PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Adaptive evolution at mRNA editing sites in soft-bodied cephalopods
items: Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador
items: Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress
items: Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients
items: Spatial and temporal activity patterns of Golden takin (Budorcas taxicolor bedfordi) recorded by camera trapping
items: The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma
items: A signature of tumor DNA repair genes associated with the prognosis of surgically-resected lung adenocarcinoma
items: Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats
items: Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery
items: Characteristics and outcomes of hemodialysis patients with COVID-19: a retrospective single center study

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods
type: item
type: AcademicArticle
description: Background The bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein. Methods We study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site. Results Here, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.
format: application/pdf
format: text/html
creator: Mikhail Moldovan
creator: Zoe Chervontseva
creator: Georgii Bazykin
creator: Mikhail S. Gelfand
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.10456
publisher: PeerJ Inc.
rights: © 2020 Moldovan et al.
abstract: Background The bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein. Methods We study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site. Results Here, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.
bibliographic citation: Moldovan et al. (2020) Adaptive evolution at mRNA editing sites in soft-bodied cephalopods. PeerJ 8:e10456 https://doi.org/10.7717/peerj.10456
date submitted: 2020-10-01
date accepted: 2020-11-09
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moldovan
  given name: Mikhail
author list: Agent
  family name: Chervontseva
  given name: Zoe
author list: Agent
  family name: Bazykin
  given name: Georgii
author list: Agent
  family name: Gelfand
  given name: Mikhail S.
doi: 10.7717/peerj.10456
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Moldovan et al.
attribution name: Moldovan et al.

Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador
type: item
type: AcademicArticle
description: Harmonia axyridis is a ladybird extensively used around the world for biological control of agricultural pests. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin Ladybird Harmonia axyridis (Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts of H. axyridis on the Ecuadorian biodiversity and agroindustry.
format: application/pdf
format: text/html
creator: Diego F. Cisneros-Heredia
creator: Emilia Peñaherrera-Romero
subject: Biodiversity
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10461
publisher: PeerJ Inc.
rights: © 2020 Cisneros-Heredia and Peñaherrera-Romero
abstract: Harmonia axyridis is a ladybird extensively used around the world for biological control of agricultural pests. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin Ladybird Harmonia axyridis (Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts of H. axyridis on the Ecuadorian biodiversity and agroindustry.
bibliographic citation: Cisneros-Heredia et al. (2020) Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador. PeerJ 8:e10461 https://doi.org/10.7717/peerj.10461
date submitted: 2019-02-28
date accepted: 2020-11-10
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Peñaherrera-Romero
  given name: Emilia
doi: 10.7717/peerj.10461
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Cisneros-Heredia and Peñaherrera-Romero
attribution name: Cisneros-Heredia and Peñaherrera-Romero

Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress
type: item
type: AcademicArticle
description: Background and objectives The timing of invasive mechanical ventilation (IMV) is controversial in COVID-19 patients with acute respiratory hypoxemia. The study aimed to develop a novel predictor called cumulative oxygen deficit (COD) for the risk stratification. Methods The study was conducted in four designated hospitals for treating COVID-19 patients in Jingmen, Wuhan, from January to March 2020. COD was defined to account for both the magnitude and duration of hypoxemia. A higher value of COD indicated more oxygen deficit. The predictive performance of COD was calculated in multivariable Cox regression models. Results A number of 111 patients including 80 in the non-IMV group and 31 in the IMV group were included. Patients with IMV had substantially lower PaO2 (62 (49, 89) vs. 90.5 (68, 125.25) mmHg; p < 0.001), and higher COD (−6.87 (−29.36, 52.38) vs. −231.68 (−1040.78, 119.83) mmHg·day) than patients without IMV. As compared to patients with COD < 0, patients with COD > 30 mmHg·day had higher risk of fatality (HR: 3.79, 95% CI [2.57–16.93]; p = 0.037), and those with COD > 50 mmHg·day were 10 times more likely to die (HR: 10.45, 95% CI [1.28–85.37]; p = 0.029). Conclusions The study developed a novel predictor COD which considered both magnitude and duration of hypoxemia, to assist risk stratification of COVID-19 patients with acute respiratory distress.
