PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica
items: The evolution of reproductive strategies in turtles
items: UAV spraying on citrus crop: impact of tank-mix adjuvant on the contact angle and droplet distribution
items: The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study
items: Comparison and correlation of cervical proprioception and muscle endurance in general joint hypermobility participants with and without non-specific neck pain—a cross-sectional study
items: Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults
items: Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses
items: Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes
items: A versatile isothermal amplification assay for the detection of leptospires from various sample types
items: Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways

Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica
type: item
type: AcademicArticle
description: Background Wildlife has been recently recognized as an environmental reservoir for antimicrobial resistance (AMR). However, less information on this topic is available in animals released back into the wild after rehabilitation in wildlife facilities, compared with studies performed exclusively in captive or free-ranging wildlife. This study aimed to evaluate the potential influence of captivity and/or treatment while in captivity of wild sloths on the AMR and virulence profiles of sloths’ Enterobacterales. Methods Oral and rectal swab samples were collected from 39 two-finger (Choloepus hoffmanni) and three-finger sloths (Bradypus variegatus) of Costa Rica (n = 78) and analyzed using conventional bacteriological techniques. A generalized linear mixed model was applied to estimate the isolates’ multiple antimicrobial resistance and virulence indices as a function of animal status. Results A considerable level of resistance was detected, especially for Citrobacter youngae and Escherichia coli, with 17.5% of isolates classified as multidrug-resistant. Virulence indices of isolates from rehabilitated sloths were significantly higher than the ones from sloths being hand-reared for shorter periods. Conclusions To our knowledge, this is the first description of sloths’ antimicrobial resistant Enterobacterales, suggesting that sloths’ rehabilitation and consequent exposure to humans, may promote the selection of bacteria with higher virulence. Ultimately, these bacteria may represent a threat to human and animal health due to their zoonotic potential and AMR and virulence profiles.
format: application/pdf
format: text/html
creator: Matilde Fernandes
creator: Carla Nóbrega Carneiro
creator: Ana Maria Villada Rosales
creator: Miguel Grilo
creator: Yolanda Ramiro
creator: Eva Cunha
creator: Telmo Nunes
creator: Luís Tavares
creator: Janet Sandi
creator: Manuela Oliveira
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12911
publisher: PeerJ Inc.
rights: © 2022 Fernandes et al.
abstract: Background Wildlife has been recently recognized as an environmental reservoir for antimicrobial resistance (AMR). However, less information on this topic is available in animals released back into the wild after rehabilitation in wildlife facilities, compared with studies performed exclusively in captive or free-ranging wildlife. This study aimed to evaluate the potential influence of captivity and/or treatment while in captivity of wild sloths on the AMR and virulence profiles of sloths’ Enterobacterales. Methods Oral and rectal swab samples were collected from 39 two-finger (Choloepus hoffmanni) and three-finger sloths (Bradypus variegatus) of Costa Rica (n = 78) and analyzed using conventional bacteriological techniques. A generalized linear mixed model was applied to estimate the isolates’ multiple antimicrobial resistance and virulence indices as a function of animal status. Results A considerable level of resistance was detected, especially for Citrobacter youngae and Escherichia coli, with 17.5% of isolates classified as multidrug-resistant. Virulence indices of isolates from rehabilitated sloths were significantly higher than the ones from sloths being hand-reared for shorter periods. Conclusions To our knowledge, this is the first description of sloths’ antimicrobial resistant Enterobacterales, suggesting that sloths’ rehabilitation and consequent exposure to humans, may promote the selection of bacteria with higher virulence. Ultimately, these bacteria may represent a threat to human and animal health due to their zoonotic potential and AMR and virulence profiles.
bibliographic citation: Fernandes et al. (2022) Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica. PeerJ 10:e12911 https://doi.org/10.7717/peerj.12911
date submitted: 2021-07-29
date accepted: 2022-01-19
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernandes
  given name: Matilde
author list: Agent
  family name: Nóbrega Carneiro
  given name: Carla
author list: Agent
  family name: Villada Rosales
  given name: Ana Maria
author list: Agent
  family name: Grilo
  given name: Miguel
author list: Agent
  family name: Ramiro
  given name: Yolanda
author list: Agent
  family name: Cunha
  given name: Eva
author list: Agent
  family name: Nunes
  given name: Telmo
author list: Agent
  family name: Tavares
  given name: Luís
author list: Agent
  family name: Sandi
  given name: Janet
author list: Agent
  family name: Oliveira
  given name: Manuela
doi: 10.7717/peerj.12911
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: © 2022 Fernandes et al.
attribution name: Fernandes et al.

