PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Resection vs. ablation for lesions characterized as resectable-ablative within the colorectal liver oligometastases criteria: a propensity score matching from retrospective study
items: Speeding up training of automated bird recognizers by data reduction of audio features
items: Airborne microbial biodiversity and seasonality in Northern and Southern Sweden
items: Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China
items: Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children
items: The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma
items: The complete genome of Banana streak GF virus Yunnan isolate infecting Cavendish Musa AAA group in China
items: Evaluation of three wheat (Triticum aestivum L.) cultivars as sensitive Cd biomarkers during the seedling stage
items: Cranial anatomy of Allosaurus jimmadseni, a new species from the lower part of the Morrison Formation (Upper Jurassic) of Western North America
items: Viability and management of the Asian elephant (Elephas maximus) population in the Endau Rompin landscape, Peninsular Malaysia

Resection vs. ablation for lesions characterized as resectable-ablative within the colorectal liver oligometastases criteria: a propensity score matching from retrospective study
type: item
type: AcademicArticle
description: Background There has been no prospective or retrospective studies reporting the comparison outcome between surgery and ablation for resectable-ablative (lesions could be treated by resection or complete ablation) colorectal liver oligometastases (CLOM). The purpose of this study was to compare the efficacy and prognostic difference in patients who underwent R0 resection vs. complete ablation within the resectable-ablative CLOM criteria. Methods From January 2008 to May 2018, a total of 2,367 patients diagnosed with colorectal liver metastases were included in this observational study. The metastasis was characterized by only limited to liver with number ≤5, size ≤5 cm, and resectable-ablative (lesions could be treated by resection or complete ablation). The evaluated indications, including liver progression-free survival (LPFS), overall survival (OS), survival rates, pattern and number of recurrences, and complications, were compared by using propensity score matching (PSM). The Kaplan−Meier curves were generated, and a log-rank test was performed. The Cox regression model was used for univariate and multivariate analyses to identify predictors of outcomes. Results A total of 421 consecutive patients were eligible for this study, with 250 and 171 undergoing R0 resection and complete ablation, respectively. PSM identified 145 patients from each group. The 1-, 3-, 5- and 8-year OS rates in the resection group and the ablation group were 95.8% vs. 95.0%, 69.8% vs. 60.1%, 53.6% vs. 42.5%, and 45.1% vs. 32.9% (p = 0.075), respectively. The median LPFS in the resection group was significantly longer than that in the ablation group (35 months vs. 15 months, p = 0.011). No statistical difference was found in LPFS between the two groups when comparing ≤3 cm liver metastases. For liver metastasis >3 cm, the median LPFS in the resection group and ablation group was 11 months and 5 months, respectively (p = 0.001). In terms of high risk of clinical risk score (CRS), the resecti…
format: application/pdf
format: text/html
creator: Ma Luo
creator: Si-Liang Chen
creator: Jiawen Chen
creator: Huzheng Yan
creator: Zhenkang Qiu
creator: Guanyu Chen
creator: Ligong Lu
creator: Fujun Zhang
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.8398
publisher: PeerJ Inc.
rights: © 2020 Luo et al.
abstract: Background There has been no prospective or retrospective studies reporting the comparison outcome between surgery and ablation for resectable-ablative (lesions could be treated by resection or complete ablation) colorectal liver oligometastases (CLOM). The purpose of this study was to compare the efficacy and prognostic difference in patients who underwent R0 resection vs. complete ablation within the resectable-ablative CLOM criteria. Methods From January 2008 to May 2018, a total of 2,367 patients diagnosed with colorectal liver metastases were included in this observational study. The metastasis was characterized by only limited to liver with number ≤5, size ≤5 cm, and resectable-ablative (lesions could be treated by resection or complete ablation). The evaluated indications, including liver progression-free survival (LPFS), overall survival (OS), survival rates, pattern and number of recurrences, and complications, were compared by using propensity score matching (PSM). The Kaplan−Meier curves were generated, and a log-rank test was performed. The Cox regression model was used for univariate and multivariate analyses to identify predictors of outcomes. Results A total of 421 consecutive patients were eligible for this study, with 250 and 171 undergoing R0 resection and complete ablation, respectively. PSM identified 145 patients from each group. The 1-, 3-, 5- and 8-year OS rates in the resection group and the ablation group were 95.8% vs. 95.0%, 69.8% vs. 60.1%, 53.6% vs. 42.5%, and 45.1% vs. 32.9% (p = 0.075), respectively. The median LPFS in the resection group was significantly longer than that in the ablation group (35 months vs. 15 months, p = 0.011). No statistical difference was found in LPFS between the two groups when comparing ≤3 cm liver metastases. For liver metastasis >3 cm, the median LPFS in the resection group and ablation group was 11 months and 5 months, respectively (p = 0.001). In terms of high risk of clinical risk score (CRS), the resecti…
bibliographic citation: Luo et al. (2020) Resection vs. ablation for lesions characterized as resectable-ablative within the colorectal liver oligometastases criteria: a propensity score matching from retrospective study. PeerJ 8:e8398 https://doi.org/10.7717/peerj.8398
date submitted: 2019-08-23
date accepted: 2019-12-16
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Ma
author list: Agent
  family name: Chen
  given name: Si-Liang
author list: Agent
  family name: Chen
  given name: Jiawen
author list: Agent
  family name: Yan
  given name: Huzheng
author list: Agent
  family name: Qiu
  given name: Zhenkang
author list: Agent
  family name: Chen
  given name: Guanyu
author list: Agent
  family name: Lu
  given name: Ligong
author list: Agent
  family name: Zhang
  given name: Fujun
doi: 10.7717/peerj.8398
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Luo et al.
