PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An observational study on risk of secondary cancers in chronic myeloid leukemia patients in the TKI era in the United States
items: Heterogenic transplantation of bone marrow-derived rhesus macaque mesenchymal stem cells ameliorates liver fibrosis induced by carbon tetrachloride in mouse
items: Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas
items: Desiccation resistance: effect of cuticular hydrocarbons and water content in Drosophila melanogaster adults
items: Estimating common dolphin bycatch in the pole-and-line tuna fishery in the Azores
items: Smartphone-based reminder system to promote pelvic floor muscle training for the management of postnatal urinary incontinence: historical control study with propensity score-matched analysis
items: Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits
items: Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México
items: Evolution of the scholarly mega-journal, 2006–2017
items: Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

An observational study on risk of secondary cancers in chronic myeloid leukemia patients in the TKI era in the United States
type: item
type: AcademicArticle
description: Introduction The treatment with tyrosine kinase inhibitors (TKIs) has drastically improved the outcome of chronic myeloid leukemia (CML) patients. This study was conducted to examine the risk of secondary cancers (SCs) in the CML patients who were diagnosed and treated in the TKI era in the United States. Methods The surveillance epidemiology and end results (SEER) database was used to identify CML patients who were diagnosed and received treatment during January 2002–December 2014. Standardized incidence ratios (SIRs) and absolute excess risks (AER) were calculated. Results Overall, 511 SCs (excluding acute leukemia) developed in 9,200 CML patients followed for 38,433 person-years. The risk of developing SCs in the CML patients was 30% higher than the age, sex and race matched standard population (SIR 1.30, 95% CI: 1.2–1.40; p < 0.001). The SIRs for CLL (SIR 3.4, 95% CI: 2–5.5; p < 0.001), thyroid (SIR 2.2, 95% CI: 1.2–3.5; p < 0.001), small intestine (SIR 3.1, 95% CI: 1.1–7; p = 0.004), gingiva (SIR 3.7, 95% CI: 1.2–8.7; p = 0.002), stomach (SIR 2.1, 95% CI: 1.1–3.5; p = 0.005), lung (SIR 1.4, 95% CI: 1.1–1.7; p = 0.006) and prostate (SIR 1.3, 95% CI: 1.02–1.6; p = 0.026) cancer among CML patients were significantly higher than the general population. The risk of SCs was higher irrespective of age and it was highest in the period 2–12 months after the diagnosis of CML. The risk of SCs in women was similar to that of the general population. Conclusion CML patients diagnosed and treated in the TKI era in the United States are at an increased risk of developing a second malignancy. The increased risk of SCs in the early period after CML diagnosis suggests that the risk of SCs may be increased due to the factors other than TKIs treatment.
format: application/pdf
format: text/html
creator: Vivek Kumar
creator: Mohit Garg
creator: Neha Chaudhary
creator: Abhinav Binod Chandra
subject: Epidemiology
subject: Internal Medicine
subject: Oncology
description: doi:10.7717/peerj.4342
publisher: PeerJ Inc.
rights: © 2018 Kumar et al.
abstract: Introduction The treatment with tyrosine kinase inhibitors (TKIs) has drastically improved the outcome of chronic myeloid leukemia (CML) patients. This study was conducted to examine the risk of secondary cancers (SCs) in the CML patients who were diagnosed and treated in the TKI era in the United States. Methods The surveillance epidemiology and end results (SEER) database was used to identify CML patients who were diagnosed and received treatment during January 2002–December 2014. Standardized incidence ratios (SIRs) and absolute excess risks (AER) were calculated. Results Overall, 511 SCs (excluding acute leukemia) developed in 9,200 CML patients followed for 38,433 person-years. The risk of developing SCs in the CML patients was 30% higher than the age, sex and race matched standard population (SIR 1.30, 95% CI: 1.2–1.40; p < 0.001). The SIRs for CLL (SIR 3.4, 95% CI: 2–5.5; p < 0.001), thyroid (SIR 2.2, 95% CI: 1.2–3.5; p < 0.001), small intestine (SIR 3.1, 95% CI: 1.1–7; p = 0.004), gingiva (SIR 3.7, 95% CI: 1.2–8.7; p = 0.002), stomach (SIR 2.1, 95% CI: 1.1–3.5; p = 0.005), lung (SIR 1.4, 95% CI: 1.1–1.7; p = 0.006) and prostate (SIR 1.3, 95% CI: 1.02–1.6; p = 0.026) cancer among CML patients were significantly higher than the general population. The risk of SCs was higher irrespective of age and it was highest in the period 2–12 months after the diagnosis of CML. The risk of SCs in women was similar to that of the general population. Conclusion CML patients diagnosed and treated in the TKI era in the United States are at an increased risk of developing a second malignancy. The increased risk of SCs in the early period after CML diagnosis suggests that the risk of SCs may be increased due to the factors other than TKIs treatment.
