PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Low composite functional movement screen score associated with decline of gait stability in young adults
items: Mycophenolate suppresses inflammation by inhibiting prostaglandin synthases: a study of molecular and experimental drug repurposing
items: The hypoferremic response to acute inflammation is maintained in thalassemia mice even under parenteral iron loading
items: Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)
items: PhyloPrimer: a taxon-specific oligonucleotide design platform
items: Evidence of integumentary scale diversity in the late Jurassic Sauropod Diplodocus sp. from the Mother’s Day Quarry, Montana
items: https://peerj.com/articles/11284
items: Identification of QTL for barley grain size
items: Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II–III breast cancer patients using CytoSorter® system: a retrospective study
items: How the fear of COVID-19 changed the way we look at human faces

Low composite functional movement screen score associated with decline of gait stability in young adults
type: item
type: AcademicArticle
description: Background The functional movement screen (FMS)TM is a screening tool used to evaluate fundamental motor function. A score of 14 for the composite total FMS score (TFMS) is generally used as the cut-off point (≤14/21). In addition, gait analysis is used to evaluate fundamental motor function in humans. Thus, evaluating the fundamental motor function using the FMSTM test and gait analysis at various speeds can provide further understanding of any decline in gait stability. In this study, we aimed to investigate the association between gait ability and fundamental movement patterns in young adults according to the cut-off point. Methods A total of 439 participants (male: 203, female: 236) successfully completed the FMS test and a 1 min treadmill test; the participants were classified into two groups: low TFMS (≤14) and high TFMS (>14). Results The low TFMS group exhibited slower and shortened walking patterns and worsen gait variability than the high TFMS group. The coefficient of variance (CV) for the double support phase at a faster speed (male) and the stride length at a slower speed (female) were classifiers between the two groups. In addition, the low TFMS group demonstrated insufficient gait adaptation at the preferred and faster speeds based on the CV of the double support phase and gait asymmetry. Lower TFMS is associated with a decline in gait ability. Therefore, participants with a lower TFMS and poor gait ability may require intervention programs to prevent risk of future injury and to enhance motor function.
format: application/pdf
format: text/html
creator: Myeounggon Lee
creator: Changhong Youm
creator: Byungjoo Noh
creator: Hwayoung Park
subject: Kinesiology
subject: Nursing
subject: Otorhinolaryngology
description: doi:10.7717/peerj.11356
publisher: PeerJ Inc.
rights: © 2021 Lee et al.
abstract: Background The functional movement screen (FMS)TM is a screening tool used to evaluate fundamental motor function. A score of 14 for the composite total FMS score (TFMS) is generally used as the cut-off point (≤14/21). In addition, gait analysis is used to evaluate fundamental motor function in humans. Thus, evaluating the fundamental motor function using the FMSTM test and gait analysis at various speeds can provide further understanding of any decline in gait stability. In this study, we aimed to investigate the association between gait ability and fundamental movement patterns in young adults according to the cut-off point. Methods A total of 439 participants (male: 203, female: 236) successfully completed the FMS test and a 1 min treadmill test; the participants were classified into two groups: low TFMS (≤14) and high TFMS (>14). Results The low TFMS group exhibited slower and shortened walking patterns and worsen gait variability than the high TFMS group. The coefficient of variance (CV) for the double support phase at a faster speed (male) and the stride length at a slower speed (female) were classifiers between the two groups. In addition, the low TFMS group demonstrated insufficient gait adaptation at the preferred and faster speeds based on the CV of the double support phase and gait asymmetry. Lower TFMS is associated with a decline in gait ability. Therefore, participants with a lower TFMS and poor gait ability may require intervention programs to prevent risk of future injury and to enhance motor function.
bibliographic citation: Lee et al. (2021) Low composite functional movement screen score associated with decline of gait stability in young adults. PeerJ 9:e11356 https://doi.org/10.7717/peerj.11356
date submitted: 2021-01-13
date accepted: 2021-04-05
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Myeounggon
author list: Agent
  family name: Youm
  given name: Changhong
author list: Agent
  family name: Noh
  given name: Byungjoo
author list: Agent
  family name: Park
  given name: Hwayoung
doi: 10.7717/peerj.11356
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: ©2021 Lee et al.
attribution name: Lee et al.

