PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes
items: Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches
items: Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max
items: Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.)
items: The emerging roles of circHECTD1 in human diseases and the specific underlying regulatory mechanisms
items: Evaluation of alanine aminotransferase/aspartate aminotransferase ratio and high-density lipoprotein for predicting neonatal adverse outcomes associated with intrahepatic cholestasis of pregnancy
items: Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling
items: Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa
items: Path for recovery: an ecological overview of the Jambato Harlequin Toad (Bufonidae: Atelopus ignescens) in its last known locality, Angamarca Valley, Ecuador
items: Taxon-dependent diversity response along a temperate elevation gradient covered by grassland

Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes
type: item
type: AcademicArticle
description: Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.
format: application/pdf
format: text/html
creator: Marina McCampbell
creator: McKayla Spencer
creator: Kristen Hart
creator: Gabrielle Link
creator: Andrew Watson
creator: Robert McCleery
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.17577
publisher: PeerJ Inc.
rights: © 2024
abstract: Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.
bibliographic citation: McCampbell et al. (2024) Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes. PeerJ 12:e17577 https://doi.org/10.7717/peerj.17577
date submitted: 2023-09-21
date accepted: 2024-05-24
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: McCampbell
  given name: Marina
author list: Agent
  family name: Spencer
  given name: McKayla
author list: Agent
  family name: Hart
  given name: Kristen
author list: Agent
  family name: Link
  given name: Gabrielle
author list: Agent
  family name: Watson
  given name: Andrew
author list: Agent
  family name: McCleery
  given name: Robert
doi: 10.7717/peerj.17577
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24

Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches
type: item
type: AcademicArticle
description: Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress.
format: application/pdf
format: text/html
creator: Hatice Kübra Gören
creator: Uğur Tan
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17584
publisher: PeerJ Inc.
rights: © 2024 Gören and Tan
abstract: Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress.
bibliographic citation: Gören et al. (2024) Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches. PeerJ 12:e17584 https://doi.org/10.7717/peerj.17584
date submitted: 2024-03-20
date accepted: 2024-05-27
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gören
  given name: Hatice Kübra
author list: Agent
  family name: Tan
  given name: Uğur
doi: 10.7717/peerj.17584
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Gören and Tan
attribution name: Gören and Tan

Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max
type: item
type: AcademicArticle
description: Background Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide. Methods In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions. Results We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
format: application/pdf
format: text/html
creator: Hind Abdelmonim Elsanosi
creator: Tiantian Zhu
creator: Guisheng Zhou
creator: Li Song
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.17590
publisher: PeerJ Inc.
rights: © 2024 Elsanosi et al.
abstract: Background Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide. Methods In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions. Results We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
bibliographic citation: Elsanosi et al. (2024) Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max. PeerJ 12:e17590 https://doi.org/10.7717/peerj.17590
date submitted: 2024-04-02
date accepted: 2024-05-28
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elsanosi
  given name: Hind Abdelmonim
author list: Agent
  family name: Zhu
  given name: Tiantian
author list: Agent
  family name: Zhou
  given name: Guisheng
author list: Agent
  family name: Song
  given name: Li
doi: 10.7717/peerj.17590
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Elsanosi et al.
attribution name: Elsanosi et al.

Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.)
type: item
type: AcademicArticle
description: Background Tungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination. Methods In this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened. Results The results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination.
format: application/pdf
format: text/html
creator: Qi Li
creator: Xiaojun Zheng
creator: Ming Chen
subject: Agricultural Science
subject: Plant Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.17601
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Tungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination. Methods In this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened. Results The results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination.
bibliographic citation: Li et al. (2024) Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.). PeerJ 12:e17601 https://doi.org/10.7717/peerj.17601
date submitted: 2024-01-09
date accepted: 2024-05-29
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qi
author list: Agent
  family name: Zheng
  given name: Xiaojun
author list: Agent
  family name: Chen
  given name: Ming
doi: 10.7717/peerj.17601
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Li et al.
attribution name: Li et al.

