PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Changing trends in elephant camp management in northern Thailand and implications for welfare
items: Optimal and near-optimal exponent-pairs for the Bertalanffy-Pütter growth model
items: Effects of a six-week weighted-implement throwing program on baseball pitching velocity, kinematics, arm stress, and arm range of motion
items: Morpho-histological development of the somatic embryos of Typha domingensis
items: Heavier- and lighter-load isolated lumbar extension resistance training produce similar strength increases, but different perceptual responses, in healthy males and females
items: Classification of the glioma grading using radiomics analysis
items: A new species of karst-dwelling freshwater crab of the genus Chinapotamon Dai & Naiyanetr, 1994 (Crustacea: Decapoda: Brachyura: Potamidae), from Guizhou, southwest China
items: A needle in a haystack: Mesozoic origin of parasitism in Strepsiptera revealed by first definite Cretaceous primary larva (Insecta)
items: Computer-aided autotransplantation of teeth with 3D printed surgical guides and arch bar: a preliminary experience
items: Identification of AaAtg8 as a marker of autophagy and a functional autophagy-related protein in Aedes albopictus

Changing trends in elephant camp management in northern Thailand and implications for welfare
type: item
type: AcademicArticle
description: Background Elephant camps are among the most attractive destinations in Thailand for tourists from many countries. A wide range of management strategies are used by these camps, which can have varied impacts on health and welfare of elephants. Methods This study surveyed 33 camps with 627 elephants in northern Thailand to quantify the types of management practices and work activities experienced by captive elephants. The survey consisted of an interview with camp owners, and direct observations of camp operations. Results Data revealed considerable variation in elephant demographics, work activities, elephant care (i.e., housing, restraint, nutrition, health care, and breeding), and mahout management among the camps. In general, older camps (those in existence for >16 years) were involved in more intensive activities, like riding with saddles and shows. By contrast, newer camps provided more one-on-one activities for tourists and elephants, and emphasized more intimate, relaxing experiences (e.g., feeding, bathing, walking) than entertainment. A demographic shift also was observed, with elephants 20 years of age and younger having a sex ratio closer to 1:1 compared to elephants in older age categories (1:4.1–1:9.8). Discussion Shifts in elephant management to less intensive activities were observed, which could have positive implications for elephant welfare. The shifting sex ratio suggests successful captive breeding is resulting in the birth of more males, which could present new welfare challenges in the future, because bulls can be more difficult to manage and socialize, and are more likely to be kept isolated during musth. Ultimately, the goal is to understand how camp activities affect welfare, and to develop science-based guidelines and standards to aid in the management of both male and female elephants used in tourism.
format: application/pdf
format: text/html
creator: Pakkanut Bansiddhi
creator: Janine L. Brown
creator: Chatchote Thitaram
creator: Veerasak Punyapornwithaya
creator: Chaleamchat Somgird
creator: Katie L. Edwards
creator: Korakot Nganvongpanit
subject: Agricultural Science
subject: Veterinary Medicine
subject: Coupled Natural and Human Systems
subject: Environmental Impacts
description: doi:10.7717/peerj.5996
publisher: PeerJ Inc.
rights: © 2018 Bansiddhi et al.
abstract: Background Elephant camps are among the most attractive destinations in Thailand for tourists from many countries. A wide range of management strategies are used by these camps, which can have varied impacts on health and welfare of elephants. Methods This study surveyed 33 camps with 627 elephants in northern Thailand to quantify the types of management practices and work activities experienced by captive elephants. The survey consisted of an interview with camp owners, and direct observations of camp operations. Results Data revealed considerable variation in elephant demographics, work activities, elephant care (i.e., housing, restraint, nutrition, health care, and breeding), and mahout management among the camps. In general, older camps (those in existence for >16 years) were involved in more intensive activities, like riding with saddles and shows. By contrast, newer camps provided more one-on-one activities for tourists and elephants, and emphasized more intimate, relaxing experiences (e.g., feeding, bathing, walking) than entertainment. A demographic shift also was observed, with elephants 20 years of age and younger having a sex ratio closer to 1:1 compared to elephants in older age categories (1:4.1–1:9.8). Discussion Shifts in elephant management to less intensive activities were observed, which could have positive implications for elephant welfare. The shifting sex ratio suggests successful captive breeding is resulting in the birth of more males, which could present new welfare challenges in the future, because bulls can be more difficult to manage and socialize, and are more likely to be kept isolated during musth. Ultimately, the goal is to understand how camp activities affect welfare, and to develop science-based guidelines and standards to aid in the management of both male and female elephants used in tourism.
bibliographic citation: Bansiddhi et al. (2018) Changing trends in elephant camp management in northern Thailand and implications for welfare. PeerJ 6:e5996 https://doi.org/10.7717/peerj.5996
date submitted: 2018-07-23
date accepted: 2018-10-25
issued: 2018-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bansiddhi
  given name: Pakkanut
author list: Agent
  family name: Brown
  given name: Janine L.
author list: Agent
  family name: Thitaram
  given name: Chatchote
author list: Agent
  family name: Punyapornwithaya
  given name: Veerasak
author list: Agent
  family name: Somgird
  given name: Chaleamchat
author list: Agent
  family name: Edwards
  given name: Katie L.
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
doi: 10.7717/peerj.5996
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-23
copyright: © 2018 Bansiddhi et al.
attribution name: Bansiddhi et al.

