PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Abstract, emotional and concrete concepts and the activation of mouth-hand effectors
items: Comparative cranial morphology of the Late Cretaceous protostegid sea turtle Desmatochelys lowii
items: Achieving the impossible: a review of magic-based interventions and their effects on wellbeing
items: Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system
items: Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice
items: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations
items: Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus
items: Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
items: Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia
items: Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America

Abstract, emotional and concrete concepts and the activation of mouth-hand effectors
type: item
type: AcademicArticle
description: According to embodied and grounded theories, concepts are grounded in sensorimotor systems. The majority of evidence supporting these views concerns concepts referring to objects or actions, while evidence on abstract concepts is more scarce. Explaining how abstract concepts such as “freedom” are represented would thus be pivotal for grounded theories. According to some recent proposals, abstract concepts are grounded in both sensorimotor and linguistic experience, thus they activate the mouth motor system more than concrete concepts. Two experiments are reported, aimed at verifying whether abstract, concrete and emotional words activate the mouth and the hand effectors. In both experiments participants performed first a lexical decision, then a recognition task. In Experiment 1 participants responded by pressing a button either with the mouth or with the hand, in Experiment 2 responses were given with the foot, while a button held either in the mouth or in the hand was used to respond to catch-trials. Abstract words were slower to process in both tasks (concreteness effect). Across the tasks and experiments, emotional concepts had instead a fluctuating pattern, different from those of both concrete and abstract concepts, suggesting that they cannot be considered as a subset of abstract concepts. The interaction between type of concept (abstract, concrete and emotional) and effector (mouth, hand) was not significant in the lexical decision task, likely because it emerged only with tasks implying a deeper processing level. It reached significance, instead, in the recognition tasks. In both experiments abstract concepts were facilitated in the mouth condition compared to the hand condition, supporting our main prediction. Emotional concepts instead had a more variable pattern. Overall, our findings indicate that various kinds of concepts differently activate the mouth and hand effectors, but they also suggest that concepts activate effectors in a flexible and task-dep…
format: application/pdf
format: text/html
creator: Claudia Mazzuca
creator: Luisa Lugli
creator: Mariagrazia Benassi
creator: Roberto Nicoletti
creator: Anna M. Borghi
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5987
publisher: PeerJ Inc.
rights: © 2018 Mazzuca et al.
abstract: According to embodied and grounded theories, concepts are grounded in sensorimotor systems. The majority of evidence supporting these views concerns concepts referring to objects or actions, while evidence on abstract concepts is more scarce. Explaining how abstract concepts such as “freedom” are represented would thus be pivotal for grounded theories. According to some recent proposals, abstract concepts are grounded in both sensorimotor and linguistic experience, thus they activate the mouth motor system more than concrete concepts. Two experiments are reported, aimed at verifying whether abstract, concrete and emotional words activate the mouth and the hand effectors. In both experiments participants performed first a lexical decision, then a recognition task. In Experiment 1 participants responded by pressing a button either with the mouth or with the hand, in Experiment 2 responses were given with the foot, while a button held either in the mouth or in the hand was used to respond to catch-trials. Abstract words were slower to process in both tasks (concreteness effect). Across the tasks and experiments, emotional concepts had instead a fluctuating pattern, different from those of both concrete and abstract concepts, suggesting that they cannot be considered as a subset of abstract concepts. The interaction between type of concept (abstract, concrete and emotional) and effector (mouth, hand) was not significant in the lexical decision task, likely because it emerged only with tasks implying a deeper processing level. It reached significance, instead, in the recognition tasks. In both experiments abstract concepts were facilitated in the mouth condition compared to the hand condition, supporting our main prediction. Emotional concepts instead had a more variable pattern. Overall, our findings indicate that various kinds of concepts differently activate the mouth and hand effectors, but they also suggest that concepts activate effectors in a flexible and task-dep…
bibliographic citation: Mazzuca et al. (2018) Abstract, emotional and concrete concepts and the activation of mouth-hand effectors. PeerJ 6:e5987 https://doi.org/10.7717/peerj.5987
date submitted: 2018-02-21
date accepted: 2018-10-23
issued: 2018-12-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mazzuca
  given name: Claudia
author list: Agent
  family name: Lugli
  given name: Luisa
author list: Agent
  family name: Benassi
  given name: Mariagrazia
author list: Agent
  family name: Nicoletti
  given name: Roberto
author list: Agent
  family name: Borghi
  given name: Anna M.
doi: 10.7717/peerj.5987
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-07
copyright: ©2018 Mazzuca et al.
attribution name: Mazzuca et al.

