PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Taurine stimulation of planarian motility: a role for the dopamine receptor pathway
items: Motor competence of children in Singapore using Movement ABC-2 test
items: Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task
items: PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites
items: CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms
items: Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens
items: A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution
items: Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods
items: Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus)
items: DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli

Taurine stimulation of planarian motility: a role for the dopamine receptor pathway
type: item
type: AcademicArticle
description: Taurine, a normal dietary component that is found in many tissues, is considered important for a number of physiological processes. It is thought to play a particular role in eye development and in the maturation of both the muscular and nervous systems, leading to its suggested use as a therapeutic for Alzheimer’s and Parkinson’s diseases. Taurine increases metabolism and has also been touted as a weight loss aid. Due to its possible benefits to health and development, taurine is added as a supplement to a wide array of products, including infant formula and energy drinks. Despite its pervasive use as a nutritional additive and implied physiological actions, there is little consensus on how taurine functions. This is likely because, mechanistically, taurine has been demonstrated to affect multiple metabolic pathways. Simple models and straightforward assay systems are required to make headway in understanding this complexity. We chose to begin this work using the planarian because these animals have basic, well-understood muscular and nervous systems and are the subjects of many well-tested assays examining how their physiology is influenced by exposure to various environmental, nutritional, and therapeutic agents. We used a simple behavioral assay, the planarian locomotor velocity test (pLmV), to gain insight into the stimulant properties of taurine. Using this assay, we observed that taurine is a mild stimulant that is not affected by sugars or subject to withdrawal. We also provide evidence that taurine makes use of the dopamine D1 receptor to mediate this stimulant effect. Given the pervasiveness of taurine in many commercial products, our findings using the planarian system provide needed insight into the stimulant properties of taurine that should be considered when adding it to the diet.
format: application/pdf
format: text/html
creator: Elisa J. Livengood
creator: Robyn A. M. V. Fong
creator: Angela M. Pratt
creator: Veronika O. Alinskas
creator: Grace Van Gorder
creator: Michael Mezzio
creator: Margaret E. Mulligan
creator: Evelyn B. Voura
subject: Animal Behavior
subject: Biochemistry
subject: Zoology
description: doi:10.7717/peerj.18671
publisher: PeerJ Inc.
rights: © 2024 Livengood et al.
abstract: Taurine, a normal dietary component that is found in many tissues, is considered important for a number of physiological processes. It is thought to play a particular role in eye development and in the maturation of both the muscular and nervous systems, leading to its suggested use as a therapeutic for Alzheimer’s and Parkinson’s diseases. Taurine increases metabolism and has also been touted as a weight loss aid. Due to its possible benefits to health and development, taurine is added as a supplement to a wide array of products, including infant formula and energy drinks. Despite its pervasive use as a nutritional additive and implied physiological actions, there is little consensus on how taurine functions. This is likely because, mechanistically, taurine has been demonstrated to affect multiple metabolic pathways. Simple models and straightforward assay systems are required to make headway in understanding this complexity. We chose to begin this work using the planarian because these animals have basic, well-understood muscular and nervous systems and are the subjects of many well-tested assays examining how their physiology is influenced by exposure to various environmental, nutritional, and therapeutic agents. We used a simple behavioral assay, the planarian locomotor velocity test (pLmV), to gain insight into the stimulant properties of taurine. Using this assay, we observed that taurine is a mild stimulant that is not affected by sugars or subject to withdrawal. We also provide evidence that taurine makes use of the dopamine D1 receptor to mediate this stimulant effect. Given the pervasiveness of taurine in many commercial products, our findings using the planarian system provide needed insight into the stimulant properties of taurine that should be considered when adding it to the diet.
bibliographic citation: Livengood et al. (2024) Taurine stimulation of planarian motility: a role for the dopamine receptor pathway. PeerJ 12:e18671 https://doi.org/10.7717/peerj.18671
date submitted: 2024-08-22
date accepted: 2024-11-19
issued: 2024-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Livengood
  given name: Elisa J.
author list: Agent
  family name: Fong
  given name: Robyn A. M. V.
author list: Agent
  family name: Pratt
  given name: Angela M.
author list: Agent
  family name: Alinskas
  given name: Veronika O.
author list: Agent
  family name: Van Gorder
  given name: Grace
author list: Agent
  family name: Mezzio
  given name: Michael
author list: Agent
  family name: Mulligan
  given name: Margaret E.
author list: Agent
  family name: Voura
  given name: Evelyn B.
doi: 10.7717/peerj.18671
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-06
copyright: © 2024 Livengood et al.
attribution name: Livengood et al.

