PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial
items: Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions
items: Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests
items: Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq
items: Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils
items: Temporal inversion of the acid-base equilibrium in newborns: an observational study
items: Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways
items: Assessment of walking disorder in community-dwelling Japanese middle-aged and elderly women using an inertial sensor
items: Natural resources to control COVID-19: could lactoferrin amend SARS-CoV-2 infectivity?
items: ZebraShare: a new venue for rapid dissemination of zebrafish mutant data

Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial
type: item
type: AcademicArticle
description: Background Despite a consistent link between obesity and increased circulating levels of fibroblast growth factor-21 (FGF21), the effect of weight-loss interventions on FGF21 is not clear. We aimed to determine the short- and long-term effects of Roux-en-Y gastric bypass (RYGB) on intact plasma FGF21 levels and to test the hypothesis that RYGB, but not diet-induced weight loss, increases fasting and postprandial responses of FGF21. Method Twenty-eight participants with obesity followed a low-calorie diet for 11 weeks. The 28 participants were randomized to undergo RYGB surgery at week 8 (RYGB group, n = 14), or to a control group scheduled for surgery at week 12 (n = 14). Fasting levels of intact, biologically active FGF21 (amino acids 1-181) and its postprandial responses to a mixed meal were assessed at week 7 and 11, and 78 weeks (18 months) after RYGB. Results At week 11 (3 weeks after RYGB), postprandial responses of intact FGF21 were enhanced in participants undergoing surgery at week 8 (change from week 7 to 11: P = 0.02), whereas no change was found in non-operated control participants in similar negative energy balance (change from week 7 to 11: P = 0.81). However, no between-group difference was found (P = 0.27 for the group-week-time interaction). Fasting, as well as postprandial responses in intact FGF21, were unchanged 18 months after RYGB when both the RYGB and control group were collapsed together (change from week 7 to 78 weeks after RYGB: P = 0.17). Conclusion Postprandial intact FGF21 levels were enhanced acutely after RYGB whereas no signs of sustained changes were found 18 months after surgery. When comparing the acute effect of RYGB with controls in similar negative energy balance, we failed to detect any significant differences between groups, probably due to the small sample size and large inter-individual variations, especially in response to surgery.
format: application/pdf
format: text/html
creator: Mette S. Nielsen
creator: Susanna Søberg
creator: Julie B. Schmidt
creator: Anne Chenchar
creator: Anders Sjödin
creator: Matthew P. Gillum
subject: Clinical Trials
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
subject: Metabolic Sciences
description: doi:10.7717/peerj.11174
publisher: PeerJ Inc.
rights: © 2021 Nielsen et al.
abstract: Background Despite a consistent link between obesity and increased circulating levels of fibroblast growth factor-21 (FGF21), the effect of weight-loss interventions on FGF21 is not clear. We aimed to determine the short- and long-term effects of Roux-en-Y gastric bypass (RYGB) on intact plasma FGF21 levels and to test the hypothesis that RYGB, but not diet-induced weight loss, increases fasting and postprandial responses of FGF21. Method Twenty-eight participants with obesity followed a low-calorie diet for 11 weeks. The 28 participants were randomized to undergo RYGB surgery at week 8 (RYGB group, n = 14), or to a control group scheduled for surgery at week 12 (n = 14). Fasting levels of intact, biologically active FGF21 (amino acids 1-181) and its postprandial responses to a mixed meal were assessed at week 7 and 11, and 78 weeks (18 months) after RYGB. Results At week 11 (3 weeks after RYGB), postprandial responses of intact FGF21 were enhanced in participants undergoing surgery at week 8 (change from week 7 to 11: P = 0.02), whereas no change was found in non-operated control participants in similar negative energy balance (change from week 7 to 11: P = 0.81). However, no between-group difference was found (P = 0.27 for the group-week-time interaction). Fasting, as well as postprandial responses in intact FGF21, were unchanged 18 months after RYGB when both the RYGB and control group were collapsed together (change from week 7 to 78 weeks after RYGB: P = 0.17). Conclusion Postprandial intact FGF21 levels were enhanced acutely after RYGB whereas no signs of sustained changes were found 18 months after surgery. When comparing the acute effect of RYGB with controls in similar negative energy balance, we failed to detect any significant differences between groups, probably due to the small sample size and large inter-individual variations, especially in response to surgery.
bibliographic citation: Nielsen et al. (2021) Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial. PeerJ 9:e11174 https://doi.org/10.7717/peerj.11174
date submitted: 2020-10-28
date accepted: 2021-03-08
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nielsen
  given name: Mette S.
author list: Agent
  family name: Søberg
  given name: Susanna
author list: Agent
  family name: Schmidt
  given name: Julie B.
author list: Agent
  family name: Chenchar
  given name: Anne
author list: Agent
  family name: Sjödin
  given name: Anders
author list: Agent
  family name: Gillum
  given name: Matthew P.
doi: 10.7717/peerj.11174
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Nielsen et al.
attribution name: Nielsen et al.

Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions
type: item
type: AcademicArticle
description: Background Hepatitis B virus (HBV) pregenomic RNA (pgRNA) has gained increasing attention owing to its role in replication of covalently closed circular DNA (cccDNA) in HBV. This marker has the potential to be used in clinical programs aimed to manage HBV infections. However, several reports on HBV pgRNA levels in clinical cases have conflicting results. RNA is easily degraded when exposed to heat and other environmental stressors. However, the stability of HBV pgRNA, during blood sample collection before the standard automated quantification, has never been estimated. This study aimed to demonstrate the effect of two different temperature conditions and storage durations on the stability of HBV pgRNA. Method Blood from forty patients with chronic hepatitis B infection, who also showed evidence of active HBV DNA replication, was collected and processed within 2 h of collection. Plasma from each patient was divided and stored at 4 °C and 25 °C (room temperature) for six different storage durations (0, 2, 6, 12, 24, and 48 h) and subsequently transferred to −80 °C for storage. The effect of multiple cycles of freezing and thawing of plasma at −20 °C or −80 °C was evaluated using samples from ten patients. Quantification of pgRNA from the samples was performed simultaneously, using the digital polymerase chain reaction (dPCR) method. The differences in pgRNA levels at baseline and each time point were compared using generalized estimating equation (GEE). A change greater than 0.5 log10 copies/mL of pgRNA is considered clinically significant. Statistical analyses were conducted using Stata 16.0. Results The mean HBV pgRNA level in the initially collected plasma samples was 5.58 log10copies/mL (ranging from 3.08 to 8.04 log10 copies/mL). The mean pgRNA levels in samples stored for different time periods compared with the initial reference sample (time 0) significantly decreased. The levels of pgRNA for 6, 12, 24, and 48 h of storage reduced by −0.05 log10 copies/mL (95% …
format: application/pdf
format: text/html
creator: Pakkapon Rattanachaisit
creator: Sirinporn Suksawatamnuay
creator: Supachaya Sriphoosanaphan
creator: Kessarin Thanapirom
creator: Panarat Thaimai
creator: Nipaporn Siripon
creator: Sukanya Sittisomwong
creator: Yong Poovorawan
creator: Piyawat Komolmit
subject: Biochemistry
subject: Biophysics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.11207
publisher: PeerJ Inc.
rights: © 2021 Rattanachaisit et al.
abstract: Background Hepatitis B virus (HBV) pregenomic RNA (pgRNA) has gained increasing attention owing to its role in replication of covalently closed circular DNA (cccDNA) in HBV. This marker has the potential to be used in clinical programs aimed to manage HBV infections. However, several reports on HBV pgRNA levels in clinical cases have conflicting results. RNA is easily degraded when exposed to heat and other environmental stressors. However, the stability of HBV pgRNA, during blood sample collection before the standard automated quantification, has never been estimated. This study aimed to demonstrate the effect of two different temperature conditions and storage durations on the stability of HBV pgRNA. Method Blood from forty patients with chronic hepatitis B infection, who also showed evidence of active HBV DNA replication, was collected and processed within 2 h of collection. Plasma from each patient was divided and stored at 4 °C and 25 °C (room temperature) for six different storage durations (0, 2, 6, 12, 24, and 48 h) and subsequently transferred to −80 °C for storage. The effect of multiple cycles of freezing and thawing of plasma at −20 °C or −80 °C was evaluated using samples from ten patients. Quantification of pgRNA from the samples was performed simultaneously, using the digital polymerase chain reaction (dPCR) method. The differences in pgRNA levels at baseline and each time point were compared using generalized estimating equation (GEE). A change greater than 0.5 log10 copies/mL of pgRNA is considered clinically significant. Statistical analyses were conducted using Stata 16.0. Results The mean HBV pgRNA level in the initially collected plasma samples was 5.58 log10copies/mL (ranging from 3.08 to 8.04 log10 copies/mL). The mean pgRNA levels in samples stored for different time periods compared with the initial reference sample (time 0) significantly decreased. The levels of pgRNA for 6, 12, 24, and 48 h of storage reduced by −0.05 log10 copies/mL (95% …
bibliographic citation: Rattanachaisit et al. (2021) Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions. PeerJ 9:e11207 https://doi.org/10.7717/peerj.11207
date submitted: 2020-10-15
date accepted: 2021-03-12
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rattanachaisit
  given name: Pakkapon
author list: Agent
  family name: Suksawatamnuay
  given name: Sirinporn
author list: Agent
  family name: Sriphoosanaphan
  given name: Supachaya
author list: Agent
  family name: Thanapirom
  given name: Kessarin
author list: Agent
  family name: Thaimai
  given name: Panarat
author list: Agent
  family name: Siripon
  given name: Nipaporn
author list: Agent
  family name: Sittisomwong
  given name: Sukanya
author list: Agent
  family name: Poovorawan
  given name: Yong
author list: Agent
  family name: Komolmit
  given name: Piyawat
doi: 10.7717/peerj.11207
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: ©2021 Rattanachaisit et al.
attribution name: Rattanachaisit et al.

Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests
type: item
type: AcademicArticle
description: The fish embryo test (FET) is an alternative to the classic freshwater toxicity test used to assess environmental hazards and risks to fish. This test has been standardized and adopted by the Organization for Economic and Cooperation and Development (OECD). As salinity may affect the substances’ toxicity, we describe the development of an alternative euryhaline test species for embryonic ecotoxicological tests: the Brazilian silverside Atherinella brasiliensis (Quoy & Gaimard, 1825). This species is broadly distributed along the coast of South America and is able to inhabit a broad range of environmental and saline conditions. Ours is the first study on the maintenance of a native South American species for natural reproduction and the generation of embryos for tests. The embryos used are transparent and possess fluorescent cells which have only been seen in a few species and which may be used as markers, making it an alternative assessment tool for the lethal and sublethal substances in marine and estuarine environments. We provide a detailed description and analysis of embryonic development under different salinities and temperatures. The embryos and larvae developed in similar ways at different salinities, however as temperatures increased, mortality also increased. We considered the effects of the reference toxicants Zn2+ and SDS using a protocol similar to the FET that was standardized for zebrafish. Brazilian silverside embryos are as sensitive as freshwater, or euryhaline fish, to the surfactant but are more resistant to metals prior to hatching. We were able to show the advantages of the Brazilian silverside as a model for a marine fish embryo test (FETm) with high levels of reproducibility and little contaminated waste.
format: application/pdf
format: text/html
creator: Natália Martins Feitosa
creator: Emiliano Nicolas Calderon
creator: Rhennã Nascimento da Silva
creator: Sônia Lopes Rezende de Melo
creator: Jackson Souza-Menezes
creator: Rodrigo Nunes-da-Fonseca
creator: Márcia Vieira Reynier
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Marine Biology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.11214
publisher: PeerJ Inc.
rights: © 2021 Feitosa et al.
abstract: The fish embryo test (FET) is an alternative to the classic freshwater toxicity test used to assess environmental hazards and risks to fish. This test has been standardized and adopted by the Organization for Economic and Cooperation and Development (OECD). As salinity may affect the substances’ toxicity, we describe the development of an alternative euryhaline test species for embryonic ecotoxicological tests: the Brazilian silverside Atherinella brasiliensis (Quoy & Gaimard, 1825). This species is broadly distributed along the coast of South America and is able to inhabit a broad range of environmental and saline conditions. Ours is the first study on the maintenance of a native South American species for natural reproduction and the generation of embryos for tests. The embryos used are transparent and possess fluorescent cells which have only been seen in a few species and which may be used as markers, making it an alternative assessment tool for the lethal and sublethal substances in marine and estuarine environments. We provide a detailed description and analysis of embryonic development under different salinities and temperatures. The embryos and larvae developed in similar ways at different salinities, however as temperatures increased, mortality also increased. We considered the effects of the reference toxicants Zn2+ and SDS using a protocol similar to the FET that was standardized for zebrafish. Brazilian silverside embryos are as sensitive as freshwater, or euryhaline fish, to the surfactant but are more resistant to metals prior to hatching. We were able to show the advantages of the Brazilian silverside as a model for a marine fish embryo test (FETm) with high levels of reproducibility and little contaminated waste.
bibliographic citation: Feitosa et al. (2021) Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests. PeerJ 9:e11214 https://doi.org/10.7717/peerj.11214
date submitted: 2020-07-29
date accepted: 2021-03-15
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feitosa
  given name: Natália Martins
author list: Agent
  family name: Calderon
  given name: Emiliano Nicolas
author list: Agent
  family name: da Silva
  given name: Rhennã Nascimento
author list: Agent
  family name: de Melo
  given name: Sônia Lopes Rezende
author list: Agent
  family name: Souza-Menezes
  given name: Jackson
author list: Agent
  family name: Nunes-da-Fonseca
  given name: Rodrigo
author list: Agent
  family name: Reynier
  given name: Márcia Vieira
doi: 10.7717/peerj.11214
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Feitosa et al.
attribution name: Feitosa et al.

Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq
type: item
type: AcademicArticle
description: Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly…
format: application/pdf
format: text/html
creator: Claudia-Anahí Pérez-Torres
creator: Enrique Ibarra-Laclette
creator: Eric-Edmundo Hernández-Domínguez
creator: Benjamín Rodríguez-Haas
creator: Alan-Josué Pérez-Lira
creator: Emanuel Villafán
creator: Alexandro Alonso-Sánchez
creator: Clemente de Jesús García-Ávila
creator: José-Abrahán Ramírez-Pool
creator: Diana Sánchez-Rangel
subject: Agricultural Science
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.11215
publisher: PeerJ Inc.
rights: © 2021 Pérez-Torres et al.
