PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction
items: Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring
items: Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children
items: Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet
items: Elevation of MPF and MAPK gene expression, GSH content and mitochondrial distribution quality induced by melatonin promotes porcine oocyte maturation and development in vitro
items: Comparison of pediatric scoring systems for mortality in septic patients and the impact of missing information on their predictive power: a retrospective analysis
items: Immune cell landscape analysis reveals prognostic immune cells and its potential mechanism in squamous cell lung carcinoma
items: Cetaceans along the southeastern Brazilian coast: occurrence, distribution and niche inference at local scale
items: Are giant clams (Tridacna maxima) distractible? A multi-modal study
items: Predictors of Gull-billed tern (Gelochelidon nilotica) nest survival in artificial coastal saltpans, Bohai Bay, China

A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction
type: item
type: AcademicArticle
description: Cerebral edema (CE) is a non-specific pathological swelling of the brain secondary to any type of neurological injury. The real-time monitoring of focal CE mostly found in early stage is of great significance to reduce mortality and disability. Magnetic Induction Phase Shift (MIPS) is expected to achieve non-invasive continuous monitoring of CE. However, most existing MIPS sensors are made of hard materials which makes it difficult to accurately retrieve CE information. In this article, we designed a conformal two-coil structure and a single-coil structure, and studied their sensitivity map using finite element method (FEM). After that, the conformal MIPS sensor that is preferable for local CE monitoring was fabricated by flexible printed circuit (FPC). Next, physical experiments were conducted to investigate its performance on different levels of simulated CE solution volume, measurement distance, and bending. Subsequently, 14 rabbits were chosen to establish CE model and another three rabbits were selected as controls. The 24-hour MIPS real-time monitoring experiments was carried out to verify that the feasibility. Results showed a gentler attenuation trend of the conformal two-coil structure, compared with the single-coil structure. In addition, the novel flexible conformal MIPS sensor has a characteristic of being robust to bending according to the physical experiments. The results of animal experiments showed that the sensor can be used for CE monitoring. It can be concluded that this flexible conformal MIPS sensor is desirable for local focusing measurement of CE and subsequent multidimensional information extraction for predicting model. Also, it enables a much more comfortable environment for long-time bedside monitoring.
format: application/pdf
format: text/html
creator: Jingbo Chen
creator: Gen Li
creator: Mingsheng Chen
creator: Gui Jin
creator: Shuanglin Zhao
creator: Zelin Bai
creator: Jun Yang
creator: Huayou Liang
creator: Jia Xu
creator: Jian Sun
creator: Mingxin Qin
subject: Bioengineering
subject: Biophysics
subject: Neurology
subject: Computational Science
description: doi:10.7717/peerj.10079
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Cerebral edema (CE) is a non-specific pathological swelling of the brain secondary to any type of neurological injury. The real-time monitoring of focal CE mostly found in early stage is of great significance to reduce mortality and disability. Magnetic Induction Phase Shift (MIPS) is expected to achieve non-invasive continuous monitoring of CE. However, most existing MIPS sensors are made of hard materials which makes it difficult to accurately retrieve CE information. In this article, we designed a conformal two-coil structure and a single-coil structure, and studied their sensitivity map using finite element method (FEM). After that, the conformal MIPS sensor that is preferable for local CE monitoring was fabricated by flexible printed circuit (FPC). Next, physical experiments were conducted to investigate its performance on different levels of simulated CE solution volume, measurement distance, and bending. Subsequently, 14 rabbits were chosen to establish CE model and another three rabbits were selected as controls. The 24-hour MIPS real-time monitoring experiments was carried out to verify that the feasibility. Results showed a gentler attenuation trend of the conformal two-coil structure, compared with the single-coil structure. In addition, the novel flexible conformal MIPS sensor has a characteristic of being robust to bending according to the physical experiments. The results of animal experiments showed that the sensor can be used for CE monitoring. It can be concluded that this flexible conformal MIPS sensor is desirable for local focusing measurement of CE and subsequent multidimensional information extraction for predicting model. Also, it enables a much more comfortable environment for long-time bedside monitoring.
