PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Patient understanding of radiation risk from medical computed tomography—A comparison of Hispanic vs. non-Hispanic emergency department populations
items: Analgesic effects of lappaconitine in leukemia bone pain in a mouse model
items: Seasonal trends in the condition of nesting females of a solitary bee: wing wear, lipid content, and oocyte size
items: Associations between lower extremity muscle mass and metabolic parameters related to obesity in Japanese obese patients with type 2 diabetes
items: Measures of skin conductance and heart rate in alcoholic men and women during memory performance
items: Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti
items: GFVO: the Genomic Feature and Variation Ontology
items: Continued Dispensing: what medications do patients believe should be available?
items: Synthetic neuronal datasets for benchmarking directed functional connectivity metrics
items: Replicability of sight word training and phonics training in poor readers: a randomised controlled trial

Patient understanding of radiation risk from medical computed tomography—A comparison of Hispanic vs. non-Hispanic emergency department populations
type: item
type: AcademicArticle
description: Background. Cultural differences and language barriers may adversely impact patients with respect to understanding the risks/benefits of medical testing. Objective. We hypothesized that there would be no difference in Hispanic vs. non-Hispanic patients’ knowledge of radiation risk that results from CT of the abdomen/pelvis (CTAP). Methods. We enrolled a convenience sample of adults at an inner-city emergency department (ED). Patients provided written answers to rate agreement on a 10-point scale for two correct statements comparing radiation exposure equality between: CTAP and 5 years of background radiation (question 1); CTAP and 200 chest x-rays (question 3). Patients also rated their agreement that multiple CT scans increase the lifetime cancer risk (question 2). Scores of >8 were considered good knowledge. Multivariate logistic regression analyses were performed to estimate the independent effect of the Hispanic variable. Results. 600 patients in the study group; 63% Hispanic, mean age 39.2 ± 13.9 years. Hispanics and non-Hispanics whites were similar with respect to good knowledge-level answers to question 1 (17.3 vs. 15.1%; OR = 1.2; 95% CI [0.74–2.0]), question 2 (31.2 vs. 39.3%; OR = 0.76; 95% CI [0.54–1.1]), and question 3 (15.2 vs. 16.5%; OR = 1.1; 95% CI [0.66–1.8]). Compared to patients who earned <20,000, patients with income >40,000 were more likely to answer question 2 with good knowledge (OR = 1.96; 95% CI [1.2–3.1]). Conclusion. The study group’s overall knowledge of radiation risk was poor, but we did not find significant differences between Hispanic vs. non-Hispanic patients.
format: application/pdf
format: text/html
creator: Afton McNierney-Moore
creator: Cynthia Smith
creator: Jose Guardiola
creator: K. Tom Xu
creator: Peter B. Richman
subject: Emergency and Critical Care
subject: Radiology and Medical Imaging
subject: Statistics
description: doi:10.7717/peerj.937
publisher: PeerJ Inc.
rights: © 2015 McNierney-Moore et al.
abstract: Background. Cultural differences and language barriers may adversely impact patients with respect to understanding the risks/benefits of medical testing. Objective. We hypothesized that there would be no difference in Hispanic vs. non-Hispanic patients’ knowledge of radiation risk that results from CT of the abdomen/pelvis (CTAP). Methods. We enrolled a convenience sample of adults at an inner-city emergency department (ED). Patients provided written answers to rate agreement on a 10-point scale for two correct statements comparing radiation exposure equality between: CTAP and 5 years of background radiation (question 1); CTAP and 200 chest x-rays (question 3). Patients also rated their agreement that multiple CT scans increase the lifetime cancer risk (question 2). Scores of >8 were considered good knowledge. Multivariate logistic regression analyses were performed to estimate the independent effect of the Hispanic variable. Results. 600 patients in the study group; 63% Hispanic, mean age 39.2 ± 13.9 years. Hispanics and non-Hispanics whites were similar with respect to good knowledge-level answers to question 1 (17.3 vs. 15.1%; OR = 1.2; 95% CI [0.74–2.0]), question 2 (31.2 vs. 39.3%; OR = 0.76; 95% CI [0.54–1.1]), and question 3 (15.2 vs. 16.5%; OR = 1.1; 95% CI [0.66–1.8]). Compared to patients who earned <20,000, patients with income >40,000 were more likely to answer question 2 with good knowledge (OR = 1.96; 95% CI [1.2–3.1]). Conclusion. The study group’s overall knowledge of radiation risk was poor, but we did not find significant differences between Hispanic vs. non-Hispanic patients.
