PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/2233
items: Delivering a medical school elective with massive open online course (MOOC) technology
items: Prediction of pKa values using the PM6 semiempirical method
items: The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled
items: Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania
items: Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation
items: Stereotactically-navigated percutaneous Irreversible Electroporation (IRE) compared to conventional IRE: a prospective trial
items: Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease
items: Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda)
items: Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation

https://peerj.com/articles/2233
type: item
type: AcademicArticle
title: Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic
description: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions a…
format: application/pdf
format: text/html
creator: Amira Chaabane
creator: Jean-Lou Justine
creator: Delphine Gey
creator: Micah D. Bakenhaster
creator: Lassad Neifar
subject: Biodiversity
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2233
publisher: PeerJ Inc.
rights: © 2016 Chaabane et al.
abstract: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions a…
bibliographic citation: Chaabane et al. (2016) Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic. PeerJ 4:e2233 https://doi.org/10.7717/peerj.2233
date submitted: 2016-04-12
date accepted: 2016-06-17
issued: 2016-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chaabane
  given name: Amira
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Bakenhaster
  given name: Micah D.
author list: Agent
  family name: Neifar
  given name: Lassad
doi: 10.7717/peerj.2233
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-16
copyright: ©2016 Chaabane et al.
attribution name: Chaabane et al.

Delivering a medical school elective with massive open online course (MOOC) technology
type: item
type: AcademicArticle
description: Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery. Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth-year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012–2015 academic years was conducted. This course was delivered by small group flipped classroom discussions for 2012–2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations. Results: Course enrollment has ranged from 6–19 students per year in the 2012–2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5-point Likert scale. The majority of all student ratings (76–95%) of this elective course are for the highest possible choice (Strongly agree or Excellent) for any criteria, regardless if the course was delivered via a traditional or MOOC format. Statistical analysis of these ratings suggests that the Effective Teacher and Overall Evaluations did not statistically differ between the two delivery formats. Discussion: Student ratings of this elective course were highly similar when delivered in a flipped classroom format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations suggest this is a change that is acceptable to the …
format: application/pdf
format: text/html
creator: Robert Robinson
subject: Science and Medical Education
subject: Human-Computer Interaction
description: doi:10.7717/peerj.2343
publisher: PeerJ Inc.
rights: © 2016 Robinson
abstract: Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery. Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth-year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012–2015 academic years was conducted. This course was delivered by small group flipped classroom discussions for 2012–2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations. Results: Course enrollment has ranged from 6–19 students per year in the 2012–2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5-point Likert scale. The majority of all student ratings (76–95%) of this elective course are for the highest possible choice (Strongly agree or Excellent) for any criteria, regardless if the course was delivered via a traditional or MOOC format. Statistical analysis of these ratings suggests that the Effective Teacher and Overall Evaluations did not statistically differ between the two delivery formats. Discussion: Student ratings of this elective course were highly similar when delivered in a flipped classroom format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations suggest this is a change that is acceptable to the …
bibliographic citation: Robinson (2016) Delivering a medical school elective with massive open online course (MOOC) technology. PeerJ 4:e2343 https://doi.org/10.7717/peerj.2343
date submitted: 2016-04-14
date accepted: 2016-07-19
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robinson
  given name: Robert
doi: 10.7717/peerj.2343
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Robinson
attribution name: Robinson

Prediction of pKa values using the PM6 semiempirical method
type: item
type: AcademicArticle
description: The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
format: application/pdf
format: text/html
creator: Jimmy C. Kromann
creator: Frej Larsen
creator: Hadeel Moustafa
creator: Jan H. Jensen
subject: Biophysics
subject: Computational Biology
description: doi:10.7717/peerj.2335
publisher: PeerJ Inc.
rights: © 2016 Kromann et al.
