PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay
items: Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study
items: Focused ultrasound-induced cell apoptosis for the treatment of tumours
items: Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study
items: Association between NKILA and some apoptotic gene expression in atherosclerosis
items: Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study
items: Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review
items: Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species
items: Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years
items: Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California

Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay
type: item
type: AcademicArticle
description: Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.
format: application/pdf
format: text/html
creator: Marianela Gastaldi
creator: M. Sabrina Pankey
creator: Guillermo Svendsen
creator: Alonso Medina
creator: Fausto Firstater
creator: Maite Narvarte
creator: Mariana Lozada
creator: Michael Lesser
subject: Biodiversity
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.17707
publisher: PeerJ Inc.
rights: © 2024 Gastaldi et al.
abstract: Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.
bibliographic citation: Gastaldi et al. (2024) Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay. PeerJ 12:e17707 https://doi.org/10.7717/peerj.17707
date submitted: 2024-02-05
date accepted: 2024-06-18
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gastaldi
  given name: Marianela
author list: Agent
  family name: Pankey
  given name: M. Sabrina
author list: Agent
  family name: Svendsen
  given name: Guillermo
author list: Agent
  family name: Medina
  given name: Alonso
author list: Agent
  family name: Firstater
  given name: Fausto
author list: Agent
  family name: Narvarte
  given name: Maite
author list: Agent
  family name: Lozada
  given name: Mariana
author list: Agent
  family name: Lesser
  given name: Michael
doi: 10.7717/peerj.17707
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: © 2024 Gastaldi et al.
attribution name: Gastaldi et al.

Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study
type: item
type: AcademicArticle
description: Background The increasing number of people living with HIV requires a simple and easy-to-use quality of life (QoL) scale for people living with HIV (PLWH). This study aims to adapt the PozQoL scale into Turkish and assess its reliability and validity for the PLWH population in Turkey. Methods Translation-back-translation methodology was employed, and face-to-face interviews were conducted with 130 patients using the PozQoL, socio-demographic, and clinical data questionnaire. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) were utilized to identify the underlying factor structure and examine the validity of the measurement model, respectively. Cronbach’s alpha and intraclass correlation coefficients (ICCs) were used to assess internal consistency and test-retest reliability, respectively. Results EFA revealed four factors with an eigenvalue of 0.88, explaining 62.1% of the cumulative variance. CFA indicated that the four-factor solution achieved good levels of fit. The total Cronbach’s alpha was 0.81, indicating high internal consistency. The ICC for the total score was 0.92 (95% confidence interval (CI) [0.90–0.94]; p < 0.05), demonstrating high test-retest reliability. Conclusion The Turkish version of the PozQoL was found to be a valid and reliable tool for assessing the health-related QoL of PLWH in Turkey.
format: application/pdf
format: text/html
creator: Sabri Atalay
creator: Zeynep Sedef Varol
creator: Sarp Singil
creator: Ufuk Sönmez
subject: Global Health
subject: HIV
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.17873
publisher: PeerJ Inc.
rights: © 2024 Atalay et al.
abstract: Background The increasing number of people living with HIV requires a simple and easy-to-use quality of life (QoL) scale for people living with HIV (PLWH). This study aims to adapt the PozQoL scale into Turkish and assess its reliability and validity for the PLWH population in Turkey. Methods Translation-back-translation methodology was employed, and face-to-face interviews were conducted with 130 patients using the PozQoL, socio-demographic, and clinical data questionnaire. Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) were utilized to identify the underlying factor structure and examine the validity of the measurement model, respectively. Cronbach’s alpha and intraclass correlation coefficients (ICCs) were used to assess internal consistency and test-retest reliability, respectively. Results EFA revealed four factors with an eigenvalue of 0.88, explaining 62.1% of the cumulative variance. CFA indicated that the four-factor solution achieved good levels of fit. The total Cronbach’s alpha was 0.81, indicating high internal consistency. The ICC for the total score was 0.92 (95% confidence interval (CI) [0.90–0.94]; p < 0.05), demonstrating high test-retest reliability. Conclusion The Turkish version of the PozQoL was found to be a valid and reliable tool for assessing the health-related QoL of PLWH in Turkey.