bibliographic citation: McNierney-Moore et al. (2015) Patient understanding of radiation risk from medical computed tomography—A comparison of Hispanic vs. non-Hispanic emergency department populations. PeerJ 3:e937 https://doi.org/10.7717/peerj.937
date submitted: 2015-03-04
date accepted: 2015-04-16
issued: 2015-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McNierney-Moore
  given name: Afton
author list: Agent
  family name: Smith
  given name: Cynthia
author list: Agent
  family name: Guardiola
  given name: Jose
author list: Agent
  family name: Xu
  given name: K. Tom
author list: Agent
  family name: Richman
  given name: Peter B.
doi: 10.7717/peerj.937
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-07
copyright: © 2015 McNierney-Moore et al.
attribution name: McNierney-Moore et al.

Analgesic effects of lappaconitine in leukemia bone pain in a mouse model
type: item
type: AcademicArticle
description: Bone pain is a common and severe symptom in cancer patients. The present study employed a mouse model of leukemia bone pain by injection K562 cells into tibia of mouse to evaluate the analgesic effects of lappacontine. Our results showed that the lappaconitine treatment at day 15, 17 and 19 could effectively reduce the spontaneous pain scoring values, restore reduced degree in the inclined-plate test induced by injection of K562 cells, as well as restore paw mechanical withdrawal threshold and paw withdrawal thermal latency induced by injection of K562 cells to the normal levels. Additionally, the molecular mechanisms of lappaconitine’s analgesic effects may be related to affect the expression levels of endogenous opioid system genes (POMC, PENK and MOR), as well as apoptosis-related genes (Xiap, Smac, Bim, NF-κB and p53). Our present results indicated that lappaconitine may become a new analgesic agent for leukemia bone pain management.
format: application/pdf
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creator: Xiao-Cui Zhu
creator: Chen-Tao Ge
creator: Pan Wang
creator: Jia-Li Zhang
creator: Yuan-Yang Yu
creator: Cai-Yun Fu
subject: Animal Behavior
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.936
publisher: PeerJ Inc.
rights: © 2015 Zhu et al.
abstract: Bone pain is a common and severe symptom in cancer patients. The present study employed a mouse model of leukemia bone pain by injection K562 cells into tibia of mouse to evaluate the analgesic effects of lappacontine. Our results showed that the lappaconitine treatment at day 15, 17 and 19 could effectively reduce the spontaneous pain scoring values, restore reduced degree in the inclined-plate test induced by injection of K562 cells, as well as restore paw mechanical withdrawal threshold and paw withdrawal thermal latency induced by injection of K562 cells to the normal levels. Additionally, the molecular mechanisms of lappaconitine’s analgesic effects may be related to affect the expression levels of endogenous opioid system genes (POMC, PENK and MOR), as well as apoptosis-related genes (Xiap, Smac, Bim, NF-κB and p53). Our present results indicated that lappaconitine may become a new analgesic agent for leukemia bone pain management.
bibliographic citation: Zhu et al. (2015) Analgesic effects of lappaconitine in leukemia bone pain in a mouse model. PeerJ 3:e936 https://doi.org/10.7717/peerj.936
date submitted: 2015-03-11
date accepted: 2015-04-15
issued: 2015-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Xiao-Cui
author list: Agent
  family name: Ge
  given name: Chen-Tao
author list: Agent
  family name: Wang
  given name: Pan
author list: Agent
  family name: Zhang
  given name: Jia-Li
author list: Agent
  family name: Yu
  given name: Yuan-Yang
author list: Agent
  family name: Fu
  given name: Cai-Yun
doi: 10.7717/peerj.936
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-07
copyright: © 2015 Zhu et al.
attribution name: Zhu et al.

