PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A descriptive study of random forest algorithm for predicting COVID-19 patients outcome
items: Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study
items: Advances and complications of regenerative medicine in diabetes therapy
items: Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system
items: Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment
items: A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering
items: Identification of priority shorebird conservation areas in the Caribbean
items: A new basal ornithopod dinosaur from the Lower Cretaceous of China
items: Cropland heterogeneity changes on the Northeast China Plain in the last three decades (1980s–2010s)
items: Reduced organizational skills in adults with ADHD are due to deficits in persistence, not in strategies

A descriptive study of random forest algorithm for predicting COVID-19 patients outcome
type: item
type: AcademicArticle
description: Background The outbreak of coronavirus disease 2019 (COVID-19) that occurred in Wuhan, China, has become a global public health threat. It is necessary to identify indicators that can be used as optimal predictors for clinical outcomes of COVID-19 patients. Methods The clinical information from 126 patients diagnosed with COVID-19 were collected from Wuhan Fourth Hospital. Specific clinical characteristics, laboratory findings, treatments and clinical outcomes were analyzed from patients hospitalized for treatment from 1 February to 15 March 2020, and subsequently died or were discharged. A random forest (RF) algorithm was used to predict the prognoses of COVID-19 patients and identify the optimal diagnostic predictors for patients’ clinical prognoses. Results Seven of the 126 patients were excluded for losing endpoints, 103 of the remaining 119 patients were discharged (alive) and 16 died in the hospital. A synthetic minority over-sampling technique (SMOTE) was used to correct the imbalanced distribution of clinical patients. Recursive feature elimination (RFE) was used to select the optimal subset for analysis. Eleven clinical parameters, Myo, CD8, age, LDH, LMR, CD45, Th/Ts, dyspnea, NLR, D-Dimer and CK were chosen with AUC approximately 0.9905. The RF algorithm was built to predict the prognoses of COVID-19 patients based on the best subset, and the area under the ROC curve (AUC) of the test data was 100%. Moreover, two optimal clinical risk predictors, lactate dehydrogenase (LDH) and Myoglobin (Myo), were selected based on the Gini index. The univariable logistic analysis revealed a substantial increase in the risk for in-hospital mortality when Myo was higher than 80 ng/ml (OR = 7.54, 95% CI [3.42–16.63]) and LDH was higher than 500 U/L (OR = 4.90, 95% CI [2.13–11.25]). Conclusion We applied an RF algorithm to predict the mortality of COVID-19 patients with high accuracy and identified LDH higher than 500 U/L and Myo higher than 80 ng/ml to be potential risk f…
format: application/pdf
format: text/html
creator: Jie Wang
creator: Heping Yu
creator: Qingquan Hua
creator: Shuili Jing
creator: Zhifen Liu
creator: Xiang Peng
creator: Cheng’an Cao
creator: Yongwen Luo
subject: Emergency and Critical Care
subject: Epidemiology
subject: Global Health
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.9945
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The outbreak of coronavirus disease 2019 (COVID-19) that occurred in Wuhan, China, has become a global public health threat. It is necessary to identify indicators that can be used as optimal predictors for clinical outcomes of COVID-19 patients. Methods The clinical information from 126 patients diagnosed with COVID-19 were collected from Wuhan Fourth Hospital. Specific clinical characteristics, laboratory findings, treatments and clinical outcomes were analyzed from patients hospitalized for treatment from 1 February to 15 March 2020, and subsequently died or were discharged. A random forest (RF) algorithm was used to predict the prognoses of COVID-19 patients and identify the optimal diagnostic predictors for patients’ clinical prognoses. Results Seven of the 126 patients were excluded for losing endpoints, 103 of the remaining 119 patients were discharged (alive) and 16 died in the hospital. A synthetic minority over-sampling technique (SMOTE) was used to correct the imbalanced distribution of clinical patients. Recursive feature elimination (RFE) was used to select the optimal subset for analysis. Eleven clinical parameters, Myo, CD8, age, LDH, LMR, CD45, Th/Ts, dyspnea, NLR, D-Dimer and CK were chosen with AUC approximately 0.9905. The RF algorithm was built to predict the prognoses of COVID-19 patients based on the best subset, and the area under the ROC curve (AUC) of the test data was 100%. Moreover, two optimal clinical risk predictors, lactate dehydrogenase (LDH) and Myoglobin (Myo), were selected based on the Gini index. The univariable logistic analysis revealed a substantial increase in the risk for in-hospital mortality when Myo was higher than 80 ng/ml (OR = 7.54, 95% CI [3.42–16.63]) and LDH was higher than 500 U/L (OR = 4.90, 95% CI [2.13–11.25]). Conclusion We applied an RF algorithm to predict the mortality of COVID-19 patients with high accuracy and identified LDH higher than 500 U/L and Myo higher than 80 ng/ml to be potential risk f…
