PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Distinctive facial features in idiopathic Moyamoya disease in Caucasians: a first systematic analysis
items: Huperzine A attenuates nonalcoholic fatty liver disease by regulating hepatocyte senescence and apoptosis: an in vitro study
items: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data
items: Single-nucleotide polymorphisms of uracil-processing genes affect the occurrence and the onset of recurrent depressive disorder
items: Association of Crohn’s disease-related chromosome 1q32 with ankylosing spondylitis is independent of bowel symptoms and faecal calprotectin
items: Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia)
items: Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease
items: A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan
items: Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification
items: Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015

Distinctive facial features in idiopathic Moyamoya disease in Caucasians: a first systematic analysis
type: item
type: AcademicArticle
description: Background Craniofacial dysmorphic features are morphological changes of the face and skull which are associated with syndromic conditions. Moyamoya angiopathy is a rare cerebral vasculopathy that can be divided into Moyamoya syndrome, which is associated or secondary to other diseases, and into idiopathic Moyamoya disease. Facial dysmorphism has been described in rare genetic syndromes with associated Moyamoya syndrome. However, a direct relationship between idiopathic Moyamoya disease with dysmorphic facial changes is not known yet. Methods Landmarks were manually placed on frontal photographs of the face of 45 patients with bilateral Moyamoya disease and 50 matched controls. After procrustes alignment of landmarks a multivariate, penalized logistic regression (elastic-net) was performed on geometric features derived from landmark data to classify patients against controls. Classifiers were visualized in importance plots that colorcode importance of geometric locations for the classification decision. Results The classification accuracy for discriminating the total patient group from controls was 82.3% (P-value = 6.3×10−11, binomial test, a-priori chance 50.2%) for an elastic-net classifier. Importance plots show that differences around the eyes and forehead were responsible for the discrimination. Subgroup analysis corrected for body mass index confirmed a similar result. Discussion Results suggest that there is a resemblance in faces of Caucasian patients with idiopathic Moyamoya disease and that there is a difference to matched controls. Replication of findings is necessary as it is difficult to control all residual confounding in study designs such as ours. If our results would be replicated in a larger cohort, this would be helpful for pathophysiological interpretation and early detection of the disease.
format: application/pdf
format: text/html
creator: Markus Kraemer
creator: Quoc Bao Huynh
creator: Dagmar Wieczorek
creator: Brunilda Balliu
creator: Barbara Mikat
creator: Stefan Boehringer
subject: Genetics
subject: Neurology
description: doi:10.7717/peerj.4740
publisher: PeerJ Inc.
rights: © 2018 Kraemer et al.
abstract: Background Craniofacial dysmorphic features are morphological changes of the face and skull which are associated with syndromic conditions. Moyamoya angiopathy is a rare cerebral vasculopathy that can be divided into Moyamoya syndrome, which is associated or secondary to other diseases, and into idiopathic Moyamoya disease. Facial dysmorphism has been described in rare genetic syndromes with associated Moyamoya syndrome. However, a direct relationship between idiopathic Moyamoya disease with dysmorphic facial changes is not known yet. Methods Landmarks were manually placed on frontal photographs of the face of 45 patients with bilateral Moyamoya disease and 50 matched controls. After procrustes alignment of landmarks a multivariate, penalized logistic regression (elastic-net) was performed on geometric features derived from landmark data to classify patients against controls. Classifiers were visualized in importance plots that colorcode importance of geometric locations for the classification decision. Results The classification accuracy for discriminating the total patient group from controls was 82.3% (P-value = 6.3×10−11, binomial test, a-priori chance 50.2%) for an elastic-net classifier. Importance plots show that differences around the eyes and forehead were responsible for the discrimination. Subgroup analysis corrected for body mass index confirmed a similar result. Discussion Results suggest that there is a resemblance in faces of Caucasian patients with idiopathic Moyamoya disease and that there is a difference to matched controls. Replication of findings is necessary as it is difficult to control all residual confounding in study designs such as ours. If our results would be replicated in a larger cohort, this would be helpful for pathophysiological interpretation and early detection of the disease.
