PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA
items: Organ health and development in larval kingfish are unaffected by ocean acidification and warming
items: Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns
items: Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands
items: Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods
items: The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study
items: Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles
items: Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania)
items: Identification of miRNA precursors in the phloem of Cucurbita maxima
items: The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer

Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA
type: item
type: AcademicArticle
description: Water pollution has been hindering the world’s sustainable development. The accurate inversion of water quality parameters in sewage with visible-near infrared spectroscopy can improve the effectiveness and rational utilization and management of water resources. However, the accuracy of spectral models of water quality parameters is usually prone to noise information and high dimensionality of spectral data. This study aimed to enhance the model accuracy through optimizing the spectral models based on the sensitive spectral intervals of different water quality parameters. To this end, six kinds of sewage water taken from a biological sewage treatment plant went through laboratory physical and chemical tests. In total, 87 samples of sewage water were obtained by adding different amount of pure water to them. The raw reflectance (Rraw) of the samples were collected with analytical spectral devices. The Rraw-SNV were obtained from the Rraw processed with the standard normal variable. Then, the sensitive spectral intervals of each of the six water quality parameters, namely, chemical oxygen demand (COD), biological oxygen demand (BOD), NH3-N, the total dissolved substances (TDS), total hardness (TH) and total alkalinity (TA), were selected using three different methods: gray correlation (GC), variable importance in projection (VIP) and set pair analysis (SPA). Finally, the performance of both extreme learning machine (ELM) and partial least squares regression (PLSR) was investigated based on the sensitive spectral intervals. The results demonstrated that the model accuracy based on the sensitive spectral ranges screened through different methods appeared different. The GC method had better performance in reducing the redundancy and the VIP method was better in information preservation. The SPA method could make the optimal trade-offs between information preservation and redundancy reduction and it could retain maximal spectral band intervals with good response to the in…
format: application/pdf
format: text/html
creator: Zheng Xing
creator: Junying Chen
creator: Xiao Zhao
creator: Yu Li
creator: Xianwen Li
creator: Zhitao Zhang
creator: Congcong Lao
creator: Haifeng Wang
subject: Agricultural Science
subject: Biochemistry
subject: Computational Science
subject: Ecohydrology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8255
publisher: PeerJ Inc.
rights: © 2019 Xing et al.
abstract: Water pollution has been hindering the world’s sustainable development. The accurate inversion of water quality parameters in sewage with visible-near infrared spectroscopy can improve the effectiveness and rational utilization and management of water resources. However, the accuracy of spectral models of water quality parameters is usually prone to noise information and high dimensionality of spectral data. This study aimed to enhance the model accuracy through optimizing the spectral models based on the sensitive spectral intervals of different water quality parameters. To this end, six kinds of sewage water taken from a biological sewage treatment plant went through laboratory physical and chemical tests. In total, 87 samples of sewage water were obtained by adding different amount of pure water to them. The raw reflectance (Rraw) of the samples were collected with analytical spectral devices. The Rraw-SNV were obtained from the Rraw processed with the standard normal variable. Then, the sensitive spectral intervals of each of the six water quality parameters, namely, chemical oxygen demand (COD), biological oxygen demand (BOD), NH3-N, the total dissolved substances (TDS), total hardness (TH) and total alkalinity (TA), were selected using three different methods: gray correlation (GC), variable importance in projection (VIP) and set pair analysis (SPA). Finally, the performance of both extreme learning machine (ELM) and partial least squares regression (PLSR) was investigated based on the sensitive spectral intervals. The results demonstrated that the model accuracy based on the sensitive spectral ranges screened through different methods appeared different. The GC method had better performance in reducing the redundancy and the VIP method was better in information preservation. The SPA method could make the optimal trade-offs between information preservation and redundancy reduction and it could retain maximal spectral band intervals with good response to the in…
bibliographic citation: Xing et al. (2019) Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA. PeerJ 7:e8255 https://doi.org/10.7717/peerj.8255
date submitted: 2019-07-31
date accepted: 2019-11-20
issued: 2019-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Zheng
author list: Agent
  family name: Chen
  given name: Junying
author list: Agent
  family name: Zhao
  given name: Xiao
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Li
  given name: Xianwen
author list: Agent
  family name: Zhang
  given name: Zhitao
author list: Agent
  family name: Lao
  given name: Congcong
author list: Agent
  family name: Wang
  given name: Haifeng
doi: 10.7717/peerj.8255
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-12
copyright: © 2019 Xing et al.
attribution name: Xing et al.