bibliographic citation: Chen et al. (2020) A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction. PeerJ 8:e10079 https://doi.org/10.7717/peerj.10079
date submitted: 2020-06-02
date accepted: 2020-09-11
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jingbo
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Chen
  given name: Mingsheng
author list: Agent
  family name: Jin
  given name: Gui
author list: Agent
  family name: Zhao
  given name: Shuanglin
author list: Agent
  family name: Bai
  given name: Zelin
author list: Agent
  family name: Yang
  given name: Jun
author list: Agent
  family name: Liang
  given name: Huayou
author list: Agent
  family name: Xu
  given name: Jia
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Qin
  given name: Mingxin
doi: 10.7717/peerj.10079
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring
type: item
type: AcademicArticle
description: The social context of social species such as sheep can modify their physiological and behavioural responses to stressors, through social buffering and social facilitation. Social buffering can lead to amelioration of stress, while social facilitation can lead to stress responses in an observer animal in the presence of a conspecific in distress. The current study investigated twin lambs undergoing ring castration, grouped either homogeneously with a castrated lamb (actor), or heterogeneously with a non-castrated lamb (observer) to examine the impact of social grouping on behavioural responses. Each lamb was scored for two classes of behaviour: pain-related behaviours and postures that are putatively related to the response to castration; and attentional behaviours directed at its twin. Thus, each lamb participated in the experiment as an actor exhibiting pain-related behaviours and postures, and as an observer of its twin. When behaviours of lambs were assessed as actors, there was a significant (P < 0.05) effect of castration but no significant effect of social grouping on expression of pain-related behaviours. When behaviours of lambs were assessed as observers, homogeneous grouping of castrated lambs increased attention towards the other twin in comparison to non-castrated lambs grouped homogeneously or lambs grouped heterogeneously (P < 0.01). Non-castrated lambs grouped homogeneously demonstrated significantly lower numbers of head direction changes (P < 0.001) and lower number of ear posture changes (P < 0.05) than heterogeneously grouped or castrated lambs. This study indicates that social attention between twin lambs is not clearly dependent on pain status of the actor lamb. It suggests that in order for the observer lamb to provide significant attention to the actor lamb displaying pain-related behaviour, the observer lamb also needs to be experiencing pain concurrently. Furthermore, there is some evidence that the presence of pain-related behaviours can le…
format: application/pdf
format: text/html
creator: Andrew Inhyuk Cho
creator: Caroline Lee
creator: Alison Small
subject: Agricultural Science
subject: Animal Behavior
subject: Veterinary Medicine
subject: Ethical Issues
description: doi:10.7717/peerj.10081
publisher: PeerJ Inc.
rights: © 2020 Cho et al.
abstract: The social context of social species such as sheep can modify their physiological and behavioural responses to stressors, through social buffering and social facilitation. Social buffering can lead to amelioration of stress, while social facilitation can lead to stress responses in an observer animal in the presence of a conspecific in distress. The current study investigated twin lambs undergoing ring castration, grouped either homogeneously with a castrated lamb (actor), or heterogeneously with a non-castrated lamb (observer) to examine the impact of social grouping on behavioural responses. Each lamb was scored for two classes of behaviour: pain-related behaviours and postures that are putatively related to the response to castration; and attentional behaviours directed at its twin. Thus, each lamb participated in the experiment as an actor exhibiting pain-related behaviours and postures, and as an observer of its twin. When behaviours of lambs were assessed as actors, there was a significant (P < 0.05) effect of castration but no significant effect of social grouping on expression of pain-related behaviours. When behaviours of lambs were assessed as observers, homogeneous grouping of castrated lambs increased attention towards the other twin in comparison to non-castrated lambs grouped homogeneously or lambs grouped heterogeneously (P < 0.01). Non-castrated lambs grouped homogeneously demonstrated significantly lower numbers of head direction changes (P < 0.001) and lower number of ear posture changes (P < 0.05) than heterogeneously grouped or castrated lambs. This study indicates that social attention between twin lambs is not clearly dependent on pain status of the actor lamb. It suggests that in order for the observer lamb to provide significant attention to the actor lamb displaying pain-related behaviour, the observer lamb also needs to be experiencing pain concurrently. Furthermore, there is some evidence that the presence of pain-related behaviours can le…
bibliographic citation: Cho et al. (2020) Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring. PeerJ 8:e10081 https://doi.org/10.7717/peerj.10081
date submitted: 2020-04-23
date accepted: 2020-09-11
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Andrew Inhyuk
author list: Agent
  family name: Lee
  given name: Caroline
author list: Agent
  family name: Small
  given name: Alison
doi: 10.7717/peerj.10081
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: © 2020 Cho et al.
attribution name: Cho et al.

Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children
type: item
type: AcademicArticle
description: Several studies have tried to establish the factors that underlie mathematical ability across development. Among them, spatial and motor abilities might play a relevant role, but no studies jointly contemplate both types of abilities to account for mathematical performance. The present study was designed to observe the roles of spatial and motor skills in mathematical performance. A total of 305 children aged between 6 and 8 years took part in this study. A generalized linear regression model with mathematical performance as a dependent variable was performed. Results revealed that Block design (as a visuospatial reasoning measure) accounted for mathematical performance, especially among 6- and 7-year-olds but not in 8-year-olds. After controlling for the effect of the block design, mental rotation and manual dexterity predicted mathematical performance. These findings highlight the role of underlying cognitive (spatial) and motor abilities in supporting mathematical achievement in primary school children.
format: application/pdf
format: text/html
creator: Laura M. Fernández-Méndez
creator: María José Contreras
creator: Irene Cristina Mammarella
creator: Tommaso Feraco
creator: Chiara Meneghetti
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.10095
publisher: PeerJ Inc.
rights: © 2020 Fernández-Méndez et al.