bibliographic citation: Kumar et al. (2018) An observational study on risk of secondary cancers in chronic myeloid leukemia patients in the TKI era in the United States. PeerJ 6:e4342 https://doi.org/10.7717/peerj.4342
date submitted: 2017-10-23
date accepted: 2018-01-18
issued: 2018-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumar
  given name: Vivek
author list: Agent
  family name: Garg
  given name: Mohit
author list: Agent
  family name: Chaudhary
  given name: Neha
author list: Agent
  family name: Chandra
  given name: Abhinav Binod
doi: 10.7717/peerj.4342
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-12
copyright: © 2018 Kumar et al.
attribution name: Kumar et al.

Heterogenic transplantation of bone marrow-derived rhesus macaque mesenchymal stem cells ameliorates liver fibrosis induced by carbon tetrachloride in mouse
type: item
type: AcademicArticle
description: Liver fibrosis is a disease that causes high morbidity and has become a major health problem. Liver fibrosis can lead to the end stage of liver diseases (livercirrhosisand hepatocellularcarcinoma). Currently, liver transplantation is the only effective treatment for end-stage liver disease. However, the shortage of organ donors, high cost of medical surgery, immunological rejection and transplantation complications severely hamper liver transplantation therapy. Mesenchymal stem cells (MSCs) have been regarded as promising cells for clinical applications in stem cell therapy in the treatment of liver diseases due to their unique multipotent differentiation capacity, immunoregulation and paracrine effects. Although liver fibrosis improvements by MSC transplantation in preclinical experiments as well as clinical trials have been reported, the in vivo fate of MSCs after transportation and their therapeutic mechanisms remain unclear. In this present study, we isolated MSCs from the bone marrow of rhesus macaques. The cells exhibited typical MSC markers and could differentiate into chondrocytes, osteocytes, and adipocytes, which were not affected by labeling with enhanced green fluorescent protein (EGFP). The harvested MSCs respond to interferon-γ stimulation and have the ability to inhibit lymphocyte proliferation in vitro. EGFP-labeled MSCs (1 × 106 cells) were transplanted into mice with carbon tetrachloride-induced liver fibrosis via tail vein injection. The ability of the heterogenic MSC infusion to ameliorate liver fibrosis in mice was evaluated by a blood plasma chemistry index, pathological examination and liver fibrosis-associated gene expression. Additionally, a small number of MSCs that homed and engrafted in the mouse liver tissues were evaluated by immunofluorescence analysis. Our results showed that the transplantation of heterogenic MSCs derived from monkey bone marrow can be used to treat liver fibrosis in the mouse model and that the paracrine effects of …
format: application/pdf
format: text/html
creator: Xufeng Fu
creator: Bin Jiang
creator: Bingrong Zheng
creator: Yaping Yan
creator: Junfeng Wang
creator: Yanchao Duan
creator: Shanshan Li
creator: Li Yan
creator: Hong Wang
creator: Bingbing Chen
creator: Xiongbo Sang
creator: Weizhi Ji
creator: Ren-He Xu
creator: Wei Si
subject: Cell Biology
subject: Gastroenterology and Hepatology
subject: Translational Medicine
description: doi:10.7717/peerj.4336
publisher: PeerJ Inc.
rights: © 2018 Fu et al.