abstract: Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly…
bibliographic citation: Pérez-Torres et al. (2021) Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PeerJ 9:e11215 https://doi.org/10.7717/peerj.11215
date submitted: 2020-10-05
date accepted: 2021-03-15
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez-Torres
  given name: Claudia-Anahí
author list: Agent
  family name: Ibarra-Laclette
  given name: Enrique
author list: Agent
  family name: Hernández-Domínguez
  given name: Eric-Edmundo
author list: Agent
  family name: Rodríguez-Haas
  given name: Benjamín
author list: Agent
  family name: Pérez-Lira
  given name: Alan-Josué
author list: Agent
  family name: Villafán
  given name: Emanuel
author list: Agent
  family name: Alonso-Sánchez
  given name: Alexandro
author list: Agent
  family name: García-Ávila
  given name: Clemente de Jesús
author list: Agent
  family name: Ramírez-Pool
  given name: José-Abrahán
author list: Agent
  family name: Sánchez-Rangel
  given name: Diana
doi: 10.7717/peerj.11215
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Pérez-Torres et al.
attribution name: Pérez-Torres et al.

Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils
type: item
type: AcademicArticle
description: Dental material attributed to Palaeoloxodon huaihoensis from the Middle to Late Pleistocene were recovered over decades from the Penghu Channel during commercial fisheries activities. The National Museum of Nature Science (NMNS) has a collection of such dental material, which differs in size and morphology and likely represents ontogenetic variation and growth trajectory of various age groups of P. huaihoensis. However, little is known regarding age determination. By using length of dental material, enamel thickness (ET), and plate counts, we established the method to distinguish the age of the species, which is directly derived from the extant African forest elephant Loxodonta africana. When measuring signs of allometric growth, we found that in both the upper and lower jaws, tooth width was correlated negatively with lamellar frequency but positively with ET. In the same age group, the number of lamellae was higher in P. huaihoensis than in L. africana. The reconstructed age distribution indicated no difference in the upper or lower jaw. Notably, within our sample, P. huaihoensis is skewed towards adult and older individuals with median age between 33–34.5 years and differed significantly from that of Mammuthus primigenius in the European Kraków Spadzista site. This age distribution pattern is speculated to be related to the harsh environmental conditions and intense intraspecific competition among P. huaihoensis during the last ice age.
format: application/pdf
format: text/html
creator: Jia-Cih Kang
creator: Chien-Hsiang Lin
creator: Chun-Hsiang Chang
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11236
publisher: PeerJ Inc.
rights: © 2021 Kang et al.
abstract: Dental material attributed to Palaeoloxodon huaihoensis from the Middle to Late Pleistocene were recovered over decades from the Penghu Channel during commercial fisheries activities. The National Museum of Nature Science (NMNS) has a collection of such dental material, which differs in size and morphology and likely represents ontogenetic variation and growth trajectory of various age groups of P. huaihoensis. However, little is known regarding age determination. By using length of dental material, enamel thickness (ET), and plate counts, we established the method to distinguish the age of the species, which is directly derived from the extant African forest elephant Loxodonta africana. When measuring signs of allometric growth, we found that in both the upper and lower jaws, tooth width was correlated negatively with lamellar frequency but positively with ET. In the same age group, the number of lamellae was higher in P. huaihoensis than in L. africana. The reconstructed age distribution indicated no difference in the upper or lower jaw. Notably, within our sample, P. huaihoensis is skewed towards adult and older individuals with median age between 33–34.5 years and differed significantly from that of Mammuthus primigenius in the European Kraków Spadzista site. This age distribution pattern is speculated to be related to the harsh environmental conditions and intense intraspecific competition among P. huaihoensis during the last ice age.
bibliographic citation: Kang et al. (2021) Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils. PeerJ 9:e11236 https://doi.org/10.7717/peerj.11236
date submitted: 2021-01-07
date accepted: 2021-03-17
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Jia-Cih
author list: Agent
  family name: Lin
  given name: Chien-Hsiang
author list: Agent
  family name: Chang
  given name: Chun-Hsiang
doi: 10.7717/peerj.11236
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: ©2021 Kang et al.
attribution name: Kang et al.

Temporal inversion of the acid-base equilibrium in newborns: an observational study
type: item
type: AcademicArticle
description: Background A considerable fraction of newborn infants experience hypoxia-ischaemia and metabolic acidosis at birth. However, little is known regarding the biological response of newborn infants to the pH drift from the physiological equilibrium. The aim of this study was to investigate the relationship between the pH drift at birth and postnatal acid-base regulation in newborn infants. Methods Clinical information of 200 spontaneously breathing newborn infants hospitalised at a neonatal intensive care centre were reviewed. Clinical variables associated with venous blood pH on days 5–7 were assessed. Results The higher blood pH on days 5–7 were explained by lower cord blood pH (−0.131, −0.210 to −0.052; regression coefficient, 95% confidence interval), greater gestational age (0.004, 0.002 to 0.005) and lower partial pressure of carbon dioxide on days 5–7 (−0.005, −0.006 to −0.004) (adjusted for sex, postnatal age and lactate on days 5–7). Conclusion In relatively stable newborn infants, blood pH drift from the physiological equilibrium at birth might trigger a system, which reverts and over-corrects blood pH within the first week of life. Given that the infants within the study cohort was spontaneously breathing, the observed phenomenon might be a common reaction of newborn infants to pH changes at birth.