bibliographic citation: Wang et al. (2020) A descriptive study of random forest algorithm for predicting COVID-19 patients outcome. PeerJ 8:e9945 https://doi.org/10.7717/peerj.9945
date submitted: 2020-05-04
date accepted: 2020-08-25
issued: 2020-09-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jie
author list: Agent
  family name: Yu
  given name: Heping
author list: Agent
  family name: Hua
  given name: Qingquan
author list: Agent
  family name: Jing
  given name: Shuili
author list: Agent
  family name: Liu
  given name: Zhifen
author list: Agent
  family name: Peng
  given name: Xiang
author list: Agent
  family name: Cao
  given name: Cheng’an
author list: Agent
  family name: Luo
  given name: Yongwen
doi: 10.7717/peerj.9945
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-09
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study
type: item
type: AcademicArticle
description: Objective To explore the relationship between body mass index (BMI) and clinicopathological characteristics in patients with papillary thyroid carcinoma (PTC). Methods The clinical data of 1,579 patients with PTC, admitted to our hospital from May 2016 to March 2017, were retrospectively analyzed. According to the different BMI of patients, it can be divided into underweight recombination (BMI < 18.5 kg/m), normal body recombination (18.5 ≤ BMI < 24.0 kg/m2), overweight recombination (24.0 ≤ BMI < 28.0 kg/m2) and obesity group (BMI ≥ 28.0 kg/m2). The clinicopathological characteristics of PTC in patients with different BMIs group were compared. Results In our study, the risk for extrathyroidal extension (ETE), advanced T stage (T III/IV), and advanced tumor-node-metastasis stage (TNM III/IV) in the overweight group were higher, with OR (odds ratio) = 1.99(1.41–2.81), OR = 2.01(1.43–2.84), OR = 2.94(1.42–6.07), respectively, relative to the normal weight group. The risk for ETE and T III/IV stage in the obese group were higher, with OR = 1.82(1.23–2.71) and OR = 1.82(1.23–2.70), respectively, relative to the normal weight group. Conclusion BMI is associated with the invasiveness of PTC. There is a higher risk for ETE and TNM III/IV stage among patients with PTC in the overweight group and for ETE among patients with PTC in the obese group.
format: application/pdf
format: text/html
creator: Huijuan Wang
creator: Pingping Wang
creator: Yu Wu
creator: Xiukun Hou
creator: Zechun Peng
creator: Weiwei Yang
creator: Lizhao Guan
creator: Linfei Hu
creator: Jingtai Zhi
creator: Ming Gao
creator: Xiangqian Zheng
subject: Epidemiology
subject: Global Health
subject: Oncology
subject: Metabolic Sciences
description: doi:10.7717/peerj.9675
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Objective To explore the relationship between body mass index (BMI) and clinicopathological characteristics in patients with papillary thyroid carcinoma (PTC). Methods The clinical data of 1,579 patients with PTC, admitted to our hospital from May 2016 to March 2017, were retrospectively analyzed. According to the different BMI of patients, it can be divided into underweight recombination (BMI < 18.5 kg/m), normal body recombination (18.5 ≤ BMI < 24.0 kg/m2), overweight recombination (24.0 ≤ BMI < 28.0 kg/m2) and obesity group (BMI ≥ 28.0 kg/m2). The clinicopathological characteristics of PTC in patients with different BMIs group were compared. Results In our study, the risk for extrathyroidal extension (ETE), advanced T stage (T III/IV), and advanced tumor-node-metastasis stage (TNM III/IV) in the overweight group were higher, with OR (odds ratio) = 1.99(1.41–2.81), OR = 2.01(1.43–2.84), OR = 2.94(1.42–6.07), respectively, relative to the normal weight group. The risk for ETE and T III/IV stage in the obese group were higher, with OR = 1.82(1.23–2.71) and OR = 1.82(1.23–2.70), respectively, relative to the normal weight group. Conclusion BMI is associated with the invasiveness of PTC. There is a higher risk for ETE and TNM III/IV stage among patients with PTC in the overweight group and for ETE among patients with PTC in the obese group.
