PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Alleviation of cadmium stress in rice by inoculation of Bacillus cereus
items: A new spatiotemporal two-stage standardized weighted procedure for regional drought analysis
items: Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions
items: Assessment of the readiness of restorations manufactured by CAD/CAM in terms of marginal fit (Part I)
items: Stress coping strategies used by nurses during the COVID-19 pandemic
items: Comparison between hydroxyapatite and polycaprolactone in inducing osteogenic differentiation and augmenting maxillary bone regeneration in rats
items: Predicting surface abundance of federally threatened Jollyville Plateau Salamanders (Eurycea tonkawae) to inform management activities at a highly modified urban spring
items: Scavenging vs hunting affects behavioral traits of an opportunistic carnivore
items: How beavers affect riverine aquatic macroinvertebrates: a review
items: The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients

Alleviation of cadmium stress in rice by inoculation of Bacillus cereus
type: item
type: AcademicArticle
description: Heavy metal resistant bacteria are of great importance because they play a crucial role in bioremediation. In the present study, 11 bacterial strains isolated from industrial waste were screened under different concentrations of cadmium (Cd) (100 µM and 200 µM). Among 11 strains, the Cd tolerant Bacillus cereus (S6D1–105) strain was selected for in vitro and in vivo studies. B. cereus was able to solubilize potassium, and phosphate as well as produce protease and siderophores during plate essays. Moreover, we observed the response of hydroponically grown rice plants, inoculated with B. cereus which was able to promote plant growth, by increasing plant biomass, chlorophyll contents, relative water content, different antioxidant enzymatic activity such as catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase and phenylalanine ammonia-lyase and reducing malondialdehyde content in both roots and leaves of rice plants under Cd stress. Our results showed that the B. cereus can be used as a biofertilizer which might be beneficial for rice cultivation in Cd contaminated soils.
format: application/pdf
format: text/html
creator: Zahra Jabeen
creator: Faiza Irshad
creator: Ayesha Habib
creator: Nazim Hussain
creator: Muhammad Sajjad
creator: Saqib Mumtaz
creator: Sidra Rehman
creator: Waseem Haider
creator: Muhammad Nadeem Hassan
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.13131
publisher: PeerJ Inc.
rights: © 2022 Jabeen et al.
abstract: Heavy metal resistant bacteria are of great importance because they play a crucial role in bioremediation. In the present study, 11 bacterial strains isolated from industrial waste were screened under different concentrations of cadmium (Cd) (100 µM and 200 µM). Among 11 strains, the Cd tolerant Bacillus cereus (S6D1–105) strain was selected for in vitro and in vivo studies. B. cereus was able to solubilize potassium, and phosphate as well as produce protease and siderophores during plate essays. Moreover, we observed the response of hydroponically grown rice plants, inoculated with B. cereus which was able to promote plant growth, by increasing plant biomass, chlorophyll contents, relative water content, different antioxidant enzymatic activity such as catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase and phenylalanine ammonia-lyase and reducing malondialdehyde content in both roots and leaves of rice plants under Cd stress. Our results showed that the B. cereus can be used as a biofertilizer which might be beneficial for rice cultivation in Cd contaminated soils.
bibliographic citation: Jabeen et al. (2022) Alleviation of cadmium stress in rice by inoculation of Bacillus cereus. PeerJ 10:e13131 https://doi.org/10.7717/peerj.13131
date submitted: 2021-10-06
date accepted: 2022-02-25
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jabeen
  given name: Zahra
author list: Agent
  family name: Irshad
  given name: Faiza
author list: Agent
  family name: Habib
  given name: Ayesha
author list: Agent
  family name: Hussain
  given name: Nazim
author list: Agent
  family name: Sajjad
  given name: Muhammad
author list: Agent
  family name: Mumtaz
  given name: Saqib
author list: Agent
  family name: Rehman
  given name: Sidra
author list: Agent
  family name: Haider
  given name: Waseem
author list: Agent
  family name: Hassan
  given name: Muhammad Nadeem
doi: 10.7717/peerj.13131
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: © 2022 Jabeen et al.
attribution name: Jabeen et al.

