PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of assisted walking-movement in patients with genetic and acquired neuromuscular disorders with the motorised Innowalk device: an international case study meta-analysis
items: Expanding global commodities trade and consumption place the world’s primates at risk of extinction
items: Repeatedly adopting power postures does not affect hormonal correlates of dominance and affiliative behavior
items: Mir-421 in plasma as a potential diagnostic biomarker for precancerous gastric lesions and early gastric cancer
items: Influence of nonylphenol exposure on basic growth, development, and thyroid tissue structure in F1 male rats
items: Symmetry preference in shapes, faces, flowers and landscapes
items: Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA
items: iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart
items: Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
items: Worldwide scientific productions with immunotherapy of sepsis: a bibliometric analysis

Effect of assisted walking-movement in patients with genetic and acquired neuromuscular disorders with the motorised Innowalk device: an international case study meta-analysis
type: item
type: AcademicArticle
description: People with physical disabilities (PD) suffer from consequences due to lack of physical activity and consequently, are at increased risk of chronic diseases. We aimed to evaluate the ability of a motorised assistive device for dynamic standing with weight-bearing in addition to standard state-of-the-art therapy to improve clinical outcome in a meta-analysis of available studies. A total of 11 studies were identified from different European countries analysing the effect of the dynamic device Innowalk. Raw data of nine studies were pooled including a total of 31 patients observed between 2009 and 2017. Standardised questionnaires and physical outcomes were examined in this exploratory meta-analysis. We recorded patients’ characteristics, duration, intensity, and location of usage as well as general clinical outcomes and improvement of passive range of motion (PROM). The analysed population consisted in 90% cases of patients younger than 18 years of age. Patients were severely disabled individuals (aged 8 (6–10) years; 58% male; 67% non-ambulatory, 86% cerebral palsy). A total of 94% used the Innowalk in a home-based or day-care setting. For nearly all individuals (94%), improvements were recorded for: walking or weight-bearing transfer (n = 13), control/strength of the trunk or head (n = 6), joint mobility (n = 14), sleep (n = 4 out of 6/67%), or muscle strength (n = 17), vital functions (n = 16), bowel function (n = 10), attention/orientation (n = 2). PROM of the hip (flexion, abduction, and adduction) significantly (p < 0.001 for multiple comparisons) increased after 1 month (p < 0.05 flexion, adduction) and further after 5 months (p < 0.05 each) in contrast (p < 0.05 each) to a control group with state-of-the-art therapy. Similarly, PROM showed a trend towards improvement in dorsal extension of the ankle (p = 0.07). In summary, this is the first report of a novel device with additional benefit to standard therapy for severe PD. These intriguing results warrant the…
format: application/pdf
format: text/html
creator: Caroline Schmidt-Lucke
creator: Jana Käferle
creator: Britt-Marie Rydh Berner
creator: Lotta Ahlborg
creator: Hege Marie Hansen
creator: Ulrika Skjellvik Tollefsen
creator: Tonje Thon
creator: Rikke Damkjær Moen
creator: Ana Pekanovic
creator: Åsa B. Tornberg
creator: Katarina Lauruschkus
subject: Clinical Trials
subject: Evidence Based Medicine
subject: Kinesiology
subject: Neurology
subject: Orthopedics
description: doi:10.7717/peerj.7098
publisher: PeerJ Inc.
rights: © 2019 Schmidt-Lucke et al.
abstract: People with physical disabilities (PD) suffer from consequences due to lack of physical activity and consequently, are at increased risk of chronic diseases. We aimed to evaluate the ability of a motorised assistive device for dynamic standing with weight-bearing in addition to standard state-of-the-art therapy to improve clinical outcome in a meta-analysis of available studies. A total of 11 studies were identified from different European countries analysing the effect of the dynamic device Innowalk. Raw data of nine studies were pooled including a total of 31 patients observed between 2009 and 2017. Standardised questionnaires and physical outcomes were examined in this exploratory meta-analysis. We recorded patients’ characteristics, duration, intensity, and location of usage as well as general clinical outcomes and improvement of passive range of motion (PROM). The analysed population consisted in 90% cases of patients younger than 18 years of age. Patients were severely disabled individuals (aged 8 (6–10) years; 58% male; 67% non-ambulatory, 86% cerebral palsy). A total of 94% used the Innowalk in a home-based or day-care setting. For nearly all individuals (94%), improvements were recorded for: walking or weight-bearing transfer (n = 13), control/strength of the trunk or head (n = 6), joint mobility (n = 14), sleep (n = 4 out of 6/67%), or muscle strength (n = 17), vital functions (n = 16), bowel function (n = 10), attention/orientation (n = 2). PROM of the hip (flexion, abduction, and adduction) significantly (p < 0.001 for multiple comparisons) increased after 1 month (p < 0.05 flexion, adduction) and further after 5 months (p < 0.05 each) in contrast (p < 0.05 each) to a control group with state-of-the-art therapy. Similarly, PROM showed a trend towards improvement in dorsal extension of the ankle (p = 0.07). In summary, this is the first report of a novel device with additional benefit to standard therapy for severe PD. These intriguing results warrant the…
bibliographic citation: Schmidt-Lucke et al. (2019) Effect of assisted walking-movement in patients with genetic and acquired neuromuscular disorders with the motorised Innowalk device: an international case study meta-analysis. PeerJ 7:e7098 https://doi.org/10.7717/peerj.7098
date submitted: 2018-12-07
date accepted: 2019-05-08
issued: 2019-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmidt-Lucke
  given name: Caroline
author list: Agent
  family name: Käferle
  given name: Jana
author list: Agent
  family name: Rydh Berner
  given name: Britt-Marie
author list: Agent
  family name: Ahlborg
  given name: Lotta
author list: Agent
  family name: Hansen
  given name: Hege Marie
author list: Agent
  family name: Skjellvik Tollefsen
  given name: Ulrika
author list: Agent
  family name: Thon
  given name: Tonje
author list: Agent
  family name: Damkjær Moen
  given name: Rikke
author list: Agent
  family name: Pekanovic
  given name: Ana
author list: Agent
  family name: Tornberg
  given name: Åsa B.