attribution name: Luo et al.

Speeding up training of automated bird recognizers by data reduction of audio features
type: item
type: AcademicArticle
description: Automated acoustic recognition of birds is considered an important technology in support of biodiversity monitoring and biodiversity conservation activities. These activities require processing large amounts of soundscape recordings. Typically, recordings are transformed to a number of acoustic features, and a machine learning method is used to build models and recognize the sound events of interest. The main problem is the scalability of data processing, either for developing models or for processing recordings made over long time periods. In those cases, the processing time and resources required might become prohibitive for the average user. To address this problem, we evaluated the applicability of three data reduction methods. These methods were applied to a series of acoustic feature vectors as an additional postprocessing step, which aims to reduce the computational demand during training. The experimental results obtained using Mel-frequency cepstral coefficients (MFCCs) and hidden Markov models (HMMs) support the finding that a reduction in training data by a factor of 10 does not significantly affect the recognition performance.
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format: text/html
creator: Allan G. de Oliveira
creator: Thiago M. Ventura
creator: Todor D. Ganchev
creator: Lucas N.S. Silva
creator: Marinêz I. Marques
creator: Karl-L. Schuchmann
subject: Ecosystem Science
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.8407
publisher: PeerJ Inc.
rights: © 2020 de Oliveira et al.
abstract: Automated acoustic recognition of birds is considered an important technology in support of biodiversity monitoring and biodiversity conservation activities. These activities require processing large amounts of soundscape recordings. Typically, recordings are transformed to a number of acoustic features, and a machine learning method is used to build models and recognize the sound events of interest. The main problem is the scalability of data processing, either for developing models or for processing recordings made over long time periods. In those cases, the processing time and resources required might become prohibitive for the average user. To address this problem, we evaluated the applicability of three data reduction methods. These methods were applied to a series of acoustic feature vectors as an additional postprocessing step, which aims to reduce the computational demand during training. The experimental results obtained using Mel-frequency cepstral coefficients (MFCCs) and hidden Markov models (HMMs) support the finding that a reduction in training data by a factor of 10 does not significantly affect the recognition performance.
bibliographic citation: de Oliveira et al. (2020) Speeding up training of automated bird recognizers by data reduction of audio features. PeerJ 8:e8407 https://doi.org/10.7717/peerj.8407
date submitted: 2019-04-05
date accepted: 2019-12-16
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Oliveira
  given name: Allan G.
author list: Agent
  family name: Ventura
  given name: Thiago M.
author list: Agent
  family name: Ganchev
  given name: Todor D.
author list: Agent
  family name: Silva
  given name: Lucas N.S.
author list: Agent
  family name: Marques
  given name: Marinêz I.
author list: Agent
  family name: Schuchmann
  given name: Karl-L.
doi: 10.7717/peerj.8407
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 de Oliveira et al.
attribution name: de Oliveira et al.

