PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling
items: Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits
items: Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers
items: Potentially inappropriate use of benzodiazepines and z-drugs in the older population—analysis of associations between long-term use and patient-related factors
items: Impact of input data (in)accuracy on overestimation of visible area in digital viewshed models
items: On the efficiency of the genetic code after frameshift mutations
items: Understanding mitochondrial myopathies: a review
items: Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications
items: Intolerance of uncertainty and conditioned place preference in opioid addiction
items: Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China

Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling
type: item
type: AcademicArticle
description: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil.
format: application/pdf
format: text/html
creator: Khadeeja Rehman
creator: Tanvir Shahzad
creator: Amna Sahar
creator: Sabir Hussain
creator: Faisal Mahmood
creator: Muhammad H. Siddique
creator: Muhammad A. Siddique
creator: Muhammad I. Rashid
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.4802
publisher: PeerJ Inc.
rights: © 2018 Rehman et al.
abstract: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil.
bibliographic citation: Rehman et al. (2018) Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling. PeerJ 6:e4802 https://doi.org/10.7717/peerj.4802
date submitted: 2018-02-21
date accepted: 2018-04-30
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Khadeeja
author list: Agent
  family name: Shahzad
  given name: Tanvir
author list: Agent
  family name: Sahar
  given name: Amna
author list: Agent
  family name: Hussain
  given name: Sabir
author list: Agent
  family name: Mahmood
  given name: Faisal
author list: Agent
  family name: Siddique
  given name: Muhammad H.
author list: Agent
  family name: Siddique
  given name: Muhammad A.
author list: Agent
  family name: Rashid
  given name: Muhammad I.
doi: 10.7717/peerj.4802
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Rehman et al.
attribution name: Rehman et al.

Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits
type: item
type: AcademicArticle
description: Background Concomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models. Methods The PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test. Results The pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant …
format: application/pdf
format: text/html
creator: Raghunandan Reddy Kura
creator: Eswar Kumar Kilari
creator: Mastan Shaik
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.4798
publisher: PeerJ Inc.
rights: © 2018 Kura et al.
abstract: Background Concomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models. Methods The PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test. Results The pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant …
bibliographic citation: Kura et al. (2018) Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits. PeerJ 6:e4798 https://doi.org/10.7717/peerj.4798
date submitted: 2018-02-23
date accepted: 2018-04-30
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kura
  given name: Raghunandan Reddy
author list: Agent
  family name: Kilari
  given name: Eswar Kumar
author list: Agent
  family name: Shaik
  given name: Mastan
doi: 10.7717/peerj.4798
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Kura et al.
attribution name: Kura et al.

Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers
type: item
type: AcademicArticle
description: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp.
format: application/pdf
format: text/html
creator: María Cristina Cardonatto
creator: Ricardo Néstor Melchor
subject: Animal Behavior
subject: Paleontology
description: doi:10.7717/peerj.4787
publisher: PeerJ Inc.
rights: © 2018 Cardonatto and Melchor
abstract: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp.
bibliographic citation: Cardonatto et al. (2018) Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers. PeerJ 6:e4787 https://doi.org/10.7717/peerj.4787
date submitted: 2018-03-05
date accepted: 2018-04-27
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardonatto
  given name: María Cristina
author list: Agent
  family name: Melchor
  given name: Ricardo Néstor
doi: 10.7717/peerj.4787
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Cardonatto and Melchor
attribution name: Cardonatto and Melchor