format: application/pdf
format: text/html
creator: Yuko Mizutani
creator: Masahiro Kinoshita
creator: Yung-Chieh Lin
creator: Satoko Fukaya
creator: Shin Kato
creator: Tadashi Hisano
creator: Hideki Hida
creator: Sachiko Iwata
creator: Shinji Saitoh
creator: Osuke Iwata
subject: Biochemistry
subject: Anatomy and Physiology
subject: Hematology
subject: Pediatrics
description: doi:10.7717/peerj.11240
publisher: PeerJ Inc.
rights: © 2021 Mizutani et al.
abstract: Background A considerable fraction of newborn infants experience hypoxia-ischaemia and metabolic acidosis at birth. However, little is known regarding the biological response of newborn infants to the pH drift from the physiological equilibrium. The aim of this study was to investigate the relationship between the pH drift at birth and postnatal acid-base regulation in newborn infants. Methods Clinical information of 200 spontaneously breathing newborn infants hospitalised at a neonatal intensive care centre were reviewed. Clinical variables associated with venous blood pH on days 5–7 were assessed. Results The higher blood pH on days 5–7 were explained by lower cord blood pH (−0.131, −0.210 to −0.052; regression coefficient, 95% confidence interval), greater gestational age (0.004, 0.002 to 0.005) and lower partial pressure of carbon dioxide on days 5–7 (−0.005, −0.006 to −0.004) (adjusted for sex, postnatal age and lactate on days 5–7). Conclusion In relatively stable newborn infants, blood pH drift from the physiological equilibrium at birth might trigger a system, which reverts and over-corrects blood pH within the first week of life. Given that the infants within the study cohort was spontaneously breathing, the observed phenomenon might be a common reaction of newborn infants to pH changes at birth.
bibliographic citation: Mizutani et al. (2021) Temporal inversion of the acid-base equilibrium in newborns: an observational study. PeerJ 9:e11240 https://doi.org/10.7717/peerj.11240
date submitted: 2020-11-20
date accepted: 2021-03-17
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mizutani
  given name: Yuko
author list: Agent
  family name: Kinoshita
  given name: Masahiro
author list: Agent
  family name: Lin
  given name: Yung-Chieh
author list: Agent
  family name: Fukaya
  given name: Satoko
author list: Agent
  family name: Kato
  given name: Shin
author list: Agent
  family name: Hisano
  given name: Tadashi
author list: Agent
  family name: Hida
  given name: Hideki
author list: Agent
  family name: Iwata
  given name: Sachiko
author list: Agent
  family name: Saitoh
  given name: Shinji
author list: Agent
  family name: Iwata
  given name: Osuke
doi: 10.7717/peerj.11240
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: ©2021 Mizutani et al.
attribution name: Mizutani et al.

Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways
type: item
type: AcademicArticle
description: Background Laryngeal squamous cell carcinoma (LSCC) is the second most aggressive head and neck squamous cell carcinoma. Although much work has been done to optimize its treatment, patients with LSCC still have poor prognosis. Therefore, figuring out differentially expressed genes (DEGs) contained in the progression of LSCC and employing them as potential therapeutic targets or biomarkers for LSCC is extremely meaningful. Methods Overlapping DEGs were screened from two standalone Gene Expression Omnibus datasets, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. By applying STRING and Cytoscape, a protein–protein network was built, and module analysis was carried out. The hub genes were selected by maximal clique centrality with the CytoHubba plugin of Cytoscape. UALCAN and GEPIA data were examined to validate the gene expression findings. Moreover, the connection of the hub genes with LSCC patient overall survival was studied employing The Cancer Genome Atlas. Then, western blot, qRT-PCR, CCK-8, wound healing and transwell assays were bring to use for further verify the key genes. Results A total of 235 DEGs were recorded, including 83 upregulated and 152 downregulated genes. A total of nine hub genes that displayed a high degree of connectivity were selected. UALCAN and GEPIA databases verified that these genes were highly expressed in LSCC tissues. High expression of the SPP1, SERPINE1 and Matrix metalloproteinases 1 (MMP1) genes was connected to worse prognosis in patients with LSCC, according to the GEPIA online tool. Western blot and qRT-PCR testify SPP1, SERPINE1 and MMP1 were upregulated in LSCC cells. Inhibition of SPP1, SERPINE1 and MMP1 suppressed cell proliferation, invasion and migration. Conclusion The work here identified effective and reliable diagnostic and prognostic molecular biomarkers by unified bioinformatics analysis and experimental verification, indicating novel and necessary therapeuti…
format: application/pdf
format: text/html
creator: Jinhua Ma
creator: Xiaodong Hu
creator: Baoqiang Dai
creator: Qiang Wang
creator: Hongqin Wang
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Otorhinolaryngology
subject: Medical Genetics
description: doi:10.7717/peerj.11259
publisher: PeerJ Inc.