The evolution of reproductive strategies in turtles
type: item
type: AcademicArticle
description: Optimal egg size theory assumes that changes in the egg and clutch are driven by selection, resulting in adjustments for the largest possible production of offspring with the highest fitness. Evidence supports the idea that large-bodied turtles tend to produce larger clutches with small and round eggs, while smaller species produce small clutches with large and elongated eggs. Our goals were to investigate whether egg and clutch size follow the predictions of egg size theory, if there are convergent reproductive strategies, and identify ecological factors that influence clutch and egg traits across all clades of living turtles. Using phylogenetic methods, we tested the covariance among reproductive traits, if they are convergent among different turtle lineages, and which ecological factors influence these traits. We found that both egg shape and size inversely correlate with clutch size, although with different evolutionary rates, following the predictions of the egg size theory. We also present compelling evidence for convergence among different turtle clades, over at least two reproductive strategies. Furthermore, climatic zone is the only ecological predictor to influence both egg size and fecundity, while diet only influences egg size. We conclude that egg and clutch traits in Testudines evolved independently several times across non-directly related clades that converged to similar reproductive strategies. Egg and clutch characteristics follow the trade-offs predicted by egg size theory and are influenced by ecological factors. Climatic zone and diet play an important role in the distribution of reproductive characteristics among turtles.
format: application/pdf
format: text/html
creator: Gabriel Jorgewich-Cohen
creator: Rafael S. Henrique
creator: Pedro Henrique Dias
creator: Marcelo R. Sánchez-Villagra
subject: Animal Behavior
subject: Biodiversity
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.13014
publisher: PeerJ Inc.
rights: © 2022 Jorgewich-Cohen et al.
abstract: Optimal egg size theory assumes that changes in the egg and clutch are driven by selection, resulting in adjustments for the largest possible production of offspring with the highest fitness. Evidence supports the idea that large-bodied turtles tend to produce larger clutches with small and round eggs, while smaller species produce small clutches with large and elongated eggs. Our goals were to investigate whether egg and clutch size follow the predictions of egg size theory, if there are convergent reproductive strategies, and identify ecological factors that influence clutch and egg traits across all clades of living turtles. Using phylogenetic methods, we tested the covariance among reproductive traits, if they are convergent among different turtle lineages, and which ecological factors influence these traits. We found that both egg shape and size inversely correlate with clutch size, although with different evolutionary rates, following the predictions of the egg size theory. We also present compelling evidence for convergence among different turtle clades, over at least two reproductive strategies. Furthermore, climatic zone is the only ecological predictor to influence both egg size and fecundity, while diet only influences egg size. We conclude that egg and clutch traits in Testudines evolved independently several times across non-directly related clades that converged to similar reproductive strategies. Egg and clutch characteristics follow the trade-offs predicted by egg size theory and are influenced by ecological factors. Climatic zone and diet play an important role in the distribution of reproductive characteristics among turtles.
bibliographic citation: Jorgewich-Cohen et al. (2022) The evolution of reproductive strategies in turtles. PeerJ 10:e13014 https://doi.org/10.7717/peerj.13014
date submitted: 2020-12-24
date accepted: 2022-02-06
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jorgewich-Cohen
  given name: Gabriel
author list: Agent
  family name: Henrique
  given name: Rafael S.
author list: Agent
  family name: Dias
  given name: Pedro Henrique
author list: Agent
  family name: Sánchez-Villagra
  given name: Marcelo R.
doi: 10.7717/peerj.13014
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: © 2022 Jorgewich-Cohen et al.
attribution name: Jorgewich-Cohen et al.