Motor competence of children in Singapore using Movement ABC-2 test
type: item
type: AcademicArticle
description: Introduction The Movement Assessment Battery for Children, 2nd Edition (MABC-2) test is a valuable tool for identifying motor delays in children globally. However, there has been a lack of data for children in Singapore. Methods This study compared 175 children in Singapore (SG) aged 3–6 years to MABC-2 data based on the United Kingdom (UK) population, using statistical tests to analyze age, country, and gender effects on motor competence. Results The results showed a positive age effect across all tasks, with SG children excelling in balance but lagging in aiming and catching tasks compared to UK children. The interaction between age and country yielded mixed results, favoring different groups at various ages. Additionally, girls displayed better manual dexterity and static balance than boys. Conclusion Encouraging more physical activities, especially those involving object manipulation, is crucial for SG children. Establishing local norms for the MABC-2 in Singapore and considering country-specific factors in motor competence evaluations can enhance early intervention strategies. These findings emphasize the importance of tailored approaches to address motor skill development in SG children.
format: application/pdf
format: text/html
creator: Jernice S.Y. Tan
creator: Michael Chia
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.18446
publisher: PeerJ Inc.
rights: © 2024 Tan and Chia
abstract: Introduction The Movement Assessment Battery for Children, 2nd Edition (MABC-2) test is a valuable tool for identifying motor delays in children globally. However, there has been a lack of data for children in Singapore. Methods This study compared 175 children in Singapore (SG) aged 3–6 years to MABC-2 data based on the United Kingdom (UK) population, using statistical tests to analyze age, country, and gender effects on motor competence. Results The results showed a positive age effect across all tasks, with SG children excelling in balance but lagging in aiming and catching tasks compared to UK children. The interaction between age and country yielded mixed results, favoring different groups at various ages. Additionally, girls displayed better manual dexterity and static balance than boys. Conclusion Encouraging more physical activities, especially those involving object manipulation, is crucial for SG children. Establishing local norms for the MABC-2 in Singapore and considering country-specific factors in motor competence evaluations can enhance early intervention strategies. These findings emphasize the importance of tailored approaches to address motor skill development in SG children.
bibliographic citation: Tan et al. (2024) Motor competence of children in Singapore using Movement ABC-2 test. PeerJ 12:e18446 https://doi.org/10.7717/peerj.18446
date submitted: 2024-06-17
date accepted: 2024-10-11
issued: 2024-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Jernice S.Y.
author list: Agent
  family name: Chia
  given name: Michael
doi: 10.7717/peerj.18446
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-05
copyright: ©2024 Tan and Chia
attribution name: Tan and Chia

Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task
type: item
type: AcademicArticle
description: Many of the complex behaviours of humans involve the production of nonadjacent dependencies between sequence elements, which in part can be generated through the hierarchical organization of sequences. To understand how these structural properties of human behaviours evolved, we can gain valuable insight from studying the sequential behaviours of nonhuman animals. Among the behaviours of nonhuman apes, tool use has been hypothesised to be a domain of behaviour which likely involves hierarchical organization, and may therefore possess nonadjacent dependencies between sequential actions. However thus far, evidence supporting hierarchical organization of great-ape tool use comes from methodologies which have been criticised in their objectivity. Additionally, the extent to which nonadjacent dependencies appear in primate action sequences during tool use has not been formally investigated. We used estimations of mutual information (MI)—a measure of dependency strength between sequence elements—to evaluate both the extent to which wild chimpanzees produce nonadjacent dependencies during a naturalistic tool-use task (nut cracking), as well as how sequences of actions are likely organized during tool use. Half of adult chimpanzees produced nonadjacent dependencies at significantly greater sequential distances than comparable, nonhierarchical Markov models once repeated actions had been accounted for. Additionally, for the majority of chimpanzees, MI decay with increasing sequential distance included a power-law relationship, which is a key indicator that the action sequences produced by chimpanzees likely entail some degree of hierarchical organization. Our analysis offered the greatest support for a system of organization where short subroutines of actions (2–8 actions long) are hierarchically arranged into longer sequences—a finding which is consistent with previous qualitative descriptions of ape tool-use behaviours. Interindividual variability was detected within our a…
format: application/pdf
format: text/html
creator: Elliot Howard-Spink
creator: Misato Hayashi
creator: Tetsuro Matsuzawa
creator: Daniel Schofield
creator: Thibaud Gruber
creator: Dora Biro
subject: Animal Behavior
subject: Anthropology
subject: Computational Biology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.18484
publisher: PeerJ Inc.
rights: © 2024 Howard-Spink et al.