bibliographic citation: Wang et al. (2020) Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study. PeerJ 8:e9675 https://doi.org/10.7717/peerj.9675
date submitted: 2020-03-30
date accepted: 2020-07-16
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Huijuan
author list: Agent
  family name: Wang
  given name: Pingping
author list: Agent
  family name: Wu
  given name: Yu
author list: Agent
  family name: Hou
  given name: Xiukun
author list: Agent
  family name: Peng
  given name: Zechun
author list: Agent
  family name: Yang
  given name: Weiwei
author list: Agent
  family name: Guan
  given name: Lizhao
author list: Agent
  family name: Hu
  given name: Linfei
author list: Agent
  family name: Zhi
  given name: Jingtai
author list: Agent
  family name: Gao
  given name: Ming
author list: Agent
  family name: Zheng
  given name: Xiangqian
doi: 10.7717/peerj.9675
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Advances and complications of regenerative medicine in diabetes therapy
type: item
type: AcademicArticle
description: The rapid development of technologies in regenerative medicine indicates clearly that their common application is not a matter of if, but of when. However, the regeneration of beta-cells for diabetes patients remains a complex challenge due to the plurality of related problems. Indeed, the generation of beta-cells masses expressing marker genes is only a first step, with maintaining permanent insulin secretion, their protection from the immune system and avoiding pathological modifications in the genome being the necessary next developments. The prospects of regenerative medicine in diabetes therapy were promoted by the emergence of promising results with embryonic stem cells (ESCs). Their pluripotency and proliferation in an undifferentiated state during culture have ensured the success of ESCs in regenerative medicine. The discovery of induced pluripotent stem cells (iPSCs) derived from the patients’ own mesenchymal cells has provided further hope for diabetes treatment. Nonetheless, the use of stem cells has significant limitations related to the pluripotent stage, such as the risk of development of teratomas. Thus, the direct conversion of mature cells into beta-cells could address this issue. Recent studies have shown the possibility of such transdifferentiation and have set trends for regeneration medicine, directed at minimizing genome modifications and invasive procedures. In this review, we will discuss the published results of beta-cell regeneration and the advantages and disadvantages illustrated by these experiments.
format: application/pdf
format: text/html
creator: Olga Brovkina
creator: Erdem Dashinimaev
subject: Cell Biology
subject: Diabetes and Endocrinology
subject: Translational Medicine
description: doi:10.7717/peerj.9746
publisher: PeerJ Inc.
rights: © 2020 Brovkina and Dashinimaev
abstract: The rapid development of technologies in regenerative medicine indicates clearly that their common application is not a matter of if, but of when. However, the regeneration of beta-cells for diabetes patients remains a complex challenge due to the plurality of related problems. Indeed, the generation of beta-cells masses expressing marker genes is only a first step, with maintaining permanent insulin secretion, their protection from the immune system and avoiding pathological modifications in the genome being the necessary next developments. The prospects of regenerative medicine in diabetes therapy were promoted by the emergence of promising results with embryonic stem cells (ESCs). Their pluripotency and proliferation in an undifferentiated state during culture have ensured the success of ESCs in regenerative medicine. The discovery of induced pluripotent stem cells (iPSCs) derived from the patients’ own mesenchymal cells has provided further hope for diabetes treatment. Nonetheless, the use of stem cells has significant limitations related to the pluripotent stage, such as the risk of development of teratomas. Thus, the direct conversion of mature cells into beta-cells could address this issue. Recent studies have shown the possibility of such transdifferentiation and have set trends for regeneration medicine, directed at minimizing genome modifications and invasive procedures. In this review, we will discuss the published results of beta-cell regeneration and the advantages and disadvantages illustrated by these experiments.
bibliographic citation: Brovkina et al. (2020) Advances and complications of regenerative medicine in diabetes therapy. PeerJ 8:e9746 https://doi.org/10.7717/peerj.9746
date submitted: 2020-05-01
date accepted: 2020-07-27
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brovkina
  given name: Olga
author list: Agent
  family name: Dashinimaev
  given name: Erdem
doi: 10.7717/peerj.9746
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Brovkina and Dashinimaev
attribution name: Brovkina and Dashinimaev

Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system
type: item
type: AcademicArticle
description: The digestive system and metabolism of the cannonball jellyfish Stomolophus sp. 2 are not well-known. The digestion study was critical to explain its ecology and bloom success. Different enzymes are involved in food digestion, which hydrolyze carbohydrates, proteins, and lipids. This study detected lipolytic activity in enzymatic extracts from gastric pouches of Stomolophus sp. 2 collected in the summer of 2013 at Bahía de Kino, Sonora, México (28°47′47″N 111°57′25″W). Lipase/esterase activity showed optimal pH at 11.0 and 50–60 °C with a half-life (t1/2) of 33 min at 55 °C, whereas halotolerance of this activity was recorded from 0-4 M NaCl. Metal ions Ca2+ and Mn2+ did not affect the activity, but Mg2+ decreased it 14.2% ± 3.15, while chelating agents as ethylenediaminetetraacetic acid reduced the activity 8.55% ± 2.13. Inhibition of lipase/esterase activity with tetrahydrolipstatin and paraoxon-ethyl decreased the activity 18.2% ± 2.3, and 62.80% ± 0.74, respectively, whereas phenylmethanesulfonyl fluoride (a protease inhibitor) did not affect it. The enzyme displayed a higher specificity for short-chain triglycerides, but triolein, coconut oil, olive oil, and fish oil were hydrolyzed. For the first time, phospholipase activity from the gastric pouch of Stomolophus sp. 2 was detected using L-α-phosphatidylethanolamine from chicken egg yolk as a substrate. These results suggest that Stomolophus sp. 2 hydrolyze several kinds of lipids, and lipolytic enzymes are active at alkaline pH under different saline conditions, which may be essential to digest different preys.