abstract: Several studies have tried to establish the factors that underlie mathematical ability across development. Among them, spatial and motor abilities might play a relevant role, but no studies jointly contemplate both types of abilities to account for mathematical performance. The present study was designed to observe the roles of spatial and motor skills in mathematical performance. A total of 305 children aged between 6 and 8 years took part in this study. A generalized linear regression model with mathematical performance as a dependent variable was performed. Results revealed that Block design (as a visuospatial reasoning measure) accounted for mathematical performance, especially among 6- and 7-year-olds but not in 8-year-olds. After controlling for the effect of the block design, mental rotation and manual dexterity predicted mathematical performance. These findings highlight the role of underlying cognitive (spatial) and motor abilities in supporting mathematical achievement in primary school children.
bibliographic citation: Fernández-Méndez et al. (2020) Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children. PeerJ 8:e10095 https://doi.org/10.7717/peerj.10095
date submitted: 2020-04-29
date accepted: 2020-09-14
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernández-Méndez
  given name: Laura M.
author list: Agent
  family name: Contreras
  given name: María José
author list: Agent
  family name: Mammarella
  given name: Irene Cristina
author list: Agent
  family name: Feraco
  given name: Tommaso
author list: Agent
  family name: Meneghetti
  given name: Chiara
doi: 10.7717/peerj.10095
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Fernández-Méndez et al.
attribution name: Fernández-Méndez et al.

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet
type: item
type: AcademicArticle
description: Background The fecal microbiota from obese individuals can induce obesity in animal models. In addition, studies in humans, animal models and dogs have revealed that the fecal microbiota of subjects with obesity is different from that of lean subjects and changes after weight loss. However, the impact of weight loss on the fecal microbiota in dogs with obesity has not been fully characterized. Methods In this study, we used 16S rRNA gene sequencing to investigate the differences in the fecal microbiota of 20 pet dogs with obesity that underwent a weight loss program. The endpoint of the weight loss program was individually tailored to the ideal body weight of each dog. In addition, we evaluated the qPCR based Dysbiosis Index before and after weight loss. Results After weight loss, the fecal microbiota structure of dogs with obesity changed significantly (weightedANOSIM; p = 0.016, R = 0.073), showing an increase in bacterial richness (p = 0.007), evenness (p = 0.007) and the number of bacterial species (p = 0.007). The fecal microbiota composition of obese dogs after weight loss was characterized by a decrease in Firmicutes (92.3% to 78.2%, q = 0.001), and increase in Bacteroidetes (1.4% to 10.1%, q = 0.002) and Fusobacteria (1.6% to 6.2%, q = 0.040). The qPCR results revealed an overall decrease in the Dysbiosis Index, driven mostly due to a significant decrease in E. coli (p = 0.030), and increase in Fusobacterium spp. (p = 0.017). Conclusion The changes observed in the fecal microbiota of dogs with obesity after weight loss with a weight loss diet rich in fiber and protein were in agreement with previous studies in humans, that reported an increase of bacterial biodiversity and a decrease of the ratio Firmicutes/Bacteroidetes.
format: application/pdf
format: text/html
creator: Sandra Bermudez Sanchez
creator: Rachel Pilla
creator: Benjamin Sarawichitr
creator: Alessandro Gramenzi
creator: Fulvio Marsilio
creator: Joerg M. Steiner
creator: Jonathan A. Lidbury
creator: Georgiana R.T. Woods
creator: Alexander J. German
creator: Jan S. Suchodolski
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9706
publisher: PeerJ Inc.
rights: © 2020 Bermudez Sanchez et al.
abstract: Background The fecal microbiota from obese individuals can induce obesity in animal models. In addition, studies in humans, animal models and dogs have revealed that the fecal microbiota of subjects with obesity is different from that of lean subjects and changes after weight loss. However, the impact of weight loss on the fecal microbiota in dogs with obesity has not been fully characterized. Methods In this study, we used 16S rRNA gene sequencing to investigate the differences in the fecal microbiota of 20 pet dogs with obesity that underwent a weight loss program. The endpoint of the weight loss program was individually tailored to the ideal body weight of each dog. In addition, we evaluated the qPCR based Dysbiosis Index before and after weight loss. Results After weight loss, the fecal microbiota structure of dogs with obesity changed significantly (weightedANOSIM; p = 0.016, R = 0.073), showing an increase in bacterial richness (p = 0.007), evenness (p = 0.007) and the number of bacterial species (p = 0.007). The fecal microbiota composition of obese dogs after weight loss was characterized by a decrease in Firmicutes (92.3% to 78.2%, q = 0.001), and increase in Bacteroidetes (1.4% to 10.1%, q = 0.002) and Fusobacteria (1.6% to 6.2%, q = 0.040). The qPCR results revealed an overall decrease in the Dysbiosis Index, driven mostly due to a significant decrease in E. coli (p = 0.030), and increase in Fusobacterium spp. (p = 0.017). Conclusion The changes observed in the fecal microbiota of dogs with obesity after weight loss with a weight loss diet rich in fiber and protein were in agreement with previous studies in humans, that reported an increase of bacterial biodiversity and a decrease of the ratio Firmicutes/Bacteroidetes.
bibliographic citation: Bermudez Sanchez et al. (2020) Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet. PeerJ 8:e9706 https://doi.org/10.7717/peerj.9706
date submitted: 2020-03-23
date accepted: 2020-07-22
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bermudez Sanchez
  given name: Sandra
author list: Agent
  family name: Pilla
  given name: Rachel
author list: Agent
  family name: Sarawichitr
  given name: Benjamin
author list: Agent
  family name: Gramenzi
  given name: Alessandro
author list: Agent
  family name: Marsilio
  given name: Fulvio
author list: Agent
  family name: Steiner
  given name: Joerg M.
author list: Agent
  family name: Lidbury
  given name: Jonathan A.
author list: Agent
  family name: Woods
  given name: Georgiana R.T.
author list: Agent
  family name: German
  given name: Alexander J.
author list: Agent
  family name: Suchodolski
  given name: Jan S.
doi: 10.7717/peerj.9706
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Bermudez Sanchez et al.
attribution name: Bermudez Sanchez et al.