Airborne microbial biodiversity and seasonality in Northern and Southern Sweden
type: item
type: AcademicArticle
description: Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by art…
format: application/pdf
format: text/html
creator: Edvin Karlsson
creator: Anna-Mia Johansson
creator: Jon Ahlinder
creator: Moa J. Lundkvist
creator: Navinder J. Singh
creator: Tomas Brodin
creator: Mats Forsman
creator: Per Stenberg
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.8424
publisher: PeerJ Inc.
rights: © 2020 Karlsson et al.
abstract: Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by art…
bibliographic citation: Karlsson et al. (2020) Airborne microbial biodiversity and seasonality in Northern and Southern Sweden. PeerJ 8:e8424 https://doi.org/10.7717/peerj.8424
date submitted: 2019-08-16
date accepted: 2019-12-17
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karlsson
  given name: Edvin
author list: Agent
  family name: Johansson
  given name: Anna-Mia
author list: Agent
  family name: Ahlinder
  given name: Jon
author list: Agent
  family name: Lundkvist
  given name: Moa J.
author list: Agent
  family name: Singh
  given name: Navinder J.
author list: Agent
  family name: Brodin
  given name: Tomas
author list: Agent
  family name: Forsman
  given name: Mats
author list: Agent
  family name: Stenberg
  given name: Per
doi: 10.7717/peerj.8424
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Karlsson et al.
attribution name: Karlsson et al.

Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China
type: item
type: AcademicArticle
description: Variation in precipitation can markedly affect the structure and function of soil microbial communities, especially in arid areas which are limited by water resources. Therefore, it is critical to understand how soil bacterial community composition and diversity will respond to variation in precipitation. In this study, we examined the soil bacterial community structure and diversity between five precipitation treatments (60% decrease, 30% decrease, control, 30% increase and 60% increase in precipitation) in the same arid site, in the Junggar desert of Xinjiang, northern China. The dominant bacterial phyla, present at similar frequencies in plots with different precipitation levels, were Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. The Shannon-Wiener and Chao1 indices of soil bacterial α-diversity were both positively correlated with plant diversity. Our results indicated that (1) extreme drought significantly decreased bacterial abundance and diversity compared with increased precipitation; (2) variation in precipitation did not change the dominant components of the bacterial communities; and (3) soil pH and total nitrogen concentration were the key factors affecting soil bacterial composition in the Junggar desert.
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format: text/html
creator: Ke Wu
creator: Wenxuan Xu
creator: Weikang Yang
subject: Ecology
subject: Microbiology
subject: Climate Change Biology
description: doi:10.7717/peerj.8433
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Variation in precipitation can markedly affect the structure and function of soil microbial communities, especially in arid areas which are limited by water resources. Therefore, it is critical to understand how soil bacterial community composition and diversity will respond to variation in precipitation. In this study, we examined the soil bacterial community structure and diversity between five precipitation treatments (60% decrease, 30% decrease, control, 30% increase and 60% increase in precipitation) in the same arid site, in the Junggar desert of Xinjiang, northern China. The dominant bacterial phyla, present at similar frequencies in plots with different precipitation levels, were Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. The Shannon-Wiener and Chao1 indices of soil bacterial α-diversity were both positively correlated with plant diversity. Our results indicated that (1) extreme drought significantly decreased bacterial abundance and diversity compared with increased precipitation; (2) variation in precipitation did not change the dominant components of the bacterial communities; and (3) soil pH and total nitrogen concentration were the key factors affecting soil bacterial composition in the Junggar desert.
bibliographic citation: Wu et al. (2020) Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China. PeerJ 8:e8433 https://doi.org/10.7717/peerj.8433
date submitted: 2019-08-27
date accepted: 2019-12-19
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Ke
author list: Agent
  family name: Xu
  given name: Wenxuan
author list: Agent
  family name: Yang
  given name: Weikang
doi: 10.7717/peerj.8433
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Wu et al.
attribution name: Wu et al.

Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children
type: item
type: AcademicArticle
description: Purpose To investigate the association between insulin-like growth factor 1 (IGF1) single-nucleotide polymorphisms (SNPs) and myopia in a young Chinese population. Methods A total of 654 Chinese children aged 6–13 years from one primary school participated in our study and underwent a series of comprehensive ocular examinations, including cycloplegic refraction and measurements of axial length. Myopia was defined as a spherical equivalence (SE) ≤ −0.5 D in the worse eye. In total, six tagging SNPs of IGF1 were genotyped using the PCR-LDR (Polymerase Chain Reaction-Ligation Detection Reaction) method. We tested four different genetic modes (the allele, dominant, recessive, and additive models) of these SNPs and used multivariate logistic regression to calculate the effect of SNPs on myopia. In addition, we conducted a haplotype analysis with a variable-sized slide-window strategy. Results Overall, 281 myopic children and 373 non-myopic controls were included in the analysis. The SNP rs2162679 showed a statistical difference between the two groups in both the allele (p = 0.0474) and additive (p = 0.0497) models. After adjusting for age and gender, children with the genotype AA in the SNP rs2162679 had a higher risk of myopia than those with the genotype GG (OR = 2.219, 95% CI [1.218–4.039], p = 0.009). All haplotypes that varied significantly between the two groups contained the SNP rs2162679, and the four-SNP window rs5742653–rs2162679 had the lowest p value (Chi square = 5.768, p = 0.0163). However, after permutation tests, none of the associations remained statistically significant. Conclusion The SNP rs2162679 in IGF1 was associated with myopia in a young Chinese population. The G allele in the SNP rs2162679 may protect against myopia.
