PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching
items: Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors
items: Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes
items: Comparison of selective laser melting and stereolithography etching templates for guided endodontics
items: Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues
items: An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh
items: Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
items: Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma
items: Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)
items: Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo

Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching
type: item
type: AcademicArticle
description: Background To train highly qualified medical talent in 5-year programs and improve students’ analytical and problem-solving abilities, it is necessary to change the traditional teaching method. This study introduces the combined teaching method of case-based learning (CBL) and clinical pathway and evaluates its role in practical gynecological teaching. Methods Medical students in a 5-year program who were enrolled in the fourth year were selected as the research subjects; these students were randomized into two groups that separately received either the traditional teaching method or the combined teaching method of CBL and clinical pathway. Before the internship, a questionnaire was administered to explore students’ views of internship in gynecology, and after the internship, the questionnaire was administered to assess the two teaching methods. Furthermore, theoretical and skill tests were performed both before and after the internship. Results A total of 206 medical students in a 5-year program who were in their fourth year were enrolled in the study. Students in the experimental group performed significantly better than those in the control group. They performed significantly better in the postinternship test than in the preinternship test (P < 0.001). The questionnaire showed that more students in the experimental group thought that their learning interests, clinical skills, case analysis ability, clinical communication ability, understanding of theoretical knowledge and clinical thinking ability had improved and significantly differed between the two groups (P < 0.05). Discussion Compared to traditional teaching methods, combined teaching method of CBL and clinical pathway can elevate students’ academic performance, improve their learning enthusiasm and help promote clinical teachers’ teaching quality. Additionally, this novel method is effective in facilitating the achievement of teaching objectives and improving the quality of talent training. Therefore, the …
format: application/pdf
format: text/html
creator: Xiaoxia Wang
creator: Xuan Che
creator: Xuedong Tang
creator: Zhengfen Xu
subject: Gynecology and Obstetrics
subject: Science and Medical Education
subject: Healthcare Services
description: doi:10.7717/peerj.17813
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background To train highly qualified medical talent in 5-year programs and improve students’ analytical and problem-solving abilities, it is necessary to change the traditional teaching method. This study introduces the combined teaching method of case-based learning (CBL) and clinical pathway and evaluates its role in practical gynecological teaching. Methods Medical students in a 5-year program who were enrolled in the fourth year were selected as the research subjects; these students were randomized into two groups that separately received either the traditional teaching method or the combined teaching method of CBL and clinical pathway. Before the internship, a questionnaire was administered to explore students’ views of internship in gynecology, and after the internship, the questionnaire was administered to assess the two teaching methods. Furthermore, theoretical and skill tests were performed both before and after the internship. Results A total of 206 medical students in a 5-year program who were in their fourth year were enrolled in the study. Students in the experimental group performed significantly better than those in the control group. They performed significantly better in the postinternship test than in the preinternship test (P < 0.001). The questionnaire showed that more students in the experimental group thought that their learning interests, clinical skills, case analysis ability, clinical communication ability, understanding of theoretical knowledge and clinical thinking ability had improved and significantly differed between the two groups (P < 0.05). Discussion Compared to traditional teaching methods, combined teaching method of CBL and clinical pathway can elevate students’ academic performance, improve their learning enthusiasm and help promote clinical teachers’ teaching quality. Additionally, this novel method is effective in facilitating the achievement of teaching objectives and improving the quality of talent training. Therefore, the …
bibliographic citation: Wang et al. (2024) Application of combined teaching method of case-based-learning and clinical pathway in practical gynecological teaching. PeerJ 12:e17813 https://doi.org/10.7717/peerj.17813
date submitted: 2024-01-02
date accepted: 2024-07-03
issued: 2024-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Xiaoxia
author list: Agent
  family name: Che
  given name: Xuan
author list: Agent
  family name: Tang
  given name: Xuedong
author list: Agent
  family name: Xu
  given name: Zhengfen
doi: 10.7717/peerj.17813
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-24
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors
type: item
type: AcademicArticle
description: Breast cancer is the most common cancer in women worldwide, and its treatment usually involves a combination of many medical procedures, including surgery, chemotherapy, radiotherapy, and hormonal therapy. One of the detrimental effects on physical function is reduced upper limb muscle strength. This study aimed to evaluate upper body strength intra-day and inter-day (test-retest) reliability using the handgrip strength test (HGS) and the bilateral isometric bench press (BIBP) and the test-retest reliability of the one repetition maximum on the bench press (BP-1RM) in breast cancer survivors (BCS). Thirty-two (52.94 ± 8.99 yrs) BCS participated in this study. The muscle strength tests were performed in two different moments, three to seven days apart. Intraclass coefficient correlation (ICC) and coefficient of variation (CV) were used to assess the reliability. Standard error of measurement (SEM), typical error of measurement (TEM), and minimally detectable change (MDC) analyses were performed. The Bland-Altman analysis was used to assess the agreement between test-retest. We found a reliability that can be described as “high” to “very high” (ICC ≥ 0.88; CV ≤ 10%) for intra-day and test-retest. SEM% and MDC% were lower than 5% and 11%, respectively, for all intra-day testing. SEM% and TEM% ranged from 3% to 11%, and MDC% ranged from 9% to 23% in the test-retest reliability. The agreement demonstrated a systematic bias ranging from 2.3% to 6.0% for all testing, and a lower systematic bias may be presented in the non-treated side assessed by HGS and BIBP. HGS, BIBP, and BP-1RM assessments are reliable for measuring upper-body muscle strength in BCS.