Comparative cranial morphology of the Late Cretaceous protostegid sea turtle Desmatochelys lowii
type: item
type: AcademicArticle
description: Background The phylogenetic placement of Cretaceous marine turtles, especially Protostegidae, is still under debate among paleontologists. Whereas protostegids were traditionally thought to be situated within the clade of recent marine turtles (Chelonioidea), some recent morphological and molecular studies suggest placement along the stem of Cryptodira. The main reason why the evolution of marine turtles is still poorly understood, is in part due to a lack of insights into the cranial anatomy of protostegids. However, a general availability of high-quality fossil material, combined with modern analysis techniques, such as X-ray microtomography, provide ample opportunity to improve this situation. The scope of this study is to help resolve its phylogenetic relationships by providing a detailed description of the external and internal cranial morphology of the extinct protostegid sea turtle Desmatochelys lowii Williston, 1894. Material and Methods This study is based on the well-preserved holotype of Desmatochelys lowii from the Late Cretaceous (middle Cenomanian to early Turonian) Greenhorn Limestone of Jefferson County, Nebraska. The skulls of two recent marine turtles, Eretmochelys imbricata (Linnaeus, 1766) (Cheloniidae) and Dermochelys coriacea Lydekker, 1889 (Dermochelyidae), as well as the snapping turtle Chelydra serpentina (Linnaeus, 1758) (Chelydridae) provide a comparative basis. All skulls were scanned using regular or micro CT scanners and the scans were then processed with the software program Amira to create 3D isosurface models. In total, 81 bones are virtually isolated, figured, and described, including the nature of their contacts. The novel bone contact data is compiled and utilized in a preliminary phenetic study. In addition, an update phylogenetic analysis is conduced that utilizes newly obtained anatomical insights. Results The detailed examination of the morphology of the herein used specimens allowed to explore some features of the skull, to r…
format: application/pdf
format: text/html
creator: Irena Raselli
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5964
publisher: PeerJ Inc.
rights: © 2018 Raselli
abstract: Background The phylogenetic placement of Cretaceous marine turtles, especially Protostegidae, is still under debate among paleontologists. Whereas protostegids were traditionally thought to be situated within the clade of recent marine turtles (Chelonioidea), some recent morphological and molecular studies suggest placement along the stem of Cryptodira. The main reason why the evolution of marine turtles is still poorly understood, is in part due to a lack of insights into the cranial anatomy of protostegids. However, a general availability of high-quality fossil material, combined with modern analysis techniques, such as X-ray microtomography, provide ample opportunity to improve this situation. The scope of this study is to help resolve its phylogenetic relationships by providing a detailed description of the external and internal cranial morphology of the extinct protostegid sea turtle Desmatochelys lowii Williston, 1894. Material and Methods This study is based on the well-preserved holotype of Desmatochelys lowii from the Late Cretaceous (middle Cenomanian to early Turonian) Greenhorn Limestone of Jefferson County, Nebraska. The skulls of two recent marine turtles, Eretmochelys imbricata (Linnaeus, 1766) (Cheloniidae) and Dermochelys coriacea Lydekker, 1889 (Dermochelyidae), as well as the snapping turtle Chelydra serpentina (Linnaeus, 1758) (Chelydridae) provide a comparative basis. All skulls were scanned using regular or micro CT scanners and the scans were then processed with the software program Amira to create 3D isosurface models. In total, 81 bones are virtually isolated, figured, and described, including the nature of their contacts. The novel bone contact data is compiled and utilized in a preliminary phenetic study. In addition, an update phylogenetic analysis is conduced that utilizes newly obtained anatomical insights. Results The detailed examination of the morphology of the herein used specimens allowed to explore some features of the skull, to r…
bibliographic citation: Raselli (2018) Comparative cranial morphology of the Late Cretaceous protostegid sea turtle Desmatochelys lowii. PeerJ 6:e5964 https://doi.org/10.7717/peerj.5964
date submitted: 2018-04-17
date accepted: 2018-10-19
issued: 2018-12-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raselli
  given name: Irena
doi: 10.7717/peerj.5964
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-07
copyright: © 2018 Raselli
attribution name: Raselli