Seasonal trends in the condition of nesting females of a solitary bee: wing wear, lipid content, and oocyte size
type: item
type: AcademicArticle
description: During the nesting season, adult females of the solitary bee Megachile rotundata (F.) face considerable physical and energy demands that could include increasing wear and tear on their bodies and decreasing lipid reserves. Consequently, their reproductive performance may be affected not only by extrinsic factors (e.g., weather and floral resource availability), but intrinsic changes in their own bodies. Because of the potential fitness effects of seasonal changes in body condition, our objectives were to determine how wing wear, lipid reserves, and oocyte sizes vary during nesting seasons, beginning when females emerge as adults. As nesting progressed, females in two populations experienced a steady increase in wing wear, which is known to reduce foraging efficiency and increase risk of mortality in other bees. Soon after emergence, females exhibited sharp declines in lipid content which remained low for the remainder of the season. Newly-emerged females ingested pollen, an activity known to be correlated with the initiation of egg maturation in this species. Additionally, the early summer drop in lipid stores was correlated with an increase in the size of the oocytes carried. However, by ∼6 weeks after emergence, oocytes began to decrease in length and volume, perhaps due to nutrient deficiencies related to loss of stored lipids. Our results suggest management of M. rotundata should include rearing bees at temperatures that maximize stored lipid reserves in adults and timing bee release so that significant pollen resources are available for both adults and offspring.
format: application/pdf
format: text/html
creator: Kevin M. O’Neill
creator: Casey M. Delphia
creator: Theresa L. Pitts-Singer
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.930
publisher: PeerJ Inc.
rights: © 2015 O’Neill et al.
abstract: During the nesting season, adult females of the solitary bee Megachile rotundata (F.) face considerable physical and energy demands that could include increasing wear and tear on their bodies and decreasing lipid reserves. Consequently, their reproductive performance may be affected not only by extrinsic factors (e.g., weather and floral resource availability), but intrinsic changes in their own bodies. Because of the potential fitness effects of seasonal changes in body condition, our objectives were to determine how wing wear, lipid reserves, and oocyte sizes vary during nesting seasons, beginning when females emerge as adults. As nesting progressed, females in two populations experienced a steady increase in wing wear, which is known to reduce foraging efficiency and increase risk of mortality in other bees. Soon after emergence, females exhibited sharp declines in lipid content which remained low for the remainder of the season. Newly-emerged females ingested pollen, an activity known to be correlated with the initiation of egg maturation in this species. Additionally, the early summer drop in lipid stores was correlated with an increase in the size of the oocytes carried. However, by ∼6 weeks after emergence, oocytes began to decrease in length and volume, perhaps due to nutrient deficiencies related to loss of stored lipids. Our results suggest management of M. rotundata should include rearing bees at temperatures that maximize stored lipid reserves in adults and timing bee release so that significant pollen resources are available for both adults and offspring.
bibliographic citation: O’Neill et al. (2015) Seasonal trends in the condition of nesting females of a solitary bee: wing wear, lipid content, and oocyte size. PeerJ 3:e930 https://doi.org/10.7717/peerj.930
date submitted: 2015-03-19
date accepted: 2015-04-13
issued: 2015-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Neill
  given name: Kevin M.
author list: Agent
  family name: Delphia
  given name: Casey M.
author list: Agent
  family name: Pitts-Singer
  given name: Theresa L.
doi: 10.7717/peerj.930
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-07
copyright: © 2015 O’Neill et al.
attribution name: O’Neill et al.

Associations between lower extremity muscle mass and metabolic parameters related to obesity in Japanese obese patients with type 2 diabetes
type: item
type: AcademicArticle
description: Background. Age-related loss of muscle mass (sarcopenia) increases the incidence of obesity in the elderly by reducing physical activity. This sarcopenic obesity may become self-perpetuating, increasing the risks for metabolic syndrome, disability, and mortality. We investigated the associations of two sarcopenic indices, the ratio of lower extremity muscle mass to body weight (L/W ratio) and the ratio of lower extremity muscle mass to upper extremity muscle mass (L/U ratio), with metabolic parameters related to obesity in patients with type 2 diabetes and obesity. Methods. Of 148 inpatients with type 2 diabetes treated between October 2013 and April 2014, we recruited 26 with obesity but no physical disability. Daily physical activity was measured by a triaxial accelerometer during a period of hospitalization, and which was also evaluated by our previously reported non-exercise activity thermogenesis questionnaire. We measured body composition by bioelectrical impedance and investigated the correlations of L/W and L/U ratios with body weight, body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), visceral fat area, subcutaneous fat area, serum lipid profile, and daily physical activity. Results. The L/W ratio was significantly and negatively correlated with BMI, WC, WHR, body fat mass, body fat percentage, subcutaneous fat area, and serum free fatty acid concentration, was positively correlated with daily physical activity: the locomotive non-exercise activity thermogenesis score, but was not correlated with visceral fat area. The L/U ratio was significantly and positively correlated with serum high-density lipoprotein cholesterol. Conclusions. High L/W and L/U ratios, indicative of relatively preserved lower extremity muscle mass, were predictive of improved metabolic parameters related to obesity. Preserved muscle fitness in obesity, especially of the lower extremities, may prevent sarcopenic obesity and lower associated risks for metabolic sy…
format: application/pdf
format: text/html
creator: Hidetaka Hamasaki
creator: Yu Kawashima
creator: Hiroki Adachi
creator: Sumie Moriyama
creator: Hisayuki Katsuyama
creator: Akahito Sako
creator: Hidekatsu Yanai
subject: Diabetes and Endocrinology
subject: Public Health
description: doi:10.7717/peerj.942
publisher: PeerJ Inc.