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creator: Tianyu Cheng
creator: Jingjing Wang
creator: Shuyu Xiong
creator: Bo Zhang
creator: Qiangqiang Li
creator: Xun Xu
creator: Xiangui He
subject: Genetics
subject: Ophthalmology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.8436
publisher: PeerJ Inc.
rights: © 2020 Cheng et al.
abstract: Purpose To investigate the association between insulin-like growth factor 1 (IGF1) single-nucleotide polymorphisms (SNPs) and myopia in a young Chinese population. Methods A total of 654 Chinese children aged 6–13 years from one primary school participated in our study and underwent a series of comprehensive ocular examinations, including cycloplegic refraction and measurements of axial length. Myopia was defined as a spherical equivalence (SE) ≤ −0.5 D in the worse eye. In total, six tagging SNPs of IGF1 were genotyped using the PCR-LDR (Polymerase Chain Reaction-Ligation Detection Reaction) method. We tested four different genetic modes (the allele, dominant, recessive, and additive models) of these SNPs and used multivariate logistic regression to calculate the effect of SNPs on myopia. In addition, we conducted a haplotype analysis with a variable-sized slide-window strategy. Results Overall, 281 myopic children and 373 non-myopic controls were included in the analysis. The SNP rs2162679 showed a statistical difference between the two groups in both the allele (p = 0.0474) and additive (p = 0.0497) models. After adjusting for age and gender, children with the genotype AA in the SNP rs2162679 had a higher risk of myopia than those with the genotype GG (OR = 2.219, 95% CI [1.218–4.039], p = 0.009). All haplotypes that varied significantly between the two groups contained the SNP rs2162679, and the four-SNP window rs5742653–rs2162679 had the lowest p value (Chi square = 5.768, p = 0.0163). However, after permutation tests, none of the associations remained statistically significant. Conclusion The SNP rs2162679 in IGF1 was associated with myopia in a young Chinese population. The G allele in the SNP rs2162679 may protect against myopia.
bibliographic citation: Cheng et al. (2020) Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children. PeerJ 8:e8436 https://doi.org/10.7717/peerj.8436
date submitted: 2019-08-28
date accepted: 2019-12-19
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Tianyu
author list: Agent
  family name: Wang
  given name: Jingjing
author list: Agent
  family name: Xiong
  given name: Shuyu
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Li
  given name: Qiangqiang
author list: Agent
  family name: Xu
  given name: Xun
author list: Agent
  family name: He
  given name: Xiangui
doi: 10.7717/peerj.8436
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Cheng et al.
attribution name: Cheng et al.

The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma
type: item
type: AcademicArticle
description: Background Ubiquitin-conjugating enzyme E2T (UBE2T) is overexpressed in several types of malignancies. However, little is known about its diagnostic significance in intrahepatic cholangiocarcinoma (ICC) and other bile duct diseases or its prognostic value in ICC. Methods The expression levels of UBE2T in the intrahepatic bile duct (IHBD, N = 13), biliary intraepithelial neoplasia (BilIN; BilIN-1/2, N = 23; BilIN-3, N = 11), and ICC (N = 401) were examined by immunohistochemistry. The differential diagnostic and prognostic values were also assessed. Results The number of UBE2T-positive cells was significantly higher in ICC tissues than in nonmalignant tissues, including the IHBD, BilIN-1/2, and BilIN-3 tissues. Kaplan–Meier analysis showed that overexpression of UBE2T was correlated with a shorter time to recurrence (TTR) and overall survival (OS). The 5-year TTR rates in the high UBE2T and low UBE2T groups were 100% and 86.2%, respectively. The corresponding OS rates were 1.9% and 22.2%, respectively. High expression of UBE2T was an independent risk factor for both TTR (hazard ratio: 1.345; 95% confidence interval: 1.047,1.728) and OS (hazard ratio: 1.420; 95% confidence interval: 1.098,1.837). Conclusions UBE2T can assist in differentiating benign bile duct diseases from ICC, and high expression of UBE2T suggests a poor prognosis for ICC.