A new spatiotemporal two-stage standardized weighted procedure for regional drought analysis
type: item
type: AcademicArticle
description: Drought is a complex phenomenon that occurs due to insufficient precipitation. It does not have immediate effects, but sustained drought can affect the hydrological, agriculture, economic sectors of the country. Therefore, there is a need for efficient methods and techniques that properly determine drought and its effects. Considering the significance and importance of drought monitoring methodologies, a new drought assessment procedure is proposed in the current study, known as the Maximum Spatio-Temporal Two-Stage Standardized Weighted Index (MSTTSSWI). The proposed MSTTSSWI is based on the weighting scheme, known as the Spatio-Temporal Two-Stage Standardized Weighting Scheme (STTSSWS). The potential of the weighting scheme is based on the Standardized Precipitation Index (SPI), Standardized Precipitation Evapotranspiration Index (SPEI), and the steady-state probabilities. Further, the STTSSWS computes spatiotemporal weights in two stages for various drought categories and stations. In the first stage of the STTSSWS, the SPI, SPEI, and the steady-state probabilities are calculated for each station at a 1-month time scale to assign weights for varying drought categories. However, in the second stage, these weights are further propagated based on spatiotemporal characteristics to obtain new weights for the various drought categories in the selected region. The STTSSWS is applied to the six meteorological stations of the Northern area, Pakistan. Moreover, the spatiotemporal weights obtained from STTSSWS are used to calculate MSTTSSWI for regional drought characterization. The MSTTSSWI may accurately provide regional spatiotemporal characteristics for the drought in the selected region and motivates researchers and policymakers to use the more comprehensive and accurate spatiotemporal characterization of drought in the selected region.
format: application/pdf
format: text/html
creator: Rizwan Niaz
creator: Nouman Iqbal
creator: Nadhir Al-Ansari
creator: Ijaz Hussain
creator: Elsayed Elsherbini Elashkar
creator: Sadaf Shamshoddin Soudagar
creator: Showkat Hussain Gani
creator: Alaa Mohamd Shoukry
creator: Saad Sh. Sammen
subject: Ecosystem Science
subject: Statistics
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13249
publisher: PeerJ Inc.
rights: © 2022 Niaz et al.
abstract: Drought is a complex phenomenon that occurs due to insufficient precipitation. It does not have immediate effects, but sustained drought can affect the hydrological, agriculture, economic sectors of the country. Therefore, there is a need for efficient methods and techniques that properly determine drought and its effects. Considering the significance and importance of drought monitoring methodologies, a new drought assessment procedure is proposed in the current study, known as the Maximum Spatio-Temporal Two-Stage Standardized Weighted Index (MSTTSSWI). The proposed MSTTSSWI is based on the weighting scheme, known as the Spatio-Temporal Two-Stage Standardized Weighting Scheme (STTSSWS). The potential of the weighting scheme is based on the Standardized Precipitation Index (SPI), Standardized Precipitation Evapotranspiration Index (SPEI), and the steady-state probabilities. Further, the STTSSWS computes spatiotemporal weights in two stages for various drought categories and stations. In the first stage of the STTSSWS, the SPI, SPEI, and the steady-state probabilities are calculated for each station at a 1-month time scale to assign weights for varying drought categories. However, in the second stage, these weights are further propagated based on spatiotemporal characteristics to obtain new weights for the various drought categories in the selected region. The STTSSWS is applied to the six meteorological stations of the Northern area, Pakistan. Moreover, the spatiotemporal weights obtained from STTSSWS are used to calculate MSTTSSWI for regional drought characterization. The MSTTSSWI may accurately provide regional spatiotemporal characteristics for the drought in the selected region and motivates researchers and policymakers to use the more comprehensive and accurate spatiotemporal characterization of drought in the selected region.
bibliographic citation: Niaz et al. (2022) A new spatiotemporal two-stage standardized weighted procedure for regional drought analysis. PeerJ 10:e13249 https://doi.org/10.7717/peerj.13249
date submitted: 2021-09-02
date accepted: 2022-03-21
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niaz
  given name: Rizwan
author list: Agent
  family name: Iqbal
  given name: Nouman
author list: Agent
  family name: Al-Ansari
  given name: Nadhir
author list: Agent
  family name: Hussain
  given name: Ijaz
author list: Agent
  family name: Elsherbini Elashkar
  given name: Elsayed
author list: Agent
  family name: Shamshoddin Soudagar
  given name: Sadaf
author list: Agent
  family name: Gani
  given name: Showkat Hussain
author list: Agent
  family name: Mohamd Shoukry
  given name: Alaa
author list: Agent
  family name: Sh. Sammen
  given name: Saad
doi: 10.7717/peerj.13249
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: © 2022 Niaz et al.
attribution name: Niaz et al.

Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions
type: item
type: AcademicArticle
description: Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting poin…
format: application/pdf
format: text/html
creator: Marina Püpke Marone
creator: Maria Fernanda Zaneli Campanari
creator: Fabio Trigo Raya
creator: Gonçalo Amarante Guimarães Pereira
creator: Marcelo Falsarella Carazzolle
subject: Bioinformatics
subject: Ecology
subject: Genetics
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13252
publisher: PeerJ Inc.
rights: © 2022 Marone et al.
abstract: Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting poin…
bibliographic citation: Marone et al. (2022) Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PeerJ 10:e13252 https://doi.org/10.7717/peerj.13252
date submitted: 2021-09-29
date accepted: 2022-03-21
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marone
  given name: Marina Püpke
author list: Agent
  family name: Campanari
  given name: Maria Fernanda Zaneli
author list: Agent
  family name: Raya
  given name: Fabio Trigo
author list: Agent
  family name: Pereira
  given name: Gonçalo Amarante Guimarães
author list: Agent
  family name: Carazzolle
  given name: Marcelo Falsarella
doi: 10.7717/peerj.13252
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: ©2022 Marone et al.
attribution name: Marone et al.

Assessment of the readiness of restorations manufactured by CAD/CAM in terms of marginal fit (Part I)
type: item
type: AcademicArticle
description: Background The master cast is the gold standard for the control and eventual adjustment of restorations produced by conventional procedures. Some digital workflow bypasses the master cast and relies completely on the precision of the CAD/CAM restoration. Aim To examine the reproducibility of the margins of CAD/CAM restorations generated from a single digital scan. Also, to check the readiness of these restorations for delivery directly after fabrication without adjustment on a master cast and thereby eliminate the need for the master cast. Methods A total of 18 metal substructures made from cobalt chrome alloy were fabricated utilizing a single STL file. The circumference was divided into eight zones. The vertical marginal discrepancy (VMD) was measured at each zone of each metal substructure, with optical microscopy at ×200 magnification. Results Measurements of vertical marginal discrepancy were in a range of (−94: 300) with a mean of 62 ± 60 μm. A one-way ANOVA test revealed that the mean VMD is significantly different among the 18 substructures (F17, 1,134 = 63.948, p < 0.001). Conclusion Although all the received substructures were fabricated from the same scan file, they were not identical and varied widely, and they were going outside the acceptable range in some zones. Within the limitations of this study, the marginal fit can be improved by extraoral adjustments on the master cast. Thus, skipping the master cast deprives the dentist of delivering a restoration of higher quality.
format: application/pdf
format: text/html
creator: Radek Mounajjed
creator: Thomas Taylor
creator: Omar Hamadah
creator: Iva Voborná
creator: Marwan Al-akkad
subject: Dentistry
description: doi:10.7717/peerj.13280
publisher: PeerJ Inc.
rights: © 2022 Mounajjed et al.
abstract: Background The master cast is the gold standard for the control and eventual adjustment of restorations produced by conventional procedures. Some digital workflow bypasses the master cast and relies completely on the precision of the CAD/CAM restoration. Aim To examine the reproducibility of the margins of CAD/CAM restorations generated from a single digital scan. Also, to check the readiness of these restorations for delivery directly after fabrication without adjustment on a master cast and thereby eliminate the need for the master cast. Methods A total of 18 metal substructures made from cobalt chrome alloy were fabricated utilizing a single STL file. The circumference was divided into eight zones. The vertical marginal discrepancy (VMD) was measured at each zone of each metal substructure, with optical microscopy at ×200 magnification. Results Measurements of vertical marginal discrepancy were in a range of (−94: 300) with a mean of 62 ± 60 μm. A one-way ANOVA test revealed that the mean VMD is significantly different among the 18 substructures (F17, 1,134 = 63.948, p < 0.001). Conclusion Although all the received substructures were fabricated from the same scan file, they were not identical and varied widely, and they were going outside the acceptable range in some zones. Within the limitations of this study, the marginal fit can be improved by extraoral adjustments on the master cast. Thus, skipping the master cast deprives the dentist of delivering a restoration of higher quality.
bibliographic citation: Mounajjed et al. (2022) Assessment of the readiness of restorations manufactured by CAD/CAM in terms of marginal fit (Part I). PeerJ 10:e13280 https://doi.org/10.7717/peerj.13280
date submitted: 2021-09-22
date accepted: 2022-03-24
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mounajjed
  given name: Radek
author list: Agent
  family name: Taylor
  given name: Thomas
author list: Agent
  family name: Hamadah
  given name: Omar
author list: Agent
  family name: Voborná
  given name: Iva
author list: Agent
  family name: Al-akkad
  given name: Marwan
doi: 10.7717/peerj.13280
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: © 2022 Mounajjed et al.
attribution name: Mounajjed et al.