Elevation of MPF and MAPK gene expression, GSH content and mitochondrial distribution quality induced by melatonin promotes porcine oocyte maturation and development in vitro
type: item
type: AcademicArticle
description: The MPF and MAPK genes play crucial roles during oocyte maturation processes. However, the pattern of MPF and MAPK gene expression induced by melatonin (MT) and its correlation to oocyte maturation quality during the process of porcine oocyte maturation in vitro remains unexplored. To unravel it, in this study, we cultured the porcine oocytes in maturation medium supplemented with 0, 10−6, 10−9, and 10−12 mol/L melatonin. Later, we analyzed the MPF and MAPK gene expression levels by RT-PCR and determined the maturation index (survival and maturation rate of oocytes). The GSH content in the single oocyte, and cytoplasmic mitochondrial maturation distribution after porcine oocyte maturation in vitro was also evaluated. We also assessed the effects of these changes on parthenogenetic embryonic developmental potential. The oocytes cultured with 10−9mol/L melatonin concentration showed higher oocyte maturation rate, and MPF and MAPK genes expression levels along with better mitochondrial distribution than the 0, 10−6, and 10−12 mol/L melatonin concentrations (p < 0.05). No significant difference was observed in the survival rates when the oocytes were cultured with different melatonin concentrations. The expression of the MPF gene in the oocytes cultured with 10−6 mol/L melatonin was higher than with 10−12 and 0 mol/L melatonin, and the expression of the MAPK gene in 10−6 and 10−12 group was higher than the control (p < 0.05). As far as the embryonic developmental potential is concerned, the cleavage and blastocyst rate of oocytes cultured with 10−6 and 10−9 mol/L melatonin was significantly higher than the 10−12 mol/L melatonin and control. In conclusion, 10−9–10−6 mol/L melatonin significantly induced the MPF and MAPK gene expression; besides, it could also be correlated with GSH content of single oocyte, mitochondrial maturation distribution, and the first polar body expulsion. These changes were also found to be associated with parthenogenetic embryo developmental po…
format: application/pdf
format: text/html
creator: Zimo Zhao
creator: Ling Yang
creator: Dan Zhang
creator: Zi Zheng
creator: Ning Li
creator: Qianjun Li
creator: Maosheng Cui
subject: Biotechnology
subject: Developmental Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.9913
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: The MPF and MAPK genes play crucial roles during oocyte maturation processes. However, the pattern of MPF and MAPK gene expression induced by melatonin (MT) and its correlation to oocyte maturation quality during the process of porcine oocyte maturation in vitro remains unexplored. To unravel it, in this study, we cultured the porcine oocytes in maturation medium supplemented with 0, 10−6, 10−9, and 10−12 mol/L melatonin. Later, we analyzed the MPF and MAPK gene expression levels by RT-PCR and determined the maturation index (survival and maturation rate of oocytes). The GSH content in the single oocyte, and cytoplasmic mitochondrial maturation distribution after porcine oocyte maturation in vitro was also evaluated. We also assessed the effects of these changes on parthenogenetic embryonic developmental potential. The oocytes cultured with 10−9mol/L melatonin concentration showed higher oocyte maturation rate, and MPF and MAPK genes expression levels along with better mitochondrial distribution than the 0, 10−6, and 10−12 mol/L melatonin concentrations (p < 0.05). No significant difference was observed in the survival rates when the oocytes were cultured with different melatonin concentrations. The expression of the MPF gene in the oocytes cultured with 10−6 mol/L melatonin was higher than with 10−12 and 0 mol/L melatonin, and the expression of the MAPK gene in 10−6 and 10−12 group was higher than the control (p < 0.05). As far as the embryonic developmental potential is concerned, the cleavage and blastocyst rate of oocytes cultured with 10−6 and 10−9 mol/L melatonin was significantly higher than the 10−12 mol/L melatonin and control. In conclusion, 10−9–10−6 mol/L melatonin significantly induced the MPF and MAPK gene expression; besides, it could also be correlated with GSH content of single oocyte, mitochondrial maturation distribution, and the first polar body expulsion. These changes were also found to be associated with parthenogenetic embryo developmental po…
bibliographic citation: Zhao et al. (2020) Elevation of MPF and MAPK gene expression, GSH content and mitochondrial distribution quality induced by melatonin promotes porcine oocyte maturation and development in vitro. PeerJ 8:e9913 https://doi.org/10.7717/peerj.9913
date submitted: 2020-04-01
date accepted: 2020-08-18
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Zimo
