PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Vkorc1 gene polymorphisms confer resistance to anticoagulant rodenticide in Turkish rats
items: Illuminating the druggable genome through patent bioactivity data
items: Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA
items: Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer
items: Can salivary lactate be used as an anaerobic biomarker?
items: Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs
items: Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile?
items: Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa
items: A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia
items: Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China

Vkorc1 gene polymorphisms confer resistance to anticoagulant rodenticide in Turkish rats
type: item
type: AcademicArticle
description: Mutations in Exon 1, 2 and 3 of the vitamin K epoxide reductase complex subunit 1 (Vkorc1) gene are known to lead to anticoagulant rodenticide resistance. In order to investigate their putative resistance in rodenticides, we studied the genetic profile of the Vkorc1 gene in Turkish black rats (Rattus rattus) and brown rats (Rattus norvegicus). In this context, previously recorded Ala21Thr mutation (R. rattus) in Exon 1 region, Ile90Leu mutation (R. rattus, R. norvegicus) in Exon 2 region and Leu120Gln mutation (R. norvegicus) in Exon 3 region were identified as “missense mutations” causing amino acid changes. Ala21Thr mutation was first detected in one specimen of Turkish black rat despite the uncertainty of its relevance to resistance. Ile90Leu mutation accepted as neutral variant was detected in most of black rat specimens. Leu120Gln mutation related to anticoagulant rodenticide resistance was found in only one brown rat specimen. Furthermore, Ser74Asn, Gln77Pro (black rat) and Ser79Pro (brown rat) mutations that cause amino acid changes in the Exon 2 region but unclear whether they cause resistance were identified. In addition, “silent mutations” which do not cause amino acid changes were also defined; these mutations were Arg12Arg mutation in Exon 1 region, His68His, Ser81Ser, Ile82Ile and Leu94Leu mutations in Exon 2 region and Ile107Ile, Thr137Thr, Ala143Ala and Gln152Gln mutations in Exon 3 region. These silent mutations were found in both species except for Ser81Ser which was determined in only brown rats.
format: application/pdf
format: text/html
creator: Nuri Yiğit
creator: Mustafa T. Duman
creator: Derya Çetintürk
creator: Fulya Saygılı-Yiğit
creator: Ercüment Çolak
creator: Reyhan Çolak
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.15055
publisher: PeerJ Inc.
rights: © 2023 Yiğit et al.
abstract: Mutations in Exon 1, 2 and 3 of the vitamin K epoxide reductase complex subunit 1 (Vkorc1) gene are known to lead to anticoagulant rodenticide resistance. In order to investigate their putative resistance in rodenticides, we studied the genetic profile of the Vkorc1 gene in Turkish black rats (Rattus rattus) and brown rats (Rattus norvegicus). In this context, previously recorded Ala21Thr mutation (R. rattus) in Exon 1 region, Ile90Leu mutation (R. rattus, R. norvegicus) in Exon 2 region and Leu120Gln mutation (R. norvegicus) in Exon 3 region were identified as “missense mutations” causing amino acid changes. Ala21Thr mutation was first detected in one specimen of Turkish black rat despite the uncertainty of its relevance to resistance. Ile90Leu mutation accepted as neutral variant was detected in most of black rat specimens. Leu120Gln mutation related to anticoagulant rodenticide resistance was found in only one brown rat specimen. Furthermore, Ser74Asn, Gln77Pro (black rat) and Ser79Pro (brown rat) mutations that cause amino acid changes in the Exon 2 region but unclear whether they cause resistance were identified. In addition, “silent mutations” which do not cause amino acid changes were also defined; these mutations were Arg12Arg mutation in Exon 1 region, His68His, Ser81Ser, Ile82Ile and Leu94Leu mutations in Exon 2 region and Ile107Ile, Thr137Thr, Ala143Ala and Gln152Gln mutations in Exon 3 region. These silent mutations were found in both species except for Ser81Ser which was determined in only brown rats.
bibliographic citation: Yiğit et al. (2023) Vkorc1 gene polymorphisms confer resistance to anticoagulant rodenticide in Turkish rats. PeerJ 11:e15055 https://doi.org/10.7717/peerj.15055
date submitted: 2022-10-05
date accepted: 2023-02-22
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yiğit
  given name: Nuri
author list: Agent
  family name: Duman
  given name: Mustafa T.
author list: Agent
  family name: Çetintürk
  given name: Derya
author list: Agent
  family name: Saygılı-Yiğit
  given name: Fulya
author list: Agent
  family name: Çolak
  given name: Ercüment
author list: Agent
  family name: Çolak
  given name: Reyhan
doi: 10.7717/peerj.15055
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: ©2023 Yiğit et al.
attribution name: Yiğit et al.