Stress coping strategies used by nurses during the COVID-19 pandemic
type: item
type: AcademicArticle
description: Introduction The risk of getting SARS-CoV-2 infection, worries about exposing loved ones, anxiety and frustration, emotional and physical exhaustion, burn out, a feeling of being overwhelmed, and struggles and challenges with parenting are a few among many factors that affect nurses’ personal lives and professional functioning. The aim of the research is to assess nurses’ level of stress during the COVID-19 pandemic and their sense of self-efficacy, and to learn what coping strategies they use. Methodology/Methods The study was carried out online and based on the diagnostic poll method, using an original survey questionnaire, the General Self-Efficacy Scale (GSES 10–40), the Mini-COPE questionnaire (0–3), and the Perceived Stress Scale PSS-10 (0–40). The respondent group was made up of nurses (n = 220) who provide health services in inpatient and outpatient health care institutions in the northeastern region of Poland. The statistical analysis was performed using the STATISTICA 13.0 package (StatSoft). The distribution of variables was checked with Shapiro-Wilk tests. The Mann–Whitney U test was used to compare two independent samples, while the Kruskal–Wallis test was used to compare more samples. The adopted statistical significance level was p < 0.05. Multivariate regression analysis was applied to determine which factors were related to the level of stress. Results The mean age of the participants was 43.3 years. The vast majority were women (96.4). The mean work experience of the nurses was over 20 years (58.2%). A total of 62.3% worked directly with patients in hospitals, including 11.8% respondents working at COVID-19 units and 37.7% working at primary care institutions. The analyses show that the respondents represented a high level of stress (PSS-10 – 20.9), related to their work experience as a nurse (β −0.250, p = 0.014), the number of hours worked a month (β 0.156, p = 0.015), and self-assessed health status (β −0.145, p = 0.037). They declared an averag…
format: application/pdf
format: text/html
creator: Matylda Sierakowska
creator: Halina Doroszkiewicz
subject: Nursing
subject: Mental Health
subject: COVID-19
description: doi:10.7717/peerj.13288
publisher: PeerJ Inc.
rights: © 2022 Sierakowska and Doroszkiewicz
abstract: Introduction The risk of getting SARS-CoV-2 infection, worries about exposing loved ones, anxiety and frustration, emotional and physical exhaustion, burn out, a feeling of being overwhelmed, and struggles and challenges with parenting are a few among many factors that affect nurses’ personal lives and professional functioning. The aim of the research is to assess nurses’ level of stress during the COVID-19 pandemic and their sense of self-efficacy, and to learn what coping strategies they use. Methodology/Methods The study was carried out online and based on the diagnostic poll method, using an original survey questionnaire, the General Self-Efficacy Scale (GSES 10–40), the Mini-COPE questionnaire (0–3), and the Perceived Stress Scale PSS-10 (0–40). The respondent group was made up of nurses (n = 220) who provide health services in inpatient and outpatient health care institutions in the northeastern region of Poland. The statistical analysis was performed using the STATISTICA 13.0 package (StatSoft). The distribution of variables was checked with Shapiro-Wilk tests. The Mann–Whitney U test was used to compare two independent samples, while the Kruskal–Wallis test was used to compare more samples. The adopted statistical significance level was p < 0.05. Multivariate regression analysis was applied to determine which factors were related to the level of stress. Results The mean age of the participants was 43.3 years. The vast majority were women (96.4). The mean work experience of the nurses was over 20 years (58.2%). A total of 62.3% worked directly with patients in hospitals, including 11.8% respondents working at COVID-19 units and 37.7% working at primary care institutions. The analyses show that the respondents represented a high level of stress (PSS-10 – 20.9), related to their work experience as a nurse (β −0.250, p = 0.014), the number of hours worked a month (β 0.156, p = 0.015), and self-assessed health status (β −0.145, p = 0.037). They declared an averag…
bibliographic citation: Sierakowska et al. (2022) Stress coping strategies used by nurses during the COVID-19 pandemic. PeerJ 10:e13288 https://doi.org/10.7717/peerj.13288
date submitted: 2021-11-15
date accepted: 2022-03-28
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sierakowska
  given name: Matylda
author list: Agent
  family name: Doroszkiewicz
  given name: Halina
doi: 10.7717/peerj.13288
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: ©2022 Sierakowska and Doroszkiewicz
attribution name: Sierakowska and Doroszkiewicz

Comparison between hydroxyapatite and polycaprolactone in inducing osteogenic differentiation and augmenting maxillary bone regeneration in rats
type: item
type: AcademicArticle