abstract: Liver fibrosis is a disease that causes high morbidity and has become a major health problem. Liver fibrosis can lead to the end stage of liver diseases (livercirrhosisand hepatocellularcarcinoma). Currently, liver transplantation is the only effective treatment for end-stage liver disease. However, the shortage of organ donors, high cost of medical surgery, immunological rejection and transplantation complications severely hamper liver transplantation therapy. Mesenchymal stem cells (MSCs) have been regarded as promising cells for clinical applications in stem cell therapy in the treatment of liver diseases due to their unique multipotent differentiation capacity, immunoregulation and paracrine effects. Although liver fibrosis improvements by MSC transplantation in preclinical experiments as well as clinical trials have been reported, the in vivo fate of MSCs after transportation and their therapeutic mechanisms remain unclear. In this present study, we isolated MSCs from the bone marrow of rhesus macaques. The cells exhibited typical MSC markers and could differentiate into chondrocytes, osteocytes, and adipocytes, which were not affected by labeling with enhanced green fluorescent protein (EGFP). The harvested MSCs respond to interferon-γ stimulation and have the ability to inhibit lymphocyte proliferation in vitro. EGFP-labeled MSCs (1 × 106 cells) were transplanted into mice with carbon tetrachloride-induced liver fibrosis via tail vein injection. The ability of the heterogenic MSC infusion to ameliorate liver fibrosis in mice was evaluated by a blood plasma chemistry index, pathological examination and liver fibrosis-associated gene expression. Additionally, a small number of MSCs that homed and engrafted in the mouse liver tissues were evaluated by immunofluorescence analysis. Our results showed that the transplantation of heterogenic MSCs derived from monkey bone marrow can be used to treat liver fibrosis in the mouse model and that the paracrine effects of …
bibliographic citation: Fu et al. (2018) Heterogenic transplantation of bone marrow-derived rhesus macaque mesenchymal stem cells ameliorates liver fibrosis induced by carbon tetrachloride in mouse. PeerJ 6:e4336 https://doi.org/10.7717/peerj.4336
date submitted: 2017-11-10
date accepted: 2018-01-17
issued: 2018-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Xufeng
author list: Agent
  family name: Jiang
  given name: Bin
author list: Agent
  family name: Zheng
  given name: Bingrong
author list: Agent
  family name: Yan
  given name: Yaping
author list: Agent
  family name: Wang
  given name: Junfeng
author list: Agent
  family name: Duan
  given name: Yanchao
author list: Agent
  family name: Li
  given name: Shanshan
author list: Agent
  family name: Yan
  given name: Li
author list: Agent
  family name: Wang
  given name: Hong
author list: Agent
  family name: Chen
  given name: Bingbing
author list: Agent
  family name: Sang
  given name: Xiongbo
author list: Agent
  family name: Ji
  given name: Weizhi
author list: Agent
  family name: Xu
  given name: Ren-He
author list: Agent
  family name: Si
  given name: Wei
doi: 10.7717/peerj.4336
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-12
copyright: ©2018 Fu et al.
attribution name: Fu et al.

Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas
type: item
type: AcademicArticle
description: Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group’s traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.
format: application/pdf
format: text/html
creator: Gustavo Sanchez
creator: Davin H.E. Setiamarga
creator: Surangkana Tuanapaya
creator: Kittichai Tongtherm
creator: Inger E. Winkelmann
creator: Hannah Schmidbaur
creator: Tetsuya Umino
creator: Caroline Albertin
creator: Louise Allcock
creator: Catalina Perales-Raya
creator: Ian Gleadall
creator: Jan M. Strugnell
creator: Oleg Simakov
creator: Jaruwat Nabhitabhata
subject: Biodiversity
subject: Ecology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.4331
publisher: PeerJ Inc.
rights: © 2018 Sanchez et al.
abstract: Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group’s traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.
bibliographic citation: Sanchez et al. (2018) Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas. PeerJ 6:e4331 https://doi.org/10.7717/peerj.4331
date submitted: 2017-06-19
date accepted: 2018-01-16
issued: 2018-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanchez
  given name: Gustavo
author list: Agent
  family name: Setiamarga
  given name: Davin H.E.
author list: Agent
  family name: Tuanapaya
  given name: Surangkana
author list: Agent
  family name: Tongtherm
  given name: Kittichai
author list: Agent
  family name: Winkelmann
  given name: Inger E.
author list: Agent
  family name: Schmidbaur
  given name: Hannah
author list: Agent
  family name: Umino
  given name: Tetsuya
author list: Agent
  family name: Albertin
  given name: Caroline
author list: Agent
  family name: Allcock
  given name: Louise
author list: Agent
  family name: Perales-Raya
  given name: Catalina
author list: Agent
  family name: Gleadall
  given name: Ian
author list: Agent
  family name: Strugnell
  given name: Jan M.
author list: Agent
  family name: Simakov
  given name: Oleg
author list: Agent
  family name: Nabhitabhata
  given name: Jaruwat
doi: 10.7717/peerj.4331
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-12
copyright: ©2018 Sanchez et al.
attribution name: Sanchez et al.