Illuminating the druggable genome through patent bioactivity data
type: item
type: AcademicArticle
description: The patent literature is a potentially valuable source of bioactivity data. In this article we describe a process to prioritise 3.7 million life science relevant patents obtained from the SureChEMBL database (https://www.surechembl.org/), according to how likely they were to contain bioactivity data for potent small molecules on less-studied targets, based on the classification developed by the Illuminating the Druggable Genome (IDG) project. The overall goal was to select a smaller number of patents that could be manually curated and incorporated into the ChEMBL database. Using relatively simple annotation and filtering pipelines, we have been able to identify a substantial number of patents containing quantitative bioactivity data for understudied targets that had not previously been reported in the peer-reviewed medicinal chemistry literature. We quantify the added value of such methods in terms of the numbers of targets that are so identified, and provide some specific illustrative examples. Our work underlines the potential value in searching the patent corpus in addition to the more traditional peer-reviewed literature. The small molecules found in these patents, together with their measured activity against the targets, are now accessible via the ChEMBL database.
format: application/pdf
format: text/html
creator: Maria P. Magariños
creator: Anna Gaulton
creator: Eloy Félix
creator: Tevfik Kiziloren
creator: Ricardo Arcila
creator: Tudor I. Oprea
creator: Andrew R. Leach
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Pharmacology
description: doi:10.7717/peerj.15153
publisher: PeerJ Inc.
rights: © 2023 Magariños et al.
abstract: The patent literature is a potentially valuable source of bioactivity data. In this article we describe a process to prioritise 3.7 million life science relevant patents obtained from the SureChEMBL database (https://www.surechembl.org/), according to how likely they were to contain bioactivity data for potent small molecules on less-studied targets, based on the classification developed by the Illuminating the Druggable Genome (IDG) project. The overall goal was to select a smaller number of patents that could be manually curated and incorporated into the ChEMBL database. Using relatively simple annotation and filtering pipelines, we have been able to identify a substantial number of patents containing quantitative bioactivity data for understudied targets that had not previously been reported in the peer-reviewed medicinal chemistry literature. We quantify the added value of such methods in terms of the numbers of targets that are so identified, and provide some specific illustrative examples. Our work underlines the potential value in searching the patent corpus in addition to the more traditional peer-reviewed literature. The small molecules found in these patents, together with their measured activity against the targets, are now accessible via the ChEMBL database.
bibliographic citation: Magariños et al. (2023) Illuminating the druggable genome through patent bioactivity data. PeerJ 11:e15153 https://doi.org/10.7717/peerj.15153
date submitted: 2022-11-25
date accepted: 2023-03-10
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Magariños
  given name: Maria P.
author list: Agent
  family name: Gaulton
  given name: Anna
author list: Agent
  family name: Félix
  given name: Eloy
author list: Agent
  family name: Kiziloren
  given name: Tevfik
author list: Agent
  family name: Arcila
  given name: Ricardo
author list: Agent
  family name: Oprea
  given name: Tudor I.
author list: Agent
  family name: Leach
  given name: Andrew R.
doi: 10.7717/peerj.15153
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: © 2023 Magariños et al.
attribution name: Magariños et al.

Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA
type: item
type: AcademicArticle
description: Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
format: application/pdf
format: text/html
creator: Maïlys H.V. Picard
creator: Anastasija Zaiko
creator: Annabel M. Tidy
creator: David J. Kelly
creator: Georgia Thomson-Laing
creator: Shaun P. Wilkinson
creator: Xavier Pochon
creator: Marcus J. Vandergoes
creator: Ian Hawes
creator: Susanna A. Wood
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Molecular Biology
subject: Computational Science
subject: Freshwater Biology
description: doi:10.7717/peerj.15210
publisher: PeerJ Inc.
rights: © 2023 Picard et al.
abstract: Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
bibliographic citation: Picard et al. (2023) Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA. PeerJ 11:e15210 https://doi.org/10.7717/peerj.15210
date submitted: 2022-06-23
date accepted: 2023-03-20
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Picard
  given name: Maïlys H.V.
author list: Agent
  family name: Zaiko
  given name: Anastasija
author list: Agent
  family name: Tidy
  given name: Annabel M.
author list: Agent
  family name: Kelly
  given name: David J.
author list: Agent
  family name: Thomson-Laing
  given name: Georgia
author list: Agent
  family name: Wilkinson
  given name: Shaun P.
author list: Agent
  family name: Pochon
  given name: Xavier
author list: Agent
  family name: Vandergoes
  given name: Marcus J.
author list: Agent
  family name: Hawes
  given name: Ian
author list: Agent
  family name: Wood
  given name: Susanna A.
doi: 10.7717/peerj.15210
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: ©2023 Picard et al.
attribution name: Picard et al.

Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer
type: item
type: AcademicArticle
description: The status of human epidermal growth factor receptor 2 (HER2) for the prognosis in colorectal cancer (CRC) is controversial, and the characteristics of the somatic mutation spectrum, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein are unknown in HER2-amplified colorectal cancer (HACC). In order to explore these characteristics along with their correlation with clinicopathological factors and prognosis in HACC. Samples of 812 CRC patients was collected. After immunohistochemistry (IHC), 59 of 812 were found to be HER2-positive, then 26 of 59 samples were further determined to be HER2 amplification by fluorescence in situ hybridization (FISH). Somatic mutation profiling of HACC was analysed using whole exome sequencing (WES). Multiplex fluorescence immunohistochemistry (mIHC) was used for tumor-infiltrating leukocytes and tertiary lymphoid structures (TLSs), while PD-L1 protein was detected by IHC. Our results indicate that the detection rates of HER2 positivity by IHC and FISH were 7.3% and 3.2% respectively, and HER2 amplification is correlated with distant tumour metastasis. The somatic mutation profiling revealed no differences between HACC and HER2-negative CRC. However, TP 53 strongly correlated with poor prognosis in HACC. Furthermore, tumor-infiltrating T cells and TLSs in the tumor immune microenvironment, as well as PD-L1 expression, were higher in HACC than in HER2-negative controls. However, none of them were associated with the prognosis of HACC. In all, HER2 amplification is correlated with distant metastasis and TP53 gene mutation may be a potential protective mechanism of HACC.
format: application/pdf
format: text/html
creator: Xiao-Ting Liu
creator: Zhi-Yong Kou
creator: Hushan Zhang
creator: Jian Dong
creator: Jian-Hua Zhang
creator: You-Jun Peng
creator: Shu Min Ma
creator: Lei Liang
creator: Xuan-Yu Meng
creator: Yuan Zhou
creator: Jun Yang
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.15261
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: The status of human epidermal growth factor receptor 2 (HER2) for the prognosis in colorectal cancer (CRC) is controversial, and the characteristics of the somatic mutation spectrum, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein are unknown in HER2-amplified colorectal cancer (HACC). In order to explore these characteristics along with their correlation with clinicopathological factors and prognosis in HACC. Samples of 812 CRC patients was collected. After immunohistochemistry (IHC), 59 of 812 were found to be HER2-positive, then 26 of 59 samples were further determined to be HER2 amplification by fluorescence in situ hybridization (FISH). Somatic mutation profiling of HACC was analysed using whole exome sequencing (WES). Multiplex fluorescence immunohistochemistry (mIHC) was used for tumor-infiltrating leukocytes and tertiary lymphoid structures (TLSs), while PD-L1 protein was detected by IHC. Our results indicate that the detection rates of HER2 positivity by IHC and FISH were 7.3% and 3.2% respectively, and HER2 amplification is correlated with distant tumour metastasis. The somatic mutation profiling revealed no differences between HACC and HER2-negative CRC. However, TP 53 strongly correlated with poor prognosis in HACC. Furthermore, tumor-infiltrating T cells and TLSs in the tumor immune microenvironment, as well as PD-L1 expression, were higher in HACC than in HER2-negative controls. However, none of them were associated with the prognosis of HACC. In all, HER2 amplification is correlated with distant metastasis and TP53 gene mutation may be a potential protective mechanism of HACC.
bibliographic citation: Liu et al. (2023) Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer. PeerJ 11:e15261 https://doi.org/10.7717/peerj.15261
date submitted: 2023-01-12
date accepted: 2023-03-28
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiao-Ting
author list: Agent
  family name: Kou
  given name: Zhi-Yong
author list: Agent
  family name: Zhang
  given name: Hushan
author list: Agent
  family name: Dong
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Jian-Hua
author list: Agent
  family name: Peng
  given name: You-Jun
author list: Agent
  family name: Ma
  given name: Shu Min
author list: Agent
  family name: Liang
  given name: Lei
author list: Agent
  family name: Meng
  given name: Xuan-Yu
author list: Agent
  family name: Zhou
  given name: Yuan
author list: Agent
  family name: Yang
  given name: Jun
doi: 10.7717/peerj.15261
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Can salivary lactate be used as an anaerobic biomarker?
