PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Ultraviolet-reflective film applied to windows reduces the likelihood of collisions for two species of songbird
items: Seasonal variations in leaf and branch trace elements and the influence of a 3-yr 100% rainfall exclusion on Pinus massoniana Lamb
items: Nitrogen form plays an important role in the growth of moso bamboo (Phyllostachys edulis) seedlings
items: An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data
items: Galectin-3 not Galectin-9 as a candidate prognosis marker for hepatocellular carcinoma
items: Effect of concurrent training on trainability performance factors in youth elite golf players
items: Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging
items: Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins
items: Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics
items: Differences in the support needs of children with developmental disabilities among groups of medical and behavioral needs

Ultraviolet-reflective film applied to windows reduces the likelihood of collisions for two species of songbird
type: item
type: AcademicArticle
description: Perhaps a billion birds die annually from colliding with residential and commercial windows. Therefore, there is a societal need to develop technologies that reduce window collisions by birds. Many current window films that are applied to the external surface of windows have human-visible patterns that are not esthetically preferable. BirdShades have developed a short wavelength (ultraviolet) reflective film that appears as a slight tint to the human eye but should be highly visible to many bird species that see in this spectral range. We performed flight tunnel tests of whether the BirdShades external window film reduced the likelihood that two species of song bird (zebra finch, Taeniopygia guttata and brown-headed cowbird, Molothrus ater) collide with windows during daylight. We paid particular attention to simulate the lighting conditions that birds will experience while flying during the day. Our results indicate a 75–90% reduction in the likelihood of collision with BirdShades-treated compared with control windows, in forced choice trials. In more ecologically relevant comparison between trials where all windows were either treated or control windows, the estimated reduction in probability of collision was 30–50%. Further, both bird species slow their flight by approximately 25% when approaching windows treated with the BirdShades film, thereby reducing the force of collisions if they were to happen. Therefore, we conclude that the BirdShades external window film will be effective in reducing the risk of and damage caused to populations and property by birds’ collision with windows. As this ultraviolet-reflective film has no human-visible patterning to it, the product might be an esthetically more acceptable low cost solution to reducing bird-window collisions. Further, we call for testing of other mitigation technologies in lighting and ecological conditions that are more similar to what birds experience in real human-built environments and make suggestions fo…
format: application/pdf
format: text/html
creator: John P. Swaddle
creator: Lauren C. Emerson
creator: Robin G. Thady
creator: Timothy J. Boycott
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.9926
publisher: PeerJ Inc.
rights: © 2020 Swaddle et al.
abstract: Perhaps a billion birds die annually from colliding with residential and commercial windows. Therefore, there is a societal need to develop technologies that reduce window collisions by birds. Many current window films that are applied to the external surface of windows have human-visible patterns that are not esthetically preferable. BirdShades have developed a short wavelength (ultraviolet) reflective film that appears as a slight tint to the human eye but should be highly visible to many bird species that see in this spectral range. We performed flight tunnel tests of whether the BirdShades external window film reduced the likelihood that two species of song bird (zebra finch, Taeniopygia guttata and brown-headed cowbird, Molothrus ater) collide with windows during daylight. We paid particular attention to simulate the lighting conditions that birds will experience while flying during the day. Our results indicate a 75–90% reduction in the likelihood of collision with BirdShades-treated compared with control windows, in forced choice trials. In more ecologically relevant comparison between trials where all windows were either treated or control windows, the estimated reduction in probability of collision was 30–50%. Further, both bird species slow their flight by approximately 25% when approaching windows treated with the BirdShades film, thereby reducing the force of collisions if they were to happen. Therefore, we conclude that the BirdShades external window film will be effective in reducing the risk of and damage caused to populations and property by birds’ collision with windows. As this ultraviolet-reflective film has no human-visible patterning to it, the product might be an esthetically more acceptable low cost solution to reducing bird-window collisions. Further, we call for testing of other mitigation technologies in lighting and ecological conditions that are more similar to what birds experience in real human-built environments and make suggestions fo…
bibliographic citation: Swaddle et al. (2020) Ultraviolet-reflective film applied to windows reduces the likelihood of collisions for two species of songbird. PeerJ 8:e9926 https://doi.org/10.7717/peerj.9926
date submitted: 2020-06-16
date accepted: 2020-08-21
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Swaddle
  given name: John P.