Desiccation resistance: effect of cuticular hydrocarbons and water content in Drosophila melanogaster adults
type: item
type: AcademicArticle
description: Background The insect cuticle covers the whole body and all appendages and has bi-directionnal selective permeability: it protects against environmental stress and pathogen infection and also helps to reduce water loss. The adult cuticle is often associated with a superficial layer of fatty acid-derived molecules such as waxes and long chain hydrocarbons that prevent rapid dehydration. The waterproofing properties of cuticular hydrocarbons (CHs) depend on their chain length and desaturation number. Drosophila CH biosynthesis involves an enzymatic pathway including several elongase and desaturase enzymes. Methods The link between desiccation resistance and CH profile remains unclear, so we tested (1) experimentally selected desiccation-resistant lines, (2) transgenic flies with altered desaturase expression and (3) natural and laboratory-induced CH variants. We also explored the possible relationship between desiccation resistance, relative water content and fecundity in females. Results We found that increased desiccation resistance is linked with the increased proportion of desaturated CHs, but not with their total amount. Experimentally-induced desiccation resistance and CH variation both remained stable after many generations without selection. Conversely, flies with a higher water content and a lower proportion of desaturated CHs showed reduced desiccation resistance. This was also the case in flies with defective desaturase expression in the fat body. Discussion We conclude that rapidly acquired desiccation resistance, depending on both CH profile and water content, can remain stable without selection in a humid environment. These three phenotypes, which might be expected to show a simple relationship, turn out to have complex physiological and genetic links.
format: application/pdf
format: text/html
creator: Jean-Francois Ferveur
creator: Jérôme Cortot
creator: Karen Rihani
creator: Matthew Cobb
creator: Claude Everaerts
subject: Ecology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.4318
publisher: PeerJ Inc.
rights: © 2018 Ferveur et al.
abstract: Background The insect cuticle covers the whole body and all appendages and has bi-directionnal selective permeability: it protects against environmental stress and pathogen infection and also helps to reduce water loss. The adult cuticle is often associated with a superficial layer of fatty acid-derived molecules such as waxes and long chain hydrocarbons that prevent rapid dehydration. The waterproofing properties of cuticular hydrocarbons (CHs) depend on their chain length and desaturation number. Drosophila CH biosynthesis involves an enzymatic pathway including several elongase and desaturase enzymes. Methods The link between desiccation resistance and CH profile remains unclear, so we tested (1) experimentally selected desiccation-resistant lines, (2) transgenic flies with altered desaturase expression and (3) natural and laboratory-induced CH variants. We also explored the possible relationship between desiccation resistance, relative water content and fecundity in females. Results We found that increased desiccation resistance is linked with the increased proportion of desaturated CHs, but not with their total amount. Experimentally-induced desiccation resistance and CH variation both remained stable after many generations without selection. Conversely, flies with a higher water content and a lower proportion of desaturated CHs showed reduced desiccation resistance. This was also the case in flies with defective desaturase expression in the fat body. Discussion We conclude that rapidly acquired desiccation resistance, depending on both CH profile and water content, can remain stable without selection in a humid environment. These three phenotypes, which might be expected to show a simple relationship, turn out to have complex physiological and genetic links.
bibliographic citation: Ferveur et al. (2018) Desiccation resistance: effect of cuticular hydrocarbons and water content in Drosophila melanogaster adults. PeerJ 6:e4318 https://doi.org/10.7717/peerj.4318
date submitted: 2017-11-22
date accepted: 2018-01-12
issued: 2018-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferveur
  given name: Jean-Francois
author list: Agent
  family name: Cortot
  given name: Jérôme
author list: Agent
  family name: Rihani
  given name: Karen
author list: Agent
  family name: Cobb
  given name: Matthew
author list: Agent
  family name: Everaerts
  given name: Claude
doi: 10.7717/peerj.4318
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-12
copyright: ©2018 Ferveur et al.
attribution name: Ferveur et al.

Estimating common dolphin bycatch in the pole-and-line tuna fishery in the Azores
type: item
type: AcademicArticle
description: Small-scale artisanal fisheries can have a significant negative impact in cetacean populations. Cetacean bycatch has been documented in the pole-and-line tuna fishery in the Azores with common dolphins being the species more frequently taken. Based on data collected by observers on ∼50% of vessels operating from 1998 to 2012, we investigate the influence of various environmental and fisheries-related factors in common dolphin bycatch and calculate fleet-wide estimates of total bycatch using design-based and model-based methods. Over the 15-year study dolphin bycatch occurred in less than 0.4% of the observed fishing events. Generalized additive modelling results suggest a significant relationship between common dolphin bycatch and duration of fishing events, sea surface temperature and location. Total bycatch calculated from the traditional stratified ratio estimation approach was 196 (95% CI: 186–205), while the negative binomial GAM estimated 262 (95% CI: 249–274) dolphins. Bycatch estimates of common dolphin were similar using statistical approaches suggesting that either of these methods may be used in future bycatch assessments for this fishery. Our work shows that rates of common dolphin bycatch in the pole-and-line tuna fishery in the Azores are low, despite considerable variations between years. Dolphins caught were released alive although the fate of these individuals is unknown. Continued monitoring will provide a better understanding of dolphin bycatch and more accurate estimates essential in the development of potential mitigation measures.