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format: text/html
creator: Huiqing Ge
creator: Jian-cang Zhou
creator: FangFang Lv
creator: Junli Zhang
creator: Jun Yi
creator: Changming Yang
creator: Lingwei Zhang
creator: Yuhan Zhou
creator: Binbin Ren
creator: Qing Pan
creator: Zhongheng Zhang
subject: Emergency and Critical Care
subject: Respiratory Medicine
description: doi:10.7717/peerj.10497
publisher: PeerJ Inc.
rights: © 2020 Ge et al.
abstract: Background and objectives The timing of invasive mechanical ventilation (IMV) is controversial in COVID-19 patients with acute respiratory hypoxemia. The study aimed to develop a novel predictor called cumulative oxygen deficit (COD) for the risk stratification. Methods The study was conducted in four designated hospitals for treating COVID-19 patients in Jingmen, Wuhan, from January to March 2020. COD was defined to account for both the magnitude and duration of hypoxemia. A higher value of COD indicated more oxygen deficit. The predictive performance of COD was calculated in multivariable Cox regression models. Results A number of 111 patients including 80 in the non-IMV group and 31 in the IMV group were included. Patients with IMV had substantially lower PaO2 (62 (49, 89) vs. 90.5 (68, 125.25) mmHg; p < 0.001), and higher COD (−6.87 (−29.36, 52.38) vs. −231.68 (−1040.78, 119.83) mmHg·day) than patients without IMV. As compared to patients with COD < 0, patients with COD > 30 mmHg·day had higher risk of fatality (HR: 3.79, 95% CI [2.57–16.93]; p = 0.037), and those with COD > 50 mmHg·day were 10 times more likely to die (HR: 10.45, 95% CI [1.28–85.37]; p = 0.029). Conclusions The study developed a novel predictor COD which considered both magnitude and duration of hypoxemia, to assist risk stratification of COVID-19 patients with acute respiratory distress.
bibliographic citation: Ge et al. (2020) Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress. PeerJ 8:e10497 https://doi.org/10.7717/peerj.10497
date submitted: 2020-09-20
date accepted: 2020-11-14
issued: 2020-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Huiqing
author list: Agent
  family name: Zhou
  given name: Jian-cang
author list: Agent
  family name: Lv
  given name: FangFang
author list: Agent
  family name: Zhang
  given name: Junli
author list: Agent
  family name: Yi
  given name: Jun
author list: Agent
  family name: Yang
  given name: Changming
author list: Agent
  family name: Zhang
  given name: Lingwei
author list: Agent
  family name: Zhou
  given name: Yuhan
author list: Agent
  family name: Ren
  given name: Binbin
author list: Agent
  family name: Pan
  given name: Qing
author list: Agent
  family name: Zhang
  given name: Zhongheng
doi: 10.7717/peerj.10497
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-27
copyright: © 2020 Ge et al.
attribution name: Ge et al.

Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients
type: item
type: AcademicArticle
description: Background Deep sedation may hamper the detection of neurological deterioration in brain-injured patients. Impaired brainstem reflexes within the first 24 h of deep sedation are associated with increased mortality in non-brain-injured patients. Our objective was to confirm this association in brain-injured patients. Methods This was an observational prospective multicenter cohort study involving four neuro-intensive care units. We included acute brain-injured patients requiring deep sedation, defined by a Richmond Assessment Sedation Scale (RASS) < −3. Neurological assessment was performed at day 1 and included pupillary diameter, pupillary light, corneal and cough reflexes, and grimace and motor response to noxious stimuli. Pre-sedation Glasgow Coma Scale (GCS) and Simplified Acute Physiology Score (SAPS-II) were collected, as well as the cause of death in the Intensive Care Unit (ICU). Results A total of 137 brain-injured patients were recruited, including 70 (51%) traumatic brain-injured patients, 40 (29%) vascular (subarachnoid hemorrhage or intracerebral hemorrhage). Thirty patients (22%) died in the ICU. At day 1, the corneal (OR 2.69, p = 0.034) and cough reflexes (OR 5.12, p = 0.0003) were more frequently abolished in patients that died in the ICU. In a multivariate analysis, abolished cough reflex was associated with ICU mortality after adjustment to pre-sedation GCS, SAPS-II, RASS (OR: 5.19, 95% CI [1.92–14.1], p = 0.001) or dose of sedatives (OR: 8.89, 95% CI [2.64–30.0], p = 0.0004). Conclusion Early (day 1) cough reflex abolition is an independent predictor of mortality in deeply sedated brain-injured patients. Abolished cough reflex likely reflects a brainstem dysfunction that might result from the combination of primary and secondary neuro-inflammatory cerebral insults revealed and/or worsened by sedation.