author list: Agent
  family name: Emerson
  given name: Lauren C.
author list: Agent
  family name: Thady
  given name: Robin G.
author list: Agent
  family name: Boycott
  given name: Timothy J.
doi: 10.7717/peerj.9926
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: © 2020 Swaddle et al.
attribution name: Swaddle et al.

Seasonal variations in leaf and branch trace elements and the influence of a 3-yr 100% rainfall exclusion on Pinus massoniana Lamb
type: item
type: AcademicArticle
description: Background Trace elements are essential for the growth and survival of plants, and their concentrations and distributions in plants are effective reflections of ecological adaptation strategies. However, this aspect has seldom been addressed. Method Changes in the leaf and branch trace elements of Pinus massoniana Lamb, induced by seasonal dynamics and in response to a 3-yr 100% rainfall exclusion, were evaluated. Results The results showed that the concentrations of Fe, Cu, Zn, Cd, Ni and Cr in leaves of P. massoniana in the control group had high seasonal resolution. There were three groups according to their patterns over the growing season: (1) nutrient elements (Cu, Zn, Ni and Cd), which continuously decreased in concentration during the growing season, with the highest concentration in spring and the lowest in autumn; (2) accumulating element (Cr), which increased in concentration from spring to autumn; and (3) indifferent element (Fe), which increased in concentration from spring to summer and decreased in concentration from summer to autumn. The concentrations of trace elements in leaves and branches showed no significant differences with mild drought stress, except for Fe and Cr in leaves and Cr in branches, which significantly increased (p < 0.05) under the result of self-selection under mild drought stress. Therefore, the resultant seasonal and drought effects on trace element cycling in P. massoniana could provide theoretical support to respond to future climate change.
format: application/pdf
format: text/html
creator: Tian Lin
creator: Xuanmei Zheng
creator: Huaizhou Zheng
subject: Plant Science
subject: Soil Science
subject: Climate Change Biology
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.9935
publisher: PeerJ Inc.
rights: © 2020 Lin et al.
abstract: Background Trace elements are essential for the growth and survival of plants, and their concentrations and distributions in plants are effective reflections of ecological adaptation strategies. However, this aspect has seldom been addressed. Method Changes in the leaf and branch trace elements of Pinus massoniana Lamb, induced by seasonal dynamics and in response to a 3-yr 100% rainfall exclusion, were evaluated. Results The results showed that the concentrations of Fe, Cu, Zn, Cd, Ni and Cr in leaves of P. massoniana in the control group had high seasonal resolution. There were three groups according to their patterns over the growing season: (1) nutrient elements (Cu, Zn, Ni and Cd), which continuously decreased in concentration during the growing season, with the highest concentration in spring and the lowest in autumn; (2) accumulating element (Cr), which increased in concentration from spring to autumn; and (3) indifferent element (Fe), which increased in concentration from spring to summer and decreased in concentration from summer to autumn. The concentrations of trace elements in leaves and branches showed no significant differences with mild drought stress, except for Fe and Cr in leaves and Cr in branches, which significantly increased (p < 0.05) under the result of self-selection under mild drought stress. Therefore, the resultant seasonal and drought effects on trace element cycling in P. massoniana could provide theoretical support to respond to future climate change.
bibliographic citation: Lin et al. (2020) Seasonal variations in leaf and branch trace elements and the influence of a 3-yr 100% rainfall exclusion on Pinus massoniana Lamb. PeerJ 8:e9935 https://doi.org/10.7717/peerj.9935
date submitted: 2020-06-09
date accepted: 2020-08-24
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Tian
author list: Agent
  family name: Zheng
  given name: Xuanmei
author list: Agent
  family name: Zheng
  given name: Huaizhou
doi: 10.7717/peerj.9935
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: ©2020 Lin et al.
attribution name: Lin et al.