bibliographic citation: Atalay et al. (2024) Validation of PozQoL scale in Turkish population living with HIV: a cross-cultural adaptation study. PeerJ 12:e17873 https://doi.org/10.7717/peerj.17873
date submitted: 2024-03-06
date accepted: 2024-07-16
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atalay
  given name: Sabri
author list: Agent
  family name: Varol
  given name: Zeynep Sedef
author list: Agent
  family name: Singil
  given name: Sarp
author list: Agent
  family name: Sönmez
  given name: Ufuk
doi: 10.7717/peerj.17873
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: © 2024 Atalay et al.
attribution name: Atalay et al.

Focused ultrasound-induced cell apoptosis for the treatment of tumours
type: item
type: AcademicArticle
description: Cancer is a serious public health problem worldwide. Traditional treatments, such as surgery, radiotherapy, chemotherapy, and immunotherapy, do not always yield satisfactory results; therefore, an efficient treatment for tumours is urgently needed. As a convenient and minimally invasive modality, focused ultrasound (FUS) has been used not only as a diagnostic tool but also as a therapeutic tool in an increasing number of studies. FUS can help treat malignant tumours by inducing apoptosis. This review describes the three apoptotic pathways, apoptotic cell clearance, and how FUS affects these three apoptotic pathways. This review also discusses the role of thermal and cavitation effects on apoptosis, including caspase activity, mitochondrial dysfunction, and Ca2+ elease. Finally, this article reviews various aspects of FUS combination therapy, including sensitization by radiotherapy and chemotherapy, gene expression upregulation, and the introduction of therapeutic gases, to provide new ideas for clinical tumour therapy.
format: application/pdf
format: text/html
creator: Na Wang
creator: Li Luo
creator: Xinzhi Xu
creator: Hang Zhou
creator: Fang Li
subject: Oncology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.17886
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Cancer is a serious public health problem worldwide. Traditional treatments, such as surgery, radiotherapy, chemotherapy, and immunotherapy, do not always yield satisfactory results; therefore, an efficient treatment for tumours is urgently needed. As a convenient and minimally invasive modality, focused ultrasound (FUS) has been used not only as a diagnostic tool but also as a therapeutic tool in an increasing number of studies. FUS can help treat malignant tumours by inducing apoptosis. This review describes the three apoptotic pathways, apoptotic cell clearance, and how FUS affects these three apoptotic pathways. This review also discusses the role of thermal and cavitation effects on apoptosis, including caspase activity, mitochondrial dysfunction, and Ca2+ elease. Finally, this article reviews various aspects of FUS combination therapy, including sensitization by radiotherapy and chemotherapy, gene expression upregulation, and the introduction of therapeutic gases, to provide new ideas for clinical tumour therapy.
bibliographic citation: Wang et al. (2024) Focused ultrasound-induced cell apoptosis for the treatment of tumours. PeerJ 12:e17886 https://doi.org/10.7717/peerj.17886
date submitted: 2024-02-01
date accepted: 2024-07-18
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Na
author list: Agent
  family name: Luo
  given name: Li
author list: Agent
  family name: Xu
  given name: Xinzhi
author list: Agent
  family name: Zhou
  given name: Hang
author list: Agent
  family name: Li
  given name: Fang
doi: 10.7717/peerj.17886
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study
type: item
type: AcademicArticle
description: Background The aging of the population highlights the need to establish empathetic connections with older adults. To achieve this, age simulation suits have been designed, allowing users to experience the physical limitations associated with aging. This study aimed to evaluate the experience of dental students with these devices, using psychometric tools to measure the impact on their understanding and empathy. Methods A pre/post-test study was conducted with the participation of 63 dental students from Rey Juan Carlos University who were fitted with an age simulation suit and asked to perform different tasks. Psychometric tools were used to assess specific parameters. Empathy was measured using the Jefferson Empathy Scale, emotional intelligence was assessed with the Trait Meta-Mood Scale-24 (TMMS-24), and the emotional attention dimension was analyzed using the Positive and Negative Affect Schedule (PANAS). Results The scores on the Jefferson Empathy Scale significantly improved from 88.44 ± 6.8 to 91.06 ± 10.11 after using the simulation suit (P < 0.026). Pearson’s product moment correlation analysis showed no significant positive association or correlation between age and scores from the three questionnaires. In the rest, a positive and significant correlation was observed (P < 0.0001). Conclusions Age simulation activities effectively enhance empathy among dental students. However, more studies are needed to foster positive attitudes toward aging and prevent negative stereotypes.