format: application/pdf
format: text/html
creator: Stanislas Kandelman
creator: Jérémy Allary
creator: Raphael Porcher
creator: Cássia Righy
creator: Clarissa Francisca Valdez
creator: Frank Rasulo
creator: Nicholas Heming
creator: Guy Moneger
creator: Eric Azabou
creator: Guillaume Savary
creator: Djillali Annane
creator: Fabrice Chretien
creator: Nicola Latronico
creator: Fernando Augusto Bozza
creator: Benjamin Rohaut
creator: Tarek Sharshar
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Emergency and Critical Care
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10326
publisher: PeerJ Inc.
rights: © 2020 Kandelman et al.
abstract: Background Deep sedation may hamper the detection of neurological deterioration in brain-injured patients. Impaired brainstem reflexes within the first 24 h of deep sedation are associated with increased mortality in non-brain-injured patients. Our objective was to confirm this association in brain-injured patients. Methods This was an observational prospective multicenter cohort study involving four neuro-intensive care units. We included acute brain-injured patients requiring deep sedation, defined by a Richmond Assessment Sedation Scale (RASS) < −3. Neurological assessment was performed at day 1 and included pupillary diameter, pupillary light, corneal and cough reflexes, and grimace and motor response to noxious stimuli. Pre-sedation Glasgow Coma Scale (GCS) and Simplified Acute Physiology Score (SAPS-II) were collected, as well as the cause of death in the Intensive Care Unit (ICU). Results A total of 137 brain-injured patients were recruited, including 70 (51%) traumatic brain-injured patients, 40 (29%) vascular (subarachnoid hemorrhage or intracerebral hemorrhage). Thirty patients (22%) died in the ICU. At day 1, the corneal (OR 2.69, p = 0.034) and cough reflexes (OR 5.12, p = 0.0003) were more frequently abolished in patients that died in the ICU. In a multivariate analysis, abolished cough reflex was associated with ICU mortality after adjustment to pre-sedation GCS, SAPS-II, RASS (OR: 5.19, 95% CI [1.92–14.1], p = 0.001) or dose of sedatives (OR: 8.89, 95% CI [2.64–30.0], p = 0.0004). Conclusion Early (day 1) cough reflex abolition is an independent predictor of mortality in deeply sedated brain-injured patients. Abolished cough reflex likely reflects a brainstem dysfunction that might result from the combination of primary and secondary neuro-inflammatory cerebral insults revealed and/or worsened by sedation.
bibliographic citation: Kandelman et al. (2020) Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients. PeerJ 8:e10326 https://doi.org/10.7717/peerj.10326
date submitted: 2020-05-06
date accepted: 2020-10-19
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandelman
  given name: Stanislas
author list: Agent
  family name: Allary
  given name: Jérémy
author list: Agent
  family name: Porcher
  given name: Raphael
author list: Agent
  family name: Righy
  given name: Cássia
author list: Agent
  family name: Valdez
  given name: Clarissa Francisca
author list: Agent
  family name: Rasulo
  given name: Frank
author list: Agent
  family name: Heming
  given name: Nicholas
author list: Agent
  family name: Moneger
  given name: Guy
author list: Agent
  family name: Azabou
  given name: Eric
author list: Agent
  family name: Savary
  given name: Guillaume
author list: Agent
  family name: Annane
  given name: Djillali
author list: Agent
  family name: Chretien
  given name: Fabrice
author list: Agent
  family name: Latronico
  given name: Nicola
author list: Agent
  family name: Bozza
  given name: Fernando Augusto
author list: Agent
  family name: Rohaut
  given name: Benjamin
author list: Agent
  family name: Sharshar
  given name: Tarek
doi: 10.7717/peerj.10326
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: © 2020 Kandelman et al.
attribution name: Kandelman et al.