Organ health and development in larval kingfish are unaffected by ocean acidification and warming
type: item
type: AcademicArticle
description: Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification.
format: application/pdf
format: text/html
creator: Andrea Y. Frommel
creator: Colin J. Brauner
creator: Bridie J.M. Allan
creator: Simon Nicol
creator: Darren M. Parsons
creator: Steve M.J. Pether
creator: Alvin N. Setiawan
creator: Neville Smith
creator: Philip L. Munday
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Histology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.8266
publisher: PeerJ Inc.
rights: © 2019 Frommel et al.
abstract: Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification.
bibliographic citation: Frommel et al. (2019) Organ health and development in larval kingfish are unaffected by ocean acidification and warming. PeerJ 7:e8266 https://doi.org/10.7717/peerj.8266
date submitted: 2019-08-15
date accepted: 2019-11-21
issued: 2019-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frommel
  given name: Andrea Y.
author list: Agent
  family name: Brauner
  given name: Colin J.
author list: Agent
  family name: Allan
  given name: Bridie J.M.
author list: Agent
  family name: Nicol
  given name: Simon
author list: Agent
  family name: Parsons
  given name: Darren M.
author list: Agent
  family name: Pether
  given name: Steve M.J.
author list: Agent
  family name: Setiawan
  given name: Alvin N.
author list: Agent
  family name: Smith
  given name: Neville
author list: Agent
  family name: Munday
  given name: Philip L.
doi: 10.7717/peerj.8266
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-12
copyright: © 2019 Frommel et al.
attribution name: Frommel et al.

Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns
type: item
type: AcademicArticle
description: Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at −20 °C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 °C and 30 °C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30–52% pollen germination between 15 °C and 20 °C. Prunus cerasifera had 40% pollen germination at 30 °C. All species studied reached the maximum pollen tube length between 10 °C and 25 °C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at −20 °C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at −20 °C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data.
format: application/pdf
format: text/html
creator: Roberto Beltrán
creator: Aina Valls
creator: Nuria Cebrián
creator: Carlos Zornoza
creator: Francisco García Breijo
creator: José Reig Armiñana
creator: Alfonso Garmendia
creator: Hugo Merle
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.8195
publisher: PeerJ Inc.
rights: © 2019 Beltrán et al.
abstract: Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at −20 °C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 °C and 30 °C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30–52% pollen germination between 15 °C and 20 °C. Prunus cerasifera had 40% pollen germination at 30 °C. All species studied reached the maximum pollen tube length between 10 °C and 25 °C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at −20 °C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at −20 °C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data.
bibliographic citation: Beltrán et al. (2019) Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns. PeerJ 7:e8195 https://doi.org/10.7717/peerj.8195
date submitted: 2019-06-20
date accepted: 2019-11-12
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beltrán
  given name: Roberto
author list: Agent
  family name: Valls
  given name: Aina
author list: Agent
  family name: Cebrián
  given name: Nuria
author list: Agent
  family name: Zornoza
  given name: Carlos
author list: Agent
  family name: García Breijo
  given name: Francisco
author list: Agent
  family name: Reig Armiñana
  given name: José
author list: Agent
  family name: Garmendia
  given name: Alfonso
author list: Agent
  family name: Merle
  given name: Hugo
doi: 10.7717/peerj.8195
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: ©2019 Beltrán et al.
attribution name: Beltrán et al.

Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands
type: item
type: AcademicArticle
description: Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
format: application/pdf
format: text/html
creator: Weike Li
creator: Xiaodong Liu
creator: Shukui Niu
subject: Biodiversity
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.8047
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
bibliographic citation: Li et al. (2019) Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands. PeerJ 7:e8047 https://doi.org/10.7717/peerj.8047
date submitted: 2018-10-16
date accepted: 2019-10-16
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Weike
author list: Agent
  family name: Liu
  given name: Xiaodong
author list: Agent
  family name: Niu
  given name: Shukui
doi: 10.7717/peerj.8047
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: ©2019 Li et al.
attribution name: Li et al.

Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods
type: item
type: AcademicArticle
description: Background Drones are reliable tools for estimating colonial seabird numbers. Although most research has focused on methods of improving the accuracy of bird counts, few studies have evaluated the impacts of these methods on bird behavior. In this study, we examined the effects of the DJI Phantom 3 drone approach (altitude, horizontal and vertical descent speeds) on changes in the intensity of behavioral response of guano birds: guanay cormorants (Phalacrocorax bougainvilli), Peruvian boobies (Sula variegata) and Peruvian pelicans (Pelecanus thagus). The breeding and non-breeding condition was also evaluated. Methods Eleven locations along the Peruvian coast were visited in 2016–2017. Drone flight tests considered an altitude range from 5 to 80 m from the colony level, a horizontal speed range from 0.5 to 15 m/s, and a vertical descent speed range from 0.5 to 3 m/s. The intensity of the behavioral response of birds was scored and categorized as: 0-no reacting, 1-head pointing to the drone (HP), 2-wing flapping (WF), 3-walking/running (WR) and 4-taking-off/flying (TK). Drone noise at specific altitudes was recorded with a sound meter close to the colony to discriminate visual from auditory effects of the drone. Results In 74% of all test flights (N = 507), guano birds did not react to the presence of the drone, whereas in the remaining flights, birds showed a sign of discomfort: HP (47.7%, N = 130), WF (18.5%), WR (16.9%) and TK (16.9%). For the drone approach tests, only flight altitude had a significant effect in the intensity of the behavioral response of guano birds (intensity behavioral response <2). No birds reacted at drone altitudes above 50 m from the colony. Birds, for all species either in breeding or non-breeding condition, reacted more often at altitudes of 5 and 10 m. Chick-rearing cormorants and pelicans were less sensitive than their non-breeding counterparts in the range of 5–30 m of drone altitude, but boobies reacted similarly irrespective of their…
format: application/pdf
format: text/html
creator: Cinthia Irigoin-Lovera
creator: Diana M. Luna
creator: Diego A. Acosta
creator: Carlos B. Zavalaga
subject: Animal Behavior
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.8129
publisher: PeerJ Inc.
rights: © 2019 Irigoin-Lovera et al.
abstract: Background Drones are reliable tools for estimating colonial seabird numbers. Although most research has focused on methods of improving the accuracy of bird counts, few studies have evaluated the impacts of these methods on bird behavior. In this study, we examined the effects of the DJI Phantom 3 drone approach (altitude, horizontal and vertical descent speeds) on changes in the intensity of behavioral response of guano birds: guanay cormorants (Phalacrocorax bougainvilli), Peruvian boobies (Sula variegata) and Peruvian pelicans (Pelecanus thagus). The breeding and non-breeding condition was also evaluated. Methods Eleven locations along the Peruvian coast were visited in 2016–2017. Drone flight tests considered an altitude range from 5 to 80 m from the colony level, a horizontal speed range from 0.5 to 15 m/s, and a vertical descent speed range from 0.5 to 3 m/s. The intensity of the behavioral response of birds was scored and categorized as: 0-no reacting, 1-head pointing to the drone (HP), 2-wing flapping (WF), 3-walking/running (WR) and 4-taking-off/flying (TK). Drone noise at specific altitudes was recorded with a sound meter close to the colony to discriminate visual from auditory effects of the drone. Results In 74% of all test flights (N = 507), guano birds did not react to the presence of the drone, whereas in the remaining flights, birds showed a sign of discomfort: HP (47.7%, N = 130), WF (18.5%), WR (16.9%) and TK (16.9%). For the drone approach tests, only flight altitude had a significant effect in the intensity of the behavioral response of guano birds (intensity behavioral response <2). No birds reacted at drone altitudes above 50 m from the colony. Birds, for all species either in breeding or non-breeding condition, reacted more often at altitudes of 5 and 10 m. Chick-rearing cormorants and pelicans were less sensitive than their non-breeding counterparts in the range of 5–30 m of drone altitude, but boobies reacted similarly irrespective of their…
bibliographic citation: Irigoin-Lovera et al. (2019) Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods. PeerJ 7:e8129 https://doi.org/10.7717/peerj.8129
date submitted: 2019-07-19
date accepted: 2019-10-31
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Irigoin-Lovera
  given name: Cinthia
author list: Agent
  family name: Luna
  given name: Diana M.
