PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Spatiotemporal expansion of human brucellosis in Shaanxi Province, Northwestern China and model for risk prediction
items: Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible
items: Photosynthetic performance and stevioside concentration are improved by the arbuscular mycorrhizal symbiosis in Stevia rebaudiana under different phosphate concentrations
items: Nursing home residents’ ADL status, institution-dwelling and association with outdoor activity: a cross-sectional study
items: A study of soil seed banks across one complete chronosequence of secondary succession in a karst landscape
items: Unique myological changes associated with ossified fabellae: a femorofabellar ligament and systematic review of the double-headed popliteus
items: A robust semi-supervised NMF model for single cell RNA-seq data
items: Broad spectrum antimicrobial activities from spore-forming bacteria isolated from the Vietnam Sea
items: High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae
items: Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study

Spatiotemporal expansion of human brucellosis in Shaanxi Province, Northwestern China and model for risk prediction
type: item
type: AcademicArticle
description: Background Human brucellosis imposes a heavy burden on the health and economy of endemic regions. Since 2011, China has reported at least 35,000 human brucellosis cases annually, with more than 90% of these cases reported in the northern. Given the alarmingly high incidence and variation in the geographical distribution of human brucellosis cases, there is an urgent need to decipher the causes of such variation in geographical distribution. Method We conducted a retrospective epidemiological study in Shaanxi Province from January 1, 2005 to December 31, 2018 to investigate the association between meteorological factors and transmission of human brucellosis according to differences in geographical distribution and seasonal fluctuation in northwestern China for the first time. Results Human brucellosis cases were mainly distributed in the Shaanbei upland plateau before 2008 and then slowly extended towards the southern region with significant seasonal fluctuation. The results of quasi-Poisson generalized additive mixed model (GAMM) indicated that air temperature, sunshine duration, rainfall, relative humidity, and evaporation with maximum lag time within 7 months played crucial roles in the transmission of human brucellosis with seasonal fluctuation. Compared with the Shaanbei upland plateau, Guanzhong basin had more obvious fluctuations in the occurrence of human brucellosis due to changes in meteorological factors. Additionally, the established GAMM model showed high accuracy in predicting the occurrence of human brucellosis based on the meteorological factors. Conclusion These findings may be used to predict the seasonal fluctuations of human brucellosis and to develop reliable and cost-effective prevention strategies in Shaanxi Province and other areas with similar environmental conditions.
format: application/pdf
format: text/html
creator: Zurong Yang
creator: Miaomiao Pang
creator: Qingyang Zhou
creator: Shuxuan Song
creator: Weifeng Liang
creator: Junjiang Chen
creator: Tianci Guo
creator: Zhongjun Shao
creator: Kun Liu
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10113
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Human brucellosis imposes a heavy burden on the health and economy of endemic regions. Since 2011, China has reported at least 35,000 human brucellosis cases annually, with more than 90% of these cases reported in the northern. Given the alarmingly high incidence and variation in the geographical distribution of human brucellosis cases, there is an urgent need to decipher the causes of such variation in geographical distribution. Method We conducted a retrospective epidemiological study in Shaanxi Province from January 1, 2005 to December 31, 2018 to investigate the association between meteorological factors and transmission of human brucellosis according to differences in geographical distribution and seasonal fluctuation in northwestern China for the first time. Results Human brucellosis cases were mainly distributed in the Shaanbei upland plateau before 2008 and then slowly extended towards the southern region with significant seasonal fluctuation. The results of quasi-Poisson generalized additive mixed model (GAMM) indicated that air temperature, sunshine duration, rainfall, relative humidity, and evaporation with maximum lag time within 7 months played crucial roles in the transmission of human brucellosis with seasonal fluctuation. Compared with the Shaanbei upland plateau, Guanzhong basin had more obvious fluctuations in the occurrence of human brucellosis due to changes in meteorological factors. Additionally, the established GAMM model showed high accuracy in predicting the occurrence of human brucellosis based on the meteorological factors. Conclusion These findings may be used to predict the seasonal fluctuations of human brucellosis and to develop reliable and cost-effective prevention strategies in Shaanxi Province and other areas with similar environmental conditions.