format: application/pdf
format: text/html
creator: Maria João Cruz
creator: Miguel Machete
creator: Gui Menezes
creator: Emer Rogan
creator: Mónica A. Silva
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.4285
publisher: PeerJ Inc.
rights: © 2018 Cruz et al.
abstract: Small-scale artisanal fisheries can have a significant negative impact in cetacean populations. Cetacean bycatch has been documented in the pole-and-line tuna fishery in the Azores with common dolphins being the species more frequently taken. Based on data collected by observers on ∼50% of vessels operating from 1998 to 2012, we investigate the influence of various environmental and fisheries-related factors in common dolphin bycatch and calculate fleet-wide estimates of total bycatch using design-based and model-based methods. Over the 15-year study dolphin bycatch occurred in less than 0.4% of the observed fishing events. Generalized additive modelling results suggest a significant relationship between common dolphin bycatch and duration of fishing events, sea surface temperature and location. Total bycatch calculated from the traditional stratified ratio estimation approach was 196 (95% CI: 186–205), while the negative binomial GAM estimated 262 (95% CI: 249–274) dolphins. Bycatch estimates of common dolphin were similar using statistical approaches suggesting that either of these methods may be used in future bycatch assessments for this fishery. Our work shows that rates of common dolphin bycatch in the pole-and-line tuna fishery in the Azores are low, despite considerable variations between years. Dolphins caught were released alive although the fate of these individuals is unknown. Continued monitoring will provide a better understanding of dolphin bycatch and more accurate estimates essential in the development of potential mitigation measures.
bibliographic citation: Cruz et al. (2018) Estimating common dolphin bycatch in the pole-and-line tuna fishery in the Azores. PeerJ 6:e4285 https://doi.org/10.7717/peerj.4285
date submitted: 2017-08-21
date accepted: 2018-01-01
issued: 2018-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz
  given name: Maria João
author list: Agent
  family name: Machete
  given name: Miguel
author list: Agent
  family name: Menezes
  given name: Gui
author list: Agent
  family name: Rogan
  given name: Emer
author list: Agent
  family name: Silva
  given name: Mónica A.
doi: 10.7717/peerj.4285
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-12
copyright: © 2018 Cruz et al.
attribution name: Cruz et al.

Smartphone-based reminder system to promote pelvic floor muscle training for the management of postnatal urinary incontinence: historical control study with propensity score-matched analysis
type: item
type: AcademicArticle
description: Background The purpose of this study was to evaluate the efficacy of a smartphone-based reminder system in promoting pelvic floor muscle training (PFMT) to help postpartum women manage urinary incontinence (UI). Methods Forty-nine and 212 postpartum women in the intervention and control groups, respectively, received PFMT guidance using a leaflet and verbal instruction as the standard care at an obstetrics clinic in Japan. Women in the intervention group also received PFMT support using the smartphone-based reminder system between January and August 2014. For analysis, they were compared with historical controls between February 2011 and January 2012, who did not receive such support and were chosen by propensity score matching. The outcomes examined were PFMT adherence and UI prevalence. The former consisted of implementation rate (i.e., the percentage of women who reported performing PFMT during the intervention period), training intensity (i.e., the number of pelvic floor muscle contractions (PFMCs) per day), and training frequency (i.e., the number of days PFMT was performed per week); the latter consisted of self-reported UI prevalence at baseline and at the end of the eight-week intervention period. Result Propensity score matching resulted in 58 postpartum women (n = 29 per group). The intervention group exhibited better PFMT adherence than the control group, in terms of PFMT implementation rate (69 vs. 31%, p = 0.008), median training intensity (15 vs. 1 PFMC reps/day, p = 0.006), and training frequency (7 vs. 3 days/week, p < 0.001). UI prevalence was not different between the groups at baseline, but was significantly reduced in the intervention group at eight weeks (0 vs. 24%, p = 0.004). Conclusion Our smartphone-based reminder system appears promising in enhancing PFMT adherence and managing postpartum UI in postpartum women. By enhancing PFMT adherence and improving women’s ability to manage the condition, the reminder system could improve the health-re…
format: application/pdf
format: text/html
creator: Kaori Kinouchi
creator: Kazutomo Ohashi
subject: Gynecology and Obstetrics
subject: Nursing
subject: Urology
subject: Women’s Health
description: doi:10.7717/peerj.4372
publisher: PeerJ Inc.