format: application/pdf
format: text/html
creator: Raul B. Martínez-Pérez
creator: Jorge A. Rodríguez
creator: Luis Alonso Leyva Soto
creator: Pablo Gortáres-Moroyoqui
creator: Lourdes M. Diaz-Tenorio
subject: Biochemistry
subject: Biotechnology
subject: Marine Biology
description: doi:10.7717/peerj.9794
publisher: PeerJ Inc.
rights: © 2020 Martínez-Pérez et al.
abstract: The digestive system and metabolism of the cannonball jellyfish Stomolophus sp. 2 are not well-known. The digestion study was critical to explain its ecology and bloom success. Different enzymes are involved in food digestion, which hydrolyze carbohydrates, proteins, and lipids. This study detected lipolytic activity in enzymatic extracts from gastric pouches of Stomolophus sp. 2 collected in the summer of 2013 at Bahía de Kino, Sonora, México (28°47′47″N 111°57′25″W). Lipase/esterase activity showed optimal pH at 11.0 and 50–60 °C with a half-life (t1/2) of 33 min at 55 °C, whereas halotolerance of this activity was recorded from 0-4 M NaCl. Metal ions Ca2+ and Mn2+ did not affect the activity, but Mg2+ decreased it 14.2% ± 3.15, while chelating agents as ethylenediaminetetraacetic acid reduced the activity 8.55% ± 2.13. Inhibition of lipase/esterase activity with tetrahydrolipstatin and paraoxon-ethyl decreased the activity 18.2% ± 2.3, and 62.80% ± 0.74, respectively, whereas phenylmethanesulfonyl fluoride (a protease inhibitor) did not affect it. The enzyme displayed a higher specificity for short-chain triglycerides, but triolein, coconut oil, olive oil, and fish oil were hydrolyzed. For the first time, phospholipase activity from the gastric pouch of Stomolophus sp. 2 was detected using L-α-phosphatidylethanolamine from chicken egg yolk as a substrate. These results suggest that Stomolophus sp. 2 hydrolyze several kinds of lipids, and lipolytic enzymes are active at alkaline pH under different saline conditions, which may be essential to digest different preys.
bibliographic citation: Martínez-Pérez et al. (2020) Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system. PeerJ 8:e9794 https://doi.org/10.7717/peerj.9794
date submitted: 2018-03-23
date accepted: 2020-08-01
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Pérez
  given name: Raul B.
author list: Agent
  family name: Rodríguez
  given name: Jorge A.
author list: Agent
  family name: Leyva Soto
  given name: Luis Alonso
author list: Agent
  family name: Gortáres-Moroyoqui
  given name: Pablo
author list: Agent
  family name: Diaz-Tenorio
  given name: Lourdes M.
doi: 10.7717/peerj.9794
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Martínez-Pérez et al.
attribution name: Martínez-Pérez et al.

Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment
type: item
type: AcademicArticle
description: Background Abundant studies have identified the association between childhood maltreatment and self-harm (SH), but little has been discussed with regard to the role of resilience in SH behaviors of adolescents who had experienced childhood maltreatment. In this study, we investigated if resilience, as well as its five dimensions, could present negative associations with presence, repetition, and severity of SH among maltreated and neglected adolescents in China. Methods A cross-sectional survey including 2,084 maltreated teenagers aged from 10 to 17 years was conducted in southwest China Yunnan province. The Childhood Trauma Questionnaire (CTQ), The Resilience Scale for Chinese Adolescents (RSCA), and the Modified version of Adolescents Self-Harm Scale (MASHS) were adopted to measure childhood maltreatment experiences, psychological resilience, and SH behaviors of the respondents, respectively. Binary univariate and multivariate logistic regression models were employed to discuss the associations between resilience and occurrence, repetition, severity of SH. Results Among the participants who met the criteria of CTQ, the prevalence rates of SH were 63.83%, 73.94%, 71.50%, 55.53%, and 58.21% for physical abuse (PA), emotional abuse (EA), sexual abuse (SA), physical neglect (PN), and emotional neglect (EN). Final regression model demonstrated that resilience was in general inversely associated with SH, repeated SH, and severe SH for all types of childhood maltreatment, with adjusted odds ratios (aORs) ranging from 0.29 (95% CI: 0.19-0.44) to 0.46 (95% CI: 0.26-0.81). Of the five dimensions of resilience, emotion regulation served as the strongest associated factor of SH among abused youths, regardless of maltreatment types. Besides, compared with those who had lower level of goal concentration and interpersonal assistance, subjects with higher resilience level reported significantly decreased risks of SH occurrence, SH repetition, and more severe SH, in adolescents wh…
format: application/pdf
format: text/html
creator: Xin Tian
creator: Guangya Yang
creator: Linling Jiang
creator: Runxu Yang
creator: Hailiang Ran
creator: Fujia Xie
creator: Xiufeng Xu
creator: Jin Lu
creator: Yuanyuan Xiao
subject: Epidemiology
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9800
publisher: PeerJ Inc.