bibliographic citation: Yang et al. (2020) Spatiotemporal expansion of human brucellosis in Shaanxi Province, Northwestern China and model for risk prediction. PeerJ 8:e10113 https://doi.org/10.7717/peerj.10113
date submitted: 2020-06-05
date accepted: 2020-09-16
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zurong
author list: Agent
  family name: Pang
  given name: Miaomiao
author list: Agent
  family name: Zhou
  given name: Qingyang
author list: Agent
  family name: Song
  given name: Shuxuan
author list: Agent
  family name: Liang
  given name: Weifeng
author list: Agent
  family name: Chen
  given name: Junjiang
author list: Agent
  family name: Guo
  given name: Tianci
author list: Agent
  family name: Shao
  given name: Zhongjun
author list: Agent
  family name: Liu
  given name: Kun
doi: 10.7717/peerj.10113
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible
type: item
type: AcademicArticle
description: Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator’s control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Isla…
format: application/pdf
format: text/html
creator: Jonas Tebbe
creator: Emily Humble
creator: Martin Adam Stoffel
creator: Lisa Johanna Tewes
creator: Caroline Müller
creator: Jaume Forcada
creator: Barbara Caspers
creator: Joseph Ivan Hoffman
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10131
publisher: PeerJ Inc.
rights: © 2020 Tebbe et al.
abstract: Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator’s control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Isla…
bibliographic citation: Tebbe et al. (2020) Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible. PeerJ 8:e10131 https://doi.org/10.7717/peerj.10131
date submitted: 2020-04-30
date accepted: 2020-09-17
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tebbe
  given name: Jonas
author list: Agent
  family name: Humble
  given name: Emily
author list: Agent
  family name: Stoffel
  given name: Martin Adam
author list: Agent
  family name: Tewes
  given name: Lisa Johanna
author list: Agent
  family name: Müller
  given name: Caroline
author list: Agent
  family name: Forcada
  given name: Jaume
author list: Agent
  family name: Caspers
  given name: Barbara
author list: Agent
  family name: Hoffman
  given name: Joseph Ivan
doi: 10.7717/peerj.10131
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: © 2020 Tebbe et al.
attribution name: Tebbe et al.

Photosynthetic performance and stevioside concentration are improved by the arbuscular mycorrhizal symbiosis in Stevia rebaudiana under different phosphate concentrations
type: item
type: AcademicArticle
description: In plants, phosphorus (P) uptake occurs via arbuscular mycorrhizal (AM) symbiosis and through plant roots. The phosphate concentration is known to affect colonization by AM fungi, and the effect depends on the plant species. Stevia rebaudiana plants are valuable sources of sweetener compounds called steviol glycosides (SGs), and the principal components of SGs are stevioside and rebaudioside A. However, a detailed analysis describing the effect of the phosphate concentration on the colonization of AM fungi in the roots and the relationship of these factors to the accumulation of SGs and photochemical performance has not been performed; such an analysis was the aim of this study. The results indicated that low phosphate concentrations (20 and 200 µM KH2PO4) induced a high percentage of colonization by Rhizophagus irregularis in the roots of S. rebaudiana, while high phosphate concentrations (500 and 1,000 µM KH2PO4) reduced colonization. The morphology of the colonization structure is a typical Arum-type mycorrhiza, and a mycorrhiza-specific phosphate transporter was identified. Colonization with low phosphate concentrations improved plant growth, chlorophyll and carotenoid concentration, and photochemical performance. The transcription of the genes that encode kaurene oxidase and glucosyltransferase (UGT74G1) was upregulated in colonized plants at 200 µM KH2PO4, which was consistent with the observed patterns of stevioside accumulation. In contrast, at 200 µM KH2PO4, the transcription of UGT76G1 and the accumulation of rebaudioside A were higher in noncolonized plants than in colonized plants. These results indicate that a low phosphate concentration improves mycorrhizal colonization and modulates the stevioside and rebaudioside A concentration by regulating the transcription of the genes that encode kaurene oxidase and glucosyltransferases, which are involved in stevioside and rebaudioside A synthesis in S. rebaudiana.
format: application/pdf
format: text/html
creator: Luis G. Sarmiento-López
creator: Melina López-Meyer
creator: Gabriela Sepúlveda-Jiménez
creator: Luis Cárdenas
creator: Mario Rodríguez-Monroy
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10173
publisher: PeerJ Inc.
rights: © 2020 Sarmiento-López et al.