abstract: The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using isodesmic reactions and compared to published ab initio results. The pKa values of pyridines, alcohols, phenols, and benzoic acids considered in this study can generally be predicted with PM6 and ab initio methods to within the same overall accuracy, with average mean absolute differences (MADs) of 0.6–0.7 pH units. For carboxylic acids, the accuracy (0.7–1.0 pH units) is also comparable to ab initio results if a single outlier is removed. For primary, secondary, and tertiary amines the accuracy is, respectively, similar (0.5–0.6), slightly worse (0.5–1.0), and worse (1.0–2.5), provided that di- and tri-ethylamine are used as reference molecules for secondary and tertiary amines. When applied to a drug-like molecule where an empirical pKa predictor exhibits a large (4.9 pH unit) error, we find that the errors for PM6-based predictions are roughly the same in magnitude but opposite in sign. As a result, most of the PM6-based methods predict the correct protonation state at physiological pH, while the empirical predictor does not. The computational cost is around 2–5 min per conformer per core processor, making PM6-based pKa prediction computationally efficient enough to be used for high-throughput screening using on the order of 100 core processors.
bibliographic citation: Kromann et al. (2016) Prediction of pKa values using the PM6 semiempirical method. PeerJ 4:e2335 https://doi.org/10.7717/peerj.2335
date submitted: 2016-06-01
date accepted: 2016-07-16
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kromann
  given name: Jimmy C.
author list: Agent
  family name: Larsen
  given name: Frej
author list: Agent
  family name: Moustafa
  given name: Hadeel
author list: Agent
  family name: Jensen
  given name: Jan H.
doi: 10.7717/peerj.2335
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Kromann et al.
attribution name: Kromann et al.

The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled
type: item
type: AcademicArticle
description: The modified Thomas test was developed to assess the presence of hip flexion contracture and to measure hip extensibility. Despite its widespread use, to the authors’ knowledge, its criterion reference validity has not yet been investigated. The purpose of this study was to assess the criterion reference validity of the modified Thomas test for measuring peak hip extension angle and hip extension deficits, as defined by the hip not being able to extend to 0º, or neutral. Twenty-nine healthy college students (age = 22.00 ± 3.80 years; height = 1.71 ± 0.09 m; body mass = 70.00 ± 15.60 kg) were recruited for this study. Bland–Altman plots revealed poor validity for the modified Thomas test’s ability to measure hip extension, which could not be explained by differences in hip flexion ability alone. The modified Thomas test displayed a sensitivity of 31.82% (95% CI [13.86–54.87]) and a specificity of 57.14% (95% CI [18.41–90.10]) for testing hip extension deficits. It appears, however, that by controlling pelvic tilt, much of this variance can be accounted for (r = 0.98). When pelvic tilt is not controlled, the modified Thomas test displays poor criterion reference validity and, as per previous studies, poor reliability. However, when pelvic tilt is controlled, the modified Thomas test appears to be a valid test for evaluating peak hip extension angle.
format: application/pdf
format: text/html
creator: Andrew D. Vigotsky
creator: Gregory J. Lehman
creator: Chris Beardsley
creator: Bret Contreras
creator: Bryan Chung
creator: Erin H. Feser
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.2325
publisher: PeerJ Inc.
rights: © 2016 Vigotsky et al.
abstract: The modified Thomas test was developed to assess the presence of hip flexion contracture and to measure hip extensibility. Despite its widespread use, to the authors’ knowledge, its criterion reference validity has not yet been investigated. The purpose of this study was to assess the criterion reference validity of the modified Thomas test for measuring peak hip extension angle and hip extension deficits, as defined by the hip not being able to extend to 0º, or neutral. Twenty-nine healthy college students (age = 22.00 ± 3.80 years; height = 1.71 ± 0.09 m; body mass = 70.00 ± 15.60 kg) were recruited for this study. Bland–Altman plots revealed poor validity for the modified Thomas test’s ability to measure hip extension, which could not be explained by differences in hip flexion ability alone. The modified Thomas test displayed a sensitivity of 31.82% (95% CI [13.86–54.87]) and a specificity of 57.14% (95% CI [18.41–90.10]) for testing hip extension deficits. It appears, however, that by controlling pelvic tilt, much of this variance can be accounted for (r = 0.98). When pelvic tilt is not controlled, the modified Thomas test displays poor criterion reference validity and, as per previous studies, poor reliability. However, when pelvic tilt is controlled, the modified Thomas test appears to be a valid test for evaluating peak hip extension angle.