Mycophenolate suppresses inflammation by inhibiting prostaglandin synthases: a study of molecular and experimental drug repurposing
type: item
type: AcademicArticle
description: Mycophenolate mofetil is an established anti-proliferative and immune-suppressive agent that minimizes the proliferation of inflammatory cells by interfering with nucleic acid synthesis. Herein, we report our discovery of the prostaglandin inhibiting properties of MMF, which offers new applications for the drug in the treatment of inflammatory diseases. The estimated values of IC50MMFCOX-1, IC50MMFCOX-2, and IC50MMF5-LOX were 5.53, 0.19, and 4.47 µM, respectively. In contrast, mycophenolic acid (MPA) showed slightly stronger inhibition: IC50MPACOX-1, IC50MPACOX-2, and IC50MPA5-LOX were 4.62, 0.14, and 4.49 µM, respectively. These results indicate that MMF and MPA are, respectively, 28.6 and 33 times more selective for cyclooxygenase-2 than for cyclooxygenase-1, which implies that MMF would have less impact on the gastric mucosa than most nonselective, nonsteroidal anti-inflammatory drugs. Furthermore, MMF provided dose-dependent relief of acute inflammation in the carrageenan-induced rat paw edema test, with results comparable to those of celecoxib and indomethacin. Molecular dynamics simulations indicated that the MMF bond with COX-2 was stable, as evidenced by a low root-mean-square deviation of atomic positions, complementary per-residue root-mean-square fluctuation, and 0–4 hydrogen bonds during the 50-ns simulation time. Therefore, MMF provides immune-suppressing, cyclooxygenase-inhibiting, and inflammation-relieving properties. Our results indicate that MMF can be 1) repositioned for inflammation treatment without the need for further expensive clinical trials, 2) used for local acute inflammations, and 3) used as a sparing agent for other steroid and non-steroid anti-inflammatory medications, especially in topical applications.
format: application/pdf
format: text/html
creator: Fahad Al-Hizab
creator: Mahmoud Kandeel
subject: Biochemistry
subject: Pharmacology
subject: Computational Science
description: doi:10.7717/peerj.11360
publisher: PeerJ Inc.
rights: © 2021 Al-Hizab and Kandeel
abstract: Mycophenolate mofetil is an established anti-proliferative and immune-suppressive agent that minimizes the proliferation of inflammatory cells by interfering with nucleic acid synthesis. Herein, we report our discovery of the prostaglandin inhibiting properties of MMF, which offers new applications for the drug in the treatment of inflammatory diseases. The estimated values of IC50MMFCOX-1, IC50MMFCOX-2, and IC50MMF5-LOX were 5.53, 0.19, and 4.47 µM, respectively. In contrast, mycophenolic acid (MPA) showed slightly stronger inhibition: IC50MPACOX-1, IC50MPACOX-2, and IC50MPA5-LOX were 4.62, 0.14, and 4.49 µM, respectively. These results indicate that MMF and MPA are, respectively, 28.6 and 33 times more selective for cyclooxygenase-2 than for cyclooxygenase-1, which implies that MMF would have less impact on the gastric mucosa than most nonselective, nonsteroidal anti-inflammatory drugs. Furthermore, MMF provided dose-dependent relief of acute inflammation in the carrageenan-induced rat paw edema test, with results comparable to those of celecoxib and indomethacin. Molecular dynamics simulations indicated that the MMF bond with COX-2 was stable, as evidenced by a low root-mean-square deviation of atomic positions, complementary per-residue root-mean-square fluctuation, and 0–4 hydrogen bonds during the 50-ns simulation time. Therefore, MMF provides immune-suppressing, cyclooxygenase-inhibiting, and inflammation-relieving properties. Our results indicate that MMF can be 1) repositioned for inflammation treatment without the need for further expensive clinical trials, 2) used for local acute inflammations, and 3) used as a sparing agent for other steroid and non-steroid anti-inflammatory medications, especially in topical applications.