The emerging roles of circHECTD1 in human diseases and the specific underlying regulatory mechanisms
type: item
type: AcademicArticle
description: Circular RNAs (circRNAs) are a class of single-stranded closed-loop RNAs that have become a popular research subject in biology. Compared to linear RNAs, they are more stable, more conserved, and more widely distributed, and they play crucial biological functions in many diseases. CircHECTD1, a newly identified member of the circRNA family, is widely distributed in humans. Recent studies have shown that circHECTD1 is abnormally expressed in various human diseases, including glioma, hepatocellular carcinoma, gastric cancer, acute ischaemic stroke, silicosis, acute lung injury, ulcerative colitis, atherosclerosis, and hypertrophic scarring. In malignant tumours, circHECTD1 is thought to be an oncogene that promotes malignant tumour behaviours and influences tumour prognosis. In nontumour diseases, it plays a dual role, promoting disease in silicosis, stroke, and other diseases, while alleviating the disease process in ulcerative colitis, acute lung injury, and atherosclerosis. This article provides a review of the regulatory roles and mechanisms of action of circHECTD1 in different diseases. We also discuss and prospectively evaluate the clinical potential of circHECTD1 as a diagnostic biomarker and a therapeutic target for related diseases, providing new insights for developing new therapeutic strategies.
format: application/pdf
format: text/html
creator: Yiran Yuan
creator: Xiaomin Zhang
creator: Xiaoxiao Wang
creator: Lei Zhang
creator: Jiefeng He
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.17612
publisher: PeerJ Inc.
rights: © 2024 Yuan et al.
abstract: Circular RNAs (circRNAs) are a class of single-stranded closed-loop RNAs that have become a popular research subject in biology. Compared to linear RNAs, they are more stable, more conserved, and more widely distributed, and they play crucial biological functions in many diseases. CircHECTD1, a newly identified member of the circRNA family, is widely distributed in humans. Recent studies have shown that circHECTD1 is abnormally expressed in various human diseases, including glioma, hepatocellular carcinoma, gastric cancer, acute ischaemic stroke, silicosis, acute lung injury, ulcerative colitis, atherosclerosis, and hypertrophic scarring. In malignant tumours, circHECTD1 is thought to be an oncogene that promotes malignant tumour behaviours and influences tumour prognosis. In nontumour diseases, it plays a dual role, promoting disease in silicosis, stroke, and other diseases, while alleviating the disease process in ulcerative colitis, acute lung injury, and atherosclerosis. This article provides a review of the regulatory roles and mechanisms of action of circHECTD1 in different diseases. We also discuss and prospectively evaluate the clinical potential of circHECTD1 as a diagnostic biomarker and a therapeutic target for related diseases, providing new insights for developing new therapeutic strategies.
bibliographic citation: Yuan et al. (2024) The emerging roles of circHECTD1 in human diseases and the specific underlying regulatory mechanisms. PeerJ 12:e17612 https://doi.org/10.7717/peerj.17612
date submitted: 2024-02-16
date accepted: 2024-05-31
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yuan
  given name: Yiran
author list: Agent
  family name: Zhang
  given name: Xiaomin
author list: Agent
  family name: Wang
  given name: Xiaoxiao
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: He
  given name: Jiefeng
doi: 10.7717/peerj.17612
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Yuan et al.
attribution name: Yuan et al.