type: item
type: AcademicArticle
description: Background Salivary lactate has been suggested as a non-invasive anaerobic biomarker in sports medicine for decades, yet has not been widely applied until now. This study aimed to explore possible issues related to its application and suggest directions for future method improvement. Methods A liquid chromatography–mass spectrometry (LC-MS) method for the determination of salivary lactate was developed, validated and applied on saliva samples collected from a group of professional sprinters (n = 20). The samples were collected via chewing a cotton ball for one minute and centrifuging it afterwards. The evaluation included variation with mouth rinse times, consistency at different sampling times, change after treadmill or cycle ergometer trainings, and association with blood lactate. Sample sizes were calculated prior to the study. One-way analysis of variance (ANOVA), intra-class correlation coefficients (ICC) and relative standard deviation (RSD) were used to evaluate data variances. Pearson correlation was applied to show correlation between salivary and blood lactate. Effect sizes and power were calculated following ANOVA and correlation analyses. Results The RSD of the LC-MS method was 19.70%. Salivary lactate concentration was affected by mouth rinse times before sampling (ANOVA p = 0.025, η2 = 0.40, 1 − β = 0.99, ICC = 0.23, mean RSD of four sampling = 55.30%), and stabilized after mouth rinsing for three times. The concentrations at resting state across three weeks were consistent at group level (ANOVA p = 0.57, η2 = 0.03, 1 − β = 0.20), but varied greatly individually (ICC = 0.22, mean RSD = 56.16%). Salivary lactate level significantly increased after treadmill and cycle ergometer trainings (ANOVA p = 0.0002, η2 = 0.46, 1 − β = 0.9999 and ANOVA p = 0.0019, η2 = 0.40, 1 − β = 0.9993, respectively), and displayed positive correlation with blood lactate concentration (r = 0.61, p = 0.0004, 1 − β = 0.9596). Significant difference between male and female partici…
format: application/pdf
format: text/html
creator: Pingping Yan
creator: Chunli Qin
creator: Zengyin Yan
creator: Chang Chen
creator: Fengjing Zhang
subject: Biochemistry
subject: Anatomy and Physiology
subject: Sports Medicine
description: doi:10.7717/peerj.15274
publisher: PeerJ Inc.
rights: © 2023 Yan et al.
abstract: Background Salivary lactate has been suggested as a non-invasive anaerobic biomarker in sports medicine for decades, yet has not been widely applied until now. This study aimed to explore possible issues related to its application and suggest directions for future method improvement. Methods A liquid chromatography–mass spectrometry (LC-MS) method for the determination of salivary lactate was developed, validated and applied on saliva samples collected from a group of professional sprinters (n = 20). The samples were collected via chewing a cotton ball for one minute and centrifuging it afterwards. The evaluation included variation with mouth rinse times, consistency at different sampling times, change after treadmill or cycle ergometer trainings, and association with blood lactate. Sample sizes were calculated prior to the study. One-way analysis of variance (ANOVA), intra-class correlation coefficients (ICC) and relative standard deviation (RSD) were used to evaluate data variances. Pearson correlation was applied to show correlation between salivary and blood lactate. Effect sizes and power were calculated following ANOVA and correlation analyses. Results The RSD of the LC-MS method was 19.70%. Salivary lactate concentration was affected by mouth rinse times before sampling (ANOVA p = 0.025, η2 = 0.40, 1 − β = 0.99, ICC = 0.23, mean RSD of four sampling = 55.30%), and stabilized after mouth rinsing for three times. The concentrations at resting state across three weeks were consistent at group level (ANOVA p = 0.57, η2 = 0.03, 1 − β = 0.20), but varied greatly individually (ICC = 0.22, mean RSD = 56.16%). Salivary lactate level significantly increased after treadmill and cycle ergometer trainings (ANOVA p = 0.0002, η2 = 0.46, 1 − β = 0.9999 and ANOVA p = 0.0019, η2 = 0.40, 1 − β = 0.9993, respectively), and displayed positive correlation with blood lactate concentration (r = 0.61, p = 0.0004, 1 − β = 0.9596). Significant difference between male and female partici…
bibliographic citation: Yan et al. (2023) Can salivary lactate be used as an anaerobic biomarker?. PeerJ 11:e15274 https://doi.org/10.7717/peerj.15274
date submitted: 2022-11-09
date accepted: 2023-03-30
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Pingping
author list: Agent
  family name: Qin
  given name: Chunli
author list: Agent
  family name: Yan
  given name: Zengyin
author list: Agent
  family name: Chen
  given name: Chang
author list: Agent
  family name: Zhang
  given name: Fengjing
doi: 10.7717/peerj.15274
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: ©2023 Yan et al.
attribution name: Yan et al.

Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs
type: item
type: AcademicArticle
description: Thalattosuchian crocodylomorphs were a diverse clade that lived from the Early Jurassic to the Early Cretaceous. The subclade Metriorhynchoidea underwent a remarkable transition, evolving from semi-aquatic ambush predators into fully aquatic forms living in the open oceans. Thalattosuchians share a peculiar palatal morphology with semi-aquatic and aquatic fossil cetaceans: paired anteroposteriorly aligned grooves along the palatal surface of the bony secondary palate. In extant cetaceans, these grooves are continuous with the greater palatine artery foramina, arteries that supply their oral thermoregulatory structures. Herein, we investigate the origins of thalattosuchian palatal grooves by examining CT scans of six thalattosuchian species (one teleosauroid, two early-diverging metriorhynchoids and three metriorhynchids), and CT scans of eleven extant crocodylian species. All thalattosuchians had paired osseous canals, enclosed by the palatines, that connect the nasal cavity to the oral cavity. These osseous canals open into the oral cavity via foramina at the posterior terminus of the palatal grooves. Extant crocodylians lack both the external grooves and the internal canals. We posit that in thalattosuchians these novel palatal canals transmitted hypertrophied medial nasal vessels (artery and vein), creating a novel heat exchange pathway connecting the palatal vascular plexus to the endocranial region. Given the general hypertrophy of thalattosuchian cephalic vasculature, and their increased blood flow and volume, thalattosuchians would have required a more extensive suite of thermoregulatory pathways to maintain stable temperatures for their neurosensory tissues.
format: application/pdf
format: text/html
creator: Mark T. Young
creator: Charlotte I. W. Bowman
creator: Arthur Erb
creator: Julia A. Schwab
creator: Lawrence M. Witmer
creator: Yanina Herrera
creator: Stephen L. Brusatte
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.15353
publisher: PeerJ Inc.
rights: © 2023 Young et al.
abstract: Thalattosuchian crocodylomorphs were a diverse clade that lived from the Early Jurassic to the Early Cretaceous. The subclade Metriorhynchoidea underwent a remarkable transition, evolving from semi-aquatic ambush predators into fully aquatic forms living in the open oceans. Thalattosuchians share a peculiar palatal morphology with semi-aquatic and aquatic fossil cetaceans: paired anteroposteriorly aligned grooves along the palatal surface of the bony secondary palate. In extant cetaceans, these grooves are continuous with the greater palatine artery foramina, arteries that supply their oral thermoregulatory structures. Herein, we investigate the origins of thalattosuchian palatal grooves by examining CT scans of six thalattosuchian species (one teleosauroid, two early-diverging metriorhynchoids and three metriorhynchids), and CT scans of eleven extant crocodylian species. All thalattosuchians had paired osseous canals, enclosed by the palatines, that connect the nasal cavity to the oral cavity. These osseous canals open into the oral cavity via foramina at the posterior terminus of the palatal grooves. Extant crocodylians lack both the external grooves and the internal canals. We posit that in thalattosuchians these novel palatal canals transmitted hypertrophied medial nasal vessels (artery and vein), creating a novel heat exchange pathway connecting the palatal vascular plexus to the endocranial region. Given the general hypertrophy of thalattosuchian cephalic vasculature, and their increased blood flow and volume, thalattosuchians would have required a more extensive suite of thermoregulatory pathways to maintain stable temperatures for their neurosensory tissues.
bibliographic citation: Young et al. (2023) Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs. PeerJ 11:e15353 https://doi.org/10.7717/peerj.15353
date submitted: 2023-01-10
date accepted: 2023-04-13
issued: 2023-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Mark T.
author list: Agent
  family name: Bowman
  given name: Charlotte I. W.
author list: Agent
  family name: Erb
  given name: Arthur
author list: Agent
  family name: Schwab
  given name: Julia A.
author list: Agent
  family name: Witmer
  given name: Lawrence M.
author list: Agent
  family name: Herrera
  given name: Yanina
author list: Agent
  family name: Brusatte
  given name: Stephen L.
doi: 10.7717/peerj.15353
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-02
copyright: © 2023 Young et al.
attribution name: Young et al.

Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile?
type: item
type: AcademicArticle
description: Global warming generates changes in environmental conditions, affecting the spatial-temporal dynamics of precipitation and temperature. Droughts, events of low rainfall, are becoming more frequent and severe. In central Chile, from 2010 to date, an unprecedented drought event has developed, affecting the ecosystem and creating pressure on the dynamics of food webs. The present study analysed the trophic ecology of Bubo magellanicus, a top predator in the Mediterranean region of Chile, between 2019 and 2020 a period with a rainfall deficit of 72.6%. Our results established a diet mainly described by invertebrates (97.75%), in particular by the Gramnostola rosea spider (87.86%), and a low contribution of small vertebrates (2.24%). The trophic niche breadth (B = 0.37) and the standardised Levin’s index (BSTA = 0.01) are the lowest recorded in the species B. magellanicus. A comparative analysis of trophic ecology with other studies developed in the same region established significant differences in the composition of the diet (frequency of occurrence of prey unit). This work provides evidence that droughts and other extreme environmental scenarios restructure the food webs of an ecosystem, with direct consequences on the trophic niche of the species, specifically top predators.