Nitrogen form plays an important role in the growth of moso bamboo (Phyllostachys edulis) seedlings
type: item
type: AcademicArticle
description: Background This study aimed to gain an understanding of the growth response of Phyllostachys edulis (moso bamboo) seedlings to nitrogen (N) and potassium (K) to benefit nutrient management practices and the design of proper fertilizer in nursery cultivation. Methods An orthogonal array L8(4×24) was used to study the effects of N forms (NH4+, NO3−), N concentrations (8, 32 mmol/L), and K+concentrations (0, 0.5, 1.5, 3 mmol/L) on seedling height, leaf number, chlorophyll content (SPAD value), biomass, root systems, and N content of P. edulis seedlings. Plants were grown in vermiculite under controlled greenhouse conditions. Results Our study showed that N form played a significant role in the overall performance of P. edulis seedlings, followed by the effect of N and K+ concentrations. Among the N forms, NH4+ significantly improved the growth of P. edulis seedlings compared with NO3−. Seedling height, leaf number, chlorophyll SPAD value, biomass, and root system architecture (root length, root surface area, root volume, and root tips) were greater with 8 mmol/L of NH4+ treatments than with 32 mmol/L of NH4+treatments, whereas root diameter and N content of P. edulis seedlings were higher with 32 mmol/L of NH4+ than with 8 mmol/L of NH4+. K displayed inconsistent effects on the growth of P. edulis seedlings. Specifically, seedling height, leaf number, biomass and root volume increased when the K+ concentration was increased from 0 to 0.5 mmol/L, followed by a decrease when the K+ concentration was further increased from 0.5 to 3 mmol/L. Root average diameter of the seedlings was the highest with a K+ concentration of 1.5 mmol/L, and K had some inhibitory effects on the chlorophyll SPAD value of the seedlings. P. edulis seedlings performed well with 8 mmol/L NH4+and further tolerated a higher concentration of both NH4+ and NO3−, although excessive N could inhibit seedling growth. A lower concertation of K (≤ 0.5 mmol/L) promoted seedling growth and increasing K+ concent…
format: application/pdf
format: text/html
creator: Na Zou
creator: Ling Huang
creator: Huijing Chen
creator: Xiaofeng Huang
creator: Qingni Song
creator: Qingpei Yang
creator: Tianchi Wang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9938
publisher: PeerJ Inc.
rights: © 2020 Zou et al.