author list: Agent
  family name: Yang
  given name: Ling
author list: Agent
  family name: Zhang
  given name: Dan
author list: Agent
  family name: Zheng
  given name: Zi
author list: Agent
  family name: Li
  given name: Ning
author list: Agent
  family name: Li
  given name: Qianjun
author list: Agent
  family name: Cui
  given name: Maosheng
doi: 10.7717/peerj.9913
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Comparison of pediatric scoring systems for mortality in septic patients and the impact of missing information on their predictive power: a retrospective analysis
type: item
type: AcademicArticle
description: Background Scores can assess the severity and course of disease and predict outcome in an objective manner. This information is needed for proper risk assessment and stratification. Furthermore, scoring systems support optimal patient care, resource management and are gaining in importance in terms of artificial intelligence. Objective This study evaluated and compared the prognostic ability of various common pediatric scoring systems (PRISM, PRISM III, PRISM IV, PIM, PIM2, PIM3, PELOD, PELOD 2) in order to determine which is the most applicable score for pediatric sepsis patients in terms of timing of disease survey and insensitivity to missing data. Methods We retrospectively examined data from 398 patients under 18 years of age, who were diagnosed with sepsis. Scores were assessed at ICU admission and re-evaluated on the day of peak C-reactive protein. The scores were compared for their ability to predict mortality in this specific patient population and for their impairment due to missing data. Results PIM (AUC 0.76 (0.68–0.76)), PIM2 (AUC 0.78 (0.72–0.78)) and PIM3 (AUC 0.76 (0.68–0.76)) scores together with PRSIM III (AUC 0.75 (0.68–0.75)) and PELOD 2 (AUC 0.75 (0.66–0.75)) are the most suitable scores for determining patient prognosis at ICU admission. Once sepsis is pronounced, PELOD 2 (AUC 0.84 (0.77–0.91)) and PRISM IV (AUC 0.8 (0.72–0.88)) become significantly better in their performance and count among the best prognostic scores for use at this time together with PRISM III (AUC 0.81 (0.73–0.89)). PELOD 2 is good for monitoring and, like the PIM scores, is also largely insensitive to missing values. Conclusion Overall, PIM scores show comparatively good performance, are stable as far as timing of the disease survey is concerned, and they are also relatively stable in terms of missing parameters. PELOD 2 is best suitable for monitoring clinical course.
format: application/pdf
format: text/html
creator: Christian Niederwanger
creator: Thomas Varga
creator: Tobias Hell
creator: Daniel Stuerzel
creator: Jennifer Prem
creator: Magdalena Gassner
creator: Franziska Rickmann
creator: Christina Schoner
creator: Daniela Hainz
creator: Gerard Cortina
creator: Benjamin Hetzer
creator: Benedikt Treml
creator: Mirjam Bachler
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.9993
publisher: PeerJ Inc.
rights: © 2020 Niederwanger et al.
abstract: Background Scores can assess the severity and course of disease and predict outcome in an objective manner. This information is needed for proper risk assessment and stratification. Furthermore, scoring systems support optimal patient care, resource management and are gaining in importance in terms of artificial intelligence. Objective This study evaluated and compared the prognostic ability of various common pediatric scoring systems (PRISM, PRISM III, PRISM IV, PIM, PIM2, PIM3, PELOD, PELOD 2) in order to determine which is the most applicable score for pediatric sepsis patients in terms of timing of disease survey and insensitivity to missing data. Methods We retrospectively examined data from 398 patients under 18 years of age, who were diagnosed with sepsis. Scores were assessed at ICU admission and re-evaluated on the day of peak C-reactive protein. The scores were compared for their ability to predict mortality in this specific patient population and for their impairment due to missing data. Results PIM (AUC 0.76 (0.68–0.76)), PIM2 (AUC 0.78 (0.72–0.78)) and PIM3 (AUC 0.76 (0.68–0.76)) scores together with PRSIM III (AUC 0.75 (0.68–0.75)) and PELOD 2 (AUC 0.75 (0.66–0.75)) are the most suitable scores for determining patient prognosis at ICU admission. Once sepsis is pronounced, PELOD 2 (AUC 0.84 (0.77–0.91)) and PRISM IV (AUC 0.8 (0.72–0.88)) become significantly better in their performance and count among the best prognostic scores for use at this time together with PRISM III (AUC 0.81 (0.73–0.89)). PELOD 2 is good for monitoring and, like the PIM scores, is also largely insensitive to missing values. Conclusion Overall, PIM scores show comparatively good performance, are stable as far as timing of the disease survey is concerned, and they are also relatively stable in terms of missing parameters. PELOD 2 is best suitable for monitoring clinical course.