Spatial and temporal activity patterns of Golden takin (Budorcas taxicolor bedfordi) recorded by camera trapping
type: item
type: AcademicArticle
description: Understanding animals’ migration, distribution and activity patterns is vital for the development of effective conservation action plans; however, such data for many species are lacking. In this study, we used camera trapping to document the spatial and temporal activity patterns of golden takins (Budorcas taxicolor bedfordi) in Changqing National Nature Reserve in the Qinling mountains, China, from April 2014 to October 2017. Our study obtained 3,323 independent detections (from a total of 12,351 detections) during a total camera trapping effort of 93,606 effective camera trap days at 573 sites. Results showed that: (1) the golden takin’s utilization distributions showed seasonal variation, with larger utilization distributions during spring and autumn compared to summer and winter; (2) the species was recorded at the highest elevations in July, and lowest elevations in December, with the species moving to higher-elevations in summer, lower-elevations in spring and autumn; (3) during all four seasons, golden takins showed bimodal activity peaks at dawn and dusk, with activity intensity higher in the second peak than the first, and overall low levels of activity recorded from 20:00–06:00; and (4) there were two annual activity peaks, the first being in April and the second in November, with camera capture rate during these two months higher than in other months, and activity levels in spring and autumn higher than in summer and winter. This study is the first application of camera traps to assess the spatial and temporal activity patterns of golden takins at a population level. Our findings suggest that the proposed national park should be designed to include golden takin habitat and that ongoing consistent monitoring efforts will be crucial to mitigating novel and ongoing threats to the species.
format: application/pdf
format: text/html
creator: Jia Li
creator: Yadong Xue
creator: Yu Zhang
creator: Wei Dong
creator: Guoyu Shan
creator: Ruiqian Sun
creator: Charlotte Hacker
creator: Bo Wu
creator: Diqiang Li
subject: Animal Behavior
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.10353
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Understanding animals’ migration, distribution and activity patterns is vital for the development of effective conservation action plans; however, such data for many species are lacking. In this study, we used camera trapping to document the spatial and temporal activity patterns of golden takins (Budorcas taxicolor bedfordi) in Changqing National Nature Reserve in the Qinling mountains, China, from April 2014 to October 2017. Our study obtained 3,323 independent detections (from a total of 12,351 detections) during a total camera trapping effort of 93,606 effective camera trap days at 573 sites. Results showed that: (1) the golden takin’s utilization distributions showed seasonal variation, with larger utilization distributions during spring and autumn compared to summer and winter; (2) the species was recorded at the highest elevations in July, and lowest elevations in December, with the species moving to higher-elevations in summer, lower-elevations in spring and autumn; (3) during all four seasons, golden takins showed bimodal activity peaks at dawn and dusk, with activity intensity higher in the second peak than the first, and overall low levels of activity recorded from 20:00–06:00; and (4) there were two annual activity peaks, the first being in April and the second in November, with camera capture rate during these two months higher than in other months, and activity levels in spring and autumn higher than in summer and winter. This study is the first application of camera traps to assess the spatial and temporal activity patterns of golden takins at a population level. Our findings suggest that the proposed national park should be designed to include golden takin habitat and that ongoing consistent monitoring efforts will be crucial to mitigating novel and ongoing threats to the species.
bibliographic citation: Li et al. (2020) Spatial and temporal activity patterns of Golden takin (Budorcas taxicolor bedfordi) recorded by camera trapping. PeerJ 8:e10353 https://doi.org/10.7717/peerj.10353
date submitted: 2019-10-25
date accepted: 2020-10-22
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Xue
  given name: Yadong
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Dong
  given name: Wei
author list: Agent
  family name: Shan
  given name: Guoyu
author list: Agent
  family name: Sun
  given name: Ruiqian
author list: Agent
  family name: Hacker
  given name: Charlotte
author list: Agent
  family name: Wu
  given name: Bo
author list: Agent
  family name: Li
  given name: Diqiang
doi: 10.7717/peerj.10353
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: ©2020 Li et al.
attribution name: Li et al.