Optimal and near-optimal exponent-pairs for the Bertalanffy-Pütter growth model
type: item
type: AcademicArticle
description: The Bertalanffy–Pütter growth model describes mass m at age t by means of the differential equation dm/dt = p * ma − q * mb. The special case using the von Bertalanffy exponent-pair a = 2/3 and b = 1 is most common (it corresponds to the von Bertalanffy growth function VBGF for length in fishery literature). Fitting VBGF to size-at-age data requires the optimization of three model parameters (the constants p, q, and an initial value for the differential equation). For the general Bertalanffy–Pütter model, two more model parameters are optimized (the pair a < b of non-negative exponents). While this reduces bias in growth estimates, it increases model complexity and more advanced optimization methods are needed, such as the Nelder–Mead amoeba method, interior point methods, or simulated annealing. Is the improved performance worth these efforts? For the case, where the exponent b = 1 remains fixed, it is known that for most fish data any exponent a < 1 could be used to model growth without affecting the fit to the data significantly (when the other parameters were optimized). We hypothesized that the optimization of both exponents would result in a significantly better fit of the optimal growth function to the data and we tested this conjecture for a data set (20,166 fish) about the mass-growth of Walleye (Sander vitreus), a fish from Lake Erie, USA. To this end, we assessed the fit on a grid of 14,281 exponent-pairs (a, b) and identified the best fitting model curve on the boundary a = b of the grid (a = b = 0.686); it corresponds to the generalized Gompertz equation dm/dt = p * ma − q * ln(m) * ma. Using the Akaike information criterion for model selection, the answer to the conjecture was no: The von Bertalanffy exponent-pair model (but not the logistic model) remained parsimonious. However, the bias reduction attained by the optimal exponent-pair may be worth the tradeoff with complexity in some situations where predictive power is solely preferred. Therefore, we…
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format: text/html
creator: Katharina Renner-Martin
creator: Norbert Brunner
creator: Manfred Kühleitner
creator: Werner-Georg Nowak
creator: Klaus Scheicher
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Biology
subject: Mathematical Biology
subject: Computational Science
subject: Natural Resource Management
description: doi:10.7717/peerj.5973
publisher: PeerJ Inc.
rights: © 2018 Renner-Martin et al.
abstract: The Bertalanffy–Pütter growth model describes mass m at age t by means of the differential equation dm/dt = p * ma − q * mb. The special case using the von Bertalanffy exponent-pair a = 2/3 and b = 1 is most common (it corresponds to the von Bertalanffy growth function VBGF for length in fishery literature). Fitting VBGF to size-at-age data requires the optimization of three model parameters (the constants p, q, and an initial value for the differential equation). For the general Bertalanffy–Pütter model, two more model parameters are optimized (the pair a < b of non-negative exponents). While this reduces bias in growth estimates, it increases model complexity and more advanced optimization methods are needed, such as the Nelder–Mead amoeba method, interior point methods, or simulated annealing. Is the improved performance worth these efforts? For the case, where the exponent b = 1 remains fixed, it is known that for most fish data any exponent a < 1 could be used to model growth without affecting the fit to the data significantly (when the other parameters were optimized). We hypothesized that the optimization of both exponents would result in a significantly better fit of the optimal growth function to the data and we tested this conjecture for a data set (20,166 fish) about the mass-growth of Walleye (Sander vitreus), a fish from Lake Erie, USA. To this end, we assessed the fit on a grid of 14,281 exponent-pairs (a, b) and identified the best fitting model curve on the boundary a = b of the grid (a = b = 0.686); it corresponds to the generalized Gompertz equation dm/dt = p * ma − q * ln(m) * ma. Using the Akaike information criterion for model selection, the answer to the conjecture was no: The von Bertalanffy exponent-pair model (but not the logistic model) remained parsimonious. However, the bias reduction attained by the optimal exponent-pair may be worth the tradeoff with complexity in some situations where predictive power is solely preferred. Therefore, we…
bibliographic citation: Renner-Martin et al. (2018) Optimal and near-optimal exponent-pairs for the Bertalanffy-Pütter growth model. PeerJ 6:e5973 https://doi.org/10.7717/peerj.5973
date submitted: 2018-08-24
date accepted: 2018-10-19
issued: 2018-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Renner-Martin
  given name: Katharina
author list: Agent
  family name: Brunner
  given name: Norbert
author list: Agent
  family name: Kühleitner
  given name: Manfred
author list: Agent
  family name: Nowak
  given name: Werner-Georg
author list: Agent
  family name: Scheicher
  given name: Klaus
doi: 10.7717/peerj.5973
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-23
copyright: © 2018 Renner-Martin et al.
attribution name: Renner-Martin et al.