bibliographic citation: Niederwanger et al. (2020) Comparison of pediatric scoring systems for mortality in septic patients and the impact of missing information on their predictive power: a retrospective analysis. PeerJ 8:e9993 https://doi.org/10.7717/peerj.9993
date submitted: 2020-04-06
date accepted: 2020-08-28
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niederwanger
  given name: Christian
author list: Agent
  family name: Varga
  given name: Thomas
author list: Agent
  family name: Hell
  given name: Tobias
author list: Agent
  family name: Stuerzel
  given name: Daniel
author list: Agent
  family name: Prem
  given name: Jennifer
author list: Agent
  family name: Gassner
  given name: Magdalena
author list: Agent
  family name: Rickmann
  given name: Franziska
author list: Agent
  family name: Schoner
  given name: Christina
author list: Agent
  family name: Hainz
  given name: Daniela
author list: Agent
  family name: Cortina
  given name: Gerard
author list: Agent
  family name: Hetzer
  given name: Benjamin
author list: Agent
  family name: Treml
  given name: Benedikt
author list: Agent
  family name: Bachler
  given name: Mirjam
doi: 10.7717/peerj.9993
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Niederwanger et al.
attribution name: Niederwanger et al.

Immune cell landscape analysis reveals prognostic immune cells and its potential mechanism in squamous cell lung carcinoma
type: item
type: AcademicArticle
description: Background Squamous cell lung carcinoma (LUSC) was closely associated with smoking which was known to have a distant immunosuppression effect. In this study, we aimed to explore the relationship between immune cells and clinical outcomes of LUSC patients with smoking history. Methods The immune cell infiltration and RNA expression profiles of LUSC patients were collected from The Cancer Genome Atlas (TCGA). Then, the correlation between immune cell infiltration and clinical characteristics was explored. According to the level of immune cell infiltration, LUSC patients with smoking history were divided into high or low group to screen the differentially expressed lncRNAs and mRNAs. The prediction of target genes was performed by miRanda. Finally, the prognostic value of a certain signature was confirmed in an independent dataset. Results Higher abundance of tumor-infiltrating T follicular helper (Tfh) cells together with a lower abundance of resting memory CD4 T cells had been found in LUSC current reformed smokers for ≤15 years and current smoking patients. Moreover, Tfh cell infiltration was not only associated with better overall survival (OS) but also varied from different degrees of TNM stage. Low expression of lncRNA PWRN1 and its potential regulating genes DMRTB1, PIRT, APOBEC1, and ZPBP2 were associated with better OS. Combining PWRN1 and four regulating genes as a signature, patients with higher-level expression of the signature had shorter survival time in not only the TCGA but also in the GEO dataset. Conclusions It was found that Tfh cells presented higher infiltration in LUSC current reformed smokers for ≤15 years and current smokers, while resting memory CD4 T cells had lower infiltration. The signature consisting of PWRN1 as well as its predicted targeted mRNAs was dysregulated in different levels of Tfh cell infiltration and might indicate patients’ OS.
format: application/pdf
format: text/html
creator: Yongyong Wang
creator: Jianji Guo
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.9996
publisher: PeerJ Inc.
rights: © 2020 Wang and Guo
abstract: Background Squamous cell lung carcinoma (LUSC) was closely associated with smoking which was known to have a distant immunosuppression effect. In this study, we aimed to explore the relationship between immune cells and clinical outcomes of LUSC patients with smoking history. Methods The immune cell infiltration and RNA expression profiles of LUSC patients were collected from The Cancer Genome Atlas (TCGA). Then, the correlation between immune cell infiltration and clinical characteristics was explored. According to the level of immune cell infiltration, LUSC patients with smoking history were divided into high or low group to screen the differentially expressed lncRNAs and mRNAs. The prediction of target genes was performed by miRanda. Finally, the prognostic value of a certain signature was confirmed in an independent dataset. Results Higher abundance of tumor-infiltrating T follicular helper (Tfh) cells together with a lower abundance of resting memory CD4 T cells had been found in LUSC current reformed smokers for ≤15 years and current smoking patients. Moreover, Tfh cell infiltration was not only associated with better overall survival (OS) but also varied from different degrees of TNM stage. Low expression of lncRNA PWRN1 and its potential regulating genes DMRTB1, PIRT, APOBEC1, and ZPBP2 were associated with better OS. Combining PWRN1 and four regulating genes as a signature, patients with higher-level expression of the signature had shorter survival time in not only the TCGA but also in the GEO dataset. Conclusions It was found that Tfh cells presented higher infiltration in LUSC current reformed smokers for ≤15 years and current smokers, while resting memory CD4 T cells had lower infiltration. The signature consisting of PWRN1 as well as its predicted targeted mRNAs was dysregulated in different levels of Tfh cell infiltration and might indicate patients’ OS.