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creator: Hua Yu
creator: Han Wang
creator: Wei Dong
creator: Zhen-Ying Cao
creator: Rong Li
creator: Chao Yang
creator: Wen-Ming Cong
creator: Hui Dong
creator: Guang-Zhi Jin
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.8454
publisher: PeerJ Inc.
rights: © 2020 Yu et al.
abstract: Background Ubiquitin-conjugating enzyme E2T (UBE2T) is overexpressed in several types of malignancies. However, little is known about its diagnostic significance in intrahepatic cholangiocarcinoma (ICC) and other bile duct diseases or its prognostic value in ICC. Methods The expression levels of UBE2T in the intrahepatic bile duct (IHBD, N = 13), biliary intraepithelial neoplasia (BilIN; BilIN-1/2, N = 23; BilIN-3, N = 11), and ICC (N = 401) were examined by immunohistochemistry. The differential diagnostic and prognostic values were also assessed. Results The number of UBE2T-positive cells was significantly higher in ICC tissues than in nonmalignant tissues, including the IHBD, BilIN-1/2, and BilIN-3 tissues. Kaplan–Meier analysis showed that overexpression of UBE2T was correlated with a shorter time to recurrence (TTR) and overall survival (OS). The 5-year TTR rates in the high UBE2T and low UBE2T groups were 100% and 86.2%, respectively. The corresponding OS rates were 1.9% and 22.2%, respectively. High expression of UBE2T was an independent risk factor for both TTR (hazard ratio: 1.345; 95% confidence interval: 1.047,1.728) and OS (hazard ratio: 1.420; 95% confidence interval: 1.098,1.837). Conclusions UBE2T can assist in differentiating benign bile duct diseases from ICC, and high expression of UBE2T suggests a poor prognosis for ICC.
bibliographic citation: Yu et al. (2020) The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma. PeerJ 8:e8454 https://doi.org/10.7717/peerj.8454
date submitted: 2019-09-20
date accepted: 2019-12-23
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Hua
author list: Agent
  family name: Wang
  given name: Han
author list: Agent
  family name: Dong
  given name: Wei
author list: Agent
  family name: Cao
  given name: Zhen-Ying
author list: Agent
  family name: Li
  given name: Rong
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Cong
  given name: Wen-Ming
author list: Agent
  family name: Dong
  given name: Hui
author list: Agent
  family name: Jin
  given name: Guang-Zhi
doi: 10.7717/peerj.8454
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Yu et al.
attribution name: Yu et al.

The complete genome of Banana streak GF virus Yunnan isolate infecting Cavendish Musa AAA group in China
type: item
type: AcademicArticle
description: Banana streak virus (BSV) belongs to the members of the genus Badnavirus, family Caulimoviridae. At present, BSV contains nine species in the International Committee on Taxonomy of Viruses (ICTV) classification report (2018b release). Previous study indicated that the viral particles of Banana streak virus Acuminata Yunnan (BSV-Acum) were purified from banana (Cavendish Musa AAA group) leaves in Yunnan Province, China, and its complete genome was obtained. To further determine whether this sample infecting with Banana streak GF virus (BSGFV), the polymerase chain reaction (PCR) cloning and complete genome analysis of the Banana streak GF virus Yunnan isolate (BSGFV-YN) isolate were carried out in this study. The result showed that BSGFV-YN infecting Cavendish Musa AAA group was co-infecting this sample. Its genome contains a total of 7,325 bp in length with 42% GC content. This complete genome sequence was deposited in GenBank under accession number MN296502. Sequence analysis showed that the complete genome of BSGFV-YN was 98.14% sequence similarity to BSGFV Goldfinger, while it was 49.10–57.09% to other BSV species. Two phylogenetic trees based on the complete genome and ORFIII polyprotein indicated that BSGFV-YN and other BSV species clustered into a group, while it was the highest homology with BSGFV Goldfinger. Although BSGFV-YN and BSGFV Goldfinger were highly homologous, their cultivating bananas are different. The former cultivating banana was from Cavendish Musa AAA group, while the latter cultivating banana was from Goldfinger Musa AAAB group. Compared with BSGFV Goldfinger, the genome of BSGFV-YN has an extra multiple repetitive sequences in the intergenetic region between ORFIII and ORFI, suggesting that this region might be related to host selection. In summary, a BSGFV-YN distant from BSV-Acum was identified from the same sample, and its complete genome sequence was determined and analyzed. The study extends the polymorphism of BSVs in China and provid…