rights: © 2015 Hamasaki et al.
abstract: Background. Age-related loss of muscle mass (sarcopenia) increases the incidence of obesity in the elderly by reducing physical activity. This sarcopenic obesity may become self-perpetuating, increasing the risks for metabolic syndrome, disability, and mortality. We investigated the associations of two sarcopenic indices, the ratio of lower extremity muscle mass to body weight (L/W ratio) and the ratio of lower extremity muscle mass to upper extremity muscle mass (L/U ratio), with metabolic parameters related to obesity in patients with type 2 diabetes and obesity. Methods. Of 148 inpatients with type 2 diabetes treated between October 2013 and April 2014, we recruited 26 with obesity but no physical disability. Daily physical activity was measured by a triaxial accelerometer during a period of hospitalization, and which was also evaluated by our previously reported non-exercise activity thermogenesis questionnaire. We measured body composition by bioelectrical impedance and investigated the correlations of L/W and L/U ratios with body weight, body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), visceral fat area, subcutaneous fat area, serum lipid profile, and daily physical activity. Results. The L/W ratio was significantly and negatively correlated with BMI, WC, WHR, body fat mass, body fat percentage, subcutaneous fat area, and serum free fatty acid concentration, was positively correlated with daily physical activity: the locomotive non-exercise activity thermogenesis score, but was not correlated with visceral fat area. The L/U ratio was significantly and positively correlated with serum high-density lipoprotein cholesterol. Conclusions. High L/W and L/U ratios, indicative of relatively preserved lower extremity muscle mass, were predictive of improved metabolic parameters related to obesity. Preserved muscle fitness in obesity, especially of the lower extremities, may prevent sarcopenic obesity and lower associated risks for metabolic sy…
bibliographic citation: Hamasaki et al. (2015) Associations between lower extremity muscle mass and metabolic parameters related to obesity in Japanese obese patients with type 2 diabetes. PeerJ 3:e942 https://doi.org/10.7717/peerj.942
date submitted: 2015-02-13
date accepted: 2015-04-16
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hamasaki
  given name: Hidetaka
author list: Agent
  family name: Kawashima
  given name: Yu
author list: Agent
  family name: Adachi
  given name: Hiroki
author list: Agent
  family name: Moriyama
  given name: Sumie
author list: Agent
  family name: Katsuyama
  given name: Hisayuki
author list: Agent
  family name: Sako
  given name: Akahito
author list: Agent
  family name: Yanai
  given name: Hidekatsu
doi: 10.7717/peerj.942
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Hamasaki et al.
attribution name: Hamasaki et al.

Measures of skin conductance and heart rate in alcoholic men and women during memory performance
type: item
type: AcademicArticle
description: We examined abnormalities in physiological responses to emotional stimuli associated with long-term chronic alcoholism. Skin conductance responses (SCR) and heart rate (HR) responses were measured in 32 abstinent alcoholic (ALC) and 30 healthy nonalcoholic (NC) men and women undergoing an emotional memory task in an MRI scanner. The task required participants to remember the identity of two emotionally-valenced faces presented at the onset of each trial during functional magnetic resonance imaging (fMRI) scanning. After viewing the faces, participants saw a distractor image (an alcoholic beverage, nonalcoholic beverage, or scrambled image) followed by a single probe face. The task was to decide whether the probe face matched one of the two encoded faces. Skin conductance measurements (before and after the encoded faces, distractor, and probe) were obtained from electrodes on the index and middle fingers on the left hand. HR measurements (beats per minute before and after the encoded faces, distractor, and probe) were obtained by a pulse oximeter placed on the little finger on the left hand. We expected that, relative to NC participants, the ALC participants would show reduced SCR and HR responses to the face stimuli, and that we would identify greater reactivity to the alcoholic beverage stimuli than to the distractor stimuli unrelated to alcohol. While the beverage type did not differentiate the groups, the ALC group did have reduced skin conductance and HR responses to elements of the task, as compared to the NC group.