rights: © 2020 Tian et al.
abstract: Background Abundant studies have identified the association between childhood maltreatment and self-harm (SH), but little has been discussed with regard to the role of resilience in SH behaviors of adolescents who had experienced childhood maltreatment. In this study, we investigated if resilience, as well as its five dimensions, could present negative associations with presence, repetition, and severity of SH among maltreated and neglected adolescents in China. Methods A cross-sectional survey including 2,084 maltreated teenagers aged from 10 to 17 years was conducted in southwest China Yunnan province. The Childhood Trauma Questionnaire (CTQ), The Resilience Scale for Chinese Adolescents (RSCA), and the Modified version of Adolescents Self-Harm Scale (MASHS) were adopted to measure childhood maltreatment experiences, psychological resilience, and SH behaviors of the respondents, respectively. Binary univariate and multivariate logistic regression models were employed to discuss the associations between resilience and occurrence, repetition, severity of SH. Results Among the participants who met the criteria of CTQ, the prevalence rates of SH were 63.83%, 73.94%, 71.50%, 55.53%, and 58.21% for physical abuse (PA), emotional abuse (EA), sexual abuse (SA), physical neglect (PN), and emotional neglect (EN). Final regression model demonstrated that resilience was in general inversely associated with SH, repeated SH, and severe SH for all types of childhood maltreatment, with adjusted odds ratios (aORs) ranging from 0.29 (95% CI: 0.19-0.44) to 0.46 (95% CI: 0.26-0.81). Of the five dimensions of resilience, emotion regulation served as the strongest associated factor of SH among abused youths, regardless of maltreatment types. Besides, compared with those who had lower level of goal concentration and interpersonal assistance, subjects with higher resilience level reported significantly decreased risks of SH occurrence, SH repetition, and more severe SH, in adolescents wh…
bibliographic citation: Tian et al. (2020) Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment. PeerJ 8:e9800 https://doi.org/10.7717/peerj.9800
date submitted: 2020-05-20
date accepted: 2020-08-03
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Xin
author list: Agent
  family name: Yang
  given name: Guangya
author list: Agent
  family name: Jiang
  given name: Linling
author list: Agent
  family name: Yang
  given name: Runxu
author list: Agent
  family name: Ran
  given name: Hailiang
author list: Agent
  family name: Xie
  given name: Fujia
author list: Agent
  family name: Xu
  given name: Xiufeng
author list: Agent
  family name: Lu
  given name: Jin
author list: Agent
  family name: Xiao
  given name: Yuanyuan
doi: 10.7717/peerj.9800
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Tian et al.
attribution name: Tian et al.

A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering
type: item
type: AcademicArticle
description: Background Sub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering. Methods To this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC. Results The biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering.
format: application/pdf
format: text/html
creator: Herbert M. Huttanus
creator: Ryan S. Senger
subject: Biotechnology
subject: Synthetic Biology
description: doi:10.7717/peerj.9805
publisher: PeerJ Inc.
rights: © 2020 Huttanus and Senger
abstract: Background Sub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering. Methods To this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC. Results The biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering.
bibliographic citation: Huttanus et al. (2020) A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering. PeerJ 8:e9805 https://doi.org/10.7717/peerj.9805
date submitted: 2020-01-28
date accepted: 2020-08-03
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huttanus
  given name: Herbert M.
author list: Agent
  family name: Senger
  given name: Ryan S.