description: Background The selection of appropriate scaffold plays an important role in ensuring the success of bone regeneration. The use of scaffolds with different materials and their effect on the osteogenic performance of cells is not well studied and this can affect the selection of suitable scaffolds for transplantation. Hence, this study aimed to investigate the comparative ability of two different synthetic scaffolds, mainly hydroxyapatite (HA) and polycaprolactone (PCL) scaffolds in promoting in vitro and in vivo bone regeneration. Method In vitro cell viability, morphology, and alkaline phosphatase (ALP) activity of MC3T3-E1 cells on HA and PCL scaffolds were determined in comparison to the accepted model outlined for two-dimensional systems. An in vivo study involving the transplantation of MC3T3-E1 cells with scaffolds into an artificial bone defect of 4 mm length and 1.5 mm depth in the rat’s left maxilla was conducted. Three-dimensional analysis using micro-computed tomography (micro-CT), hematoxylin and eosin (H&E), and immunohistochemistry analyses evaluation were performed after six weeks of transplantation. Results MC3T3-E1 cells on the HA scaffold showed the highest cell viability. The cell viability on both scaffolds decreased after 14 days of culture, which reflects the dominant occurrence of osteoblast differentiation. An early sign of osteoblast differentiation can be detected on the PCL scaffold. However, cells on the HA scaffold showed more prominent results with intense mineralized nodules and significantly (p < 0.05) high levels of ALP activity with prolonged osteoblast induction. Micro-CT and H&E analyses confirmed the in vitro results with bone formation were significantly (p < 0.05) greater in HA scaffold and was supported by IHC analysis which confirmed stronger expression of osteogenic markers ALP and osteocalcin. Conclusion Different scaffold materials of HA and PCL might have influenced the bone regeneration ability of MC3T3-E1. Regardless, in…
format: application/pdf
format: text/html
creator: Nur Atmaliya Luchman
creator: Rohaya Megat Abdul Wahab
creator: Shahrul Hisham Zainal Ariffin
creator: Nurrul Shaqinah Nasruddin
creator: Seng Fong Lau
creator: Farinawati Yazid
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Orthopedics
subject: Histology
description: doi:10.7717/peerj.13356
publisher: PeerJ Inc.
rights: © 2022 Luchman et al.
abstract: Background The selection of appropriate scaffold plays an important role in ensuring the success of bone regeneration. The use of scaffolds with different materials and their effect on the osteogenic performance of cells is not well studied and this can affect the selection of suitable scaffolds for transplantation. Hence, this study aimed to investigate the comparative ability of two different synthetic scaffolds, mainly hydroxyapatite (HA) and polycaprolactone (PCL) scaffolds in promoting in vitro and in vivo bone regeneration. Method In vitro cell viability, morphology, and alkaline phosphatase (ALP) activity of MC3T3-E1 cells on HA and PCL scaffolds were determined in comparison to the accepted model outlined for two-dimensional systems. An in vivo study involving the transplantation of MC3T3-E1 cells with scaffolds into an artificial bone defect of 4 mm length and 1.5 mm depth in the rat’s left maxilla was conducted. Three-dimensional analysis using micro-computed tomography (micro-CT), hematoxylin and eosin (H&E), and immunohistochemistry analyses evaluation were performed after six weeks of transplantation. Results MC3T3-E1 cells on the HA scaffold showed the highest cell viability. The cell viability on both scaffolds decreased after 14 days of culture, which reflects the dominant occurrence of osteoblast differentiation. An early sign of osteoblast differentiation can be detected on the PCL scaffold. However, cells on the HA scaffold showed more prominent results with intense mineralized nodules and significantly (p < 0.05) high levels of ALP activity with prolonged osteoblast induction. Micro-CT and H&E analyses confirmed the in vitro results with bone formation were significantly (p < 0.05) greater in HA scaffold and was supported by IHC analysis which confirmed stronger expression of osteogenic markers ALP and osteocalcin. Conclusion Different scaffold materials of HA and PCL might have influenced the bone regeneration ability of MC3T3-E1. Regardless, in…
bibliographic citation: Luchman et al. (2022) Comparison between hydroxyapatite and polycaprolactone in inducing osteogenic differentiation and augmenting maxillary bone regeneration in rats. PeerJ 10:e13356 https://doi.org/10.7717/peerj.13356
date submitted: 2021-10-25
date accepted: 2022-04-08
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luchman
  given name: Nur Atmaliya
author list: Agent
  family name: Megat Abdul Wahab
  given name: Rohaya
author list: Agent
  family name: Zainal Ariffin
  given name: Shahrul Hisham
author list: Agent
  family name: Nasruddin
  given name: Nurrul Shaqinah
author list: Agent
  family name: Lau
  given name: Seng Fong
author list: Agent
  family name: Yazid
  given name: Farinawati
doi: 10.7717/peerj.13356
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: ©2022 Luchman et al.
attribution name: Luchman et al.