Potentially inappropriate use of benzodiazepines and z-drugs in the older population—analysis of associations between long-term use and patient-related factors
type: item
type: AcademicArticle
description: Introduction The long-term use of benzodiazepines (BZD) and z-drugs in older populations is associated with a variety of sociodemographic and health-related factors. Recent studies reported that long-term BZD and z-drugs use is associated with increased age, female sex, and severe negative psychological (e.g., depression) and somatic (e.g., chronic disease) factors. The current study explores the sociodemographic and health-related factors associated with long-term BZD and z-drugs use in the elderly. Methods We conducted a cross-sectional survey among randomly selected patients of one health insurance plan (“AOK North-West”) with BZD and z-drugs prescriptions in the past 12 months. The sample was stratified by appropriate German prescription guidelines (yes vs. no) and age (50–65 vs. >65 years). To examine the association of selected sociodemographic and psychological variables (e.g., sex, employment status, quality of life, depression) with long-term use, a binary logistic regression analysis was conducted. Results In total, data from 340 patients were analyzed. The mean age was 72.1 (SD = 14.5) years, and the most commonly used substances were zopiclon (38.1%), oxazepam (18.1%), and lorazepam (13.8%). The mean defined daily dose (DDD) was 0.73 (SD = 0.47). Insomnia was the main reason for prescribing BZD and z-drugs. The long-term use of BZD and z-drugs was significantly associated with unemployment (OR = 2.9, 95% CI [1.2–7.1]) and generally problematic medication use (OR = 0.5, 95% CI [0.2–1.0]). Discussion Unemployment status and problematic medication use had a significant association with the patient-reported, long-term use of BZD and z-drugs. Divergent prescription patterns might suggest problematic patterns of BZD and z-drugs use. The causal connection between the identified factors and problematic BZD and z-drugs prescription is not discussed in this paper. Nevertheless, employment status and possible evidence of general problematic drug use may be a warnin…
format: application/pdf
format: text/html
creator: Aliaksandra Mokhar
creator: Niklas Tillenburg
creator: Jörg Dirmaier
creator: Silke Kuhn
creator: Martin Härter
creator: Uwe Verthein
subject: Geriatrics
subject: Pharmacology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.4614
publisher: PeerJ Inc.
rights: © 2018 Mokhar et al.
abstract: Introduction The long-term use of benzodiazepines (BZD) and z-drugs in older populations is associated with a variety of sociodemographic and health-related factors. Recent studies reported that long-term BZD and z-drugs use is associated with increased age, female sex, and severe negative psychological (e.g., depression) and somatic (e.g., chronic disease) factors. The current study explores the sociodemographic and health-related factors associated with long-term BZD and z-drugs use in the elderly. Methods We conducted a cross-sectional survey among randomly selected patients of one health insurance plan (“AOK North-West”) with BZD and z-drugs prescriptions in the past 12 months. The sample was stratified by appropriate German prescription guidelines (yes vs. no) and age (50–65 vs. >65 years). To examine the association of selected sociodemographic and psychological variables (e.g., sex, employment status, quality of life, depression) with long-term use, a binary logistic regression analysis was conducted. Results In total, data from 340 patients were analyzed. The mean age was 72.1 (SD = 14.5) years, and the most commonly used substances were zopiclon (38.1%), oxazepam (18.1%), and lorazepam (13.8%). The mean defined daily dose (DDD) was 0.73 (SD = 0.47). Insomnia was the main reason for prescribing BZD and z-drugs. The long-term use of BZD and z-drugs was significantly associated with unemployment (OR = 2.9, 95% CI [1.2–7.1]) and generally problematic medication use (OR = 0.5, 95% CI [0.2–1.0]). Discussion Unemployment status and problematic medication use had a significant association with the patient-reported, long-term use of BZD and z-drugs. Divergent prescription patterns might suggest problematic patterns of BZD and z-drugs use. The causal connection between the identified factors and problematic BZD and z-drugs prescription is not discussed in this paper. Nevertheless, employment status and possible evidence of general problematic drug use may be a warnin…
bibliographic citation: Mokhar et al. (2018) Potentially inappropriate use of benzodiazepines and z-drugs in the older population—analysis of associations between long-term use and patient-related factors. PeerJ 6:e4614 https://doi.org/10.7717/peerj.4614
date submitted: 2017-12-18
date accepted: 2018-03-23
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mokhar
  given name: Aliaksandra
author list: Agent
  family name: Tillenburg
  given name: Niklas
author list: Agent
  family name: Dirmaier
  given name: Jörg
author list: Agent
  family name: Kuhn
  given name: Silke
author list: Agent
  family name: Härter
  given name: Martin
author list: Agent
  family name: Verthein
  given name: Uwe
doi: 10.7717/peerj.4614
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Mokhar et al.
attribution name: Mokhar et al.