doi: 10.7717/peerj.9805
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Huttanus and Senger
attribution name: Huttanus and Senger

Identification of priority shorebird conservation areas in the Caribbean
type: item
type: AcademicArticle
description: Despite being geographically central to the Atlantic Americas Flyway for migratory birds, the Caribbean is often overlooked or underappreciated when addressing the conservation of North American shorebirds. To our knowledge, this is the first Caribbean-wide assessment of shorebird use in the region. We analyzed 211,013 shorebird species observations in the insular Caribbean from 2010–2019, representing 78,794 eBird checklists and cumulative total of 2.1 million shorebirds of 45 species. We conclude that priority areas for shorebird conservation include Humedal Sur de Pinar del Río (Humedal Sur de Los Palacios) in Cuba, and Monte Cristi in the Dominican Republic as they each likely support more than 20,000 shorebirds annually, and they host large abundances of geographic populations for particular taxa. Specifically, the former site hosts >10% of Short-billed Dowitchers (Limnodromus griseus griseus/hendersoni), and >1% of Black-bellied Plovers (Pluvialis squatarola cynosurae) and Wilson’s Plovers (Charadrius wilsonia wilsonia), while the latter site supports large numbers of Black-necked Stilts (Himantopus mexicanus). We also identified at least 15 additional sites that likely cross the 1% population threshold for one or more shorebird taxa. These sites may qualify for special international designations such as Important Bird and Biodiversity Areas or as part of the Western Hemisphere Shorebird Reserve Network; 11 of the 17 sites we identified do not hold either of these titles. Data on subspecific or geographic distributions of three species, Snowy Plover (C. nivosus), Black-necked Stilt, and Killdeer (C. vociferous), are insufficient to reveal if the sites with the highest abundances were mostly comprised of Caribbean populations or migrants, but the limited information suggests that they also likely exceed 1% thresholds on several islands. Based on our results, we recommend more extensive systematic surveys of shorebirds in the Caribbean, including research on tur…
format: application/pdf
format: text/html
creator: Jessica R. Cañizares
creator: J. Michael Reed
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9831
publisher: PeerJ Inc.
rights: © 2020 Cañizares and Reed
abstract: Despite being geographically central to the Atlantic Americas Flyway for migratory birds, the Caribbean is often overlooked or underappreciated when addressing the conservation of North American shorebirds. To our knowledge, this is the first Caribbean-wide assessment of shorebird use in the region. We analyzed 211,013 shorebird species observations in the insular Caribbean from 2010–2019, representing 78,794 eBird checklists and cumulative total of 2.1 million shorebirds of 45 species. We conclude that priority areas for shorebird conservation include Humedal Sur de Pinar del Río (Humedal Sur de Los Palacios) in Cuba, and Monte Cristi in the Dominican Republic as they each likely support more than 20,000 shorebirds annually, and they host large abundances of geographic populations for particular taxa. Specifically, the former site hosts >10% of Short-billed Dowitchers (Limnodromus griseus griseus/hendersoni), and >1% of Black-bellied Plovers (Pluvialis squatarola cynosurae) and Wilson’s Plovers (Charadrius wilsonia wilsonia), while the latter site supports large numbers of Black-necked Stilts (Himantopus mexicanus). We also identified at least 15 additional sites that likely cross the 1% population threshold for one or more shorebird taxa. These sites may qualify for special international designations such as Important Bird and Biodiversity Areas or as part of the Western Hemisphere Shorebird Reserve Network; 11 of the 17 sites we identified do not hold either of these titles. Data on subspecific or geographic distributions of three species, Snowy Plover (C. nivosus), Black-necked Stilt, and Killdeer (C. vociferous), are insufficient to reveal if the sites with the highest abundances were mostly comprised of Caribbean populations or migrants, but the limited information suggests that they also likely exceed 1% thresholds on several islands. Based on our results, we recommend more extensive systematic surveys of shorebirds in the Caribbean, including research on tur…
bibliographic citation: Cañizares et al. (2020) Identification of priority shorebird conservation areas in the Caribbean. PeerJ 8:e9831 https://doi.org/10.7717/peerj.9831
date submitted: 2020-05-21
date accepted: 2020-08-06
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cañizares
  given name: Jessica R.
author list: Agent
  family name: Reed
  given name: J. Michael
doi: 10.7717/peerj.9831
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Cañizares and Reed
attribution name: Cañizares and Reed

A new basal ornithopod dinosaur from the Lower Cretaceous of China
type: item
type: AcademicArticle
description: A new basal ornithopod dinosaur, based on two nearly complete articulated skeletons, is reported from the Lujiatun Beds (Yixian Fm, Lower Cretaceous) of western Liaoning Province (China). Some of the diagnostic features of Changmiania liaoningensis nov. gen., nov. sp. are tentatively interpreted as adaptations to a fossorial behavior, including: fused premaxillae; nasal laterally expanded, overhanging the maxilla; shortened neck formed by only six cervical vertebrae; neural spines of the sacral vertebrae completely fused together, forming a craniocaudally-elongated continuous bar; fused scapulocoracoid with prominent scapular spine; and paired ilia symmetrically inclined dorsomedially, partially covering the sacrum in dorsal view. A phylogenetic analysis places Changmiania liaoningensis as the most basal ornithopod dinosaur described so far. It is tentatively hypothesized that both Changmiania liaoningensis specimens were suddenly entrapped in a collapsed underground burrow while they were resting, which would explain their perfect lifelike postures and the complete absence of weathering and scavenging traces. However, further behavioural inference remains problematic, because those specimens lack extensive sedimentological and taphonomic data, as it is also the case for most specimens collected in the Lujiatun Beds so far.