Predicting surface abundance of federally threatened Jollyville Plateau Salamanders (Eurycea tonkawae) to inform management activities at a highly modified urban spring
type: item
type: AcademicArticle
description: Urban expansion has contributed to the loss of habitat for range restricted species across the globe. Managing wildlife populations within these urban settings presents the challenge of balancing human and wildlife needs. Jollyville Plateau Salamanders (Eurycea tonkawae) are a range restricted, federally threatened, species of neotenic brook salamander endemic to central Texas. Almost the entire geographic range of E. tonkawae is embedded in the Austin, Cedar Park, and Round Rock metropolitan areas of Travis and Williamson counties, Texas. Among E. tonkawae occupied sites, Brushy Creek Spring has experienced some of the most extensive anthropogenic disturbance. Today the site consists of small groundwater outlets that emerge in the seams within a concrete culvert underlying a highway. Salamanders persist within this system though they are rarely detected. Here, we model the occurrence of salamanders within the surface habitat of Brushy Creek Spring using generalized linear models. In the absence of available data regarding the amount of water that is discharged from the spring, we use accumulated rainfall as a proxy for discharge to estimate salamander abundance. Additionally, we present evidence of reproduction, recruitment, and subterranean movement by E. tonkawae throughout this site. Infrastructure maintenance is inevitable at Brushy Creek Spring. We intend for our results to inform when maintenance should occur, i.e., during environmental conditions when salamanders are less likely to be observed in the surface habitat, to avoid unnecessary impacts to this federally threatened species.
format: application/pdf
format: text/html
creator: Zachary C. Adcock
creator: Andrew R. MacLaren
creator: Ryan M. Jones
creator: Andrea Villamizar-Gomez
creator: Ashley E. Wall
creator: Kemble White IV
creator: Michael R. J. Forstner
subject: Conservation Biology
subject: Ecology
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.13359
publisher: PeerJ Inc.
rights: © 2022 Adcock et al.
abstract: Urban expansion has contributed to the loss of habitat for range restricted species across the globe. Managing wildlife populations within these urban settings presents the challenge of balancing human and wildlife needs. Jollyville Plateau Salamanders (Eurycea tonkawae) are a range restricted, federally threatened, species of neotenic brook salamander endemic to central Texas. Almost the entire geographic range of E. tonkawae is embedded in the Austin, Cedar Park, and Round Rock metropolitan areas of Travis and Williamson counties, Texas. Among E. tonkawae occupied sites, Brushy Creek Spring has experienced some of the most extensive anthropogenic disturbance. Today the site consists of small groundwater outlets that emerge in the seams within a concrete culvert underlying a highway. Salamanders persist within this system though they are rarely detected. Here, we model the occurrence of salamanders within the surface habitat of Brushy Creek Spring using generalized linear models. In the absence of available data regarding the amount of water that is discharged from the spring, we use accumulated rainfall as a proxy for discharge to estimate salamander abundance. Additionally, we present evidence of reproduction, recruitment, and subterranean movement by E. tonkawae throughout this site. Infrastructure maintenance is inevitable at Brushy Creek Spring. We intend for our results to inform when maintenance should occur, i.e., during environmental conditions when salamanders are less likely to be observed in the surface habitat, to avoid unnecessary impacts to this federally threatened species.
bibliographic citation: Adcock et al. (2022) Predicting surface abundance of federally threatened Jollyville Plateau Salamanders (Eurycea tonkawae) to inform management activities at a highly modified urban spring. PeerJ 10:e13359 https://doi.org/10.7717/peerj.13359
date submitted: 2022-01-25
date accepted: 2022-04-08
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adcock
  given name: Zachary C.
author list: Agent
  family name: MacLaren
  given name: Andrew R.
author list: Agent
  family name: Jones
  given name: Ryan M.
author list: Agent
  family name: Villamizar-Gomez
  given name: Andrea
author list: Agent
  family name: Wall
  given name: Ashley E.
author list: Agent
  family name: White IV
  given name: Kemble
author list: Agent
  family name: Forstner
  given name: Michael R. J.
doi: 10.7717/peerj.13359
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: © 2022 Adcock et al.
attribution name: Adcock et al.

Scavenging vs hunting affects behavioral traits of an opportunistic carnivore
type: item
type: AcademicArticle
description: Background Human-induced changes to ecosystems transform the availability of resources to predators, including altering prey populations and increasing access to anthropogenic foods. Opportunistic predators are likely to respond to altered food resources by changing the proportion of food they hunt versus scavenge. These shifts in foraging behavior will affect species interactions through multiple pathways, including by changing other aspects of predator behavior such as boldness, innovation, and social structure. Methods To understand how foraging behavior impacts predator behavior, we conducted a controlled experiment to simulate hunting by introducing a prey model to captive coyotes (Canis latrans) and compared their behavior to coyotes that continued to scavenge over one year. We used focal observations to construct behavioral budgets, and conducted novel object, puzzle box, and conspecific tests to evaluate boldness, innovation, and response to conspecifics. Results We documented increased time spent resting by hunting coyotes paired with decreased time spent active. Hunting coyotes increased boldness and persistence but there were no changes in innovation. Our results illustrate how foraging behavior can impact other aspects of behavior, with potential ecological consequences to predator ecology, predator-prey dynamics, and human-wildlife conflict; however, the captive nature of our study limits specific conclusions related to wild predators. We conclude that human-induced behavioral changes could have cascading ecological implications that are not fully understood.