Impact of input data (in)accuracy on overestimation of visible area in digital viewshed models
type: item
type: AcademicArticle
description: Viewshed analysis is a GIS tool in standard use for more than two decades to perform numerous scientific and practical tasks. The reliability of the resulting viewshed model depends on the computational algorithm and the quality of the input digital surface model (DSM). Although many studies have dealt with improving viewshed algorithms, only a few studies have focused on the effect of the spatial accuracy of input data. Here, we compare simple binary viewshed models based on DSMs having varying levels of detail with viewshed models created using LiDAR DSM. The compared DSMs were calculated as the sums of digital terrain models (DTMs) and layers of forests and buildings with expertly assigned heights. Both elevation data and the visibility obstacle layers were prepared using digital vector maps differing in scale (1:5,000, 1:25,000, and 1:500,000) as well as using a combination of a LiDAR DTM with objects vectorized on an orthophotomap. All analyses were performed for 104 sample locations of 5 km2, covering areas from lowlands to mountains and including farmlands as well as afforested landscapes. We worked with two observer point heights, the first (1.8 m) simulating observation by a person standing on the ground and the second (80 m) as observation from high structures such as wind turbines, and with five estimates of forest heights (15, 20, 25, 30, and 35 m). At all height estimations, all of the vector-based DSMs used resulted in overestimations of visible areas considerably greater than those from the LiDAR DSM. In comparison to the effect from input data scale, the effect from object height estimation was shown to be secondary.
format: application/pdf
format: text/html
creator: Ondřej Lagner
creator: Tomáš Klouček
creator: Petra Šímová
subject: Ecosystem Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4835
publisher: PeerJ Inc.
rights: © 2018 Lagner et al.
abstract: Viewshed analysis is a GIS tool in standard use for more than two decades to perform numerous scientific and practical tasks. The reliability of the resulting viewshed model depends on the computational algorithm and the quality of the input digital surface model (DSM). Although many studies have dealt with improving viewshed algorithms, only a few studies have focused on the effect of the spatial accuracy of input data. Here, we compare simple binary viewshed models based on DSMs having varying levels of detail with viewshed models created using LiDAR DSM. The compared DSMs were calculated as the sums of digital terrain models (DTMs) and layers of forests and buildings with expertly assigned heights. Both elevation data and the visibility obstacle layers were prepared using digital vector maps differing in scale (1:5,000, 1:25,000, and 1:500,000) as well as using a combination of a LiDAR DTM with objects vectorized on an orthophotomap. All analyses were performed for 104 sample locations of 5 km2, covering areas from lowlands to mountains and including farmlands as well as afforested landscapes. We worked with two observer point heights, the first (1.8 m) simulating observation by a person standing on the ground and the second (80 m) as observation from high structures such as wind turbines, and with five estimates of forest heights (15, 20, 25, 30, and 35 m). At all height estimations, all of the vector-based DSMs used resulted in overestimations of visible areas considerably greater than those from the LiDAR DSM. In comparison to the effect from input data scale, the effect from object height estimation was shown to be secondary.
bibliographic citation: Lagner et al. (2018) Impact of input data (in)accuracy on overestimation of visible area in digital viewshed models. PeerJ 6:e4835 https://doi.org/10.7717/peerj.4835
date submitted: 2018-02-23
date accepted: 2018-05-03
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lagner
  given name: Ondřej
author list: Agent
  family name: Klouček
  given name: Tomáš
author list: Agent
  family name: Šímová
  given name: Petra
doi: 10.7717/peerj.4835
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Lagner et al.
attribution name: Lagner et al.

