57.7% of the sample). Employing variance-based structural equation modeling, we attempted to identify whether social connectedness, social support, and loneliness were variables predictive of the QoL of young Italians. We also sought to identify specific psychological factors, such as symbolic threat, realistic threat, and the threat from potentially contaminated objects, was correlated to COVID-19 fear and whether engaging in particular behaviors was likely to improve the QoL. Results Our results suggest that social connectedness and loneliness are significant predictors of QoL, while social support did not have a significant effect on QoL. Furthermore, we observed that symbolic and realistic threats and the threat from potentially contaminated objects are significant and positive predictors of COVID-19 fear. Moreover, COVID-19 fear had significant and positive relationships with the carrying out of specific behaviors, such as creative activities during the isolation period and that this related to affirming individuals’ country-specific identity. Finally, COVID-19 fear is a significant predictor of behavioral factors related to the adherence to public health advice in line with national guidance regarding the containment of COVID-19; this factor, however, did not correlate with QoL. Conclusion Our res…
format: application/pdf
format: text/html
creator: Anna Lardone
creator: Pierpaolo Sorrentino
creator: Francesco Giancamilli
creator: Tommaso Palombi
creator: Trevor Simper
creator: Laura Mandolesi
creator: Fabio Lucidi
creator: Andrea Chirico
creator: Federica Galli
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.10611
publisher: PeerJ Inc.
rights: © 2020 Lardone et al.
abstract: Background In 2020, to limit the spread of Coronavirus (COVID-19), many countries, including Italy, have issued a lengthy quarantine period for the entire population. For this reason lifestyle has changed, bringing inevitable repercussions to the Quality of Life (QoL). The present study aims to identify which psychosocial variables predict behaviors capable of affecting the QoL during the lockdown period, potentially highlighting factors that might promote well-being and health in the Italian population during the epidemic. Methods Between 27 April 2020 and 11 May 2020, we administered a web-survey to a sample of young Italian people (age M = 21.2; SD = 3.5; female = 57.7% of the sample). Employing variance-based structural equation modeling, we attempted to identify whether social connectedness, social support, and loneliness were variables predictive of the QoL of young Italians. We also sought to identify specific psychological factors, such as symbolic threat, realistic threat, and the threat from potentially contaminated objects, was correlated to COVID-19 fear and whether engaging in particular behaviors was likely to improve the QoL. Results Our results suggest that social connectedness and loneliness are significant predictors of QoL, while social support did not have a significant effect on QoL. Furthermore, we observed that symbolic and realistic threats and the threat from potentially contaminated objects are significant and positive predictors of COVID-19 fear. Moreover, COVID-19 fear had significant and positive relationships with the carrying out of specific behaviors, such as creative activities during the isolation period and that this related to affirming individuals’ country-specific identity. Finally, COVID-19 fear is a significant predictor of behavioral factors related to the adherence to public health advice in line with national guidance regarding the containment of COVID-19; this factor, however, did not correlate with QoL. Conclusion Our res…
bibliographic citation: Lardone et al. (2020) Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians. PeerJ 8:e10611 https://doi.org/10.7717/peerj.10611
date submitted: 2020-08-13
date accepted: 2020-11-30
issued: 2020-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lardone
  given name: Anna
author list: Agent
  family name: Sorrentino
  given name: Pierpaolo
author list: Agent
  family name: Giancamilli
  given name: Francesco
author list: Agent
  family name: Palombi
  given name: Tommaso
author list: Agent
  family name: Simper
  given name: Trevor
author list: Agent
  family name: Mandolesi
  given name: Laura
author list: Agent
  family name: Lucidi
  given name: Fabio
author list: Agent
  family name: Chirico
  given name: Andrea
author list: Agent
  family name: Galli
  given name: Federica
doi: 10.7717/peerj.10611
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-18
copyright: © 2020 Lardone et al.
attribution name: Lardone et al.

Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island
type: item
type: AcademicArticle
description: In 2005, a chikungunya virus outbreak devastated the tropical island of Reunion, infecting a third of the total population. Motivated by the Reunion Island case study, we investigate the theoretic potential for two intervention measures under both voluntary and mandatory protocols to control a vector-borne disease when there is risk of the disease becoming endemic. The first measure uses insect repellent to prevent mosquito bites, while the second involves emigrating to the neighboring Mauritius Island to avoid infection. There is a threshold on the cost of using repellent above which both voluntary and mandatory regimes find it optimal to forgo usage. Below that threshold, mandatory usage protocols will eradicate the disease; however, voluntary adoption leaves the disease at a small endemic level. Emigrating from the island to avoid infection results in a tragedy-of-the-commons effect: while being potentially beneficial to specific susceptible individuals, the remaining islanders paradoxically face a higher risk of infection. Mandated relocation of susceptible individuals away from the epidemic is viable only if the cost of this relocation is several magnitudes lower than the cost of infection. Since this assumption is unlikely to hold for chikungunya, it is optimal to discourage such emigration for the benefit of the entire population. An underlying assumption about the conservation of human-vector encounter rates in mosquito biting behavior informs our conclusions and may warrant additional experimental verification.
format: application/pdf
format: text/html
creator: Sylvia R.M. Klein
creator: Alex O. Foster
creator: David A. Feagins
creator: Jonathan T. Rowell
creator: Igor V. Erovenko
subject: Mathematical Biology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.10151
publisher: PeerJ Inc.
rights: © 2020 Klein et al.
abstract: In 2005, a chikungunya virus outbreak devastated the tropical island of Reunion, infecting a third of the total population. Motivated by the Reunion Island case study, we investigate the theoretic potential for two intervention measures under both voluntary and mandatory protocols to control a vector-borne disease when there is risk of the disease becoming endemic. The first measure uses insect repellent to prevent mosquito bites, while the second involves emigrating to the neighboring Mauritius Island to avoid infection. There is a threshold on the cost of using repellent above which both voluntary and mandatory regimes find it optimal to forgo usage. Below that threshold, mandatory usage protocols will eradicate the disease; however, voluntary adoption leaves the disease at a small endemic level. Emigrating from the island to avoid infection results in a tragedy-of-the-commons effect: while being potentially beneficial to specific susceptible individuals, the remaining islanders paradoxically face a higher risk of infection. Mandated relocation of susceptible individuals away from the epidemic is viable only if the cost of this relocation is several magnitudes lower than the cost of infection. Since this assumption is unlikely to hold for chikungunya, it is optimal to discourage such emigration for the benefit of the entire population. An underlying assumption about the conservation of human-vector encounter rates in mosquito biting behavior informs our conclusions and may warrant additional experimental verification.
bibliographic citation: Klein et al. (2020) Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island. PeerJ 8:e10151 https://doi.org/10.7717/peerj.10151
date submitted: 2019-08-28
date accepted: 2020-09-21
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klein
  given name: Sylvia R.M.
author list: Agent
  family name: Foster
  given name: Alex O.
author list: Agent
  family name: Feagins
  given name: David A.
author list: Agent
  family name: Rowell
  given name: Jonathan T.
author list: Agent
  family name: Erovenko
  given name: Igor V.
doi: 10.7717/peerj.10151
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: ©2020 Klein et al.
attribution name: Klein et al.

A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment
type: item
type: AcademicArticle
description: Background The importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown featherback (Chitala ornata) is popularly consumed and is an economically important fish in Thailand which is often used in food products such as fish balls and fish cakes. Along with other fish species, the clown featherback is one of fish of inland fisheries at Phayao Lake. Recent fish surveys from 2016-2018 at Phayao Lake using netting and electrofishing found that the number of clown featherback have been reducing since 2016 and could not be detected at all by 2018. This is despite the fact that there are still reports of their presence in the lake from locals. Methods We developed an eDNA-based method for detection of the clown featherback in Phayao Lake as an alternative tool. Water samples were collected in three different sampling months (February, June and September) at six sites located in the lake. Species-specific primers and the probe were designed to amplify a 183 bp fragment of the cytB region of the clown featherback. Results eDNA of the clown featherback can be detected in all different sampling months and sites. Concentration of the clown featherback found in Prayao Lake showed no difference over sampling month but between collecting sites. This proves that eDNA based survey is a sensitive and useful tool for monitoring and surveying the clown featherback at any time of the year.