bibliographic citation: Vigotsky et al. (2016) The modified Thomas test is not a valid measure of hip extension unless pelvic tilt is controlled. PeerJ 4:e2325 https://doi.org/10.7717/peerj.2325
date submitted: 2016-05-24
date accepted: 2016-07-14
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vigotsky
  given name: Andrew D.
author list: Agent
  family name: Lehman
  given name: Gregory J.
author list: Agent
  family name: Beardsley
  given name: Chris
author list: Agent
  family name: Contreras
  given name: Bret
author list: Agent
  family name: Chung
  given name: Bryan
author list: Agent
  family name: Feser
  given name: Erin H.
doi: 10.7717/peerj.2325
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Vigotsky et al.
attribution name: Vigotsky et al.

Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania
type: item
type: AcademicArticle
description: The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens.
format: application/pdf
format: text/html
creator: Joyce M. Sakamoto
creator: Terry Fei Fan Ng
creator: Yasutsugu Suzuki
creator: Hitoshi Tsujimoto
creator: Xutao Deng
creator: Eric Delwart
creator: Jason L. Rasgon
subject: Ecology
subject: Entomology
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.2324
publisher: PeerJ Inc.
rights: © 2016 Sakamoto et al.
abstract: The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens.
bibliographic citation: Sakamoto et al. (2016) Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania. PeerJ 4:e2324 https://doi.org/10.7717/peerj.2324
date submitted: 2016-06-14
date accepted: 2016-07-13
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakamoto
  given name: Joyce M.
author list: Agent
  family name: Ng
  given name: Terry Fei Fan
author list: Agent
  family name: Suzuki
  given name: Yasutsugu
author list: Agent
  family name: Tsujimoto
  given name: Hitoshi
author list: Agent
  family name: Deng
  given name: Xutao
author list: Agent
  family name: Delwart
  given name: Eric
author list: Agent
  family name: Rasgon
  given name: Jason L.
doi: 10.7717/peerj.2324
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: © 2016 Sakamoto et al.
attribution name: Sakamoto et al.

Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation
type: item
type: AcademicArticle
description: Background. Mammalian hibernation in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) is characterized by dramatic changes on a physiological and molecular level. During hibernation, mammalian hearts show a propensity to hypertrophy due to the need for increasing contractility to pump colder and more viscous blood. While cardiac hypertrophy is quite often a process characterized by decompensation, the ground squirrel studied is an excellent model of cardiac plasticity and cardioprotection under conditions of hypothermia and ischemia. The forkhead box O (Foxo) family of proteins and myogenin (MyoG) are transcription factors that control protein degradation and muscle atrophy by regulating the expression of the E3 ubiquitin ligases, MAFbx and MuRF1. These ligases are part of the ubiquitin proteasome system by transferring ubiquitin to proteins and targeting these proteins for degradation. Regulation of Foxo1 and 3a occurs through phosphorylation at different residues. The threonine-24 (Thr-24) and serine-319 (Ser-319) residues on Foxo1, and the Thr-32 residue on Foxo3a are phosphorylated by Akt, leading to cytoplasmic localization of Foxo. We propose that the described mechanism contributes to the changes taking place in cardiac muscle throughout hibernation. Methods. Total and phosphorylated protein levels of Foxo1 and Foxo3a, as well as total protein levels of MyoG, MAFbx, and MuRF1, were studied using immunoblotting. Results. Immunoblotting results demonstrated upregulations in Foxo1 and Foxo3a total protein levels (1.3- and 4.5-fold increases relative to euthermic control, for Foxo1 and 3a respectively) during late torpor, and protein levels remained elevated throughout the rest of torpor and at interbout arousal. We also observed decreases in inactive, phosphorylated Foxo1 and 3a proteins during throughout torpor, where levels of p-Foxo1 Ser319 and Thr24, as well as p-Foxo3a Thr32 decreased by at least 45% throughout torpor. MyoG was upregulated only …
format: application/pdf
format: text/html
creator: Yichi Zhang
creator: Oscar A. Aguilar
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Cardiology
description: doi:10.7717/peerj.2317
publisher: PeerJ Inc.
rights: © 2016 Zhang et al.