format: application/pdf
format: text/html
creator: Wanderson Santos
creator: Vitor Marques
creator: Claudio Andre B. de Lira
creator: Wagner Martins
creator: Amilton Vieira
creator: Diba Mani
creator: Claudio Battaglini
creator: Carlos Vieira
subject: Kinesiology
subject: Oncology
subject: Women’s Health
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17576
publisher: PeerJ Inc.
rights: © 2024 Santos et al.
abstract: Breast cancer is the most common cancer in women worldwide, and its treatment usually involves a combination of many medical procedures, including surgery, chemotherapy, radiotherapy, and hormonal therapy. One of the detrimental effects on physical function is reduced upper limb muscle strength. This study aimed to evaluate upper body strength intra-day and inter-day (test-retest) reliability using the handgrip strength test (HGS) and the bilateral isometric bench press (BIBP) and the test-retest reliability of the one repetition maximum on the bench press (BP-1RM) in breast cancer survivors (BCS). Thirty-two (52.94 ± 8.99 yrs) BCS participated in this study. The muscle strength tests were performed in two different moments, three to seven days apart. Intraclass coefficient correlation (ICC) and coefficient of variation (CV) were used to assess the reliability. Standard error of measurement (SEM), typical error of measurement (TEM), and minimally detectable change (MDC) analyses were performed. The Bland-Altman analysis was used to assess the agreement between test-retest. We found a reliability that can be described as “high” to “very high” (ICC ≥ 0.88; CV ≤ 10%) for intra-day and test-retest. SEM% and MDC% were lower than 5% and 11%, respectively, for all intra-day testing. SEM% and TEM% ranged from 3% to 11%, and MDC% ranged from 9% to 23% in the test-retest reliability. The agreement demonstrated a systematic bias ranging from 2.3% to 6.0% for all testing, and a lower systematic bias may be presented in the non-treated side assessed by HGS and BIBP. HGS, BIBP, and BP-1RM assessments are reliable for measuring upper-body muscle strength in BCS.
bibliographic citation: Santos et al. (2024) Reliability of dynamic and isometric upper muscle strength testing in breast cancer survivors. PeerJ 12:e17576 https://doi.org/10.7717/peerj.17576
date submitted: 2024-03-13
date accepted: 2024-05-24
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Wanderson
author list: Agent
  family name: Marques
  given name: Vitor
author list: Agent
  family name: de Lira
  given name: Claudio Andre B.
author list: Agent
  family name: Martins
  given name: Wagner
author list: Agent
  family name: Vieira
  given name: Amilton
author list: Agent
  family name: Mani
  given name: Diba
author list: Agent
  family name: Battaglini
  given name: Claudio
author list: Agent
  family name: Vieira
  given name: Carlos
doi: 10.7717/peerj.17576
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: © 2024 Santos et al.
attribution name: Santos et al.

Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes
type: item
type: AcademicArticle
description: Pre-harvest sprouting (PHS) is one of the important abiotic stresses in mungbean which significantly reduces yield and quality of the produce. This study was conducted to evaluate the genetic variability for tolerance to pre-harvest sprouting in diverse mungbean genotypes while simultaneously deciphering the association of yield contributing traits with PHS. Eighty-three diverse mungbean genotypes (23 released varieties, 23 advanced breeding lines and 37 exotic germplasm lines) were investigated for tolerance to PHS, water imbibition capacities by pods, pod and seed physical traits. Wide variation in PHS was recorded which ranged between 17.8% to 81% (mean value 54.34%). Germplasm lines exhibited higher tolerance to PHS than the high-yielding released varieties. Correlation analysis revealed PHS to be positively associated with water imbibition capacity by pods (r = 0.21) and germinated pod % (r = 0.78). Pod length (r = −0.13) and seeds per pod (r = −0.13) were negatively influencing PHS. Positive associations between PHS and water imbibition capacity by pods, germinated pod % and 100-seed weight was further confirmed by multivariate analysis. Small-seeded genotypes having 100-seed weight <3 g exhibited higher tolerance to PHS compared to bold-seeded genotypes having 100-seed weight more than 3.5 g. Fresh seed germination among the selected PHS tolerant and susceptible genotypes ranged from 42% (M 204) to 98% (Pusa 1131). A positive association (r = 0.79) was recorded between fresh seed germination and PHS. Genotypes M 1255, M 145, M 422, M 1421 identified as potential genetic donors against PHS could be utilized in mungbean breeding programs.
format: application/pdf
format: text/html
creator: Soma Gupta
creator: Muraleedhar Aski
creator: Gyan Prakash Mishra
creator: Prachi S. Yadav
creator: Kuldeep Tripathi
creator: Sandeep Kumar Lal
creator: Simran Jain
creator: Ramakrishnan Madhavan Nair
creator: Harsh Kumar Dikshit
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17609
publisher: PeerJ Inc.
rights: © 2024 Gupta et al.
abstract: Pre-harvest sprouting (PHS) is one of the important abiotic stresses in mungbean which significantly reduces yield and quality of the produce. This study was conducted to evaluate the genetic variability for tolerance to pre-harvest sprouting in diverse mungbean genotypes while simultaneously deciphering the association of yield contributing traits with PHS. Eighty-three diverse mungbean genotypes (23 released varieties, 23 advanced breeding lines and 37 exotic germplasm lines) were investigated for tolerance to PHS, water imbibition capacities by pods, pod and seed physical traits. Wide variation in PHS was recorded which ranged between 17.8% to 81% (mean value 54.34%). Germplasm lines exhibited higher tolerance to PHS than the high-yielding released varieties. Correlation analysis revealed PHS to be positively associated with water imbibition capacity by pods (r = 0.21) and germinated pod % (r = 0.78). Pod length (r = −0.13) and seeds per pod (r = −0.13) were negatively influencing PHS. Positive associations between PHS and water imbibition capacity by pods, germinated pod % and 100-seed weight was further confirmed by multivariate analysis. Small-seeded genotypes having 100-seed weight <3 g exhibited higher tolerance to PHS compared to bold-seeded genotypes having 100-seed weight more than 3.5 g. Fresh seed germination among the selected PHS tolerant and susceptible genotypes ranged from 42% (M 204) to 98% (Pusa 1131). A positive association (r = 0.79) was recorded between fresh seed germination and PHS. Genotypes M 1255, M 145, M 422, M 1421 identified as potential genetic donors against PHS could be utilized in mungbean breeding programs.
bibliographic citation: Gupta et al. (2024) Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes. PeerJ 12:e17609 https://doi.org/10.7717/peerj.17609
date submitted: 2024-02-14
date accepted: 2024-05-30
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gupta
  given name: Soma
author list: Agent
  family name: Aski
  given name: Muraleedhar
author list: Agent
  family name: Mishra
  given name: Gyan Prakash
author list: Agent
  family name: Yadav
  given name: Prachi S.
author list: Agent
  family name: Tripathi
  given name: Kuldeep
author list: Agent
  family name: Lal
  given name: Sandeep Kumar
author list: Agent
  family name: Jain
  given name: Simran
author list: Agent
  family name: Nair
  given name: Ramakrishnan Madhavan
author list: Agent
  family name: Dikshit
  given name: Harsh Kumar
doi: 10.7717/peerj.17609
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: © 2024 Gupta et al.
attribution name: Gupta et al.