bibliographic citation: Al-Hizab et al. (2021) Mycophenolate suppresses inflammation by inhibiting prostaglandin synthases: a study of molecular and experimental drug repurposing. PeerJ 9:e11360 https://doi.org/10.7717/peerj.11360
date submitted: 2021-01-12
date accepted: 2021-04-06
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Hizab
  given name: Fahad
author list: Agent
  family name: Kandeel
  given name: Mahmoud
doi: 10.7717/peerj.11360
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Al-Hizab and Kandeel
attribution name: Al-Hizab and Kandeel

The hypoferremic response to acute inflammation is maintained in thalassemia mice even under parenteral iron loading
type: item
type: AcademicArticle
description: Background Hepcidin controls iron homeostasis by inducing the degradation of the iron efflux protein, ferroportin (FPN1), and subsequently reducing serum iron levels. Hepcidin expression is influenced by multiple factors, including iron stores, ineffective erythropoiesis, and inflammation. However, the interactions between these factors under thalassemic condition remain unclear. This study aimed to determine the hypoferremic and transcriptional responses of iron homeostasis to acute inflammatory induction by lipopolysaccharide (LPS) in thalassemic (Hbbth3/+) mice with/without parenteral iron loading with iron dextran. Methods Wild type and Hbbth3/+ mice were intramuscularly injected with 5 mg of iron dextran once daily for two consecutive days. After a 2-week equilibration, acute inflammation was induced by an intraperitoneal injection of a single dose of 1 µg/g body weight of LPS. Control groups for both iron loading and acute inflammation received equal volume(s) of saline solution. Blood and tissue samples were collected at 6 hours after LPS (or saline) injection. Iron parameters and mRNA expression of hepcidin as well as genes involved in iron transport and metabolism in wild type and Hbbth3/+ mice were analyzed and compared by Kruskal–Wallis test with pairwise Mann–Whitney U test. Results We found the inductive effects of LPS on liver IL-6 mRNA expression to be more pronounced under parenteral iron loading. Upon LPS administration, splenic erythroferrone (ERFE) mRNA levels were reduced only in iron-treated mice, whereas, liver bone morphogenetic protein 6 (BMP6) mRNA levels were decreased under both control and parenteral iron loading conditions. Despite the altered expression of the aforementioned hepcidin regulators, the stimulatory effect of LPS on hepcidin mRNA expression was blunt in iron-treated Hbbth3/+ mice. Contrary to the blunted hepcidin response, LPS treatment suppressed FPN1 mRNA expression in the liver, spleen, and duodenum, as well as reduced se…
format: application/pdf
format: text/html
creator: Chanita Sanyear
creator: Buraporn Chiawtada
creator: Punnee Butthep
creator: Saovaros Svasti
creator: Suthat Fucharoen
creator: Patarabutr Masaratana
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.11367
publisher: PeerJ Inc.
rights: © 2021 Sanyear et al.