bibliographic citation: Kraemer et al. (2018) Distinctive facial features in idiopathic Moyamoya disease in Caucasians: a first systematic analysis. PeerJ 6:e4740 https://doi.org/10.7717/peerj.4740
date submitted: 2017-05-15
date accepted: 2018-04-19
issued: 2018-06-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraemer
  given name: Markus
author list: Agent
  family name: Huynh
  given name: Quoc Bao
author list: Agent
  family name: Wieczorek
  given name: Dagmar
author list: Agent
  family name: Balliu
  given name: Brunilda
author list: Agent
  family name: Mikat
  given name: Barbara
author list: Agent
  family name: Boehringer
  given name: Stefan
doi: 10.7717/peerj.4740
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-27
copyright: ©2018 Kraemer et al.
attribution name: Kraemer et al.

Huperzine A attenuates nonalcoholic fatty liver disease by regulating hepatocyte senescence and apoptosis: an in vitro study
type: item
type: AcademicArticle
description: Objective This study was undertaken to detect if free fatty acids (FFA) induce hepatocyte senescence in L-02 cells and if huperzine A has an anti-aging effect in fatty liver cells. Methods L-02 cells were treated with a FFA mixture (oleate/palmitate, at 3:0, 2:1, 1:1, 1:2 and 0:3 ratios) at different concentrations. Cell viability and fat accumulation rate were assessed by a Cell Counting Kit 8 and Nile Red staining, respectively. The mixture with the highest cell viability and fat accumulation rate was selected to continue with the following experiment. The L-02 cells were divided into five groups, including the control group, FFA group, FFA + 0.1 μmol/L huperzine A (LH) group, FFA + 1.0 μmol/L huperzine A (MH) group and FFA + 10 μmol/L huperzine A (HH) group, and were cultured for 24 h. The expression of senescence-associated β-galactosidase (SA-β-gal) was detected by an SA-β-gal staining kit. The expression levels of aging genes were measured by qRT-PCR. The expression levels of apoptosis proteins were detected by a Western blot. ELISA kits were used to detect inflammatory factors and oxidative stress products. The expression of nuclear factor (NF-κB) and IκBα were detected by immunofluorescence. Results The FFA mixture (oleate/palmitate, at a 2:1 ratio) of 0.5 mmol/L had the highest cell viability and fat accumulation rate, which was preferable for establishing an in vitro fatty liver model. The expression of inflammatory factors (TNF-α and IL-6) and oxidants Malonaldehyde (MDA), 4-hydroxynonenal (HNE) and reactive oxygen species (ROS) also increased in the L-02 fatty liver cells. The expression levels of aging markers and aging genes, such as SA-β-gal, p16, p21, p53 and pRb, increased more in the L-02 fatty liver cells than in the L-02 cells. The total levels of the apoptosis-associated proteins Bcl2, Bax, Bax/Bcl-2, CyCt and cleaved caspase 9 were also upregulated in the L-02 fatty liver cells. All of the above genes and proteins were downregulated in the hupe…
format: application/pdf
format: text/html
creator: Xiao-na Hu
creator: Jiao-feng Wang
creator: Yi-qin Huang
creator: Zheng Wang
creator: Fang-yuan Dong
creator: Hai-fen Ma
creator: Zhi-jun Bao
subject: Gastroenterology and Hepatology
subject: Pharmacology
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.5145
publisher: PeerJ Inc.
rights: © 2018 Hu et al.