format: application/pdf
format: text/html
creator: Kayle S. Sawyer
creator: Alan Poey
creator: Susan Mosher Ruiz
creator: Ksenija Marinkovic
creator: Marlene Oscar-Berman
subject: Neuroscience
subject: Anatomy and Physiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.941
publisher: PeerJ Inc.
rights: © 2015 Sawyer et al.
abstract: We examined abnormalities in physiological responses to emotional stimuli associated with long-term chronic alcoholism. Skin conductance responses (SCR) and heart rate (HR) responses were measured in 32 abstinent alcoholic (ALC) and 30 healthy nonalcoholic (NC) men and women undergoing an emotional memory task in an MRI scanner. The task required participants to remember the identity of two emotionally-valenced faces presented at the onset of each trial during functional magnetic resonance imaging (fMRI) scanning. After viewing the faces, participants saw a distractor image (an alcoholic beverage, nonalcoholic beverage, or scrambled image) followed by a single probe face. The task was to decide whether the probe face matched one of the two encoded faces. Skin conductance measurements (before and after the encoded faces, distractor, and probe) were obtained from electrodes on the index and middle fingers on the left hand. HR measurements (beats per minute before and after the encoded faces, distractor, and probe) were obtained by a pulse oximeter placed on the little finger on the left hand. We expected that, relative to NC participants, the ALC participants would show reduced SCR and HR responses to the face stimuli, and that we would identify greater reactivity to the alcoholic beverage stimuli than to the distractor stimuli unrelated to alcohol. While the beverage type did not differentiate the groups, the ALC group did have reduced skin conductance and HR responses to elements of the task, as compared to the NC group.
bibliographic citation: Sawyer et al. (2015) Measures of skin conductance and heart rate in alcoholic men and women during memory performance. PeerJ 3:e941 https://doi.org/10.7717/peerj.941
date submitted: 2014-05-22
date accepted: 2015-04-16
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sawyer
  given name: Kayle S.
author list: Agent
  family name: Poey
  given name: Alan
author list: Agent
  family name: Ruiz
  given name: Susan Mosher
author list: Agent
  family name: Marinkovic
  given name: Ksenija
author list: Agent
  family name: Oscar-Berman
  given name: Marlene
doi: 10.7717/peerj.941
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Sawyer et al.
attribution name: Sawyer et al.

Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti
type: item
type: AcademicArticle
description: Aedes aegypti is the major vector of dengue, yellow fever and chikungunya viruses that put millions of people in endemic countries at risk. Mass rearing of this mosquito is crucial for strategies that use modified insects to reduce vector populations and transmission of pathogens, such as sterile insect technique or population replacement. A major problem for vector mosquito mass rearing is the requirement of vertebrate blood for egg production since it poses significant costs as well as potential health hazards. Also, regulations for human and animal use as blood source can pose a significant obstacle. A completely artificial diet that supports egg production in vector mosquitoes can solve this problem. In this study, we compared different blood fractions, serum and red blood cells, as dietary protein sources for mosquito egg production. We also tested artificial diets made from commercially available blood proteins (bovine serum albumin (BSA) and hemoglobin). We found that Ae. aegypti performed vitellogenesis and produced eggs when given whole bovine blood, serum, or an artificial diet containing BSA. Conversely, egg production was impaired after feeding of the red blood cell fraction or an artificial diet containing only hemoglobin. We also found that egg viability of serum-fed mosquitoes were comparable to that of whole blood and an iron supplemented BSA meal produced more viable eggs than a meal containing BSA alone. Our results indicate that serum proteins, not hemoglobin, may replace vertebrate blood in artificial diets for mass mosquito rearing.