Effects of a six-week weighted-implement throwing program on baseball pitching velocity, kinematics, arm stress, and arm range of motion
type: item
type: AcademicArticle
description: Background Weighted-baseball training programs are used at the high school, collegiate, and professional levels of baseball. The purpose of this study was to evaluate the effects of a six-week training period consisting of weighted implements, manual therapy, weightlifting, and other modalities on shoulder external rotation, elbow valgus stress, pitching velocity, and kinematics. Hypothesis A six-week training program that includes weighted implements will increase pitching velocity along with concomitant increases in arm angular velocities, joint kinetics, and shoulder external rotation. Methods Seventeen collegiate and professional baseball pitchers (age range 18–23, average: 19.9 ± 1.3) training at Driveline Baseball were evaluated via a combination of an eight-camera motion-capture system, range-of-motion measurements and radar- and pitch-tracking equipment, both before and after a six-week training period. Each participant received individualized training programs, with significant overlap in training methods for all athletes. Twenty-eight biomechanical parameters were computed for each bullpen trial, four arm range-of-motion measurements were taken, and pitching velocities were recorded before and after the training period. Pre- and post-training period data were compared via post-hoc paired t tests. Results There was no change in pitching velocity across the seventeen subjects. Four biomechanical parameters for the holistic group were significantly changed after the training period: internal rotational velocity was higher (from 4,527 ± 470 to 4,759 ± 542 degrees/second), shoulder abduction was lower at ball release (96 ± 7.6 to 93 ± 5.4°), the shoulder was less externally rotated at ball release (95 ± 15 to 86 ± 18°) and shoulder adduction torque was higher (from 103 ± 39 to 138 ± 53 N-m). Among the arm range of motion measurements, four were significantly different after the training period: the shoulder internal rotation range of motion and total range of m…
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format: text/html
creator: Joseph A. Marsh
creator: Matthew I. Wagshol
creator: Kyle J. Boddy
creator: Michael E. O’Connell
creator: Sam J. Briend
creator: Kyle E. Lindley
creator: Alex Caravan
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.6003
publisher: PeerJ Inc.
rights: © 2018 Marsh et al.
abstract: Background Weighted-baseball training programs are used at the high school, collegiate, and professional levels of baseball. The purpose of this study was to evaluate the effects of a six-week training period consisting of weighted implements, manual therapy, weightlifting, and other modalities on shoulder external rotation, elbow valgus stress, pitching velocity, and kinematics. Hypothesis A six-week training program that includes weighted implements will increase pitching velocity along with concomitant increases in arm angular velocities, joint kinetics, and shoulder external rotation. Methods Seventeen collegiate and professional baseball pitchers (age range 18–23, average: 19.9 ± 1.3) training at Driveline Baseball were evaluated via a combination of an eight-camera motion-capture system, range-of-motion measurements and radar- and pitch-tracking equipment, both before and after a six-week training period. Each participant received individualized training programs, with significant overlap in training methods for all athletes. Twenty-eight biomechanical parameters were computed for each bullpen trial, four arm range-of-motion measurements were taken, and pitching velocities were recorded before and after the training period. Pre- and post-training period data were compared via post-hoc paired t tests. Results There was no change in pitching velocity across the seventeen subjects. Four biomechanical parameters for the holistic group were significantly changed after the training period: internal rotational velocity was higher (from 4,527 ± 470 to 4,759 ± 542 degrees/second), shoulder abduction was lower at ball release (96 ± 7.6 to 93 ± 5.4°), the shoulder was less externally rotated at ball release (95 ± 15 to 86 ± 18°) and shoulder adduction torque was higher (from 103 ± 39 to 138 ± 53 N-m). Among the arm range of motion measurements, four were significantly different after the training period: the shoulder internal rotation range of motion and total range of m…
bibliographic citation: Marsh et al. (2018) Effects of a six-week weighted-implement throwing program on baseball pitching velocity, kinematics, arm stress, and arm range of motion. PeerJ 6:e6003 https://doi.org/10.7717/peerj.6003
date submitted: 2018-05-30
date accepted: 2018-10-25
issued: 2018-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marsh
  given name: Joseph A.
author list: Agent
  family name: Wagshol
  given name: Matthew I.
author list: Agent
  family name: Boddy
  given name: Kyle J.
author list: Agent
  family name: O’Connell
  given name: Michael E.
author list: Agent
  family name: Briend
  given name: Sam J.
author list: Agent
  family name: Lindley
  given name: Kyle E.
author list: Agent
  family name: Caravan
  given name: Alex
doi: 10.7717/peerj.6003
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-23
copyright: ©2018 Marsh et al.
attribution name: Marsh et al.

Morpho-histological development of the somatic embryos of Typha domingensis
type: item
type: AcademicArticle
description: Background Sustainable methods of propagation of Typha domingensis through somatic embryogenesis can help mitigate its current condition of ecological marginalization and overexploitation. This study examined whether differentiation up to coleoptilar embryos could be obtained in an embryogenic line proliferated with light and high auxin concentration. Methods Murashige and Skoog medium at half ionic strength and containing 3% sucrose and 0.1% ascorbic acid was used for the three embryogenic phases. Induction started with aseptic 9-day-old germinated seeds cultured in 0.5 mg L−1 2,4-dichlorophenoxyacetic (2,4-D). Proliferation of the embryogenic callus was evaluated at 2,4-D concentrations ranging from 0 to 2 mg L−1 in cultures maintained in the dark. The dominant embryogenic products obtained in each treatment were used as embryogenic lines in the third phase. Thus, maturation of the somatic embryos (SEs) was analyzed using four embryogenic lines and under light vs. dark conditions. Embryogenic differentiation was also monitored histologically. Results Proliferation of the nine morphogenetic products was greater in the presence of 2,4-D, regardless of the concentration, than in the absence of auxin. Among the products, a yellow callus was invariably associated with the presence of an oblong SE and suspended cells in the 2,4-D treatments, and a brown callus with scutellar somatic embryos (scSEs) in the treatment without 2,4-D. During the maturation phase, especially the embryogenic line but also the light condition resulted in significant differences, with the highest averages of the nine morphogenetic products obtained under light conditions and the maximum concentration of auxin (YC3 embryogenic line). Only this line achieved scSE growth, under both light and dark conditions. Structurally complete coleoptilar somatic embryos (colSEs) could be anatomically confirmed only during the maturation phase. Discussion In the embryogenic line cultured with the highest auxin …
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format: text/html
creator: Guadalupe Hernández-Piedra
creator: Violeta Ruiz-Carrera
creator: Alberto J. Sánchez
creator: Arlette Hernández-Franyutti
creator: Alfonso Azpeitia-Morales
subject: Biotechnology
subject: Developmental Biology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.5952
publisher: PeerJ Inc.