rights: © 2018 Kinouchi and Ohashi
abstract: Background The purpose of this study was to evaluate the efficacy of a smartphone-based reminder system in promoting pelvic floor muscle training (PFMT) to help postpartum women manage urinary incontinence (UI). Methods Forty-nine and 212 postpartum women in the intervention and control groups, respectively, received PFMT guidance using a leaflet and verbal instruction as the standard care at an obstetrics clinic in Japan. Women in the intervention group also received PFMT support using the smartphone-based reminder system between January and August 2014. For analysis, they were compared with historical controls between February 2011 and January 2012, who did not receive such support and were chosen by propensity score matching. The outcomes examined were PFMT adherence and UI prevalence. The former consisted of implementation rate (i.e., the percentage of women who reported performing PFMT during the intervention period), training intensity (i.e., the number of pelvic floor muscle contractions (PFMCs) per day), and training frequency (i.e., the number of days PFMT was performed per week); the latter consisted of self-reported UI prevalence at baseline and at the end of the eight-week intervention period. Result Propensity score matching resulted in 58 postpartum women (n = 29 per group). The intervention group exhibited better PFMT adherence than the control group, in terms of PFMT implementation rate (69 vs. 31%, p = 0.008), median training intensity (15 vs. 1 PFMC reps/day, p = 0.006), and training frequency (7 vs. 3 days/week, p < 0.001). UI prevalence was not different between the groups at baseline, but was significantly reduced in the intervention group at eight weeks (0 vs. 24%, p = 0.004). Conclusion Our smartphone-based reminder system appears promising in enhancing PFMT adherence and managing postpartum UI in postpartum women. By enhancing PFMT adherence and improving women’s ability to manage the condition, the reminder system could improve the health-re…
bibliographic citation: Kinouchi et al. (2018) Smartphone-based reminder system to promote pelvic floor muscle training for the management of postnatal urinary incontinence: historical control study with propensity score-matched analysis. PeerJ 6:e4372 https://doi.org/10.7717/peerj.4372
date submitted: 2017-12-22
date accepted: 2018-01-25
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kinouchi
  given name: Kaori
author list: Agent
  family name: Ohashi
  given name: Kazutomo
doi: 10.7717/peerj.4372
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Kinouchi and Ohashi
attribution name: Kinouchi and Ohashi

Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits
type: item
type: AcademicArticle
description: There is currently unprecedented interest in quantifying variation in thermal physiology among organisms, especially in order to understand and predict the biological impacts of climate change. A key parameter in this quantification of thermal physiology is the performance or value of a rate, across individuals or species, at a common temperature (temperature normalisation). An increasingly popular model for fitting thermal performance curves to data—the Sharpe-Schoolfield equation—can yield strongly inflated estimates of temperature-normalised rate values. These deviations occur whenever a key thermodynamic assumption of the model is violated, i.e., when the enzyme governing the performance of the rate is not fully functional at the chosen reference temperature. Using data on 1,758 thermal performance curves across a wide range of species, we identify the conditions that exacerbate this inflation. We then demonstrate that these biases can compromise tests to detect metabolic cold adaptation, which requires comparison of fitness or rate performance of different species or genotypes at some fixed low temperature. Finally, we suggest alternative methods for obtaining unbiased estimates of temperature-normalised rate values for meta-analyses of thermal performance across species in climate change impact studies.
format: application/pdf
format: text/html
creator: Dimitrios - Georgios Kontopoulos
creator: Bernardo García-Carreras
creator: Sofía Sal
creator: Thomas P. Smith
creator: Samraat Pawar
subject: Ecology
subject: Mathematical Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.4363
publisher: PeerJ Inc.
rights: © 2018 Kontopoulos et al.
abstract: There is currently unprecedented interest in quantifying variation in thermal physiology among organisms, especially in order to understand and predict the biological impacts of climate change. A key parameter in this quantification of thermal physiology is the performance or value of a rate, across individuals or species, at a common temperature (temperature normalisation). An increasingly popular model for fitting thermal performance curves to data—the Sharpe-Schoolfield equation—can yield strongly inflated estimates of temperature-normalised rate values. These deviations occur whenever a key thermodynamic assumption of the model is violated, i.e., when the enzyme governing the performance of the rate is not fully functional at the chosen reference temperature. Using data on 1,758 thermal performance curves across a wide range of species, we identify the conditions that exacerbate this inflation. We then demonstrate that these biases can compromise tests to detect metabolic cold adaptation, which requires comparison of fitness or rate performance of different species or genotypes at some fixed low temperature. Finally, we suggest alternative methods for obtaining unbiased estimates of temperature-normalised rate values for meta-analyses of thermal performance across species in climate change impact studies.