format: application/pdf
format: text/html
creator: Kristina K. Gonzales
creator: Hitoshi Tsujimoto
creator: Immo A. Hansen
subject: Animal Behavior
subject: Developmental Biology
subject: Entomology
subject: Parasitology
description: doi:10.7717/peerj.938
publisher: PeerJ Inc.
rights: © 2015 Gonzales et al.
abstract: Aedes aegypti is the major vector of dengue, yellow fever and chikungunya viruses that put millions of people in endemic countries at risk. Mass rearing of this mosquito is crucial for strategies that use modified insects to reduce vector populations and transmission of pathogens, such as sterile insect technique or population replacement. A major problem for vector mosquito mass rearing is the requirement of vertebrate blood for egg production since it poses significant costs as well as potential health hazards. Also, regulations for human and animal use as blood source can pose a significant obstacle. A completely artificial diet that supports egg production in vector mosquitoes can solve this problem. In this study, we compared different blood fractions, serum and red blood cells, as dietary protein sources for mosquito egg production. We also tested artificial diets made from commercially available blood proteins (bovine serum albumin (BSA) and hemoglobin). We found that Ae. aegypti performed vitellogenesis and produced eggs when given whole bovine blood, serum, or an artificial diet containing BSA. Conversely, egg production was impaired after feeding of the red blood cell fraction or an artificial diet containing only hemoglobin. We also found that egg viability of serum-fed mosquitoes were comparable to that of whole blood and an iron supplemented BSA meal produced more viable eggs than a meal containing BSA alone. Our results indicate that serum proteins, not hemoglobin, may replace vertebrate blood in artificial diets for mass mosquito rearing.
bibliographic citation: Gonzales et al. (2015) Blood serum and BSA, but neither red blood cells nor hemoglobin can support vitellogenesis and egg production in the dengue vector Aedes aegypti. PeerJ 3:e938 https://doi.org/10.7717/peerj.938
date submitted: 2014-12-08
date accepted: 2015-04-16
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzales
  given name: Kristina K.
author list: Agent
  family name: Tsujimoto
  given name: Hitoshi
author list: Agent
  family name: Hansen
  given name: Immo A.
doi: 10.7717/peerj.938
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Gonzales et al.
attribution name: Gonzales et al.

GFVO: the Genomic Feature and Variation Ontology
type: item
type: AcademicArticle
description: Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.
format: application/pdf
format: text/html
creator: Joachim Baran
creator: Bibi Sehnaaz Begum Durgahee
creator: Karen Eilbeck
creator: Erick Antezana
creator: Robert Hoehndorf
creator: Michel Dumontier
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.933
publisher: PeerJ Inc.
rights: © 2015 Baran et al.
abstract: Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.
bibliographic citation: Baran et al. (2015) GFVO: the Genomic Feature and Variation Ontology. PeerJ 3:e933 https://doi.org/10.7717/peerj.933
date submitted: 2014-11-04
date accepted: 2015-04-14
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baran
  given name: Joachim
author list: Agent
  family name: Durgahee
  given name: Bibi Sehnaaz Begum
author list: Agent
  family name: Eilbeck
  given name: Karen
author list: Agent
  family name: Antezana
  given name: Erick
author list: Agent
  family name: Hoehndorf
  given name: Robert
author list: Agent
  family name: Dumontier
  given name: Michel
doi: 10.7717/peerj.933
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Baran et al.
attribution name: Baran et al.

Continued Dispensing: what medications do patients believe should be available?
type: item
type: AcademicArticle
description: Background. Continued Dispensing (CD) is a new medication supply method for certain medications in Australia. It aims to prevent treatment interruption as a result of patients’ inability to obtain a new valid prescription. The only currently eligible patients for this service are statin and/or oral contraceptives users who have been using these medications for 6 months or more, have not utilized the CD method during the last 12 months, and cannot obtain an immediate appointment with the prescriber in order to get a new prescription. This study aimed to investigate patients’ attitudes towards potential extension and expansion of this medication supply method. Methods. A randomly selected 301 users of these medications from all Australian States were recruited using Computer Assisted Telephone Interview (CATI). Result. The response rate was 79%. The majority of the participants (73.3%) did not agree with current restriction on CD utilization frequency. They also supported, to varying degrees, inclusion of all the proposed medications (support ranged from 44.2–78.4%). In this regard, participants who suffered from a specific disease did not differ significantly from those without the disease except in case of patients with depression (p = 0.001). Conclusions. Participants of this study strongly supported both CD extension and expansion. A future critical review of the current version of CD is highly recommended in order to enhance CD capability to achieve its goals.