abstract: Many of the complex behaviours of humans involve the production of nonadjacent dependencies between sequence elements, which in part can be generated through the hierarchical organization of sequences. To understand how these structural properties of human behaviours evolved, we can gain valuable insight from studying the sequential behaviours of nonhuman animals. Among the behaviours of nonhuman apes, tool use has been hypothesised to be a domain of behaviour which likely involves hierarchical organization, and may therefore possess nonadjacent dependencies between sequential actions. However thus far, evidence supporting hierarchical organization of great-ape tool use comes from methodologies which have been criticised in their objectivity. Additionally, the extent to which nonadjacent dependencies appear in primate action sequences during tool use has not been formally investigated. We used estimations of mutual information (MI)—a measure of dependency strength between sequence elements—to evaluate both the extent to which wild chimpanzees produce nonadjacent dependencies during a naturalistic tool-use task (nut cracking), as well as how sequences of actions are likely organized during tool use. Half of adult chimpanzees produced nonadjacent dependencies at significantly greater sequential distances than comparable, nonhierarchical Markov models once repeated actions had been accounted for. Additionally, for the majority of chimpanzees, MI decay with increasing sequential distance included a power-law relationship, which is a key indicator that the action sequences produced by chimpanzees likely entail some degree of hierarchical organization. Our analysis offered the greatest support for a system of organization where short subroutines of actions (2–8 actions long) are hierarchically arranged into longer sequences—a finding which is consistent with previous qualitative descriptions of ape tool-use behaviours. Interindividual variability was detected within our a…
bibliographic citation: Howard-Spink et al. (2024) Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task. PeerJ 12:e18484 https://doi.org/10.7717/peerj.18484
date submitted: 2024-05-16
date accepted: 2024-10-16
issued: 2024-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Howard-Spink
  given name: Elliot
author list: Agent
  family name: Hayashi
  given name: Misato
author list: Agent
  family name: Matsuzawa
  given name: Tetsuro
author list: Agent
  family name: Schofield
  given name: Daniel
author list: Agent
  family name: Gruber
  given name: Thibaud
author list: Agent
  family name: Biro
  given name: Dora
doi: 10.7717/peerj.18484
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-05
copyright: © 2024 Howard-Spink et al.
attribution name: Howard-Spink et al.

PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites
type: item
type: AcademicArticle
description: In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.
format: application/pdf
format: text/html
creator: Wayne P. Maddison
subject: Biodiversity
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.18504
publisher: PeerJ Inc.
rights: © 2024 Maddison
abstract: In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.
bibliographic citation: Maddison (2024) PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites. PeerJ 12:e18504 https://doi.org/10.7717/peerj.18504
date submitted: 2024-07-22
date accepted: 2024-10-18
issued: 2024-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maddison
  given name: Wayne P.
doi: 10.7717/peerj.18504
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-05
copyright: ©2024 Maddison
attribution name: Maddison

CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms
type: item
type: AcademicArticle
description: CYP3A, a key member of the cytochrome P450 (CYP450) superfamily, is integral to drug metabolism, processing a substantial portion of medications. Their role in drug metabolism is particularly prominent, as CYP3A4 and CYP3A5 metabolize approximately 30–50% of known drugs. The genetic polymorphism of CYP3A4/5 is significant inter-individual variability in enzymatic activity, which can result in different pharmacokinetic profiles in response to the same drug among individuals. These polymorphisms can lead to either increased drug toxicity or reduced therapeutic effects, requiring dosage adjustments based on genetic profiles. Consequently, the study of the enzymatic activity of CYP3A4/5 gene variants is of great importance for the formulation of personalized treatment regimens. This article first reviews the role of CYP3A4/5 in drug metabolism in the human body, including inhibitors and inducers of CYP3A4/5 and drug-drug interactions. In terms of genetic polymorphism, it discusses the detection methods, enzymatic kinetic characteristics, and clinical guidelines for CYP3A5. Finally, the article summarizes the importance of CYP3A4/5 in clinical applications, including personalized therapy, management of drug-drug interactions, and adjustment of drug doses. This review contributes to the understanding of the functions and genetic characteristics of CYP3A4/5, allowing for more effective clinical outcomes through optimized drug therapy.