rights: © 2018 Hernández-Piedra et al.
abstract: Background Sustainable methods of propagation of Typha domingensis through somatic embryogenesis can help mitigate its current condition of ecological marginalization and overexploitation. This study examined whether differentiation up to coleoptilar embryos could be obtained in an embryogenic line proliferated with light and high auxin concentration. Methods Murashige and Skoog medium at half ionic strength and containing 3% sucrose and 0.1% ascorbic acid was used for the three embryogenic phases. Induction started with aseptic 9-day-old germinated seeds cultured in 0.5 mg L−1 2,4-dichlorophenoxyacetic (2,4-D). Proliferation of the embryogenic callus was evaluated at 2,4-D concentrations ranging from 0 to 2 mg L−1 in cultures maintained in the dark. The dominant embryogenic products obtained in each treatment were used as embryogenic lines in the third phase. Thus, maturation of the somatic embryos (SEs) was analyzed using four embryogenic lines and under light vs. dark conditions. Embryogenic differentiation was also monitored histologically. Results Proliferation of the nine morphogenetic products was greater in the presence of 2,4-D, regardless of the concentration, than in the absence of auxin. Among the products, a yellow callus was invariably associated with the presence of an oblong SE and suspended cells in the 2,4-D treatments, and a brown callus with scutellar somatic embryos (scSEs) in the treatment without 2,4-D. During the maturation phase, especially the embryogenic line but also the light condition resulted in significant differences, with the highest averages of the nine morphogenetic products obtained under light conditions and the maximum concentration of auxin (YC3 embryogenic line). Only this line achieved scSE growth, under both light and dark conditions. Structurally complete coleoptilar somatic embryos (colSEs) could be anatomically confirmed only during the maturation phase. Discussion In the embryogenic line cultured with the highest auxin …
bibliographic citation: Hernández-Piedra et al. (2018) Morpho-histological development of the somatic embryos of Typha domingensis. PeerJ 6:e5952 https://doi.org/10.7717/peerj.5952
date submitted: 2018-04-25
date accepted: 2018-10-18
issued: 2018-11-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Piedra
  given name: Guadalupe
author list: Agent
  family name: Ruiz-Carrera
  given name: Violeta
author list: Agent
  family name: Sánchez
  given name: Alberto J.
author list: Agent
  family name: Hernández-Franyutti
  given name: Arlette
author list: Agent
  family name: Azpeitia-Morales
  given name: Alfonso
doi: 10.7717/peerj.5952
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-23
copyright: © 2018 Hernández-Piedra et al.
attribution name: Hernández-Piedra et al.

Heavier- and lighter-load isolated lumbar extension resistance training produce similar strength increases, but different perceptual responses, in healthy males and females
type: item
type: AcademicArticle
description: Objectives Muscles dominant in type I muscle fibres, such as the lumbar extensors, are often trained using lighter loads and higher repetition ranges. However, literature suggests that similar strength adaptations can be attained by the use of both heavier- (HL) and lighter-load (LL) resistance training across a number of appendicular muscle groups. Furthermore, LL resistance exercise to momentary failure might result in greater discomfort. Design The aims of the present study were to compare strength adaptations, as well as perceptual responses of effort (RPE-E) and discomfort (RPE-D), to isolated lumbar extension (ILEX) exercise using HL (80% of maximum voluntary contraction; MVC) and LL (50% MVC) in healthy males and females. Methods Twenty-six participants (n = 14 males, n = 12 females) were divided in to sex counter-balanced HL (23 ± 5 years; 172.3 ± 9.8 cm; 71.0 ± 13.1 kg) and LL (22 ± 2 years; 175.3 ± 6.3 cm; 72.8 ± 9.5 kg) resistance training groups. All participants performed a single set of dynamic ILEX exercise 1 day/week for 6 weeks using either 80% (HL) or 50% (LL) of their MVC to momentary failure. Results Analyses revealed significant pre- to post-intervention increases in isometric strength for both HL and LL, with no significant between-group differences (p > 0.05). Changes in strength index (area under torque curves) were 2,891 Nm degrees 95% CIs [1,612–4,169] and 2,865 Nm degrees 95% CIs [1,587–4,144] for HL and LL respectively. Changes in MVC were 51.7 Nm 95% CIs [24.4–79.1] and 46.0 Nm 95% CIs [18.6–73.3] for HL and LL respectively. Mean repetitions per set, total training time and discomfort were all significantly higher for LL compared to HL (26 ± 8 vs. 8 ± 3 repetitions, 158.5 ± 47 vs. 50.5 ± 15 s, and 7.8 ± 1.8 vs. 4.8 ± 2.5, respectively; all p < 0.005). Conclusions The present study supports that that low-volume, low-frequency ILEX resistance exercise can produce similar strength increases in the lumbar extensors using either HL or LL. As …
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format: text/html
creator: James P. Fisher
creator: Charlotte Stuart
creator: James Steele
creator: Paulo Gentil
creator: Jürgen Giessing
subject: Anatomy and Physiology
subject: Evidence Based Medicine
subject: Health Policy
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.6001
publisher: PeerJ Inc.
