PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
items: A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
items: Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
items: Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
items: Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery
items: Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management
items: Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks
items: The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study
items: GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
items: P-curve accurately rejects evidence for homeopathic ultramolecular dilutions

Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
type: item
type: AcademicArticle
description: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
format: application/pdf
format: text/html
creator: Tahneal Hawke
creator: Hayley Bates
creator: Suzanne Hand
creator: Michael Archer
creator: Linda Broome
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6307
publisher: PeerJ Inc.
rights: © 2019 Hawke et al.
abstract: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
bibliographic citation: Hawke et al. (2019) Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia. PeerJ 7:e6307 https://doi.org/10.7717/peerj.6307
date submitted: 2018-07-17
date accepted: 2018-12-18
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hawke
  given name: Tahneal
author list: Agent
  family name: Bates
  given name: Hayley
author list: Agent
  family name: Hand
  given name: Suzanne
author list: Agent
  family name: Archer
  given name: Michael
author list: Agent
  family name: Broome
  given name: Linda
doi: 10.7717/peerj.6307
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Hawke et al.
attribution name: Hawke et al.

A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
type: item
type: AcademicArticle
description: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
format: application/pdf
format: text/html
creator: Philip D. Mannion
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6348
publisher: PeerJ Inc.
rights: © 2019 Mannion
abstract: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
bibliographic citation: Mannion (2019) A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom. PeerJ 7:e6348 https://doi.org/10.7717/peerj.6348
date submitted: 2018-10-08
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannion
  given name: Philip D.
doi: 10.7717/peerj.6348
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Mannion
attribution name: Mannion

Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
type: item
type: AcademicArticle
description: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
format: application/pdf
format: text/html
creator: Jie Chen
creator: Chaofeng Xing
creator: Li Yan
creator: Yabing Wang
creator: Haosen Wang
creator: Zongmeng Zhang
creator: Daolun Yu
creator: Jie Li
creator: Honglin Li
creator: Jun Li
creator: Yafei Cai
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.6352
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
bibliographic citation: Chen et al. (2019) Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ 7:e6352 https://doi.org/10.7717/peerj.6352
date submitted: 2018-09-25
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Xing
  given name: Chaofeng
author list: Agent
  family name: Yan
  given name: Li
author list: Agent
  family name: Wang
  given name: Yabing
author list: Agent
  family name: Wang
  given name: Haosen
author list: Agent
  family name: Zhang
  given name: Zongmeng
author list: Agent
  family name: Yu
  given name: Daolun
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Li
  given name: Honglin
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Cai
  given name: Yafei
doi: 10.7717/peerj.6352
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
type: item
type: AcademicArticle
description: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
format: application/pdf
format: text/html
creator: Ji Qing
creator: Wang Dawei
creator: Zhou Jun
creator: Xu Yulan
creator: Shen Bingqi
creator: Zhou Fan
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6353
publisher: PeerJ Inc.
rights: © 2019 Qing et al.
abstract: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
bibliographic citation: Qing et al. (2019) Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PeerJ 7:e6353 https://doi.org/10.7717/peerj.6353
date submitted: 2018-10-16
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qing
  given name: Ji
author list: Agent
  family name: Dawei
  given name: Wang
author list: Agent
  family name: Jun
  given name: Zhou
author list: Agent
  family name: Yulan
  given name: Xu
author list: Agent
  family name: Bingqi
  given name: Shen
author list: Agent
  family name: Fan
  given name: Zhou
doi: 10.7717/peerj.6353
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Qing et al.
attribution name: Qing et al.

Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery
type: item
type: AcademicArticle
description: Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/…
format: application/pdf
format: text/html
creator: Kyle J. Boddy
creator: Joseph A. Marsh
creator: Alex Caravan
creator: Kyle E. Lindley
creator: John O. Scheffey
creator: Michael E. O’Connell
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.6365
publisher: PeerJ Inc.
rights: © 2019 Boddy et al.
abstract: Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/…
bibliographic citation: Boddy et al. (2019) Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery. PeerJ 7:e6365 https://doi.org/10.7717/peerj.6365
date submitted: 2018-07-10
date accepted: 2018-12-30
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boddy
  given name: Kyle J.
author list: Agent
  family name: Marsh
  given name: Joseph A.
author list: Agent
  family name: Caravan
  given name: Alex
author list: Agent
  family name: Lindley
  given name: Kyle E.
author list: Agent
  family name: Scheffey
  given name: John O.
author list: Agent
  family name: O’Connell
  given name: Michael E.
doi: 10.7717/peerj.6365
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Boddy et al.
attribution name: Boddy et al.

Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management
type: item
type: AcademicArticle
description: Background The red swamp crayfish, Procambarus clarkii (Girard, 1852), is one of the most promising freshwater species for aquaculture in China. Understanding its reproductive pattern and population dynamics is crucial for sustainable management, but there is currently a lack of fundamental knowledge of commercial P. clarkii populations. Therefore, the purpose of this study was to investigate the reproductive pattern and population dynamics of commercial P. clarkii throughout the yearly cycle. Methods A total of 2,051 crayfish (1,012 females and 1,039 males) were collected from March 2016 to February 2017 in the area of Selection and Reproduction Center of Crayfish. The reproductive pattern was evaluated by the gonadosomatic index (GSI), hepatosomatic index (HSI), ovarian development and fecundity. Growth, mortality rates and exploitation rate were estimated by electronic length frequency analysis by R package “TropFishR” based on data of cephalothorax length (CTL). Results Our results demonstrated that spawning activities of P. clarkii took place from September to November, with a mean fecundity of 429 ± 9 eggs per female. There were two recruitments yearly, a major one from October to November and a minor one from March to May. With respect to population growth, five growth cohorts were identified for both females and males. Crayfish grew faster but attained smaller asymptotic maximum CTL as indicated by higher growth coefficient (K), growth parameter index (Ø′) and lower asymptotic CTL (Linf). The estimates of total mortality rate (Z), natural mortality rate (M) and fishing mortality rate (F) were 1.93, 1.02, 0.91 year−1 for females and 2.32, 0.93, 1.39 year−1 for males, which showed that the mortality of male crayfish was mainly caused by fishing. The estimates of exploitation rate (E) indicated that male crayfish were overexploited, with the values of 0.47 and 0.60 year−1 for females and males, respectively. Discussion P. clarkii spawned from September to Novem…
format: application/pdf
format: text/html
creator: Shiyu Jin
creator: Lisa Jacquin
creator: Mantang Xiong
creator: Ruojing Li
creator: Sovan Lek
creator: Wei Li
creator: Tanglin Zhang
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6214
publisher: PeerJ Inc.
rights: © 2019 Jin et al.
abstract: Background The red swamp crayfish, Procambarus clarkii (Girard, 1852), is one of the most promising freshwater species for aquaculture in China. Understanding its reproductive pattern and population dynamics is crucial for sustainable management, but there is currently a lack of fundamental knowledge of commercial P. clarkii populations. Therefore, the purpose of this study was to investigate the reproductive pattern and population dynamics of commercial P. clarkii throughout the yearly cycle. Methods A total of 2,051 crayfish (1,012 females and 1,039 males) were collected from March 2016 to February 2017 in the area of Selection and Reproduction Center of Crayfish. The reproductive pattern was evaluated by the gonadosomatic index (GSI), hepatosomatic index (HSI), ovarian development and fecundity. Growth, mortality rates and exploitation rate were estimated by electronic length frequency analysis by R package “TropFishR” based on data of cephalothorax length (CTL). Results Our results demonstrated that spawning activities of P. clarkii took place from September to November, with a mean fecundity of 429 ± 9 eggs per female. There were two recruitments yearly, a major one from October to November and a minor one from March to May. With respect to population growth, five growth cohorts were identified for both females and males. Crayfish grew faster but attained smaller asymptotic maximum CTL as indicated by higher growth coefficient (K), growth parameter index (Ø′) and lower asymptotic CTL (Linf). The estimates of total mortality rate (Z), natural mortality rate (M) and fishing mortality rate (F) were 1.93, 1.02, 0.91 year−1 for females and 2.32, 0.93, 1.39 year−1 for males, which showed that the mortality of male crayfish was mainly caused by fishing. The estimates of exploitation rate (E) indicated that male crayfish were overexploited, with the values of 0.47 and 0.60 year−1 for females and males, respectively. Discussion P. clarkii spawned from September to Novem…
bibliographic citation: Jin et al. (2019) Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management. PeerJ 7:e6214 https://doi.org/10.7717/peerj.6214
date submitted: 2018-09-21
date accepted: 2018-12-04
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Shiyu
author list: Agent
  family name: Jacquin
  given name: Lisa
author list: Agent
  family name: Xiong
  given name: Mantang
author list: Agent
  family name: Li
  given name: Ruojing
author list: Agent
  family name: Lek
  given name: Sovan
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Tanglin
doi: 10.7717/peerj.6214
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Jin et al.
attribution name: Jin et al.

Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks
type: item
type: AcademicArticle
description: Purpose Myopia (short-sightedness) is the commonest visual disorder and greatest risk factor for sight threatening secondary pathologies. Myopia and hyperopia can be induced in animal models by rearing with optical lens defocus of opposite sign. The degree of refractive compensation to lens-induced defocus in chicks has been shown to be modified by directionally drifting sawtooth spatio-temporal luminance diamond plaids, with Fast-ON sawtooth spatio-temporal luminance profiles inhibiting the myopic shift in response to negative lenses, and Fast-OFF profiles inhibiting the hyperopic shift in response to positive lenses. What is unknown is whether similar sign-of-defocus dependent results produced by spatio-temporal modulation of sawtooth patterns could be achieved by rearing chicks under whole field low temporal frequency sawtooth luminance profiles at 1 or 4 Hz without a spatial component, or whether such stimuli would indiscriminately elicit a myopic shift such as that previously shown with symmetrical (or near-symmetrical) low frequency flicker across a range of species. Methods Hatchling chicks (n = 166) were reared from days five to nine under one of three defocus conditions (No Lens, +10D lens, or −10D lens) and five light conditions (No Flicker, 1 Hz Fast-ON/Slow-OFF sawtooth flicker, 4 Hz Fast-ON/Slow-OFF sawtooth flicker, 1 Hz Fast-OFF/Slow-ON sawtooth flicker, or 4Hz Fast-OFF/Slow-ON sawtooth flicker). The sawtooth flicker was produced by light emitting diodes (white LEDs, 1.2 –183 Lux), and had no measurable dark phase. Biometrics (refraction and ocular axial dimensions) were measured on day nine. Results Both 1 Hz and 4 Hz Fast-ON and Fast-OFF sawtooth flicker induced an increase in vitreous chamber depth that was greater in the presence of negative compared to positive lens defocus. Both sawtooth profiles at both temporal frequencies inhibited the hyperopic shift in response to +10D lenses, whilst full myopic compensation (or over-compensation) in respon…
format: application/pdf
format: text/html
creator: Melanie J. Murphy
creator: Nina Riddell
creator: David P. Crewther
creator: David Simpson
creator: Sheila G. Crewther
subject: Neuroscience
subject: Ophthalmology
description: doi:10.7717/peerj.6277
publisher: PeerJ Inc.
rights: © 2019 Murphy et al.
abstract: Purpose Myopia (short-sightedness) is the commonest visual disorder and greatest risk factor for sight threatening secondary pathologies. Myopia and hyperopia can be induced in animal models by rearing with optical lens defocus of opposite sign. The degree of refractive compensation to lens-induced defocus in chicks has been shown to be modified by directionally drifting sawtooth spatio-temporal luminance diamond plaids, with Fast-ON sawtooth spatio-temporal luminance profiles inhibiting the myopic shift in response to negative lenses, and Fast-OFF profiles inhibiting the hyperopic shift in response to positive lenses. What is unknown is whether similar sign-of-defocus dependent results produced by spatio-temporal modulation of sawtooth patterns could be achieved by rearing chicks under whole field low temporal frequency sawtooth luminance profiles at 1 or 4 Hz without a spatial component, or whether such stimuli would indiscriminately elicit a myopic shift such as that previously shown with symmetrical (or near-symmetrical) low frequency flicker across a range of species. Methods Hatchling chicks (n = 166) were reared from days five to nine under one of three defocus conditions (No Lens, +10D lens, or −10D lens) and five light conditions (No Flicker, 1 Hz Fast-ON/Slow-OFF sawtooth flicker, 4 Hz Fast-ON/Slow-OFF sawtooth flicker, 1 Hz Fast-OFF/Slow-ON sawtooth flicker, or 4Hz Fast-OFF/Slow-ON sawtooth flicker). The sawtooth flicker was produced by light emitting diodes (white LEDs, 1.2 –183 Lux), and had no measurable dark phase. Biometrics (refraction and ocular axial dimensions) were measured on day nine. Results Both 1 Hz and 4 Hz Fast-ON and Fast-OFF sawtooth flicker induced an increase in vitreous chamber depth that was greater in the presence of negative compared to positive lens defocus. Both sawtooth profiles at both temporal frequencies inhibited the hyperopic shift in response to +10D lenses, whilst full myopic compensation (or over-compensation) in respon…
bibliographic citation: Murphy et al. (2019) Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks. PeerJ 7:e6277 https://doi.org/10.7717/peerj.6277
date submitted: 2018-03-12
date accepted: 2018-12-11
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murphy
  given name: Melanie J.
author list: Agent
  family name: Riddell
  given name: Nina
author list: Agent
  family name: Crewther
  given name: David P.
author list: Agent
  family name: Simpson
  given name: David
author list: Agent
  family name: Crewther
  given name: Sheila G.
doi: 10.7717/peerj.6277
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Murphy et al.
attribution name: Murphy et al.