author list: Agent
  family name: Acosta
  given name: Diego A.
author list: Agent
  family name: Zavalaga
  given name: Carlos B.
doi: 10.7717/peerj.8129
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: © 2019 Irigoin-Lovera et al.
attribution name: Irigoin-Lovera et al.

The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study
type: item
type: AcademicArticle
description: Background Motor impairments are relatively common in children with obesity and evidence suggests that these difficulties go beyond those expected based on the extra weight. This study aimed to investigate the mental rotation capacity in children with obesity, i.e., the ability to mentally view and rotate spatial information, which is a function of both visual-spatial and action representation processes. In particular, we examined whether children with obesity solved mental hand rotation tasks using an egocentric perspective (i.e., motor imagery) and if performance was related to their motor competence. Methods Fifty children (age range: 7–11 y) of which 19 with obesity and motor impairments (OB-) as assessed by the Movement Assessment Battery for Children (2nd version), 13 with obesity without motor impairments (OB+) and 18 control children with a healthy weight (HW) and normal motor competence, were submitted to a classic hand rotation task. Sitting at a desk the children were instructed to indicate the laterality of a picture of a hand displayed on a monitor as quickly and as accurately as possible. Results The results indicate no differences in response time between groups (2,648 ms, 2,558 ms, 2,664 ms for OB-, OB+ and HW respectively). The OB- group, however, had significantly lower accuracy rates and inverse efficiency scores than the HW group (Accuracy: 72% vs. 89%; Inverse efficiency: 4,428 vs. 3,238). No difference was observed in accuracy and inverse efficiency between the OB+ and HW group (Accuracy: 86%; Inverse efficiency: 3,432). In all groups, slower and more error-prone responses were observed when the angle of rotation was larger and when the hand on display was incongruent with the posture of the participants, which indicates that judgments were made from an egocentric perspective and involved motor imagery. Conclusion All children, including those with obesity, appear to engage in motor imagery. This notion needs to be investigated further in child…
format: application/pdf
format: text/html
creator: Frederik J.A. Deconinck
creator: Eva D’Hondt
creator: Karen Caeyenberghs
creator: Matthieu Lenoir
creator: Mireille J.C.M. Augustijn
subject: Kinesiology
subject: Neurology
subject: Pediatrics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8150
publisher: PeerJ Inc.
rights: © 2019 Deconinck et al.
