PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods
items: Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
items: Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot
items: Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet
items: Pro-inflammatory effect of obesity on rats with burn wounds
items: Self-reports vs. physical measures of spinal stiffness
items: Identification of key genes and pathways in endometriosis by integrated expression profiles analysis
items: Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies
items: Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery
items: Trials in developing a nanoscale material for extravascular contrast-enhanced ultrasound targeting hepatocellular carcinoma

Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods
type: item
type: AcademicArticle
description: Background Existing studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer. Methods A total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays. Results A total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.9…
format: application/pdf
format: text/html
creator: Li Gao
creator: Yu-Yan Pang
creator: Xian-Yu Guo
creator: Jing-Jing Zeng
creator: Zhong-Qing Tang
creator: Dan-Dan Xiong
creator: Xia Yang
creator: Ying Li
creator: Fu-Chao Ma
creator: Lin-Jiang Pan
creator: Zhen-Bo Feng
creator: Gang Chen
subject: Computational Biology
subject: Genetics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10458
publisher: PeerJ Inc.
rights: © 2020 Gao et al.
abstract: Background Existing studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer. Methods A total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays. Results A total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.9…
bibliographic citation: Gao et al. (2020) Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods. PeerJ 8:e10458 https://doi.org/10.7717/peerj.10458
date submitted: 2020-08-20
date accepted: 2020-11-10
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Li
author list: Agent
  family name: Pang
  given name: Yu-Yan
author list: Agent
  family name: Guo
  given name: Xian-Yu
author list: Agent
  family name: Zeng
  given name: Jing-Jing
author list: Agent
  family name: Tang
  given name: Zhong-Qing
author list: Agent
  family name: Xiong
  given name: Dan-Dan
author list: Agent
  family name: Yang
  given name: Xia
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Ma
  given name: Fu-Chao
author list: Agent
  family name: Pan
  given name: Lin-Jiang
author list: Agent
  family name: Feng
  given name: Zhen-Bo
author list: Agent
  family name: Chen
  given name: Gang
doi: 10.7717/peerj.10458
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Gao et al.
attribution name: Gao et al.

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
type: item
type: AcademicArticle
description: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
format: application/pdf
format: text/html
creator: Zhixin Wang
creator: Yalin Sun
creator: Xinfang Huang
creator: Feng Li
creator: Yuping Liu
creator: Honglian Zhu
creator: Zhengwei Liu
creator: Weidong Ke
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10485
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
bibliographic citation: Wang et al. (2020) Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers. PeerJ 8:e10485 https://doi.org/10.7717/peerj.10485
date submitted: 2020-07-13
date accepted: 2020-11-12
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhixin
author list: Agent
  family name: Sun
  given name: Yalin
author list: Agent
  family name: Huang
  given name: Xinfang
author list: Agent
  family name: Li
  given name: Feng
author list: Agent
  family name: Liu
  given name: Yuping
author list: Agent
  family name: Zhu
  given name: Honglian
author list: Agent
  family name: Liu
  given name: Zhengwei
author list: Agent
  family name: Ke
  given name: Weidong
doi: 10.7717/peerj.10485
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot
type: item
type: AcademicArticle
description: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.
format: application/pdf
format: text/html
creator: Ahmed Khadr
creator: Guang-Long Wang
creator: Ya-Hui Wang
creator: Rong-Rong Zhang
creator: Xin-Rui Wang
creator: Zhi-Sheng Xu
creator: Yong-Sheng Tian
creator: Ai-Sheng Xiong
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10492
publisher: PeerJ Inc.
rights: © 2020 Khadr et al.
abstract: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.
bibliographic citation: Khadr et al. (2020) Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot. PeerJ 8:e10492 https://doi.org/10.7717/peerj.10492
date submitted: 2020-06-05
date accepted: 2020-11-13
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khadr
  given name: Ahmed
author list: Agent
  family name: Wang
  given name: Guang-Long
author list: Agent
  family name: Wang
  given name: Ya-Hui
author list: Agent
  family name: Zhang
  given name: Rong-Rong
author list: Agent
  family name: Wang
  given name: Xin-Rui
author list: Agent
  family name: Xu
  given name: Zhi-Sheng
author list: Agent
  family name: Tian
  given name: Yong-Sheng
author list: Agent
  family name: Xiong
  given name: Ai-Sheng
doi: 10.7717/peerj.10492
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Khadr et al.
attribution name: Khadr et al.

Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet
type: item
type: AcademicArticle
description: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and intersp…
format: application/pdf
format: text/html
creator: Zeferino Blanco-Martínez
creator: Roberto Pérez-Castañeda
creator: Jesús Genaro Sánchez-Martínez
creator: Flaviano Benavides-González
creator: Jaime Luis Rábago-Castro
creator: María de la Luz Vázquez-Sauceda
creator: Lorena Garrido-Olvera
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10496
publisher: PeerJ Inc.
rights: © 2020 Blanco-Martínez et al.
abstract: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and intersp…
bibliographic citation: Blanco-Martínez et al. (2020) Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet. PeerJ 8:e10496 https://doi.org/10.7717/peerj.10496
date submitted: 2020-07-06
date accepted: 2020-11-14
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blanco-Martínez
  given name: Zeferino
author list: Agent
  family name: Pérez-Castañeda
  given name: Roberto
author list: Agent
  family name: Sánchez-Martínez
  given name: Jesús Genaro
author list: Agent
  family name: Benavides-González
  given name: Flaviano
author list: Agent
  family name: Rábago-Castro
  given name: Jaime Luis
author list: Agent
  family name: Vázquez-Sauceda
  given name: María de la Luz
author list: Agent
  family name: Garrido-Olvera
  given name: Lorena
doi: 10.7717/peerj.10496
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Blanco-Martínez et al.
attribution name: Blanco-Martínez et al.

Pro-inflammatory effect of obesity on rats with burn wounds
type: item
type: AcademicArticle
description: Objective A burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study. Materials and methods Different degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted. Results The ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14. Conclusion Burn injury and obesity have a mutually synergistic effect on the body’s inflammatory response.
format: application/pdf
format: text/html
creator: Chan Nie
creator: Huiting Yu
creator: Xue Wang
creator: Xiahong Li
creator: Zairong Wei
creator: Xiuquan Shi
subject: Molecular Biology
subject: Dermatology
subject: Internal Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.10499
publisher: PeerJ Inc.
rights: © 2020 Nie et al.
abstract: Objective A burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study. Materials and methods Different degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted. Results The ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14. Conclusion Burn injury and obesity have a mutually synergistic effect on the body’s inflammatory response.
bibliographic citation: Nie et al. (2020) Pro-inflammatory effect of obesity on rats with burn wounds. PeerJ 8:e10499 https://doi.org/10.7717/peerj.10499
date submitted: 2020-07-23
date accepted: 2020-11-15
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nie
  given name: Chan
author list: Agent
  family name: Yu
  given name: Huiting
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Li
  given name: Xiahong
author list: Agent
  family name: Wei
  given name: Zairong
author list: Agent
  family name: Shi
  given name: Xiuquan
doi: 10.7717/peerj.10499
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Nie et al.
attribution name: Nie et al.