UAV spraying on citrus crop: impact of tank-mix adjuvant on the contact angle and droplet distribution
type: item
type: AcademicArticle
description: Adding tank-mix adjuvants into the spray mixture is a common practice to improve droplet distribution for field crops (e.g., rice, wheat, corn, etc.) when using Unmanned Aerial Vehicle (UAV) sprayers. However, the effectiveness of tank-mix adjuvant for UAV spraying in orchard crops is still an open problem, considering their special canopy structure and leaf features. This study aims to evaluate the effects of a typical tank-mix adjuvant concentrations (i.e., Nong Jian Fei (NJF)) on Contact Angle (CA) and droplet distribution in the citrus tree canopy. Three commonly used parameters, namely dynamic CA, droplet coverage, and Volume Median Diameter (VMD), are adopted for performance evaluation. The dynamic CAs on the adaxial surface of citrus leaves, for water-only and NJF-presence sprays, respectively, are measured with five concentration levels, where three replications are performed for each concentration. The sprays with 0.5‰ NJF are adopted in the field experiment for evaluating droplet distributions, where Water Sensitive Papers (WSPs) are used as collectors. Two multi-rotor UAVs (DJI T20 and T30) which consist of different sizes of pesticide tanks and rotor diameters are used as the spraying platforms. Both water-only and NJF-presence treatments are conducted for the two UAVs, respectively. The results of the CA experiment show that NJF addition can significantly reduce the CAs of the sprays. The sprays with 0.5‰ NJF obtain the lowest CA within the observing time, suggesting a better spread ability on solid surface (e.g., WSPs or/and leaves). With respect to the effects of NJF addition on individual UAVs, the field trial results indicate that NJF addition can remarkably increase both the droplet coverage and VMD at three canopy layers, except for T30 droplet coverage of the inside and bottom layers. Comparing the difference of droplet coverage between two UAVs, while significant difference is found in the same layer before NJF addition, there is no notable diff…
format: application/pdf
format: text/html
creator: Yanhua Meng
creator: Wanqiang Zhong
creator: Cunjia Liu
creator: Jinya Su
creator: Jiyuan Su
creator: Yubin Lan
creator: Zhiguo Wang
creator: Meimei Wang
subject: Agricultural Science
subject: Bioengineering
subject: Plant Science
subject: Atmospheric Chemistry
description: doi:10.7717/peerj.13064
publisher: PeerJ Inc.
rights: © 2022 Meng et al.
abstract: Adding tank-mix adjuvants into the spray mixture is a common practice to improve droplet distribution for field crops (e.g., rice, wheat, corn, etc.) when using Unmanned Aerial Vehicle (UAV) sprayers. However, the effectiveness of tank-mix adjuvant for UAV spraying in orchard crops is still an open problem, considering their special canopy structure and leaf features. This study aims to evaluate the effects of a typical tank-mix adjuvant concentrations (i.e., Nong Jian Fei (NJF)) on Contact Angle (CA) and droplet distribution in the citrus tree canopy. Three commonly used parameters, namely dynamic CA, droplet coverage, and Volume Median Diameter (VMD), are adopted for performance evaluation. The dynamic CAs on the adaxial surface of citrus leaves, for water-only and NJF-presence sprays, respectively, are measured with five concentration levels, where three replications are performed for each concentration. The sprays with 0.5‰ NJF are adopted in the field experiment for evaluating droplet distributions, where Water Sensitive Papers (WSPs) are used as collectors. Two multi-rotor UAVs (DJI T20 and T30) which consist of different sizes of pesticide tanks and rotor diameters are used as the spraying platforms. Both water-only and NJF-presence treatments are conducted for the two UAVs, respectively. The results of the CA experiment show that NJF addition can significantly reduce the CAs of the sprays. The sprays with 0.5‰ NJF obtain the lowest CA within the observing time, suggesting a better spread ability on solid surface (e.g., WSPs or/and leaves). With respect to the effects of NJF addition on individual UAVs, the field trial results indicate that NJF addition can remarkably increase both the droplet coverage and VMD at three canopy layers, except for T30 droplet coverage of the inside and bottom layers. Comparing the difference of droplet coverage between two UAVs, while significant difference is found in the same layer before NJF addition, there is no notable diff…
bibliographic citation: Meng et al. (2022) UAV spraying on citrus crop: impact of tank-mix adjuvant on the contact angle and droplet distribution. PeerJ 10:e13064 https://doi.org/10.7717/peerj.13064
date submitted: 2021-11-11
date accepted: 2022-02-14
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Yanhua
author list: Agent
  family name: Zhong
  given name: Wanqiang
author list: Agent
  family name: Liu
  given name: Cunjia
author list: Agent
  family name: Su
  given name: Jinya
author list: Agent
  family name: Su
  given name: Jiyuan
author list: Agent
  family name: Lan
  given name: Yubin
author list: Agent
  family name: Wang
  given name: Zhiguo
author list: Agent
  family name: Wang
  given name: Meimei
doi: 10.7717/peerj.13064
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: © 2022 Meng et al.
