PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Agrichemicals and antibiotics in combination increase antibiotic resistance evolution
items: Assessment of the kidney and lung as immune barriers and hematopoietic sites in the invasive apple snail Pomacea canaliculata
items: A new specimen of Palvennia hoybergeti: implications for cranial and pectoral girdle anatomy in ophthalmosaurid ichthyosaurs
items: Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory
items: Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient
items: Building interpretable models for polypharmacy prediction in older chronic patients based on drug prescription records
items: Bite marks on the frill of a juvenile Centrosaurus from the Late Cretaceous Dinosaur Provincial Park Formation, Alberta, Canada
items: Movements and dispersal of brown trout (Salmo trutta Linnaeus, 1758) in Mediterranean streams: influence of habitat and biotic factors
items: Nutritional value of several commercially important river fish species from the Czech Republic
items: Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics

Agrichemicals and antibiotics in combination increase antibiotic resistance evolution
type: item
type: AcademicArticle
description: Antibiotic resistance in our pathogens is medicine’s climate change: caused by human activity, and resulting in more extreme outcomes. Resistance emerges in microbial populations when antibiotics act on phenotypic variance within the population. This can arise from either genotypic diversity (resulting from a mutation or horizontal gene transfer), or from differences in gene expression due to environmental variation, referred to as adaptive resistance. Adaptive changes can increase fitness allowing bacteria to survive at higher concentrations of antibiotics. They can also decrease fitness, potentially leading to selection for antibiotic resistance at lower concentrations. There are opportunities for other environmental stressors to promote antibiotic resistance in ways that are hard to predict using conventional assays. Exploiting our previous observation that commonly used herbicides can increase or decrease the minimum inhibitory concentration (MIC) of different antibiotics, we provide the first comprehensive test of the hypothesis that the rate of antibiotic resistance evolution under specified conditions can increase, regardless of whether a herbicide increases or decreases the antibiotic MIC. Short term evolution experiments were used for various herbicide and antibiotic combinations. We found conditions where acquired resistance arises more frequently regardless of whether the exogenous non-antibiotic agent increased or decreased antibiotic effectiveness. This is attributed to the effect of the herbicide on either MIC or the minimum selective concentration (MSC) of a paired antibiotic. The MSC is the lowest concentration of antibiotic at which the fitness of individuals varies because of the antibiotic, and is lower than MIC. Our results suggest that additional environmental factors influencing competition between bacteria could enhance the ability of antibiotics to select antibiotic resistance. Our work demonstrates that bacteria may acquire antibiotic resist…
format: application/pdf
format: text/html
creator: Brigitta Kurenbach
creator: Amy M. Hill
creator: William Godsoe
creator: Sophie van Hamelsveld
creator: Jack A. Heinemann
subject: Agricultural Science
subject: Evolutionary Studies
subject: Microbiology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.5801
publisher: PeerJ Inc.
rights: © 2018 Kurenbach et al.
abstract: Antibiotic resistance in our pathogens is medicine’s climate change: caused by human activity, and resulting in more extreme outcomes. Resistance emerges in microbial populations when antibiotics act on phenotypic variance within the population. This can arise from either genotypic diversity (resulting from a mutation or horizontal gene transfer), or from differences in gene expression due to environmental variation, referred to as adaptive resistance. Adaptive changes can increase fitness allowing bacteria to survive at higher concentrations of antibiotics. They can also decrease fitness, potentially leading to selection for antibiotic resistance at lower concentrations. There are opportunities for other environmental stressors to promote antibiotic resistance in ways that are hard to predict using conventional assays. Exploiting our previous observation that commonly used herbicides can increase or decrease the minimum inhibitory concentration (MIC) of different antibiotics, we provide the first comprehensive test of the hypothesis that the rate of antibiotic resistance evolution under specified conditions can increase, regardless of whether a herbicide increases or decreases the antibiotic MIC. Short term evolution experiments were used for various herbicide and antibiotic combinations. We found conditions where acquired resistance arises more frequently regardless of whether the exogenous non-antibiotic agent increased or decreased antibiotic effectiveness. This is attributed to the effect of the herbicide on either MIC or the minimum selective concentration (MSC) of a paired antibiotic. The MSC is the lowest concentration of antibiotic at which the fitness of individuals varies because of the antibiotic, and is lower than MIC. Our results suggest that additional environmental factors influencing competition between bacteria could enhance the ability of antibiotics to select antibiotic resistance. Our work demonstrates that bacteria may acquire antibiotic resist…
bibliographic citation: Kurenbach et al. (2018) Agrichemicals and antibiotics in combination increase antibiotic resistance evolution. PeerJ 6:e5801 https://doi.org/10.7717/peerj.5801
date submitted: 2018-05-03
date accepted: 2018-09-21
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kurenbach
  given name: Brigitta
author list: Agent
  family name: Hill
  given name: Amy M.