format: application/pdf
format: text/html
creator: Wei-li Li
creator: Nai-tong Yu
creator: Jian-hua Wang
creator: Jun-cheng Li
creator: Zhi-xin Liu
subject: Genomics
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.8459
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Banana streak virus (BSV) belongs to the members of the genus Badnavirus, family Caulimoviridae. At present, BSV contains nine species in the International Committee on Taxonomy of Viruses (ICTV) classification report (2018b release). Previous study indicated that the viral particles of Banana streak virus Acuminata Yunnan (BSV-Acum) were purified from banana (Cavendish Musa AAA group) leaves in Yunnan Province, China, and its complete genome was obtained. To further determine whether this sample infecting with Banana streak GF virus (BSGFV), the polymerase chain reaction (PCR) cloning and complete genome analysis of the Banana streak GF virus Yunnan isolate (BSGFV-YN) isolate were carried out in this study. The result showed that BSGFV-YN infecting Cavendish Musa AAA group was co-infecting this sample. Its genome contains a total of 7,325 bp in length with 42% GC content. This complete genome sequence was deposited in GenBank under accession number MN296502. Sequence analysis showed that the complete genome of BSGFV-YN was 98.14% sequence similarity to BSGFV Goldfinger, while it was 49.10–57.09% to other BSV species. Two phylogenetic trees based on the complete genome and ORFIII polyprotein indicated that BSGFV-YN and other BSV species clustered into a group, while it was the highest homology with BSGFV Goldfinger. Although BSGFV-YN and BSGFV Goldfinger were highly homologous, their cultivating bananas are different. The former cultivating banana was from Cavendish Musa AAA group, while the latter cultivating banana was from Goldfinger Musa AAAB group. Compared with BSGFV Goldfinger, the genome of BSGFV-YN has an extra multiple repetitive sequences in the intergenetic region between ORFIII and ORFI, suggesting that this region might be related to host selection. In summary, a BSGFV-YN distant from BSV-Acum was identified from the same sample, and its complete genome sequence was determined and analyzed. The study extends the polymorphism of BSVs in China and provid…
bibliographic citation: Li et al. (2020) The complete genome of Banana streak GF virus Yunnan isolate infecting Cavendish Musa AAA group in China. PeerJ 8:e8459 https://doi.org/10.7717/peerj.8459
date submitted: 2019-09-20
date accepted: 2019-12-24
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wei-li
author list: Agent
  family name: Yu
  given name: Nai-tong
author list: Agent
  family name: Wang
  given name: Jian-hua
author list: Agent
  family name: Li
  given name: Jun-cheng
author list: Agent
  family name: Liu
  given name: Zhi-xin
doi: 10.7717/peerj.8459
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Li et al.
attribution name: Li et al.

Evaluation of three wheat (Triticum aestivum L.) cultivars as sensitive Cd biomarkers during the seedling stage
type: item
type: AcademicArticle
description: Sensitive seedling crops have been developed to monitor Cadmium (Cd) contamination in agricultural soil. In the present study, 18 parameters involving growth conditions and physiological performances were assessed to evaluate Cd-responses of three wheat (Triticum aestivum L.) cultivars, Xihan1 (XH), Longzhong1 (LZ) and Dingfeng16 (DF). Principle component analysis illustrated that Factor 1, representing growth performance, soluble sugar content and catalase activity, responded to the Cd treatments in a dose dependent manner, while Factor 2 represented by chlorophyll content and germinating root growth was mainly dependent on cultivar differences. Higher inhibition rates were observed in growth performance than in physiological responses, with the highest inhibition rates of shoot biomasses (39.6%), root length (58.7%), root tip number (57.8%) and bifurcation number (83.2%), even under the lowest Cd treatment (2.5 mg·L−1). According to the Cd toxicity sensitivity evaluation, DF exerted highest tolerance to Cd stress in root growth while LZ was more sensitive to Cd stress, suggesting LZ as an ideal Cd contaminant biomarker. This study will provide novel insight into the cultivar-dependent response during using wheat seedlings as Cd biomarkers.