rights: © 2018 Fisher et al.
abstract: Objectives Muscles dominant in type I muscle fibres, such as the lumbar extensors, are often trained using lighter loads and higher repetition ranges. However, literature suggests that similar strength adaptations can be attained by the use of both heavier- (HL) and lighter-load (LL) resistance training across a number of appendicular muscle groups. Furthermore, LL resistance exercise to momentary failure might result in greater discomfort. Design The aims of the present study were to compare strength adaptations, as well as perceptual responses of effort (RPE-E) and discomfort (RPE-D), to isolated lumbar extension (ILEX) exercise using HL (80% of maximum voluntary contraction; MVC) and LL (50% MVC) in healthy males and females. Methods Twenty-six participants (n = 14 males, n = 12 females) were divided in to sex counter-balanced HL (23 ± 5 years; 172.3 ± 9.8 cm; 71.0 ± 13.1 kg) and LL (22 ± 2 years; 175.3 ± 6.3 cm; 72.8 ± 9.5 kg) resistance training groups. All participants performed a single set of dynamic ILEX exercise 1 day/week for 6 weeks using either 80% (HL) or 50% (LL) of their MVC to momentary failure. Results Analyses revealed significant pre- to post-intervention increases in isometric strength for both HL and LL, with no significant between-group differences (p > 0.05). Changes in strength index (area under torque curves) were 2,891 Nm degrees 95% CIs [1,612–4,169] and 2,865 Nm degrees 95% CIs [1,587–4,144] for HL and LL respectively. Changes in MVC were 51.7 Nm 95% CIs [24.4–79.1] and 46.0 Nm 95% CIs [18.6–73.3] for HL and LL respectively. Mean repetitions per set, total training time and discomfort were all significantly higher for LL compared to HL (26 ± 8 vs. 8 ± 3 repetitions, 158.5 ± 47 vs. 50.5 ± 15 s, and 7.8 ± 1.8 vs. 4.8 ± 2.5, respectively; all p < 0.005). Conclusions The present study supports that that low-volume, low-frequency ILEX resistance exercise can produce similar strength increases in the lumbar extensors using either HL or LL. As …
bibliographic citation: Fisher et al. (2018) Heavier- and lighter-load isolated lumbar extension resistance training produce similar strength increases, but different perceptual responses, in healthy males and females. PeerJ 6:e6001 https://doi.org/10.7717/peerj.6001
date submitted: 2018-07-27
date accepted: 2018-10-23
issued: 2018-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fisher
  given name: James P.
author list: Agent
  family name: Stuart
  given name: Charlotte
author list: Agent
  family name: Steele
  given name: James
author list: Agent
  family name: Gentil
  given name: Paulo
author list: Agent
  family name: Giessing
  given name: Jürgen
doi: 10.7717/peerj.6001
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-22
copyright: ©2018 Fisher et al.
attribution name: Fisher et al.

Classification of the glioma grading using radiomics analysis
type: item
type: AcademicArticle
description: Background Grading of gliomas is critical information related to prognosis and survival. We aimed to apply a radiomics approach using various machine learning classifiers to determine the glioma grading. Methods We considered 285 (high grade n = 210, low grade n = 75) cases obtained from the Brain Tumor Segmentation 2017 Challenge. Manual annotations of enhancing tumors, non-enhancing tumors, necrosis, and edema were provided by the database. Each case was multi-modal with T1-weighted, T1-contrast enhanced, T2-weighted, and FLAIR images. A five-fold cross validation was adopted to separate the training and test data. A total of 468 radiomics features were calculated for three types of regions of interest. The minimum redundancy maximum relevance algorithm was used to select features useful for classifying glioma grades in the training cohort. The selected features were used to build three classifier models of logistics, support vector machines, and random forest classifiers. The classification performance of the models was measured in the training cohort using accuracy, sensitivity, specificity, and area under the curve (AUC) of the receiver operating characteristic curve. The trained classifier models were applied to the test cohort. Results Five significant features were selected for the machine learning classifiers and the three classifiers showed an average AUC of 0.9400 for training cohorts and 0.9030 (logistic regression 0.9010, support vector machine 0.8866, and random forest 0.9213) for test cohorts. Discussion Glioma grading could be accurately determined using machine learning and feature selection techniques in conjunction with a radiomics approach. The results of our study might contribute to high-throughput computer aided diagnosis system for gliomas.