The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Increasing evidence has shown that N6-methyladenosine (m6A) RNA methylation regulators have important biological functions in human cancers. However, there are few studies on the value of m6A reader protein YTHDC2 in the diagnosis and tumor-infiltrating of head and neck squamous cell carcinoma (HNSCC). Therefore, it is important to understand the potential clinical value of YTHDC2 in the prognosis and immune infiltration of HNSCC. Methods In this study, gene expression profiles and the corresponding clinical information of 270 HNSCC patients were downloaded from the Gene Expression Omnibus (GEO) database. The gene co-expression network was established to verify whether YTHDC2 was related to the prognosis of HNSCC and verified again in the public database. The correlations between YTHDC2 and immune infiltration was investigated via Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA). Results The results showed that YTHDC2 appeared in the blue module related to survival time and survival state and had a close correlation with the prognosis and immune infiltration level of HNSCC in public database. Patients with low expression of YTHDC2 had poor overall survival (OS) and recurrence-free survival (RFS) than those with high expression. In addition, the expression of YTHDC2 was positively correlated with the level of CD4+ T cell subpopulations infiltration in HNSCC. Conclusions Through this study, we found that YTHDC2 is a tumor suppressor gene with high expression in normal tissues and low expression in tumor tissues. In addition, YTHDC2 is correlated with the immune infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells in HNSCC, which may become a potential marker for prognosis and immune infiltration of HNSCC.
format: application/pdf
format: text/html
creator: Yang Li
creator: Ji-Na Zheng
creator: En-Hao Wang
creator: Chan-Juan Gong
creator: Keng-Fu Lan
creator: XiaoJun Ding
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.10385
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Increasing evidence has shown that N6-methyladenosine (m6A) RNA methylation regulators have important biological functions in human cancers. However, there are few studies on the value of m6A reader protein YTHDC2 in the diagnosis and tumor-infiltrating of head and neck squamous cell carcinoma (HNSCC). Therefore, it is important to understand the potential clinical value of YTHDC2 in the prognosis and immune infiltration of HNSCC. Methods In this study, gene expression profiles and the corresponding clinical information of 270 HNSCC patients were downloaded from the Gene Expression Omnibus (GEO) database. The gene co-expression network was established to verify whether YTHDC2 was related to the prognosis of HNSCC and verified again in the public database. The correlations between YTHDC2 and immune infiltration was investigated via Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA). Results The results showed that YTHDC2 appeared in the blue module related to survival time and survival state and had a close correlation with the prognosis and immune infiltration level of HNSCC in public database. Patients with low expression of YTHDC2 had poor overall survival (OS) and recurrence-free survival (RFS) than those with high expression. In addition, the expression of YTHDC2 was positively correlated with the level of CD4+ T cell subpopulations infiltration in HNSCC. Conclusions Through this study, we found that YTHDC2 is a tumor suppressor gene with high expression in normal tissues and low expression in tumor tissues. In addition, YTHDC2 is correlated with the immune infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells in HNSCC, which may become a potential marker for prognosis and immune infiltration of HNSCC.
bibliographic citation: Li et al. (2020) The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma. PeerJ 8:e10385 https://doi.org/10.7717/peerj.10385
date submitted: 2020-05-21
date accepted: 2020-10-27
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yang
author list: Agent
  family name: Zheng
  given name: Ji-Na
author list: Agent
  family name: Wang
  given name: En-Hao
author list: Agent
  family name: Gong
  given name: Chan-Juan
author list: Agent
  family name: Lan
  given name: Keng-Fu
author list: Agent
  family name: Ding
  given name: XiaoJun
doi: 10.7717/peerj.10385
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: ©2020 Li et al.
attribution name: Li et al.