author list: Agent
  family name: Godsoe
  given name: William
author list: Agent
  family name: van Hamelsveld
  given name: Sophie
author list: Agent
  family name: Heinemann
  given name: Jack A.
doi: 10.7717/peerj.5801
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Kurenbach et al.
attribution name: Kurenbach et al.

Assessment of the kidney and lung as immune barriers and hematopoietic sites in the invasive apple snail Pomacea canaliculata
type: item
type: AcademicArticle
description: Knowledge on the immune system of Pomacea canaliculata is becoming increasingly important, because of this gastropod’s role as intermediate host and vector of Angiostrongylus cantonensis, the etiologic agent of eosinophilic meningitis in humans and domestic animals. Immune defenses of this gastropod comprise both humoral and cellular components, but they may also involve organs that act as immune barriers to prevent the spread of alien molecules and organisms. Both the kidney and lung are here shown to serve this function, because of (1) their positions in blood circulation, (2) the intricate architecture of their blood spaces, and (3) the proliferative and nodulation reactions of hemocytes to an immune challenge. However, these organs differ in that only the kidney shows permanent hemocyte aggregations. Microcirculation in the kidney was found to flow through an intricate vascular bed containing the permanent aggregations, which occurred either as hemocyte islets anchored by cytoplasmic projections of the renal epithelium or as perivascular accretions. Within 96 h of the injection of yeast cells, hemocyte nodules were formed both in the kidney and lung. Moreover, cell proliferation in renal hemocyte islets was measured by bromodeoxyuridine (BrdU) incorporation. The proportion of BrdU positive nuclei increased 48 h after injection. Signs of nodule regression (apoptotic bodies, lipofuscin-like deposits) and a decrease in the proportion of BrdU positive nuclei were found at 96 h. In addition, the area of renal hemocyte islets was significantly increased 96 h after injection. Nevertheless, the high complexity of the small vascular chambers that constitute the lung’s respiratory lamina would also facilitate hemocyte-antigen contacts, required to elicit cellular aggregation, and hence, nodulation. To our knowledge, this paper includes the first quantitative indication of hemocyte proliferation after an immune challenge among Caenogastropoda.
format: application/pdf
format: text/html
creator: Cristian Rodriguez
creator: Guido I. Prieto
creator: Israel A. Vega
creator: Alfredo Castro-Vazquez
subject: Zoology
subject: Anatomy and Physiology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.5789
publisher: PeerJ Inc.
rights: © 2018 Rodriguez et al.
abstract: Knowledge on the immune system of Pomacea canaliculata is becoming increasingly important, because of this gastropod’s role as intermediate host and vector of Angiostrongylus cantonensis, the etiologic agent of eosinophilic meningitis in humans and domestic animals. Immune defenses of this gastropod comprise both humoral and cellular components, but they may also involve organs that act as immune barriers to prevent the spread of alien molecules and organisms. Both the kidney and lung are here shown to serve this function, because of (1) their positions in blood circulation, (2) the intricate architecture of their blood spaces, and (3) the proliferative and nodulation reactions of hemocytes to an immune challenge. However, these organs differ in that only the kidney shows permanent hemocyte aggregations. Microcirculation in the kidney was found to flow through an intricate vascular bed containing the permanent aggregations, which occurred either as hemocyte islets anchored by cytoplasmic projections of the renal epithelium or as perivascular accretions. Within 96 h of the injection of yeast cells, hemocyte nodules were formed both in the kidney and lung. Moreover, cell proliferation in renal hemocyte islets was measured by bromodeoxyuridine (BrdU) incorporation. The proportion of BrdU positive nuclei increased 48 h after injection. Signs of nodule regression (apoptotic bodies, lipofuscin-like deposits) and a decrease in the proportion of BrdU positive nuclei were found at 96 h. In addition, the area of renal hemocyte islets was significantly increased 96 h after injection. Nevertheless, the high complexity of the small vascular chambers that constitute the lung’s respiratory lamina would also facilitate hemocyte-antigen contacts, required to elicit cellular aggregation, and hence, nodulation. To our knowledge, this paper includes the first quantitative indication of hemocyte proliferation after an immune challenge among Caenogastropoda.