abstract: Objective This study was undertaken to detect if free fatty acids (FFA) induce hepatocyte senescence in L-02 cells and if huperzine A has an anti-aging effect in fatty liver cells. Methods L-02 cells were treated with a FFA mixture (oleate/palmitate, at 3:0, 2:1, 1:1, 1:2 and 0:3 ratios) at different concentrations. Cell viability and fat accumulation rate were assessed by a Cell Counting Kit 8 and Nile Red staining, respectively. The mixture with the highest cell viability and fat accumulation rate was selected to continue with the following experiment. The L-02 cells were divided into five groups, including the control group, FFA group, FFA + 0.1 μmol/L huperzine A (LH) group, FFA + 1.0 μmol/L huperzine A (MH) group and FFA + 10 μmol/L huperzine A (HH) group, and were cultured for 24 h. The expression of senescence-associated β-galactosidase (SA-β-gal) was detected by an SA-β-gal staining kit. The expression levels of aging genes were measured by qRT-PCR. The expression levels of apoptosis proteins were detected by a Western blot. ELISA kits were used to detect inflammatory factors and oxidative stress products. The expression of nuclear factor (NF-κB) and IκBα were detected by immunofluorescence. Results The FFA mixture (oleate/palmitate, at a 2:1 ratio) of 0.5 mmol/L had the highest cell viability and fat accumulation rate, which was preferable for establishing an in vitro fatty liver model. The expression of inflammatory factors (TNF-α and IL-6) and oxidants Malonaldehyde (MDA), 4-hydroxynonenal (HNE) and reactive oxygen species (ROS) also increased in the L-02 fatty liver cells. The expression levels of aging markers and aging genes, such as SA-β-gal, p16, p21, p53 and pRb, increased more in the L-02 fatty liver cells than in the L-02 cells. The total levels of the apoptosis-associated proteins Bcl2, Bax, Bax/Bcl-2, CyCt and cleaved caspase 9 were also upregulated in the L-02 fatty liver cells. All of the above genes and proteins were downregulated in the hupe…
bibliographic citation: Hu et al. (2018) Huperzine A attenuates nonalcoholic fatty liver disease by regulating hepatocyte senescence and apoptosis: an in vitro study. PeerJ 6:e5145 https://doi.org/10.7717/peerj.5145
date submitted: 2017-12-29
date accepted: 2018-06-11
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Xiao-na
author list: Agent
  family name: Wang
  given name: Jiao-feng
author list: Agent
  family name: Huang
  given name: Yi-qin
author list: Agent
  family name: Wang
  given name: Zheng
author list: Agent
  family name: Dong
  given name: Fang-yuan
author list: Agent
  family name: Ma
  given name: Hai-fen
author list: Agent
  family name: Bao
  given name: Zhi-jun
doi: 10.7717/peerj.5145
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: © 2018 Hu et al.
attribution name: Hu et al.

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data
type: item
type: AcademicArticle
description: Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcodi…
format: application/pdf
format: text/html
creator: Rodney T. Richardson
creator: Johan Bengtsson-Palme
creator: Mary M. Gardiner
creator: Reed M. Johnson
subject: Bioinformatics
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.5126
publisher: PeerJ Inc.
rights: © 2018 Richardson et al.
abstract: Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcodi…
bibliographic citation: Richardson et al. (2018) A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data. PeerJ 6:e5126 https://doi.org/10.7717/peerj.5126
date submitted: 2018-03-16
date accepted: 2018-06-07
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Richardson
  given name: Rodney T.
author list: Agent
  family name: Bengtsson-Palme
  given name: Johan
author list: Agent
  family name: Gardiner
  given name: Mary M.
author list: Agent
  family name: Johnson
  given name: Reed M.
doi: 10.7717/peerj.5126
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Richardson et al.
attribution name: Richardson et al.