format: application/pdf
format: text/html
creator: Mitchell A. Parsons
creator: Andrew Garcia
creator: Julie K. Young
subject: Animal Behavior
subject: Ecology
description: doi:10.7717/peerj.13366
publisher: PeerJ Inc.
rights: © 2022 Parsons et al.
abstract: Background Human-induced changes to ecosystems transform the availability of resources to predators, including altering prey populations and increasing access to anthropogenic foods. Opportunistic predators are likely to respond to altered food resources by changing the proportion of food they hunt versus scavenge. These shifts in foraging behavior will affect species interactions through multiple pathways, including by changing other aspects of predator behavior such as boldness, innovation, and social structure. Methods To understand how foraging behavior impacts predator behavior, we conducted a controlled experiment to simulate hunting by introducing a prey model to captive coyotes (Canis latrans) and compared their behavior to coyotes that continued to scavenge over one year. We used focal observations to construct behavioral budgets, and conducted novel object, puzzle box, and conspecific tests to evaluate boldness, innovation, and response to conspecifics. Results We documented increased time spent resting by hunting coyotes paired with decreased time spent active. Hunting coyotes increased boldness and persistence but there were no changes in innovation. Our results illustrate how foraging behavior can impact other aspects of behavior, with potential ecological consequences to predator ecology, predator-prey dynamics, and human-wildlife conflict; however, the captive nature of our study limits specific conclusions related to wild predators. We conclude that human-induced behavioral changes could have cascading ecological implications that are not fully understood.
bibliographic citation: Parsons et al. (2022) Scavenging vs hunting affects behavioral traits of an opportunistic carnivore. PeerJ 10:e13366 https://doi.org/10.7717/peerj.13366
date submitted: 2022-01-20
date accepted: 2022-04-11
issued: 2022-05-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parsons
  given name: Mitchell A.
author list: Agent
  family name: Garcia
  given name: Andrew
author list: Agent
  family name: Young
  given name: Julie K.
doi: 10.7717/peerj.13366
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-02
copyright: ©2022 Parsons et al.
attribution name: Parsons et al.

How beavers affect riverine aquatic macroinvertebrates: a review
type: item
type: AcademicArticle
description: Background As ecosystem engineers, the construction of dams by beavers alters stream habitat physically and biologically, making them a species of interest for habitat restoration. Beaver-created habitat changes affect a wide range of aquatic invertebrate species. However, despite numerous individual studies of how beavers affect aquatic macroinvertebrate assemblages, there has been no evaluation of the consensus of these effects across studies. Methodology We collated and examined studies comparing beaver-created ponds to nearby lotic reaches to determine general trends in aquatic macroinvertebrate richness, density, biomass, and functional composition between habitats. From this evidence, we highight knowledge gaps in how beaver activity affects aquatic macroinvertebrates. Results Overall, in the majority of studies, aquatic macroinvertebrate richness was higher in nearby lotic reaches compared to beaver-created ponds, but richness at coarser scales (gamma diversity) increased with the addition of beaver ponds due to increased habitat heterogeneity. Functional feeding group (FFG) patterns were highly context-dependent, though predator taxa were generally more abundant in beaver ponds than adjacent lotic reaches. Site-specific geomorphological changes, coupled with dam or riparian zone characteristics and resulting differences in basal food resources likely shape other FFG responses. Conclusions We identify a lack of long-term studies at single or multiple sites and conclude that fine-scale approaches may improve our understanding of the dynamics of macroinvertebrates within the freshwater realm and beyond. Due to the context-dependent nature of each study, further systematic studies of beaver engineering effects across a wider variety of environmental conditions and wetland types will also help inform land and species management decisions, such as where to prioritize protection of beaver habitats in the face of a global freshwater biodiversity crisis, or where to …
format: application/pdf
format: text/html
creator: Susan Washko
creator: Nigel Willby
creator: Alan Law
subject: Ecology
subject: Entomology
subject: Freshwater Biology
description: doi:10.7717/peerj.13180
publisher: PeerJ Inc.
rights: © 2022 Washko et al.