abstract: In plants, phosphorus (P) uptake occurs via arbuscular mycorrhizal (AM) symbiosis and through plant roots. The phosphate concentration is known to affect colonization by AM fungi, and the effect depends on the plant species. Stevia rebaudiana plants are valuable sources of sweetener compounds called steviol glycosides (SGs), and the principal components of SGs are stevioside and rebaudioside A. However, a detailed analysis describing the effect of the phosphate concentration on the colonization of AM fungi in the roots and the relationship of these factors to the accumulation of SGs and photochemical performance has not been performed; such an analysis was the aim of this study. The results indicated that low phosphate concentrations (20 and 200 µM KH2PO4) induced a high percentage of colonization by Rhizophagus irregularis in the roots of S. rebaudiana, while high phosphate concentrations (500 and 1,000 µM KH2PO4) reduced colonization. The morphology of the colonization structure is a typical Arum-type mycorrhiza, and a mycorrhiza-specific phosphate transporter was identified. Colonization with low phosphate concentrations improved plant growth, chlorophyll and carotenoid concentration, and photochemical performance. The transcription of the genes that encode kaurene oxidase and glucosyltransferase (UGT74G1) was upregulated in colonized plants at 200 µM KH2PO4, which was consistent with the observed patterns of stevioside accumulation. In contrast, at 200 µM KH2PO4, the transcription of UGT76G1 and the accumulation of rebaudioside A were higher in noncolonized plants than in colonized plants. These results indicate that a low phosphate concentration improves mycorrhizal colonization and modulates the stevioside and rebaudioside A concentration by regulating the transcription of the genes that encode kaurene oxidase and glucosyltransferases, which are involved in stevioside and rebaudioside A synthesis in S. rebaudiana.
bibliographic citation: Sarmiento-López et al. (2020) Photosynthetic performance and stevioside concentration are improved by the arbuscular mycorrhizal symbiosis in Stevia rebaudiana under different phosphate concentrations. PeerJ 8:e10173 https://doi.org/10.7717/peerj.10173
date submitted: 2020-07-10
date accepted: 2020-09-22
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarmiento-López
  given name: Luis G.
author list: Agent
  family name: López-Meyer
  given name: Melina
author list: Agent
  family name: Sepúlveda-Jiménez
  given name: Gabriela
author list: Agent
  family name: Cárdenas
  given name: Luis
author list: Agent
  family name: Rodríguez-Monroy
  given name: Mario
doi: 10.7717/peerj.10173
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Sarmiento-López et al.
attribution name: Sarmiento-López et al.

Nursing home residents’ ADL status, institution-dwelling and association with outdoor activity: a cross-sectional study
type: item
type: AcademicArticle
description: Introduction The Norwegian regulations for nursing homes consider access to meaningful activities to be an indicator for the quality of nursing homes. Activities of daily living (ADL) provide important basic self-care skills for nursing home residents. Due to the physical changes caused by ageing and comorbidities, nursing home residents may experience functional decline over time, which may affect their ability to perform meaningful ADL, such as outdoor activity, which is considered a valuable and meaningful activity in Norwegian culture. This study aimed to investigate the association between ADL status, institution-dwelling and outdoor activity among nursing home residents. Methods This cross-sectional study included 784 residents aged >67 years living in 21 nursing homes in 15 Norwegian municipalities between November 2016 and May 2018. The Barthel Index was used to assess the nursing home residents’ ADL status. Other variables collected were age, gender, body weight and height, visits per month, institution, ward, and participation in weekly outdoor activities. Descriptive statistics were used to provide an overview of the residents’ characteristics. A Poisson regression model was used to test the association between the outdoor activity level as the dependent variable and ADL score, institution, and other control variables as independent variables. Results More than half (57%) of the nursing home residents in this sample did not go outdoors. More than 50% of the residents had an ADL score <10, which indicates low performance status. Further, we found that residents’ ADL status, institution, ward, and number of visits had an impact on how often the residents went outdoors. Discussion The nursing home residents in this study rarely went outdoors, which is interesting because Norwegians appreciate this activity. Differences in the number of visits might explain why some residents went outdoors more often than other residents did. Our findings also highlight that …
format: application/pdf
format: text/html
creator: Anne Marie Sandvoll
creator: Ellen Karine Grov
creator: Morten Simonsen
subject: Geriatrics
subject: Nursing
subject: Statistics
description: doi:10.7717/peerj.10202
publisher: PeerJ Inc.
rights: © 2020 Sandvoll et al.