abstract: Background This study aimed to gain an understanding of the growth response of Phyllostachys edulis (moso bamboo) seedlings to nitrogen (N) and potassium (K) to benefit nutrient management practices and the design of proper fertilizer in nursery cultivation. Methods An orthogonal array L8(4×24) was used to study the effects of N forms (NH4+, NO3−), N concentrations (8, 32 mmol/L), and K+concentrations (0, 0.5, 1.5, 3 mmol/L) on seedling height, leaf number, chlorophyll content (SPAD value), biomass, root systems, and N content of P. edulis seedlings. Plants were grown in vermiculite under controlled greenhouse conditions. Results Our study showed that N form played a significant role in the overall performance of P. edulis seedlings, followed by the effect of N and K+ concentrations. Among the N forms, NH4+ significantly improved the growth of P. edulis seedlings compared with NO3−. Seedling height, leaf number, chlorophyll SPAD value, biomass, and root system architecture (root length, root surface area, root volume, and root tips) were greater with 8 mmol/L of NH4+ treatments than with 32 mmol/L of NH4+treatments, whereas root diameter and N content of P. edulis seedlings were higher with 32 mmol/L of NH4+ than with 8 mmol/L of NH4+. K displayed inconsistent effects on the growth of P. edulis seedlings. Specifically, seedling height, leaf number, biomass and root volume increased when the K+ concentration was increased from 0 to 0.5 mmol/L, followed by a decrease when the K+ concentration was further increased from 0.5 to 3 mmol/L. Root average diameter of the seedlings was the highest with a K+ concentration of 1.5 mmol/L, and K had some inhibitory effects on the chlorophyll SPAD value of the seedlings. P. edulis seedlings performed well with 8 mmol/L NH4+and further tolerated a higher concentration of both NH4+ and NO3−, although excessive N could inhibit seedling growth. A lower concertation of K (≤ 0.5 mmol/L) promoted seedling growth and increasing K+ concent…
bibliographic citation: Zou et al. (2020) Nitrogen form plays an important role in the growth of moso bamboo (Phyllostachys edulis) seedlings. PeerJ 8:e9938 https://doi.org/10.7717/peerj.9938
date submitted: 2020-05-27
date accepted: 2020-08-24
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Na
author list: Agent
  family name: Huang
  given name: Ling
author list: Agent
  family name: Chen
  given name: Huijing
author list: Agent
  family name: Huang
  given name: Xiaofeng
author list: Agent
  family name: Song
  given name: Qingni
author list: Agent
  family name: Yang
  given name: Qingpei
author list: Agent
  family name: Wang
  given name: Tianchi
doi: 10.7717/peerj.9938
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: ©2020 Zou et al.
attribution name: Zou et al.

An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data
type: item
type: AcademicArticle
description: Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populatio…
format: application/pdf
format: text/html
creator: Jessica F. McLaughlin
creator: Kevin Winker
subject: Biodiversity
subject: Evolutionary Studies
subject: Genomics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9939
publisher: PeerJ Inc.
rights: © 2020 McLaughlin and Winker
abstract: Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populatio…
bibliographic citation: McLaughlin et al. (2020) An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data. PeerJ 8:e9939 https://doi.org/10.7717/peerj.9939
date submitted: 2020-04-27
date accepted: 2020-08-24
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McLaughlin
  given name: Jessica F.
author list: Agent
  family name: Winker
  given name: Kevin
doi: 10.7717/peerj.9939
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: © 2020 McLaughlin and Winker
attribution name: McLaughlin and Winker

Galectin-3 not Galectin-9 as a candidate prognosis marker for hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Galectins (Gal) are a family of protein that bind to the β-galactoside of glycoproteins. It modulates a variety of biological functions, such as tumor growth, angiogenesis and tumor metastasis. A series of experimental and clinical evidences have been reported to support a correlation between galectin expressions and neoplastic transformation, progression and prognosis. The objective of this study was to estimate the expression of Gal-3 and Gal-9 in order to evaluate their relation to hepatocellular carcinoma (HCC) -related clinical features and their prognostic values. Methods We evaluated Gal-3 and Gal-9 expression in 247 HCC patients by a tissue microarray immunohistochemistry method, then analyzed the relationship between expression levels of Gal-3 and Gal-9 protein and tumor parameters or clinical outcomes. Results The Gal-3 expression was significantly higher in tumor tissues compared with adjacent non-tumor tissues (P < 0.001), while no significant differences of Gal-9 was detected (P = 0.222). A higher Gal-3 expression was significantly associated with lymph-vascular invasion (P = 0.049), poor histological differentiation (P = 0.016), and no cirrhosis (P = 0.040). In contrast, a lower Gal-9 expression was related to lymph-vascular invasion (P = 0.012) and poor histological differentiation (P = 0.002). Survival analysis showed that patients with higher Gal-3 expression had worse overall survival (P = 0.012) , however no correlation was found between Gal-9 expression and survival (P = 0.185). Multivariate analysis showed that multiple tumor (HR = 1.94, 95% CI [1.36–2.78]), tumor size ≥ 5 cm (HR = 1.51, 95% CI [1.07–2.12]), Lymph-vascular invasion (HR = 1.45, 95% CI [1.00–2.10]) and Gal-3 expression (HR = 1.57, 95% CI [1.06–2.33]) were independent influencing factors of prognosis in patients with hepatocellular carcinoma. Conclusion Gal-3 was expected to serve as a novel prognostic marker of hepatocellular carcinoma, while Gal-9 expression was only r…
format: application/pdf
format: text/html
creator: Fei Kong
creator: Meishan Jin
creator: Donghui Cao
creator: Zhifang Jia
creator: Yawen Liu
creator: Jing Jiang
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.9949
publisher: PeerJ Inc.