abstract: Background Motor impairments are relatively common in children with obesity and evidence suggests that these difficulties go beyond those expected based on the extra weight. This study aimed to investigate the mental rotation capacity in children with obesity, i.e., the ability to mentally view and rotate spatial information, which is a function of both visual-spatial and action representation processes. In particular, we examined whether children with obesity solved mental hand rotation tasks using an egocentric perspective (i.e., motor imagery) and if performance was related to their motor competence. Methods Fifty children (age range: 7–11 y) of which 19 with obesity and motor impairments (OB-) as assessed by the Movement Assessment Battery for Children (2nd version), 13 with obesity without motor impairments (OB+) and 18 control children with a healthy weight (HW) and normal motor competence, were submitted to a classic hand rotation task. Sitting at a desk the children were instructed to indicate the laterality of a picture of a hand displayed on a monitor as quickly and as accurately as possible. Results The results indicate no differences in response time between groups (2,648 ms, 2,558 ms, 2,664 ms for OB-, OB+ and HW respectively). The OB- group, however, had significantly lower accuracy rates and inverse efficiency scores than the HW group (Accuracy: 72% vs. 89%; Inverse efficiency: 4,428 vs. 3,238). No difference was observed in accuracy and inverse efficiency between the OB+ and HW group (Accuracy: 86%; Inverse efficiency: 3,432). In all groups, slower and more error-prone responses were observed when the angle of rotation was larger and when the hand on display was incongruent with the posture of the participants, which indicates that judgments were made from an egocentric perspective and involved motor imagery. Conclusion All children, including those with obesity, appear to engage in motor imagery. This notion needs to be investigated further in child…
bibliographic citation: Deconinck et al. (2019) The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study. PeerJ 7:e8150 https://doi.org/10.7717/peerj.8150
date submitted: 2019-06-03
date accepted: 2019-11-04
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deconinck
  given name: Frederik J.A.
author list: Agent
  family name: D’Hondt
  given name: Eva
author list: Agent
  family name: Caeyenberghs
  given name: Karen
author list: Agent
  family name: Lenoir
  given name: Matthieu
author list: Agent
  family name: Augustijn
  given name: Mireille J.C.M.
doi: 10.7717/peerj.8150
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: ©2019 Deconinck et al.
attribution name: Deconinck et al.

Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles
type: item
type: AcademicArticle
description: The prospective study including 166 participants aims to evaluate the association between seminal prosaposin and the outcomes of in vitro fertilization (IVF) cycles in humans. The generalized linear model (GLM) was used to analyze the associations between seminal prosaposin concentrations and normal fertilization rates and good embryos proportion. The generalized estimating equation (GEE) was used to evaluate the association between embryo parameters and the prosaposin concentrations. Each model was adjusted for age of the couples, female basal FSH, AFC and BMI, starting dose and oocyte yield of IVF cycles and smoker. GLM models suggested that prosaposin was significantly associated with fertilization rate (P = 0.005) and good embryo proportion (P = 0.038) while none of the semen parameters (sperm concentration, motility, progressive motility, normal morphology rate, postwash sperm concentration and motility) was significantly associated with the parameters in the cohort. Using GEE, it was also shown that prosaposin was positively associated with the occurrence of early cleavage and negatively associated with uneven cleavage pattern on day 3. In both the overall population and the normozoospermia patients, the prosaposin was significantly associated with pregnancy with adjustment with covariates. In conclusion, our data suggested that seminal prosaposin concentration could provide more information regarding normal fertilization and embryo development in IVF than traditional semen parameters.
format: application/pdf
format: text/html
creator: Chun Xu
creator: Jiali Cai
creator: Lanlan Liu
creator: Jianzhi Ren
subject: Developmental Biology
subject: Andrology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.8177
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: The prospective study including 166 participants aims to evaluate the association between seminal prosaposin and the outcomes of in vitro fertilization (IVF) cycles in humans. The generalized linear model (GLM) was used to analyze the associations between seminal prosaposin concentrations and normal fertilization rates and good embryos proportion. The generalized estimating equation (GEE) was used to evaluate the association between embryo parameters and the prosaposin concentrations. Each model was adjusted for age of the couples, female basal FSH, AFC and BMI, starting dose and oocyte yield of IVF cycles and smoker. GLM models suggested that prosaposin was significantly associated with fertilization rate (P = 0.005) and good embryo proportion (P = 0.038) while none of the semen parameters (sperm concentration, motility, progressive motility, normal morphology rate, postwash sperm concentration and motility) was significantly associated with the parameters in the cohort. Using GEE, it was also shown that prosaposin was positively associated with the occurrence of early cleavage and negatively associated with uneven cleavage pattern on day 3. In both the overall population and the normozoospermia patients, the prosaposin was significantly associated with pregnancy with adjustment with covariates. In conclusion, our data suggested that seminal prosaposin concentration could provide more information regarding normal fertilization and embryo development in IVF than traditional semen parameters.