format: application/pdf
format: text/html
creator: Sam Catchpole Ahumada
creator: Luis Carrera Suárez
creator: Reinaldo Rivera
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.15020
publisher: PeerJ Inc.
rights: © 2023 Catchpole Ahumada et al.
abstract: Global warming generates changes in environmental conditions, affecting the spatial-temporal dynamics of precipitation and temperature. Droughts, events of low rainfall, are becoming more frequent and severe. In central Chile, from 2010 to date, an unprecedented drought event has developed, affecting the ecosystem and creating pressure on the dynamics of food webs. The present study analysed the trophic ecology of Bubo magellanicus, a top predator in the Mediterranean region of Chile, between 2019 and 2020 a period with a rainfall deficit of 72.6%. Our results established a diet mainly described by invertebrates (97.75%), in particular by the Gramnostola rosea spider (87.86%), and a low contribution of small vertebrates (2.24%). The trophic niche breadth (B = 0.37) and the standardised Levin’s index (BSTA = 0.01) are the lowest recorded in the species B. magellanicus. A comparative analysis of trophic ecology with other studies developed in the same region established significant differences in the composition of the diet (frequency of occurrence of prey unit). This work provides evidence that droughts and other extreme environmental scenarios restructure the food webs of an ecosystem, with direct consequences on the trophic niche of the species, specifically top predators.
bibliographic citation: Catchpole Ahumada et al. (2023) Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile?. PeerJ 11:e15020 https://doi.org/10.7717/peerj.15020
date submitted: 2022-08-22
date accepted: 2023-02-17
issued: 2023-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catchpole Ahumada
  given name: Sam
author list: Agent
  family name: Carrera Suárez
  given name: Luis
author list: Agent
  family name: Rivera
  given name: Reinaldo
doi: 10.7717/peerj.15020
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-01
copyright: ©2023 Catchpole Ahumada et al.
attribution name: Catchpole Ahumada et al.

Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa
type: item
type: AcademicArticle
description: Introduction Over-grazing by livestock has resulted in the widespread degradation of South Africa’s succulent thicket ecosystems. This is characterised by a significant reduction in the cover of the dominant succulent shrub, Portulacaria afra. Because this species is unable to regenerate naturally in degraded habitat, active reintroduction is required to restore ecosystem function. However, reintroduction success is relatively low, and the recruitment barriers for this species are poorly understood. Methods By conducting pairwise plot surveys in actively restored and adjacent degraded succulent thicket habitats, the extent of P. afra seedling abundance in these contrasting ecosystem conditions is quantified. Results Seedling abundance was significantly greater in restored ecosystems (W = 23, p = 0.03225). Additionally, seedlings found in restored habitats were strongly associated with open habitat, whereas seedlings in degraded ecosystems were more restricted to nurse sites (X2 = 122.84, df = 2, p-value < 2.2e–16). A weak (R2 = 0,237), but significant (p = 0, 0295) correlation between P. afra cover and seedling abundance was recorded. Conclusion Active restoration of succulent thicket habitat through P. afra reintroduction appears to overcome recruitment barriers. This may suggest that, despite the poor survival of introduced individuals, natural recruitment could contribute to the regeneration of restored succulent thicket ecosystems.
format: application/pdf
format: text/html
creator: Nicholas C. Galuszynski
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.15081
publisher: PeerJ Inc.
rights: © 2023 Galuszynski
abstract: Introduction Over-grazing by livestock has resulted in the widespread degradation of South Africa’s succulent thicket ecosystems. This is characterised by a significant reduction in the cover of the dominant succulent shrub, Portulacaria afra. Because this species is unable to regenerate naturally in degraded habitat, active reintroduction is required to restore ecosystem function. However, reintroduction success is relatively low, and the recruitment barriers for this species are poorly understood. Methods By conducting pairwise plot surveys in actively restored and adjacent degraded succulent thicket habitats, the extent of P. afra seedling abundance in these contrasting ecosystem conditions is quantified. Results Seedling abundance was significantly greater in restored ecosystems (W = 23, p = 0.03225). Additionally, seedlings found in restored habitats were strongly associated with open habitat, whereas seedlings in degraded ecosystems were more restricted to nurse sites (X2 = 122.84, df = 2, p-value < 2.2e–16). A weak (R2 = 0,237), but significant (p = 0, 0295) correlation between P. afra cover and seedling abundance was recorded. Conclusion Active restoration of succulent thicket habitat through P. afra reintroduction appears to overcome recruitment barriers. This may suggest that, despite the poor survival of introduced individuals, natural recruitment could contribute to the regeneration of restored succulent thicket ecosystems.