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format: text/html
creator: Hwan-ho Cho
creator: Seung-hak Lee
creator: Jonghoon Kim
creator: Hyunjin Park
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.5982
publisher: PeerJ Inc.
rights: © 2018 Cho et al.
abstract: Background Grading of gliomas is critical information related to prognosis and survival. We aimed to apply a radiomics approach using various machine learning classifiers to determine the glioma grading. Methods We considered 285 (high grade n = 210, low grade n = 75) cases obtained from the Brain Tumor Segmentation 2017 Challenge. Manual annotations of enhancing tumors, non-enhancing tumors, necrosis, and edema were provided by the database. Each case was multi-modal with T1-weighted, T1-contrast enhanced, T2-weighted, and FLAIR images. A five-fold cross validation was adopted to separate the training and test data. A total of 468 radiomics features were calculated for three types of regions of interest. The minimum redundancy maximum relevance algorithm was used to select features useful for classifying glioma grades in the training cohort. The selected features were used to build three classifier models of logistics, support vector machines, and random forest classifiers. The classification performance of the models was measured in the training cohort using accuracy, sensitivity, specificity, and area under the curve (AUC) of the receiver operating characteristic curve. The trained classifier models were applied to the test cohort. Results Five significant features were selected for the machine learning classifiers and the three classifiers showed an average AUC of 0.9400 for training cohorts and 0.9030 (logistic regression 0.9010, support vector machine 0.8866, and random forest 0.9213) for test cohorts. Discussion Glioma grading could be accurately determined using machine learning and feature selection techniques in conjunction with a radiomics approach. The results of our study might contribute to high-throughput computer aided diagnosis system for gliomas.
bibliographic citation: Cho et al. (2018) Classification of the glioma grading using radiomics analysis. PeerJ 6:e5982 https://doi.org/10.7717/peerj.5982
date submitted: 2018-08-07
date accepted: 2018-10-22
issued: 2018-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Hwan-ho
author list: Agent
  family name: Lee
  given name: Seung-hak
author list: Agent
  family name: Kim
  given name: Jonghoon
author list: Agent
  family name: Park
  given name: Hyunjin
doi: 10.7717/peerj.5982
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-22
copyright: ©2018 Cho et al.
attribution name: Cho et al.

A new species of karst-dwelling freshwater crab of the genus Chinapotamon Dai & Naiyanetr, 1994 (Crustacea: Decapoda: Brachyura: Potamidae), from Guizhou, southwest China
type: item
type: AcademicArticle
description: Chinapotamon maolanense sp. n. from Maolan National Nature Reserve, Guizhou, southwest China, is described. C. maolanense sp. n. has diagnostic features of Chinapotamon, such as a slender and sinuous male first gonopod, prominently convex carapace, and one-third ratio of frons to carapace width. This new species can be distinguished from congeners by the combination of the following characters: relatively slender subterminal segment of the first gonopods, nearly oval-shaped carapace, anterolateral margin cristate of carapace and an oval-shaped gap between the fingers of the male major chela. In addition, we used a 16S rRNA gene fragment to explore the relationship between C. maolanense sp. n. and C. glabrum, C. depressum and other freshwater crabs distributed in Guizhou; the results support the new species being assigned to Chinapotamon and clearly different from other species used in the analysis.
format: application/pdf
format: text/html
creator: Jie-xin Zou
creator: Jun Bai
creator: Xian-min Zhou
subject: Aquaculture, Fisheries and Fish Science
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5947
publisher: PeerJ Inc.
rights: © 2018 Zou et al.
abstract: Chinapotamon maolanense sp. n. from Maolan National Nature Reserve, Guizhou, southwest China, is described. C. maolanense sp. n. has diagnostic features of Chinapotamon, such as a slender and sinuous male first gonopod, prominently convex carapace, and one-third ratio of frons to carapace width. This new species can be distinguished from congeners by the combination of the following characters: relatively slender subterminal segment of the first gonopods, nearly oval-shaped carapace, anterolateral margin cristate of carapace and an oval-shaped gap between the fingers of the male major chela. In addition, we used a 16S rRNA gene fragment to explore the relationship between C. maolanense sp. n. and C. glabrum, C. depressum and other freshwater crabs distributed in Guizhou; the results support the new species being assigned to Chinapotamon and clearly different from other species used in the analysis.
bibliographic citation: Zou et al. (2018) A new species of karst-dwelling freshwater crab of the genus Chinapotamon Dai & Naiyanetr, 1994 (Crustacea: Decapoda: Brachyura: Potamidae), from Guizhou, southwest China. PeerJ 6:e5947 https://doi.org/10.7717/peerj.5947
date submitted: 2018-04-24
date accepted: 2018-10-17
issued: 2018-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Jie-xin
author list: Agent
  family name: Bai
  given name: Jun
author list: Agent
  family name: Zhou
  given name: Xian-min
doi: 10.7717/peerj.5947
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-22
copyright: © 2018 Zou et al.
attribution name: Zou et al.

A needle in a haystack: Mesozoic origin of parasitism in Strepsiptera revealed by first definite Cretaceous primary larva (Insecta)
type: item
type: AcademicArticle
description: Twisted winged insects (Strepsiptera) are a highly specialized small order of parasitic insects. Whether parasitism developed at an early or late stage in the evolution of the group was unknown. Here we record and describe the first definite Mesozoic strepsipteran primary larva embedded in Burmese amber (∼99 million years ago). This extends the origin of parasitism back by at least ∼50 million years, and reveals that this specialized life style has evolved in the Mesozoic or even earlier in the group. The extremely small first instar displays all diagnostic characters of strepsipteran immatures of this stage and is nearly identical with those of Mengenillidae, one of the most “ancestral” extant strepsipteran taxa. This demonstrates a remarkable evolutionary stasis over 100 million years. The new finding strongly weakens the case of small larvae embedded in Cretaceous amber interpreted as strepsipteran immatures. They differ in many structural features from extant strepsipteran primary larvae and are very likely parasitic beetle larvae.