Achieving the impossible: a review of magic-based interventions and their effects on wellbeing
type: item
type: AcademicArticle
description: Research has demonstrated that involvement with mainstream performing arts, such as music and dance, can boost wellbeing. This article extends this work by reviewing little-known research on whether learning magic tricks can have an equally beneficial effect. We first present an historic overview of several magic-based interventions created by magicians, psychologists and occupational therapists. We then identify the potential benefits of such interventions, and review studies that have attempted to systematically assess these interventions. The studies have mostly revealed beneficial outcomes, but much of the work is of poor methodological quality (involving small numbers of participants and no control group), and has tended to focus on clinical populations. Finally, we present guidelines for future research in the area, emphasizing the need for more systematic and better-controlled studies.
format: application/pdf
format: text/html
creator: Richard Wiseman
creator: Caroline Watt
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.6081
publisher: PeerJ Inc.
rights: © 2018 Wiseman and Watt
abstract: Research has demonstrated that involvement with mainstream performing arts, such as music and dance, can boost wellbeing. This article extends this work by reviewing little-known research on whether learning magic tricks can have an equally beneficial effect. We first present an historic overview of several magic-based interventions created by magicians, psychologists and occupational therapists. We then identify the potential benefits of such interventions, and review studies that have attempted to systematically assess these interventions. The studies have mostly revealed beneficial outcomes, but much of the work is of poor methodological quality (involving small numbers of participants and no control group), and has tended to focus on clinical populations. Finally, we present guidelines for future research in the area, emphasizing the need for more systematic and better-controlled studies.
bibliographic citation: Wiseman et al. (2018) Achieving the impossible: a review of magic-based interventions and their effects on wellbeing. PeerJ 6:e6081 https://doi.org/10.7717/peerj.6081
date submitted: 2018-10-15
date accepted: 2018-11-07
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiseman
  given name: Richard
author list: Agent
  family name: Watt
  given name: Caroline
doi: 10.7717/peerj.6081
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Wiseman and Watt
attribution name: Wiseman and Watt

Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system
type: item
type: AcademicArticle
description: Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were g…
format: application/pdf
format: text/html
creator: Laura E. Williams
creator: Claire E. Kleinschmidt
creator: Stephen Mecca
subject: Microbiology
subject: Public Health
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6077
publisher: PeerJ Inc.
rights: © 2018 Williams et al.
abstract: Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were g…
bibliographic citation: Williams et al. (2018) Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system. PeerJ 6:e6077 https://doi.org/10.7717/peerj.6077
date submitted: 2018-09-05
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Laura E.
author list: Agent
  family name: Kleinschmidt
  given name: Claire E.
author list: Agent
  family name: Mecca
  given name: Stephen
doi: 10.7717/peerj.6077
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Williams et al.
attribution name: Williams et al.

Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice
type: item
type: AcademicArticle
description: Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis …
format: application/pdf
format: text/html
creator: Wang Jin
creator: Xiaowen Liang
creator: Anastasia Brooks
creator: Kathryn Futrega
creator: Xin Liu
creator: Michael R. Doran
creator: Matthew J. Simpson
creator: Michael S. Roberts
creator: Haolu Wang
subject: Cell Biology
subject: Mathematical Biology
subject: Drugs and Devices
description: doi:10.7717/peerj.6072
publisher: PeerJ Inc.
rights: © 2018 Jin et al.
abstract: Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis …
bibliographic citation: Jin et al. (2018) Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice. PeerJ 6:e6072 https://doi.org/10.7717/peerj.6072
date submitted: 2018-08-22
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Wang
author list: Agent
  family name: Liang
  given name: Xiaowen
author list: Agent
  family name: Brooks
  given name: Anastasia
author list: Agent
  family name: Futrega
  given name: Kathryn
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Doran
  given name: Michael R.
author list: Agent
  family name: Simpson
  given name: Matthew J.
author list: Agent
  family name: Roberts
  given name: Michael S.
author list: Agent
  family name: Wang
  given name: Haolu
doi: 10.7717/peerj.6072
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Jin et al.
attribution name: Jin et al.

Conservation implications of primate trade in China over 18 years based on web news reports of confiscations
type: item
type: AcademicArticle
description: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in res…
format: application/pdf
format: text/html
creator: Qingyong Ni
creator: Yu Wang
creator: Ariana Weldon
creator: Meng Xie
creator: Huailiang Xu
creator: Yongfang Yao
creator: Mingwang Zhang
creator: Ying Li
creator: Yan Li
creator: Bo Zeng
creator: K.A.I. Nekaris
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.6069
publisher: PeerJ Inc.
rights: © 2018 Ni et al.
abstract: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in res…
bibliographic citation: Ni et al. (2018) Conservation implications of primate trade in China over 18 years based on web news reports of confiscations. PeerJ 6:e6069 https://doi.org/10.7717/peerj.6069
date submitted: 2018-08-20
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ni
  given name: Qingyong
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Weldon
  given name: Ariana
author list: Agent
  family name: Xie
  given name: Meng
author list: Agent
  family name: Xu
  given name: Huailiang
author list: Agent
  family name: Yao
  given name: Yongfang
author list: Agent
  family name: Zhang
  given name: Mingwang
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Zeng
  given name: Bo
author list: Agent
  family name: Nekaris
  given name: K.A.I.
doi: 10.7717/peerj.6069
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Ni et al.
attribution name: Ni et al.

Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus
type: item
type: AcademicArticle
description: Background Diabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI). Methods A cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment. Results Included in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile…
format: application/pdf
format: text/html
creator: Alan Uriel García-Tejeda
creator: Clara Luz Sampieri
creator: Irene Suárez-Torres
creator: Jaime Morales-Romero
creator: Verónica Patricia Demeneghi-Marini
creator: Magda Elena Hernández-Hernández
creator: Arturo Rodríguez-Hernández
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Urology
description: doi:10.7717/peerj.6067
publisher: PeerJ Inc.
rights: © 2018 García-Tejeda et al.
abstract: Background Diabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI). Methods A cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment. Results Included in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile…
bibliographic citation: García-Tejeda et al. (2018) Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus. PeerJ 6:e6067 https://doi.org/10.7717/peerj.6067
date submitted: 2018-06-21
date accepted: 2018-11-04
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Tejeda
  given name: Alan Uriel
author list: Agent
  family name: Sampieri
  given name: Clara Luz
author list: Agent
  family name: Suárez-Torres
  given name: Irene
author list: Agent
  family name: Morales-Romero
  given name: Jaime
author list: Agent
  family name: Demeneghi-Marini
  given name: Verónica Patricia
author list: Agent
  family name: Hernández-Hernández
  given name: Magda Elena
author list: Agent
  family name: Rodríguez-Hernández
  given name: Arturo
doi: 10.7717/peerj.6067
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 García-Tejeda et al.
attribution name: García-Tejeda et al.

Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
type: item
type: AcademicArticle
description: Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and Methods The original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information. Results A nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001). Discussion The present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients.
format: application/pdf
format: text/html
creator: Zhiqiao Zhang
creator: Qingbo Liu
creator: Peng Wang
creator: Jing Li
creator: Tingshan He
creator: Yanling Ouyang
creator: Yiyan Huang
creator: Weidong Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.6061
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and Methods The original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information. Results A nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001). Discussion The present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients.
bibliographic citation: Zhang et al. (2018) Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients. PeerJ 6:e6061 https://doi.org/10.7717/peerj.6061
date submitted: 2018-08-27
date accepted: 2018-11-03
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zhiqiao
author list: Agent
  family name: Liu
  given name: Qingbo
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: He
  given name: Tingshan
author list: Agent
  family name: Ouyang
  given name: Yanling
author list: Agent
  family name: Huang
  given name: Yiyan
author list: Agent
  family name: Wang
  given name: Weidong
doi: 10.7717/peerj.6061
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia
type: item
type: AcademicArticle
description: We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status.
format: application/pdf
format: text/html
creator: Vladimir G. Grinkov
creator: Andreas Bauer
creator: Sergey I. Gashkov
creator: Helmut Sternberg
creator: Michael Wink
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.6059
publisher: PeerJ Inc.
rights: © 2018 Grinkov et al.
abstract: We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status.
bibliographic citation: Grinkov et al. (2018) Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia. PeerJ 6:e6059 https://doi.org/10.7717/peerj.6059
date submitted: 2018-03-13
date accepted: 2018-11-04
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grinkov
  given name: Vladimir G.
author list: Agent
  family name: Bauer
  given name: Andreas
author list: Agent
  family name: Gashkov
  given name: Sergey I.
author list: Agent
  family name: Sternberg
  given name: Helmut
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.6059
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Grinkov et al.
attribution name: Grinkov et al.

Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America
type: item
type: AcademicArticle
description: Background A scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales. Methods I selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization. Results In general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected. Discussion The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structu…
format: application/pdf
format: text/html
creator: Lucas Matías Leveau
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6056
publisher: PeerJ Inc.
rights: © 2018 Leveau
abstract: Background A scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales. Methods I selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization. Results In general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected. Discussion The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structu…
bibliographic citation: Leveau (2018) Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America. PeerJ 6:e6056 https://doi.org/10.7717/peerj.6056
date submitted: 2018-02-08
date accepted: 2018-11-01
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leveau
  given name: Lucas Matías
doi: 10.7717/peerj.6056
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Leveau
attribution name: Leveau

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