format: application/pdf
format: text/html
creator: Maslin Osathanunkul
creator: Toshifumi Minamoto
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.10338
publisher: PeerJ Inc.
rights: © 2020 Osathanunkul and Minamoto
abstract: Background The importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown featherback (Chitala ornata) is popularly consumed and is an economically important fish in Thailand which is often used in food products such as fish balls and fish cakes. Along with other fish species, the clown featherback is one of fish of inland fisheries at Phayao Lake. Recent fish surveys from 2016-2018 at Phayao Lake using netting and electrofishing found that the number of clown featherback have been reducing since 2016 and could not be detected at all by 2018. This is despite the fact that there are still reports of their presence in the lake from locals. Methods We developed an eDNA-based method for detection of the clown featherback in Phayao Lake as an alternative tool. Water samples were collected in three different sampling months (February, June and September) at six sites located in the lake. Species-specific primers and the probe were designed to amplify a 183 bp fragment of the cytB region of the clown featherback. Results eDNA of the clown featherback can be detected in all different sampling months and sites. Concentration of the clown featherback found in Prayao Lake showed no difference over sampling month but between collecting sites. This proves that eDNA based survey is a sensitive and useful tool for monitoring and surveying the clown featherback at any time of the year.
bibliographic citation: Osathanunkul et al. (2020) A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ 8:e10338 https://doi.org/10.7717/peerj.10338
date submitted: 2020-06-30
date accepted: 2020-10-20
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Osathanunkul
  given name: Maslin
author list: Agent
  family name: Minamoto
  given name: Toshifumi
doi: 10.7717/peerj.10338
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: ©2020 Osathanunkul and Minamoto
attribution name: Osathanunkul and Minamoto

The effect of decay and lexical uncertainty on processing long-distance dependencies in reading
type: item
type: AcademicArticle
description: To make sense of a sentence, a reader must keep track of dependent relationships between words, such as between a verb and its particle (e.g. turn the music down). In languages such as German, verb-particle dependencies often span long distances, with the particle only appearing at the end of the clause. This means that it may be necessary to process a large amount of intervening sentence material before the full verb of the sentence is known. To facilitate processing, previous studies have shown that readers can preactivate the lexical information of neighbouring upcoming words, but less is known about whether such preactivation can be sustained over longer distances. We asked the question, do readers preactivate lexical information about long-distance verb particles? In one self-paced reading and one eye tracking experiment, we delayed the appearance of an obligatory verb particle that varied only in the predictability of its lexical identity. We additionally manipulated the length of the delay in order to test two contrasting accounts of dependency processing: that increased distance between dependent elements may sharpen expectation of the distant word and facilitate its processing (an antilocality effect), or that it may slow processing via temporal activation decay (a locality effect). We isolated decay by delaying the particle with a neutral noun modifier containing no information about the identity of the upcoming particle, and no known sources of interference or working memory load. Under the assumption that readers would preactivate the lexical representations of plausible verb particles, we hypothesised that a smaller number of plausible particles would lead to stronger preactivation of each particle, and thus higher predictability of the target. This in turn should have made predictable target particles more resistant to the effects of decay than less predictable target particles. The eye tracking experiment provided evidence that higher predictability d…
format: application/pdf
format: text/html
creator: Kate Stone
creator: Titus von der Malsburg
creator: Shravan Vasishth
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.10438
publisher: PeerJ Inc.
rights: © 2020 Stone et al.