format: application/pdf
format: text/html
creator: Yuqing Yang
creator: Wenhao Wu
creator: Paul-Emile Dieudonné
creator: Pascal Godefroit
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9832
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: A new basal ornithopod dinosaur, based on two nearly complete articulated skeletons, is reported from the Lujiatun Beds (Yixian Fm, Lower Cretaceous) of western Liaoning Province (China). Some of the diagnostic features of Changmiania liaoningensis nov. gen., nov. sp. are tentatively interpreted as adaptations to a fossorial behavior, including: fused premaxillae; nasal laterally expanded, overhanging the maxilla; shortened neck formed by only six cervical vertebrae; neural spines of the sacral vertebrae completely fused together, forming a craniocaudally-elongated continuous bar; fused scapulocoracoid with prominent scapular spine; and paired ilia symmetrically inclined dorsomedially, partially covering the sacrum in dorsal view. A phylogenetic analysis places Changmiania liaoningensis as the most basal ornithopod dinosaur described so far. It is tentatively hypothesized that both Changmiania liaoningensis specimens were suddenly entrapped in a collapsed underground burrow while they were resting, which would explain their perfect lifelike postures and the complete absence of weathering and scavenging traces. However, further behavioural inference remains problematic, because those specimens lack extensive sedimentological and taphonomic data, as it is also the case for most specimens collected in the Lujiatun Beds so far.
bibliographic citation: Yang et al. (2020) A new basal ornithopod dinosaur from the Lower Cretaceous of China. PeerJ 8:e9832 https://doi.org/10.7717/peerj.9832
date submitted: 2020-05-18
date accepted: 2020-08-07
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yuqing
author list: Agent
  family name: Wu
  given name: Wenhao
author list: Agent
  family name: Dieudonné
  given name: Paul-Emile
author list: Agent
  family name: Godefroit
  given name: Pascal
doi: 10.7717/peerj.9832
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: © 2020 Yang et al.
attribution name: Yang et al.

Cropland heterogeneity changes on the Northeast China Plain in the last three decades (1980s–2010s)
type: item
type: AcademicArticle
description: The Northeast China Plain is one of the major grain-producing areas of China because of its fertile black soil and large fields adapted for agricultural machinery. It has experienced some land-use changes, such as urbanization, deforestation, and wetland reclamation in recent decades. A comprehensive understanding of these changes in terms of the total cropping land and its heterogeneity during this period is important for policymakers. In this study, we used a series of cropland products at the 30-m resolution for the period 1980–2015. The heterogeneity for dominant cropland decreased slowly over the three decades, especially for the large pieces of cropland, showing a general trend of increased cropland homogeneity. The spatial patterns of the averaged heterogeneity index were nearly the same, varying from 0.5 to 0.6, and the most heterogeneous areas were mainly located in some separate counties. Cropland expansion occurred across most of Northeast China, while cropland shrinking occurred only in the northern and eastern sections of Northeast China and around the capital cities, in the flat areas. Also, changes in land use away from cropland mainly occurred in areas with low elevation (50–200 m) and a gentle slope (less than 1 degree). The predominant changes in cropland were gross gain and homogeneity, occurring across most of the area except capital cities and boundary areas. Possible reasons for the total cropland heterogeneity changes were urbanization, restoration of cropland to forest, and some government land-use policies. Moreover, this study evaluates the effectiveness of cropland policies influencing in Northeast China.
format: application/pdf
format: text/html
creator: Xiaoxuan Liu
creator: Le Yu
creator: Qinghan Dong
creator: Dailiang Peng
creator: Wenbin Wu
creator: Qiangyi Yu
creator: Yuqi Cheng
creator: Yidi Xu
creator: Xiaomeng Huang
creator: Zheng Zhou
creator: Dong Wang
creator: Lei Fang
creator: Peng Gong
subject: Agricultural Science
subject: Ecology
subject: Ecosystem Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9835
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: The Northeast China Plain is one of the major grain-producing areas of China because of its fertile black soil and large fields adapted for agricultural machinery. It has experienced some land-use changes, such as urbanization, deforestation, and wetland reclamation in recent decades. A comprehensive understanding of these changes in terms of the total cropping land and its heterogeneity during this period is important for policymakers. In this study, we used a series of cropland products at the 30-m resolution for the period 1980–2015. The heterogeneity for dominant cropland decreased slowly over the three decades, especially for the large pieces of cropland, showing a general trend of increased cropland homogeneity. The spatial patterns of the averaged heterogeneity index were nearly the same, varying from 0.5 to 0.6, and the most heterogeneous areas were mainly located in some separate counties. Cropland expansion occurred across most of Northeast China, while cropland shrinking occurred only in the northern and eastern sections of Northeast China and around the capital cities, in the flat areas. Also, changes in land use away from cropland mainly occurred in areas with low elevation (50–200 m) and a gentle slope (less than 1 degree). The predominant changes in cropland were gross gain and homogeneity, occurring across most of the area except capital cities and boundary areas. Possible reasons for the total cropland heterogeneity changes were urbanization, restoration of cropland to forest, and some government land-use policies. Moreover, this study evaluates the effectiveness of cropland policies influencing in Northeast China.