format: application/pdf
format: text/html
creator: Jesus Rodriguez-Molinero
creator: Esther Delgado-Somolinos
creator: Blanca C. Miguelañez-Medrán
creator: Rosario Ramirez-Puerta
creator: Inmaculada Corral-Liria
creator: Raquel Jiménez-Fernández
creator: Marta Elena Losa-Iglesias
creator: Antonio F. López-Sánchez
subject: Dentistry
subject: Geriatrics
subject: Science and Medical Education
description: doi:10.7717/peerj.17908
publisher: PeerJ Inc.
rights: © 2024 Rodriguez-Molinero et al.
abstract: Background The aging of the population highlights the need to establish empathetic connections with older adults. To achieve this, age simulation suits have been designed, allowing users to experience the physical limitations associated with aging. This study aimed to evaluate the experience of dental students with these devices, using psychometric tools to measure the impact on their understanding and empathy. Methods A pre/post-test study was conducted with the participation of 63 dental students from Rey Juan Carlos University who were fitted with an age simulation suit and asked to perform different tasks. Psychometric tools were used to assess specific parameters. Empathy was measured using the Jefferson Empathy Scale, emotional intelligence was assessed with the Trait Meta-Mood Scale-24 (TMMS-24), and the emotional attention dimension was analyzed using the Positive and Negative Affect Schedule (PANAS). Results The scores on the Jefferson Empathy Scale significantly improved from 88.44 ± 6.8 to 91.06 ± 10.11 after using the simulation suit (P < 0.026). Pearson’s product moment correlation analysis showed no significant positive association or correlation between age and scores from the three questionnaires. In the rest, a positive and significant correlation was observed (P < 0.0001). Conclusions Age simulation activities effectively enhance empathy among dental students. However, more studies are needed to foster positive attitudes toward aging and prevent negative stereotypes.
bibliographic citation: Rodriguez-Molinero et al. (2024) Use of an age-simulation suit as an empathy-building method for dental students: a pre-post study. PeerJ 12:e17908 https://doi.org/10.7717/peerj.17908
date submitted: 2024-04-18
date accepted: 2024-07-22
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez-Molinero
  given name: Jesus
author list: Agent
  family name: Delgado-Somolinos
  given name: Esther
author list: Agent
  family name: Miguelañez-Medrán
  given name: Blanca C.
author list: Agent
  family name: Ramirez-Puerta
  given name: Rosario
author list: Agent
  family name: Corral-Liria
  given name: Inmaculada
author list: Agent
  family name: Jiménez-Fernández
  given name: Raquel
author list: Agent
  family name: Losa-Iglesias
  given name: Marta Elena
author list: Agent
  family name: López-Sánchez
  given name: Antonio F.
doi: 10.7717/peerj.17908
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: ©2024 Rodriguez-Molinero et al.
attribution name: Rodriguez-Molinero et al.