Comparison of selective laser melting and stereolithography etching templates for guided endodontics
type: item
type: AcademicArticle
description: Background With the increasing application of guided endodontics to treat complex root canal treatment, the entire process of root canal treatment has become more precise, reducing damage to tooth structure and improving success rates. However, due to the limitations of the operating space, the use of guided endodontic templates in posterior root canal treatment is less common. This study aims to compare the accuracy and reliability of selective laser melting (SLM) and traditional stereolithography etching (SLA) guided endodontic templates for posterior root canals, providing better treatment strategies for posterior root canal treatment. Methods The teeth were randomly assigned to either SLM or SLA group. Preoperative cone-beam computed tomography (CBCT) and a three-dimensional (3D) scanner were used to establish the 3D root canal system and the accurate occlusal models of the teeth. The virtual access to the canal access was designed using Mimics 19.0 and 3-Matic 11.0. The endodontic access was performed based on either SLM or SLA templates. The accuracy of endodontic preparation was measured in three-dimensions by calculating deviations from planned accesses. The template height and tooth substance loss rates in each group were measured. Results SLM-guided templates have a low average deviation at the entry point and apical portion of the bur of total posterior teeth (including premolars and molars) and individual molars (P < 0.05). Moreover, there was a significant difference in angular deviations and height of template in total posterior teeth and individual molars (P < 0.05). The mean substance loss rate of the SLA group was slightly greater than that of the SLM group, but the difference was not statistically (P > 0.05). Conclusions SLM-guided endodontics provides a more predictable and precise location of root canal orifice for the treatment of posterior teeth.
format: application/pdf
format: text/html
creator: Ting Zhang
creator: Du Chen
creator: Fei Zhang
creator: Sijing Xie
creator: Guofeng Wu
creator: Qingang Hu
creator: Fuhua Yan
creator: Xuna Tang
subject: Computational Biology
subject: Dentistry
description: doi:10.7717/peerj.17646
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background With the increasing application of guided endodontics to treat complex root canal treatment, the entire process of root canal treatment has become more precise, reducing damage to tooth structure and improving success rates. However, due to the limitations of the operating space, the use of guided endodontic templates in posterior root canal treatment is less common. This study aims to compare the accuracy and reliability of selective laser melting (SLM) and traditional stereolithography etching (SLA) guided endodontic templates for posterior root canals, providing better treatment strategies for posterior root canal treatment. Methods The teeth were randomly assigned to either SLM or SLA group. Preoperative cone-beam computed tomography (CBCT) and a three-dimensional (3D) scanner were used to establish the 3D root canal system and the accurate occlusal models of the teeth. The virtual access to the canal access was designed using Mimics 19.0 and 3-Matic 11.0. The endodontic access was performed based on either SLM or SLA templates. The accuracy of endodontic preparation was measured in three-dimensions by calculating deviations from planned accesses. The template height and tooth substance loss rates in each group were measured. Results SLM-guided templates have a low average deviation at the entry point and apical portion of the bur of total posterior teeth (including premolars and molars) and individual molars (P < 0.05). Moreover, there was a significant difference in angular deviations and height of template in total posterior teeth and individual molars (P < 0.05). The mean substance loss rate of the SLA group was slightly greater than that of the SLM group, but the difference was not statistically (P > 0.05). Conclusions SLM-guided endodontics provides a more predictable and precise location of root canal orifice for the treatment of posterior teeth.
bibliographic citation: Zhang et al. (2024) Comparison of selective laser melting and stereolithography etching templates for guided endodontics. PeerJ 12:e17646 https://doi.org/10.7717/peerj.17646
date submitted: 2024-04-01
date accepted: 2024-06-06
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ting
author list: Agent
  family name: Chen
  given name: Du
author list: Agent
  family name: Zhang
  given name: Fei
author list: Agent
  family name: Xie
  given name: Sijing
author list: Agent
  family name: Wu
  given name: Guofeng
author list: Agent
  family name: Hu
  given name: Qingang
author list: Agent
  family name: Yan
  given name: Fuhua
author list: Agent
  family name: Tang
  given name: Xuna
doi: 10.7717/peerj.17646
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues
type: item
type: AcademicArticle
description: The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host.