abstract: Introduction The Norwegian regulations for nursing homes consider access to meaningful activities to be an indicator for the quality of nursing homes. Activities of daily living (ADL) provide important basic self-care skills for nursing home residents. Due to the physical changes caused by ageing and comorbidities, nursing home residents may experience functional decline over time, which may affect their ability to perform meaningful ADL, such as outdoor activity, which is considered a valuable and meaningful activity in Norwegian culture. This study aimed to investigate the association between ADL status, institution-dwelling and outdoor activity among nursing home residents. Methods This cross-sectional study included 784 residents aged >67 years living in 21 nursing homes in 15 Norwegian municipalities between November 2016 and May 2018. The Barthel Index was used to assess the nursing home residents’ ADL status. Other variables collected were age, gender, body weight and height, visits per month, institution, ward, and participation in weekly outdoor activities. Descriptive statistics were used to provide an overview of the residents’ characteristics. A Poisson regression model was used to test the association between the outdoor activity level as the dependent variable and ADL score, institution, and other control variables as independent variables. Results More than half (57%) of the nursing home residents in this sample did not go outdoors. More than 50% of the residents had an ADL score <10, which indicates low performance status. Further, we found that residents’ ADL status, institution, ward, and number of visits had an impact on how often the residents went outdoors. Discussion The nursing home residents in this study rarely went outdoors, which is interesting because Norwegians appreciate this activity. Differences in the number of visits might explain why some residents went outdoors more often than other residents did. Our findings also highlight that …
bibliographic citation: Sandvoll et al. (2020) Nursing home residents’ ADL status, institution-dwelling and association with outdoor activity: a cross-sectional study. PeerJ 8:e10202 https://doi.org/10.7717/peerj.10202
date submitted: 2019-11-14
date accepted: 2020-09-27
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sandvoll
  given name: Anne Marie
author list: Agent
  family name: Grov
  given name: Ellen Karine
author list: Agent
  family name: Simonsen
  given name: Morten
doi: 10.7717/peerj.10202
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 Sandvoll et al.
attribution name: Sandvoll et al.

A study of soil seed banks across one complete chronosequence of secondary succession in a karst landscape
type: item
type: AcademicArticle
description: Anthropogenic disturbance and distinctive geochemistry have resulted in rocky desertification in many karst regions of the world. Seed banks are crucial to vegetation regeneration in degraded karst ecosystems characterized by a discontinuous distribution of soil and seasonal drought stress. However, the dynamics of seed banks across one complete series of secondary succession and the underlying mechanisms remain unclear. We selected eight typical stages during secondary succession, conducted aboveground vegetation survey and collected 960 soil samples in the Guiyang karst landscape of China. Seed density, species richness and plant life forms in seed banks were determined via the germination method. The results indicated that the seed density in seed banks before and after field seed germination was significantly different among most succession stages. Community succession had impacts on the seed density of seed banks before and after field seed germination. Seed density ranged from 1,042 seedlings.m−2 in evergreen broadleaf forests to 3,755 seedlings.m−2 in the herb community, which was a relatively high density. The seed density and similar species composition between the seed banks and vegetation declined with succession from early to later stages. Species richness in seed banks was highest in middle succession stages and increased with increasing species richness of aboveground vegetation. The species richness of the five life forms in the seed banks showed different variations across these succession stages. The conservation of diverse aboveground vegetation can maintain the diversity of seed banks for restoration.
format: application/pdf
format: text/html
creator: Xiaole He
creator: Li Yuan
creator: Zhen Hong Wang
creator: Zizong Zhou
creator: Li Wan
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.10226
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Anthropogenic disturbance and distinctive geochemistry have resulted in rocky desertification in many karst regions of the world. Seed banks are crucial to vegetation regeneration in degraded karst ecosystems characterized by a discontinuous distribution of soil and seasonal drought stress. However, the dynamics of seed banks across one complete series of secondary succession and the underlying mechanisms remain unclear. We selected eight typical stages during secondary succession, conducted aboveground vegetation survey and collected 960 soil samples in the Guiyang karst landscape of China. Seed density, species richness and plant life forms in seed banks were determined via the germination method. The results indicated that the seed density in seed banks before and after field seed germination was significantly different among most succession stages. Community succession had impacts on the seed density of seed banks before and after field seed germination. Seed density ranged from 1,042 seedlings.m−2 in evergreen broadleaf forests to 3,755 seedlings.m−2 in the herb community, which was a relatively high density. The seed density and similar species composition between the seed banks and vegetation declined with succession from early to later stages. Species richness in seed banks was highest in middle succession stages and increased with increasing species richness of aboveground vegetation. The species richness of the five life forms in the seed banks showed different variations across these succession stages. The conservation of diverse aboveground vegetation can maintain the diversity of seed banks for restoration.
bibliographic citation: He et al. (2020) A study of soil seed banks across one complete chronosequence of secondary succession in a karst landscape. PeerJ 8:e10226 https://doi.org/10.7717/peerj.10226
date submitted: 2020-05-15
date accepted: 2020-10-01
issued: 2020-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Xiaole
author list: Agent
  family name: Yuan
  given name: Li
author list: Agent
  family name: Wang
  given name: Zhen Hong
author list: Agent
  family name: Zhou
  given name: Zizong
author list: Agent
  family name: Wan
  given name: Li
doi: 10.7717/peerj.10226
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-19
copyright: ©2020 He et al.
attribution name: He et al.