Self-reports vs. physical measures of spinal stiffness
type: item
type: AcademicArticle
description: Background Objectively measured reduction in lumbar posterior-to-anterior (PA) stiffness is associated with pain relief in some, but not all persons with low back pain. Unfortunately, these measurements can be time consuming to perform. In comparison, the Lumbar Spine Instability Questionnaire (LSIQ) is intended to measure spinal instability and the Lumbar Spine Disability Index (LSDI) is created for self-reporting functional disability due to increased spinal stiffness. Given the above, the aim of this study is to compare measures of the LSIQ and LSDI with objective measures of lumbar PA stiffness as measured by a mechanical device, Vertetrack (VT), in patients with persistent non-specific low back pain (nsLBP). Methods Twenty-nine patients with nsLBP completed the LSIQ and LSDI at baseline and after two weeks. On these same occasions, PA spinal stiffness was measured using the VT. Between measurements, patients received four sessions of spinal manipulation. The resulting data was analyzed to determine the correlation between the self-report and objective measures of stiffness at both time points. Further, the patients were categorized into responders and non-responders based on pre-established cut points depending on values from the VT and compared those to self-report measures in order to determine whether the LSIQ and the LSDI were sensitive to change. Results Twenty-nine participants completed the study. Measures from the LSIQ and LSDI correlated poorly with objectively measured lumbar PA stiffness at baseline and also with the change scores. The change in objectively measured lumbar PA stiffness following spinal manipulation did not differ between those who improved, and those who did not improve according to the pre-specified cut-points. Finally, a reduction in lumbar PA stiffness following intervention was not associated with improvement in LSIQ and LSDI outcomes. Conclusions The current data indicate that the LSIQ and LSDI questionnaires do not correlate wi…
format: application/pdf
format: text/html
creator: Jonas Nielsen
creator: Casper Glissmann Nim
creator: Søren O’Neill
creator: Eleanor Boyle
creator: Jan Hartvigsen
creator: Gregory N. Kawchuk
subject: Anatomy and Physiology
subject: Global Health
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.9598
publisher: PeerJ Inc.
rights: © 2020 Nielsen et al.
abstract: Background Objectively measured reduction in lumbar posterior-to-anterior (PA) stiffness is associated with pain relief in some, but not all persons with low back pain. Unfortunately, these measurements can be time consuming to perform. In comparison, the Lumbar Spine Instability Questionnaire (LSIQ) is intended to measure spinal instability and the Lumbar Spine Disability Index (LSDI) is created for self-reporting functional disability due to increased spinal stiffness. Given the above, the aim of this study is to compare measures of the LSIQ and LSDI with objective measures of lumbar PA stiffness as measured by a mechanical device, Vertetrack (VT), in patients with persistent non-specific low back pain (nsLBP). Methods Twenty-nine patients with nsLBP completed the LSIQ and LSDI at baseline and after two weeks. On these same occasions, PA spinal stiffness was measured using the VT. Between measurements, patients received four sessions of spinal manipulation. The resulting data was analyzed to determine the correlation between the self-report and objective measures of stiffness at both time points. Further, the patients were categorized into responders and non-responders based on pre-established cut points depending on values from the VT and compared those to self-report measures in order to determine whether the LSIQ and the LSDI were sensitive to change. Results Twenty-nine participants completed the study. Measures from the LSIQ and LSDI correlated poorly with objectively measured lumbar PA stiffness at baseline and also with the change scores. The change in objectively measured lumbar PA stiffness following spinal manipulation did not differ between those who improved, and those who did not improve according to the pre-specified cut-points. Finally, a reduction in lumbar PA stiffness following intervention was not associated with improvement in LSIQ and LSDI outcomes. Conclusions The current data indicate that the LSIQ and LSDI questionnaires do not correlate wi…
bibliographic citation: Nielsen et al. (2020) Self-reports vs. physical measures of spinal stiffness. PeerJ 8:e9598 https://doi.org/10.7717/peerj.9598
date submitted: 2019-11-04
date accepted: 2020-07-02
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nielsen
  given name: Jonas
author list: Agent
  family name: Glissmann Nim
  given name: Casper
author list: Agent
  family name: O’Neill
  given name: Søren
author list: Agent
  family name: Boyle
  given name: Eleanor
author list: Agent
  family name: Hartvigsen
  given name: Jan
author list: Agent
  family name: Kawchuk
  given name: Gregory N.
doi: 10.7717/peerj.9598
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: ©2020 Nielsen et al.
attribution name: Nielsen et al.

Identification of key genes and pathways in endometriosis by integrated expression profiles analysis
type: item
type: AcademicArticle
description: The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis.
format: application/pdf
format: text/html
creator: Ding Cui
creator: Yang Liu
creator: Junyan Ma
creator: Kaiqing Lin
creator: Kaihong Xu
creator: Jun Lin
subject: Genomics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.10171
publisher: PeerJ Inc.
rights: © 2020 Cui et al.
abstract: The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis.
bibliographic citation: Cui et al. (2020) Identification of key genes and pathways in endometriosis by integrated expression profiles analysis. PeerJ 8:e10171 https://doi.org/10.7717/peerj.10171
date submitted: 2019-10-15
date accepted: 2020-09-22
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Ding
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Ma
  given name: Junyan
author list: Agent
  family name: Lin
  given name: Kaiqing
author list: Agent
  family name: Xu
  given name: Kaihong
author list: Agent
  family name: Lin
  given name: Jun
doi: 10.7717/peerj.10171
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: ©2020 Cui et al.
attribution name: Cui et al.

Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies
type: item
type: AcademicArticle
description: Background Blow flies are a family of dipterans of medical, veterinary and sanitary importance. We aim to predict the current geographical distribution of six neotropical blowfly species with different altitudinal ranges of distribution (high, medium, and lowlands) and degree of synanthropy (eusynanthropic, hemisynanthropic and asynanthropic) based on their existing fundamental niche (EA) in Northwestern South America. Methods Geographical records were compiled based on data from museum specimens and literature. The accessible area hypothesis (M) was calculated based on three criteria: (1) Altitudinal range, (2) Synanthropy values deducted based on the Human Influence Index (HII) raster dataset, and (3). The mean dispersal capability of flies. The modeling was performed using the Maxent entropy modeling software. The selection of parameters was made with the R Program ENMeval package. Results The models were assessed using the area under the operator-partial receiver curve (ROCp). The high statistical performance was evidenced in every modeling prediction. The modeling allowed identifying possible taxonomic inaccuracies and the lack of exhaustive collection in the field, especially for lowlands species. Geographical distribution predicted by the modeling and empirical data was remarkably coherent in montane species. Discussion The data obtained evidence that montane elevational ranges affect the performance of the distribution models. These models will allow a more precise predicting of medium and high elevation blow flies than lowlands species. Montane species modeling will accurately predict the fly occurrence to use such biological information for medical, legal, veterinary, and conservation purposes.
format: application/pdf
format: text/html
creator: Mariano Altamiranda-Saavedra
creator: Eduardo Amat
creator: Luz Miryam Gómez-P
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Zoology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10370
publisher: PeerJ Inc.
rights: © 2020 Altamiranda-Saavedra et al.
abstract: Background Blow flies are a family of dipterans of medical, veterinary and sanitary importance. We aim to predict the current geographical distribution of six neotropical blowfly species with different altitudinal ranges of distribution (high, medium, and lowlands) and degree of synanthropy (eusynanthropic, hemisynanthropic and asynanthropic) based on their existing fundamental niche (EA) in Northwestern South America. Methods Geographical records were compiled based on data from museum specimens and literature. The accessible area hypothesis (M) was calculated based on three criteria: (1) Altitudinal range, (2) Synanthropy values deducted based on the Human Influence Index (HII) raster dataset, and (3). The mean dispersal capability of flies. The modeling was performed using the Maxent entropy modeling software. The selection of parameters was made with the R Program ENMeval package. Results The models were assessed using the area under the operator-partial receiver curve (ROCp). The high statistical performance was evidenced in every modeling prediction. The modeling allowed identifying possible taxonomic inaccuracies and the lack of exhaustive collection in the field, especially for lowlands species. Geographical distribution predicted by the modeling and empirical data was remarkably coherent in montane species. Discussion The data obtained evidence that montane elevational ranges affect the performance of the distribution models. These models will allow a more precise predicting of medium and high elevation blow flies than lowlands species. Montane species modeling will accurately predict the fly occurrence to use such biological information for medical, legal, veterinary, and conservation purposes.
bibliographic citation: Altamiranda-Saavedra et al. (2020) Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies. PeerJ 8:e10370 https://doi.org/10.7717/peerj.10370
date submitted: 2020-07-10
date accepted: 2020-10-26
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Altamiranda-Saavedra
  given name: Mariano
author list: Agent
  family name: Amat
  given name: Eduardo
author list: Agent
  family name: Gómez-P
  given name: Luz Miryam
doi: 10.7717/peerj.10370
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: ©2020 Altamiranda-Saavedra et al.
attribution name: Altamiranda-Saavedra et al.

Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery
type: item
type: AcademicArticle
description: Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored.
format: application/pdf
format: text/html
creator: Rohit Nandakumar
creator: Valentin Dinu
subject: Bioinformatics
subject: Computational Biology
subject: Drugs and Devices
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.10381
publisher: PeerJ Inc.
rights: © 2020 Nandakumar and Dinu
abstract: Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored.
bibliographic citation: Nandakumar et al. (2020) Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery. PeerJ 8:e10381 https://doi.org/10.7717/peerj.10381
date submitted: 2020-05-20
date accepted: 2020-10-27
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nandakumar
  given name: Rohit
author list: Agent
  family name: Dinu
  given name: Valentin
doi: 10.7717/peerj.10381
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: © 2020 Nandakumar and Dinu
attribution name: Nandakumar and Dinu

Trials in developing a nanoscale material for extravascular contrast-enhanced ultrasound targeting hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Medical imaging is an important approach for the diagnosis of hepatocellular carcinoma (HCC), a common life threaten disease, however, the diagnostic efficiency is still not optimal. Developing a novel method to improve diagnosis is necessary. The aim of this project was to formulate a material that can combine with GPC3 of HCC for targeted enhanced ultrasound. Methods A material of sulfur hexafluoride (SF6) filled liposome microbubbles and conjugated with synthesized peptide (LSPMbs) was prepared and assessed in vitro and vivo. Liposome microbubbles were made of DPPC, DPPG, DSPE-PEG2000,and SF6, using thin film method to form shell, followed filling SF6, and conjugating peptide. A carbodiimide method was used for covalent conjugation of peptide to LSMbs. Results The prepared LSPMbs appeared round shaped, with size of 380.9 ± 176.5 nm, and Zeta potential of −51.4 ± 10.4mV. LSPMbs showed high affinity to Huh-7 cells in vitro, presented good enhanced ultrasound effects, did not show cytotoxicity, and did not exhibit targeted fluorescence and enhanced ultrasound in animal xenograft tumors. Conclusion Extravascular contrast-enhanced ultrasound targeted GPC3 on HCC may not be realized, and the reason may be that targeted contrast agents of microbubbles are hard to access and accumulate in the tumor stroma and matrix.
format: application/pdf
format: text/html
creator: Size Wu
creator: Xiyuan Lin
subject: Gastroenterology and Hepatology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10403
publisher: PeerJ Inc.
rights: © 2020 Wu and Lin
abstract: Background Medical imaging is an important approach for the diagnosis of hepatocellular carcinoma (HCC), a common life threaten disease, however, the diagnostic efficiency is still not optimal. Developing a novel method to improve diagnosis is necessary. The aim of this project was to formulate a material that can combine with GPC3 of HCC for targeted enhanced ultrasound. Methods A material of sulfur hexafluoride (SF6) filled liposome microbubbles and conjugated with synthesized peptide (LSPMbs) was prepared and assessed in vitro and vivo. Liposome microbubbles were made of DPPC, DPPG, DSPE-PEG2000,and SF6, using thin film method to form shell, followed filling SF6, and conjugating peptide. A carbodiimide method was used for covalent conjugation of peptide to LSMbs. Results The prepared LSPMbs appeared round shaped, with size of 380.9 ± 176.5 nm, and Zeta potential of −51.4 ± 10.4mV. LSPMbs showed high affinity to Huh-7 cells in vitro, presented good enhanced ultrasound effects, did not show cytotoxicity, and did not exhibit targeted fluorescence and enhanced ultrasound in animal xenograft tumors. Conclusion Extravascular contrast-enhanced ultrasound targeted GPC3 on HCC may not be realized, and the reason may be that targeted contrast agents of microbubbles are hard to access and accumulate in the tumor stroma and matrix.
bibliographic citation: Wu et al. (2020) Trials in developing a nanoscale material for extravascular contrast-enhanced ultrasound targeting hepatocellular carcinoma. PeerJ 8:e10403 https://doi.org/10.7717/peerj.10403
date submitted: 2020-08-12
date accepted: 2020-10-31
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Size
author list: Agent
  family name: Lin
  given name: Xiyuan
doi: 10.7717/peerj.10403
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: ©2020 Wu and Lin
attribution name: Wu and Lin

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