Evaluation of alanine aminotransferase/aspartate aminotransferase ratio and high-density lipoprotein for predicting neonatal adverse outcomes associated with intrahepatic cholestasis of pregnancy
type: item
type: AcademicArticle
description: Background To determine the association between lipid metabolism and intrahepatic cholestasis of pregnancy (ICP), and explore the value of maternal alanine aminotransferase/aspartate aminotransferase (ALT/AST) and high-density lipoprotein (HDL) in predicting adverse neonatal outcomes in women with ICP. Methods A total of 147 pregnant women with ICP admitted to The Fourth Hospital of Shijiazhuang and 120 normal pregnant women in the same period were selected in this study. The Mann-Whitney U test and Chi-square tests were used to compare the differences in clinical data. Multivariate logistic regression was used to analyze the relationship between ALT/AST and the occurrence of adverse pregnancy outcomes in patients with ICP. The combined predictive value of ALT/AST and HDL was determined by receiver operating characteristic (ROC) curve analysis. Results Among 147 women with ICP, 122 women had total bile acid (TBA) levels of 10–39.9 µmol/L, and 25 had TBA ≥ 40 µmol/L. There was significantly lower gestational age in patients with severe ICP than in those with mild and control groups (all p < 0.05), and the weight of newborns in the maternal ICP group was significantly lower than in the control group (p < 0.05). Increasing TBA levels was associated with higher AST, ALT, ALT/AST, and lower HDL level (all p < 0.05). Meanwhile, higher levels of ALT/AST was positively associated with neonatal hyperbilirubinemia [adjusted odds ratio (AOR) = 4.019, 95% CI [1.757–9.194, p = 0.001] and cardiac injury [AOR = 3.500, 95% CI [1.535–7.987], p = 0.003]. HDL was a significant protective factor for neonatal hyperbilirubinemia and cardiac injury [AOR = 0.315, 95% CI [0.126–0.788], p = 0.014; AOR = 0.134 (0.039–0.461), p = 0.001]. The area under the ROC curve (AUC) for prediction of neonatal hyperbilirubinemia by ALT/AST combined with HDL was 0.668 [95% CI [56.3–77.3%], p = 0.002], and the sensitivity and specificity were 47.1% and 84.0%, respectively. To predict neonatal cardiac injury…
format: application/pdf
format: text/html
creator: Xizhenzi Fan
creator: Xia Li
creator: Tianxiao Yu
creator: Ruifen Jiao
creator: Wenhui Song
creator: Achou Su
creator: Mingwei Li
creator: Qing Guo
subject: Gynecology and Obstetrics
subject: Pediatrics
subject: Women’s Health
description: doi:10.7717/peerj.17613
publisher: PeerJ Inc.
rights: © 2024 Fan et al.
abstract: Background To determine the association between lipid metabolism and intrahepatic cholestasis of pregnancy (ICP), and explore the value of maternal alanine aminotransferase/aspartate aminotransferase (ALT/AST) and high-density lipoprotein (HDL) in predicting adverse neonatal outcomes in women with ICP. Methods A total of 147 pregnant women with ICP admitted to The Fourth Hospital of Shijiazhuang and 120 normal pregnant women in the same period were selected in this study. The Mann-Whitney U test and Chi-square tests were used to compare the differences in clinical data. Multivariate logistic regression was used to analyze the relationship between ALT/AST and the occurrence of adverse pregnancy outcomes in patients with ICP. The combined predictive value of ALT/AST and HDL was determined by receiver operating characteristic (ROC) curve analysis. Results Among 147 women with ICP, 122 women had total bile acid (TBA) levels of 10–39.9 µmol/L, and 25 had TBA ≥ 40 µmol/L. There was significantly lower gestational age in patients with severe ICP than in those with mild and control groups (all p < 0.05), and the weight of newborns in the maternal ICP group was significantly lower than in the control group (p < 0.05). Increasing TBA levels was associated with higher AST, ALT, ALT/AST, and lower HDL level (all p < 0.05). Meanwhile, higher levels of ALT/AST was positively associated with neonatal hyperbilirubinemia [adjusted odds ratio (AOR) = 4.019, 95% CI [1.757–9.194, p = 0.001] and cardiac injury [AOR = 3.500, 95% CI [1.535–7.987], p = 0.003]. HDL was a significant protective factor for neonatal hyperbilirubinemia and cardiac injury [AOR = 0.315, 95% CI [0.126–0.788], p = 0.014; AOR = 0.134 (0.039–0.461), p = 0.001]. The area under the ROC curve (AUC) for prediction of neonatal hyperbilirubinemia by ALT/AST combined with HDL was 0.668 [95% CI [56.3–77.3%], p = 0.002], and the sensitivity and specificity were 47.1% and 84.0%, respectively. To predict neonatal cardiac injury…
bibliographic citation: Fan et al. (2024) Evaluation of alanine aminotransferase/aspartate aminotransferase ratio and high-density lipoprotein for predicting neonatal adverse outcomes associated with intrahepatic cholestasis of pregnancy. PeerJ 12:e17613 https://doi.org/10.7717/peerj.17613
date submitted: 2024-02-01
date accepted: 2024-05-31
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Fan
  given name: Xizhenzi
author list: Agent
  family name: Li
  given name: Xia
author list: Agent
  family name: Yu
  given name: Tianxiao
author list: Agent
  family name: Jiao
  given name: Ruifen
author list: Agent
  family name: Song
  given name: Wenhui
author list: Agent
  family name: Su
  given name: Achou
author list: Agent
  family name: Li
  given name: Mingwei
author list: Agent
  family name: Guo
  given name: Qing
doi: 10.7717/peerj.17613
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Fan et al.
attribution name: Fan et al.

Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling
type: item
type: AcademicArticle
description: While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model’s accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a “hot” immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment.
format: application/pdf
format: text/html
creator: Jinglu Yu
creator: Yabin Gong
creator: Zhenye Xu
creator: Lei Chen
creator: Shuang Li
creator: Yongkang Cui
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.17629
publisher: PeerJ Inc.
rights: © 2024 Yu et al.
abstract: While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model’s accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a “hot” immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment.
bibliographic citation: Yu et al. (2024) Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling. PeerJ 12:e17629 https://doi.org/10.7717/peerj.17629
date submitted: 2024-01-17
date accepted: 2024-06-03
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Jinglu
author list: Agent
  family name: Gong
  given name: Yabin
author list: Agent
  family name: Xu
  given name: Zhenye
author list: Agent
  family name: Chen
  given name: Lei
author list: Agent
  family name: Li
  given name: Shuang
author list: Agent
  family name: Cui
  given name: Yongkang
doi: 10.7717/peerj.17629
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Yu et al.
attribution name: Yu et al.

Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa
type: item
type: AcademicArticle
description: In this review, we examine the current landscape of point-of-care testing (POCT) diagnostic tools designed for poverty-related infectious diseases (PRIDs) in sub-Saharan Africa (sSA) while delineating key avenues for future advancements. Our analysis encompasses both established and emerging diagnostic methods for PRIDs, addressing the persistent challenges in POCT tool development and deployment, such as cost, accessibility, and reliability. We emphasize recent advancements in POCT diagnostic tools as well as platforms poised to enhance diagnostic testing in sSA. Recognizing the urgency for affordable and widely accessible POCT diagnostic tools to detect PRIDs in sSA, we advocate for a multidisciplinary approach. This approach integrates current and emerging diagnostic methods, explicitly addressing challenges hindering point-of-care (POC) tool development. Furthermore, it recognizes the profound impact of misdiagnosis on public and global health, emphasizing the need for effective tools. To facilitate the successful development and implementation of POCT diagnostic tools in sSA, we propose strategies including the creation of multi-analyte detection POCT tools, the implementation of education and training programs, community engagement initiatives, fostering public-private collaborations, and the establishment of reliable supply chains. Through these concerted efforts, we aim to accelerate the development of POCT in the sSA region, ensuring its effectiveness and accessibility in addressing the diagnostic challenges associated with PRIDs.
format: application/pdf
format: text/html
creator: Benedict Ofori
creator: Seth Twum
creator: Silas Nkansah Yeboah
creator: Felix Ansah
creator: Kwabena Amofa Nketia Sarpong
subject: Drugs and Devices
subject: Global Health
subject: Infectious Diseases
subject: Healthcare Services
description: doi:10.7717/peerj.17198
publisher: PeerJ Inc.
rights: © 2024 Ofori et al.
abstract: In this review, we examine the current landscape of point-of-care testing (POCT) diagnostic tools designed for poverty-related infectious diseases (PRIDs) in sub-Saharan Africa (sSA) while delineating key avenues for future advancements. Our analysis encompasses both established and emerging diagnostic methods for PRIDs, addressing the persistent challenges in POCT tool development and deployment, such as cost, accessibility, and reliability. We emphasize recent advancements in POCT diagnostic tools as well as platforms poised to enhance diagnostic testing in sSA. Recognizing the urgency for affordable and widely accessible POCT diagnostic tools to detect PRIDs in sSA, we advocate for a multidisciplinary approach. This approach integrates current and emerging diagnostic methods, explicitly