rights: © 2021 Ma et al.
abstract: Background Laryngeal squamous cell carcinoma (LSCC) is the second most aggressive head and neck squamous cell carcinoma. Although much work has been done to optimize its treatment, patients with LSCC still have poor prognosis. Therefore, figuring out differentially expressed genes (DEGs) contained in the progression of LSCC and employing them as potential therapeutic targets or biomarkers for LSCC is extremely meaningful. Methods Overlapping DEGs were screened from two standalone Gene Expression Omnibus datasets, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. By applying STRING and Cytoscape, a protein–protein network was built, and module analysis was carried out. The hub genes were selected by maximal clique centrality with the CytoHubba plugin of Cytoscape. UALCAN and GEPIA data were examined to validate the gene expression findings. Moreover, the connection of the hub genes with LSCC patient overall survival was studied employing The Cancer Genome Atlas. Then, western blot, qRT-PCR, CCK-8, wound healing and transwell assays were bring to use for further verify the key genes. Results A total of 235 DEGs were recorded, including 83 upregulated and 152 downregulated genes. A total of nine hub genes that displayed a high degree of connectivity were selected. UALCAN and GEPIA databases verified that these genes were highly expressed in LSCC tissues. High expression of the SPP1, SERPINE1 and Matrix metalloproteinases 1 (MMP1) genes was connected to worse prognosis in patients with LSCC, according to the GEPIA online tool. Western blot and qRT-PCR testify SPP1, SERPINE1 and MMP1 were upregulated in LSCC cells. Inhibition of SPP1, SERPINE1 and MMP1 suppressed cell proliferation, invasion and migration. Conclusion The work here identified effective and reliable diagnostic and prognostic molecular biomarkers by unified bioinformatics analysis and experimental verification, indicating novel and necessary therapeuti…
bibliographic citation: Ma et al. (2021) Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways. PeerJ 9:e11259 https://doi.org/10.7717/peerj.11259
date submitted: 2020-11-26
date accepted: 2021-03-22
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jinhua
author list: Agent
  family name: Hu
  given name: Xiaodong
author list: Agent
  family name: Dai
  given name: Baoqiang
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Wang
  given name: Hongqin
doi: 10.7717/peerj.11259
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Ma et al.
attribution name: Ma et al.

Assessment of walking disorder in community-dwelling Japanese middle-aged and elderly women using an inertial sensor
type: item
type: AcademicArticle
description: Background Decreased walking speed has been revealed to be related to many negative events. Several researchers support the importance of triceps surae function as a cause of decreased walking speed. The purpose of this study was to investigate the relationship between walking speed and plantar flexor power during the terminal stance of gait in community-dwelling middle-aged and elderly women using an inertial sensor. Methods One hundred thirty-six healthy female middle-aged to elderly community-dwelling women were included in this study. We measured two-step score, grip strength, walking speed and accelerometer data from which we estimated ankle power (estimated ankle power) during walking using an inertial sensor. All participants were classified into the four different age strata, fifties (50–59), sixties (60–69), seventies (70–79) and eighties (80–89). The differences in each parameter between the four age groups were compared using repeated analysis of variance and post-hoc Bonferroni corrections for multiple comparisons to establish significance. Multiple regression analysis was carried out using a stepwise method to determine the correlations with comfortable walking speed. Comfortable walking speed was considered a dependent variable. Results The normalized estimated ankle power of the eighties group was significantly decreased in comparison with seventies age groups and fifties age groups (P < 0.05), but there were no significant differences in normalized estimated ankle power between the sixties and eighties age-groups. The results of stepwise multiple regression analysis revealed that the normalized estimated ankle power, two-step value and body weight were highly-significant partial regression coefficients (adjusted R2 = 0.57).
format: application/pdf
format: text/html
creator: Toshinori Miyashita
creator: Shintarou Kudo
creator: Yoshihiro Maekawa
subject: Drugs and Devices
subject: Geriatrics
subject: Kinesiology
subject: Orthopedics
subject: Women’s Health
description: doi:10.7717/peerj.11269
publisher: PeerJ Inc.
rights: © 2021 Miyashita et al.
abstract: Background Decreased walking speed has been revealed to be related to many negative events. Several researchers support the importance of triceps surae function as a cause of decreased walking speed. The purpose of this study was to investigate the relationship between walking speed and plantar flexor power during the terminal stance of gait in community-dwelling middle-aged and elderly women using an inertial sensor. Methods One hundred thirty-six healthy female middle-aged to elderly community-dwelling women were included in this study. We measured two-step score, grip strength, walking speed and accelerometer data from which we estimated ankle power (estimated ankle power) during walking using an inertial sensor. All participants were classified into the four different age strata, fifties (50–59), sixties (60–69), seventies (70–79) and eighties (80–89). The differences in each parameter between the four age groups were compared using repeated analysis of variance and post-hoc Bonferroni corrections for multiple comparisons to establish significance. Multiple regression analysis was carried out using a stepwise method to determine the correlations with comfortable walking speed. Comfortable walking speed was considered a dependent variable. Results The normalized estimated ankle power of the eighties group was significantly decreased in comparison with seventies age groups and fifties age groups (P < 0.05), but there were no significant differences in normalized estimated ankle power between the sixties and eighties age-groups. The results of stepwise multiple regression analysis revealed that the normalized estimated ankle power, two-step value and body weight were highly-significant partial regression coefficients (adjusted R2 = 0.57).