A signature of tumor DNA repair genes associated with the prognosis of surgically-resected lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung cancer has the highest morbidity and mortality of cancers worldwide. Lung adenocarcinoma (LUAD) is the most common pathological subtype of lung cancer and surgery is its most common treatment. The dysregulated expression of DNA repair genes is found in a variety of cancers and has been shown to affect the origin and progression of these diseases. However, the function of DNA repair genes in surgically-treated LUAD is unclear. Methods We sought to determine the association between the signature of DNA repair genes for patients with surgical LUAD and their overall prognosis. We obtained gene expression data and corresponding clinical information of LUAD from The Cancer Genome Atlas (TCGA) database. The differently expressed DNA repair genes of surgically-treated LUAD and normal tissues were identified using the Wilcoxon rank-sum test. We used uni- and multivariate Cox regression analyses to shrink the aberrantly expressed genes, which were then used to construct the prognostic signature and the risk score formula associated with the independent prognosis of surgically-treated LUAD. We used Kaplan–Meier and Cox hazard ratio analyses to confirm the diagnostic and prognostic roles. Two validation sets (GSE31210 and GSE37745) were downloaded from the Gene Expression Omnibus (GEO) and were used to externally verify the prognostic value of the signature. OSluca online database verifies the hazard ratio for the DNA repair genes by which the signature was constructed. We investigated the correlation between the signature of the DNA repair genes and the clinical parameters. The potential molecular mechanisms and pathways of the prognostic signature were explored using Gene Set Enrichment Analysis (GSEA). Results We determined the prognostic signature based on six DNA repair genes (PLK1, FOXM1, PTTG1, CCNO, HIST3H2A, and BLM) and calculated the risk score based on this formula. Patients with surgically-treated LUAD were divided into high-risk and low-risk groups…
format: application/pdf
format: text/html
creator: Xiongtao Yang
creator: Guohui Wang
creator: Runchuan Gu
creator: Xiaohong Xu
creator: Guangying Zhu
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10418
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Lung cancer has the highest morbidity and mortality of cancers worldwide. Lung adenocarcinoma (LUAD) is the most common pathological subtype of lung cancer and surgery is its most common treatment. The dysregulated expression of DNA repair genes is found in a variety of cancers and has been shown to affect the origin and progression of these diseases. However, the function of DNA repair genes in surgically-treated LUAD is unclear. Methods We sought to determine the association between the signature of DNA repair genes for patients with surgical LUAD and their overall prognosis. We obtained gene expression data and corresponding clinical information of LUAD from The Cancer Genome Atlas (TCGA) database. The differently expressed DNA repair genes of surgically-treated LUAD and normal tissues were identified using the Wilcoxon rank-sum test. We used uni- and multivariate Cox regression analyses to shrink the aberrantly expressed genes, which were then used to construct the prognostic signature and the risk score formula associated with the independent prognosis of surgically-treated LUAD. We used Kaplan–Meier and Cox hazard ratio analyses to confirm the diagnostic and prognostic roles. Two validation sets (GSE31210 and GSE37745) were downloaded from the Gene Expression Omnibus (GEO) and were used to externally verify the prognostic value of the signature. OSluca online database verifies the hazard ratio for the DNA repair genes by which the signature was constructed. We investigated the correlation between the signature of the DNA repair genes and the clinical parameters. The potential molecular mechanisms and pathways of the prognostic signature were explored using Gene Set Enrichment Analysis (GSEA). Results We determined the prognostic signature based on six DNA repair genes (PLK1, FOXM1, PTTG1, CCNO, HIST3H2A, and BLM) and calculated the risk score based on this formula. Patients with surgically-treated LUAD were divided into high-risk and low-risk groups…
bibliographic citation: Yang et al. (2020) A signature of tumor DNA repair genes associated with the prognosis of surgically-resected lung adenocarcinoma. PeerJ 8:e10418 https://doi.org/10.7717/peerj.10418
date submitted: 2020-07-03
date accepted: 2020-11-02
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Xiongtao
author list: Agent
  family name: Wang
  given name: Guohui
author list: Agent
  family name: Gu
  given name: Runchuan
author list: Agent
  family name: Xu
  given name: Xiaohong
author list: Agent
  family name: Zhu
  given name: Guangying
doi: 10.7717/peerj.10418
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats
type: item
type: AcademicArticle
description: Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3–1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.
format: application/pdf
format: text/html
creator: Babatunde O. Motayo
creator: Olukunle Oluwapamilerin Oluwasemowo
creator: Paul A. Akinduti
subject: Evolutionary Studies
subject: Veterinary Medicine
subject: Virology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.10434
publisher: PeerJ Inc.
rights: © 2020 Motayo et al.
abstract: Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3–1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.
bibliographic citation: Motayo et al. (2020) Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats. PeerJ 8:e10434 https://doi.org/10.7717/peerj.10434
date submitted: 2020-06-04
date accepted: 2020-11-06
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Motayo
  given name: Babatunde O.
author list: Agent
  family name: Oluwasemowo
  given name: Olukunle Oluwapamilerin
author list: Agent
  family name: Akinduti
  given name: Paul A.
doi: 10.7717/peerj.10434
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: © 2020 Motayo et al.
attribution name: Motayo et al.

Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery
type: item
type: AcademicArticle
description: We studied the impact of bariatric surgery on the intestinal microbiota of morbidly obese study subjects. A total of 13 morbidly obese women (five of which had type 2 diabetes) and 14 healthy age- and gender-matched controls were recruited and the microbiota composition of fecal samples were determined by using a phylogenetic microarray. Sampling of the patients took place just one month before and 6 months after the operation. Within six months after bariatric surgery, the obese subjects had lost on average a quarter of their weight whereas four of the five of the diabetic subjects were in remission. Bariatric surgery was associated with an increased microbial community richness and Bacteroidetes/Firmicutes ratio. In addition, we observed an increased relative abundance of facultative anaerobes, such as Streptococcus spp., and a reduction in specific butyrate-producing Firmicutes. The observed postoperative alterations in intestinal microbiota reflect adaptation to the changing conditions in the gastrointestinal tract, such as energy restriction and the inability to process fiber-rich foods after bariatric surgery.
format: application/pdf
format: text/html
creator: Jukka Koffert
creator: Leo Lahti
creator: Lotta Nylund
creator: Seppo Salminen
creator: Jarna C. Hannukainen
creator: Paulina Salminen
creator: Willem M. de Vos
creator: Pirjo Nuutila
subject: Microbiology
subject: Clinical Trials
subject: Diabetes and Endocrinology
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.10442
publisher: PeerJ Inc.
rights: © 2020 Koffert et al.
abstract: We studied the impact of bariatric surgery on the intestinal microbiota of morbidly obese study subjects. A total of 13 morbidly obese women (five of which had type 2 diabetes) and 14 healthy age- and gender-matched controls were recruited and the microbiota composition of fecal samples were determined by using a phylogenetic microarray. Sampling of the patients took place just one month before and 6 months after the operation. Within six months after bariatric surgery, the obese subjects had lost on average a quarter of their weight whereas four of the five of the diabetic subjects were in remission. Bariatric surgery was associated with an increased microbial community richness and Bacteroidetes/Firmicutes ratio. In addition, we observed an increased relative abundance of facultative anaerobes, such as Streptococcus spp., and a reduction in specific butyrate-producing Firmicutes. The observed postoperative alterations in intestinal microbiota reflect adaptation to the changing conditions in the gastrointestinal tract, such as energy restriction and the inability to process fiber-rich foods after bariatric surgery.
bibliographic citation: Koffert et al. (2020) Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery. PeerJ 8:e10442 https://doi.org/10.7717/peerj.10442
date submitted: 2020-05-29
date accepted: 2020-11-06
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Koffert
  given name: Jukka
author list: Agent
  family name: Lahti
  given name: Leo
author list: Agent
  family name: Nylund
  given name: Lotta
author list: Agent
  family name: Salminen
  given name: Seppo
author list: Agent
  family name: Hannukainen
  given name: Jarna C.
author list: Agent
  family name: Salminen
  given name: Paulina
author list: Agent
  family name: de Vos
  given name: Willem M.
author list: Agent
  family name: Nuutila
  given name: Pirjo
doi: 10.7717/peerj.10442
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: ©2020 Koffert et al.
attribution name: Koffert et al.