bibliographic citation: Galuszynski (2023) Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa. PeerJ 11:e15081 https://doi.org/10.7717/peerj.15081
date submitted: 2022-09-13
date accepted: 2023-02-25
issued: 2023-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galuszynski
  given name: Nicholas C.
doi: 10.7717/peerj.15081
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-01
copyright: ©2023 Galuszynski
attribution name: Galuszynski

A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia
type: item
type: AcademicArticle
description: Background Malaysia is strongly supported by the agriculture sector as the backbone to drive the economy. However, COVID-19 has significantly affected agriculture across the production, supply, and marketing chains. It also disturbs the balance of food supply and demand in Malaysia. COVID-19 was an unexpected pandemic that resulted in shock and panic and caused a huge global impact. However, the impacts of this pandemic on the agriculture sector in Malaysia, particularly in the production and supply chains, are still unclear and scarce. This review offers insights into the challenges, particularly in sustaining agri-food production and supply chains. It also highlights the opportunity and relevant measures towards sustainability in agriculture to avoid agri-food disasters in the future. Methods This study was carried out through a desk review of the secondary source of information covering the impact of COVID-19 in Malaysia particularly in the agri-food aspect, and a wide range of strategies and initiatives as the effective measures to overcome the crisis of this pandemic. Online desk research of the government published data and customer desk research were utilized to complete this study. Search engines such as Google Scholar and the statistical data from the official websites including the Department of Statistics Malaysia (DOSM) and the Food and Fertilizer Technology Center for the Asian and Pacific Region (FFTC-AP), were utilized. Keywords such as impact of COVID-19, pandemic, and agri-food supply chain were used to conduct the searches. The articles identified to be related to the study’s objective were then downloaded and included in the study. Descriptive methods were used as the primary analysis technique following the descriptive analysis and visual data analysis in performing the sources obtained. Results This devastating impact damages the lives by causing 4.3 million confirmed infections and more than 290,000 deaths. This disease presents an unprecedente…
format: application/pdf
format: text/html
creator: Say Peng Tan
creator: Lee Chuen Ng
creator: Novel Lyndon
creator: Zaki Aman
creator: Parthiban Kannan
creator: Khairuman Hashim
creator: Han Meng Teo
creator: Muhamad Syazlie Che Ibrahim
subject: Agricultural Science
subject: Food Science and Technology
subject: Natural Resource Management
description: doi:10.7717/peerj.15228
publisher: PeerJ Inc.
rights: © 2023 Tan et al.
abstract: Background Malaysia is strongly supported by the agriculture sector as the backbone to drive the economy. However, COVID-19 has significantly affected agriculture across the production, supply, and marketing chains. It also disturbs the balance of food supply and demand in Malaysia. COVID-19 was an unexpected pandemic that resulted in shock and panic and caused a huge global impact. However, the impacts of this pandemic on the agriculture sector in Malaysia, particularly in the production and supply chains, are still unclear and scarce. This review offers insights into the challenges, particularly in sustaining agri-food production and supply chains. It also highlights the opportunity and relevant measures towards sustainability in agriculture to avoid agri-food disasters in the future. Methods This study was carried out through a desk review of the secondary source of information covering the impact of COVID-19 in Malaysia particularly in the agri-food aspect, and a wide range of strategies and initiatives as the effective measures to overcome the crisis of this pandemic. Online desk research of the government published data and customer desk research were utilized to complete this study. Search engines such as Google Scholar and the statistical data from the official websites including the Department of Statistics Malaysia (DOSM) and the Food and Fertilizer Technology Center for the Asian and Pacific Region (FFTC-AP), were utilized. Keywords such as impact of COVID-19, pandemic, and agri-food supply chain were used to conduct the searches. The articles identified to be related to the study’s objective were then downloaded and included in the study. Descriptive methods were used as the primary analysis technique following the descriptive analysis and visual data analysis in performing the sources obtained. Results This devastating impact damages the lives by causing 4.3 million confirmed infections and more than 290,000 deaths. This disease presents an unprecedente…
bibliographic citation: Tan et al. (2023) A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia. PeerJ 11:e15228 https://doi.org/10.7717/peerj.15228
date submitted: 2022-12-23
date accepted: 2023-03-24
issued: 2023-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Say Peng
author list: Agent
  family name: Ng
  given name: Lee Chuen
author list: Agent
  family name: Lyndon
  given name: Novel
author list: Agent
  family name: Aman
  given name: Zaki
author list: Agent
  family name: Kannan
  given name: Parthiban
author list: Agent
  family name: Hashim
  given name: Khairuman
author list: Agent
  family name: Teo
  given name: Han Meng
author list: Agent
  family name: Che Ibrahim
  given name: Muhamad Syazlie
doi: 10.7717/peerj.15228
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-01
copyright: © 2023 Tan et al.
attribution name: Tan et al.

Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China
type: item
type: AcademicArticle
description: Background With the improvement in diagnosis and treatment of gastric cancer (GC), the survival time of patients has been gradually prolonged. However, these survivors are at increased risk for other diseases, including second primary cancers (SPCs). Currently, there remain few central studies concerning double primary cancers with first gastric cancer (DPCFGC). Thus, this study aimed to investigate these patients’ clinical characteristics and perform prognostic nomogram analysis. Methods The clinical data of 78 DPCFGC patients were retrospectively collected and analyzed through the hospital electronic medical record system. Univariate and multivariate Cox regression analyses were performed to screen independent risk factors, based on which the prognostic nomogram was further constructed and validated using the R software package. Finally, Kaplan–Meier curves were plotted to explore the association of overall survival (OS) with prognostic factors and the model. Results The prevalence of DPCFGC was 0.86%, of which the proportions of synchronous and metachronous patients were 47.44% and 52.56% , respectively; 65.38% (51/78) and 34.62% (27/78) of patients were male and female, respectively. The median age at GC and SPC diagnosis was 63 and 65 years, respectively, and 52.57% of GC patients developed SPCs within 1 year. The top three SPCs were in the esophagus (19.24%), colon (16.67%), and rectum (15.39%). The most common features of GC and SPCs were adenocarcinoma, poorly and moderately differentiated histology, and pathological stages I and II. The radical resection rate of GC was significantly lower in synchronous patients than in metachronous patients (45.94% vs. 100.00%, P < 0.001), but no significant difference was noted in the radical resection rate of SPCs (35.13% vs. 46.34%, P = 0.315). The OS of DPCFGC patients was 31.03 ± 4.14 months. The pathological stage of GC and SPCs, whether to operate for GC, and diagnostic interval were independent risk factors. The pr…
format: application/pdf
format: text/html
creator: Bing Wang
creator: Lu Liu
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.15278
publisher: PeerJ Inc.
rights: © 2023 Wang and Liu
abstract: Background With the improvement in diagnosis and treatment of gastric cancer (GC), the survival time of patients has been gradually prolonged. However, these survivors are at increased risk for other diseases, including second primary cancers (SPCs). Currently, there remain few central studies concerning double primary cancers with first gastric cancer (DPCFGC). Thus, this study aimed to investigate these patients’ clinical characteristics and perform prognostic nomogram analysis. Methods The clinical data of 78 DPCFGC patients were retrospectively collected and analyzed through the hospital electronic medical record system. Univariate and multivariate Cox regression analyses were performed to screen independent risk factors, based on which the prognostic nomogram was further constructed and validated using the R software package. Finally, Kaplan–Meier curves were plotted to explore the association of overall survival (OS) with prognostic factors and the model. Results The prevalence of DPCFGC was 0.86%, of which the proportions of synchronous and metachronous patients were 47.44% and 52.56% , respectively; 65.38% (51/78) and 34.62% (27/78) of patients were male and female, respectively. The median age at GC and SPC diagnosis was 63 and 65 years, respectively, and 52.57% of GC patients developed SPCs within 1 year. The top three SPCs were in the esophagus (19.24%), colon (16.67%), and rectum (15.39%). The most common features of GC and SPCs were adenocarcinoma, poorly and moderately differentiated histology, and pathological stages I and II. The radical resection rate of GC was significantly lower in synchronous patients than in metachronous patients (45.94% vs. 100.00%, P < 0.001), but no significant difference was noted in the radical resection rate of SPCs (35.13% vs. 46.34%, P = 0.315). The OS of DPCFGC patients was 31.03 ± 4.14 months. The pathological stage of GC and SPCs, whether to operate for GC, and diagnostic interval were independent risk factors. The pr…
bibliographic citation: Wang et al. (2023) Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China. PeerJ 11:e15278 https://doi.org/10.7717/peerj.15278
date submitted: 2022-11-22
date accepted: 2023-04-01
issued: 2023-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Bing
author list: Agent
  family name: Liu
  given name: Lu
doi: 10.7717/peerj.15278
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-01
copyright: ©2023 Wang and Liu
attribution name: Wang and Liu

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