bibliographic citation: Rodriguez et al. (2018) Assessment of the kidney and lung as immune barriers and hematopoietic sites in the invasive apple snail Pomacea canaliculata. PeerJ 6:e5789 https://doi.org/10.7717/peerj.5789
date submitted: 2018-06-01
date accepted: 2018-09-19
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez
  given name: Cristian
author list: Agent
  family name: Prieto
  given name: Guido I.
author list: Agent
  family name: Vega
  given name: Israel A.
author list: Agent
  family name: Castro-Vazquez
  given name: Alfredo
doi: 10.7717/peerj.5789
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Rodriguez et al.
attribution name: Rodriguez et al.

A new specimen of Palvennia hoybergeti: implications for cranial and pectoral girdle anatomy in ophthalmosaurid ichthyosaurs
type: item
type: AcademicArticle
description: The Late Jurassic Slottsmøya Member Lagerstätte on Spitsbergen preserves a diverse array of marine reptiles, including four named taxa of ophthalmosaurid ichthyosaurs. One of these, Palvennia hoybergeti, is based on the single holotype specimen (SVB 1451) with an incomplete skull. A newly discovered specimen (PMO 222.669) with a disarticulated but largely complete skull and anterior postcranium is described, which considerably expands our knowledge of this taxon. Two additional new ophthalmosaurid specimens with pectoral girdles from the same member are described. The taxonomic utility of the ophthalmosaurid pectoral girdle is contentious, and an assessment of seven pectoral girdles from the Slottsmøya Member provides a basis for addressing this question via a 2D landmark principal component analysis of baracromian coracoids. The analysis reveals a taxonomic signal in the coracoids but also highlights the degree of individual variation. Commonly used phylogenetic characters do not fully encapsulate the degree of variation seen in coracoids and in some cases combine analogous features.
format: application/pdf
format: text/html
creator: Lene Liebe Delsett
creator: Patrick Scott Druckenmiller
creator: Aubrey Jane Roberts
creator: Jørn Harald Hurum
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5776
publisher: PeerJ Inc.
rights: © 2018 Delsett et al.
abstract: The Late Jurassic Slottsmøya Member Lagerstätte on Spitsbergen preserves a diverse array of marine reptiles, including four named taxa of ophthalmosaurid ichthyosaurs. One of these, Palvennia hoybergeti, is based on the single holotype specimen (SVB 1451) with an incomplete skull. A newly discovered specimen (PMO 222.669) with a disarticulated but largely complete skull and anterior postcranium is described, which considerably expands our knowledge of this taxon. Two additional new ophthalmosaurid specimens with pectoral girdles from the same member are described. The taxonomic utility of the ophthalmosaurid pectoral girdle is contentious, and an assessment of seven pectoral girdles from the Slottsmøya Member provides a basis for addressing this question via a 2D landmark principal component analysis of baracromian coracoids. The analysis reveals a taxonomic signal in the coracoids but also highlights the degree of individual variation. Commonly used phylogenetic characters do not fully encapsulate the degree of variation seen in coracoids and in some cases combine analogous features.
bibliographic citation: Delsett et al. (2018) A new specimen of Palvennia hoybergeti: implications for cranial and pectoral girdle anatomy in ophthalmosaurid ichthyosaurs. PeerJ 6:e5776 https://doi.org/10.7717/peerj.5776
date submitted: 2018-05-30
date accepted: 2018-09-15
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delsett
  given name: Lene Liebe
author list: Agent
  family name: Druckenmiller
  given name: Patrick Scott
author list: Agent
  family name: Roberts
  given name: Aubrey Jane
author list: Agent
  family name: Hurum
  given name: Jørn Harald
doi: 10.7717/peerj.5776
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: © 2018 Delsett et al.
attribution name: Delsett et al.

Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory
type: item
type: AcademicArticle
description: We studied the relationship between plant functional foliar traits and the endophytic bacterial communities associated in trees, taking the example of sessile oak (Quercus petraea (Matt.) Liebl). Forty-five samples with replicates of eight leaves per sample were collected in spring, summer and autumn. Bacterial community diversity was analyzed via Automated Ribosomal Intergenic Spacer Analysis (ARISA). The leaf traits specific leaf area, level of herbivory, stomatal number, stomatal length, carbon and nitrogen concentration were measured for the leaves of each sample. For statistical analysis, linear mixed effect models, the Canonical Correlation Analysis (CCA) and Non-Parametric Multivariate Analysis of Variance (NPMANOVA) were applied. Herbivory, nitrogen and carbon concentration were significantly different in autumn compared to spring and summer (p value < 0.05), while stomatal length was differentiated between spring and the other two seasons (p value < 0.01). The seasonal differentiation of the bacterial community structure was explained by the first and second axes (29.7% and 25.3%, respectively) in the CCA. The bacterial community structure significantly correlated with herbivory, nitrogen concentration and stomatal length. We conclude that herbivory, nitrogen content, and size of stomatal aperture at the leaf level are important for endophyte colonization in oaks growth in alpine forest environments.
format: application/pdf
format: text/html
creator: Luigimaria Borruso
creator: Camilla Wellstein
creator: Alessia Bani
creator: Sara Casagrande Bacchiocchi
creator: Ania Margoni
creator: Rita Tonin
creator: Stefan Zerbe
creator: Lorenzo Brusetti
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.5769
publisher: PeerJ Inc.
rights: © 2018 Borruso et al.
abstract: We studied the relationship between plant functional foliar traits and the endophytic bacterial communities associated in trees, taking the example of sessile oak (Quercus petraea (Matt.) Liebl). Forty-five samples with replicates of eight leaves per sample were collected in spring, summer and autumn. Bacterial community diversity was analyzed via Automated Ribosomal Intergenic Spacer Analysis (ARISA). The leaf traits specific leaf area, level of herbivory, stomatal number, stomatal length, carbon and nitrogen concentration were measured for the leaves of each sample. For statistical analysis, linear mixed effect models, the Canonical Correlation Analysis (CCA) and Non-Parametric Multivariate Analysis of Variance (NPMANOVA) were applied. Herbivory, nitrogen and carbon concentration were significantly different in autumn compared to spring and summer (p value < 0.05), while stomatal length was differentiated between spring and the other two seasons (p value < 0.01). The seasonal differentiation of the bacterial community structure was explained by the first and second axes (29.7% and 25.3%, respectively) in the CCA. The bacterial community structure significantly correlated with herbivory, nitrogen concentration and stomatal length. We conclude that herbivory, nitrogen content, and size of stomatal aperture at the leaf level are important for endophyte colonization in oaks growth in alpine forest environments.
bibliographic citation: Borruso et al. (2018) Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory. PeerJ 6:e5769 https://doi.org/10.7717/peerj.5769
date submitted: 2018-02-28
date accepted: 2018-09-17
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borruso
  given name: Luigimaria
author list: Agent
  family name: Wellstein
  given name: Camilla
author list: Agent
  family name: Bani
  given name: Alessia
author list: Agent
  family name: Casagrande Bacchiocchi
  given name: Sara
author list: Agent
  family name: Margoni
  given name: Ania
author list: Agent
  family name: Tonin
  given name: Rita
author list: Agent
  family name: Zerbe
  given name: Stefan
author list: Agent
  family name: Brusetti
  given name: Lorenzo
doi: 10.7717/peerj.5769
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Borruso et al.
attribution name: Borruso et al.

Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient
type: item
type: AcademicArticle
description: The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.
format: application/pdf
format: text/html
creator: Xin Qian
creator: Liang Chen
creator: Xiaoming Guo
creator: Dan He
creator: Miaomiao Shi
creator: Dianxiang Zhang
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.5767
publisher: PeerJ Inc.
rights: © 2018 Qian et al.
abstract: The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.
bibliographic citation: Qian et al. (2018) Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient. PeerJ 6:e5767 https://doi.org/10.7717/peerj.5767
date submitted: 2018-04-30
date accepted: 2018-09-17
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qian
  given name: Xin
author list: Agent
  family name: Chen
  given name: Liang
author list: Agent
  family name: Guo
  given name: Xiaoming
author list: Agent
  family name: He
  given name: Dan
author list: Agent
  family name: Shi
  given name: Miaomiao
author list: Agent
  family name: Zhang
  given name: Dianxiang
doi: 10.7717/peerj.5767
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Qian et al.
attribution name: Qian et al.