abstract: Background Hepcidin controls iron homeostasis by inducing the degradation of the iron efflux protein, ferroportin (FPN1), and subsequently reducing serum iron levels. Hepcidin expression is influenced by multiple factors, including iron stores, ineffective erythropoiesis, and inflammation. However, the interactions between these factors under thalassemic condition remain unclear. This study aimed to determine the hypoferremic and transcriptional responses of iron homeostasis to acute inflammatory induction by lipopolysaccharide (LPS) in thalassemic (Hbbth3/+) mice with/without parenteral iron loading with iron dextran. Methods Wild type and Hbbth3/+ mice were intramuscularly injected with 5 mg of iron dextran once daily for two consecutive days. After a 2-week equilibration, acute inflammation was induced by an intraperitoneal injection of a single dose of 1 µg/g body weight of LPS. Control groups for both iron loading and acute inflammation received equal volume(s) of saline solution. Blood and tissue samples were collected at 6 hours after LPS (or saline) injection. Iron parameters and mRNA expression of hepcidin as well as genes involved in iron transport and metabolism in wild type and Hbbth3/+ mice were analyzed and compared by Kruskal–Wallis test with pairwise Mann–Whitney U test. Results We found the inductive effects of LPS on liver IL-6 mRNA expression to be more pronounced under parenteral iron loading. Upon LPS administration, splenic erythroferrone (ERFE) mRNA levels were reduced only in iron-treated mice, whereas, liver bone morphogenetic protein 6 (BMP6) mRNA levels were decreased under both control and parenteral iron loading conditions. Despite the altered expression of the aforementioned hepcidin regulators, the stimulatory effect of LPS on hepcidin mRNA expression was blunt in iron-treated Hbbth3/+ mice. Contrary to the blunted hepcidin response, LPS treatment suppressed FPN1 mRNA expression in the liver, spleen, and duodenum, as well as reduced se…
bibliographic citation: Sanyear et al. (2021) The hypoferremic response to acute inflammation is maintained in thalassemia mice even under parenteral iron loading. PeerJ 9:e11367 https://doi.org/10.7717/peerj.11367
date submitted: 2020-12-11
date accepted: 2021-04-07
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanyear
  given name: Chanita
author list: Agent
  family name: Chiawtada
  given name: Buraporn
author list: Agent
  family name: Butthep
  given name: Punnee
author list: Agent
  family name: Svasti
  given name: Saovaros
author list: Agent
  family name: Fucharoen
  given name: Suthat
author list: Agent
  family name: Masaratana
  given name: Patarabutr
doi: 10.7717/peerj.11367
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Sanyear et al.
attribution name: Sanyear et al.

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)
type: item
type: AcademicArticle
description: Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1–CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16–17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.
format: application/pdf
format: text/html
creator: Yuanyuan Dan
creator: Yuan Niu
creator: Chunlei Wang
creator: Mei Yan
creator: Weibiao Liao
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11398
publisher: PeerJ Inc.
rights: © 2021 Dan et al.
abstract: Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1–CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16–17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.
bibliographic citation: Dan et al. (2021) Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.). PeerJ 9:e11398 https://doi.org/10.7717/peerj.11398
date submitted: 2020-12-15
date accepted: 2021-04-13
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dan
  given name: Yuanyuan
author list: Agent
  family name: Niu
  given name: Yuan
author list: Agent
  family name: Wang
  given name: Chunlei
author list: Agent
  family name: Yan
  given name: Mei
author list: Agent
  family name: Liao
  given name: Weibiao
doi: 10.7717/peerj.11398
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Dan et al.
attribution name: Dan et al.

PhyloPrimer: a taxon-specific oligonucleotide design platform
type: item
type: AcademicArticle
description: Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
format: application/pdf
format: text/html
creator: Gilda Varliero
creator: Jared Wray
creator: Cédric Malandain
creator: Gary Barker
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.11120
publisher: PeerJ Inc.
rights: © 2021 Varliero et al.
abstract: Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
bibliographic citation: Varliero et al. (2021) PhyloPrimer: a taxon-specific oligonucleotide design platform. PeerJ 9:e11120 https://doi.org/10.7717/peerj.11120
date submitted: 2020-11-13
date accepted: 2021-02-25
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Varliero
  given name: Gilda
author list: Agent
  family name: Wray
  given name: Jared
author list: Agent
  family name: Malandain
  given name: Cédric
author list: Agent
  family name: Barker
  given name: Gary
doi: 10.7717/peerj.11120
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: ©2021 Varliero et al.
attribution name: Varliero et al.