format: application/pdf
format: text/html
creator: Yuqing Zhang
creator: Ziying Wang
creator: Yuchao Wang
creator: Weikai Jin
creator: Zheyan Zhang
creator: Lehao Jin
creator: Jianchang Qian
creator: Long Zheng
subject: Cell Biology
subject: Genetics
subject: Pharmacology
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.18636
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: CYP3A, a key member of the cytochrome P450 (CYP450) superfamily, is integral to drug metabolism, processing a substantial portion of medications. Their role in drug metabolism is particularly prominent, as CYP3A4 and CYP3A5 metabolize approximately 30–50% of known drugs. The genetic polymorphism of CYP3A4/5 is significant inter-individual variability in enzymatic activity, which can result in different pharmacokinetic profiles in response to the same drug among individuals. These polymorphisms can lead to either increased drug toxicity or reduced therapeutic effects, requiring dosage adjustments based on genetic profiles. Consequently, the study of the enzymatic activity of CYP3A4/5 gene variants is of great importance for the formulation of personalized treatment regimens. This article first reviews the role of CYP3A4/5 in drug metabolism in the human body, including inhibitors and inducers of CYP3A4/5 and drug-drug interactions. In terms of genetic polymorphism, it discusses the detection methods, enzymatic kinetic characteristics, and clinical guidelines for CYP3A5. Finally, the article summarizes the importance of CYP3A4/5 in clinical applications, including personalized therapy, management of drug-drug interactions, and adjustment of drug doses. This review contributes to the understanding of the functions and genetic characteristics of CYP3A4/5, allowing for more effective clinical outcomes through optimized drug therapy.
bibliographic citation: Zhang et al. (2024) CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms. PeerJ 12:e18636 https://doi.org/10.7717/peerj.18636
date submitted: 2024-08-08
date accepted: 2024-11-12
issued: 2024-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yuqing
author list: Agent
  family name: Wang
  given name: Ziying
author list: Agent
  family name: Wang
  given name: Yuchao
author list: Agent
  family name: Jin
  given name: Weikai
author list: Agent
  family name: Zhang
  given name: Zheyan
author list: Agent
  family name: Jin
  given name: Lehao
author list: Agent
  family name: Qian
  given name: Jianchang
author list: Agent
  family name: Zheng
  given name: Long
doi: 10.7717/peerj.18636
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-05
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens
type: item
type: AcademicArticle
description: Biochar, a carbon-rich material that has attracted considerable interest in interdisciplinary research, is produced through a process known as pyrolysis, which involves the thermal decomposition of organic material in the absence of oxygen. Bamboo biochar is a specific type of biochar, manufactured from bamboo straw through carbonisation at 800 °C and subsequent filtration through a 100-mesh sieve. There is currently a lack of research into the potential benefits of bamboo biochar in improving soil quality in tea gardens. The aim of this study was to investigate the effect of bamboo biochar on the physicochemical properties, enzymatic activity, and microbial community structure of tea garden soils. The results demonstrate that the integration of bamboo biochar into the soil significantly enhanced the soil pH, total nitrogen, available nitrogen, total phosphorus, available phosphorus, available potassium, and slowly available potassium by 15.3%, 52.0%, 91.5%, 91%, 48.4%, 94.2%, and 107.7%, respectively. In addition, soil acid phosphatase activity decreased significantly by 52.5%. In contrast, the activities of sucrase, catalase, and β-glucosidase increased substantially by 54.0%, 68.7%, and 68.4%, respectively, when organic fertilizer and bamboo biochar were applied concurrently. Additionally, the Shannon, Simpson, and Pielou diversity indices of the microbial communities were significantly enhanced. Following the incorporation of bamboo biochar in the soil samples, the relative abundance of Proteobacteria increased significantly, whereas that of Acidobacteria decreased. Various concentrations of bamboo biochar markedly influenced microbial markers in the soil. The results of this study suggest that the application of bamboo biochar to soil may modestly improve its physicochemical properties, enzyme activity, and microbial community structure. These findings provide a foundation for future investigations on soil ecological restoration.