Single-nucleotide polymorphisms of uracil-processing genes affect the occurrence and the onset of recurrent depressive disorder
type: item
type: AcademicArticle
description: Depressive disorders (DD) are known to be associated with increased DNA damage, the impairment of DNA damage repair, and the presence of single-nucleotide polymorphisms (SNPs) in DNA damage repair genes. Some indirect evidence also suggests that uracil metabolism may be disrupted in depressed patients. Therefore, the current study genotypes three SNPs localized in genes encoding uracil-processing proteins: two glycosylases, i.e., UNG g.7245G>C (rs34259), SMUG1 c.-31A>G (rs3087404), and dUTPase, i.e., DUT g.48638795G>T (rs4775748). The polymorphisms were analyzed in 585 DNA samples (282 cases and 303 controls) using TaqMan probes. The G/G genotype and G allele of UNG polymorphism decreased the risk of depression, while the G/C genotype and C allele of the same SNP increased it. It was also found that G/G carriers had their first episode significantly later than the heterozygotes. Although there was no association between the occurrence of depression and the SMUG1 SNP, a significant difference was found between the homozygotes regarding the onset of DD. In conclusion, the SNPs localized in the uracil-processing genes may modulate the occurrence and the onset of depression, which further supports the hypothesis that impairment of DNA damage repair, especially base-excision repair, may play an important role in the pathogenesis of the disease.
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format: text/html
creator: Piotr Czarny
creator: Paulina Wigner
creator: Justyna Strycharz
creator: Cezary Watala
creator: Ewa Swiderska
creator: Ewelina Synowiec
creator: Piotr Galecki
creator: Monika Talarowska
creator: Janusz Szemraj
creator: Kuan-Pin Su
creator: Tomasz Sliwinski
subject: Genetics
subject: Cognitive Disorders
subject: Pharmacology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5116
publisher: PeerJ Inc.
rights: © 2018 Czarny et al.
abstract: Depressive disorders (DD) are known to be associated with increased DNA damage, the impairment of DNA damage repair, and the presence of single-nucleotide polymorphisms (SNPs) in DNA damage repair genes. Some indirect evidence also suggests that uracil metabolism may be disrupted in depressed patients. Therefore, the current study genotypes three SNPs localized in genes encoding uracil-processing proteins: two glycosylases, i.e., UNG g.7245G>C (rs34259), SMUG1 c.-31A>G (rs3087404), and dUTPase, i.e., DUT g.48638795G>T (rs4775748). The polymorphisms were analyzed in 585 DNA samples (282 cases and 303 controls) using TaqMan probes. The G/G genotype and G allele of UNG polymorphism decreased the risk of depression, while the G/C genotype and C allele of the same SNP increased it. It was also found that G/G carriers had their first episode significantly later than the heterozygotes. Although there was no association between the occurrence of depression and the SMUG1 SNP, a significant difference was found between the homozygotes regarding the onset of DD. In conclusion, the SNPs localized in the uracil-processing genes may modulate the occurrence and the onset of depression, which further supports the hypothesis that impairment of DNA damage repair, especially base-excision repair, may play an important role in the pathogenesis of the disease.
bibliographic citation: Czarny et al. (2018) Single-nucleotide polymorphisms of uracil-processing genes affect the occurrence and the onset of recurrent depressive disorder. PeerJ 6:e5116 https://doi.org/10.7717/peerj.5116
date submitted: 2018-03-09
date accepted: 2018-06-07
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Czarny
  given name: Piotr
author list: Agent
  family name: Wigner
  given name: Paulina
author list: Agent
  family name: Strycharz
  given name: Justyna
author list: Agent
  family name: Watala
  given name: Cezary
author list: Agent
  family name: Swiderska
  given name: Ewa
author list: Agent
  family name: Synowiec
  given name: Ewelina
author list: Agent
  family name: Galecki
  given name: Piotr
author list: Agent
  family name: Talarowska
  given name: Monika
author list: Agent
  family name: Szemraj
  given name: Janusz
author list: Agent
  family name: Su
  given name: Kuan-Pin
author list: Agent
  family name: Sliwinski
  given name: Tomasz
doi: 10.7717/peerj.5116
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Czarny et al.
attribution name: Czarny et al.