Unique myological changes associated with ossified fabellae: a femorofabellar ligament and systematic review of the double-headed popliteus
type: item
type: AcademicArticle
description: Introduction The fabella is a sesamoid bone embedded in the tendon of the lateral head of the gastrocnemius. It is the only bone in the human body to increase in prevalence in the last 100 years. As the fabella can serve as an origin/insertion for muscles, tendons, and/or ligaments (e.g., the oblique popliteal and fabellofibular ligaments), temporal changes in fabella prevalence could lead to temporal changes in “standard” knee anatomy. The aim of this study was to investigate unique myological changes to the posterolateral corner knee associated with ossified fabella presence and perform a systematic review to contextualize our results. Methods Thirty-three fresh frozen cadaveric knees were considered. As the knees were all used for previous experimentation, the knees were in variable levels of preservation. Those with adequate preservation were used to determine ossified fabella presence/absence. When ossified fabellae were present, unique myologies associated with the fabella were recorded. A systematic review was performed on the double-headed popliteus to investigate possible correlations between this anatomical variant and the fabella. Results Of the 33 knees, 30 preserved enough soft tissue to determine fabella presence/absence: 16/30 knees had fabellae (five cartilaginous and 11 ossified). Eight of the eleven knees with ossified fabellae retained enough soft tissue to investigate the posterolateral knee anatomy. Of these, 4/8 exhibited unique myological changes. One knee had a double-headed popliteus muscle where one head originated from the medial side of a large, bulbous fabella. A systematic review revealed double-headed popliteus muscles are rare, but individuals are 3.7 times more likely to have a fabella if they have a double-headed popliteus. Another knee had a large, thick ligament stretching from the lateral edge of the fabella to the inferoposterior edge of the lateral femoral epicondyle, deep to the lateral collateral ligament (LCL) and near the p…
format: application/pdf
format: text/html
creator: Michael A. Berthaume
creator: Spencer Barnes
creator: Kiron K. Athwal
creator: Lukas Willinger
subject: Bioengineering
subject: Evolutionary Studies
subject: Anatomy and Physiology
subject: Orthopedics
description: doi:10.7717/peerj.10028
publisher: PeerJ Inc.
rights: © 2020 Berthaume et al.
abstract: Introduction The fabella is a sesamoid bone embedded in the tendon of the lateral head of the gastrocnemius. It is the only bone in the human body to increase in prevalence in the last 100 years. As the fabella can serve as an origin/insertion for muscles, tendons, and/or ligaments (e.g., the oblique popliteal and fabellofibular ligaments), temporal changes in fabella prevalence could lead to temporal changes in “standard” knee anatomy. The aim of this study was to investigate unique myological changes to the posterolateral corner knee associated with ossified fabella presence and perform a systematic review to contextualize our results. Methods Thirty-three fresh frozen cadaveric knees were considered. As the knees were all used for previous experimentation, the knees were in variable levels of preservation. Those with adequate preservation were used to determine ossified fabella presence/absence. When ossified fabellae were present, unique myologies associated with the fabella were recorded. A systematic review was performed on the double-headed popliteus to investigate possible correlations between this anatomical variant and the fabella. Results Of the 33 knees, 30 preserved enough soft tissue to determine fabella presence/absence: 16/30 knees had fabellae (five cartilaginous and 11 ossified). Eight of the eleven knees with ossified fabellae retained enough soft tissue to investigate the posterolateral knee anatomy. Of these, 4/8 exhibited unique myological changes. One knee had a double-headed popliteus muscle where one head originated from the medial side of a large, bulbous fabella. A systematic review revealed double-headed popliteus muscles are rare, but individuals are 3.7 times more likely to have a fabella if they have a double-headed popliteus. Another knee had a large, thick ligament stretching from the lateral edge of the fabella to the inferoposterior edge of the lateral femoral epicondyle, deep to the lateral collateral ligament (LCL) and near the p…
bibliographic citation: Berthaume et al. (2020) Unique myological changes associated with ossified fabellae: a femorofabellar ligament and systematic review of the double-headed popliteus. PeerJ 8:e10028 https://doi.org/10.7717/peerj.10028
date submitted: 2020-04-21
date accepted: 2020-09-02
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berthaume
  given name: Michael A.
author list: Agent
  family name: Barnes
  given name: Spencer
author list: Agent
  family name: Athwal
  given name: Kiron K.
author list: Agent
  family name: Willinger
  given name: Lukas
doi: 10.7717/peerj.10028
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: © 2020 Berthaume et al.
attribution name: Berthaume et al.

