PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Dopamine and eye movement control in Parkinson’s disease: deficits in corollary discharge signals?
items: RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
items: Bait-attending amphipods of the Tonga Trench and depth-stratified population structure in the scavenging amphipod Hirondellea dubia Dahl, 1959
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

Dopamine and eye movement control in Parkinson’s disease: deficits in corollary discharge signals?
type: item
type: AcademicArticle
description: Movement in Parkinson’s disease (PD) is fragmented, and the patients depend on visual information in their behavior. This suggests that the patients may have deficits in internally monitoring their own movements. Internal monitoring of movements is assumed to rely on corollary discharge signals that enable the brain to predict the sensory consequences of actions. We studied early-stage PD patients (N = 14), and age-matched healthy control participants (N = 14) to examine whether PD patients reveal deficits in updating their sensory representations after eye movements. The participants performed a double-saccade task where, in order to accurately fixate a second target, the participant must correct for the displacement caused by the first saccade. In line with previous reports, the patients had difficulties in fixating the second target when the eye movement was performed without visual guidance. Furthermore, the patients had difficulties in taking into account the error in the first saccade when making a saccade toward the second target, especially when eye movements were made toward the side with dominant motor symptoms. Across PD patients, the impairments in saccadic eye movements correlated with the integrity of the dopaminergic system as measured with [123I]FP-CIT SPECT: Patients with lower striatal (caudate, anterior putamen, and posterior putamen) dopamine transporter binding made larger errors in saccades. This effect was strongest when patients made memory-guided saccades toward the second target. Our results provide tentative evidence that the motor deficits in PD may be partly due to deficits in internal monitoring of movements.
format: application/pdf
format: text/html
creator: Henry Railo
creator: Henri Olkoniemi
creator: Enni Eeronheimo
creator: Oona Pääkkönen
creator: Juho Joutsa
creator: Valtteri Kaasinen
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6038
publisher: PeerJ Inc.
rights: © 2018 Railo et al.
abstract: Movement in Parkinson’s disease (PD) is fragmented, and the patients depend on visual information in their behavior. This suggests that the patients may have deficits in internally monitoring their own movements. Internal monitoring of movements is assumed to rely on corollary discharge signals that enable the brain to predict the sensory consequences of actions. We studied early-stage PD patients (N = 14), and age-matched healthy control participants (N = 14) to examine whether PD patients reveal deficits in updating their sensory representations after eye movements. The participants performed a double-saccade task where, in order to accurately fixate a second target, the participant must correct for the displacement caused by the first saccade. In line with previous reports, the patients had difficulties in fixating the second target when the eye movement was performed without visual guidance. Furthermore, the patients had difficulties in taking into account the error in the first saccade when making a saccade toward the second target, especially when eye movements were made toward the side with dominant motor symptoms. Across PD patients, the impairments in saccadic eye movements correlated with the integrity of the dopaminergic system as measured with [123I]FP-CIT SPECT: Patients with lower striatal (caudate, anterior putamen, and posterior putamen) dopamine transporter binding made larger errors in saccades. This effect was strongest when patients made memory-guided saccades toward the second target. Our results provide tentative evidence that the motor deficits in PD may be partly due to deficits in internal monitoring of movements.
bibliographic citation: Railo et al. (2018) Dopamine and eye movement control in Parkinson’s disease: deficits in corollary discharge signals?. PeerJ 6:e6038 https://doi.org/10.7717/peerj.6038
date submitted: 2018-08-17
date accepted: 2018-10-30
issued: 2018-12-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Railo
  given name: Henry
author list: Agent
  family name: Olkoniemi
  given name: Henri
author list: Agent
  family name: Eeronheimo
  given name: Enni
author list: Agent
  family name: Pääkkönen
  given name: Oona
author list: Agent
  family name: Joutsa
  given name: Juho
author list: Agent
  family name: Kaasinen
  given name: Valtteri
doi: 10.7717/peerj.6038
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-07
copyright: © 2018 Railo et al.
attribution name: Railo et al.

RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
type: item
type: AcademicArticle
description: Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd.
format: application/pdf
format: text/html
creator: Sebastián Contreras-Riquelme
creator: Jose-Antonio Garate
creator: Tomas Perez-Acle
creator: Alberto J.M. Martin
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
description: doi:10.7717/peerj.5998
publisher: PeerJ Inc.
rights: © 2018 Contreras-Riquelme et al.
abstract: Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd.
bibliographic citation: Contreras-Riquelme et al. (2018) RIP-MD: a tool to study residue interaction networks in protein molecular dynamics. PeerJ 6:e5998 https://doi.org/10.7717/peerj.5998
date submitted: 2018-03-25
date accepted: 2018-10-25
issued: 2018-12-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Contreras-Riquelme
  given name: Sebastián
author list: Agent
  family name: Garate
  given name: Jose-Antonio
author list: Agent
  family name: Perez-Acle
  given name: Tomas
author list: Agent
  family name: Martin
  given name: Alberto J.M.
doi: 10.7717/peerj.5998
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-07
copyright: © 2018 Contreras-Riquelme et al.
attribution name: Contreras-Riquelme et al.