author list: Agent
  family name: Lauruschkus
  given name: Katarina
doi: 10.7717/peerj.7098
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-18
copyright: © 2019 Schmidt-Lucke et al.
attribution name: Schmidt-Lucke et al.

Expanding global commodities trade and consumption place the world’s primates at risk of extinction
type: item
type: AcademicArticle
description: As a consequence of recent human activities. populations of approximately 75% of the world’s primates are in decline, and more than 60% of species (n = 512) are threatened with extinction. Major anthropogenic pressures on primate persistence include the widespread loss and degradation of natural habitats caused by the expansion of industrial agriculture, pastureland for cattle, logging, mining, and fossil fuel extraction. This is the result of growing global market demands for agricultural and nonagricultural commodities. Here, we profile the effects of international trade of forest-risk agricultural and nonagricultural commodities, namely soybean, oil palm, natural rubber, beef, forestry products, fossil fuels, metals, minerals, and gemstones on habitat conversion in the Neotropics, Africa, and South and Southeast Asia. Total estimated forest loss for these regions between 2001 and 2017 was ca 179 million ha. The average percent of commodity-driven permanent deforestation for the period 2001–2015 was highest in Southeast Asia (47%) followed by the Neotropics (26%), South Asia (26%), and Africa (7%). Commodities exports increased significantly between 2000 and 2016 in all primate range regions leading to the widespread conversion of forested land to agricultural fields and an increase in natural resource extraction. In 2016, US $1.1 trillion of natural-resource commodities were traded by countries in primate range regions. The Neotropics accounted for 41% of the total value of these exports, Southeast Asia for 27%, Africa 21%, and South Asia 11%. Major commodity exporters in 2016 were Brazil, India, Indonesia, Malaysia and South Africa, countries of high primate diversity and endemism. Among the top 10 importers were China, the US, Japan, and Switzerland. Primate range countries lag far behind importer nations in food security and gross domestic product per capita, suggesting that trade and commodity-driven land-use have done little to generate wealth and well-being…
format: application/pdf
format: text/html
creator: Alejandro Estrada
creator: Paul A. Garber
creator: Abhishek Chaudhary
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.7068
publisher: PeerJ Inc.
rights: © 2019 Estrada et al.
abstract: As a consequence of recent human activities. populations of approximately 75% of the world’s primates are in decline, and more than 60% of species (n = 512) are threatened with extinction. Major anthropogenic pressures on primate persistence include the widespread loss and degradation of natural habitats caused by the expansion of industrial agriculture, pastureland for cattle, logging, mining, and fossil fuel extraction. This is the result of growing global market demands for agricultural and nonagricultural commodities. Here, we profile the effects of international trade of forest-risk agricultural and nonagricultural commodities, namely soybean, oil palm, natural rubber, beef, forestry products, fossil fuels, metals, minerals, and gemstones on habitat conversion in the Neotropics, Africa, and South and Southeast Asia. Total estimated forest loss for these regions between 2001 and 2017 was ca 179 million ha. The average percent of commodity-driven permanent deforestation for the period 2001–2015 was highest in Southeast Asia (47%) followed by the Neotropics (26%), South Asia (26%), and Africa (7%). Commodities exports increased significantly between 2000 and 2016 in all primate range regions leading to the widespread conversion of forested land to agricultural fields and an increase in natural resource extraction. In 2016, US $1.1 trillion of natural-resource commodities were traded by countries in primate range regions. The Neotropics accounted for 41% of the total value of these exports, Southeast Asia for 27%, Africa 21%, and South Asia 11%. Major commodity exporters in 2016 were Brazil, India, Indonesia, Malaysia and South Africa, countries of high primate diversity and endemism. Among the top 10 importers were China, the US, Japan, and Switzerland. Primate range countries lag far behind importer nations in food security and gross domestic product per capita, suggesting that trade and commodity-driven land-use have done little to generate wealth and well-being…
bibliographic citation: Estrada et al. (2019) Expanding global commodities trade and consumption place the world’s primates at risk of extinction. PeerJ 7:e7068 https://doi.org/10.7717/peerj.7068
date submitted: 2019-03-13
date accepted: 2019-05-06
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Estrada
  given name: Alejandro
author list: Agent
  family name: Garber
  given name: Paul A.
author list: Agent
  family name: Chaudhary
  given name: Abhishek
doi: 10.7717/peerj.7068
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Estrada et al.
attribution name: Estrada et al.