format: application/pdf
format: text/html
creator: Si-Hai Zhang
creator: Yi Shen
creator: Le-Feng Lin
creator: Su-Lei Tang
creator: Chun-Xiao Liu
creator: Xiang-Hua Fang
creator: Zhi-Ping Guo
creator: Ying-Ying Wang
creator: Yang-Chun Zhu
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.18642
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Biochar, a carbon-rich material that has attracted considerable interest in interdisciplinary research, is produced through a process known as pyrolysis, which involves the thermal decomposition of organic material in the absence of oxygen. Bamboo biochar is a specific type of biochar, manufactured from bamboo straw through carbonisation at 800 °C and subsequent filtration through a 100-mesh sieve. There is currently a lack of research into the potential benefits of bamboo biochar in improving soil quality in tea gardens. The aim of this study was to investigate the effect of bamboo biochar on the physicochemical properties, enzymatic activity, and microbial community structure of tea garden soils. The results demonstrate that the integration of bamboo biochar into the soil significantly enhanced the soil pH, total nitrogen, available nitrogen, total phosphorus, available phosphorus, available potassium, and slowly available potassium by 15.3%, 52.0%, 91.5%, 91%, 48.4%, 94.2%, and 107.7%, respectively. In addition, soil acid phosphatase activity decreased significantly by 52.5%. In contrast, the activities of sucrase, catalase, and β-glucosidase increased substantially by 54.0%, 68.7%, and 68.4%, respectively, when organic fertilizer and bamboo biochar were applied concurrently. Additionally, the Shannon, Simpson, and Pielou diversity indices of the microbial communities were significantly enhanced. Following the incorporation of bamboo biochar in the soil samples, the relative abundance of Proteobacteria increased significantly, whereas that of Acidobacteria decreased. Various concentrations of bamboo biochar markedly influenced microbial markers in the soil. The results of this study suggest that the application of bamboo biochar to soil may modestly improve its physicochemical properties, enzyme activity, and microbial community structure. These findings provide a foundation for future investigations on soil ecological restoration.
bibliographic citation: Zhang et al. (2024) Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens. PeerJ 12:e18642 https://doi.org/10.7717/peerj.18642
date submitted: 2024-07-18
date accepted: 2024-11-13
issued: 2024-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Si-Hai
author list: Agent
  family name: Shen
  given name: Yi
author list: Agent
  family name: Lin
  given name: Le-Feng
author list: Agent
  family name: Tang
  given name: Su-Lei
author list: Agent
  family name: Liu
  given name: Chun-Xiao
author list: Agent
  family name: Fang
  given name: Xiang-Hua
author list: Agent
  family name: Guo
  given name: Zhi-Ping
author list: Agent
  family name: Wang
  given name: Ying-Ying
author list: Agent
  family name: Zhu
  given name: Yang-Chun
doi: 10.7717/peerj.18642
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-05
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution
type: item
type: AcademicArticle
description: Processing large collections of earth observation (EO) time-series, often petabyte-sized, such as NASA’s Landsat and ESA’s Sentinel missions, can be computationally prohibitive and costly. Despite their name, even the Analysis Ready Data (ARD) versions of such collections can rarely be used as direct input for modeling because of cloud presence and/or prohibitive storage size. Existing solutions for readily using these data are not openly available, are poor in performance, or lack flexibility. Addressing this issue, we developed TSIRF (Time-Series Iteration-free Reconstruction Framework), a computational framework that can be used to apply diverse time-series processing tasks, such as temporal aggregation and time-series reconstruction by simply adjusting the convolution kernel. As the first large-scale application, TSIRF was employed to process the entire Global Land Analysis and Discovery (GLAD) ARD Landsat archive, producing a cloud-free bi-monthly aggregated product. This process, covering seven Landsat bands globally from 1997 to 2022, with more than two trillion pixels and for each one a time-series of 156 samples in the aggregated product, required approximately 28 hours of computation using 1248 Intel® Xeon® Gold 6248R CPUs. The quality of the result was assessed using a benchmark dataset derived from the aggregated product and comparing different imputation strategies. The resulting reconstructed images can be used as input for machine learning models or to map biophysical indices. To further limit the storage size the produced data was saved as 8-bit Cloud-Optimized GeoTIFFs (COG). With the hosting of about 20 TB per band/index for an entire 30 m resolution bi-monthly historical time-series distributed as open data, the product enables seamless, fast, and affordable access to the Landsat archive for environmental monitoring and analysis applications.
format: application/pdf
format: text/html
creator: Davide Consoli
creator: Leandro Parente
creator: Rolf Simoes
creator: Murat Şahin
creator: Xuemeng Tian
creator: Martijn Witjes
creator: Lindsey Sloat
creator: Tomislav Hengl
subject: Environmental Sciences
subject: Computational Science
subject: Data Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.18585
publisher: PeerJ Inc.
rights: © 2024 Consoli et al.