format: application/pdf
format: text/html
creator: Hans Pohl
creator: Jan Batelka
creator: Jakub Prokop
creator: Patrick Müller
creator: Margarita I. Yavorskaya
creator: Rolf G. Beutel
subject: Entomology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.5943
publisher: PeerJ Inc.
rights: © 2018 Pohl et al.
abstract: Twisted winged insects (Strepsiptera) are a highly specialized small order of parasitic insects. Whether parasitism developed at an early or late stage in the evolution of the group was unknown. Here we record and describe the first definite Mesozoic strepsipteran primary larva embedded in Burmese amber (∼99 million years ago). This extends the origin of parasitism back by at least ∼50 million years, and reveals that this specialized life style has evolved in the Mesozoic or even earlier in the group. The extremely small first instar displays all diagnostic characters of strepsipteran immatures of this stage and is nearly identical with those of Mengenillidae, one of the most “ancestral” extant strepsipteran taxa. This demonstrates a remarkable evolutionary stasis over 100 million years. The new finding strongly weakens the case of small larvae embedded in Cretaceous amber interpreted as strepsipteran immatures. They differ in many structural features from extant strepsipteran primary larvae and are very likely parasitic beetle larvae.
bibliographic citation: Pohl et al. (2018) A needle in a haystack: Mesozoic origin of parasitism in Strepsiptera revealed by first definite Cretaceous primary larva (Insecta). PeerJ 6:e5943 https://doi.org/10.7717/peerj.5943
date submitted: 2018-08-15
date accepted: 2018-10-10
issued: 2018-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pohl
  given name: Hans
author list: Agent
  family name: Batelka
  given name: Jan
author list: Agent
  family name: Prokop
  given name: Jakub
author list: Agent
  family name: Müller
  given name: Patrick
author list: Agent
  family name: Yavorskaya
  given name: Margarita I.
author list: Agent
  family name: Beutel
  given name: Rolf G.
doi: 10.7717/peerj.5943
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-22
copyright: ©2018 Pohl et al.
attribution name: Pohl et al.

Computer-aided autotransplantation of teeth with 3D printed surgical guides and arch bar: a preliminary experience
type: item
type: AcademicArticle
description: Background/Aim Autotransplantation of teeth is a method to restore the missing teeth and computer-aided techniques have been applied in this field. The aim of this study was to describe a novel approach for computer-aided autotransplantation of teeth and to preliminarily assess its feasibility, accuracy, and stability. Methods Eight wisdom teeth with complete root formation of eight adult patients were autotransplanted. Individual replicas of donor teeth with local splints, surgical templates, and arch bars were virtually designed and fabricated using three-dimensional printing, these were then applied in the autotransplantation surgeries. Clinical and radiological outcomes were observed, the extra-alveolar time, success rate, and 1-year survival rate were analyzed, and accuracy and stability of this approach were evaluated. Results The extra-alveolar time of donor teeth were less than 3 min. The average follow-up duration was 2.00 ± 1.06 years. All autotransplanted teeth showed normal masticatory function. Ankylosis was found in one patient, and the overall success rate was 87.5%, whereas the 1-year survival rate was 100%. Linear differences between the designed and the immediate autotransplanted positions at crowns and apexes of the donor teeth were 1.43 ± 0.57 and 1.77 ± 0.67 mm, respectively. Linear differences between immediate and the stable positions at crowns and apexes of the donor teeth were 0.66 ± 0.36 and 0.67 ± 0.48 mm, respectively. Conclusion The present study illustrated the feasibility, clinical satisfied accuracy, and stability of a novel approach for computer-aided autotransplantation of teeth. This new approach facilitated the surgical procedure and might be a viable and predictable method for autotransplantation of teeth.
format: application/pdf
format: text/html
creator: Wei He
creator: Kaiyue Tian
creator: Xiaoyan Xie
creator: Enbo Wang
creator: Nianhui Cui
subject: Dentistry
description: doi:10.7717/peerj.5939
publisher: PeerJ Inc.
rights: © 2018 He et al.
abstract: Background/Aim Autotransplantation of teeth is a method to restore the missing teeth and computer-aided techniques have been applied in this field. The aim of this study was to describe a novel approach for computer-aided autotransplantation of teeth and to preliminarily assess its feasibility, accuracy, and stability. Methods Eight wisdom teeth with complete root formation of eight adult patients were autotransplanted. Individual replicas of donor teeth with local splints, surgical templates, and arch bars were virtually designed and fabricated using three-dimensional printing, these were then applied in the autotransplantation surgeries. Clinical and radiological outcomes were observed, the extra-alveolar time, success rate, and 1-year survival rate were analyzed, and accuracy and stability of this approach were evaluated. Results The extra-alveolar time of donor teeth were less than 3 min. The average follow-up duration was 2.00 ± 1.06 years. All autotransplanted teeth showed normal masticatory function. Ankylosis was found in one patient, and the overall success rate was 87.5%, whereas the 1-year survival rate was 100%. Linear differences between the designed and the immediate autotransplanted positions at crowns and apexes of the donor teeth were 1.43 ± 0.57 and 1.77 ± 0.67 mm, respectively. Linear differences between immediate and the stable positions at crowns and apexes of the donor teeth were 0.66 ± 0.36 and 0.67 ± 0.48 mm, respectively. Conclusion The present study illustrated the feasibility, clinical satisfied accuracy, and stability of a novel approach for computer-aided autotransplantation of teeth. This new approach facilitated the surgical procedure and might be a viable and predictable method for autotransplantation of teeth.
bibliographic citation: He et al. (2018) Computer-aided autotransplantation of teeth with 3D printed surgical guides and arch bar: a preliminary experience. PeerJ 6:e5939 https://doi.org/10.7717/peerj.5939
date submitted: 2018-07-26
date accepted: 2018-10-16
issued: 2018-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Wei
author list: Agent
  family name: Tian
  given name: Kaiyue
author list: Agent
  family name: Xie
  given name: Xiaoyan
author list: Agent
  family name: Wang
  given name: Enbo
author list: Agent
  family name: Cui
  given name: Nianhui
doi: 10.7717/peerj.5939
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-22
copyright: © 2018 He et al.
attribution name: He et al.