attribution name: Meng et al.

The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study
type: item
type: AcademicArticle
description: Background We explored the relationship between the platelet-lymphocyte ratio (PLR), the prognostic nutritional index (PNI), the lactate dehydrogenase-albumin ratio (LDH/albumin ratio; LAR), the controlling nutritional status (CONUT) score, and the long-term survival of colon cancer patients. Methods We conducted a retrospective analysis of the clinical data and follow-up materials of 126 patients with colon cancer who underwent surgical treatment in the Department of Gastrointestinal Surgery of Jiangnan University Affiliated Hospital from June 2012 to December 2015. The receiver operating characteristic curve (ROC) was used to distinguish the high ratio group from the low ratio group. The Kaplan Meier method was used to draw the survival curve in our survival analysis. The log rank test was used for the univariate analysis and the Cox multivariate regression analysis was used to analyze the correlation between preoperative PLR, PNI, LAR, conut scores, and overall survival (OS) and progression free survival (PFS) of patients with colon cancer. Results The median follow-up time was 72 months. The OS rates at 3 and 5 years were 83.3% and 78.5%, respectively. The PFS rates at 3 and 5 years were 79.3% and 77.6%, respectively. The 3-year and 5-year OS rates in the low LAR group (≤4.91) were 90.9% and 87.1%, respectively, and were 56.0% and 44.0% in the high LAR group (>4.91) respectively. Univariate and multivariate analyses showed that the LAR value was correlated with OS and PFS (P < 0.05). Conclusion A high preoperative LAR is an independent predictor of the prognosis of colon cancer patients.
format: application/pdf
format: text/html
creator: Zhihui Xie
creator: Hui Zhou
creator: Lei Wang
creator: Yibo Wu
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Immunology
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.13091
publisher: PeerJ Inc.
rights: © 2022 Xie et al.
abstract: Background We explored the relationship between the platelet-lymphocyte ratio (PLR), the prognostic nutritional index (PNI), the lactate dehydrogenase-albumin ratio (LDH/albumin ratio; LAR), the controlling nutritional status (CONUT) score, and the long-term survival of colon cancer patients. Methods We conducted a retrospective analysis of the clinical data and follow-up materials of 126 patients with colon cancer who underwent surgical treatment in the Department of Gastrointestinal Surgery of Jiangnan University Affiliated Hospital from June 2012 to December 2015. The receiver operating characteristic curve (ROC) was used to distinguish the high ratio group from the low ratio group. The Kaplan Meier method was used to draw the survival curve in our survival analysis. The log rank test was used for the univariate analysis and the Cox multivariate regression analysis was used to analyze the correlation between preoperative PLR, PNI, LAR, conut scores, and overall survival (OS) and progression free survival (PFS) of patients with colon cancer. Results The median follow-up time was 72 months. The OS rates at 3 and 5 years were 83.3% and 78.5%, respectively. The PFS rates at 3 and 5 years were 79.3% and 77.6%, respectively. The 3-year and 5-year OS rates in the low LAR group (≤4.91) were 90.9% and 87.1%, respectively, and were 56.0% and 44.0% in the high LAR group (>4.91) respectively. Univariate and multivariate analyses showed that the LAR value was correlated with OS and PFS (P < 0.05). Conclusion A high preoperative LAR is an independent predictor of the prognosis of colon cancer patients.
bibliographic citation: Xie et al. (2022) The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study. PeerJ 10:e13091 https://doi.org/10.7717/peerj.13091
date submitted: 2021-07-21
date accepted: 2022-02-18
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Zhihui
author list: Agent
  family name: Zhou
  given name: Hui
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Wu
  given name: Yibo
doi: 10.7717/peerj.13091
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: © 2022 Xie et al.
attribution name: Xie et al.