A robust semi-supervised NMF model for single cell RNA-seq data
type: item
type: AcademicArticle
description: Background Single-cell RNA-sequencing (scRNA-seq) technology is a powerful tool to study organism from a single cell perspective and explore the heterogeneity between cells. Clustering is a fundamental step in scRNA-seq data analysis and it is the key to understand cell function and constitutes the basis of other advanced analysis. Nonnegative Matrix Factorization (NMF) has been widely used in clustering analysis of transcriptome data and achieved good performance. However, the existing NMF model is unsupervised and ignores known gene functions in the process of clustering. Knowledges of cell markers genes (genes that only express in specific cells) in human and model organisms have been accumulated a lot, such as the Molecular Signatures Database (MSigDB), which can be used as prior information in the clustering analysis of scRNA-seq data. Because the same kind of cells is likely to have similar biological functions and specific gene expression patterns, the marker genes of cells can be utilized as prior knowledge in the clustering analysis. Methods We propose a robust and semi-supervised NMF (rssNMF) model, which introduces a new variable to absorb noises of data and incorporates marker genes as prior information into a graph regularization term. We use rssNMF to solve the clustering problem of scRNA-seq data. Results Twelve scRNA-seq datasets with true labels are used to test the model performance and the results illustrate that our model outperforms original NMF and other common methods such as KMeans and Hierarchical Clustering. Biological significance analysis shows that rssNMF can identify key subclasses and latent biological processes. To our knowledge, this study is the first method that incorporates prior knowledge into the clustering analysis of scRNA-seq data.
format: application/pdf
format: text/html
creator: Peng Wu
creator: Mo An
creator: Hai-Ren Zou
creator: Cai-Ying Zhong
creator: Wei Wang
creator: Chang-Peng Wu
subject: Bioinformatics
subject: Molecular Biology
subject: Computational Science
description: doi:10.7717/peerj.10091
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Background Single-cell RNA-sequencing (scRNA-seq) technology is a powerful tool to study organism from a single cell perspective and explore the heterogeneity between cells. Clustering is a fundamental step in scRNA-seq data analysis and it is the key to understand cell function and constitutes the basis of other advanced analysis. Nonnegative Matrix Factorization (NMF) has been widely used in clustering analysis of transcriptome data and achieved good performance. However, the existing NMF model is unsupervised and ignores known gene functions in the process of clustering. Knowledges of cell markers genes (genes that only express in specific cells) in human and model organisms have been accumulated a lot, such as the Molecular Signatures Database (MSigDB), which can be used as prior information in the clustering analysis of scRNA-seq data. Because the same kind of cells is likely to have similar biological functions and specific gene expression patterns, the marker genes of cells can be utilized as prior knowledge in the clustering analysis. Methods We propose a robust and semi-supervised NMF (rssNMF) model, which introduces a new variable to absorb noises of data and incorporates marker genes as prior information into a graph regularization term. We use rssNMF to solve the clustering problem of scRNA-seq data. Results Twelve scRNA-seq datasets with true labels are used to test the model performance and the results illustrate that our model outperforms original NMF and other common methods such as KMeans and Hierarchical Clustering. Biological significance analysis shows that rssNMF can identify key subclasses and latent biological processes. To our knowledge, this study is the first method that incorporates prior knowledge into the clustering analysis of scRNA-seq data.
bibliographic citation: Wu et al. (2020) A robust semi-supervised NMF model for single cell RNA-seq data. PeerJ 8:e10091 https://doi.org/10.7717/peerj.10091
date submitted: 2020-04-27
date accepted: 2020-09-13
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Peng
author list: Agent
  family name: An
  given name: Mo
author list: Agent
  family name: Zou
  given name: Hai-Ren
author list: Agent
  family name: Zhong
  given name: Cai-Ying
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Wu
  given name: Chang-Peng
doi: 10.7717/peerj.10091
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: ©2020 Wu et al.
attribution name: Wu et al.