addressing challenges hindering point-of-care (POC) tool development. Furthermore, it recognizes the profound impact of misdiagnosis on public and global health, emphasizing the need for effective tools. To facilitate the successful development and implementation of POCT diagnostic tools in sSA, we propose strategies including the creation of multi-analyte detection POCT tools, the implementation of education and training programs, community engagement initiatives, fostering public-private collaborations, and the establishment of reliable supply chains. Through these concerted efforts, we aim to accelerate the development of POCT in the sSA region, ensuring its effectiveness and accessibility in addressing the diagnostic challenges associated with PRIDs.
bibliographic citation: Ofori et al. (2024) Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa. PeerJ 12:e17198 https://doi.org/10.7717/peerj.17198
date submitted: 2023-08-21
date accepted: 2024-03-14
issued: 2024-06-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ofori
  given name: Benedict
author list: Agent
  family name: Twum
  given name: Seth
author list: Agent
  family name: Nkansah Yeboah
  given name: Silas
author list: Agent
  family name: Ansah
  given name: Felix
author list: Agent
  family name: Amofa Nketia Sarpong
  given name: Kwabena
doi: 10.7717/peerj.17198
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-21
copyright: © 2024 Ofori et al.
attribution name: Ofori et al.

Path for recovery: an ecological overview of the Jambato Harlequin Toad (Bufonidae: Atelopus ignescens) in its last known locality, Angamarca Valley, Ecuador
type: item
type: AcademicArticle
description: The Jambato Harlequin toad (Atelopus ignescens), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen Batrachochytrium dendrobatidis (Bd), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato.
format: application/pdf
format: text/html
creator: Mateo A. Vega-Yánez
creator: Amanda B. Quezada-Riera
creator: Blanca Rios-Touma
creator: María del Carmen Vizcaíno-Barba
creator: William Millingalli
creator: Orlando Ganzino
creator: Luis A. Coloma
creator: Elicio E. Tapia
creator: Nadine Dupérré
creator: Mónica Páez-Vacas
creator: David Parra-Puente
creator: Daniela Franco-Mena
creator: Gabriela Gavilanes
creator: David Salazar-Valenzuela
creator: Carlos A. Valle
creator: Juan M. Guayasamin
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.17344
publisher: PeerJ Inc.
rights: © 2024 Vega-Yánez et al.
abstract: The Jambato Harlequin toad (Atelopus ignescens), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen Batrachochytrium dendrobatidis (Bd), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato.
bibliographic citation: Vega-Yánez et al. (2024) Path for recovery: an ecological overview of the Jambato Harlequin Toad (Bufonidae: Atelopus ignescens) in its last known locality, Angamarca Valley, Ecuador. PeerJ 12:e17344 https://doi.org/10.7717/peerj.17344
date submitted: 2024-02-23
date accepted: 2024-04-15
issued: 2024-06-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vega-Yánez
  given name: Mateo A.
author list: Agent
  family name: Quezada-Riera
  given name: Amanda B.
author list: Agent
  family name: Rios-Touma
  given name: Blanca
author list: Agent
  family name: Vizcaíno-Barba
  given name: María del Carmen
author list: Agent
  family name: Millingalli
  given name: William
author list: Agent
  family name: Ganzino
  given name: Orlando
author list: Agent
  family name: Coloma
  given name: Luis A.
author list: Agent
  family name: Tapia
  given name: Elicio E.
author list: Agent
  family name: Dupérré
  given name: Nadine
author list: Agent
  family name: Páez-Vacas
  given name: Mónica
author list: Agent
  family name: Parra-Puente
  given name: David
author list: Agent
  family name: Franco-Mena
  given name: Daniela
author list: Agent
  family name: Gavilanes
  given name: Gabriela
author list: Agent
  family name: Salazar-Valenzuela
  given name: David
author list: Agent
  family name: Valle
  given name: Carlos A.
author list: Agent
  family name: Guayasamin
  given name: Juan M.
doi: 10.7717/peerj.17344
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-21
copyright: ©2024 Vega-Yánez et al.
attribution name: Vega-Yánez et al.