format: application/pdf
format: text/html
creator: Salem Hasn Abukres
creator: Kreshnik Hoti
creator: Jeffery David Hughes
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.924
publisher: PeerJ Inc.
rights: © 2015 Abukres et al.
abstract: Background. Continued Dispensing (CD) is a new medication supply method for certain medications in Australia. It aims to prevent treatment interruption as a result of patients’ inability to obtain a new valid prescription. The only currently eligible patients for this service are statin and/or oral contraceptives users who have been using these medications for 6 months or more, have not utilized the CD method during the last 12 months, and cannot obtain an immediate appointment with the prescriber in order to get a new prescription. This study aimed to investigate patients’ attitudes towards potential extension and expansion of this medication supply method. Methods. A randomly selected 301 users of these medications from all Australian States were recruited using Computer Assisted Telephone Interview (CATI). Result. The response rate was 79%. The majority of the participants (73.3%) did not agree with current restriction on CD utilization frequency. They also supported, to varying degrees, inclusion of all the proposed medications (support ranged from 44.2–78.4%). In this regard, participants who suffered from a specific disease did not differ significantly from those without the disease except in case of patients with depression (p = 0.001). Conclusions. Participants of this study strongly supported both CD extension and expansion. A future critical review of the current version of CD is highly recommended in order to enhance CD capability to achieve its goals.
bibliographic citation: Abukres et al. (2015) Continued Dispensing: what medications do patients believe should be available?. PeerJ 3:e924 https://doi.org/10.7717/peerj.924
date submitted: 2014-11-19
date accepted: 2015-04-09
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abukres
  given name: Salem Hasn
author list: Agent
  family name: Hoti
  given name: Kreshnik
author list: Agent
  family name: Hughes
  given name: Jeffery David
doi: 10.7717/peerj.924
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Abukres et al.
attribution name: Abukres et al.

Synthetic neuronal datasets for benchmarking directed functional connectivity metrics
type: item
type: AcademicArticle
description: Background. Datasets consisting of synthetic neural data generated with quantifiable and controlled parameters are a valuable asset in the process of testing and validating directed functional connectivity metrics. Considering the recent debate in the neuroimaging community concerning the use of these metrics for fMRI data, synthetic datasets that emulate the BOLD signal dynamics have played a central role by supporting claims that argue in favor or against certain choices. Generative models often used in studies that simulate neuronal activity, with the aim of gaining insight into specific brain regions and functions, have different requirements from the generative models for benchmarking datasets. Even though the latter must be realistic, there is a tradeoff between realism and computational demand that needs to be contemplated and simulations that efficiently mimic the real behavior of single neurons or neuronal populations are preferred, instead of more cumbersome and marginally precise ones. Methods. This work explores how simple generative models are able to produce neuronal datasets, for benchmarking purposes, that reflect the simulated effective connectivity and, how these can be used to obtain synthetic recordings of EEG and fMRI BOLD signals. The generative models covered here are AR processes, neural mass models consisting of linear and nonlinear stochastic differential equations and populations with thousands of spiking units. Forward models for EEG consist in the simple three-shell head model while the fMRI BOLD signal is modeled with the Balloon-Windkessel model or by convolution with a hemodynamic response function. Results. The simulated datasets are tested for causality with the original spectral formulation for Granger causality. Modeled effective connectivity can be detected in the generated data for varying connection strengths and interaction delays. Discussion. All generative models produce synthetic neuronal data with detectable causal effects…
format: application/pdf
format: text/html
creator: João Rodrigues
creator: Alexandre Andrade
subject: Biophysics
subject: Neuroscience
subject: Computational Science
description: doi:10.7717/peerj.923
publisher: PeerJ Inc.