abstract: To make sense of a sentence, a reader must keep track of dependent relationships between words, such as between a verb and its particle (e.g. turn the music down). In languages such as German, verb-particle dependencies often span long distances, with the particle only appearing at the end of the clause. This means that it may be necessary to process a large amount of intervening sentence material before the full verb of the sentence is known. To facilitate processing, previous studies have shown that readers can preactivate the lexical information of neighbouring upcoming words, but less is known about whether such preactivation can be sustained over longer distances. We asked the question, do readers preactivate lexical information about long-distance verb particles? In one self-paced reading and one eye tracking experiment, we delayed the appearance of an obligatory verb particle that varied only in the predictability of its lexical identity. We additionally manipulated the length of the delay in order to test two contrasting accounts of dependency processing: that increased distance between dependent elements may sharpen expectation of the distant word and facilitate its processing (an antilocality effect), or that it may slow processing via temporal activation decay (a locality effect). We isolated decay by delaying the particle with a neutral noun modifier containing no information about the identity of the upcoming particle, and no known sources of interference or working memory load. Under the assumption that readers would preactivate the lexical representations of plausible verb particles, we hypothesised that a smaller number of plausible particles would lead to stronger preactivation of each particle, and thus higher predictability of the target. This in turn should have made predictable target particles more resistant to the effects of decay than less predictable target particles. The eye tracking experiment provided evidence that higher predictability d…
bibliographic citation: Stone et al. (2020) The effect of decay and lexical uncertainty on processing long-distance dependencies in reading. PeerJ 8:e10438 https://doi.org/10.7717/peerj.10438
date submitted: 2019-11-27
date accepted: 2020-11-06
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stone
  given name: Kate
author list: Agent
  family name: von der Malsburg
  given name: Titus
author list: Agent
  family name: Vasishth
  given name: Shravan
doi: 10.7717/peerj.10438
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: © 2020 Stone et al.
attribution name: Stone et al.

Digitizing abdominal palpation with a pressure measurement and positioning device
type: item
type: AcademicArticle
description: An abdominal physical examination is one of the most important tools in evaluating patients with acute abdominal pain. We focused on palpation, in which assessment is made according to the patient’s response and force feedback. Since palpation is performed manually by the examiner, the uniformity of force and location is difficult to achieve during examinations. We propose an integrated system to quantify palpation pressure and location. A force sensor continuously collects pressure data, while a camera locates the precise position of contact. The system recorded, displayed average and maximum pressure by creating a pressure/time curve for computer-aided diagnosis. Compared with previous work on pressure sensors of quantifying abdominal palpation, our proposed system is the integrated approach to measure palpation force and track the corresponding position at the same time, for further diagnosis. In addition, we only make use of a sensing device and a general web camera, rather than commercial algometry and infrared cameras used in the previous work. Based on our clinical trials, the statistics of palpation pressure values and the corresponding findings are also reported. We performed abdominal palpation with our system for twenty-three healthy participants, including fourteen males and nine females. We applied two grades of force on the abdomen (light and deep) by four-quadrant and nine-region schemes, record the value of pressure and location. In the four-quadrant scheme, the average pressures of abdominal palpation with light and deep force levels were 0.506(N) and 0.552(N), respectively. In the nine-region scheme, the average pressures were 0.496(N) and 0.577(N), respectively. Two episodes of contact dermal reaction were identified. According to our experiment statistics, there is no significant difference in the force level between the four-quadrant and nine-region scheme. Our results have the potential to be used as a reference guide while designing digital ab…
format: application/pdf
format: text/html
creator: Jia-Lien Hsu
creator: Chia-Hui Lee
creator: Chung-Ho Hsieh
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Nursing
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.10511
publisher: PeerJ Inc.
rights: © 2020 Hsu et al.
abstract: An abdominal physical examination is one of the most important tools in evaluating patients with acute abdominal pain. We focused on palpation, in which assessment is made according to the patient’s response and force feedback. Since palpation is performed manually by the examiner, the uniformity of force and location is difficult to achieve during examinations. We propose an integrated system to quantify palpation pressure and location. A force sensor continuously collects pressure data, while a camera locates the precise position of contact. The system recorded, displayed average and maximum pressure by creating a pressure/time curve for computer-aided diagnosis. Compared with previous work on pressure sensors of quantifying abdominal palpation, our proposed system is the integrated approach to measure palpation force and track the corresponding position at the same time, for further diagnosis. In addition, we only make use of a sensing device and a general web camera, rather than commercial algometry and infrared cameras used in the previous work. Based on our clinical trials, the statistics of palpation pressure values and the corresponding findings are also reported. We performed abdominal palpation with our system for twenty-three healthy participants, including fourteen males and nine females. We applied two grades of force on the abdomen (light and deep) by four-quadrant and nine-region schemes, record the value of pressure and location. In the four-quadrant scheme, the average pressures of abdominal palpation with light and deep force levels were 0.506(N) and 0.552(N), respectively. In the nine-region scheme, the average pressures were 0.496(N) and 0.577(N), respectively. Two episodes of contact dermal reaction were identified. According to our experiment statistics, there is no significant difference in the force level between the four-quadrant and nine-region scheme. Our results have the potential to be used as a reference guide while designing digital ab…
bibliographic citation: Hsu et al. (2020) Digitizing abdominal palpation with a pressure measurement and positioning device. PeerJ 8:e10511 https://doi.org/10.7717/peerj.10511
date submitted: 2020-06-09
date accepted: 2020-11-16
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hsu
  given name: Jia-Lien
author list: Agent
  family name: Lee
  given name: Chia-Hui
author list: Agent
  family name: Hsieh
  given name: Chung-Ho
doi: 10.7717/peerj.10511
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: ©2020 Hsu et al.