Repeatedly adopting power postures does not affect hormonal correlates of dominance and affiliative behavior
type: item
type: AcademicArticle
description: Background Adopting expansive vs. constrictive postures related to high vs. low levels of social power has been suggested to induce changes in testosterone and cortisol levels, and thereby to mimic hormonal correlates of dominance behavior. However, these findings have been challenged by several non-replications recently. Despite this growing body of evidence that does not support posture effects on hormone levels, the question remains as to whether repeatedly holding postures over time and/or assessing hormonal responses at different time points would yield different outcomes. The current study assesses these methodological characteristics as possible reasons for previous null-findings. Additionally, it investigates for the first time whether expansive and constrictive postures impact progesterone levels, a suggested correlate of affiliative motives and behavior. By testing the effects of repeated but short posture manipulations in between the blocks of a social task while using a cover story, it further fulfills the conditions previously raised as potentially necessary for the effects to occur. Methods A total of 82 male participants repeatedly adopted an expansive or constrictive posture for 2 min in between blocks of a task that consisted in categorizing faces based on first impressions. Saliva samples were taken at two different time points in a time window in which hormonal responses to stress, competition and other manipulations are known to be strongest. Results Neither testosterone and cortisol levels linked to dominance behaviors, nor progesterone levels related to affiliative tendencies, responded differently to adopting expansive as opposed to constrictive postures. The present results suggest that even repeated power posing in a context where social stimuli are task-relevant does not elicit changes in hormone levels.
format: application/pdf
format: text/html
creator: Hannah Metzler
creator: Julie Grèzes
subject: Anthropology
subject: Anatomy and Physiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6726
publisher: PeerJ Inc.
rights: © 2019 Metzler & Grèzes
abstract: Background Adopting expansive vs. constrictive postures related to high vs. low levels of social power has been suggested to induce changes in testosterone and cortisol levels, and thereby to mimic hormonal correlates of dominance behavior. However, these findings have been challenged by several non-replications recently. Despite this growing body of evidence that does not support posture effects on hormone levels, the question remains as to whether repeatedly holding postures over time and/or assessing hormonal responses at different time points would yield different outcomes. The current study assesses these methodological characteristics as possible reasons for previous null-findings. Additionally, it investigates for the first time whether expansive and constrictive postures impact progesterone levels, a suggested correlate of affiliative motives and behavior. By testing the effects of repeated but short posture manipulations in between the blocks of a social task while using a cover story, it further fulfills the conditions previously raised as potentially necessary for the effects to occur. Methods A total of 82 male participants repeatedly adopted an expansive or constrictive posture for 2 min in between blocks of a task that consisted in categorizing faces based on first impressions. Saliva samples were taken at two different time points in a time window in which hormonal responses to stress, competition and other manipulations are known to be strongest. Results Neither testosterone and cortisol levels linked to dominance behaviors, nor progesterone levels related to affiliative tendencies, responded differently to adopting expansive as opposed to constrictive postures. The present results suggest that even repeated power posing in a context where social stimuli are task-relevant does not elicit changes in hormone levels.
bibliographic citation: Metzler et al. (2019) Repeatedly adopting power postures does not affect hormonal correlates of dominance and affiliative behavior. PeerJ 7:e6726 https://doi.org/10.7717/peerj.6726
date submitted: 2018-11-21
date accepted: 2019-03-06
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Metzler
  given name: Hannah
author list: Agent
  family name: Grèzes
  given name: Julie
doi: 10.7717/peerj.6726
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Metzler and Grèzes
attribution name: Metzler & Grèzes

Mir-421 in plasma as a potential diagnostic biomarker for precancerous gastric lesions and early gastric cancer
type: item
type: AcademicArticle
description: Objective MicroRNA (miR)-421 plays a key role in cancer progression. It has been reported that circulating miR-421may be a potential tumor marker for the diagnosis of several cancers. However, the role of miR-421 in plasma as a potential biomarker in the diagnosis of precancerous gastric lesions (Pre) and early-stage gastric cancer (GC) remains poorly understood. In this study, we investigated miR-421 in plasma as a novel potential biomarker for the detection of precancerous gastric lesions and early-stage (GC). Materials & Methods The miRNA content was determined by quantitative real-time polymerase chain reaction (qRT-PCR). MiR-421 content in all subjects was normalized by endogenous miRNA (miR-16). The diagnostic value of miR-421 for Pre and GC was assessed by comparing receiver operating characteristic (ROC) analysis with traditional tumor markers, including CEA, CA125, CA153, CA211 and