Association between NKILA and some apoptotic gene expression in atherosclerosis
type: item
type: AcademicArticle
description: Oxidized light-density lipoprotein (ox-LDL) causes endothelial dysfunction, which is an important determinant of atherogenesis, and subsequently leads to apoptosis. Atherosclerosis is one of the most significant cardiovascular diseases (CVDs) threatening human health and causes death worldwide. Recently, long noncoding RNAs (lncRNAs) have been suggested to involved in vascular biology. Ox-LDL activates nuclear factor kappa-B (NF-κB), and NF-κB interacting lncRNA (NKILA) inhibits NF-κB signaling. In this study, the hypothesis is that NKILA may regulate endothelial cell (EC) apoptosis and, therefore, play a role in the pathogenesis of atherosclerosis. This hypothesis is based on the knowledge that EC apoptosis contributes to atherosclerosis development and that NKILA has become a prominent lncRNA in CVDs. The expression of Bcl-2-associated X protein (BAX), caspase 9 (CASP9), cytochrome c (Cyt c, CYCS), apoptotic protease activating factor 1 (APAF1), and B-cell lymphoma 2 (BCL-2) genes in human umbilical vein endothelial cells (HUVEC) treated with ox-LDL and transfected with NKILA siRNA was analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR). BAX, CASP9, CYCS, APAF1, and BCL-2 gene expression was downregulated in ox-LDL and NKILA siRNA-treated HUVEC. In addition, when threshold/quantification cycle (Cq) values of NKILA gene expression increased, Cq values of BAX, CASP9, APAF1, and BCL-2 gene expression increased statistics significantly. The expression detection of all these genes, resulting from NKILA gene silencing, may provide guidance for epigenetic studies on EC apoptosis in atherosclerosis.
format: application/pdf
format: text/html
creator: Burcu Bayyurt
creator: Şeyda Akın
creator: Nil Özbilüm Şahin
creator: İzzet Yelkuvan
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Medical Genetics
description: doi:10.7717/peerj.17915
publisher: PeerJ Inc.
rights: © 2024 Bayyurt et al.
abstract: Oxidized light-density lipoprotein (ox-LDL) causes endothelial dysfunction, which is an important determinant of atherogenesis, and subsequently leads to apoptosis. Atherosclerosis is one of the most significant cardiovascular diseases (CVDs) threatening human health and causes death worldwide. Recently, long noncoding RNAs (lncRNAs) have been suggested to involved in vascular biology. Ox-LDL activates nuclear factor kappa-B (NF-κB), and NF-κB interacting lncRNA (NKILA) inhibits NF-κB signaling. In this study, the hypothesis is that NKILA may regulate endothelial cell (EC) apoptosis and, therefore, play a role in the pathogenesis of atherosclerosis. This hypothesis is based on the knowledge that EC apoptosis contributes to atherosclerosis development and that NKILA has become a prominent lncRNA in CVDs. The expression of Bcl-2-associated X protein (BAX), caspase 9 (CASP9), cytochrome c (Cyt c, CYCS), apoptotic protease activating factor 1 (APAF1), and B-cell lymphoma 2 (BCL-2) genes in human umbilical vein endothelial cells (HUVEC) treated with ox-LDL and transfected with NKILA siRNA was analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR). BAX, CASP9, CYCS, APAF1, and BCL-2 gene expression was downregulated in ox-LDL and NKILA siRNA-treated HUVEC. In addition, when threshold/quantification cycle (Cq) values of NKILA gene expression increased, Cq values of BAX, CASP9, APAF1, and BCL-2 gene expression increased statistics significantly. The expression detection of all these genes, resulting from NKILA gene silencing, may provide guidance for epigenetic studies on EC apoptosis in atherosclerosis.
bibliographic citation: Bayyurt et al. (2024) Association between NKILA and some apoptotic gene expression in atherosclerosis. PeerJ 12:e17915 https://doi.org/10.7717/peerj.17915
date submitted: 2024-04-19
date accepted: 2024-07-23
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bayyurt
  given name: Burcu
author list: Agent
  family name: Akın
  given name: Şeyda
author list: Agent
  family name: Özbilüm Şahin
  given name: Nil
author list: Agent
  family name: Yelkuvan
  given name: İzzet
doi: 10.7717/peerj.17915
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: ©2024 Bayyurt et al.
attribution name: Bayyurt et al.

Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study
type: item
type: AcademicArticle
description: Purpose To compare the visual quality after wavefront-guided femtosecond LASIK (WFG FS-LASIK) in patients with different levels of preoperative total ocular higher-order aberrations to guide clinical decision-making regarding patient selection and treatment strategies. Methods This study included 112 right eyes of 112 patients who previously underwent WFG FS-LASIK for correcting myopia and myopic astigmatism. The patients were divided into two groups based on the mean values of preoperative total ocular HOAs (0.30 ± 0.09 µm): HOA ≤ 0.3 and > 0.3 groups. The visual acuity, manifest refraction, corneal Strehl ratio (SR), root mean square (RMS) of corneal and ocular aberrations, and area under the log contrast sensitivity function (AULCSF) of both groups were compared preoperatively and at 1, 3, 6, and 12 months postoperatively. Results The induced ocular HOAs and coma (Δ = 1 mo − Preop) were significantly lower in the HOAs > 0.3 group than in the HOAs ≤ 0.3 group (ΔHOAs: 0.39 ± 0.19 vs. 0.29 ± 0.18 μm, t = 2.797, P = 0.006; Δ coma: 0.30 ± 0.19 vs. 0.20 ± 0.21 μm, t = 2.542, P = 0.012). In the HOAs > 0.3 group, ΔHOAs were negatively correlated with the preoperative ocular HOAs (r = −0.315, P = 0.019). In the HOAs ≤ 0.3 group, the regression equation for Δ HOAs = 0.098 + 0.053 |SE| (F = 21.756, P < 0.001). In the HOAs > 0.3 group, the regression equation for ΔHOAs = 0.534 − 1.081 HOAs + 0.038|Sphere| (F = 7.954, P = 0.001). The postoperative uncorrected distance visual acuity, spherical equivalent, corneal aberrations, SR and AULCSF of both groups were similar (all P > 0.05). Furthermore, the ocular aberrations were not significantly different between both groups at 3, 6, and 12 months postoperatively (all P > 0.05). In addition, compared with the preoperative period, the AULCSF of both groups were significantly increased in the postoperative period (all P < 0.05). Conclusions The induced ocular HOAs and coma in HOAs > 0.3 group were lower. However, both groups achieved…
format: application/pdf
format: text/html
creator: Yu Zhang
creator: Yangrui Du
creator: Ming He
creator: Youdan Zhang
creator: Zhiyu Du
subject: Ophthalmology
subject: Pathology
subject: Pharmacology
subject: Translational Medicine
description: doi:10.7717/peerj.17940
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Purpose To compare the visual quality after wavefront-guided femtosecond LASIK (WFG FS-LASIK) in patients with different levels of preoperative total ocular higher-order aberrations to guide clinical decision-making regarding patient selection and treatment strategies. Methods This study included 112 right eyes of 112 patients who previously underwent WFG FS-LASIK for correcting myopia and myopic astigmatism. The patients were divided into two groups based on the mean values of preoperative total ocular HOAs (0.30 ± 0.09 µm): HOA ≤ 0.3 and > 0.3 groups. The visual acuity, manifest refraction, corneal Strehl ratio (SR), root mean square (RMS) of corneal and ocular aberrations, and area under the log contrast sensitivity function (AULCSF) of both groups were compared preoperatively and at 1, 3, 6, and 12 months postoperatively. Results The induced ocular HOAs and coma (Δ = 1 mo − Preop) were significantly lower in the HOAs > 0.3 group than in the HOAs ≤ 0.3 group (ΔHOAs: 0.39 ± 0.19 vs. 0.29 ± 0.18 μm, t = 2.797, P = 0.006; Δ coma: 0.30 ± 0.19 vs. 0.20 ± 0.21 μm, t = 2.542, P = 0.012). In the HOAs > 0.3 group, ΔHOAs were negatively correlated with the preoperative ocular HOAs (r = −0.315, P = 0.019). In the HOAs ≤ 0.3 group, the regression equation for Δ HOAs = 0.098 + 0.053 |SE| (F = 21.756, P < 0.001). In the HOAs > 0.3 group, the regression equation for ΔHOAs = 0.534 − 1.081 HOAs + 0.038|Sphere| (F = 7.954, P = 0.001). The postoperative uncorrected distance visual acuity, spherical equivalent, corneal aberrations, SR and AULCSF of both groups were similar (all P > 0.05). Furthermore, the ocular aberrations were not significantly different between both groups at 3, 6, and 12 months postoperatively (all P > 0.05). In addition, compared with the preoperative period, the AULCSF of both groups were significantly increased in the postoperative period (all P < 0.05). Conclusions The induced ocular HOAs and coma in HOAs > 0.3 group were lower. However, both groups achieved…
bibliographic citation: Zhang et al. (2024) Comparison of visual quality after wavefront-guided LASIK in patients with different levels of preoperative total ocular higher-order aberrations: a retrospective study. PeerJ 12:e17940 https://doi.org/10.7717/peerj.17940
date submitted: 2024-05-16
date accepted: 2024-07-28
issued: 2024-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Du
  given name: Yangrui
author list: Agent
  family name: He
  given name: Ming
author list: Agent
  family name: Zhang
  given name: Youdan
author list: Agent
  family name: Du
  given name: Zhiyu
doi: 10.7717/peerj.17940
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-21
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review
type: item
type: AcademicArticle
description: Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants’ stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities.