bibliographic citation: Liu et al. (2020) Cropland heterogeneity changes on the Northeast China Plain in the last three decades (1980s–2010s). PeerJ 8:e9835 https://doi.org/10.7717/peerj.9835
date submitted: 2020-06-22
date accepted: 2020-08-07
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaoxuan
author list: Agent
  family name: Yu
  given name: Le
author list: Agent
  family name: Dong
  given name: Qinghan
author list: Agent
  family name: Peng
  given name: Dailiang
author list: Agent
  family name: Wu
  given name: Wenbin
author list: Agent
  family name: Yu
  given name: Qiangyi
author list: Agent
  family name: Cheng
  given name: Yuqi
author list: Agent
  family name: Xu
  given name: Yidi
author list: Agent
  family name: Huang
  given name: Xiaomeng
author list: Agent
  family name: Zhou
  given name: Zheng
author list: Agent
  family name: Wang
  given name: Dong
author list: Agent
  family name: Fang
  given name: Lei
author list: Agent
  family name: Gong
  given name: Peng
doi: 10.7717/peerj.9835
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Reduced organizational skills in adults with ADHD are due to deficits in persistence, not in strategies
type: item
type: AcademicArticle
description: Background Attention Deficit Hyperactivity Disorder (ADHD) is commonly associated with poor organizational skills, as per the definition of ADHD. However, the contribution of each of the following factors (and their interactions) to the aforementioned poor organization, while comparing individuals with and without ADHD, has not been analyzed in-depth: Work Organization; Communication Clarity; Punctuality; Goal-oriented behaviour; Assiduity; Workspace Organization; Strategies; and Attentiveness. The purpose is to examine the self-reported levels of organizational skills in adults with and without ADHD. Methods Seven hundred seventy-four (n = 303 with a diagnosis of ADHD) adults from the community were recruited online. Participants completed a measure of organizational skills and a screening measure of ADHD. Results Participants with a diagnosis of ADHD displayed lower scores than individuals without a diagnosis of ADHD on all organizational skills with the exception of using strategies to remain organized and learn new information. Higher levels of education were associated with higher levels of organizational skills. While there was no difference between males and females with ADHD, females without ADHD scored higher than males without ADHD. Conclusion This study supports that individuals with ADHD can efficiently develop strategies, but may have difficulties using those strategies in a continuous manner. Suggestions to increase organizational skills in adults with ADHD are presented.
format: application/pdf
format: text/html
creator: Guillaume Durand
creator: Ioana-Smarandita Arbone
creator: Monica Wharton
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9844
publisher: PeerJ Inc.
rights: © 2020 Durand et al.
abstract: Background Attention Deficit Hyperactivity Disorder (ADHD) is commonly associated with poor organizational skills, as per the definition of ADHD. However, the contribution of each of the following factors (and their interactions) to the aforementioned poor organization, while comparing individuals with and without ADHD, has not been analyzed in-depth: Work Organization; Communication Clarity; Punctuality; Goal-oriented behaviour; Assiduity; Workspace Organization; Strategies; and Attentiveness. The purpose is to examine the self-reported levels of organizational skills in adults with and without ADHD. Methods Seven hundred seventy-four (n = 303 with a diagnosis of ADHD) adults from the community were recruited online. Participants completed a measure of organizational skills and a screening measure of ADHD. Results Participants with a diagnosis of ADHD displayed lower scores than individuals without a diagnosis of ADHD on all organizational skills with the exception of using strategies to remain organized and learn new information. Higher levels of education were associated with higher levels of organizational skills. While there was no difference between males and females with ADHD, females without ADHD scored higher than males without ADHD. Conclusion This study supports that individuals with ADHD can efficiently develop strategies, but may have difficulties using those strategies in a continuous manner. Suggestions to increase organizational skills in adults with ADHD are presented.
bibliographic citation: Durand et al. (2020) Reduced organizational skills in adults with ADHD are due to deficits in persistence, not in strategies. PeerJ 8:e9844 https://doi.org/10.7717/peerj.9844
date submitted: 2020-05-04
date accepted: 2020-08-11
issued: 2020-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Durand
  given name: Guillaume
author list: Agent
  family name: Arbone
  given name: Ioana-Smarandita
author list: Agent
  family name: Wharton
  given name: Monica
doi: 10.7717/peerj.9844
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-08
copyright: ©2020 Durand et al.
attribution name: Durand et al.

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