CA50. The correlation between the expression of miR-421 and the pathological characteristics of Pre and GC was analyzed. Results Elevated expression of miR-421 in plasma can robustly distinguish the normal population from Pre and GC cases, especially in the early stages of gastric cancer cases (all p < 0.05). The ROC analyses showed that the area under the ROC curve (AUC), sensitivity, accuracy and Youden index of miR-421 were superior to traditional tumor markers (CEA, CA125, CA153, CA211, and CA50) in GC diagnosis, while its specificity was higher than CEA, CA153 and CA50 (all p < 0.05). MiR-421 in plasma had higher AUC value than AFP, CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05), while specificity, accuracy and Youden index of miR-421 was only lower than CA211. The efficiency of miR-421 in the diagnosis of GC was significantly higher than that of CA211 and CA50, and it was significantly higher than CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05). In addition, up-regulation of miR-421 occurred initially in precancerous gastric lesions as well as in …
format: application/pdf
format: text/html
creator: Jianlin Chen
creator: Lihua Wu
creator: Yifan Sun
creator: Qi Yin
creator: Xianhua Chen
creator: Siqun Liang
creator: Qingyan Meng
creator: Haihua Long
creator: Fangying Li
creator: Changjun Luo
creator: Xiaorong Xiao
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Pathology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7002
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Objective MicroRNA (miR)-421 plays a key role in cancer progression. It has been reported that circulating miR-421may be a potential tumor marker for the diagnosis of several cancers. However, the role of miR-421 in plasma as a potential biomarker in the diagnosis of precancerous gastric lesions (Pre) and early-stage gastric cancer (GC) remains poorly understood. In this study, we investigated miR-421 in plasma as a novel potential biomarker for the detection of precancerous gastric lesions and early-stage (GC). Materials & Methods The miRNA content was determined by quantitative real-time polymerase chain reaction (qRT-PCR). MiR-421 content in all subjects was normalized by endogenous miRNA (miR-16). The diagnostic value of miR-421 for Pre and GC was assessed by comparing receiver operating characteristic (ROC) analysis with traditional tumor markers, including CEA, CA125, CA153, CA211 and CA50. The correlation between the expression of miR-421 and the pathological characteristics of Pre and GC was analyzed. Results Elevated expression of miR-421 in plasma can robustly distinguish the normal population from Pre and GC cases, especially in the early stages of gastric cancer cases (all p < 0.05). The ROC analyses showed that the area under the ROC curve (AUC), sensitivity, accuracy and Youden index of miR-421 were superior to traditional tumor markers (CEA, CA125, CA153, CA211, and CA50) in GC diagnosis, while its specificity was higher than CEA, CA153 and CA50 (all p < 0.05). MiR-421 in plasma had higher AUC value than AFP, CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05), while specificity, accuracy and Youden index of miR-421 was only lower than CA211. The efficiency of miR-421 in the diagnosis of GC was significantly higher than that of CA211 and CA50, and it was significantly higher than CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05). In addition, up-regulation of miR-421 occurred initially in precancerous gastric lesions as well as in …
bibliographic citation: Chen et al. (2019) Mir-421 in plasma as a potential diagnostic biomarker for precancerous gastric lesions and early gastric cancer. PeerJ 7:e7002 https://doi.org/10.7717/peerj.7002
date submitted: 2018-12-13
date accepted: 2019-04-23
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jianlin
author list: Agent
  family name: Wu
  given name: Lihua
author list: Agent
  family name: Sun
  given name: Yifan
author list: Agent
  family name: Yin
  given name: Qi
author list: Agent
  family name: Chen
  given name: Xianhua
author list: Agent
  family name: Liang
  given name: Siqun
author list: Agent
  family name: Meng
  given name: Qingyan
author list: Agent
  family name: Long
  given name: Haihua
author list: Agent
  family name: Li
  given name: Fangying
author list: Agent
  family name: Luo
  given name: Changjun
author list: Agent
  family name: Xiao
  given name: Xiaorong
doi: 10.7717/peerj.7002
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Influence of nonylphenol exposure on basic growth, development, and thyroid tissue structure in F1 male rats
type: item
type: AcademicArticle
description: Objective Environmental endocrine disruptors (EEDs) with a weak ability to mimic estrogen have been associated with thyroid dysfunction. However, little is known about the effect of nonylphenol (NP), a well-known EED, on thyroid structure. The present study evaluates whether gestational and lactational exposure to NP impacts growth and thyroid structure in F1 male rats. Methods A total of 60 rats were gavaged with NP (25, 50, and 100 mg/kg), estradiol (E2, 30 μg/kg/day), and corn oil alone (vehicle control) from gestational day 6 to postnatal day (PND) 21. Serum thyroid hormones free triiodothyronine (FT3), free thyroxine (FT4) and thyroid stimulating hormone levels were detected by automated chemiluminescence immunoassay analyzer. The NP level in the thyroid was measured using high-performance liquid chromatography. The ultrastructure of follicular epithelial cells was examined using transmission electron microscopy. Histopathology was conducted using hematoxylin and eosin staining. Results On PND 0, exposure to 50 and 100 mg/kg/day NP led to a