rights: © 2015 Rodrigues and Andrade
abstract: Background. Datasets consisting of synthetic neural data generated with quantifiable and controlled parameters are a valuable asset in the process of testing and validating directed functional connectivity metrics. Considering the recent debate in the neuroimaging community concerning the use of these metrics for fMRI data, synthetic datasets that emulate the BOLD signal dynamics have played a central role by supporting claims that argue in favor or against certain choices. Generative models often used in studies that simulate neuronal activity, with the aim of gaining insight into specific brain regions and functions, have different requirements from the generative models for benchmarking datasets. Even though the latter must be realistic, there is a tradeoff between realism and computational demand that needs to be contemplated and simulations that efficiently mimic the real behavior of single neurons or neuronal populations are preferred, instead of more cumbersome and marginally precise ones. Methods. This work explores how simple generative models are able to produce neuronal datasets, for benchmarking purposes, that reflect the simulated effective connectivity and, how these can be used to obtain synthetic recordings of EEG and fMRI BOLD signals. The generative models covered here are AR processes, neural mass models consisting of linear and nonlinear stochastic differential equations and populations with thousands of spiking units. Forward models for EEG consist in the simple three-shell head model while the fMRI BOLD signal is modeled with the Balloon-Windkessel model or by convolution with a hemodynamic response function. Results. The simulated datasets are tested for causality with the original spectral formulation for Granger causality. Modeled effective connectivity can be detected in the generated data for varying connection strengths and interaction delays. Discussion. All generative models produce synthetic neuronal data with detectable causal effects…
bibliographic citation: Rodrigues et al. (2015) Synthetic neuronal datasets for benchmarking directed functional connectivity metrics. PeerJ 3:e923 https://doi.org/10.7717/peerj.923
date submitted: 2014-12-20
date accepted: 2015-04-09
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodrigues
  given name: João
author list: Agent
  family name: Andrade
  given name: Alexandre
doi: 10.7717/peerj.923
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 Rodrigues and Andrade
attribution name: Rodrigues and Andrade

Replicability of sight word training and phonics training in poor readers: a randomised controlled trial
type: item
type: AcademicArticle
description: Given the importance of effective treatments for children with reading impairment, paired with growing concern about the lack of scientific replication in psychological science, the aim of this study was to replicate a quasi-randomised trial of sight word and phonics training using a randomised controlled trial (RCT) design. One group of poor readers (N = 41) did 8 weeks of phonics training (i.e., phonological decoding) and then 8 weeks of sight word training (i.e., whole-word recognition). A second group did the reverse order of training. Sight word and phonics training each had a large and significant valid treatment effect on trained irregular words and word reading fluency. In addition, combined sight word and phonics training had a moderate and significant valid treatment effect on nonword reading accuracy and fluency. These findings demonstrate the reliability of both phonics and sight word training in treating poor readers in an era where the importance of scientific reliability is under close scrutiny.
format: application/pdf
format: text/html
creator: G McArthur
creator: S Kohnen
creator: K Jones
creator: P Eve
creator: E Banales
creator: L Larsen
creator: A Castles
subject: Clinical Trials
subject: Cognitive Disorders
description: doi:10.7717/peerj.922
publisher: PeerJ Inc.
rights: © 2015 McArthur et al.
abstract: Given the importance of effective treatments for children with reading impairment, paired with growing concern about the lack of scientific replication in psychological science, the aim of this study was to replicate a quasi-randomised trial of sight word and phonics training using a randomised controlled trial (RCT) design. One group of poor readers (N = 41) did 8 weeks of phonics training (i.e., phonological decoding) and then 8 weeks of sight word training (i.e., whole-word recognition). A second group did the reverse order of training. Sight word and phonics training each had a large and significant valid treatment effect on trained irregular words and word reading fluency. In addition, combined sight word and phonics training had a moderate and significant valid treatment effect on nonword reading accuracy and fluency. These findings demonstrate the reliability of both phonics and sight word training in treating poor readers in an era where the importance of scientific reliability is under close scrutiny.
bibliographic citation: McArthur et al. (2015) Replicability of sight word training and phonics training in poor readers: a randomised controlled trial. PeerJ 3:e922 https://doi.org/10.7717/peerj.922
date submitted: 2014-10-22
date accepted: 2015-04-09
issued: 2015-05-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McArthur
  given name: G
author list: Agent
  family name: Kohnen
  given name: S
author list: Agent
  family name: Jones
  given name: K
author list: Agent
  family name: Eve
  given name: P
author list: Agent
  family name: Banales
  given name: E
author list: Agent
  family name: Larsen
  given name: L
author list: Agent
  family name: Castles
  given name: A
doi: 10.7717/peerj.922
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-05
copyright: © 2015 McArthur et al.
attribution name: McArthur et al.

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