Comparison and correlation of cervical proprioception and muscle endurance in general joint hypermobility participants with and without non-specific neck pain—a cross-sectional study
type: item
type: AcademicArticle
description: Background Cervical proprioception and muscle endurance are essential for maintaining cervical functional joint stability. Proprioception and muscle endurance may be impaired in those with general joint hypermobility (GJH). Examining these aspects is crucial. This study’s aims are to (1) compare the cervical joint position error (JPE) and muscle endurance holding capacities in GJH individuals with and without non-specific neck pain (NSNP) (2) to assess the relationship between hypermobility Beighton scores, cervical JPE’s, and muscle endurance in GJH individuals with and without NSNP. Methods In this cross-sectional comparative study, 33 GJH participants with NSNP (mean age 21.7 ± 1.8 years) and 35 asymptomatic participants GJH (mean age 22.42 ± 1.7 years) participated. Beighton’s score of ≥4 of 9 tests was used as criteria to diagnose GJH. Cervical JPEs were estimated in degrees using a cervical range of motion device, and muscle endurance (flexor and extensor) were estimated in seconds using a stopwatch. Results GJH participants with NSNP showed significantly larger cervical JPEs (p < 0.001) and decreased muscle endurance holding times (p < 0.001) compared to asymptomatic participants. Beighton hypermobility scores showed a significant moderate positive correlation with cervical JPEs (flexion: r = 0.43, p = 0.013), left rotation: r = 0.47, p = 0.005, right rotation: r = 0.57, p = 0.001) in NSNP individuals. Also, Beighton hypermobility scores showed a moderate negative correlation with muscle endurance in NSNP (flexor muscles: r = −0.40, p = 0.020, extensor muscles: r = −0.41, p = 0.020, and asymptomatic individuals (flexor muscles: −0.34, p = 0.045, extensor muscles: r = −0.45, p = 0.007). Conclusion GJH individuals with NSNP showed increased cervical JPEs and reduced muscle endurance compared to asymptomatic. Individuals with GJH with higher Beighton scores demonstrated increased cervical JPEs and reduced neck muscle endurance holding ability. In clinical practi…
format: application/pdf
format: text/html
creator: Ravi Shankar Reddy
creator: Jaya Shanker Tedla
creator: Mastour Saeed Alshahrani
creator: Faisal Asiri
creator: Venkata Nagaraj Kakaraparthi
subject: Anesthesiology and Pain Management
subject: Orthopedics
subject: Rheumatology
subject: Rehabilitation
description: doi:10.7717/peerj.13097
publisher: PeerJ Inc.
rights: © 2022 Reddy et al.
abstract: Background Cervical proprioception and muscle endurance are essential for maintaining cervical functional joint stability. Proprioception and muscle endurance may be impaired in those with general joint hypermobility (GJH). Examining these aspects is crucial. This study’s aims are to (1) compare the cervical joint position error (JPE) and muscle endurance holding capacities in GJH individuals with and without non-specific neck pain (NSNP) (2) to assess the relationship between hypermobility Beighton scores, cervical JPE’s, and muscle endurance in GJH individuals with and without NSNP. Methods In this cross-sectional comparative study, 33 GJH participants with NSNP (mean age 21.7 ± 1.8 years) and 35 asymptomatic participants GJH (mean age 22.42 ± 1.7 years) participated. Beighton’s score of ≥4 of 9 tests was used as criteria to diagnose GJH. Cervical JPEs were estimated in degrees using a cervical range of motion device, and muscle endurance (flexor and extensor) were estimated in seconds using a stopwatch. Results GJH participants with NSNP showed significantly larger cervical JPEs (p < 0.001) and decreased muscle endurance holding times (p < 0.001) compared to asymptomatic participants. Beighton hypermobility scores showed a significant moderate positive correlation with cervical JPEs (flexion: r = 0.43, p = 0.013), left rotation: r = 0.47, p = 0.005, right rotation: r = 0.57, p = 0.001) in NSNP individuals. Also, Beighton hypermobility scores showed a moderate negative correlation with muscle endurance in NSNP (flexor muscles: r = −0.40, p = 0.020, extensor muscles: r = −0.41, p = 0.020, and asymptomatic individuals (flexor muscles: −0.34, p = 0.045, extensor muscles: r = −0.45, p = 0.007). Conclusion GJH individuals with NSNP showed increased cervical JPEs and reduced muscle endurance compared to asymptomatic. Individuals with GJH with higher Beighton scores demonstrated increased cervical JPEs and reduced neck muscle endurance holding ability. In clinical practi…
bibliographic citation: Reddy et al. (2022) Comparison and correlation of cervical proprioception and muscle endurance in general joint hypermobility participants with and without non-specific neck pain—a cross-sectional study. PeerJ 10:e13097 https://doi.org/10.7717/peerj.13097