format: application/pdf
format: text/html
creator: Awmpuizeli Fanai
creator: Beirachhitha Bohia
creator: Felicia Lalremruati
creator: Nancy Lalhriatpuii
creator: Lalrokimi
creator: Rosie Lalmuanpuii
creator: Prashant Kumar Singh
creator: Zothanpuia
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.17882
publisher: PeerJ Inc.
rights: © 2024 Fanai et al.
abstract: Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants’ stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities.
bibliographic citation: Fanai et al. (2024) Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review. PeerJ 12:e17882 https://doi.org/10.7717/peerj.17882
date submitted: 2024-05-02
date accepted: 2024-07-17
issued: 2024-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fanai
  given name: Awmpuizeli
author list: Agent
  family name: Bohia
  given name: Beirachhitha
author list: Agent
  family name: Lalremruati
  given name: Felicia
author list: Agent
  family name: Lalhriatpuii
  given name: Nancy
author list: Agent
  family name: Lalrokimi
author list: Agent
  family name: Lalmuanpuii
  given name: Rosie
author list: Agent
  family name: Singh
  given name: Prashant Kumar
author list: Agent
  family name: Zothanpuia
doi: 10.7717/peerj.17882
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-20
copyright: © 2024 Fanai et al.
attribution name: Fanai et al.

Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species
type: item
type: AcademicArticle
description: Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated in the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to species with broad geographic distributions. In this study, we assessed and redefined the species boundaries of the Centrolene buckleyi species complex, and formally described two new species from the Andes of Ecuador. These new taxa are recognized by a combination of morphometric, osteological, acoustic, and genetic data. Following IUCN criteria, we propose that the two new species should to be considered as Endangered (EN), mainly because of their small distributions and habitat loss. The C. buckleyi complex provides insights into the biogeography of closely related Andean species. As in other glassfrogs, speciation in Centrolene seems to be mediated by the linearity of the Andes, where gene flow can be restricted by topography and, also, local extinctions.
format: application/pdf
format: text/html
creator: Daniela Franco-Mena
creator: Ignacio De la Riva
creator: Mateo A. Vega-Yánez
creator: Paul Székely
creator: Luis Amador
creator: Diego Batallas
creator: Juan P. Reyes-Puig
creator: Diego F. Cisneros-Heredia
creator: Khristian Venegas-Valencia
creator: Sandra P. Galeano
creator: Jaime Culebras
creator: Juan M. Guayasamin
subject: Biodiversity
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.17712
publisher: PeerJ Inc.
rights: © 2024 Franco-Mena et al.
abstract: Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated in the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to species with broad geographic distributions. In this study, we assessed and redefined the species boundaries of the Centrolene buckleyi species complex, and formally described two new species from the Andes of Ecuador. These new taxa are recognized by a combination of morphometric, osteological, acoustic, and genetic data. Following IUCN criteria, we propose that the two new species should to be considered as Endangered (EN), mainly because of their small distributions and habitat loss. The C. buckleyi complex provides insights into the biogeography of closely related Andean species. As in other glassfrogs, speciation in Centrolene seems to be mediated by the linearity of the Andes, where gene flow can be restricted by topography and, also, local extinctions.