abstract: Background. Mammalian hibernation in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) is characterized by dramatic changes on a physiological and molecular level. During hibernation, mammalian hearts show a propensity to hypertrophy due to the need for increasing contractility to pump colder and more viscous blood. While cardiac hypertrophy is quite often a process characterized by decompensation, the ground squirrel studied is an excellent model of cardiac plasticity and cardioprotection under conditions of hypothermia and ischemia. The forkhead box O (Foxo) family of proteins and myogenin (MyoG) are transcription factors that control protein degradation and muscle atrophy by regulating the expression of the E3 ubiquitin ligases, MAFbx and MuRF1. These ligases are part of the ubiquitin proteasome system by transferring ubiquitin to proteins and targeting these proteins for degradation. Regulation of Foxo1 and 3a occurs through phosphorylation at different residues. The threonine-24 (Thr-24) and serine-319 (Ser-319) residues on Foxo1, and the Thr-32 residue on Foxo3a are phosphorylated by Akt, leading to cytoplasmic localization of Foxo. We propose that the described mechanism contributes to the changes taking place in cardiac muscle throughout hibernation. Methods. Total and phosphorylated protein levels of Foxo1 and Foxo3a, as well as total protein levels of MyoG, MAFbx, and MuRF1, were studied using immunoblotting. Results. Immunoblotting results demonstrated upregulations in Foxo1 and Foxo3a total protein levels (1.3- and 4.5-fold increases relative to euthermic control, for Foxo1 and 3a respectively) during late torpor, and protein levels remained elevated throughout the rest of torpor and at interbout arousal. We also observed decreases in inactive, phosphorylated Foxo1 and 3a proteins during throughout torpor, where levels of p-Foxo1 Ser319 and Thr24, as well as p-Foxo3a Thr32 decreased by at least 45% throughout torpor. MyoG was upregulated only …
bibliographic citation: Zhang et al. (2016) Transcriptional activation of muscle atrophy promotes cardiac muscle remodeling during mammalian hibernation. PeerJ 4:e2317 https://doi.org/10.7717/peerj.2317
date submitted: 2016-05-26
date accepted: 2016-07-12
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yichi
author list: Agent
  family name: Aguilar
  given name: Oscar A.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.2317
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Zhang et al.
attribution name: Zhang et al.

Stereotactically-navigated percutaneous Irreversible Electroporation (IRE) compared to conventional IRE: a prospective trial
type: item
type: AcademicArticle
description: Purpose. The purpose of this study was to compare CT-navigated stereotactic IRE (SIRE) needle placement to non-navigated conventional IRE (CIRE) for percutaneous ablation of liver malignancies. Materials and Methods. A prospective trial including a total of 20 patients was conducted with 10 patients in each arm of the study. IRE procedures were guided using either CT fluoroscopy (CIRE) or a stereotactic planning and navigation system (SIRE). Primary endpoint was procedure time. Secondary endpoints were accuracy of needle placement, technical success rate, complication rate and dose-length product (DLP). Results. A total of 20 IRE procedures were performed to ablate hepatic malignancies (16 HCC, 4 liver metastases), 10 procedures in each arm. Mean time for placement of IRE electrodes in SIRE was significantly shorter with 27 ± 8 min compared to 87 ± 30 min for CIRE (p < 0.001). Accuracy of needle placement for SIRE was higher than CIRE (2.2 mm vs. 3.3 mm mean deviation, p < 0.001). The total DLP and the fluoroscopy DLP were significantly lower in SIRE compared to CIRE. Technical success rate and complication rates were equal in both arms. Conclusion. SIRE demonstrated a significant reduction of procedure length and higher accuracy compared to CIRE. Stereotactic navigation has the potential to reduce radiation dose for the patient and the radiologist without increasing the risk of complications or impaired technical success compared to CIRE.
format: application/pdf
format: text/html
creator: Lukas P. Beyer
creator: Benedikt Pregler
creator: Christoph Nießen
creator: Andreas Schicho
creator: Michael Haimerl
creator: Ernst Michael Jung
creator: Christian Stroszczynski
creator: Philipp Wiggermann
subject: Oncology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.2277
publisher: PeerJ Inc.
rights: © 2016 Beyer et al.