The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study
type: item
type: AcademicArticle
description: Objective In evidence synthesis practice, dealing with binary rare adverse events (AEs) is a challenging problem. The pooled estimates for rare AEs through traditional inverse variance (IV), Mantel-Haenszel (MH), and Yusuf-Peto (Peto) methods are suboptimal, as the biases tend to be large. We proposed the “one-stage” approach based on multilevel variance component logistic regression (MVCL) to handle this problem. Methods We used simulations to generate trials of individual participant data (IPD) with a series of predefined parameters. We compared the performance of the MVCL “one-stage” approach and the five classical methods (fixed/random effect IV, fixed/random effect MH, and Peto) for rare binary AEs under different scenarios, which included different sample size setting rules, effect sizes, between-study heterogeneity, and numbers of studies in each meta-analysis. The percentage bias, mean square error (MSE), coverage probability, and average width of the 95% confidence intervals were used as performance indicators. Results We set 52 scenarios and each scenario was simulated 1,000 times. Under the rule of three (a sample size setting rule to ensure a 95% chance of detecting at least one AE case), the MVCL “one-stage” IPD method had the lowest percentage bias in most of the situations and the bias remained at a very low level (<10%), when compared to IV, MH, and Peto methods. In addition, the MVCL “one-stage” IPD method generally had the lowest MSE and the narrowest average width of 95% confidence intervals. However, it did not show better coverage probability over the other five methods. Conclusions The MVCL “one-stage” IPD meta-analysis is a useful method to handle binary rare events and superior compared to traditional methods under the rule of three. Further meta-analyses may take account of the “one-stage” IPD method for pooling rare event data.
format: application/pdf
format: text/html
creator: Liang-Liang Cheng
creator: Ke Ju
creator: Rui-Lie Cai
creator: Chang Xu
subject: Clinical Trials
subject: Epidemiology
subject: Evidence Based Medicine
subject: Statistics
description: doi:10.7717/peerj.6295
publisher: PeerJ Inc.
rights: © 2019 Cheng et al.
abstract: Objective In evidence synthesis practice, dealing with binary rare adverse events (AEs) is a challenging problem. The pooled estimates for rare AEs through traditional inverse variance (IV), Mantel-Haenszel (MH), and Yusuf-Peto (Peto) methods are suboptimal, as the biases tend to be large. We proposed the “one-stage” approach based on multilevel variance component logistic regression (MVCL) to handle this problem. Methods We used simulations to generate trials of individual participant data (IPD) with a series of predefined parameters. We compared the performance of the MVCL “one-stage” approach and the five classical methods (fixed/random effect IV, fixed/random effect MH, and Peto) for rare binary AEs under different scenarios, which included different sample size setting rules, effect sizes, between-study heterogeneity, and numbers of studies in each meta-analysis. The percentage bias, mean square error (MSE), coverage probability, and average width of the 95% confidence intervals were used as performance indicators. Results We set 52 scenarios and each scenario was simulated 1,000 times. Under the rule of three (a sample size setting rule to ensure a 95% chance of detecting at least one AE case), the MVCL “one-stage” IPD method had the lowest percentage bias in most of the situations and the bias remained at a very low level (<10%), when compared to IV, MH, and Peto methods. In addition, the MVCL “one-stage” IPD method generally had the lowest MSE and the narrowest average width of 95% confidence intervals. However, it did not show better coverage probability over the other five methods. Conclusions The MVCL “one-stage” IPD meta-analysis is a useful method to handle binary rare events and superior compared to traditional methods under the rule of three. Further meta-analyses may take account of the “one-stage” IPD method for pooling rare event data.
bibliographic citation: Cheng et al. (2019) The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study. PeerJ 7:e6295 https://doi.org/10.7717/peerj.6295
date submitted: 2018-07-02
date accepted: 2018-12-15
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Liang-Liang
author list: Agent
  family name: Ju
  given name: Ke
author list: Agent
  family name: Cai
  given name: Rui-Lie
author list: Agent
  family name: Xu
  given name: Chang
doi: 10.7717/peerj.6295
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: © 2019 Cheng et al.
attribution name: Cheng et al.