significant decrease in the average litter size, litter weight and number of live pups per litter compared to the control group (P < 0.05). Dams exposed to NP during perinatal period demonstrated decreased serum levels of FT3 and FT4 in F1 male rats, when compared to the control group (P < 0.05). The NP level in the control group was 3.39 ± 0.08 ng/mg, while NP levels in the low, middle, and high dose groups ranged from 5.20 to 11.00 ng/mg. Exposure caused a dose-related increase in NP level in the thyroid of male pups (P < 0.01). The thicknesses of the thyroid follicular epithelium were 2.06 ± 0.37 μm in the control group and 3.97 ± 1.61 μm in the high-dose group. The thickness of the thyroid follicular epithelium increased with an increase in treatment dose in a dose-dependent manner (P < 0.05). The sizes of the thyroid follicles were 1,405.53 ± 866.62 μm2 in the control group and 317.49 ± 231.15 μm2 in the high-dose group…
format: application/pdf
format: text/html
creator: Lin Wang
creator: Jie Xu
creator: Feng Zeng
creator: Xiangjun Fu
creator: Weihong Xu
creator: Jie Yu
subject: Toxicology
subject: Public Health
subject: Environmental Impacts
description: doi:10.7717/peerj.7039
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Objective Environmental endocrine disruptors (EEDs) with a weak ability to mimic estrogen have been associated with thyroid dysfunction. However, little is known about the effect of nonylphenol (NP), a well-known EED, on thyroid structure. The present study evaluates whether gestational and lactational exposure to NP impacts growth and thyroid structure in F1 male rats. Methods A total of 60 rats were gavaged with NP (25, 50, and 100 mg/kg), estradiol (E2, 30 μg/kg/day), and corn oil alone (vehicle control) from gestational day 6 to postnatal day (PND) 21. Serum thyroid hormones free triiodothyronine (FT3), free thyroxine (FT4) and thyroid stimulating hormone levels were detected by automated chemiluminescence immunoassay analyzer. The NP level in the thyroid was measured using high-performance liquid chromatography. The ultrastructure of follicular epithelial cells was examined using transmission electron microscopy. Histopathology was conducted using hematoxylin and eosin staining. Results On PND 0, exposure to 50 and 100 mg/kg/day NP led to a significant decrease in the average litter size, litter weight and number of live pups per litter compared to the control group (P < 0.05). Dams exposed to NP during perinatal period demonstrated decreased serum levels of FT3 and FT4 in F1 male rats, when compared to the control group (P < 0.05). The NP level in the control group was 3.39 ± 0.08 ng/mg, while NP levels in the low, middle, and high dose groups ranged from 5.20 to 11.00 ng/mg. Exposure caused a dose-related increase in NP level in the thyroid of male pups (P < 0.01). The thicknesses of the thyroid follicular epithelium were 2.06 ± 0.37 μm in the control group and 3.97 ± 1.61 μm in the high-dose group. The thickness of the thyroid follicular epithelium increased with an increase in treatment dose in a dose-dependent manner (P < 0.05). The sizes of the thyroid follicles were 1,405.53 ± 866.62 μm2 in the control group and 317.49 ± 231.15 μm2 in the high-dose group…
bibliographic citation: Wang et al. (2019) Influence of nonylphenol exposure on basic growth, development, and thyroid tissue structure in F1 male rats. PeerJ 7:e7039 https://doi.org/10.7717/peerj.7039
date submitted: 2019-02-19
date accepted: 2019-04-29
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lin
author list: Agent
  family name: Xu
  given name: Jie
author list: Agent
  family name: Zeng
  given name: Feng
author list: Agent
  family name: Fu
  given name: Xiangjun
author list: Agent
  family name: Xu
  given name: Weihong
author list: Agent
  family name: Yu
  given name: Jie
doi: 10.7717/peerj.7039
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Symmetry preference in shapes, faces, flowers and landscapes
type: item
type: AcademicArticle
description: Most people like symmetry, and symmetry has been extensively used in visual art and architecture. In this study, we compared preference for images of abstract and familiar objects in the original format or when containing perfect bilateral symmetry. We created pairs of images for different categories: male faces, female faces, polygons, smoothed version of the polygons, flowers, and landscapes. This design allows us to compare symmetry preference in different domains. Each observer saw all categories randomly interleaved but saw only one of the two images in a pair. After recording preference, we recorded a rating of how salient the symmetry was for each image, and measured how quickly observers could decide which of the two images in a pair was symmetrical. Results reveal a general preference for symmetry in the case of shapes and faces. For landscapes, natural (no perfect symmetry) images were preferred. Correlations with judgments of saliency were present but generally low, and for landscapes the salience of symmetry was negatively related to preference. However, even within the category where symmetry was not liked (landscapes), the separate analysis of original and modified stimuli showed an interesting pattern: Salience of symmetry was correlated positively (artificial) or negatively (original) with preference, suggesting different effects of symmetry within the same class of stimuli based on context and categorization.
format: application/pdf
format: text/html
creator: Marco Bertamini
creator: Giulia Rampone
creator: Alexis D.J. Makin
creator: Andrew Jessop
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7078
publisher: PeerJ Inc.
rights: © 2019 Bertamini et al.