Characteristics and outcomes of hemodialysis patients with COVID-19: a retrospective single center study
type: item
type: AcademicArticle
description: Background The coronavirus 19 (COVID-19) pandemic has heightened the threat to the health and lives of patients with comorbid diseases. Infection by COVID-19 is especially detrimental to patients on hemodialysis. In this study, we evaluated the clinical characteristics, laboratory findings, treatments and prognoses of hemodialysis patients with COVID-19. Methods A total of 16 hemodialysis patients with COVID-19 were recruited from Wuhan Fourth Hospital from 5 February to 20 March 2020 for a retrospective, single-center study. A total of 62 non-dialysis patients with COVID-19 were the control group. We collected data on the clinical characteristics, laboratory findings, treatments, and clinical outcomes of patients affected by the virus. Results Hemodialysis patients with COVID-19 had a lower incidence of fever (P = 0.001) and relatively higher incidence of pre-admission comorbidities and shortness of breath than non-dialysis patients with COVID-19 (75% vs. 61%, P = 0.467 50% vs. 33.87%, P = 0.248 ). Hemodialysis patients had lower levels of hemoglobin (P < 0.001), white blood cell counts (P = 0.015), neutrophils (P = 0.016), AST (P = 0.037), ALT (P < 0.001) and procalcitonin (P < 0.001), and higher levels of D-dimer (P < 0.001) and thrombin time (P < 0.001). Hemodialysis patients had a higher incidence of pulmonary effusion, cord-like high-density shadows, pleural thickening, and atelectasis (P < 0.05). Hemodialysis patients also had relatively higher rates of mortality and prolonged hospital stays compared with the control group. Conclusions Hemodialysis patients typically present with multiple comorbidities and are considered to be a high-risk group for COVID-19 infections. Hemodialysis patients with COVID-19 may have prolonged hospital stays and unfavorable prognoses and should be closely monitored.
format: application/pdf
format: text/html
creator: Yongwen Luo
creator: Junli Li
creator: Zhifen Liu
creator: Heping Yu
creator: Xiang Peng
creator: Cheng’an Cao
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10459
publisher: PeerJ Inc.
rights: © 2020 Luo et al.
abstract: Background The coronavirus 19 (COVID-19) pandemic has heightened the threat to the health and lives of patients with comorbid diseases. Infection by COVID-19 is especially detrimental to patients on hemodialysis. In this study, we evaluated the clinical characteristics, laboratory findings, treatments and prognoses of hemodialysis patients with COVID-19. Methods A total of 16 hemodialysis patients with COVID-19 were recruited from Wuhan Fourth Hospital from 5 February to 20 March 2020 for a retrospective, single-center study. A total of 62 non-dialysis patients with COVID-19 were the control group. We collected data on the clinical characteristics, laboratory findings, treatments, and clinical outcomes of patients affected by the virus. Results Hemodialysis patients with COVID-19 had a lower incidence of fever (P = 0.001) and relatively higher incidence of pre-admission comorbidities and shortness of breath than non-dialysis patients with COVID-19 (75% vs. 61%, P = 0.467 50% vs. 33.87%, P = 0.248 ). Hemodialysis patients had lower levels of hemoglobin (P < 0.001), white blood cell counts (P = 0.015), neutrophils (P = 0.016), AST (P = 0.037), ALT (P < 0.001) and procalcitonin (P < 0.001), and higher levels of D-dimer (P < 0.001) and thrombin time (P < 0.001). Hemodialysis patients had a higher incidence of pulmonary effusion, cord-like high-density shadows, pleural thickening, and atelectasis (P < 0.05). Hemodialysis patients also had relatively higher rates of mortality and prolonged hospital stays compared with the control group. Conclusions Hemodialysis patients typically present with multiple comorbidities and are considered to be a high-risk group for COVID-19 infections. Hemodialysis patients with COVID-19 may have prolonged hospital stays and unfavorable prognoses and should be closely monitored.
bibliographic citation: Luo et al. (2020) Characteristics and outcomes of hemodialysis patients with COVID-19: a retrospective single center study. PeerJ 8:e10459 https://doi.org/10.7717/peerj.10459
date submitted: 2020-05-14
date accepted: 2020-11-10
issued: 2020-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Yongwen
author list: Agent
  family name: Li
  given name: Junli
author list: Agent
  family name: Liu
  given name: Zhifen
author list: Agent
  family name: Yu
  given name: Heping
author list: Agent
  family name: Peng
  given name: Xiang
author list: Agent
  family name: Cao
  given name: Cheng’an
doi: 10.7717/peerj.10459
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-26
copyright: © 2020 Luo et al.
attribution name: Luo et al.

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