date submitted: 2021-11-22
date accepted: 2022-02-20
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reddy
  given name: Ravi Shankar
author list: Agent
  family name: Tedla
  given name: Jaya Shanker
author list: Agent
  family name: Alshahrani
  given name: Mastour Saeed
author list: Agent
  family name: Asiri
  given name: Faisal
author list: Agent
  family name: Kakaraparthi
  given name: Venkata Nagaraj
doi: 10.7717/peerj.13097
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: © 2022 Reddy et al.
attribution name: Reddy et al.

Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults
type: item
type: AcademicArticle
description: Social communication difficulties are a diagnostic feature in autism. These difficulties are sometimes attributed, at least in part, to impaired ability in making inferences about what other people mean. In this registered report, we tested a competing hypothesis that the communication profile of adults on the autism spectrum can be more strongly characterised by reduced confidence in making inferences in the face of uncertain information. We tested this hypothesis by comparing the performance of 102 autistic and 109 non-autistic adults on a test of implied meaning, using a test of grammaticality judgements as a control task. We hypothesised that autistic adults would report substantially lower confidence, allowing for differences in accuracy, than non-autistic adults on the test of implied meaning compared to the grammaticality test. However, our results did not suggest this. Instead, we found that accuracy and confidence were both reduced to a similar extent on the test of implied meaning in the autistic group compared to the control group, although these were only subtle differences. This pattern of results was specific to inference-making, as the autistic and non-autistic groups did not differ on the grammar test. This supports the idea that specific differences in pragmatic language processing can exist in autism in the absence of core language problems. Importantly, this pattern of results (differences on the test of implied meaning and no differences on the grammar test) was reversed in a group with self-reported reading difficulties, indicating that the differences in inference-making were specific to the autistic group. Lastly, we found relationships between Intolerance of Uncertainty, performance on the test of implied meaning, and self-reported social communication challenges. This supports the idea that discomfort with uncertainty plays a role in the pragmatic language and communication challenges in autism.
format: application/pdf
format: text/html
creator: Alexander C. Wilson
creator: Dorothy V.M. Bishop
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13110
publisher: PeerJ Inc.
rights: © 2022 Wilson and Bishop
abstract: Social communication difficulties are a diagnostic feature in autism. These difficulties are sometimes attributed, at least in part, to impaired ability in making inferences about what other people mean. In this registered report, we tested a competing hypothesis that the communication profile of adults on the autism spectrum can be more strongly characterised by reduced confidence in making inferences in the face of uncertain information. We tested this hypothesis by comparing the performance of 102 autistic and 109 non-autistic adults on a test of implied meaning, using a test of grammaticality judgements as a control task. We hypothesised that autistic adults would report substantially lower confidence, allowing for differences in accuracy, than non-autistic adults on the test of implied meaning compared to the grammaticality test. However, our results did not suggest this. Instead, we found that accuracy and confidence were both reduced to a similar extent on the test of implied meaning in the autistic group compared to the control group, although these were only subtle differences. This pattern of results was specific to inference-making, as the autistic and non-autistic groups did not differ on the grammar test. This supports the idea that specific differences in pragmatic language processing can exist in autism in the absence of core language problems. Importantly, this pattern of results (differences on the test of implied meaning and no differences on the grammar test) was reversed in a group with self-reported reading difficulties, indicating that the differences in inference-making were specific to the autistic group. Lastly, we found relationships between Intolerance of Uncertainty, performance on the test of implied meaning, and self-reported social communication challenges. This supports the idea that discomfort with uncertainty plays a role in the pragmatic language and communication challenges in autism.