format: application/pdf
format: text/html
creator: Thomson M. Paris
creator: Nicholas Johnston
creator: Iris Strzyzewski
creator: Jessica L. Griesheimer
creator: Benjamin Reimer
creator: Kathi Malfa
creator: Sandra A. Allan
creator: Xavier Martini
subject: Agricultural Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.17665
publisher: PeerJ Inc.
rights: © 2024 Paris et al.
abstract: The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host.
bibliographic citation: Paris et al. (2024) Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues. PeerJ 12:e17665 https://doi.org/10.7717/peerj.17665
date submitted: 2024-03-15
date accepted: 2024-06-11
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paris
  given name: Thomson M.
author list: Agent
  family name: Johnston
  given name: Nicholas
author list: Agent
  family name: Strzyzewski
  given name: Iris
author list: Agent
  family name: Griesheimer
  given name: Jessica L.
author list: Agent
  family name: Reimer
  given name: Benjamin
author list: Agent
  family name: Malfa
  given name: Kathi
author list: Agent
  family name: Allan
  given name: Sandra A.
author list: Agent
  family name: Martini
  given name: Xavier
doi: 10.7717/peerj.17665
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Paris et al.
attribution name: Paris et al.

An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh
type: item
type: AcademicArticle
description: Despite their overlooked status, weeds are increasingly recognized for their therapeutic value, aligning with historical reliance on plants for medicine and nutrition. This study investigates the medicinal potential of native weed species in Bangladesh, specifically pigments, antioxidants, and free radical scavenging abilities. Twenty different medicinal weed species were collected from the vicinity of Khulna Agricultural University and processed in the Crop Botany Department Laboratory. Pigment levels were determined using spectrophotometer analysis, and phenolics, flavonoids, and DPPH were quantified accordingly. Chlorophyll levels in leaves ranged from 216.70 ± 9.41 to 371.14 ± 28.67 µg g−1 FW, and in stems from 51.98 ± 3.21 to 315.89 ± 17.19 µg g−1 FW. Flavonoid content also varied widely, from 1,624.62 ± 102.03 to 410.00 ± 115.58 mg CE 100 g−1 FW in leaves, and from 653.08 ± 32.42 to 80.00 ± 18.86 mg CE 100 g−1 FW in stems. In case of phenolics content Euphorbia hirta L. displaying the highest total phenolic content in leaves (1,722.33 ± 417.89 mg GAE 100 g−1 FW) and Ruellia tuberosa L. in stems (977.70 ± 145.58 mg GAE 100 g−1 FW). The lowest DPPH 2.505 ± 1.028 mg mL−1was found in Heliotropium indicum L. leaves. Hierarchical clustering links species with pigment, phenolic/flavonoid content, and antioxidant activity. PCA, involving 20 species and seven traits, explained 70.07% variability, with significant PC1 (14.82%) and PC2 (55.25%). Leaves were shown to be superior, and high-performing plants such as E. hirta and H. indicum stood out for their chemical composition and antioxidant activity. Thus, this research emphasizes the value of efficient selection while concentrating on the therapeutic potential of native weed species.
format: application/pdf
format: text/html
creator: Mousumi Jahan Sumi
creator: Samia Binta Zaman
creator: Shahin Imran
creator: Prosenjit Sarker
creator: Mohammad Saidur Rhaman
creator: Ahmed Gaber
creator: Milan Skalicky
creator: Debojyoti Moulick
creator: Akbar Hossain
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.17698
publisher: PeerJ Inc.
rights: © 2024 Sumi et al.