bibliographic citation: Franco-Mena et al. (2024) Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species. PeerJ 12:e17712 https://doi.org/10.7717/peerj.17712
date submitted: 2023-09-28
date accepted: 2024-06-18
issued: 2024-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Franco-Mena
  given name: Daniela
author list: Agent
  family name: De la Riva
  given name: Ignacio
author list: Agent
  family name: Vega-Yánez
  given name: Mateo A.
author list: Agent
  family name: Székely
  given name: Paul
author list: Agent
  family name: Amador
  given name: Luis
author list: Agent
  family name: Batallas
  given name: Diego
author list: Agent
  family name: Reyes-Puig
  given name: Juan P.
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Venegas-Valencia
  given name: Khristian
author list: Agent
  family name: Galeano
  given name: Sandra P.
author list: Agent
  family name: Culebras
  given name: Jaime
author list: Agent
  family name: Guayasamin
  given name: Juan M.
doi: 10.7717/peerj.17712
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-20
copyright: © 2024 Franco-Mena et al.
attribution name: Franco-Mena et al.

Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years
type: item
type: AcademicArticle
description: The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard’s dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard’s dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species.
format: application/pdf
format: text/html
creator: Ubaldo Márquez-Luna
creator: Pablo Arenas
creator: M. Isabel Herrera-Juárez
creator: Hilda Marcela Pérez-Escobedo
creator: Gustavo Hernández-Orta
creator: Guillermo Gil-Alarcón
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.17888
publisher: PeerJ Inc.
rights: © 2024 Márquez-Luna et al.
abstract: The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard’s dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard’s dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species.
bibliographic citation: Márquez-Luna et al. (2024) Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years. PeerJ 12:e17888 https://doi.org/10.7717/peerj.17888
date submitted: 2024-03-13
date accepted: 2024-07-18
issued: 2024-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Márquez-Luna
  given name: Ubaldo
author list: Agent
  family name: Arenas
  given name: Pablo
author list: Agent
  family name: Herrera-Juárez
  given name: M. Isabel
author list: Agent
  family name: Pérez-Escobedo
  given name: Hilda Marcela
author list: Agent
  family name: Hernández-Orta
  given name: Gustavo
author list: Agent
  family name: Gil-Alarcón
  given name: Guillermo
doi: 10.7717/peerj.17888
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-20
copyright: © 2024 Márquez-Luna et al.
attribution name: Márquez-Luna et al.

Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California
type: item
type: AcademicArticle
description: Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ‘ja ‘ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
format: application/pdf
format: text/html
creator: Manet E. Peña-Salinas
creator: Daan R. Speth
creator: Daniel R. Utter
creator: Ronald M. Spelz
creator: Sujung Lim
creator: Robert Zierenberg
creator: David W. Caress
creator: Patricia G. Núñez
creator: Roberto Vázquez
creator: Victoria J. Orphan
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.17724
publisher: PeerJ Inc.
rights: © 2024 Peña-Salinas et al.
abstract: Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ‘ja ‘ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
bibliographic citation: Peña-Salinas et al. (2024) Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa ‘ja ‘ag hydrothermal vent fields in the Pescadero Basin, Gulf of California. PeerJ 12:e17724 https://doi.org/10.7717/peerj.17724
date submitted: 2023-12-06
date accepted: 2024-06-20
issued: 2024-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peña-Salinas
  given name: Manet E.
author list: Agent
  family name: Speth
  given name: Daan R.
author list: Agent
  family name: Utter
  given name: Daniel R.
author list: Agent
  family name: Spelz
  given name: Ronald M.
author list: Agent
  family name: Lim
  given name: Sujung
author list: Agent
  family name: Zierenberg
  given name: Robert
author list: Agent
  family name: Caress
  given name: David W.
author list: Agent
  family name: Núñez
  given name: Patricia G.
author list: Agent
  family name: Vázquez
  given name: Roberto
author list: Agent
  family name: Orphan
  given name: Victoria J.
doi: 10.7717/peerj.17724
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-19
copyright: © 2024 Peña-Salinas et al.
attribution name: Peña-Salinas et al.

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