Evidence of integumentary scale diversity in the late Jurassic Sauropod Diplodocus sp. from the Mother’s Day Quarry, Montana
type: item
type: AcademicArticle
description: The life appearance of dinosaurs is a hotly debated topic in the world of paleontology, especially when it comes to dinosaur integument. In the case of sauropods, however, the topic is harder to properly discuss due to the limited amount of fossilized skin impressions that have been discovered. Thus far, the fossil record of sauropod integument fossils include titanosaur embryos from Patagonia, possible keratinous diplodocid dorsal spines, track ways with foot impressions, and other isolated skin impressions found in association with sauropod body fossils. Several prominent integument fossils have been found at the Mother’s Day Quarry, located in the Bighorn Basin, Montana. These discoveries may bring new important information about diplodocids, specifically Diplodocus sp. Here we describe newly uncovered fossilized skin that gives evidence of scale diversity in the genus Diplodocus. The scales themselves represent tubercles, and exhibit various shapes including rectangular, ovoid, polygonal, and globular scales. The tubercles are small in size, the biggest of which only reach about 10mm in length. Considering how diverse the scale shapes are in such a small area of skin, it is possible that these distinct scale shapes may represent a transition on the body from one region to another: perhaps from the abdomen to dorsal side, or abdomen to shoulder. Based on analysis of extant integument and scale orientation of crocodilians, it is possible to hypothesize on the location of the integument relative to the body as well as the size and relative maturational status of the individual.
format: application/pdf
format: text/html
creator: Tess Gallagher
creator: Jason Poole
creator: Jason P. Schein
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11202
publisher: PeerJ Inc.
rights: © 2021 Gallagher et al.
abstract: The life appearance of dinosaurs is a hotly debated topic in the world of paleontology, especially when it comes to dinosaur integument. In the case of sauropods, however, the topic is harder to properly discuss due to the limited amount of fossilized skin impressions that have been discovered. Thus far, the fossil record of sauropod integument fossils include titanosaur embryos from Patagonia, possible keratinous diplodocid dorsal spines, track ways with foot impressions, and other isolated skin impressions found in association with sauropod body fossils. Several prominent integument fossils have been found at the Mother’s Day Quarry, located in the Bighorn Basin, Montana. These discoveries may bring new important information about diplodocids, specifically Diplodocus sp. Here we describe newly uncovered fossilized skin that gives evidence of scale diversity in the genus Diplodocus. The scales themselves represent tubercles, and exhibit various shapes including rectangular, ovoid, polygonal, and globular scales. The tubercles are small in size, the biggest of which only reach about 10mm in length. Considering how diverse the scale shapes are in such a small area of skin, it is possible that these distinct scale shapes may represent a transition on the body from one region to another: perhaps from the abdomen to dorsal side, or abdomen to shoulder. Based on analysis of extant integument and scale orientation of crocodilians, it is possible to hypothesize on the location of the integument relative to the body as well as the size and relative maturational status of the individual.
bibliographic citation: Gallagher et al. (2021) Evidence of integumentary scale diversity in the late Jurassic Sauropod Diplodocus sp. from the Mother’s Day Quarry, Montana. PeerJ 9:e11202 https://doi.org/10.7717/peerj.11202
date submitted: 2020-12-16
date accepted: 2021-03-11
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gallagher
  given name: Tess
author list: Agent
  family name: Poole
  given name: Jason
author list: Agent
  family name: Schein
  given name: Jason P.
doi: 10.7717/peerj.11202
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: © 2021 Gallagher et al.
attribution name: Gallagher et al.

https://peerj.com/articles/11284
type: item
type: AcademicArticle
title: DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea
description: In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.
format: application/pdf
format: text/html
creator: Hyun Kyong Kim
creator: Benny K.K. Chan
creator: Sung Joon Song
creator: Jong Seong Khim
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11284
publisher: PeerJ Inc.
rights: © 2021 Kim et al.
abstract: In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.
bibliographic citation: Kim et al. (2021) DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea. PeerJ 9:e11284 https://doi.org/10.7717/peerj.11284
date submitted: 2021-01-26
date accepted: 2021-03-24
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Hyun Kyong
author list: Agent
  family name: Chan
  given name: Benny K.K.
author list: Agent
  family name: Song
  given name: Sung Joon
author list: Agent
  family name: Khim
  given name: Jong Seong
doi: 10.7717/peerj.11284
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: ©2021 Kim et al.
attribution name: Kim et al.