bibliographic citation: Kontopoulos et al. (2018) Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits. PeerJ 6:e4363 https://doi.org/10.7717/peerj.4363
date submitted: 2017-07-10
date accepted: 2018-01-23
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kontopoulos
  given name: Dimitrios - Georgios
author list: Agent
  family name: García-Carreras
  given name: Bernardo
author list: Agent
  family name: Sal
  given name: Sofía
author list: Agent
  family name: Smith
  given name: Thomas P.
author list: Agent
  family name: Pawar
  given name: Samraat
doi: 10.7717/peerj.4363
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Kontopoulos et al.
attribution name: Kontopoulos et al.

Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México
type: item
type: AcademicArticle
description: Cancer cases result in 13% of all deaths worldwide. Unwanted side effects in patients under conventional treatments have led to the search for beneficial alternative therapies. Microalgae synthesize compounds with known in vitro and in vivo biological activity against different tumor cell lines. Therefore, native microalgae from the State of Nuevo Leon, Mexico may become a potential source of antitumor agents. The aim of the present study was to evaluate the in vitro cytotoxic effect of Nuevo Leon regional Chlorella sorokiniana (Chlorellales: Chlorellaceae) and Scenedesmus sp. (Chlorococcales: Scenedesmaceae). Native microalgae crude organic extracts cytotoxicity against murine L5178Y-R lymphoma cell line and normal lymphocyte proliferation were evaluated using the MTT reduction colorimetric assay. Cell death pathway was analyzed by acridine orange and ethidium bromide staining, DNA degradation in 2% agarose gel electrophoresis and caspases activity. Results indicated significant (p < 0.05) 61.89% ± 3.26% and 74.77% ± 1.84% tumor cytotoxicity by C. sorokiniana and Scenedesmus sp. methanol extracts, respectively, at 500 µg/mL, by the mechanism of apoptosis. This study contributes to Mexican microalgae biodiversity knowledge and their potential as antitumor agent sources.
format: application/pdf
format: text/html
creator: Raul Reyna-Martinez
creator: Ricardo Gomez-Flores
creator: Ulrico López-Chuken
creator: Ramiro Quintanilla-Licea
creator: Diana Caballero-Hernandez
creator: Cristina Rodríguez-Padilla
creator: Julio Cesar Beltrán-Rocha
creator: Patricia Tamez-Guerra
subject: Biotechnology
subject: Ecosystem Science
subject: Oncology
subject: Freshwater Biology
description: doi:10.7717/peerj.4358
publisher: PeerJ Inc.
rights: © 2018 Reyna-Martinez et al.
abstract: Cancer cases result in 13% of all deaths worldwide. Unwanted side effects in patients under conventional treatments have led to the search for beneficial alternative therapies. Microalgae synthesize compounds with known in vitro and in vivo biological activity against different tumor cell lines. Therefore, native microalgae from the State of Nuevo Leon, Mexico may become a potential source of antitumor agents. The aim of the present study was to evaluate the in vitro cytotoxic effect of Nuevo Leon regional Chlorella sorokiniana (Chlorellales: Chlorellaceae) and Scenedesmus sp. (Chlorococcales: Scenedesmaceae). Native microalgae crude organic extracts cytotoxicity against murine L5178Y-R lymphoma cell line and normal lymphocyte proliferation were evaluated using the MTT reduction colorimetric assay. Cell death pathway was analyzed by acridine orange and ethidium bromide staining, DNA degradation in 2% agarose gel electrophoresis and caspases activity. Results indicated significant (p < 0.05) 61.89% ± 3.26% and 74.77% ± 1.84% tumor cytotoxicity by C. sorokiniana and Scenedesmus sp. methanol extracts, respectively, at 500 µg/mL, by the mechanism of apoptosis. This study contributes to Mexican microalgae biodiversity knowledge and their potential as antitumor agent sources.
bibliographic citation: Reyna-Martinez et al. (2018) Antitumor activity of Chlorella sorokiniana and Scenedesmus sp. microalgae native of Nuevo León State, México. PeerJ 6:e4358 https://doi.org/10.7717/peerj.4358
date submitted: 2017-09-27
date accepted: 2018-01-22
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reyna-Martinez
  given name: Raul
author list: Agent
  family name: Gomez-Flores
  given name: Ricardo
author list: Agent
  family name: López-Chuken
  given name: Ulrico
author list: Agent
  family name: Quintanilla-Licea
  given name: Ramiro
author list: Agent
  family name: Caballero-Hernandez
  given name: Diana
author list: Agent
  family name: Rodríguez-Padilla
  given name: Cristina
author list: Agent
  family name: Beltrán-Rocha
  given name: Julio Cesar
author list: Agent
  family name: Tamez-Guerra
  given name: Patricia
doi: 10.7717/peerj.4358
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Reyna-Martinez et al.
attribution name: Reyna-Martinez et al.