abstract: Purpose. The purpose of this study was to compare CT-navigated stereotactic IRE (SIRE) needle placement to non-navigated conventional IRE (CIRE) for percutaneous ablation of liver malignancies. Materials and Methods. A prospective trial including a total of 20 patients was conducted with 10 patients in each arm of the study. IRE procedures were guided using either CT fluoroscopy (CIRE) or a stereotactic planning and navigation system (SIRE). Primary endpoint was procedure time. Secondary endpoints were accuracy of needle placement, technical success rate, complication rate and dose-length product (DLP). Results. A total of 20 IRE procedures were performed to ablate hepatic malignancies (16 HCC, 4 liver metastases), 10 procedures in each arm. Mean time for placement of IRE electrodes in SIRE was significantly shorter with 27 ± 8 min compared to 87 ± 30 min for CIRE (p < 0.001). Accuracy of needle placement for SIRE was higher than CIRE (2.2 mm vs. 3.3 mm mean deviation, p < 0.001). The total DLP and the fluoroscopy DLP were significantly lower in SIRE compared to CIRE. Technical success rate and complication rates were equal in both arms. Conclusion. SIRE demonstrated a significant reduction of procedure length and higher accuracy compared to CIRE. Stereotactic navigation has the potential to reduce radiation dose for the patient and the radiologist without increasing the risk of complications or impaired technical success compared to CIRE.
bibliographic citation: Beyer et al. (2016) Stereotactically-navigated percutaneous Irreversible Electroporation (IRE) compared to conventional IRE: a prospective trial. PeerJ 4:e2277 https://doi.org/10.7717/peerj.2277
date submitted: 2016-05-18
date accepted: 2016-07-01
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beyer
  given name: Lukas P.
author list: Agent
  family name: Pregler
  given name: Benedikt
author list: Agent
  family name: Nießen
  given name: Christoph
author list: Agent
  family name: Schicho
  given name: Andreas
author list: Agent
  family name: Haimerl
  given name: Michael
author list: Agent
  family name: Jung
  given name: Ernst Michael
author list: Agent
  family name: Stroszczynski
  given name: Christian
author list: Agent
  family name: Wiggermann
  given name: Philipp
doi: 10.7717/peerj.2277
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Beyer et al.
attribution name: Beyer et al.

Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease
type: item
type: AcademicArticle
description: Background. Cystic fibrosis (CF) is a genetic disease that results in chronic infections of the lungs. CF patients experience intermittent pulmonary exacerbations (CFPE) that are associated with poor clinical outcomes. CFPE involves an increase in disease symptoms requiring more aggressive therapy. Methods. Longitudinal sputum samples were collected from 11 patients (n = 44 samples) to assess the effect of exacerbations on the sputum metabolome using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data was analyzed with MS/MS molecular networking and multivariate statistics. Results. The individual patient source had a larger influence on the metabolome of sputum than the clinical state (exacerbation, treatment, post-treatment, or stable). Of the 4,369 metabolites detected, 12% were unique to CFPE samples; however, the only known metabolites significantly elevated at exacerbation across the dataset were platelet activating factor (PAF) and a related monacylglycerophosphocholine lipid. Due to the personalized nature of the sputum metabolome, a single patient was followed for 4.2 years (capturing four separate exacerbation events) as a case study for the detection of personalized biomarkers with metabolomics. PAF and related lipids were significantly elevated during CFPEs of this patient and ceramide was elevated during CFPE treatment. Correlating the abundance of bacterial 16S rRNA gene amplicons to metabolomics data from the same samples during a CFPE demonstrated that antibiotics were positively correlated to Stenotrophomonas and Pseudomonas, while ceramides and other lipids were correlated with Streptococcus, Rothia, and anaerobes. Conclusions. This study identified PAF and other inflammatory lipids as potential biomarkers of CFPE, but overall, the metabolome of CF sputum was patient specific, supporting a personalized approach to molecular detection of CFPE onset.
format: application/pdf
format: text/html
creator: Robert A. Quinn
creator: Yan Wei Lim
creator: Tytus D. Mak
creator: Katrine Whiteson
creator: Mike Furlan
creator: Douglas Conrad
creator: Forest Rohwer
creator: Pieter Dorrestein
subject: Bioinformatics
subject: Infectious Diseases
subject: Respiratory Medicine
description: doi:10.7717/peerj.2174
publisher: PeerJ Inc.