Identification of QTL for barley grain size
type: item
type: AcademicArticle
description: Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
format: application/pdf
format: text/html
creator: Junmei Wang
creator: Xiaojian Wu
creator: Wenhao Yue
creator: Chenchen Zhao
creator: Jianming Yang
creator: Meixue Zhou
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11287
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
bibliographic citation: Wang et al. (2021) Identification of QTL for barley grain size. PeerJ 9:e11287 https://doi.org/10.7717/peerj.11287
date submitted: 2021-01-08
date accepted: 2021-03-25
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Junmei
author list: Agent
  family name: Wu
  given name: Xiaojian
author list: Agent
  family name: Yue
  given name: Wenhao
author list: Agent
  family name: Zhao
  given name: Chenchen
author list: Agent
  family name: Yang
  given name: Jianming
author list: Agent
  family name: Zhou
  given name: Meixue
doi: 10.7717/peerj.11287
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II–III breast cancer patients using CytoSorter® system: a retrospective study
type: item
type: AcademicArticle
description: Purpose Circulating tumor cells (CTCs) are known to be associated with late recurrence and poor prognosis in breast cancer (BC). Different CTC enrichment platforms have different CTC cut-off values for poor prognosis. This study aimed to evaluate whether preoperative CTCs could be a prognostic factor for early recurrence of disease in BC patients with resectable tumors, and to ascertain the CTC cut-off value for early recurrence with CytoSorter® CTC system. Methods Thirty-six stage II and III BC patients who had preoperative (pre-op) CTC detection and underwent a mastectomy or lumpectomy for curative intent between January and May 2018 were enrolled in this retrospective study. CTC detection was performed using CytoSorter® CTC system. Correlations of patients’ demographics, clinicopathological characteristics, adjuvant therapies and CTCs with relapse and survival were evaluated. Results CTCs were detected in 32 out of 36 patients before surgery. Nine patients developed relapses during follow-up, and seven of them were distant recurrence. Univariate analysis showed that CTCs were correlated with two-year recurrence free survival (RFS) and distant RFS (D-RFS) (P = 0.013 and 0.029, respectively). Two-year RFS and D-RFS were 85.2% and 88.9%, respectively, for patients with <4 CTCs, while 44.4% and 55.6%, respectively, for patients with ≧4 CTCs. In multivariate analysis, only CTC was shown to be correlated with two-year RFS (HR: 0.219, 95% CI: [0.058–0.82], P = 0.024) and D-RFS (HR: 0.218, 95% CI [0.048–0.977], P = 0.047). Conclusion BC patients with pre-op CTCs ≥4 per four mL of blood have significantly reduced two-year RFS and D-RFS. A pre-op CTC cut-off of four per four mL of blood was found for CytoSorter® to identify BC patients with a higher risk for early recurrence.
format: application/pdf
format: text/html
creator: Lidan Jin
creator: Wan-Hung Fan
creator: Yi Luan
creator: Meiqiong Wu
creator: Wenhe Zhao
subject: Drugs and Devices
subject: Hematology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.11366
publisher: PeerJ Inc.
rights: © 2021 Jin et al.