abstract: Processing large collections of earth observation (EO) time-series, often petabyte-sized, such as NASA’s Landsat and ESA’s Sentinel missions, can be computationally prohibitive and costly. Despite their name, even the Analysis Ready Data (ARD) versions of such collections can rarely be used as direct input for modeling because of cloud presence and/or prohibitive storage size. Existing solutions for readily using these data are not openly available, are poor in performance, or lack flexibility. Addressing this issue, we developed TSIRF (Time-Series Iteration-free Reconstruction Framework), a computational framework that can be used to apply diverse time-series processing tasks, such as temporal aggregation and time-series reconstruction by simply adjusting the convolution kernel. As the first large-scale application, TSIRF was employed to process the entire Global Land Analysis and Discovery (GLAD) ARD Landsat archive, producing a cloud-free bi-monthly aggregated product. This process, covering seven Landsat bands globally from 1997 to 2022, with more than two trillion pixels and for each one a time-series of 156 samples in the aggregated product, required approximately 28 hours of computation using 1248 Intel® Xeon® Gold 6248R CPUs. The quality of the result was assessed using a benchmark dataset derived from the aggregated product and comparing different imputation strategies. The resulting reconstructed images can be used as input for machine learning models or to map biophysical indices. To further limit the storage size the produced data was saved as 8-bit Cloud-Optimized GeoTIFFs (COG). With the hosting of about 20 TB per band/index for an entire 30 m resolution bi-monthly historical time-series distributed as open data, the product enables seamless, fast, and affordable access to the Landsat archive for environmental monitoring and analysis applications.
bibliographic citation: Consoli et al. (2024) A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution. PeerJ 12:e18585 https://doi.org/10.7717/peerj.18585
date submitted: 2024-05-22
date accepted: 2024-11-04
issued: 2024-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Consoli
  given name: Davide
author list: Agent
  family name: Parente
  given name: Leandro
author list: Agent
  family name: Simoes
  given name: Rolf
author list: Agent
  family name: Şahin
  given name: Murat
author list: Agent
  family name: Tian
  given name: Xuemeng
author list: Agent
  family name: Witjes
  given name: Martijn
author list: Agent
  family name: Sloat
  given name: Lindsey
author list: Agent
  family name: Hengl
  given name: Tomislav
doi: 10.7717/peerj.18585
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-04
copyright: © 2024 Consoli et al.
attribution name: Consoli et al.

Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods
type: item
type: AcademicArticle
description: Background Acute myocardial infarction (AMI) is one of the most serious cardiovascular diseases. Apoptosis is a type of programmed cell death that causes DNA degradation and chromatin condensation. The role of apoptosis in AMI progression remains unclear. Methods Three AMI-related microarray datasets (GSE48060, GSE66360 and GSE97320) were obtained from the Gene Expression Omnibus database and combined for further analysis. Differential expression analysis and enrichment analysis were performed on the combined dataset to identify differentially expressed genes (DEGs). Apoptosis-related genes (ARGs) were screened through the intersection of genes associated with apoptosis in previous studies and DEGs. The expression pattern of ARGs was studied on the basis of their raw expression data. Three machine learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and Random Forest (RF) were utilized to screen crucial genes in these ARGs. Immune infiltration was estimated by single sample gene set enrichment analysis (ssGSEA). Corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of crucial genes. A nomogram clinical prediction model of the crucial genes was constructed and evaluated. The Mendelian randomization analysis was employed to investigate whether there is a causal relationship between apoptosis and AMI. Finally, an AMI mouse model was established, and apoptosis in the hearts of AMI mice was assessed via TUNEL staining. qRT-PCR was employed to validate these crucial genes in the hearts of AMI mice. The external dataset GSE59867 was used for further validating the crucial genes. Results Fifteen ARGs (GADD45A, DDIT3, FEZ1, PMAIP1, IER3, IFNGR1, CDKN1A, GNA15, IL1B, EREG, BCL10, JUN, EGR3, GADD45B, and CD14) were identified. Six crucial genes (CDKN1A, BCL10, PMAIP1, IL1B, GNA15, and CD14) were screened from ARGs by machine learning…
format: application/pdf
format: text/html
creator: Haoyan Zhu
creator: Mengyao Li
creator: Jiahe Wu
creator: Liqiu Yan
creator: Wei Xiong
creator: Xiaorong Hu
creator: Zhibing Lu
creator: Chenze Li
creator: Huanhuan Cai
subject: Bioinformatics
subject: Cardiology
description: doi:10.7717/peerj.18591
publisher: PeerJ Inc.
rights: © 2024 Zhu et al.