bibliographic citation: Xu et al. (2019) Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles. PeerJ 7:e8177 https://doi.org/10.7717/peerj.8177
date submitted: 2019-09-03
date accepted: 2019-11-07
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Chun
author list: Agent
  family name: Cai
  given name: Jiali
author list: Agent
  family name: Liu
  given name: Lanlan
author list: Agent
  family name: Ren
  given name: Jianzhi
doi: 10.7717/peerj.8177
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania)
type: item
type: AcademicArticle
description: This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi–square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record.
format: application/pdf
format: text/html
creator: Julio Mercader
creator: Siobhán Clarke
creator: Mariam Bundala
creator: Julien Favreau
creator: Jamie Inwood
creator: Makarius Itambu
creator: Fergus Larter
creator: Patrick Lee
creator: Garnet Lewiski-McQuaid
creator: Neduvoto Mollel
creator: Aloyce Mwambwiga
creator: Robert Patalano
creator: María Soto
creator: Laura Tucker
creator: Dale Walde
subject: Anthropology
subject: Ecology
subject: Evolutionary Studies
subject: Soil Science
description: doi:10.7717/peerj.8211
publisher: PeerJ Inc.
rights: © 2019 Mercader et al.
abstract: This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi–square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record.
bibliographic citation: Mercader et al. (2019) Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania). PeerJ 7:e8211 https://doi.org/10.7717/peerj.8211
date submitted: 2019-08-28
date accepted: 2019-11-14
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mercader
  given name: Julio
author list: Agent
  family name: Clarke
  given name: Siobhán
author list: Agent
  family name: Bundala
  given name: Mariam
author list: Agent
  family name: Favreau
  given name: Julien
author list: Agent
  family name: Inwood
  given name: Jamie
author list: Agent
  family name: Itambu
  given name: Makarius
author list: Agent
  family name: Larter
  given name: Fergus
author list: Agent
  family name: Lee
  given name: Patrick
author list: Agent
  family name: Lewiski-McQuaid
  given name: Garnet
author list: Agent
  family name: Mollel
  given name: Neduvoto
author list: Agent
  family name: Mwambwiga
  given name: Aloyce
author list: Agent
  family name: Patalano
  given name: Robert
author list: Agent
  family name: Soto
  given name: María
author list: Agent
  family name: Tucker
  given name: Laura
author list: Agent
  family name: Walde
  given name: Dale
doi: 10.7717/peerj.8211
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: ©2019 Mercader et al.
attribution name: Mercader et al.

Identification of miRNA precursors in the phloem of Cucurbita maxima
type: item
type: AcademicArticle
description: Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.
format: application/pdf
format: text/html
creator: Eugeny Tolstyko
creator: Alexander Lezzhov
creator: Andrey Solovyev
subject: Cell Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8269
publisher: PeerJ Inc.
rights: © 2019 Tolstyko et al.
abstract: Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.
bibliographic citation: Tolstyko et al. (2019) Identification of miRNA precursors in the phloem of Cucurbita maxima. PeerJ 7:e8269 https://doi.org/10.7717/peerj.8269
date submitted: 2019-10-07
date accepted: 2019-11-22
issued: 2019-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tolstyko
  given name: Eugeny
author list: Agent
  family name: Lezzhov
  given name: Alexander
author list: Agent
  family name: Solovyev
  given name: Andrey
doi: 10.7717/peerj.8269
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-11
copyright: © 2019 Tolstyko et al.
attribution name: Tolstyko et al.