bibliographic citation: Miyashita et al. (2021) Assessment of walking disorder in community-dwelling Japanese middle-aged and elderly women using an inertial sensor. PeerJ 9:e11269 https://doi.org/10.7717/peerj.11269
date submitted: 2020-07-22
date accepted: 2021-03-23
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miyashita
  given name: Toshinori
author list: Agent
  family name: Kudo
  given name: Shintarou
author list: Agent
  family name: Maekawa
  given name: Yoshihiro
doi: 10.7717/peerj.11269
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Miyashita et al.
attribution name: Miyashita et al.

Natural resources to control COVID-19: could lactoferrin amend SARS-CoV-2 infectivity?
type: item
type: AcademicArticle
description: The world population is still facing the second wave of the COVID-19 pandemic. Such a challenge requires complicated tools to control, namely vaccines, effective cures, and complementary agents. Here we present one candidate for the role of an effective cure and/or complementary agent: lactoferrin. It is the cross-talking mediator between many organs/cellular systems in the body. It serves as a physiological, immunological, and anti-microbial barrier, and acts as a regulator molecule. Furthermore, lactoferrin has receptors on most tissues cells, and is a rich source for bioactive peptides, particularly in the digestive system. In the past months, in vitro and in vivo evidence has accumulated regarding lactoferrin’s ability to control SARS-CoV-2 infectivity in different indicated scenarios. Also, lactoferrin or whey milk (of human or other mammal’s origin) is a cheap, easily available, and safe agent, the use of which can produce promising results. Pharmaceutical and/or food supplementary formulas of lactoferrin could be particularly effective in controlling the gastrointestinal COVID-19-associated symptoms and could limit the fecal-oral viral infection transmission, through mechanisms that mimic that of norovirus infection control by lactoferrin via induction of intestinal innate immunity. This natural avenue may be effective not only in symptomatic patients, but could also be more helpful in asymptomatic patients as a main or adjuvant treatment.
format: application/pdf
format: text/html
creator: Ehab H. Mattar
creator: Fatma Elrashdy
creator: Hussein A. Almehdar
creator: Vladimir N. Uversky
creator: Elrashdy M. Redwan
subject: Biochemistry
subject: Molecular Biology
subject: Virology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.11303
publisher: PeerJ Inc.
rights: © 2021 Mattar et al.
abstract: The world population is still facing the second wave of the COVID-19 pandemic. Such a challenge requires complicated tools to control, namely vaccines, effective cures, and complementary agents. Here we present one candidate for the role of an effective cure and/or complementary agent: lactoferrin. It is the cross-talking mediator between many organs/cellular systems in the body. It serves as a physiological, immunological, and anti-microbial barrier, and acts as a regulator molecule. Furthermore, lactoferrin has receptors on most tissues cells, and is a rich source for bioactive peptides, particularly in the digestive system. In the past months, in vitro and in vivo evidence has accumulated regarding lactoferrin’s ability to control SARS-CoV-2 infectivity in different indicated scenarios. Also, lactoferrin or whey milk (of human or other mammal’s origin) is a cheap, easily available, and safe agent, the use of which can produce promising results. Pharmaceutical and/or food supplementary formulas of lactoferrin could be particularly effective in controlling the gastrointestinal COVID-19-associated symptoms and could limit the fecal-oral viral infection transmission, through mechanisms that mimic that of norovirus infection control by lactoferrin via induction of intestinal innate immunity. This natural avenue may be effective not only in symptomatic patients, but could also be more helpful in asymptomatic patients as a main or adjuvant treatment.
bibliographic citation: Mattar et al. (2021) Natural resources to control COVID-19: could lactoferrin amend SARS-CoV-2 infectivity?. PeerJ 9:e11303 https://doi.org/10.7717/peerj.11303
date submitted: 2021-01-24
date accepted: 2021-03-29
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mattar
  given name: Ehab H.
author list: Agent
  family name: Elrashdy
  given name: Fatma
author list: Agent
  family name: Almehdar
  given name: Hussein A.
author list: Agent
  family name: Uversky
  given name: Vladimir N.
author list: Agent
  family name: Redwan
  given name: Elrashdy M.
doi: 10.7717/peerj.11303
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Mattar et al.
attribution name: Mattar et al.