abstract: Background Acute myocardial infarction (AMI) is one of the most serious cardiovascular diseases. Apoptosis is a type of programmed cell death that causes DNA degradation and chromatin condensation. The role of apoptosis in AMI progression remains unclear. Methods Three AMI-related microarray datasets (GSE48060, GSE66360 and GSE97320) were obtained from the Gene Expression Omnibus database and combined for further analysis. Differential expression analysis and enrichment analysis were performed on the combined dataset to identify differentially expressed genes (DEGs). Apoptosis-related genes (ARGs) were screened through the intersection of genes associated with apoptosis in previous studies and DEGs. The expression pattern of ARGs was studied on the basis of their raw expression data. Three machine learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and Random Forest (RF) were utilized to screen crucial genes in these ARGs. Immune infiltration was estimated by single sample gene set enrichment analysis (ssGSEA). Corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of crucial genes. A nomogram clinical prediction model of the crucial genes was constructed and evaluated. The Mendelian randomization analysis was employed to investigate whether there is a causal relationship between apoptosis and AMI. Finally, an AMI mouse model was established, and apoptosis in the hearts of AMI mice was assessed via TUNEL staining. qRT-PCR was employed to validate these crucial genes in the hearts of AMI mice. The external dataset GSE59867 was used for further validating the crucial genes. Results Fifteen ARGs (GADD45A, DDIT3, FEZ1, PMAIP1, IER3, IFNGR1, CDKN1A, GNA15, IL1B, EREG, BCL10, JUN, EGR3, GADD45B, and CD14) were identified. Six crucial genes (CDKN1A, BCL10, PMAIP1, IL1B, GNA15, and CD14) were screened from ARGs by machine learning…
bibliographic citation: Zhu et al. (2024) Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods. PeerJ 12:e18591 https://doi.org/10.7717/peerj.18591
date submitted: 2024-05-16
date accepted: 2024-11-05
issued: 2024-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Haoyan
author list: Agent
  family name: Li
  given name: Mengyao
author list: Agent
  family name: Wu
  given name: Jiahe
author list: Agent
  family name: Yan
  given name: Liqiu
author list: Agent
  family name: Xiong
  given name: Wei
author list: Agent
  family name: Hu
  given name: Xiaorong
author list: Agent
  family name: Lu
  given name: Zhibing
author list: Agent
  family name: Li
  given name: Chenze
author list: Agent
  family name: Cai
  given name: Huanhuan
doi: 10.7717/peerj.18591
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-04
copyright: © 2024 Zhu et al.
attribution name: Zhu et al.

Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus)
type: item
type: AcademicArticle
description: Management of wildlife populations is most effective with a thorough understanding of the interplay among vital rates, population growth, and density-dependent feedback; however, measuring all relevant vital rates and assessing density-dependence can prove challenging. Integrated population models have been proposed as a method to address these issues, as they allow for direct modeling of density-dependent pathways and inference on parameters without direct data. We developed integrated population models from a 25-year demography dataset of Northern Bobwhites (Colinus virginianus) from southern Georgia, USA, to assess the demographic drivers of population growth rates and to estimate the strength of multiple density-dependent processes simultaneously. Furthermore, we utilize a novel approach combining breeding productivity and post-breeding abundance and age-and-sex ratio data to infer juvenile survival. Population abundance was relatively stable for the first 14 years of the study but began growing after 2012, showing that bobwhite populations may be stable or exhibit positive population growth in areas of intensive management. Variation in breeding and non-breeding survival drove changes in population growth in a few years; however, population growth rates were most affected by productivity across the entire study duration. A similar pattern was observed for density-dependence, with relatively stronger negative effects of density on productivity than on survival. Our novel modeling approach required an informative prior but was successful at updating the prior distribution for juvenile survival. Our results show that integrated population models provide an attractive and flexible method for directly modeling all relevant density-dependent processes and for combining breeding and post-breeding data to estimate juvenile survival in the absence of direct data.
format: application/pdf
format: text/html
creator: William B. Lewis
creator: Chloé R. Nater
creator: Justin A. Rectenwald
creator: D. Clay Sisson
creator: James A. Martin
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.18625
publisher: PeerJ Inc.
rights: © 2024 Lewis et al.
abstract: Management of wildlife populations is most effective with a thorough understanding of the interplay among vital rates, population growth, and density-dependent feedback; however, measuring all relevant vital rates and assessing density-dependence can prove challenging. Integrated population models have been proposed as a method to address these issues, as they allow for direct modeling of density-dependent pathways and inference on parameters without direct data. We developed integrated population models from a 25-year demography dataset of Northern Bobwhites (Colinus virginianus) from southern Georgia, USA, to assess the demographic drivers of population growth rates and to estimate the strength of multiple density-dependent processes simultaneously. Furthermore, we utilize a novel approach combining breeding productivity and post-breeding abundance and age-and-sex ratio data to infer juvenile survival. Population abundance was relatively stable for the first 14 years of the study but began growing after 2012, showing that bobwhite populations may be stable or exhibit positive population growth in areas of intensive management. Variation in breeding and non-breeding survival drove changes in population growth in a few years; however, population growth rates were most affected by productivity across the entire study duration. A similar pattern was observed for density-dependence, with relatively stronger negative effects of density on productivity than on survival. Our novel modeling approach required an informative prior but was successful at updating the prior distribution for juvenile survival. Our results show that integrated population models provide an attractive and flexible method for directly modeling all relevant density-dependent processes and for combining breeding and post-breeding data to estimate juvenile survival in the absence of direct data.