bibliographic citation: Wilson et al. (2022) Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults. PeerJ 10:e13110 https://doi.org/10.7717/peerj.13110
date submitted: 2021-12-20
date accepted: 2022-02-22
issued: 2022-03-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilson
  given name: Alexander C.
author list: Agent
  family name: Bishop
  given name: Dorothy V.M.
doi: 10.7717/peerj.13110
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-11
copyright: ©2022 Wilson and Bishop
attribution name: Wilson and Bishop

Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses
type: item
type: AcademicArticle
description: Background The rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment. Methods In this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions. Results As a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs.
format: application/pdf
format: text/html
creator: Muhammad Abdul Rehman Rashid
creator: Rana Muhammad Atif
creator: Yan Zhao
creator: Farrukh Azeem
creator: Hafiz Ghulam Muhu-Din Ahmed
creator: Yinghua Pan
creator: Danting Li
creator: Yong Zhao
creator: Zhanying Zhang
creator: Hongliang Zhang
creator: Jinjie Li
creator: Zichao Li
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12674
publisher: PeerJ Inc.
rights: © 2022 Rashid et al.
abstract: Background The rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment. Methods In this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions. Results As a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs.
bibliographic citation: Rashid et al. (2022) Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses. PeerJ 10:e12674 https://doi.org/10.7717/peerj.12674
date submitted: 2021-08-12
date accepted: 2021-12-02
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rashid
  given name: Muhammad Abdul Rehman
author list: Agent
  family name: Atif
  given name: Rana Muhammad
author list: Agent
  family name: Zhao
  given name: Yan
author list: Agent
  family name: Azeem
  given name: Farrukh
author list: Agent
  family name: Ahmed
  given name: Hafiz Ghulam Muhu-Din
author list: Agent
  family name: Pan
  given name: Yinghua
author list: Agent
  family name: Li
  given name: Danting
author list: Agent
  family name: Zhao
  given name: Yong
author list: Agent
  family name: Zhang
  given name: Zhanying
author list: Agent
  family name: Zhang
  given name: Hongliang
author list: Agent
  family name: Li
  given name: Jinjie
author list: Agent
  family name: Li
  given name: Zichao
doi: 10.7717/peerj.12674
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Rashid et al.
attribution name: Rashid et al.

Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes
type: item
type: AcademicArticle
description: The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H′) revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly ineffi…
format: application/pdf
format: text/html
creator: Muraleedhar Aski
creator: Reena Mehra
creator: Gyan Prakash Mishra
creator: Dharmendra Singh
creator: Prachi Yadav
creator: Neha Rai
creator: Venkata Ravi Prakash Reddy
creator: Arun Kumar MB
creator: Renu Pandey
creator: Madan Pal Singh
creator: Gayacharan
creator: Ruchi Bansal
creator: Kuldeep Tripathi
creator: Sripada M. Udupa
creator: Shiv Kumar
creator: Ashutosh Sarker
creator: Harsh Kumar Dikshit
subject: Agricultural Science
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12766
publisher: PeerJ Inc.
rights: © 2022 Aski et al.
abstract: The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H′) revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly ineffi…
bibliographic citation: Aski et al. (2022) Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes. PeerJ 10:e12766 https://doi.org/10.7717/peerj.12766
date submitted: 2021-07-07
date accepted: 2021-12-17
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aski
  given name: Muraleedhar
author list: Agent
  family name: Mehra
  given name: Reena
author list: Agent
  family name: Mishra
  given name: Gyan Prakash
author list: Agent
  family name: Singh
  given name: Dharmendra
author list: Agent
  family name: Yadav
  given name: Prachi
author list: Agent
  family name: Rai
  given name: Neha
author list: Agent
  family name: Reddy
  given name: Venkata Ravi Prakash
author list: Agent
  family name: MB
  given name: Arun Kumar
author list: Agent
  family name: Pandey
  given name: Renu
author list: Agent
  family name: Singh
  given name: Madan Pal
author list: Agent
  family name: Gayacharan
author list: Agent
  family name: Bansal
  given name: Ruchi
author list: Agent
  family name: Tripathi
  given name: Kuldeep
author list: Agent
  family name: Udupa
  given name: Sripada M.