Building interpretable models for polypharmacy prediction in older chronic patients based on drug prescription records
type: item
type: AcademicArticle
description: Background Multimorbidity presents an increasingly common problem in older population, and is tightly related to polypharmacy, i.e., concurrent use of multiple medications by one individual. Detecting polypharmacy from drug prescription records is not only related to multimorbidity, but can also point at incorrect use of medicines. In this work, we build models for predicting polypharmacy from drug prescription records for newly diagnosed chronic patients. We evaluate the models’ performance with a strong focus on interpretability of the results. Methods A centrally collected nationwide dataset of prescription records was used to perform electronic phenotyping of patients for the following two chronic conditions: type 2 diabetes mellitus (T2D) and cardiovascular disease (CVD). In addition, a hospital discharge dataset was linked to the prescription records. A regularized regression model was built for 11 different experimental scenarios on two datasets, and complexity of the model was controlled with a maximum number of dimensions (MND) parameter. Performance and interpretability of the model were evaluated with AUC, AUPRC, calibration plots, and interpretation by a medical doctor. Results For the CVD model, AUC and AUPRC values of 0.900 (95% [0.898–0.901]) and 0.640 (0.635–0.645) were reached, respectively, while for the T2D model the values were 0.808 (0.803–0.812) and 0.732 (0.725–0.739). Reducing complexity of the model by 65% and 48% for CVD and T2D, resulted in 3% and 4% lower AUC, and 4% and 5% lower AUPRC values, respectively. Calibration plots for our models showed that we can achieve moderate calibration with reducing the models’ complexity without significant loss of predictive performance. Discussion In this study, we found that it is possible to use drug prescription data to build a model for polypharmacy prediction in older population. In addition, the study showed that it is possible to find a balance between good performance and interpretability of t…
format: application/pdf
format: text/html
creator: Simon Kocbek
creator: Primoz Kocbek
creator: Andraz Stozer
creator: Tina Zupanic
creator: Tudor Groza
creator: Gregor Stiglic
subject: Drugs and Devices
subject: Public Health
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.5765
publisher: PeerJ Inc.
rights: © 2018 Kocbek et al.
abstract: Background Multimorbidity presents an increasingly common problem in older population, and is tightly related to polypharmacy, i.e., concurrent use of multiple medications by one individual. Detecting polypharmacy from drug prescription records is not only related to multimorbidity, but can also point at incorrect use of medicines. In this work, we build models for predicting polypharmacy from drug prescription records for newly diagnosed chronic patients. We evaluate the models’ performance with a strong focus on interpretability of the results. Methods A centrally collected nationwide dataset of prescription records was used to perform electronic phenotyping of patients for the following two chronic conditions: type 2 diabetes mellitus (T2D) and cardiovascular disease (CVD). In addition, a hospital discharge dataset was linked to the prescription records. A regularized regression model was built for 11 different experimental scenarios on two datasets, and complexity of the model was controlled with a maximum number of dimensions (MND) parameter. Performance and interpretability of the model were evaluated with AUC, AUPRC, calibration plots, and interpretation by a medical doctor. Results For the CVD model, AUC and AUPRC values of 0.900 (95% [0.898–0.901]) and 0.640 (0.635–0.645) were reached, respectively, while for the T2D model the values were 0.808 (0.803–0.812) and 0.732 (0.725–0.739). Reducing complexity of the model by 65% and 48% for CVD and T2D, resulted in 3% and 4% lower AUC, and 4% and 5% lower AUPRC values, respectively. Calibration plots for our models showed that we can achieve moderate calibration with reducing the models’ complexity without significant loss of predictive performance. Discussion In this study, we found that it is possible to use drug prescription data to build a model for polypharmacy prediction in older population. In addition, the study showed that it is possible to find a balance between good performance and interpretability of t…
bibliographic citation: Kocbek et al. (2018) Building interpretable models for polypharmacy prediction in older chronic patients based on drug prescription records. PeerJ 6:e5765 https://doi.org/10.7717/peerj.5765
date submitted: 2018-04-11
date accepted: 2018-09-17
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kocbek
  given name: Simon
author list: Agent
  family name: Kocbek
  given name: Primoz
author list: Agent
  family name: Stozer
  given name: Andraz
author list: Agent
  family name: Zupanic
  given name: Tina
author list: Agent
  family name: Groza
  given name: Tudor
author list: Agent
  family name: Stiglic
  given name: Gregor
doi: 10.7717/peerj.5765
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Kocbek et al.
attribution name: Kocbek et al.