abstract: Most people like symmetry, and symmetry has been extensively used in visual art and architecture. In this study, we compared preference for images of abstract and familiar objects in the original format or when containing perfect bilateral symmetry. We created pairs of images for different categories: male faces, female faces, polygons, smoothed version of the polygons, flowers, and landscapes. This design allows us to compare symmetry preference in different domains. Each observer saw all categories randomly interleaved but saw only one of the two images in a pair. After recording preference, we recorded a rating of how salient the symmetry was for each image, and measured how quickly observers could decide which of the two images in a pair was symmetrical. Results reveal a general preference for symmetry in the case of shapes and faces. For landscapes, natural (no perfect symmetry) images were preferred. Correlations with judgments of saliency were present but generally low, and for landscapes the salience of symmetry was negatively related to preference. However, even within the category where symmetry was not liked (landscapes), the separate analysis of original and modified stimuli showed an interesting pattern: Salience of symmetry was correlated positively (artificial) or negatively (original) with preference, suggesting different effects of symmetry within the same class of stimuli based on context and categorization.
bibliographic citation: Bertamini et al. (2019) Symmetry preference in shapes, faces, flowers and landscapes. PeerJ 7:e7078 https://doi.org/10.7717/peerj.7078
date submitted: 2019-01-09
date accepted: 2019-05-06
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bertamini
  given name: Marco
author list: Agent
  family name: Rampone
  given name: Giulia
author list: Agent
  family name: Makin
  given name: Alexis D.J.
author list: Agent
  family name: Jessop
  given name: Andrew
doi: 10.7717/peerj.7078
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Bertamini et al.
attribution name: Bertamini et al.

Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA
type: item
type: AcademicArticle
description: Background Gypsophila paniculata (baby’s breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby’s breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby’s breath in order to assess whether alternative management strategies should be employed to control these populations. Methods We sequenced two chloroplast regions, ribulose-bisphosphate carboxylase gene (rbcL), and maturase K (matK), and one nuclear region, internal transcribed spacer 2 (ITS2), from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to reference sequences from other Gypsophila species obtained from the Barcode of Life Database and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after 5-months of growth. Results Phylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong to G. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs. Discussion Based upon these results, we propose that the two color morphs are variants of G. paniculata. Given…
format: application/pdf
format: text/html
creator: Marisa L. Yang
creator: Emma Rice
creator: Hailee Leimbach-Maus
creator: Charlyn G. Partridge
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.7100
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Gypsophila paniculata (baby’s breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby’s breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby’s breath in order to assess whether alternative management strategies should be employed to control these populations. Methods We sequenced two chloroplast regions, ribulose-bisphosphate carboxylase gene (rbcL), and maturase K (matK), and one nuclear region, internal transcribed spacer 2 (ITS2), from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to reference sequences from other Gypsophila species obtained from the Barcode of Life Database and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after 5-months of growth. Results Phylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong to G. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs. Discussion Based upon these results, we propose that the two color morphs are variants of G. paniculata. Given…
bibliographic citation: Yang et al. (2019) Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA. PeerJ 7:e7100 https://doi.org/10.7717/peerj.7100
date submitted: 2018-03-14
date accepted: 2019-05-08
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Marisa L.
author list: Agent
  family name: Rice
  given name: Emma
author list: Agent
  family name: Leimbach-Maus
  given name: Hailee
author list: Agent
  family name: Partridge
  given name: Charlyn G.
doi: 10.7717/peerj.7100
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Yang et al.
attribution name: Yang et al.

iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart
type: item
type: AcademicArticle
description: Background Wheat is one of the most important staple crops worldwide. Fusarium head blight (FHB) severely affects wheat yield and quality. A novel bread wheat mutant, ZK001, characterized as cleistogamic was isolated from a non-cleistogamous variety Yumai 18 (YM18) through static magnetic field mutagenesis. Cleistogamy is a promising strategy for controlling FHB. However, little is known about the mechanism of cleistogamy in wheat. Methods We performed a FHB resistance test to identify the FHB infection rate of ZK001. We also measured the agronomic traits of ZK001 and the starch and total soluble sugar contents of lodicules in YM18 and ZK001. Finally, we performed comparative studies at the proteome level between YM18 and ZK001 based on the proteomic technique of isobaric tags for relative and absolute quantification. Results The infection rate of ZK001 was lower than that of its wild-type and Aikang 58. The abnormal lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Proteome analysis showed that the main differentially abundant proteins (DAPs) were related to carbohydrate metabolism, protein transport, and calcium ion binding. These DAPs may work together to regulate cellular homeostasis, osmotic pressure and the development of lodicules. This hypothesis is supported by the analysis of starch, soluble sugar content in the lodicules as well as the results of Quantitative reverse transcription polymerase chain reaction. Conclusions Proteomic analysis has provided comprehensive information that should be useful for further research on the lodicule development mechanism in wheat. The ZK001 mutant is optimal for studying flower development in wheat and could be very important for FHB resistant projects via conventional crossing.