author list: Agent
  family name: Kumar
  given name: Shiv
author list: Agent
  family name: Sarker
  given name: Ashutosh
author list: Agent
  family name: Dikshit
  given name: Harsh Kumar
doi: 10.7717/peerj.12766
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Aski et al.
attribution name: Aski et al.

A versatile isothermal amplification assay for the detection of leptospires from various sample types
type: item
type: AcademicArticle
description: Background Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene. Results Several reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease. Conclusions In short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study.
format: application/pdf
format: text/html
creator: Shuhaidah Othman
creator: Pui-Yuei Lee
creator: Jia-Yong Lam
creator: Noraini Philip
creator: Nurul Natasya Azhari
creator: Norliza Bahtiar Affendy
creator: Siti Norbaya Masri
creator: Vasantha Kumari Neela
creator: Farah Shafawati Mohd-Taib
creator: Hui-Yee Chee
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12850
publisher: PeerJ Inc.
rights: © 2022 Othman et al.
abstract: Background Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene. Results Several reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease. Conclusions In short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study.
bibliographic citation: Othman et al. (2022) A versatile isothermal amplification assay for the detection of leptospires from various sample types. PeerJ 10:e12850 https://doi.org/10.7717/peerj.12850
date submitted: 2021-10-05
date accepted: 2022-01-07
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Othman
  given name: Shuhaidah
author list: Agent
  family name: Lee
  given name: Pui-Yuei
author list: Agent
  family name: Lam
  given name: Jia-Yong
author list: Agent
  family name: Philip
  given name: Noraini
author list: Agent
  family name: Azhari
  given name: Nurul Natasya
author list: Agent
  family name: Affendy
  given name: Norliza Bahtiar
author list: Agent
  family name: Masri
  given name: Siti Norbaya
author list: Agent
  family name: Neela
  given name: Vasantha Kumari
author list: Agent
  family name: Mohd-Taib
  given name: Farah Shafawati
author list: Agent
  family name: Chee
  given name: Hui-Yee
doi: 10.7717/peerj.12850
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: ©2022 Othman et al.
attribution name: Othman et al.

Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways
type: item
type: AcademicArticle
description: Background Immediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown. Methods The expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation. Results A significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09–0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61–0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03–1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-relat…
format: application/pdf
format: text/html
creator: Fei-Yan He
creator: Gang Chen
creator: Rong-quan He
creator: Zhi-Guang Huang
creator: Jian-Di Li
creator: Wei-Zi Wu
creator: Ji-Tian Chen
creator: Yu-Lu Tang
creator: Dong-Ming Li
creator: Shang-Ling Pan
creator: Zhen-Bo Feng
creator: Yi-wu Dang
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.12944
publisher: PeerJ Inc.
rights: © 2022 He et al.
abstract: Background Immediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown. Methods The expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation. Results A significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09–0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61–0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03–1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-relat…
bibliographic citation: He et al. (2022) Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways. PeerJ 10:e12944 https://doi.org/10.7717/peerj.12944
date submitted: 2021-08-27
date accepted: 2022-01-24
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Fei-Yan
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: He
  given name: Rong-quan
author list: Agent
  family name: Huang
  given name: Zhi-Guang
author list: Agent
  family name: Li
  given name: Jian-Di
author list: Agent
  family name: Wu
  given name: Wei-Zi
author list: Agent
  family name: Chen
  given name: Ji-Tian
author list: Agent
  family name: Tang
  given name: Yu-Lu
author list: Agent
  family name: Li
  given name: Dong-Ming
author list: Agent
  family name: Pan
  given name: Shang-Ling
author list: Agent
  family name: Feng
  given name: Zhen-Bo
author list: Agent
  family name: Dang
  given name: Yi-wu
doi: 10.7717/peerj.12944
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: ©2022 He et al.
attribution name: He et al.

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