Evolution of the scholarly mega-journal, 2006–2017
type: item
type: AcademicArticle
description: Mega-journals are a new kind of scholarly journal made possible by electronic publishing. They are open access (OA) and funded by charges, which authors pay for the publishing services. What distinguishes mega-journals from other OA journals is, in particular, a peer review focusing only on scientific trustworthiness. The journals can easily publish thousands of articles per year and there is no need to filter articles due to restricted slots in the publishing schedule. This study updates some earlier longitudinal studies of the evolution of mega-journals and their publication volumes. After very rapid growth in 2010–2013, the increase in overall article volumes has slowed down. Mega-journals are also increasingly dependent for sustained growth on Chinese authors, who now contribute 25% of all articles in such journals. There has also been an internal shift in market shares. PLOS ONE, which totally dominated mega-journal publishing in the early years, currently publishes around one-third of all articles. Scientific Reports has grown rapidly since 2014 and is now the biggest journal.
format: application/pdf
format: text/html
creator: Bo-Christer Björk
subject: Science Policy
description: doi:10.7717/peerj.4357
publisher: PeerJ Inc.
rights: © 2018 Björk
abstract: Mega-journals are a new kind of scholarly journal made possible by electronic publishing. They are open access (OA) and funded by charges, which authors pay for the publishing services. What distinguishes mega-journals from other OA journals is, in particular, a peer review focusing only on scientific trustworthiness. The journals can easily publish thousands of articles per year and there is no need to filter articles due to restricted slots in the publishing schedule. This study updates some earlier longitudinal studies of the evolution of mega-journals and their publication volumes. After very rapid growth in 2010–2013, the increase in overall article volumes has slowed down. Mega-journals are also increasingly dependent for sustained growth on Chinese authors, who now contribute 25% of all articles in such journals. There has also been an internal shift in market shares. PLOS ONE, which totally dominated mega-journal publishing in the early years, currently publishes around one-third of all articles. Scientific Reports has grown rapidly since 2014 and is now the biggest journal.
bibliographic citation: Björk (2018) Evolution of the scholarly mega-journal, 2006–2017. PeerJ 6:e4357 https://doi.org/10.7717/peerj.4357
date submitted: 2017-10-05
date accepted: 2018-01-22
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Björk
  given name: Bo-Christer
doi: 10.7717/peerj.4357
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Björk
attribution name: Björk

Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method
type: item
type: AcademicArticle
description: Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.
format: application/pdf
format: text/html
creator: Aristóteles Góes-Neto
creator: Marcelo V.C. Diniz
creator: Daniel S. Carvalho
creator: Gilberto C. Bomfim
creator: Angelo A. Duarte
creator: Jerzy A. Brzozowski
creator: Thierry C. Petit Lobão
creator: Suani T.R. Pinho
creator: Charbel N. El-Hani
creator: Roberto F.S. Andrade
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.4349
publisher: PeerJ Inc.
rights: © 2018 Góes-Neto et al.
abstract: Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.
bibliographic citation: Góes-Neto et al. (2018) Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method. PeerJ 6:e4349 https://doi.org/10.7717/peerj.4349
date submitted: 2017-09-19
date accepted: 2018-01-19
issued: 2018-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Góes-Neto
  given name: Aristóteles
author list: Agent
  family name: Diniz
  given name: Marcelo V.C.
author list: Agent
  family name: Carvalho
  given name: Daniel S.
author list: Agent
  family name: Bomfim
  given name: Gilberto C.
author list: Agent
  family name: Duarte
  given name: Angelo A.
author list: Agent
  family name: Brzozowski
  given name: Jerzy A.
author list: Agent
  family name: Petit Lobão
  given name: Thierry C.
author list: Agent
  family name: Pinho
  given name: Suani T.R.
author list: Agent
  family name: El-Hani
  given name: Charbel N.
author list: Agent
  family name: Andrade
  given name: Roberto F.S.
doi: 10.7717/peerj.4349
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-02-09
copyright: ©2018 Góes-Neto et al.
attribution name: Góes-Neto et al.

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