rights: © 2020 Kong et al.
abstract: Background Galectins (Gal) are a family of protein that bind to the β-galactoside of glycoproteins. It modulates a variety of biological functions, such as tumor growth, angiogenesis and tumor metastasis. A series of experimental and clinical evidences have been reported to support a correlation between galectin expressions and neoplastic transformation, progression and prognosis. The objective of this study was to estimate the expression of Gal-3 and Gal-9 in order to evaluate their relation to hepatocellular carcinoma (HCC) -related clinical features and their prognostic values. Methods We evaluated Gal-3 and Gal-9 expression in 247 HCC patients by a tissue microarray immunohistochemistry method, then analyzed the relationship between expression levels of Gal-3 and Gal-9 protein and tumor parameters or clinical outcomes. Results The Gal-3 expression was significantly higher in tumor tissues compared with adjacent non-tumor tissues (P < 0.001), while no significant differences of Gal-9 was detected (P = 0.222). A higher Gal-3 expression was significantly associated with lymph-vascular invasion (P = 0.049), poor histological differentiation (P = 0.016), and no cirrhosis (P = 0.040). In contrast, a lower Gal-9 expression was related to lymph-vascular invasion (P = 0.012) and poor histological differentiation (P = 0.002). Survival analysis showed that patients with higher Gal-3 expression had worse overall survival (P = 0.012) , however no correlation was found between Gal-9 expression and survival (P = 0.185). Multivariate analysis showed that multiple tumor (HR = 1.94, 95% CI [1.36–2.78]), tumor size ≥ 5 cm (HR = 1.51, 95% CI [1.07–2.12]), Lymph-vascular invasion (HR = 1.45, 95% CI [1.00–2.10]) and Gal-3 expression (HR = 1.57, 95% CI [1.06–2.33]) were independent influencing factors of prognosis in patients with hepatocellular carcinoma. Conclusion Gal-3 was expected to serve as a novel prognostic marker of hepatocellular carcinoma, while Gal-9 expression was only r…
bibliographic citation: Kong et al. (2020) Galectin-3 not Galectin-9 as a candidate prognosis marker for hepatocellular carcinoma. PeerJ 8:e9949 https://doi.org/10.7717/peerj.9949
date submitted: 2020-04-21
date accepted: 2020-08-25
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Fei
author list: Agent
  family name: Jin
  given name: Meishan
author list: Agent
  family name: Cao
  given name: Donghui
author list: Agent
  family name: Jia
  given name: Zhifang
author list: Agent
  family name: Liu
  given name: Yawen
author list: Agent
  family name: Jiang
  given name: Jing
doi: 10.7717/peerj.9949
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: ©2020 Kong et al.
attribution name: Kong et al.