format: application/pdf
format: text/html
creator: Chuntao He
creator: Zhihai Ding
creator: Samavia Mubeen
creator: Xuying Guo
creator: Huiling Fu
creator: Guorong Xin
subject: Agricultural Science
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.8478
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Sensitive seedling crops have been developed to monitor Cadmium (Cd) contamination in agricultural soil. In the present study, 18 parameters involving growth conditions and physiological performances were assessed to evaluate Cd-responses of three wheat (Triticum aestivum L.) cultivars, Xihan1 (XH), Longzhong1 (LZ) and Dingfeng16 (DF). Principle component analysis illustrated that Factor 1, representing growth performance, soluble sugar content and catalase activity, responded to the Cd treatments in a dose dependent manner, while Factor 2 represented by chlorophyll content and germinating root growth was mainly dependent on cultivar differences. Higher inhibition rates were observed in growth performance than in physiological responses, with the highest inhibition rates of shoot biomasses (39.6%), root length (58.7%), root tip number (57.8%) and bifurcation number (83.2%), even under the lowest Cd treatment (2.5 mg·L−1). According to the Cd toxicity sensitivity evaluation, DF exerted highest tolerance to Cd stress in root growth while LZ was more sensitive to Cd stress, suggesting LZ as an ideal Cd contaminant biomarker. This study will provide novel insight into the cultivar-dependent response during using wheat seedlings as Cd biomarkers.
bibliographic citation: He et al. (2020) Evaluation of three wheat (Triticum aestivum L.) cultivars as sensitive Cd biomarkers during the seedling stage. PeerJ 8:e8478 https://doi.org/10.7717/peerj.8478
date submitted: 2019-10-31
date accepted: 2019-12-27
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Chuntao
author list: Agent
  family name: Ding
  given name: Zhihai
author list: Agent
  family name: Mubeen
  given name: Samavia
author list: Agent
  family name: Guo
  given name: Xuying
author list: Agent
  family name: Fu
  given name: Huiling
author list: Agent
  family name: Xin
  given name: Guorong
doi: 10.7717/peerj.8478
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: © 2020 He et al.
attribution name: He et al.

Cranial anatomy of Allosaurus jimmadseni, a new species from the lower part of the Morrison Formation (Upper Jurassic) of Western North America
type: item
type: AcademicArticle
description: Allosaurus is one of the best known theropod dinosaurs from the Jurassic and a crucial taxon in phylogenetic analyses. On the basis of an in-depth, firsthand study of the bulk of Allosaurus specimens housed in North American institutions, we describe here a new theropod dinosaur from the Upper Jurassic Morrison Formation of Western North America, Allosaurus jimmadseni sp. nov., based upon a remarkably complete articulated skeleton and skull and a second specimen with an articulated skull and associated skeleton. The present study also assigns several other specimens to this new species, Allosaurus jimmadseni, which is characterized by a number of autapomorphies present on the dermal skull roof and additional characters present in the postcrania. In particular, whereas the ventral margin of the jugal of Allosaurus fragilis has pronounced sigmoidal convexity, the ventral margin is virtually straight in Allosaurus jimmadseni. The paired nasals of Allosaurus jimmadseni possess bilateral, blade-like crests along the lateral margin, forming a pronounced nasolacrimal crest that is absent in Allosaurus fragilis.
format: application/pdf
format: text/html
creator: Daniel J. Chure
creator: Mark A. Loewen
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7803
publisher: PeerJ Inc.
rights: © 2020 Chure and Loewen
abstract: Allosaurus is one of the best known theropod dinosaurs from the Jurassic and a crucial taxon in phylogenetic analyses. On the basis of an in-depth, firsthand study of the bulk of Allosaurus specimens housed in North American institutions, we describe here a new theropod dinosaur from the Upper Jurassic Morrison Formation of Western North America, Allosaurus jimmadseni sp. nov., based upon a remarkably complete articulated skeleton and skull and a second specimen with an articulated skull and associated skeleton. The present study also assigns several other specimens to this new species, Allosaurus jimmadseni, which is characterized by a number of autapomorphies present on the dermal skull roof and additional characters present in the postcrania. In particular, whereas the ventral margin of the jugal of Allosaurus fragilis has pronounced sigmoidal convexity, the ventral margin is virtually straight in Allosaurus jimmadseni. The paired nasals of Allosaurus jimmadseni possess bilateral, blade-like crests along the lateral margin, forming a pronounced nasolacrimal crest that is absent in Allosaurus fragilis.
bibliographic citation: Chure et al. (2020) Cranial anatomy of Allosaurus jimmadseni, a new species from the lower part of the Morrison Formation (Upper Jurassic) of Western North America. PeerJ 8:e7803 https://doi.org/10.7717/peerj.7803
date submitted: 2018-07-20
date accepted: 2019-08-31
issued: 2020-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chure
  given name: Daniel J.
author list: Agent
  family name: Loewen
  given name: Mark A.