format: application/pdf
format: text/html
creator: Caiguo Tang
creator: Huilan Zhang
creator: Pingping Zhang
creator: Yuhan Ma
creator: Minghui Cao
creator: Hao Hu
creator: Faheem Afzal Shah
creator: Weiwei Zhao
creator: Minghao Li
creator: Lifang Wu
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7104
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Background Wheat is one of the most important staple crops worldwide. Fusarium head blight (FHB) severely affects wheat yield and quality. A novel bread wheat mutant, ZK001, characterized as cleistogamic was isolated from a non-cleistogamous variety Yumai 18 (YM18) through static magnetic field mutagenesis. Cleistogamy is a promising strategy for controlling FHB. However, little is known about the mechanism of cleistogamy in wheat. Methods We performed a FHB resistance test to identify the FHB infection rate of ZK001. We also measured the agronomic traits of ZK001 and the starch and total soluble sugar contents of lodicules in YM18 and ZK001. Finally, we performed comparative studies at the proteome level between YM18 and ZK001 based on the proteomic technique of isobaric tags for relative and absolute quantification. Results The infection rate of ZK001 was lower than that of its wild-type and Aikang 58. The abnormal lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Proteome analysis showed that the main differentially abundant proteins (DAPs) were related to carbohydrate metabolism, protein transport, and calcium ion binding. These DAPs may work together to regulate cellular homeostasis, osmotic pressure and the development of lodicules. This hypothesis is supported by the analysis of starch, soluble sugar content in the lodicules as well as the results of Quantitative reverse transcription polymerase chain reaction. Conclusions Proteomic analysis has provided comprehensive information that should be useful for further research on the lodicule development mechanism in wheat. The ZK001 mutant is optimal for studying flower development in wheat and could be very important for FHB resistant projects via conventional crossing.
bibliographic citation: Tang et al. (2019) iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart. PeerJ 7:e7104 https://doi.org/10.7717/peerj.7104
date submitted: 2019-01-06
date accepted: 2019-05-08
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Caiguo
author list: Agent
  family name: Zhang
  given name: Huilan
author list: Agent
  family name: Zhang
  given name: Pingping
author list: Agent
  family name: Ma
  given name: Yuhan
author list: Agent
  family name: Cao
  given name: Minghui
author list: Agent
  family name: Hu
  given name: Hao
author list: Agent
  family name: Shah
  given name: Faheem Afzal
author list: Agent
  family name: Zhao
  given name: Weiwei
author list: Agent
  family name: Li
  given name: Minghao
author list: Agent
  family name: Wu
  given name: Lifang
doi: 10.7717/peerj.7104
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Tang et al.
attribution name: Tang et al.

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
type: item
type: AcademicArticle
description: The “bidirectional gene pair” indicates a particular head-to-head gene organization in which transcription start sites of two genes are located on opposite strands of genomic DNA within a region of one kb. Despite bidirectional gene pairs are well characterized, little is known about their expression profiles and regulation features in tumorigenesis. We used RNA-seq data from The Cancer Genome Atlas (TCGA) dataset for a systematic analysis of the expression profiles of bidirectional gene pairs in 13 cancer datasets. Gene pairs on the opposite strand with transcription end site distance within one kb or on the same strand with the distance of two genes between 1–10 kb and gene pairs comprising two randomly chosen genes were used as control gene pairs (CG1, CG2, and random). We identified and characterized up-/down-regulated genes by comparing the expression level between tumors and adjacent normal tissues in 13 TCGA datasets. There were no consistently significant difference in the percentage of up-/down-regulated genes between bidirectional and control/random genes in most of TCGA datasets. However, the percentage of bidirectional gene pairs comprising two up- or two down-regulated genes was significantly higher than gene pairs from CG1/2 in 12/11 analyzed TCGA datasets and the random gene pairs in all 13 TCGA datasets. Then we identified the methylation correlated bidirectional genes to explore the regulatory mechanism of bidirectional genes. Like the differentially expressed gene pairs, the bidirectional genes in a pair were significantly prone to be both hypo- or hyper-methylation correlated genes in 12/13 TCGA datasets when comparing to the CG2/random gene pairs despite no significant difference between the percentages of hypo-/hyper-methylation correlated genes in bidirectional and CG2/random genes in most of TCGA datasets. Finally, we explored the correlation between bidirectional genes and patient’s survival, identifying prognostic bidirectional genes and pro…
format: application/pdf
format: text/html
creator: Juchuanli Tu
creator: Xiaolu Li
creator: Jianjun Wang
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.7107
publisher: PeerJ Inc.
rights: © 2019 Tu et al.
abstract: The “bidirectional gene pair” indicates a particular head-to-head gene organization in which transcription start sites of two genes are located on opposite strands of genomic DNA within a region of one kb. Despite bidirectional gene pairs are well characterized, little is known about their expression profiles and regulation features in tumorigenesis. We used RNA-seq data from The Cancer Genome Atlas (TCGA) dataset for a systematic analysis of the expression profiles of bidirectional gene pairs in 13 cancer datasets. Gene pairs on the opposite strand with transcription end site distance within one kb or on the same strand with the distance of two genes between 1–10 kb and gene pairs comprising two randomly chosen genes were used as control gene pairs (CG1, CG2, and random). We identified and characterized up-/down-regulated genes by comparing the expression level between tumors and adjacent normal tissues in 13 TCGA datasets. There were no consistently significant difference in the percentage of up-/down-regulated genes between bidirectional and control/random genes in most of TCGA datasets. However, the percentage of bidirectional gene pairs comprising two up- or two down-regulated genes was significantly higher than gene pairs from CG1/2 in 12/11 analyzed TCGA datasets and the random gene pairs in all 13 TCGA datasets. Then we identified the methylation correlated bidirectional genes to explore the regulatory mechanism of bidirectional genes. Like the differentially expressed gene pairs, the bidirectional genes in a pair were significantly prone to be both hypo- or hyper-methylation correlated genes in 12/13 TCGA datasets when comparing to the CG2/random gene pairs despite no significant difference between the percentages of hypo-/hyper-methylation correlated genes in bidirectional and CG2/random genes in most of TCGA datasets. Finally, we explored the correlation between bidirectional genes and patient’s survival, identifying prognostic bidirectional genes and pro…
bibliographic citation: Tu et al. (2019) Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset. PeerJ 7:e7107 https://doi.org/10.7717/peerj.7107
date submitted: 2019-02-15
date accepted: 2019-05-09
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tu
  given name: Juchuanli
author list: Agent
  family name: Li
  given name: Xiaolu
author list: Agent
  family name: Wang
  given name: Jianjun
doi: 10.7717/peerj.7107
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Tu et al.