Effect of concurrent training on trainability performance factors in youth elite golf players
type: item
type: AcademicArticle
description: Background Due to the early specialization of golf players, examining the within session sequence of training should be considered to enhance performance and prevent injury risk. The present study analyzed the effects of an 18-week concurrent training developed before or after a specific golf session in adolescence elite golfers on several performance factors. Methods Sixteen right-handed male golfers, were randomly divided into two groups: after golf specific training (AG) (n = 8, age: 16.77 ± 0.58 years) and before golf specific training (BG) (n = 8, age: 16.93 ± 0.59 years). AG and BG players followed a concurrent physical conditioning program (CT) after or before the golf specific training, respectively. Body mass, body fat, muscle mass, jumping ability (CMJ), ball speed (Sball), golf movements screens (GMS), power in a golf swing-specific cable woodchop (Wmax) and the perceived training load (TL) in golf specific training (TL-G) and TL in CT (TL-CT) were measured on three separate occasions. Results BG demonstrates a lower TL-CT than AG (p < .001, ${\eta }_{p}^{2}=0.90$ η p 2 = 0 . 90 ) along the training program without effects on TL-G, achieving significant percentage of change on CMJ (9.38%; p = .165; d = 0.73), GMS (50.52%; p = .41, d = 0.91), Wmax (16.93%; p = .001; d = 2.02) and Sball (1.82%; p = .018; d = 0.92) without interaction effects on anthropometric measures. Conclusions Performing CT sessions before the regular golf training can improve specific performance factors with a lower perceived TL than the same training carried out after the regular golf training.
format: application/pdf
format: text/html
creator: Juan Carlos Redondo
creator: Ana María de Benito
creator: José María Izquierdo
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.9963
publisher: PeerJ Inc.
rights: © 2020 Redondo et al.
abstract: Background Due to the early specialization of golf players, examining the within session sequence of training should be considered to enhance performance and prevent injury risk. The present study analyzed the effects of an 18-week concurrent training developed before or after a specific golf session in adolescence elite golfers on several performance factors. Methods Sixteen right-handed male golfers, were randomly divided into two groups: after golf specific training (AG) (n = 8, age: 16.77 ± 0.58 years) and before golf specific training (BG) (n = 8, age: 16.93 ± 0.59 years). AG and BG players followed a concurrent physical conditioning program (CT) after or before the golf specific training, respectively. Body mass, body fat, muscle mass, jumping ability (CMJ), ball speed (Sball), golf movements screens (GMS), power in a golf swing-specific cable woodchop (Wmax) and the perceived training load (TL) in golf specific training (TL-G) and TL in CT (TL-CT) were measured on three separate occasions. Results BG demonstrates a lower TL-CT than AG (p < .001, ${\eta }_{p}^{2}=0.90$ η p 2 = 0 . 90 ) along the training program without effects on TL-G, achieving significant percentage of change on CMJ (9.38%; p = .165; d = 0.73), GMS (50.52%; p = .41, d = 0.91), Wmax (16.93%; p = .001; d = 2.02) and Sball (1.82%; p = .018; d = 0.92) without interaction effects on anthropometric measures. Conclusions Performing CT sessions before the regular golf training can improve specific performance factors with a lower perceived TL than the same training carried out after the regular golf training.
bibliographic citation: Redondo et al. (2020) Effect of concurrent training on trainability performance factors in youth elite golf players. PeerJ 8:e9963 https://doi.org/10.7717/peerj.9963
date submitted: 2020-05-27
date accepted: 2020-08-25
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Redondo
  given name: Juan Carlos
author list: Agent
  family name: de Benito
  given name: Ana María
author list: Agent
  family name: Izquierdo
  given name: José María
doi: 10.7717/peerj.9963
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: ©2020 Redondo et al.
attribution name: Redondo et al.

Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging
type: item
type: AcademicArticle
description: Knowledge on the extent and mechanisms of fish damage caused by hydropower facilities is important for the conservation of fish populations. Herein, we assessed the effects of hydropower turbine passage on internal fish injuries using X-ray technology. A total of 902 specimens from seven native European fish species were screened for 36 types of internal injuries and 86 external injuries evaluated with a previously published protocol. The applied systematic visual evaluation of X-ray images successfully detected skeletal injuries, swim bladder anomalies, emphysema, free intraperitoneal gas and hemorrhages. Injuries related to handling and to impacts of different parts of the hydropower structure could be clearly distinguished applying multivariate statistics and the data often explained delayed mortality within 96 h after turbine passage. The internal injuries could clearly be assigned to specific physical impacts resulting from turbine passage such as swim bladder rupture due to abrupt pressure change or fractures of skeletal parts due to blade-strike, fluid shear or severe turbulence. Generally, internal injuries were rarely depicted by external evaluation. For example, 29% of individuals with vertebral fractures did not present externally visible signs of severe injury. A combination of the external and internal injury evaluation allows quantifying and comparing fish injuries across sites, and can help to identify the technologies and operational procedures which minimize harm to fish in the context of assessing hydropower-related fish injuries as well as in assessing fish welfare.
format: application/pdf
format: text/html
creator: Melanie Mueller
creator: Katharina Sternecker
creator: Stefan Milz
creator: Juergen Geist
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
subject: Environmental Impacts
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.9977
publisher: PeerJ Inc.
rights: © 2020 Mueller et al.
abstract: Knowledge on the extent and mechanisms of fish damage caused by hydropower facilities is important for the conservation of fish populations. Herein, we assessed the effects of hydropower turbine passage on internal fish injuries using X-ray technology. A total of 902 specimens from seven native European fish species were screened for 36 types of internal injuries and 86 external injuries evaluated with a previously published protocol. The applied systematic visual evaluation of X-ray images successfully detected skeletal injuries, swim bladder anomalies, emphysema, free intraperitoneal gas and hemorrhages. Injuries related to handling and to impacts of different parts of the hydropower structure could be clearly distinguished applying multivariate statistics and the data often explained delayed mortality within 96 h after turbine passage. The internal injuries could clearly be assigned to specific physical impacts resulting from turbine passage such as swim bladder rupture due to abrupt pressure change or fractures of skeletal parts due to blade-strike, fluid shear or severe turbulence. Generally, internal injuries were rarely depicted by external evaluation. For example, 29% of individuals with vertebral fractures did not present externally visible signs of severe injury. A combination of the external and internal injury evaluation allows quantifying and comparing fish injuries across sites, and can help to identify the technologies and operational procedures which minimize harm to fish in the context of assessing hydropower-related fish injuries as well as in assessing fish welfare.
bibliographic citation: Mueller et al. (2020) Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging. PeerJ 8:e9977 https://doi.org/10.7717/peerj.9977
date submitted: 2020-02-10
date accepted: 2020-08-26
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mueller
  given name: Melanie
author list: Agent
  family name: Sternecker
  given name: Katharina
author list: Agent
  family name: Milz
  given name: Stefan
author list: Agent
  family name: Geist
  given name: Juergen
doi: 10.7717/peerj.9977
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: © 2020 Mueller et al.
attribution name: Mueller et al.

Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins
type: item
type: AcademicArticle
description: The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.
format: application/pdf
format: text/html
creator: Mingrui Wang
creator: Dapeng Wang
creator: Jun Yu
creator: Shi Huang
subject: Computational Biology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.9983
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.
bibliographic citation: Wang et al. (2020) Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins. PeerJ 8:e9983 https://doi.org/10.7717/peerj.9983
date submitted: 2019-12-13
date accepted: 2020-08-27
issued: 2020-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mingrui
author list: Agent
  family name: Wang
  given name: Dapeng
author list: Agent
  family name: Yu
  given name: Jun
author list: Agent
  family name: Huang
  given name: Shi
doi: 10.7717/peerj.9983
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-16
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics
type: item
type: AcademicArticle
description: Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism.
format: application/pdf
format: text/html
creator: Luis Fernando Lozano Aguirre
creator: Juan Carlos Salazar
creator: José Ignacio Vásquez
creator: Víctor Antonio García-Angulo
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.9553
publisher: PeerJ Inc.