The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer
type: item
type: AcademicArticle
description: Background Gastric cancer (GC) is the fourth most frequently diagnosed malignancy and the second leading cause of cancer-associated mortality worldwide. The tumor microenvironment, especially tumor-infiltrating immune cells (TIICs), exhibits crucial roles both in promoting and inhibiting cancer growth. The aim of the present study was to evaluate the landscape of TIICs and develop a prognostic nomogram in GC. Materials and Methods A gene expression profile obtained from a dataset from The Cancer Genome Atlas (TCGA) was used to quantify the proportion of 22 TIICs in GC by the CIBERSORT algorithm. LASSO regression analysis and multivariate Cox regression were applied to select the best survival-related TIICs and develop an immunoscore formula. Based on the immunoscore and clinical information, a prognostic nomogram was built, and the predictive accuracy of it was evaluated by the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and the calibration plot. Furthermore, the nomogram was validated by data from the International Cancer Genome Consortium (ICGC) dataset. Results In the GC samples, macrophages (25.3%), resting memory CD4 T cells (16.2%) and CD8 T cells (9.7%) were the most abundant among 22 TIICs. Seven TIICs were filtered out and used to develop an immunoscore formula. The AUC of the prognostic nomogram in the TCGA set was 0.772, similar to that in the ICGC set (0.730) and whole set (0.748), and significantly superior to that of TNM staging alone (0.591). The calibration plot demonstrated an outstanding consistency between the prediction and actual observation. Survival analysis revealed that patients with GC in the high-immunoscore group exhibited a poor clinical outcome. The result of multivariate analysis revealed that the immunoscore was an independent prognostic factor. Discussion The immunoscore could be used to reinforce the clinical outcome prediction ability of the TNM staging system and provide a convenient tool for ri…
format: application/pdf
format: text/html
creator: Linhai Li
creator: Yiming Ouyang
creator: Wenrong Wang
creator: Dezhi Hou
creator: Yu Zhu
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.7993
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Gastric cancer (GC) is the fourth most frequently diagnosed malignancy and the second leading cause of cancer-associated mortality worldwide. The tumor microenvironment, especially tumor-infiltrating immune cells (TIICs), exhibits crucial roles both in promoting and inhibiting cancer growth. The aim of the present study was to evaluate the landscape of TIICs and develop a prognostic nomogram in GC. Materials and Methods A gene expression profile obtained from a dataset from The Cancer Genome Atlas (TCGA) was used to quantify the proportion of 22 TIICs in GC by the CIBERSORT algorithm. LASSO regression analysis and multivariate Cox regression were applied to select the best survival-related TIICs and develop an immunoscore formula. Based on the immunoscore and clinical information, a prognostic nomogram was built, and the predictive accuracy of it was evaluated by the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and the calibration plot. Furthermore, the nomogram was validated by data from the International Cancer Genome Consortium (ICGC) dataset. Results In the GC samples, macrophages (25.3%), resting memory CD4 T cells (16.2%) and CD8 T cells (9.7%) were the most abundant among 22 TIICs. Seven TIICs were filtered out and used to develop an immunoscore formula. The AUC of the prognostic nomogram in the TCGA set was 0.772, similar to that in the ICGC set (0.730) and whole set (0.748), and significantly superior to that of TNM staging alone (0.591). The calibration plot demonstrated an outstanding consistency between the prediction and actual observation. Survival analysis revealed that patients with GC in the high-immunoscore group exhibited a poor clinical outcome. The result of multivariate analysis revealed that the immunoscore was an independent prognostic factor. Discussion The immunoscore could be used to reinforce the clinical outcome prediction ability of the TNM staging system and provide a convenient tool for ri…
bibliographic citation: Li et al. (2019) The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer. PeerJ 7:e7993 https://doi.org/10.7717/peerj.7993
date submitted: 2019-06-18
date accepted: 2019-10-04
issued: 2019-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Linhai
author list: Agent
  family name: Ouyang
  given name: Yiming
author list: Agent
  family name: Wang
  given name: Wenrong
author list: Agent
  family name: Hou
  given name: Dezhi
author list: Agent
  family name: Zhu
  given name: Yu
doi: 10.7717/peerj.7993
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-10
copyright: ©2019 Li et al.
attribution name: Li et al.

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