rights: © 2016 Quinn et al.
abstract: Background. Cystic fibrosis (CF) is a genetic disease that results in chronic infections of the lungs. CF patients experience intermittent pulmonary exacerbations (CFPE) that are associated with poor clinical outcomes. CFPE involves an increase in disease symptoms requiring more aggressive therapy. Methods. Longitudinal sputum samples were collected from 11 patients (n = 44 samples) to assess the effect of exacerbations on the sputum metabolome using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data was analyzed with MS/MS molecular networking and multivariate statistics. Results. The individual patient source had a larger influence on the metabolome of sputum than the clinical state (exacerbation, treatment, post-treatment, or stable). Of the 4,369 metabolites detected, 12% were unique to CFPE samples; however, the only known metabolites significantly elevated at exacerbation across the dataset were platelet activating factor (PAF) and a related monacylglycerophosphocholine lipid. Due to the personalized nature of the sputum metabolome, a single patient was followed for 4.2 years (capturing four separate exacerbation events) as a case study for the detection of personalized biomarkers with metabolomics. PAF and related lipids were significantly elevated during CFPEs of this patient and ceramide was elevated during CFPE treatment. Correlating the abundance of bacterial 16S rRNA gene amplicons to metabolomics data from the same samples during a CFPE demonstrated that antibiotics were positively correlated to Stenotrophomonas and Pseudomonas, while ceramides and other lipids were correlated with Streptococcus, Rothia, and anaerobes. Conclusions. This study identified PAF and other inflammatory lipids as potential biomarkers of CFPE, but overall, the metabolome of CF sputum was patient specific, supporting a personalized approach to molecular detection of CFPE onset.
bibliographic citation: Quinn et al. (2016) Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease. PeerJ 4:e2174 https://doi.org/10.7717/peerj.2174
date submitted: 2016-02-06
date accepted: 2016-06-04
issued: 2016-08-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quinn
  given name: Robert A.
author list: Agent
  family name: Lim
  given name: Yan Wei
author list: Agent
  family name: Mak
  given name: Tytus D.
author list: Agent
  family name: Whiteson
  given name: Katrine
author list: Agent
  family name: Furlan
  given name: Mike
author list: Agent
  family name: Conrad
  given name: Douglas
author list: Agent
  family name: Rohwer
  given name: Forest
author list: Agent
  family name: Dorrestein
  given name: Pieter
doi: 10.7717/peerj.2174
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-11
copyright: ©2016 Quinn et al.
attribution name: Quinn et al.

Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda)
type: item
type: AcademicArticle
description: This study describes the segmentation and setation at different developmental stages of the homonomous trunk limbs of the remipede Speleonectes tulumensis Yager, 1987 collected in anchialine caves of the Yucatan Peninsula. Most homonomous trunk limbs originate ventrolaterally and are composed of two protopodal segments, three exopodal segments and four endopodal segments; contralateral limb pairs are united by a sternal bar. However, the last few posterior limbs originate ventrally, are smaller sized, and have regressively fewer segments, suggesting that limb development passes through several intermediate steps beginning with a limb bud. A terminal stage of development is proposed for specimens on which the posterior somite bears a simple bilobate limb bud, and the adjacent somite bears a limb with a protopod comprised of a coxapod and basipod, and with three exopodal and four endopodal segments. On each trunk limb there are 20 serially homologous groups of setae, and the numbers of setae on different limbs usually varies. These groups of setae are arranged linearly and are identified based on the morphology of the setae and their position on the segments. The number of setae in these groups increases gradually from the anterior homonomous limb to a maximum between limbs 8–12; the number then decreases sharply on the more posterior limbs. Changes in the number of setae, which reach a maximum between trunk limbs 8–12, differ from changes in segmentation which vary only over the last few posterior trunk limbs. Following a vector analysis that identified a spatial pattern for these 20 groups of setae among the different homonomous limbs, the hypothesis was confirmed that the number of setae in any given group and any given limb is correlated with the group, with the position of the somite along the body axis, and with the number of somites present on the specimens. This is the first vector analysis used to analyze a pattern of developmental changes in serially homolog…
format: application/pdf
format: text/html
creator: Viacheslav N. Ivanenko
creator: Ekaterina A. Antonenko
creator: Mikhail S. Gelfand
creator: Jill Yager
creator: Frank D. Ferrari
subject: Biodiversity
subject: Developmental Biology
subject: Evolutionary Studies
subject: Marine Biology
subject: Mathematical Biology
description: doi:10.7717/peerj.2305
publisher: PeerJ Inc.