rights: © 2020 Lozano Aguirre et al.
abstract: Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism.
bibliographic citation: Lozano Aguirre et al. (2020) Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics. PeerJ 8:e9553 https://doi.org/10.7717/peerj.9553
date submitted: 2019-09-26
date accepted: 2020-06-24
issued: 2020-09-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lozano Aguirre
  given name: Luis Fernando
author list: Agent
  family name: Salazar
  given name: Juan Carlos
author list: Agent
  family name: Vásquez
  given name: José Ignacio
author list: Agent
  family name: García-Angulo
  given name: Víctor Antonio
doi: 10.7717/peerj.9553
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-15
copyright: ©2020 Lozano Aguirre et al.
attribution name: Lozano Aguirre et al.

Differences in the support needs of children with developmental disabilities among groups of medical and behavioral needs
type: item
type: AcademicArticle
description: Background/Aims Medical and behavioral needs are relevant in organizing and providing support strategies that improve the quality of life for children, along with their families. The present study aims to examine the impact of medical and behavioral needs on the need for support of children with disabilities. Methods Health and education professionals were interviewed using the Supports Intensity Scale-Children’s version to estimate the support needs of 911 children and adolescents (5–16 years) with an intellectual disability, including 55.32% with an additional disability. For data analysis, a model for measuring support needs was specified, consisting of seven support needs factors and three method factors. In estimating the model, four groups of medical and behavioral needs were considered. The factor scores’ means of the groups were compared through t-tests. Results Medical and behavioral needs had an impact on overall support needs. Differences were found in all support domains for medical needs. The greatest influence of behavioral needs was found in the Social and School participation areas but was indistinguishable between the mild and moderate levels of needs. Conclusions Medical and behavioral needs greatly affect the need for support in a child’s daily life, so they need to be considered a priority for support services. The importance of standardized assessments is emphasized to help develop support strategies.
format: application/pdf
format: text/html
creator: Victor B. Arias
creator: Virginia Aguayo
creator: Miguel A. Verdugo
creator: Antonio M. Amor
subject: Cognitive Disorders
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.9557
publisher: PeerJ Inc.
rights: © 2020 Arias et al.
abstract: Background/Aims Medical and behavioral needs are relevant in organizing and providing support strategies that improve the quality of life for children, along with their families. The present study aims to examine the impact of medical and behavioral needs on the need for support of children with disabilities. Methods Health and education professionals were interviewed using the Supports Intensity Scale-Children’s version to estimate the support needs of 911 children and adolescents (5–16 years) with an intellectual disability, including 55.32% with an additional disability. For data analysis, a model for measuring support needs was specified, consisting of seven support needs factors and three method factors. In estimating the model, four groups of medical and behavioral needs were considered. The factor scores’ means of the groups were compared through t-tests. Results Medical and behavioral needs had an impact on overall support needs. Differences were found in all support domains for medical needs. The greatest influence of behavioral needs was found in the Social and School participation areas but was indistinguishable between the mild and moderate levels of needs. Conclusions Medical and behavioral needs greatly affect the need for support in a child’s daily life, so they need to be considered a priority for support services. The importance of standardized assessments is emphasized to help develop support strategies.
bibliographic citation: Arias et al. (2020) Differences in the support needs of children with developmental disabilities among groups of medical and behavioral needs. PeerJ 8:e9557 https://doi.org/10.7717/peerj.9557
date submitted: 2020-04-01
date accepted: 2020-06-25
issued: 2020-09-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arias
  given name: Victor B.
author list: Agent
  family name: Aguayo
  given name: Virginia
author list: Agent
  family name: Verdugo
  given name: Miguel A.
author list: Agent
  family name: Amor
  given name: Antonio M.
doi: 10.7717/peerj.9557
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-15
copyright: ©2020 Arias et al.
attribution name: Arias et al.

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