attribution name: Tu et al.

Worldwide scientific productions with immunotherapy of sepsis: a bibliometric analysis
type: item
type: AcademicArticle
description: Background Sepsis represents a significant healthcare problem worldwide and causes a high number of deaths every year but remains to be fully understood. During and after sepsis, the host immune response is complex and involves an initial excessive host inflammatory response to infection that is closely related to tissue damage and leads to organ failure. Over the past three decades, immunotherapy for sepsis has vastly improved, but in this area, the most influential articles, journals, authors, and countries have not yet been completely summarized and analyzed. Objective Performed a bibliometric analysis on all the articles concerning immunotherapy for sepsis from 1962 to 2019 was our objective, and we also explored the potential correlations between publications of different countries and their gross domestic product (GDP). Methods All articles about immunotherapy for sepsis were extracted from the Scopus database and analyzed. We also retrieved GDP data from all the countries that have published information from the World Bank. Results In summary, we have retrieved 1,483 related articles from the Scopus database starting from the first publication on immunotherapy for sepsis in 1962 through March 16, 2019. Over the past decade, the number of the articles published has increased year by year to reach 866 in total, which accounts for about 58% of all publications, with 2017 being the most prolific year when 179 articles were published. The US published 604 articles (41%), followed by China (n = 163, 11%), and Germany (n = 158, 11%). In terms of publishing media, the journal that published the highest number of the articles was Journal of Critical Care Medicine with 65 articles (4%), followed by Shock with 55 articles (4%), and Critical Care with 35 articles (2%). There was a strong correlation between the GDP of the different countries and their publication numbers (r = 0.811, P < 0.001). Conclusions Our present study analyzed all types of articles concerning immun…
format: application/pdf
format: text/html
creator: Ronghao Wan
creator: Lei Li
creator: Chenwei Xing
creator: Ronggang Peng
creator: Liang Gao
subject: Emergency and Critical Care
subject: Hematology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.7116
publisher: PeerJ Inc.
rights: © 2019 Wan et al.
abstract: Background Sepsis represents a significant healthcare problem worldwide and causes a high number of deaths every year but remains to be fully understood. During and after sepsis, the host immune response is complex and involves an initial excessive host inflammatory response to infection that is closely related to tissue damage and leads to organ failure. Over the past three decades, immunotherapy for sepsis has vastly improved, but in this area, the most influential articles, journals, authors, and countries have not yet been completely summarized and analyzed. Objective Performed a bibliometric analysis on all the articles concerning immunotherapy for sepsis from 1962 to 2019 was our objective, and we also explored the potential correlations between publications of different countries and their gross domestic product (GDP). Methods All articles about immunotherapy for sepsis were extracted from the Scopus database and analyzed. We also retrieved GDP data from all the countries that have published information from the World Bank. Results In summary, we have retrieved 1,483 related articles from the Scopus database starting from the first publication on immunotherapy for sepsis in 1962 through March 16, 2019. Over the past decade, the number of the articles published has increased year by year to reach 866 in total, which accounts for about 58% of all publications, with 2017 being the most prolific year when 179 articles were published. The US published 604 articles (41%), followed by China (n = 163, 11%), and Germany (n = 158, 11%). In terms of publishing media, the journal that published the highest number of the articles was Journal of Critical Care Medicine with 65 articles (4%), followed by Shock with 55 articles (4%), and Critical Care with 35 articles (2%). There was a strong correlation between the GDP of the different countries and their publication numbers (r = 0.811, P < 0.001). Conclusions Our present study analyzed all types of articles concerning immun…
bibliographic citation: Wan et al. (2019) Worldwide scientific productions with immunotherapy of sepsis: a bibliometric analysis. PeerJ 7:e7116 https://doi.org/10.7717/peerj.7116
date submitted: 2019-02-01
date accepted: 2019-05-11
issued: 2019-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Ronghao
author list: Agent
  family name: Li
  given name: Lei
author list: Agent
  family name: Xing
  given name: Chenwei
author list: Agent
  family name: Peng
  given name: Ronggang
author list: Agent
  family name: Gao
  given name: Liang
doi: 10.7717/peerj.7116
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-17
copyright: © 2019 Wan et al.
attribution name: Wan et al.

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