bibliographic citation: Wang et al. (2020) Immune cell landscape analysis reveals prognostic immune cells and its potential mechanism in squamous cell lung carcinoma. PeerJ 8:e9996 https://doi.org/10.7717/peerj.9996
date submitted: 2020-04-28
date accepted: 2020-08-28
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yongyong
author list: Agent
  family name: Guo
  given name: Jianji
doi: 10.7717/peerj.9996
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Wang and Guo
attribution name: Wang and Guo

Cetaceans along the southeastern Brazilian coast: occurrence, distribution and niche inference at local scale
type: item
type: AcademicArticle
description: It is deemed important to understand cetacean occurrence and distribution to comprehend their ecological roles. The geographical occurrence of species’ niche can be used to better describe their potential distribution. The niche can be defined using environmental variables. Those variables are considered static and not affected by biological activities. The present study goal was to assess the occurrence and distribution of cetaceans along the southeastern Brazilian coast, as well as to define the fundamental and realized niche of each species and to investigate niche overlap at local scale. The environmental requirements for each species were also investigated throughout statistical tests. Sighting data were obtained through oceanographic surveys conducted between 2012 and 2015. The environmental variables available on MARSPEC and the software NicheA were used for the ecological niche modeling. A total of twelve cetacean species were identified and the potential distribution areas of the six commonest ones were defined. Even though the species presented different environmental preferences, most of them had partial overlap among niches and potential distribution areas. The environmental heterogeneity of the study area might support the co-occurrence of different species with different environmental requirements.
format: application/pdf
format: text/html
creator: Giovanna Corrêa e Figueiredo
creator: Karina Bohrer do Amaral
creator: Marcos César de Oliveira Santos
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.10000
publisher: PeerJ Inc.
rights: © 2020 Figueiredo et al.
abstract: It is deemed important to understand cetacean occurrence and distribution to comprehend their ecological roles. The geographical occurrence of species’ niche can be used to better describe their potential distribution. The niche can be defined using environmental variables. Those variables are considered static and not affected by biological activities. The present study goal was to assess the occurrence and distribution of cetaceans along the southeastern Brazilian coast, as well as to define the fundamental and realized niche of each species and to investigate niche overlap at local scale. The environmental requirements for each species were also investigated throughout statistical tests. Sighting data were obtained through oceanographic surveys conducted between 2012 and 2015. The environmental variables available on MARSPEC and the software NicheA were used for the ecological niche modeling. A total of twelve cetacean species were identified and the potential distribution areas of the six commonest ones were defined. Even though the species presented different environmental preferences, most of them had partial overlap among niches and potential distribution areas. The environmental heterogeneity of the study area might support the co-occurrence of different species with different environmental requirements.
bibliographic citation: Figueiredo et al. (2020) Cetaceans along the southeastern Brazilian coast: occurrence, distribution and niche inference at local scale. PeerJ 8:e10000 https://doi.org/10.7717/peerj.10000
date submitted: 2019-12-09
date accepted: 2020-08-29
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Figueiredo
  given name: Giovanna Corrêa e
author list: Agent
  family name: do Amaral
  given name: Karina Bohrer
author list: Agent
  family name: Santos
  given name: Marcos César de Oliveira
doi: 10.7717/peerj.10000
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Figueiredo et al.
attribution name: Figueiredo et al.

Are giant clams (Tridacna maxima) distractible? A multi-modal study
type: item
type: AcademicArticle
description: To properly assess risk, an animal must focus its attention on relevant external stimuli; however, attention can be reallocated when distracting stimuli are present. This reallocation of attention may interfere with an individual’s ability to effectively assess risk and may impede its response. Multiple stimuli presented together can have additive effects as distractors, and these include stimuli in different modalities. Although changes in noise and water flow are detectable by some bivalves, this has not been studied in the context of risk assessment or distraction. We experimentally exposed giant clams (Tridacna maxima) to changes in water particle movement through underwater sound (motorboat noise) and increased water flow to determine whether these stimuli, individually or together, modified risk assessment or caused distraction. We found that clams responded to sound, flow, and their combination by increasing frequency of mantle retractions (a potential anti-predator response) when exposed to a stimulus. Sound alone did not change risk assessment in either the latency to close or to reemerge following closure. However, when exposed to both stimuli simultaneously, clams increased their latency to close. We suggest that clams perceive sound and flow in an additive way, and are thus distracted. Interestingly, and uniquely, clams discriminate these multimodal stimuli through a single sensory modality. For sessile clams, anthropogenic noise is detectable, yet unavoidable, suggesting that they be especially vulnerable to marine noise pollution.
format: application/pdf
format: text/html
creator: Ryan Doyle
creator: Jonathan Kim
creator: Angelika Pe
creator: Daniel T. Blumstein
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10050
publisher: PeerJ Inc.
rights: © 2020 Doyle et al.
abstract: To properly assess risk, an animal must focus its attention on relevant external stimuli; however, attention can be reallocated when distracting stimuli are present. This reallocation of attention may interfere with an individual’s ability to effectively assess risk and may impede its response. Multiple stimuli presented together can have additive effects as distractors, and these include stimuli in different modalities. Although changes in noise and water flow are detectable by some bivalves, this has not been studied in the context of risk assessment or distraction. We experimentally exposed giant clams (Tridacna maxima) to changes in water particle movement through underwater sound (motorboat noise) and increased water flow to determine whether these stimuli, individually or together, modified risk assessment or caused distraction. We found that clams responded to sound, flow, and their combination by increasing frequency of mantle retractions (a potential anti-predator response) when exposed to a stimulus. Sound alone did not change risk assessment in either the latency to close or to reemerge following closure. However, when exposed to both stimuli simultaneously, clams increased their latency to close. We suggest that clams perceive sound and flow in an additive way, and are thus distracted. Interestingly, and uniquely, clams discriminate these multimodal stimuli through a single sensory modality. For sessile clams, anthropogenic noise is detectable, yet unavoidable, suggesting that they be especially vulnerable to marine noise pollution.