bibliographic citation: Lewis et al. (2024) Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus). PeerJ 12:e18625 https://doi.org/10.7717/peerj.18625
date submitted: 2024-08-13
date accepted: 2024-11-11
issued: 2024-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lewis
  given name: William B.
author list: Agent
  family name: Nater
  given name: Chloé R.
author list: Agent
  family name: Rectenwald
  given name: Justin A.
author list: Agent
  family name: Sisson
  given name: D. Clay
author list: Agent
  family name: Martin
  given name: James A.
doi: 10.7717/peerj.18625
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-04
copyright: © 2024 Lewis et al.
attribution name: Lewis et al.

DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli
type: item
type: AcademicArticle
description: Surfactants are molecules derived primarily from petroleum that can reduce the surface tension at interfaces. Their slow degradation is a characteristic that could cause environmental issues. This and other factors contribute to the allure of biosurfactants today. Progress has been made in this area of research, which aims to satisfy the need for effective surfactants that are not harmful to the environment. In previous studies, we demonstrated the surface tension activity of the Escherichia coli transmembrane protein OmpA. Here, we carried out DNA shuffling on ompA to improve its interfacial activity. We evaluated changes in interfacial tension when exposing mutants to a water-oil interface to identify the most promising candidates. Two mutants reached an interfacial tension value lower (9.10 mN/m and 4.24 mN/m) than the original protein OmpA (14.98 mN/m). Since predicted isoelectric point values are far from neutral pH, the charge of the protein was a crucial factor in explaining the migration of proteins towards the interface. Low molecular weight mutants did not exhibit a significant difference in their migration to the interface.
format: application/pdf
format: text/html
creator: Vanessa Lucía Nuñez Velez
creator: Liseth Daniela Villamizar Gomez
creator: Jhon E. Mendoza Ospina
creator: Yasser Hayek-Orduz
creator: Miguel Fernandez-Niño
creator: Silvia Restrepo Restrepo
creator: Óscar Alberto Álvarez Solano
creator: Luis H. Reyes Barrios
creator: Andres F. Gonzalez Barrios
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.17239
publisher: PeerJ Inc.
rights: © 2024 Nuñez Velez et al.
abstract: Surfactants are molecules derived primarily from petroleum that can reduce the surface tension at interfaces. Their slow degradation is a characteristic that could cause environmental issues. This and other factors contribute to the allure of biosurfactants today. Progress has been made in this area of research, which aims to satisfy the need for effective surfactants that are not harmful to the environment. In previous studies, we demonstrated the surface tension activity of the Escherichia coli transmembrane protein OmpA. Here, we carried out DNA shuffling on ompA to improve its interfacial activity. We evaluated changes in interfacial tension when exposing mutants to a water-oil interface to identify the most promising candidates. Two mutants reached an interfacial tension value lower (9.10 mN/m and 4.24 mN/m) than the original protein OmpA (14.98 mN/m). Since predicted isoelectric point values are far from neutral pH, the charge of the protein was a crucial factor in explaining the migration of proteins towards the interface. Low molecular weight mutants did not exhibit a significant difference in their migration to the interface.
bibliographic citation: Nuñez Velez et al. (2024) DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli. PeerJ 12:e17239 https://doi.org/10.7717/peerj.17239
date submitted: 2023-09-11
date accepted: 2024-03-25
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nuñez Velez
  given name: Vanessa Lucía
author list: Agent
  family name: Villamizar Gomez
  given name: Liseth Daniela
author list: Agent
  family name: Mendoza Ospina
  given name: Jhon E.
author list: Agent
  family name: Hayek-Orduz
  given name: Yasser
author list: Agent
  family name: Fernandez-Niño
  given name: Miguel
author list: Agent
  family name: Restrepo Restrepo
  given name: Silvia
author list: Agent
  family name: Álvarez Solano
  given name: Óscar Alberto
author list: Agent
  family name: Reyes Barrios
  given name: Luis H.
author list: Agent
  family name: Gonzalez Barrios
  given name: Andres F.
doi: 10.7717/peerj.17239
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: ©2024 Nuñez Velez et al.
attribution name: Nuñez Velez et al.

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