Bite marks on the frill of a juvenile Centrosaurus from the Late Cretaceous Dinosaur Provincial Park Formation, Alberta, Canada
type: item
type: AcademicArticle
description: Bite marks on bones can provide critical information about interactions between carnivores and animals they consumed (or attempted to) in the fossil record. Data from such interactions is somewhat sparse and is hampered by a lack of records in the scientific literature. Here, we present a rare instance of feeding traces on the frill of a juvenile ceratopsian dinosaur from the late Campanian Dinosaur Park Formation of Alberta. It is difficult to determine the likely tracemaker(s) but the strongest candidate is a small-bodied theropod such as a dromaeosaur or juvenile tyrannosaur. This marks the first documented case of carnivore consumption of a juvenile ceratopsid, but may represent scavenging as opposed to predation.
format: application/pdf
format: text/html
creator: David W.E. Hone
creator: Darren H. Tanke
creator: Caleb M. Brown
subject: Animal Behavior
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.5748
publisher: PeerJ Inc.
rights: © 2018 Hone et al.
abstract: Bite marks on bones can provide critical information about interactions between carnivores and animals they consumed (or attempted to) in the fossil record. Data from such interactions is somewhat sparse and is hampered by a lack of records in the scientific literature. Here, we present a rare instance of feeding traces on the frill of a juvenile ceratopsian dinosaur from the late Campanian Dinosaur Park Formation of Alberta. It is difficult to determine the likely tracemaker(s) but the strongest candidate is a small-bodied theropod such as a dromaeosaur or juvenile tyrannosaur. This marks the first documented case of carnivore consumption of a juvenile ceratopsid, but may represent scavenging as opposed to predation.
bibliographic citation: Hone et al. (2018) Bite marks on the frill of a juvenile Centrosaurus from the Late Cretaceous Dinosaur Provincial Park Formation, Alberta, Canada. PeerJ 6:e5748 https://doi.org/10.7717/peerj.5748
date submitted: 2018-02-06
date accepted: 2018-09-11
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hone
  given name: David W.E.
author list: Agent
  family name: Tanke
  given name: Darren H.
author list: Agent
  family name: Brown
  given name: Caleb M.
doi: 10.7717/peerj.5748
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: © 2018 Hone et al.
attribution name: Hone et al.

Movements and dispersal of brown trout (Salmo trutta Linnaeus, 1758) in Mediterranean streams: influence of habitat and biotic factors
type: item
type: AcademicArticle
description: Dispersal is a critical determinant of animal distribution and population dynamics, and is essential information for management planning. We studied the movement patterns and the influence of habitat and biotic factors on Mediterranean brown trout (Salmo trutta) by mark-recapture methods in three headwater streams of the Ebro Basin (NE Iberian Peninsula). Fish were sampled by electrofishing on five occasions over 18–24 months and movements of over 3,000 individually tagged trout (age 1+ onwards) were recorded. Most of the tagged fish exhibited limited movement and were recaptured within 100 m from the initial capture section. Small seasonal differences in the movement pattern were observed, but in two of the streams, displacement distances increased prior the spawning period in autumn. The frequency distributions of dispersal distances were highly leptokurtic and skewed to the right and fitted well to a two-group exponential model, thus trout populations were composed of mobile and stationary individuals, the latter being the predominant component in the populations (71.1–87.5% of individuals). The mean dispersal distances, for fish captured at least in three sampling events, ranged 20.7–45.4 m for the stationary group and 229.4–540.5 m for the mobile group. Moving brown trout were larger than non-moving individuals and exhibited higher growth rates in two of the streams. Habitat features were not consistently linked to movement rates, but there were some interaction effects between stream and habitat characteristics such as depth, cover and water velocity.
format: application/pdf
format: text/html
creator: Enric Aparicio
creator: Rafel Rocaspana
creator: Adolfo de Sostoa
creator: Antoni Palau-Ibars
creator: Carles Alcaraz
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.5730
publisher: PeerJ Inc.
rights: © 2018 Aparicio et al.
abstract: Dispersal is a critical determinant of animal distribution and population dynamics, and is essential information for management planning. We studied the movement patterns and the influence of habitat and biotic factors on Mediterranean brown trout (Salmo trutta) by mark-recapture methods in three headwater streams of the Ebro Basin (NE Iberian Peninsula). Fish were sampled by electrofishing on five occasions over 18–24 months and movements of over 3,000 individually tagged trout (age 1+ onwards) were recorded. Most of the tagged fish exhibited limited movement and were recaptured within 100 m from the initial capture section. Small seasonal differences in the movement pattern were observed, but in two of the streams, displacement distances increased prior the spawning period in autumn. The frequency distributions of dispersal distances were highly leptokurtic and skewed to the right and fitted well to a two-group exponential model, thus trout populations were composed of mobile and stationary individuals, the latter being the predominant component in the populations (71.1–87.5% of individuals). The mean dispersal distances, for fish captured at least in three sampling events, ranged 20.7–45.4 m for the stationary group and 229.4–540.5 m for the mobile group. Moving brown trout were larger than non-moving individuals and exhibited higher growth rates in two of the streams. Habitat features were not consistently linked to movement rates, but there were some interaction effects between stream and habitat characteristics such as depth, cover and water velocity.