Identification of AaAtg8 as a marker of autophagy and a functional autophagy-related protein in Aedes albopictus
type: item
type: AcademicArticle
description: Aedes albopictus is a primary vector of hundreds of pathogens. Strong environmental adaptability and extensive global distribution of Aedes albopictus make it a severe threat to human health. Autophagy is a cellular process involved in maintenance of cellular homeostasis and recirculation of cytoplasm to generate macromolecule constituents and energy under different stress conditions. Many autophagy-related (Atg) proteins have been identified in yeast and were found in various organisms subsequently, indicating that the basic mechanism of autophagy is well conserved in eukaryotes. Among all Atg proteins, Atg8 plays important roles in autophagy and is widely used as a marker to monitor autophagic activity in yeast, Drosophila, nematodes, zebrafish and mammals. By now, Atg proteins in Aedes albopictus have not been reported yet and the autophagy pathway in Aedes albopictus remains unclear. This study identified a homolog of Atg8 from Aedes albopictus and named it AaAtg8. Sequence analysis revealed that AaAtg8 was highly conserved in the Atg8 family. This work proved that AaAtg8 was a functional Atg protein of Aedes albopictus and expressed during developmental and adult stages of Aedes albopictus. Moreover, the study also established the basic methods for autophagy study in C6/36 cells. First, it was proved that both rapamycin and starvation were applicable ways to induce autophagy in C6/36 cells, and that 3-methyladenine and chloroquine could be used to inhibit early and late stages of autophagy in C6/36 cells, respectively. Second, the results in this study showed that monodansylcadaverine staining could be used to detect autophagy in C6/36 cells. Additionally, the study revealed that the level of autophagy in C6/36 cells could be monitored by the turnover assay of AaAtg8 or fluorescent AaAtg8. Taken together, this study identified AaAtg8, the first reported Atg protein in Aedes albopictus. It also provided useful methods for studying autophagy in Aedes albopictus. …
format: application/pdf
format: text/html
creator: Jialu Qiao
creator: Dandan Zhang
creator: Yu Wang
creator: Xiaomei Li
creator: Shengya Wang
creator: Qingzhen Liu
subject: Biochemistry
subject: Cell Biology
subject: Entomology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.5988
publisher: PeerJ Inc.
rights: © 2018 Qiao et al.
abstract: Aedes albopictus is a primary vector of hundreds of pathogens. Strong environmental adaptability and extensive global distribution of Aedes albopictus make it a severe threat to human health. Autophagy is a cellular process involved in maintenance of cellular homeostasis and recirculation of cytoplasm to generate macromolecule constituents and energy under different stress conditions. Many autophagy-related (Atg) proteins have been identified in yeast and were found in various organisms subsequently, indicating that the basic mechanism of autophagy is well conserved in eukaryotes. Among all Atg proteins, Atg8 plays important roles in autophagy and is widely used as a marker to monitor autophagic activity in yeast, Drosophila, nematodes, zebrafish and mammals. By now, Atg proteins in Aedes albopictus have not been reported yet and the autophagy pathway in Aedes albopictus remains unclear. This study identified a homolog of Atg8 from Aedes albopictus and named it AaAtg8. Sequence analysis revealed that AaAtg8 was highly conserved in the Atg8 family. This work proved that AaAtg8 was a functional Atg protein of Aedes albopictus and expressed during developmental and adult stages of Aedes albopictus. Moreover, the study also established the basic methods for autophagy study in C6/36 cells. First, it was proved that both rapamycin and starvation were applicable ways to induce autophagy in C6/36 cells, and that 3-methyladenine and chloroquine could be used to inhibit early and late stages of autophagy in C6/36 cells, respectively. Second, the results in this study showed that monodansylcadaverine staining could be used to detect autophagy in C6/36 cells. Additionally, the study revealed that the level of autophagy in C6/36 cells could be monitored by the turnover assay of AaAtg8 or fluorescent AaAtg8. Taken together, this study identified AaAtg8, the first reported Atg protein in Aedes albopictus. It also provided useful methods for studying autophagy in Aedes albopictus. …
bibliographic citation: Qiao et al. (2018) Identification of AaAtg8 as a marker of autophagy and a functional autophagy-related protein in Aedes albopictus. PeerJ 6:e5988 https://doi.org/10.7717/peerj.5988
date submitted: 2018-06-29
date accepted: 2018-10-23
issued: 2018-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiao
  given name: Jialu
author list: Agent
  family name: Zhang
  given name: Dandan
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Li
  given name: Xiaomei
author list: Agent
  family name: Wang
  given name: Shengya
author list: Agent
  family name: Liu
  given name: Qingzhen
doi: 10.7717/peerj.5988
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-21
copyright: ©2018 Qiao et al.
attribution name: Qiao et al.

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