Taxon-dependent diversity response along a temperate elevation gradient covered by grassland
type: item
type: AcademicArticle
description: Elevational gradients constitute excellent systems for understanding the mechanisms that generate and maintain global biodiversity patterns. Climatic gradients associated with elevation show strong influence on species distribution in mountains. The study of mountains covered by the same habitat type is an ideal scenario to compare alternatives to the energy hypotheses. Our aim was to investigate how changes in climatic conditions along the elevational gradient drive α- and β-diversity of four taxa in a mountain system located within a grassland biome. We sampled ants, spiders, birds and plants, and measured climatic variables at six elevational bands (with 10 sampling sites each) established between 470 and 1,000 masl on a mountain from the Ventania Mountain System, Argentina. Species richness per site and β-diversity (turnover and nestedness) between the lowest band and upper sites were estimated. For most taxa, species richness declined at high elevations and energy, through temperature, was the major driver of species richness for ants, plants and birds, prevailing over productivity and water availability. The major β-diversity component was turnover for plants, spiders and birds, and nestedness for ants. The unique environmental conditions of the upper bands could favour the occurrence of specialist and endemic species.
format: application/pdf
format: text/html
creator: Santiago Santoandré
creator: Carolina Samanta Ramos
creator: Pablo Picca
creator: Julieta Filloy
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.17375
publisher: PeerJ Inc.
rights: © 2024 Santoandré et al.
abstract: Elevational gradients constitute excellent systems for understanding the mechanisms that generate and maintain global biodiversity patterns. Climatic gradients associated with elevation show strong influence on species distribution in mountains. The study of mountains covered by the same habitat type is an ideal scenario to compare alternatives to the energy hypotheses. Our aim was to investigate how changes in climatic conditions along the elevational gradient drive α- and β-diversity of four taxa in a mountain system located within a grassland biome. We sampled ants, spiders, birds and plants, and measured climatic variables at six elevational bands (with 10 sampling sites each) established between 470 and 1,000 masl on a mountain from the Ventania Mountain System, Argentina. Species richness per site and β-diversity (turnover and nestedness) between the lowest band and upper sites were estimated. For most taxa, species richness declined at high elevations and energy, through temperature, was the major driver of species richness for ants, plants and birds, prevailing over productivity and water availability. The major β-diversity component was turnover for plants, spiders and birds, and nestedness for ants. The unique environmental conditions of the upper bands could favour the occurrence of specialist and endemic species.
bibliographic citation: Santoandré et al. (2024) Taxon-dependent diversity response along a temperate elevation gradient covered by grassland. PeerJ 12:e17375 https://doi.org/10.7717/peerj.17375
date submitted: 2023-08-16
date accepted: 2024-04-19
issued: 2024-06-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santoandré
  given name: Santiago
author list: Agent
  family name: Ramos
  given name: Carolina Samanta
author list: Agent
  family name: Picca
  given name: Pablo
author list: Agent
  family name: Filloy
  given name: Julieta
doi: 10.7717/peerj.17375
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-21
copyright: ©2024 Santoandré et al.
attribution name: Santoandré et al.

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