bibliographic citation: Aparicio et al. (2018) Movements and dispersal of brown trout (Salmo trutta Linnaeus, 1758) in Mediterranean streams: influence of habitat and biotic factors. PeerJ 6:e5730 https://doi.org/10.7717/peerj.5730
date submitted: 2018-03-16
date accepted: 2018-09-11
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aparicio
  given name: Enric
author list: Agent
  family name: Rocaspana
  given name: Rafel
author list: Agent
  family name: de Sostoa
  given name: Adolfo
author list: Agent
  family name: Palau-Ibars
  given name: Antoni
author list: Agent
  family name: Alcaraz
  given name: Carles
doi: 10.7717/peerj.5730
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Aparicio et al.
attribution name: Aparicio et al.

Nutritional value of several commercially important river fish species from the Czech Republic
type: item
type: AcademicArticle
description: Proximate and fatty acid (FA) composition of seven freshwater fish species from the Czech Republic were examined. Moreover, the index of atherogenicity (IA) and the index of thrombogenicity (IT) were calculated from the obtained data. These two indices along with the total content of the essential n-3 FAs, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) as well as the ratio of n-6/n3 FAs, provide good indicators for the nutritional value of the fish. The species had been selected owing to the limited amount of information about their nutritional composition available. Furthermore, they are not typically subject to aquaculture, being almost exclusively obtained by angling. The protein content was relatively stable in all species (17.1 ± 1.55 to 19.2 ± 2.20 g/100 g). The content of carbohydrates ranged from 0.02 ± 0.1 to 0.99 ± 0.0 g/100 g and ash from 1.08 ± 0.20 to 2.54 ± 1.57 g/100 g. As expected, a high variability was observed in the fat content (0.74 ± 0.04 to 4.04 ± 0.81 g/100 g) and the FA composition, as well as the contents of EPA and DHA. IA and IT were close to the values stated for the Eskimo diet, indicating a high nutritional value with a positive effect for human health.
format: application/pdf
format: text/html
creator: Sarvenaz Khalili Tilami
creator: Sabine Sampels
creator: Tomáš Zajíc
creator: Jakub Krejsa
creator: Jan Másílko
creator: Jan Mráz
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
description: doi:10.7717/peerj.5729
publisher: PeerJ Inc.
rights: © 2018 Khalili Tilami et al.
abstract: Proximate and fatty acid (FA) composition of seven freshwater fish species from the Czech Republic were examined. Moreover, the index of atherogenicity (IA) and the index of thrombogenicity (IT) were calculated from the obtained data. These two indices along with the total content of the essential n-3 FAs, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) as well as the ratio of n-6/n3 FAs, provide good indicators for the nutritional value of the fish. The species had been selected owing to the limited amount of information about their nutritional composition available. Furthermore, they are not typically subject to aquaculture, being almost exclusively obtained by angling. The protein content was relatively stable in all species (17.1 ± 1.55 to 19.2 ± 2.20 g/100 g). The content of carbohydrates ranged from 0.02 ± 0.1 to 0.99 ± 0.0 g/100 g and ash from 1.08 ± 0.20 to 2.54 ± 1.57 g/100 g. As expected, a high variability was observed in the fat content (0.74 ± 0.04 to 4.04 ± 0.81 g/100 g) and the FA composition, as well as the contents of EPA and DHA. IA and IT were close to the values stated for the Eskimo diet, indicating a high nutritional value with a positive effect for human health.
bibliographic citation: Khalili Tilami et al. (2018) Nutritional value of several commercially important river fish species from the Czech Republic. PeerJ 6:e5729 https://doi.org/10.7717/peerj.5729
date submitted: 2018-05-25
date accepted: 2018-09-12
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khalili Tilami
  given name: Sarvenaz
author list: Agent
  family name: Sampels
  given name: Sabine
author list: Agent
  family name: Zajíc
  given name: Tomáš
author list: Agent
  family name: Krejsa
  given name: Jakub
author list: Agent
  family name: Másílko
  given name: Jan
author list: Agent
  family name: Mráz
  given name: Jan
doi: 10.7717/peerj.5729
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: © 2018 Khalili Tilami et al.
attribution name: Khalili Tilami et al.

Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics
type: item
type: AcademicArticle
description: Background HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified the lncRNA that might be involved in HIVE, and explored the possible mechanism. Methods In the GEO public database, the microarray expression profile (GSE35864) of three regions of brain tissues (white matter, frontal cortex and basal ganglia brain tissues) was chosen, updated annotation was performed to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the differential expressed ncRNA, and Genbank of NCBI was used to identify lncRNAs. The StarBase, PITA and miRDB databases were used to predict the target miRNAs of lncRNA. The TargetScan, PicTar and MiRanda databases were used to predict the target genes of miRNAs. The GO and KEGG pathway analysis were used to make function analysis on the targets genes. Results Seventeen differentially expressed lncRNAs were observed in the white matter of brain tissues, for which 352 target miRNAs and 6,659 target genes were predicted. The GO function analysis indicated that the lncRNAs were mainly involved in the nuclear transcription and translation processes. The KEGG pathway analysis showed that the target genes were significantly enriched in 33 signal pathways, of which 11 were clearly related to the nervous system function. Discussion The brand-new and different microarray results can be obtained through the updated annotation of the chips, and it is feasible to identify lncRNAs from ordinary chips. The results suggest that lncRNA may be involved in the occurrence and development of HIVE, which provides a new direction for further research on the diagnosis and treatment of HIVE.
format: application/pdf
format: text/html
creator: Diangeng Li
creator: Pengtao Bao
creator: Zhiwei Yin
creator: Lei Sun
creator: Jin Feng
creator: Zheng He
creator: Meiling Jin
creator: Changting Liu
subject: Bioinformatics
subject: HIV
description: doi:10.7717/peerj.5721
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Background HIV-associated encephalitis (HIVE) is one of the common complications of HIV infection, and the pathogenesis of HIVE remains unclear, while lncRNA might be involved it. In this study, we made re-annotation on the expression profiling from the HIVE study in the public database, identified the lncRNA that might be involved in HIVE, and explored the possible mechanism. Methods In the GEO public database, the microarray expression profile (GSE35864) of three regions of brain tissues (white matter, frontal cortex and basal ganglia brain tissues) was chosen, updated annotation was performed to construct the non-cording-RNA (ncRNA) microarray data. Morpheus was used to identify the differential expressed ncRNA, and Genbank of NCBI was used to identify lncRNAs. The StarBase, PITA and miRDB databases were used to predict the target miRNAs of lncRNA. The TargetScan, PicTar and MiRanda databases were used to predict the target genes of miRNAs. The GO and KEGG pathway analysis were used to make function analysis on the targets genes. Results Seventeen differentially expressed lncRNAs were observed in the white matter of brain tissues, for which 352 target miRNAs and 6,659 target genes were predicted. The GO function analysis indicated that the lncRNAs were mainly involved in the nuclear transcription and translation processes. The KEGG pathway analysis showed that the target genes were significantly enriched in 33 signal pathways, of which 11 were clearly related to the nervous system function. Discussion The brand-new and different microarray results can be obtained through the updated annotation of the chips, and it is feasible to identify lncRNAs from ordinary chips. The results suggest that lncRNA may be involved in the occurrence and development of HIVE, which provides a new direction for further research on the diagnosis and treatment of HIVE.
bibliographic citation: Li et al. (2018) Exploration of the involvement of LncRNA in HIV-associated encephalitis using bioinformatics. PeerJ 6:e5721 https://doi.org/10.7717/peerj.5721
date submitted: 2018-04-27
date accepted: 2018-09-05
issued: 2018-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Diangeng
author list: Agent
  family name: Bao
  given name: Pengtao
author list: Agent
  family name: Yin
  given name: Zhiwei
author list: Agent
  family name: Sun
  given name: Lei
author list: Agent
  family name: Feng
  given name: Jin
author list: Agent
  family name: He
  given name: Zheng
author list: Agent
  family name: Jin
  given name: Meiling
author list: Agent
  family name: Liu
  given name: Changting
doi: 10.7717/peerj.5721
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-12
copyright: ©2018 Li et al.
attribution name: Li et al.

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