abstract: Purpose Circulating tumor cells (CTCs) are known to be associated with late recurrence and poor prognosis in breast cancer (BC). Different CTC enrichment platforms have different CTC cut-off values for poor prognosis. This study aimed to evaluate whether preoperative CTCs could be a prognostic factor for early recurrence of disease in BC patients with resectable tumors, and to ascertain the CTC cut-off value for early recurrence with CytoSorter® CTC system. Methods Thirty-six stage II and III BC patients who had preoperative (pre-op) CTC detection and underwent a mastectomy or lumpectomy for curative intent between January and May 2018 were enrolled in this retrospective study. CTC detection was performed using CytoSorter® CTC system. Correlations of patients’ demographics, clinicopathological characteristics, adjuvant therapies and CTCs with relapse and survival were evaluated. Results CTCs were detected in 32 out of 36 patients before surgery. Nine patients developed relapses during follow-up, and seven of them were distant recurrence. Univariate analysis showed that CTCs were correlated with two-year recurrence free survival (RFS) and distant RFS (D-RFS) (P = 0.013 and 0.029, respectively). Two-year RFS and D-RFS were 85.2% and 88.9%, respectively, for patients with <4 CTCs, while 44.4% and 55.6%, respectively, for patients with ≧4 CTCs. In multivariate analysis, only CTC was shown to be correlated with two-year RFS (HR: 0.219, 95% CI: [0.058–0.82], P = 0.024) and D-RFS (HR: 0.218, 95% CI [0.048–0.977], P = 0.047). Conclusion BC patients with pre-op CTCs ≥4 per four mL of blood have significantly reduced two-year RFS and D-RFS. A pre-op CTC cut-off of four per four mL of blood was found for CytoSorter® to identify BC patients with a higher risk for early recurrence.
bibliographic citation: Jin et al. (2021) Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II–III breast cancer patients using CytoSorter® system: a retrospective study. PeerJ 9:e11366 https://doi.org/10.7717/peerj.11366
date submitted: 2020-12-16
date accepted: 2021-04-07
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Lidan
author list: Agent
  family name: Fan
  given name: Wan-Hung
author list: Agent
  family name: Luan
  given name: Yi
author list: Agent
  family name: Wu
  given name: Meiqiong
author list: Agent
  family name: Zhao
  given name: Wenhe
doi: 10.7717/peerj.11366
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: © 2021 Jin et al.
attribution name: Jin et al.

How the fear of COVID-19 changed the way we look at human faces
type: item
type: AcademicArticle
description: Do we look at persons currently or previously affected by COVID-19 the same way as we do with healthy ones? In this eye-tracking study, we investigated how participants (N = 54) looked at faces of individuals presented as “COVID-19 Free”, “Sick with COVID-19”, or “Recovered from COVID-19”. Results showed that participants tend to look at the eyes of COVID-19-free faces longer than at those of both COVID-19-related faces. Crucially, we also found an increase of visual attention for the mouth of the COVID-19-related faces, possibly due to the threatening characterisation of such area as a transmission vehicle for SARS-CoV-2. Thus, by detailing how people dynamically changed the way of looking at faces as a function of the perceived risk of contagion, we provide the first evidence in the literature about the impact of the pandemic on the most basic level of social interaction.
format: application/pdf
format: text/html
creator: Giovanni Federico
creator: Donatella Ferrante
creator: Francesco Marcatto
creator: Maria Antonella Brandimonte
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11380
publisher: PeerJ Inc.
rights: © 2021 Federico et al.
abstract: Do we look at persons currently or previously affected by COVID-19 the same way as we do with healthy ones? In this eye-tracking study, we investigated how participants (N = 54) looked at faces of individuals presented as “COVID-19 Free”, “Sick with COVID-19”, or “Recovered from COVID-19”. Results showed that participants tend to look at the eyes of COVID-19-free faces longer than at those of both COVID-19-related faces. Crucially, we also found an increase of visual attention for the mouth of the COVID-19-related faces, possibly due to the threatening characterisation of such area as a transmission vehicle for SARS-CoV-2. Thus, by detailing how people dynamically changed the way of looking at faces as a function of the perceived risk of contagion, we provide the first evidence in the literature about the impact of the pandemic on the most basic level of social interaction.
bibliographic citation: Federico et al. (2021) How the fear of COVID-19 changed the way we look at human faces. PeerJ 9:e11380 https://doi.org/10.7717/peerj.11380
date submitted: 2021-02-11
date accepted: 2021-04-09
issued: 2021-04-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Federico
  given name: Giovanni
author list: Agent
  family name: Ferrante
  given name: Donatella
author list: Agent
  family name: Marcatto
  given name: Francesco
author list: Agent
  family name: Brandimonte
  given name: Maria Antonella
doi: 10.7717/peerj.11380
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-29
copyright: © 2021 Federico et al.
attribution name: Federico et al.

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