bibliographic citation: Doyle et al. (2020) Are giant clams (Tridacna maxima) distractible? A multi-modal study. PeerJ 8:e10050 https://doi.org/10.7717/peerj.10050
date submitted: 2020-05-15
date accepted: 2020-09-06
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doyle
  given name: Ryan
author list: Agent
  family name: Kim
  given name: Jonathan
author list: Agent
  family name: Pe
  given name: Angelika
author list: Agent
  family name: Blumstein
  given name: Daniel T.
doi: 10.7717/peerj.10050
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Doyle et al.
attribution name: Doyle et al.

Predictors of Gull-billed tern (Gelochelidon nilotica) nest survival in artificial coastal saltpans, Bohai Bay, China
type: item
type: AcademicArticle
description: Background Coastal saltpans are a common supratidal human-modified wetland habitat found within many coastal landscape mosaics. Commercial salt production and aquaculture practices often result in the creation of exposed coastal substrates that could provide suitable breeding habitat for waterbird populations; however, few studies have quantified waterbird breeding success in these artificial wetlands. Methods Here we examine the nesting behavior of the Gull-billed tern (Gelochelidon nilotica) breeding in the Nanpu coastal saltpans of Bohai Bay, Yellow Sea, China over three consecutive nesting seasons (2017–2019) by using nest survival model in Program MARK. Results The results revealed that nest survival of Gull-billed terns in coastal saltpans (0.697) was higher than previously published estimates from other regions, with an estimated daily survival rate (DSR) of 0.982 ± 0.001 (±95% CI). High nest survival was mainly attributed to low levels of human disturbances and low predation rates, while exposure to strong winds, flooding and silting were the main factors causing nest failure. Model-averaged estimates revealed that eggs laid in nests located on ‘habitat islands’ with feather or clam shell substrates were most likely to hatch. Initiation date, nest age, clutch size and quadratic effects of nearest-neighbor distance, nearest distance to road and nearest distance to water were all significant predictors of nest success, but the nest survival declined overall from 2017 to 2019 due to the degradation and loss of breeding habitat anthropogenically caused by rising water levels. Discussion Coastal saltpans represent an alternative breeding habitat for the Gull-billed tern populations in Bohai Bay, but conservation management should prioritize flood prevention to improve the extent and quality of breeding habitat, concurrent with efforts to create further ‘habitat islands’ with suitable nesting substrate.
format: application/pdf
format: text/html
creator: Fuxing Wu
creator: Weipan Lei
creator: Huw Lloyd
creator: Zhengwang Zhang
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.10054
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Background Coastal saltpans are a common supratidal human-modified wetland habitat found within many coastal landscape mosaics. Commercial salt production and aquaculture practices often result in the creation of exposed coastal substrates that could provide suitable breeding habitat for waterbird populations; however, few studies have quantified waterbird breeding success in these artificial wetlands. Methods Here we examine the nesting behavior of the Gull-billed tern (Gelochelidon nilotica) breeding in the Nanpu coastal saltpans of Bohai Bay, Yellow Sea, China over three consecutive nesting seasons (2017–2019) by using nest survival model in Program MARK. Results The results revealed that nest survival of Gull-billed terns in coastal saltpans (0.697) was higher than previously published estimates from other regions, with an estimated daily survival rate (DSR) of 0.982 ± 0.001 (±95% CI). High nest survival was mainly attributed to low levels of human disturbances and low predation rates, while exposure to strong winds, flooding and silting were the main factors causing nest failure. Model-averaged estimates revealed that eggs laid in nests located on ‘habitat islands’ with feather or clam shell substrates were most likely to hatch. Initiation date, nest age, clutch size and quadratic effects of nearest-neighbor distance, nearest distance to road and nearest distance to water were all significant predictors of nest success, but the nest survival declined overall from 2017 to 2019 due to the degradation and loss of breeding habitat anthropogenically caused by rising water levels. Discussion Coastal saltpans represent an alternative breeding habitat for the Gull-billed tern populations in Bohai Bay, but conservation management should prioritize flood prevention to improve the extent and quality of breeding habitat, concurrent with efforts to create further ‘habitat islands’ with suitable nesting substrate.
bibliographic citation: Wu et al. (2020) Predictors of Gull-billed tern (Gelochelidon nilotica) nest survival in artificial coastal saltpans, Bohai Bay, China. PeerJ 8:e10054 https://doi.org/10.7717/peerj.10054
date submitted: 2020-05-21
date accepted: 2020-09-07
issued: 2020-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Fuxing
author list: Agent
  family name: Lei
  given name: Weipan
author list: Agent
  family name: Lloyd
  given name: Huw
author list: Agent
  family name: Zhang
  given name: Zhengwang
doi: 10.7717/peerj.10054
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-05
copyright: ©2020 Wu et al.
attribution name: Wu et al.

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