ZebraShare: a new venue for rapid dissemination of zebrafish mutant data
type: item
type: AcademicArticle
description: Background In the past decade, the zebrafish community has widely embraced targeted mutagenesis technologies, resulting in an abundance of mutant lines. While many lines have proven to be useful for investigating gene function, many have also shown no apparent phenotype, or phenotypes not of interest to the originating lab. In order for labs to document and share information about these lines, we have created ZebraShare as a new resource offered within ZFIN. Methods ZebraShare involves a form-based submission process generated by ZFIN. The ZebraShare interface (https://zfin.org/action/zebrashare) can be accessed on ZFIN under “Submit Data”. Users download the Submission Workbook and complete the required fields, then submit the completed workbook with associated images and captions, generating a new ZFIN publication record. ZFIN curators add the submitted phenotype and mutant information to the ZFIN database, provide mapping information about mutations, and cross reference this information across the appropriate ZFIN databases. We present here examples of ZebraShare submissions, including phf21aa, kdm1a, ctnnd1, snu13a, and snu13b mutant lines. Results Users can find ZebraShare submissions by searching ZFIN for specific alleles or line designations, just as for alleles submitted through the normal process. We present several potential examples of submission types to ZebraShare including a phenotypic mutants, mildly phenotypic, and early lethal mutants. Mutants for kdm1a show no apparent skeletal phenotype, and phf21aa mutants show only a mild skeletal phenotype, yet these genes have specific human disease relevance and therefore may be useful for further studies. The p120-catenin encoding gene, ctnnd1, was knocked out to investigate a potential role in brain development or function. The homozygous ctnnd1 mutant disintegrates during early somitogenesis and the heterozygote has localized defects, revealing vital roles in early development. Two snu13 genes were knocked…
format: application/pdf
format: text/html
creator: April DeLaurier
creator: Douglas G. Howe
creator: Leyla Ruzicka
creator: Adam N. Carte
creator: Lacie Mishoe Hernandez
creator: Kali J Wiggins
creator: Mika M. Gallati
creator: Kayce Vanpelt
creator: Frances Loyo Rosado
creator: Katlin G. Pugh
creator: Chasey J. Shabdue
creator: Khadijah Jihad
creator: Summer B. Thyme
creator: Jared C. Talbot
subject: Bioinformatics
subject: Developmental Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.11007
publisher: PeerJ Inc.
rights: © 2021 DeLaurier et al.
abstract: Background In the past decade, the zebrafish community has widely embraced targeted mutagenesis technologies, resulting in an abundance of mutant lines. While many lines have proven to be useful for investigating gene function, many have also shown no apparent phenotype, or phenotypes not of interest to the originating lab. In order for labs to document and share information about these lines, we have created ZebraShare as a new resource offered within ZFIN. Methods ZebraShare involves a form-based submission process generated by ZFIN. The ZebraShare interface (https://zfin.org/action/zebrashare) can be accessed on ZFIN under “Submit Data”. Users download the Submission Workbook and complete the required fields, then submit the completed workbook with associated images and captions, generating a new ZFIN publication record. ZFIN curators add the submitted phenotype and mutant information to the ZFIN database, provide mapping information about mutations, and cross reference this information across the appropriate ZFIN databases. We present here examples of ZebraShare submissions, including phf21aa, kdm1a, ctnnd1, snu13a, and snu13b mutant lines. Results Users can find ZebraShare submissions by searching ZFIN for specific alleles or line designations, just as for alleles submitted through the normal process. We present several potential examples of submission types to ZebraShare including a phenotypic mutants, mildly phenotypic, and early lethal mutants. Mutants for kdm1a show no apparent skeletal phenotype, and phf21aa mutants show only a mild skeletal phenotype, yet these genes have specific human disease relevance and therefore may be useful for further studies. The p120-catenin encoding gene, ctnnd1, was knocked out to investigate a potential role in brain development or function. The homozygous ctnnd1 mutant disintegrates during early somitogenesis and the heterozygote has localized defects, revealing vital roles in early development. Two snu13 genes were knocked…
bibliographic citation: DeLaurier et al. (2021) ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. PeerJ 9:e11007 https://doi.org/10.7717/peerj.11007
date submitted: 2020-09-03
date accepted: 2021-02-02
issued: 2021-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeLaurier
  given name: April
author list: Agent
  family name: Howe
  given name: Douglas G.
author list: Agent
  family name: Ruzicka
  given name: Leyla
author list: Agent
  family name: Carte
  given name: Adam N.
author list: Agent
  family name: Mishoe Hernandez
  given name: Lacie
author list: Agent
  family name: Wiggins
  given name: Kali J
author list: Agent
  family name: Gallati
  given name: Mika M.
author list: Agent
  family name: Vanpelt
  given name: Kayce
author list: Agent
  family name: Loyo Rosado
  given name: Frances
author list: Agent
  family name: Pugh
  given name: Katlin G.
author list: Agent
  family name: Shabdue
  given name: Chasey J.
author list: Agent
  family name: Jihad
  given name: Khadijah
author list: Agent
  family name: Thyme
  given name: Summer B.
author list: Agent
  family name: Talbot
  given name: Jared C.
doi: 10.7717/peerj.11007
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-13
copyright: ©2021 DeLaurier et al.
attribution name: DeLaurier et al.

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