abstract: Despite their overlooked status, weeds are increasingly recognized for their therapeutic value, aligning with historical reliance on plants for medicine and nutrition. This study investigates the medicinal potential of native weed species in Bangladesh, specifically pigments, antioxidants, and free radical scavenging abilities. Twenty different medicinal weed species were collected from the vicinity of Khulna Agricultural University and processed in the Crop Botany Department Laboratory. Pigment levels were determined using spectrophotometer analysis, and phenolics, flavonoids, and DPPH were quantified accordingly. Chlorophyll levels in leaves ranged from 216.70 ± 9.41 to 371.14 ± 28.67 µg g−1 FW, and in stems from 51.98 ± 3.21 to 315.89 ± 17.19 µg g−1 FW. Flavonoid content also varied widely, from 1,624.62 ± 102.03 to 410.00 ± 115.58 mg CE 100 g−1 FW in leaves, and from 653.08 ± 32.42 to 80.00 ± 18.86 mg CE 100 g−1 FW in stems. In case of phenolics content Euphorbia hirta L. displaying the highest total phenolic content in leaves (1,722.33 ± 417.89 mg GAE 100 g−1 FW) and Ruellia tuberosa L. in stems (977.70 ± 145.58 mg GAE 100 g−1 FW). The lowest DPPH 2.505 ± 1.028 mg mL−1was found in Heliotropium indicum L. leaves. Hierarchical clustering links species with pigment, phenolic/flavonoid content, and antioxidant activity. PCA, involving 20 species and seven traits, explained 70.07% variability, with significant PC1 (14.82%) and PC2 (55.25%). Leaves were shown to be superior, and high-performing plants such as E. hirta and H. indicum stood out for their chemical composition and antioxidant activity. Thus, this research emphasizes the value of efficient selection while concentrating on the therapeutic potential of native weed species.
bibliographic citation: Sumi et al. (2024) An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh. PeerJ 12:e17698 https://doi.org/10.7717/peerj.17698
date submitted: 2024-02-28
date accepted: 2024-06-17
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sumi
  given name: Mousumi Jahan
author list: Agent
  family name: Zaman
  given name: Samia Binta
author list: Agent
  family name: Imran
  given name: Shahin
author list: Agent
  family name: Sarker
  given name: Prosenjit
author list: Agent
  family name: Rhaman
  given name: Mohammad Saidur
author list: Agent
  family name: Gaber
  given name: Ahmed
author list: Agent
  family name: Skalicky
  given name: Milan
author list: Agent
  family name: Moulick
  given name: Debojyoti
author list: Agent
  family name: Hossain
  given name: Akbar
doi: 10.7717/peerj.17698
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Sumi et al.
attribution name: Sumi et al.

Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
type: item
type: AcademicArticle
description: Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism.
format: application/pdf
format: text/html
creator: Kayla T. Wilhoit
creator: Emmarie P. Alexander
creator: Heath Blackmon
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.17740
publisher: PeerJ Inc.
rights: © 2024 Wilhoit et al.
abstract: Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism.
bibliographic citation: Wilhoit et al. (2024) Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes. PeerJ 12:e17740 https://doi.org/10.7717/peerj.17740
date submitted: 2023-07-25
date accepted: 2024-06-24
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilhoit
  given name: Kayla T.
author list: Agent
  family name: Alexander
  given name: Emmarie P.
author list: Agent
  family name: Blackmon
  given name: Heath
doi: 10.7717/peerj.17740
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Wilhoit et al.
attribution name: Wilhoit et al.

Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma
type: item
type: AcademicArticle
description: Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performe…
format: application/pdf
format: text/html
creator: Yong Li
creator: Yunxiang Cai
creator: Longfei Ji
creator: Binyu Wang
creator: Danfei Shi
creator: Xinmin Li
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17746
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performe…
bibliographic citation: Li et al. (2024) Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma. PeerJ 12:e17746 https://doi.org/10.7717/peerj.17746
date submitted: 2024-03-28
date accepted: 2024-06-24
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Yong
author list: Agent
  family name: Cai
  given name: Yunxiang
author list: Agent
  family name: Ji
  given name: Longfei
author list: Agent
  family name: Wang
  given name: Binyu
author list: Agent
  family name: Shi
  given name: Danfei
author list: Agent
  family name: Li
  given name: Xinmin
doi: 10.7717/peerj.17746
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Li et al.
attribution name: Li et al.

Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)
type: item
type: AcademicArticle
description: The “paradox of sex” refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have aris…
format: application/pdf
format: text/html
creator: Emily Yarbrough
creator: Christopher Chandler
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.17780
publisher: PeerJ Inc.