Broad spectrum antimicrobial activities from spore-forming bacteria isolated from the Vietnam Sea
type: item
type: AcademicArticle
description: The widespread occurrence of pathogenic bacteria resistant to last-line antibiotics has resulted in significant challenges in human and veterinary medicine. There is an urgent need for new antimicrobial agents that can be used to control these life threating pathogens. We report the identification of antimicrobial activities, against a broad range of bacterial pathogens, from a collection of marine-derived spore-forming bacteria. Although marine environments have been previously investigated as sources of novel antibiotics, studies on such environments are still limited and there remain opportunities for further discoveries and this study has used resources derived from an under-exploited region, the Vietnam Sea. Antimicrobial activity was assessed against a panel of Gram-positive and Gram-negative bacteria, including several multi-drug resistant pathogens. From a total of 489 isolates, 16.4% had antimicrobial activity. Of 23 shortlisted isolates with the greatest antimicrobial activity, 22 were Bacillus spp. isolates and one was a Paenibacillus polymyxa isolate. Most of the antimicrobial compounds were sensitive to proteases, indicating that they were proteins rather than secondary metabolites. The study demonstrated that marine bacteria derived from the Vietnam Sea represent a rich resource, producing antimicrobial compounds with activity against a broad range of clinically relevant bacterial pathogens, including important antibiotic resistant pathogens. Several isolates were identified that have particularly broad range activities and produce antimicrobial compounds that may have value for future drug development.
format: application/pdf
format: text/html
creator: Khanh Minh Chau
creator: Dong Van Quyen
creator: Joshua M. Fraser
creator: Andrew T. Smith
creator: Thi Thu Hao Van
creator: Robert J. Moore
subject: Biotechnology
subject: Microbiology
subject: Drugs and Devices
description: doi:10.7717/peerj.10117
publisher: PeerJ Inc.
rights: © 2020 Chau et al.
abstract: The widespread occurrence of pathogenic bacteria resistant to last-line antibiotics has resulted in significant challenges in human and veterinary medicine. There is an urgent need for new antimicrobial agents that can be used to control these life threating pathogens. We report the identification of antimicrobial activities, against a broad range of bacterial pathogens, from a collection of marine-derived spore-forming bacteria. Although marine environments have been previously investigated as sources of novel antibiotics, studies on such environments are still limited and there remain opportunities for further discoveries and this study has used resources derived from an under-exploited region, the Vietnam Sea. Antimicrobial activity was assessed against a panel of Gram-positive and Gram-negative bacteria, including several multi-drug resistant pathogens. From a total of 489 isolates, 16.4% had antimicrobial activity. Of 23 shortlisted isolates with the greatest antimicrobial activity, 22 were Bacillus spp. isolates and one was a Paenibacillus polymyxa isolate. Most of the antimicrobial compounds were sensitive to proteases, indicating that they were proteins rather than secondary metabolites. The study demonstrated that marine bacteria derived from the Vietnam Sea represent a rich resource, producing antimicrobial compounds with activity against a broad range of clinically relevant bacterial pathogens, including important antibiotic resistant pathogens. Several isolates were identified that have particularly broad range activities and produce antimicrobial compounds that may have value for future drug development.
bibliographic citation: Chau et al. (2020) Broad spectrum antimicrobial activities from spore-forming bacteria isolated from the Vietnam Sea. PeerJ 8:e10117 https://doi.org/10.7717/peerj.10117
date submitted: 2020-07-24
date accepted: 2020-09-16
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chau
  given name: Khanh Minh
author list: Agent
  family name: Van Quyen
  given name: Dong
author list: Agent
  family name: Fraser
  given name: Joshua M.
author list: Agent
  family name: Smith
  given name: Andrew T.
author list: Agent
  family name: Van
  given name: Thi Thu Hao
author list: Agent
  family name: Moore
  given name: Robert J.
doi: 10.7717/peerj.10117
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: ©2020 Chau et al.
attribution name: Chau et al.

High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae
type: item
type: AcademicArticle
description: Background Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge. Results We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics. Conclusions Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
format: application/pdf
format: text/html
creator: Vincent J. Fasanello
creator: Ping Liu
creator: Carlos A. Botero
creator: Justin C. Fay
subject: Evolutionary Studies
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.10118
publisher: PeerJ Inc.
rights: © 2020 Fasanello et al.
abstract: Background Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge. Results We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics. Conclusions Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
bibliographic citation: Fasanello et al. (2020) High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae. PeerJ 8:e10118 https://doi.org/10.7717/peerj.10118
date submitted: 2020-07-20
date accepted: 2020-09-16
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fasanello
  given name: Vincent J.
author list: Agent
  family name: Liu
  given name: Ping
author list: Agent
  family name: Botero
  given name: Carlos A.
author list: Agent
  family name: Fay
  given name: Justin C.
doi: 10.7717/peerj.10118
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: ©2020 Fasanello et al.
attribution name: Fasanello et al.

Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study
type: item
type: AcademicArticle
description: Background The COVID-19 pandemic is found to affect the mental health of the population. Undergraduate medical students are especially prone to mental health disorders and hence could be more vulnerable to the impact of the pandemic. Methods A prospective longitudinal study was conducted on 217 undergraduate medical students in a medical college at Chennai, India. Depression, anxiety, and stress levels were recorded using Depression Anxiety Stress Scale 21 Items (DASS21) before and during the COVID-19 outbreak in India in December 2019 and June 2020, respectively. In the follow-up survey, in addition to DASS21, the Pittsburgh Sleep Quality Index to assess sleep quality and a self-administered questionnaire to assess the impact of COVID-19 related stressors were used. The self-administered questionnaire assessed the status of COVID-19 testing, interactions with COVID-19 patients, self-perceived levels of concerns and worries related to academics (COVID-19-AA (academic apprehensions)) and those pertaining to the self and family/friends (COVID-19-GA (general apprehensions)). Cross-sectional and longitudinal comparison of overall scores of depression, anxiety, and stress and scores stratified by gender, year of study, place of residence and monthly family income were performed. Predictors for depression, anxiety, and stress during COVID-19 were investigated using adjusted binary logistic regression analysis and results were expressed as adjusted odds ratio with 95% confidence interval (CI). A P value < 0.05 was considered statistically significant. Results The average scores of depression, anxiety, and stress during the baseline survey were 7.55 ± 7.86, 4.6 ± 6.19 and 7.31 ± 7.34 with the prevalence (95% Cl) of 33.2% [27–39.9%], 21.2% [16–27.2%] and 20.7% [15.5–26.7%]; in follow-up survey, the mean scores were 8.16 ± 8.9, 6.11 ± 7.13 and 9.31 ± 8.18 with the prevalence being 35.5% [29.1–42.2%], 33.2% [27–39.9%] and 24.9% [19.3–31.2%] for depression, anxiety, and stress …
format: application/pdf
format: text/html
creator: Ilango Saraswathi
creator: Jayakumar Saikarthik
creator: K. Senthil Kumar
creator: Kumar Madhan Srinivasan
creator: M. Ardhanaari
creator: Raghunath Gunapriya
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.10164
publisher: PeerJ Inc.
rights: © 2020 Saraswathi et al.
abstract: Background The COVID-19 pandemic is found to affect the mental health of the population. Undergraduate medical students are especially prone to mental health disorders and hence could be more vulnerable to the impact of the pandemic. Methods A prospective longitudinal study was conducted on 217 undergraduate medical students in a medical college at Chennai, India. Depression, anxiety, and stress levels were recorded using Depression Anxiety Stress Scale 21 Items (DASS21) before and during the COVID-19 outbreak in India in December 2019 and June 2020, respectively. In the follow-up survey, in addition to DASS21, the Pittsburgh Sleep Quality Index to assess sleep quality and a self-administered questionnaire to assess the impact of COVID-19 related stressors were used. The self-administered questionnaire assessed the status of COVID-19 testing, interactions with COVID-19 patients, self-perceived levels of concerns and worries related to academics (COVID-19-AA (academic apprehensions)) and those pertaining to the self and family/friends (COVID-19-GA (general apprehensions)). Cross-sectional and longitudinal comparison of overall scores of depression, anxiety, and stress and scores stratified by gender, year of study, place of residence and monthly family income were performed. Predictors for depression, anxiety, and stress during COVID-19 were investigated using adjusted binary logistic regression analysis and results were expressed as adjusted odds ratio with 95% confidence interval (CI). A P value < 0.05 was considered statistically significant. Results The average scores of depression, anxiety, and stress during the baseline survey were 7.55 ± 7.86, 4.6 ± 6.19 and 7.31 ± 7.34 with the prevalence (95% Cl) of 33.2% [27–39.9%], 21.2% [16–27.2%] and 20.7% [15.5–26.7%]; in follow-up survey, the mean scores were 8.16 ± 8.9, 6.11 ± 7.13 and 9.31 ± 8.18 with the prevalence being 35.5% [29.1–42.2%], 33.2% [27–39.9%] and 24.9% [19.3–31.2%] for depression, anxiety, and stress …
bibliographic citation: Saraswathi et al. (2020) Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study. PeerJ 8:e10164 https://doi.org/10.7717/peerj.10164
date submitted: 2020-08-05
date accepted: 2020-09-22
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saraswathi
  given name: Ilango
author list: Agent
  family name: Saikarthik
  given name: Jayakumar
author list: Agent
  family name: Senthil Kumar
  given name: K.
author list: Agent
  family name: Madhan Srinivasan
  given name: Kumar
author list: Agent
  family name: Ardhanaari
  given name: M.
author list: Agent
  family name: Gunapriya
  given name: Raghunath
doi: 10.7717/peerj.10164
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: © 2020 Saraswathi et al.
attribution name: Saraswathi et al.

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