abstract: Background As ecosystem engineers, the construction of dams by beavers alters stream habitat physically and biologically, making them a species of interest for habitat restoration. Beaver-created habitat changes affect a wide range of aquatic invertebrate species. However, despite numerous individual studies of how beavers affect aquatic macroinvertebrate assemblages, there has been no evaluation of the consensus of these effects across studies. Methodology We collated and examined studies comparing beaver-created ponds to nearby lotic reaches to determine general trends in aquatic macroinvertebrate richness, density, biomass, and functional composition between habitats. From this evidence, we highight knowledge gaps in how beaver activity affects aquatic macroinvertebrates. Results Overall, in the majority of studies, aquatic macroinvertebrate richness was higher in nearby lotic reaches compared to beaver-created ponds, but richness at coarser scales (gamma diversity) increased with the addition of beaver ponds due to increased habitat heterogeneity. Functional feeding group (FFG) patterns were highly context-dependent, though predator taxa were generally more abundant in beaver ponds than adjacent lotic reaches. Site-specific geomorphological changes, coupled with dam or riparian zone characteristics and resulting differences in basal food resources likely shape other FFG responses. Conclusions We identify a lack of long-term studies at single or multiple sites and conclude that fine-scale approaches may improve our understanding of the dynamics of macroinvertebrates within the freshwater realm and beyond. Due to the context-dependent nature of each study, further systematic studies of beaver engineering effects across a wider variety of environmental conditions and wetland types will also help inform land and species management decisions, such as where to prioritize protection of beaver habitats in the face of a global freshwater biodiversity crisis, or where to …
bibliographic citation: Washko et al. (2022) How beavers affect riverine aquatic macroinvertebrates: a review. PeerJ 10:e13180 https://doi.org/10.7717/peerj.13180
date submitted: 2022-01-25
date accepted: 2022-03-07
issued: 2022-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Washko
  given name: Susan
author list: Agent
  family name: Willby
  given name: Nigel
author list: Agent
  family name: Law
  given name: Alan
doi: 10.7717/peerj.13180
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-29
copyright: © 2022 Washko et al.
attribution name: Washko et al.

The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients
type: item
type: AcademicArticle
description: The latitudinal and elevational patterns of species richness of resident and migrant birds have been of interest to researchers over the past few decades, and various hypotheses have been proposed to explain the factors that may affect these patterns. This study aimed to shed light on the elevational distribution patterns of resident and migrant bird species richness by examining biotic and abiotic factors such as climate, and habitat heterogeneity using a piecewise structural equation model (pSEM). The overall pattern of resident species richness showed a decreasing trend with increasing elevation, whereas that of migrant species richness showed an increasing trend. The mid-peak pattern of species richness was affected by a combination of resident and migrant species and not by either resident or migrant species. Our results showed that resident species were distributed in lower elevation regions with higher mean spring temperatures, whereas migrant species were found in higher elevation regions with lower mean spring temperatures and higher overstory vegetation coverage. Although high elevation conditions might adversely affect the reproduction of migrant birds, higher overstory vegetation coverage at high elevations seemed to compensate for this by providing a better nesting and roosting environment. Despite the significance of habitat diversity and understory vegetation coverage in univariate linear regression models, multiple regression models of the interconnection of ecological processes demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables.
format: application/pdf
format: text/html
creator: Jin-Yong Kim
creator: Jongmin Yoon
creator: Yu-Seong Choi
creator: Soo Hyung Eo
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13258
publisher: PeerJ Inc.
rights: © 2022 Kim et al.
abstract: The latitudinal and elevational patterns of species richness of resident and migrant birds have been of interest to researchers over the past few decades, and various hypotheses have been proposed to explain the factors that may affect these patterns. This study aimed to shed light on the elevational distribution patterns of resident and migrant bird species richness by examining biotic and abiotic factors such as climate, and habitat heterogeneity using a piecewise structural equation model (pSEM). The overall pattern of resident species richness showed a decreasing trend with increasing elevation, whereas that of migrant species richness showed an increasing trend. The mid-peak pattern of species richness was affected by a combination of resident and migrant species and not by either resident or migrant species. Our results showed that resident species were distributed in lower elevation regions with higher mean spring temperatures, whereas migrant species were found in higher elevation regions with lower mean spring temperatures and higher overstory vegetation coverage. Although high elevation conditions might adversely affect the reproduction of migrant birds, higher overstory vegetation coverage at high elevations seemed to compensate for this by providing a better nesting and roosting environment. Despite the significance of habitat diversity and understory vegetation coverage in univariate linear regression models, multiple regression models of the interconnection of ecological processes demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables.
bibliographic citation: Kim et al. (2022) The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients. PeerJ 10:e13258 https://doi.org/10.7717/peerj.13258
date submitted: 2021-05-12
date accepted: 2022-03-22
issued: 2022-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Jin-Yong
author list: Agent
  family name: Yoon
  given name: Jongmin
author list: Agent
  family name: Choi
  given name: Yu-Seong
author list: Agent
  family name: Eo
  given name: Soo Hyung
doi: 10.7717/peerj.13258
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-29
copyright: © 2022 Kim et al.
attribution name: Kim et al.

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