attribution name: Hsu et al.

Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea
type: item
type: AcademicArticle
description: Massive floating green macroalgae have formed harmful green tides in the Yellow Sea since 2007. To study the early development and the associated environmental factors for the green tide, a field survey was carried out in the Subei Shoal, southwestern Yellow Sea. Multiple species were identified in both floating green macroalgae and micro-propagules , while their abundances showed distinct spatial variations. The floating macroalgal biomass was widespread in the northern Subei Shoal and most abundant at 34°N. Ulva prolifera dominated (91.2% in average) the floating macroalgae, and the majority (88.5%) of U. prolifera was the ‘floating type’. In comparison, the micro-propagules were most abundant around the aquaculture rafts, and decreased significantly with the distance to the rafts. The dominant species of micro-propagules was U. linza (48.5%), followed by U. prolifera (35.1%). Their distinct distribution patterns and species diversity suggested little direct contribution of micro-propagules for the floating macroalgae. The spatial variation of the floating macroalgae was probably a combined result from the biomass source and environmental factors, while the abundance of micro-propagules was closely associated with the rafts. A positive correlation between the floating macroalgae and DO was observed and suggested active photosynthesis of the initial biomass in Subei Shoal. This study revealed specific distributional pattern and relationships among the floating macroalgae, micro-propagules and the environmental factors in the source region, which helps understanding the early blooming dynamics of the green tides in Yellow Sea.
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format: text/html
creator: Xiaoxiang Miao
creator: Jie Xiao
creator: Qinzeng Xu
creator: Shiliang Fan
creator: Zongling Wang
creator: Xiao Wang
creator: Xuelei Zhang
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Plant Science
subject: Biological Oceanography
description: doi:10.7717/peerj.10538
publisher: PeerJ Inc.
rights: © 2020 Miao et al.
abstract: Massive floating green macroalgae have formed harmful green tides in the Yellow Sea since 2007. To study the early development and the associated environmental factors for the green tide, a field survey was carried out in the Subei Shoal, southwestern Yellow Sea. Multiple species were identified in both floating green macroalgae and micro-propagules , while their abundances showed distinct spatial variations. The floating macroalgal biomass was widespread in the northern Subei Shoal and most abundant at 34°N. Ulva prolifera dominated (91.2% in average) the floating macroalgae, and the majority (88.5%) of U. prolifera was the ‘floating type’. In comparison, the micro-propagules were most abundant around the aquaculture rafts, and decreased significantly with the distance to the rafts. The dominant species of micro-propagules was U. linza (48.5%), followed by U. prolifera (35.1%). Their distinct distribution patterns and species diversity suggested little direct contribution of micro-propagules for the floating macroalgae. The spatial variation of the floating macroalgae was probably a combined result from the biomass source and environmental factors, while the abundance of micro-propagules was closely associated with the rafts. A positive correlation between the floating macroalgae and DO was observed and suggested active photosynthesis of the initial biomass in Subei Shoal. This study revealed specific distributional pattern and relationships among the floating macroalgae, micro-propagules and the environmental factors in the source region, which helps understanding the early blooming dynamics of the green tides in Yellow Sea.
bibliographic citation: Miao et al. (2020) Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea. PeerJ 8:e10538 https://doi.org/10.7717/peerj.10538
date submitted: 2020-07-16
date accepted: 2020-11-19
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miao
  given name: Xiaoxiang
author list: Agent
  family name: Xiao
  given name: Jie
author list: Agent
  family name: Xu
  given name: Qinzeng
author list: Agent
  family name: Fan
  given name: Shiliang
author list: Agent
  family name: Wang
  given name: Zongling
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Zhang
  given name: Xuelei
doi: 10.7717/peerj.10538
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: ©2020 Miao et al.
attribution name: Miao et al.

Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
type: item
type: AcademicArticle
description: Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region. Methods This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus. Results Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.
format: application/pdf
format: text/html
creator: J. Antonio Baeza
subject: Genetics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10554
publisher: PeerJ Inc.
rights: © 2020 Baeza
abstract: Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region. Methods This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus. Results Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.
bibliographic citation: Baeza (2020) Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery. PeerJ 8:e10554 https://doi.org/10.7717/peerj.10554
date submitted: 2020-09-29
date accepted: 2020-11-22
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baeza
  given name: J. Antonio
doi: 10.7717/peerj.10554
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: © 2020 Baeza
attribution name: Baeza

bmd: an R package for benchmark dose estimation
type: item
type: AcademicArticle
description: The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper’s objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R. It allows the rapid implementation of available, novel, and future statistical methods and the integration of other statistical analyses.
format: application/pdf
format: text/html
creator: Signe M. Jensen
creator: Felix M. Kluxen
creator: Jens C. Streibig
creator: Nina Cedergreen
creator: Christian Ritz
subject: Computational Biology
subject: Toxicology
subject: Statistics
subject: Computational Science
subject: Ecotoxicology
description: doi:10.7717/peerj.10557
publisher: PeerJ Inc.
rights: © 2020 Jensen et al.
abstract: The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper’s objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R. It allows the rapid implementation of available, novel, and future statistical methods and the integration of other statistical analyses.
bibliographic citation: Jensen et al. (2020) bmd: an R package for benchmark dose estimation. PeerJ 8:e10557 https://doi.org/10.7717/peerj.10557
date submitted: 2020-07-08
date accepted: 2020-11-22
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jensen
  given name: Signe M.
author list: Agent
  family name: Kluxen
  given name: Felix M.
author list: Agent
  family name: Streibig
  given name: Jens C.
author list: Agent
  family name: Cedergreen
  given name: Nina
author list: Agent
  family name: Ritz
  given name: Christian
doi: 10.7717/peerj.10557
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: ©2020 Jensen et al.
attribution name: Jensen et al.

Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas
type: item
type: AcademicArticle
description: Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
format: application/pdf
format: text/html
creator: Timothy P. Driscoll
creator: Victoria I. Verhoeve
creator: Cassia Brockway
creator: Darin L. Shrewsberry
creator: Mariah Plumer
creator: Spiridon E. Sevdalis
creator: John F. Beckmann
creator: Laura M. Krueger
creator: Kevin R. Macaluso
creator: Abdu F. Azad
creator: Joseph J. Gillespie
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10646
publisher: PeerJ Inc.
rights: © 2020 Driscoll et al.
abstract: Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
bibliographic citation: Driscoll et al. (2020) Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas. PeerJ 8:e10646 https://doi.org/10.7717/peerj.10646
date submitted: 2020-08-14
date accepted: 2020-12-03
issued: 2020-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Driscoll
  given name: Timothy P.
author list: Agent
  family name: Verhoeve
  given name: Victoria I.
author list: Agent
  family name: Brockway
  given name: Cassia
author list: Agent
  family name: Shrewsberry
  given name: Darin L.
author list: Agent
  family name: Plumer
  given name: Mariah
author list: Agent
  family name: Sevdalis
  given name: Spiridon E.
author list: Agent
  family name: Beckmann
  given name: John F.
author list: Agent
  family name: Krueger
  given name: Laura M.
author list: Agent
  family name: Macaluso
  given name: Kevin R.
author list: Agent
  family name: Azad
  given name: Abdu F.
author list: Agent
  family name: Gillespie
  given name: Joseph J.
doi: 10.7717/peerj.10646
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-17
copyright: © 2020 Driscoll et al.
attribution name: Driscoll et al.

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