doi: 10.7717/peerj.7803
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-24
copyright: © 2020 Chure and Loewen
attribution name: Chure and Loewen

Viability and management of the Asian elephant (Elephas maximus) population in the Endau Rompin landscape, Peninsular Malaysia
type: item
type: AcademicArticle
description: The need for conservation scientists to produce research of greater relevance to practitioners is now increasingly recognized. This study provides an example of scientists working alongside practitioners and policy makers to address a question of immediate relevance to elephant conservation in Malaysia and using the results to inform wildlife management policy and practice including the National Elephant Conservation Action Plan for Peninsular Malaysia. Since ensuring effective conservation of elephants in the Endau Rompin Landscape (ERL) in Peninsular Malaysia is difficult without data on population parameters we (1) conducted a survey to assess the size of the elephant population, (2) used that information to assess the viability of the population under different management scenarios including translocation of elephants out of the ERL (a technique long used in Malaysia to mitigate human–elephant conflict (HEC)), and (3) assessed a number of options for managing the elephant population and HEC in the future. Our dung-count based survey in the ERL produced an estimate of 135 (95% CI [80–225]) elephants in the 2,500 km2 area. The population is thus of national significance, containing possibly the second largest elephant population in Peninsular Malaysia, and with effective management elephant numbers could probably double. We used the data from our survey plus other sources to conduct a population viability analysis to assess relative extinction risk under different management scenarios. Our results demonstrate that the population cannot sustain even very low levels of removal for translocation or anything other than occasional poaching. We describe, therefore, an alternative approach, informed by this analysis, which focuses on in situ management and non-translocation-based methods for preventing or mitigating HEC. The recommended approach includes an increase in law enforcement to protect the elephants and their habitat, maintenance of habitat connectivity between…
format: application/pdf
format: text/html
creator: Salman Saaban
creator: Mohd Nawayai Yasak
creator: Melvin Gumal
creator: Aris Oziar
creator: Francis Cheong
creator: Zaleha Shaari
creator: Martin Tyson
creator: Simon Hedges
subject: Biodiversity
subject: Conservation Biology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.8209
publisher: PeerJ Inc.
rights: © 2020 Saaban et al.
abstract: The need for conservation scientists to produce research of greater relevance to practitioners is now increasingly recognized. This study provides an example of scientists working alongside practitioners and policy makers to address a question of immediate relevance to elephant conservation in Malaysia and using the results to inform wildlife management policy and practice including the National Elephant Conservation Action Plan for Peninsular Malaysia. Since ensuring effective conservation of elephants in the Endau Rompin Landscape (ERL) in Peninsular Malaysia is difficult without data on population parameters we (1) conducted a survey to assess the size of the elephant population, (2) used that information to assess the viability of the population under different management scenarios including translocation of elephants out of the ERL (a technique long used in Malaysia to mitigate human–elephant conflict (HEC)), and (3) assessed a number of options for managing the elephant population and HEC in the future. Our dung-count based survey in the ERL produced an estimate of 135 (95% CI [80–225]) elephants in the 2,500 km2 area. The population is thus of national significance, containing possibly the second largest elephant population in Peninsular Malaysia, and with effective management elephant numbers could probably double. We used the data from our survey plus other sources to conduct a population viability analysis to assess relative extinction risk under different management scenarios. Our results demonstrate that the population cannot sustain even very low levels of removal for translocation or anything other than occasional poaching. We describe, therefore, an alternative approach, informed by this analysis, which focuses on in situ management and non-translocation-based methods for preventing or mitigating HEC. The recommended approach includes an increase in law enforcement to protect the elephants and their habitat, maintenance of habitat connectivity between…
bibliographic citation: Saaban et al. (2020) Viability and management of the Asian elephant (Elephas maximus) population in the Endau Rompin landscape, Peninsular Malaysia. PeerJ 8:e8209 https://doi.org/10.7717/peerj.8209
date submitted: 2019-05-14
date accepted: 2019-11-13
issued: 2020-01-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saaban
  given name: Salman
author list: Agent
  family name: Yasak
  given name: Mohd Nawayai
author list: Agent
  family name: Gumal
  given name: Melvin
author list: Agent
  family name: Oziar
  given name: Aris
author list: Agent
  family name: Cheong
  given name: Francis
author list: Agent
  family name: Shaari
  given name: Zaleha
author list: Agent
  family name: Tyson
  given name: Martin
author list: Agent
  family name: Hedges
  given name: Simon
doi: 10.7717/peerj.8209
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-24
copyright: ©2020 Saaban et al.
attribution name: Saaban et al.

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