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
type: item
type: AcademicArticle
description: Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.
format: application/pdf
format: text/html
creator: Yafei Mao
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6303
publisher: PeerJ Inc.
rights: © 2019 Mao
abstract: Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.
bibliographic citation: Mao (2019) GenoDup Pipeline: a tool to detect genome duplication using the dS-based method. PeerJ 7:e6303 https://doi.org/10.7717/peerj.6303
date submitted: 2018-10-05
date accepted: 2018-12-16
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Yafei
doi: 10.7717/peerj.6303
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Mao
attribution name: Mao

P-curve accurately rejects evidence for homeopathic ultramolecular dilutions
type: item
type: AcademicArticle
description: Background P-curve has been proposed as a statistical test of evidential value. The distributions of sets of statistically significant p-values are tested for skewness. P-curves of true effects are right-skewed, with greater density at lower p-values than higher p-values. Analyses of null effects result in a flat or left-skewed distribution. The accuracy of p-curve has not been tested using published research analyses of a null effect. We examined whether p-curve accurately rejects a set of significant p-values obtained for a nonexistent effect. Methods Homeopathic ultramolecular dilutions are medicinal preparations with active substances diluted beyond Avogadro’s number. Such dilute mixtures are unlikely to contain a single molecule of an active substance. We tested whether p-curve accurately rejects the evidential value of significant results obtained in placebo-controlled clinical trials of homeopathic ultramolecular dilutions. Results P-curve accurately rejected the evidential value of significant results obtained in placebo-controlled clinical trials of ultramolecular dilutions. Robustness testing using alternate p-values yielded similar results. Conclusion Our results suggest that p-curve can accurately detect when sets of statistically significant results lack evidential value.
format: application/pdf
format: text/html
creator: Samuel Reisman
creator: Mostafa Balboul
creator: Tashzna Jones
subject: Science Policy
subject: Statistics
description: doi:10.7717/peerj.6318
publisher: PeerJ Inc.
rights: © 2019 Reisman et al.
abstract: Background P-curve has been proposed as a statistical test of evidential value. The distributions of sets of statistically significant p-values are tested for skewness. P-curves of true effects are right-skewed, with greater density at lower p-values than higher p-values. Analyses of null effects result in a flat or left-skewed distribution. The accuracy of p-curve has not been tested using published research analyses of a null effect. We examined whether p-curve accurately rejects a set of significant p-values obtained for a nonexistent effect. Methods Homeopathic ultramolecular dilutions are medicinal preparations with active substances diluted beyond Avogadro’s number. Such dilute mixtures are unlikely to contain a single molecule of an active substance. We tested whether p-curve accurately rejects the evidential value of significant results obtained in placebo-controlled clinical trials of homeopathic ultramolecular dilutions. Results P-curve accurately rejected the evidential value of significant results obtained in placebo-controlled clinical trials of ultramolecular dilutions. Robustness testing using alternate p-values yielded similar results. Conclusion Our results suggest that p-curve can accurately detect when sets of statistically significant results lack evidential value.
bibliographic citation: Reisman et al. (2019) P-curve accurately rejects evidence for homeopathic ultramolecular dilutions. PeerJ 7:e6318 https://doi.org/10.7717/peerj.6318
date submitted: 2018-10-12
date accepted: 2018-12-16
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reisman
  given name: Samuel
author list: Agent
  family name: Balboul
  given name: Mostafa
author list: Agent
  family name: Jones
  given name: Tashzna
doi: 10.7717/peerj.6318
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Reisman et al.
attribution name: Reisman et al.

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