On the efficiency of the genetic code after frameshift mutations
type: item
type: AcademicArticle
description: Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
format: application/pdf
format: text/html
creator: Regine Geyer
creator: Amir Madany Mamlouk
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.4825
publisher: PeerJ Inc.
rights: © 2018 Geyer and Madany Mamlouk
abstract: Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
bibliographic citation: Geyer et al. (2018) On the efficiency of the genetic code after frameshift mutations. PeerJ 6:e4825 https://doi.org/10.7717/peerj.4825
date submitted: 2017-10-02
date accepted: 2018-05-02
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geyer
  given name: Regine
author list: Agent
  family name: Madany Mamlouk
  given name: Amir
doi: 10.7717/peerj.4825
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Geyer and Madany Mamlouk
attribution name: Geyer and Madany Mamlouk

Understanding mitochondrial myopathies: a review
type: item
type: AcademicArticle
description: Mitochondria are small, energy-producing structures vital to the energy needs of the body. Genetic mutations cause mitochondria to fail to produce the energy needed by cells and organs which can cause severe disease and death. These genetic mutations are likely to be in the mitochondrial DNA (mtDNA), or possibly in the nuclear DNA (nDNA). The goal of this review is to assess the current understanding of mitochondrial diseases. This review focuses on the pathology, causes, risk factors, symptoms, prevalence data, symptomatic treatments, and new research aimed at possible preventions and/or treatments of mitochondrial diseases. Mitochondrial myopathies are mitochondrial diseases that cause prominent muscular symptoms such as muscle weakness and usually present with a multitude of symptoms and can affect virtually all organ systems. There is no cure for these diseases as of today. Treatment is generally supportive and emphasizes symptom management. Mitochondrial diseases occur infrequently and hence research funding levels tend to be low in comparison with more common diseases. On the positive side, quite a few genetic defects responsible for mitochondrial diseases have been identified, which are in turn being used to investigate potential treatments. Speech therapy, physical therapy, and respiratory therapy have been used in mitochondrial diseases with variable results. These therapies are not curative and at best help with maintaining a patient’s current abilities to move and function.
format: application/pdf
format: text/html
creator: Abhimanyu S. Ahuja
subject: Genetics
subject: Internal Medicine
subject: Neurology
subject: Medical Genetics
description: doi:10.7717/peerj.4790
publisher: PeerJ Inc.
rights: © 2018 Ahuja
abstract: Mitochondria are small, energy-producing structures vital to the energy needs of the body. Genetic mutations cause mitochondria to fail to produce the energy needed by cells and organs which can cause severe disease and death. These genetic mutations are likely to be in the mitochondrial DNA (mtDNA), or possibly in the nuclear DNA (nDNA). The goal of this review is to assess the current understanding of mitochondrial diseases. This review focuses on the pathology, causes, risk factors, symptoms, prevalence data, symptomatic treatments, and new research aimed at possible preventions and/or treatments of mitochondrial diseases. Mitochondrial myopathies are mitochondrial diseases that cause prominent muscular symptoms such as muscle weakness and usually present with a multitude of symptoms and can affect virtually all organ systems. There is no cure for these diseases as of today. Treatment is generally supportive and emphasizes symptom management. Mitochondrial diseases occur infrequently and hence research funding levels tend to be low in comparison with more common diseases. On the positive side, quite a few genetic defects responsible for mitochondrial diseases have been identified, which are in turn being used to investigate potential treatments. Speech therapy, physical therapy, and respiratory therapy have been used in mitochondrial diseases with variable results. These therapies are not curative and at best help with maintaining a patient’s current abilities to move and function.
bibliographic citation: Ahuja (2018) Understanding mitochondrial myopathies: a review. PeerJ 6:e4790 https://doi.org/10.7717/peerj.4790
date submitted: 2018-02-14
date accepted: 2018-04-27
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahuja
  given name: Abhimanyu S.
doi: 10.7717/peerj.4790
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Ahuja
attribution name: Ahuja

Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications
type: item
type: AcademicArticle
description: Background Parasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control. Methods Using a combination of three genes (COI, 28S, and CAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset. Results The monophyly of the tribe Euphorini and the two genera Peristenus and Leiophron were confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications of Leiophron sensu lato were not supported, and the monotypic genus Mama was also not supported. Discussion Euphoriella, Euphoriana, Euphorus, and Mama syn. n, have been synonymized under Leiophron. Mama mariae syn. n was placed as a junior synonym of Leiophron reclinator. The generic concepts of Peristenus and Leiophron were refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe.
format: application/pdf
format: text/html
creator: Yuanmeng Miles Zhang
creator: Julia Stigenberg
creator: Jacqueline Hope Meyer
creator: Barbara Jo-Anne Sharanowski
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.4783
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Background Parasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control. Methods Using a combination of three genes (COI, 28S, and CAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset. Results The monophyly of the tribe Euphorini and the two genera Peristenus and Leiophron were confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications of Leiophron sensu lato were not supported, and the monotypic genus Mama was also not supported. Discussion Euphoriella, Euphoriana, Euphorus, and Mama syn. n, have been synonymized under Leiophron. Mama mariae syn. n was placed as a junior synonym of Leiophron reclinator. The generic concepts of Peristenus and Leiophron were refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe.
bibliographic citation: Zhang et al. (2018) Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications. PeerJ 6:e4783 https://doi.org/10.7717/peerj.4783
date submitted: 2018-02-22
date accepted: 2018-04-25
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yuanmeng Miles
author list: Agent
  family name: Stigenberg
  given name: Julia
author list: Agent
  family name: Meyer
  given name: Jacqueline Hope
author list: Agent
  family name: Sharanowski
  given name: Barbara Jo-Anne
doi: 10.7717/peerj.4783
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

Intolerance of uncertainty and conditioned place preference in opioid addiction
type: item
type: AcademicArticle
description: Several personality factors have been implicated in vulnerability to addiction by impacting learning and decision making. One such factor is intolerance of uncertainty (IU), the tendency to perceive uncertain situations negatively and avoid them. Conditioned place preference (CPP), which compares preference for contexts paired with reward, has been used to examine the motivation for both drug and non-drug rewards. However, preference for locations associated with non-drug reward, as well as the potential influence of IU, has not been thoroughly studied in individuals with addiction. In the current study, we examined CPP using a computer-based task in a sample of addicted individuals undergoing opioid maintenance treatment and never-addicted controls. Patients were confirmed to have higher IU than controls. In the CPP task, the two groups did not differ in overall time spent in the previously-rewarded context. However, controls were more likely than patients to immediately return to this context. Contrary to our predictions, IU was not a significant predictor of preference for the previously-rewarded context, although higher IU in controls was associated with a higher number of rewards obtained in the task. No such relationship was found in patients.
format: application/pdf
format: text/html
creator: Milen L. Radell
creator: Michael Todd Allen
creator: Belinda Favaloro
creator: Catherine E. Myers
creator: Paul Haber
creator: Kirsten Morley
creator: Ahmed A. Moustafa
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.4775
publisher: PeerJ Inc.
rights: © 2018 Radell et al.
abstract: Several personality factors have been implicated in vulnerability to addiction by impacting learning and decision making. One such factor is intolerance of uncertainty (IU), the tendency to perceive uncertain situations negatively and avoid them. Conditioned place preference (CPP), which compares preference for contexts paired with reward, has been used to examine the motivation for both drug and non-drug rewards. However, preference for locations associated with non-drug reward, as well as the potential influence of IU, has not been thoroughly studied in individuals with addiction. In the current study, we examined CPP using a computer-based task in a sample of addicted individuals undergoing opioid maintenance treatment and never-addicted controls. Patients were confirmed to have higher IU than controls. In the CPP task, the two groups did not differ in overall time spent in the previously-rewarded context. However, controls were more likely than patients to immediately return to this context. Contrary to our predictions, IU was not a significant predictor of preference for the previously-rewarded context, although higher IU in controls was associated with a higher number of rewards obtained in the task. No such relationship was found in patients.
bibliographic citation: Radell et al. (2018) Intolerance of uncertainty and conditioned place preference in opioid addiction. PeerJ 6:e4775 https://doi.org/10.7717/peerj.4775
date submitted: 2018-01-15
date accepted: 2018-04-25
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Radell
  given name: Milen L.
author list: Agent
  family name: Allen
  given name: Michael Todd
author list: Agent
  family name: Favaloro
  given name: Belinda
author list: Agent
  family name: Myers
  given name: Catherine E.
author list: Agent
  family name: Haber
  given name: Paul
author list: Agent
  family name: Morley
  given name: Kirsten
author list: Agent
  family name: Moustafa
  given name: Ahmed A.
doi: 10.7717/peerj.4775
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Radell et al.
attribution name: Radell et al.

Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China
type: item
type: AcademicArticle
description: Background Long-term fertilisation has a large influence on soil physical and chemical properties in agro-ecosystems. The effects on the distribution of aggregates, however, are not fully understood. We determined the dynamic change of the distribution of aggregates and soil organic carbon (SOC) content over time in a long-term field experiment established in 1998 on the Loess Plateau of China and illustrated the relationship between them. Methods We determined SOC content and the distribution of aggregates in nine fertiliser treatments: manure (M); nitrogen (N); phosphorus (P); M and N; M, N, and P; M and P; N and P; bare land; and an unfertilised control. These parameters were then used for a path analysis and to analyse the fractal dimension (Dv). Results The organic fertiliser increased SOC content. The proportions of 0.1–0.25 mm microaggregates and 0.25–0.5 mm macroaggregates were higher and the proportion of the 0.01–0.05 mm size class of the silt + clay fraction was lower in the treatments receiving organic fertiliser (M, MN, MNP, and MP) than that in the control, indicating that the addition of organic fertiliser promoted aggregation. The distribution of aggregates characterised by their fractal dimension (Dv), however, did not differ among the treatments. Discussion Dv was strongly correlated with the proportion of the <0.002 mm size class of the silt + clay fraction that did not differ significantly among the treatments. The change in the distribution of aggregates was strongly correlated with SOC content, which could produce organic polymer binding agents to increase the proportion of larger particles. Long-term application of organic fertiliser is thus necessary for the improvement and maintenance of soil quality in semi-arid agricultural land when residues are removed.
format: application/pdf
format: text/html
creator: Jiaoyang Zhang
creator: Caili Sun
creator: Guobin Liu
creator: Sha Xue
subject: Environmental Sciences
subject: Soil Science
description: doi:10.7717/peerj.4758
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Background Long-term fertilisation has a large influence on soil physical and chemical properties in agro-ecosystems. The effects on the distribution of aggregates, however, are not fully understood. We determined the dynamic change of the distribution of aggregates and soil organic carbon (SOC) content over time in a long-term field experiment established in 1998 on the Loess Plateau of China and illustrated the relationship between them. Methods We determined SOC content and the distribution of aggregates in nine fertiliser treatments: manure (M); nitrogen (N); phosphorus (P); M and N; M, N, and P; M and P; N and P; bare land; and an unfertilised control. These parameters were then used for a path analysis and to analyse the fractal dimension (Dv). Results The organic fertiliser increased SOC content. The proportions of 0.1–0.25 mm microaggregates and 0.25–0.5 mm macroaggregates were higher and the proportion of the 0.01–0.05 mm size class of the silt + clay fraction was lower in the treatments receiving organic fertiliser (M, MN, MNP, and MP) than that in the control, indicating that the addition of organic fertiliser promoted aggregation. The distribution of aggregates characterised by their fractal dimension (Dv), however, did not differ among the treatments. Discussion Dv was strongly correlated with the proportion of the <0.002 mm size class of the silt + clay fraction that did not differ significantly among the treatments. The change in the distribution of aggregates was strongly correlated with SOC content, which could produce organic polymer binding agents to increase the proportion of larger particles. Long-term application of organic fertiliser is thus necessary for the improvement and maintenance of soil quality in semi-arid agricultural land when residues are removed.
bibliographic citation: Zhang et al. (2018) Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China. PeerJ 6:e4758 https://doi.org/10.7717/peerj.4758
date submitted: 2017-11-12
date accepted: 2018-04-23
issued: 2018-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jiaoyang
author list: Agent
  family name: Sun
  given name: Caili
author list: Agent
  family name: Liu
  given name: Guobin
author list: Agent
  family name: Xue
  given name: Sha
doi: 10.7717/peerj.4758
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-21
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

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