rights: © 2024 Yarbrough and Chandler
abstract: The “paradox of sex” refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have aris…
bibliographic citation: Yarbrough et al. (2024) Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus). PeerJ 12:e17780 https://doi.org/10.7717/peerj.17780
date submitted: 2024-01-18
date accepted: 2024-06-30
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yarbrough
  given name: Emily
author list: Agent
  family name: Chandler
  given name: Christopher
doi: 10.7717/peerj.17780
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Yarbrough and Chandler
attribution name: Yarbrough and Chandler

Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo
type: item
type: AcademicArticle
description: Background Colletotrichum fructicola is a predominant anthracnose species in Camellia oleifera, causing various adverse effects. Traditional intercropping Vernicia fordii with C. oleifera may enhance anthracnose resistance, but the mechanism remains elusive. Methods We utilized UPLC-MS/MS and acid-base detection to identify the major antimicrobial alkaloid components in the V. fordii leaf extract. Subsequently, by adding different concentrations of V. fordii leaf extract for cultivating C. fructicola, with untreated C. fructicola as a control, we investigated the impact of the V. fordii leaf extract, cell wall integrity, cell membrane permeability, MDA, and ROS content changes. Additionally, analysis of key pathogenic genes of C. fructicola confirmed that the V. fordii leaf extract inhibits the growth of the fungus through gene regulation. Results This study discovered the alkaloid composition of V. fordii leaf extract by UPLC-MS/MS and acid-base detection, such as trigonelline, stachydrine, betaine, and O-Phosphocholine. V. fordii leaf extract successfully penetrated C. fructicola mycelia, damaged cellular integrity, and increased ROS and MDA levels by 1.75 and 2.05 times respectively, thereby inhibiting C. fructicola proliferation. By analyzing the key pathogenic genes of C. fructicola, it was demonstrated that the antifungal function of V. fordii leaf extract depends mainly on the regulation of RAB7 and HAC1 gene expression. Therefore, this study elucidates the mechanism of V. fordii -C. oleifera intercropping in strengthening anthracnose resistance in C. oleifera, contributing to efficient C. oleifera cultivation.
format: application/pdf
format: text/html
creator: Luyao Ge
creator: Yanling Zeng
creator: Xinyun Liu
creator: Xinhai Pan
creator: Guliang Yang
creator: Qinhui Du
creator: Wenlin He
subject: Biochemistry
subject: Conservation Biology
subject: Mycology
subject: Toxicology
description: doi:10.7717/peerj.17607
publisher: PeerJ Inc.
rights: © 2024 Ge et al.
abstract: Background Colletotrichum fructicola is a predominant anthracnose species in Camellia oleifera, causing various adverse effects. Traditional intercropping Vernicia fordii with C. oleifera may enhance anthracnose resistance, but the mechanism remains elusive. Methods We utilized UPLC-MS/MS and acid-base detection to identify the major antimicrobial alkaloid components in the V. fordii leaf extract. Subsequently, by adding different concentrations of V. fordii leaf extract for cultivating C. fructicola, with untreated C. fructicola as a control, we investigated the impact of the V. fordii leaf extract, cell wall integrity, cell membrane permeability, MDA, and ROS content changes. Additionally, analysis of key pathogenic genes of C. fructicola confirmed that the V. fordii leaf extract inhibits the growth of the fungus through gene regulation. Results This study discovered the alkaloid composition of V. fordii leaf extract by UPLC-MS/MS and acid-base detection, such as trigonelline, stachydrine, betaine, and O-Phosphocholine. V. fordii leaf extract successfully penetrated C. fructicola mycelia, damaged cellular integrity, and increased ROS and MDA levels by 1.75 and 2.05 times respectively, thereby inhibiting C. fructicola proliferation. By analyzing the key pathogenic genes of C. fructicola, it was demonstrated that the antifungal function of V. fordii leaf extract depends mainly on the regulation of RAB7 and HAC1 gene expression. Therefore, this study elucidates the mechanism of V. fordii -C. oleifera intercropping in strengthening anthracnose resistance in C. oleifera, contributing to efficient C. oleifera cultivation.
bibliographic citation: Ge et al. (2024) Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo. PeerJ 12:e17607 https://doi.org/10.7717/peerj.17607
date submitted: 2024-02-23
date accepted: 2024-05-30
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Luyao
author list: Agent
  family name: Zeng
  given name: Yanling
author list: Agent
  family name: Liu
  given name: Xinyun
author list: Agent
  family name: Pan
  given name: Xinhai
author list: Agent
  family name: Yang
  given name: Guliang
author list: Agent
  family name: Du
  given name: Qinhui
author list: Agent
  family name: He
  given name: Wenlin
doi: 10.7717/peerj.17607
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: ©2024 Ge et al.
attribution name: Ge et al.

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