Bait-attending amphipods of the Tonga Trench and depth-stratified population structure in the scavenging amphipod Hirondellea dubia Dahl, 1959
type: item
type: AcademicArticle
description: Background The hadal zone encompasses the deepest parts of the world’s ocean trenches from depths of ∼6,000–11,000 m. The communities observed at these depths are dominated by scavenging amphipods that rapidly intercept and consume carrion as it falls to the deepest parts of the trenches. New samples collected in the Tonga Trench provide an opportunity to compare the amphipod assemblages and the population structure of a dominant species, Hirondellea dubia Dahl, 1959, between trenches and with earlier data presented for the Tonga Trench, and other trenches in the South Pacific. Methods Over 3,600 individual scavenging amphipods across 10 species were collected in seven baited traps at two sites; in the Horizon Deep site, the deepest part of the Tonga Trench (10,800 m) and a site directly up-slope at the trench edge (6,250 m). The composition of the bait-attending amphipods is described and a morphometric analysis of H. dubia examines the bathymetric distribution of the different life stages encountered. Results The amphipod assemblage was more diverse than previously reported, seven species were recorded for the first time from the Tonga Trench. The species diversity was highest at the shallower depth, with H. dubia the only species captured at the deepest site. At the same time, the abundance of amphipods collected at 10,800 m was around sevenfold higher than at the shallower site. H. dubia showed clear ontogenetic vertical structuring, with juveniles dominant at the shallow site and adults dominant at the deep site. The amphipods of the deeper site were always larger at comparable life stage. Discussion The numbers of species encountered in the Tonga Trench is less than reported from the New Hebrides and Kermadec trenches, and six species encountered are shared across trenches. These findings support the previous suggestion that the fauna of the New Hebrides, Tonga and Kermadec Trenches may represent a single biogeographic province. The ontogenetic shift in H. dub…
format: application/pdf
format: text/html
creator: James P.A. Wilson
creator: Kareen E. Schnabel
creator: Ashley A. Rowden
creator: Rachael A. Peart
creator: Hiroshi Kitazato
creator: Ken G. Ryan
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.5994
publisher: PeerJ Inc.
rights: © 2018 Wilson et al.
abstract: Background The hadal zone encompasses the deepest parts of the world’s ocean trenches from depths of ∼6,000–11,000 m. The communities observed at these depths are dominated by scavenging amphipods that rapidly intercept and consume carrion as it falls to the deepest parts of the trenches. New samples collected in the Tonga Trench provide an opportunity to compare the amphipod assemblages and the population structure of a dominant species, Hirondellea dubia Dahl, 1959, between trenches and with earlier data presented for the Tonga Trench, and other trenches in the South Pacific. Methods Over 3,600 individual scavenging amphipods across 10 species were collected in seven baited traps at two sites; in the Horizon Deep site, the deepest part of the Tonga Trench (10,800 m) and a site directly up-slope at the trench edge (6,250 m). The composition of the bait-attending amphipods is described and a morphometric analysis of H. dubia examines the bathymetric distribution of the different life stages encountered. Results The amphipod assemblage was more diverse than previously reported, seven species were recorded for the first time from the Tonga Trench. The species diversity was highest at the shallower depth, with H. dubia the only species captured at the deepest site. At the same time, the abundance of amphipods collected at 10,800 m was around sevenfold higher than at the shallower site. H. dubia showed clear ontogenetic vertical structuring, with juveniles dominant at the shallow site and adults dominant at the deep site. The amphipods of the deeper site were always larger at comparable life stage. Discussion The numbers of species encountered in the Tonga Trench is less than reported from the New Hebrides and Kermadec trenches, and six species encountered are shared across trenches. These findings support the previous suggestion that the fauna of the New Hebrides, Tonga and Kermadec Trenches may represent a single biogeographic province. The ontogenetic shift in H. dub…
bibliographic citation: Wilson et al. (2018) Bait-attending amphipods of the Tonga Trench and depth-stratified population structure in the scavenging amphipod Hirondellea dubia Dahl, 1959. PeerJ 6:e5994 https://doi.org/10.7717/peerj.5994
date submitted: 2018-08-15
date accepted: 2018-10-24
issued: 2018-12-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilson
  given name: James P.A.
author list: Agent
  family name: Schnabel
  given name: Kareen E.
author list: Agent
  family name: Rowden
  given name: Ashley A.
author list: Agent
  family name: Peart
  given name: Rachael A.
author list: Agent
  family name: Kitazato
  given name: Hiroshi
author list: Agent
  family name: Ryan
  given name: Ken G.
doi: 10.7717/peerj.5994
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-07
copyright: © 2018 Wilson et al.
attribution name: Wilson et al.

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.

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