rights: © 2016 Ivanenko et al.
abstract: This study describes the segmentation and setation at different developmental stages of the homonomous trunk limbs of the remipede Speleonectes tulumensis Yager, 1987 collected in anchialine caves of the Yucatan Peninsula. Most homonomous trunk limbs originate ventrolaterally and are composed of two protopodal segments, three exopodal segments and four endopodal segments; contralateral limb pairs are united by a sternal bar. However, the last few posterior limbs originate ventrally, are smaller sized, and have regressively fewer segments, suggesting that limb development passes through several intermediate steps beginning with a limb bud. A terminal stage of development is proposed for specimens on which the posterior somite bears a simple bilobate limb bud, and the adjacent somite bears a limb with a protopod comprised of a coxapod and basipod, and with three exopodal and four endopodal segments. On each trunk limb there are 20 serially homologous groups of setae, and the numbers of setae on different limbs usually varies. These groups of setae are arranged linearly and are identified based on the morphology of the setae and their position on the segments. The number of setae in these groups increases gradually from the anterior homonomous limb to a maximum between limbs 8–12; the number then decreases sharply on the more posterior limbs. Changes in the number of setae, which reach a maximum between trunk limbs 8–12, differ from changes in segmentation which vary only over the last few posterior trunk limbs. Following a vector analysis that identified a spatial pattern for these 20 groups of setae among the different homonomous limbs, the hypothesis was confirmed that the number of setae in any given group and any given limb is correlated with the group, with the position of the somite along the body axis, and with the number of somites present on the specimens. This is the first vector analysis used to analyze a pattern of developmental changes in serially homolog…
bibliographic citation: Ivanenko et al. (2016) Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda). PeerJ 4:e2305 https://doi.org/10.7717/peerj.2305
date submitted: 2016-06-05
date accepted: 2016-07-08
issued: 2016-08-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ivanenko
  given name: Viacheslav N.
author list: Agent
  family name: Antonenko
  given name: Ekaterina A.
author list: Agent
  family name: Gelfand
  given name: Mikhail S.
author list: Agent
  family name: Yager
  given name: Jill
author list: Agent
  family name: Ferrari
  given name: Frank D.
doi: 10.7717/peerj.2305
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-10
copyright: ©2016 Ivanenko et al.
attribution name: Ivanenko et al.

Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation
type: item
type: AcademicArticle
description: Vegemite is an iconic Australian food spread made from spent brewers’ yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers’ yeast. No fermentation occurred in any condition without addition of extra brewer’s yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers’ yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers’ yeast had been added. We estimate that the real-world cost of home brewed “Vegemite Beer” would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings.
format: application/pdf
format: text/html
creator: Edward D. Kerr
creator: Benjamin L. Schulz
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.2271
publisher: PeerJ Inc.
rights: © 2016 Kerr and Schulz
abstract: Vegemite is an iconic Australian food spread made from spent brewers’ yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers’ yeast. No fermentation occurred in any condition without addition of extra brewer’s yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers’ yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers’ yeast had been added. We estimate that the real-world cost of home brewed “Vegemite Beer” would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings.
bibliographic citation: Kerr et al. (2016) Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation. PeerJ 4:e2271 https://doi.org/10.7717/peerj.2271
date submitted: 2016-01-06
date accepted: 2016-06-29
issued: 2016-08-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerr
  given name: Edward D.
author list: Agent
  family name: Schulz
  given name: Benjamin L.
doi: 10.7717/peerj.2271
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-10
copyright: ©2016 Kerr and Schulz
attribution name: Kerr and Schulz

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