Association of Crohn’s disease-related chromosome 1q32 with ankylosing spondylitis is independent of bowel symptoms and faecal calprotectin
type: item
type: AcademicArticle
description: Background Genome-wide association studies have identified a plethora of risk genes for both Crohn’s disease (CD) and ankylosing spondylitis (AS). A subset of genes found to be risk factors for CD have also been found to be risk factors for AS. The objective of our study was to assess whether CD risk genes were associated with non-invasive clinical markers of gut inflammation in patients with AS, indicating a potential subset of patients with clinical as well as genetic overlap. Methods A total of 308 Caucasian patients who fulfilled the modified New York Criteria for AS, were assessed for bowel symptoms using the Dudley Inflammatory Bowel Symptom Questionnaire (DISQ). Of these patients, 157 also had faecal calprotectin measured. All AS patients and 568 healthy controls were genotyped for 10 CD risk loci using predesigned single nucleotide polymorphism (SNP) genotyping assays. Chi-square analysis was used to test for association between genotype and DISQ score and faecal calprotectin level. Results The minor allele of two SNPs, one in chromosome region 1q32 SNP (rs11584383), and one in the gene coding for IL23R (rs11209026) conferred protection against AS. Only the association of 1q32 remained significant after Bonferroni correction for multiple testing. Stratification by DISQ score and faecal calprotectin did not influence the association of 1q32 with AS. Conclusion In patients with AS, the association of the CD 1q32 SNP was independent of non-invasive markers of bowel inflammation. Other CD related SNPs were not found have a significant association with AS.
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format: text/html
creator: Rebecca L. Roberts
creator: Mary C. Wallace
creator: Andrew A. Harrison
creator: Douglas White
creator: Nicola Dalbeth
creator: Lisa K. Stamp
creator: Daniel Ching
creator: John Highton
creator: Tony R. Merriman
creator: Philip C. Robinson
creator: Matthew A. Brown
creator: Simon M. Stebbings
subject: Genetics
subject: Rheumatology
description: doi:10.7717/peerj.5088
publisher: PeerJ Inc.
rights: © 2018 Roberts et al.
abstract: Background Genome-wide association studies have identified a plethora of risk genes for both Crohn’s disease (CD) and ankylosing spondylitis (AS). A subset of genes found to be risk factors for CD have also been found to be risk factors for AS. The objective of our study was to assess whether CD risk genes were associated with non-invasive clinical markers of gut inflammation in patients with AS, indicating a potential subset of patients with clinical as well as genetic overlap. Methods A total of 308 Caucasian patients who fulfilled the modified New York Criteria for AS, were assessed for bowel symptoms using the Dudley Inflammatory Bowel Symptom Questionnaire (DISQ). Of these patients, 157 also had faecal calprotectin measured. All AS patients and 568 healthy controls were genotyped for 10 CD risk loci using predesigned single nucleotide polymorphism (SNP) genotyping assays. Chi-square analysis was used to test for association between genotype and DISQ score and faecal calprotectin level. Results The minor allele of two SNPs, one in chromosome region 1q32 SNP (rs11584383), and one in the gene coding for IL23R (rs11209026) conferred protection against AS. Only the association of 1q32 remained significant after Bonferroni correction for multiple testing. Stratification by DISQ score and faecal calprotectin did not influence the association of 1q32 with AS. Conclusion In patients with AS, the association of the CD 1q32 SNP was independent of non-invasive markers of bowel inflammation. Other CD related SNPs were not found have a significant association with AS.
bibliographic citation: Roberts et al. (2018) Association of Crohn’s disease-related chromosome 1q32 with ankylosing spondylitis is independent of bowel symptoms and faecal calprotectin. PeerJ 6:e5088 https://doi.org/10.7717/peerj.5088
date submitted: 2017-08-21
date accepted: 2018-06-05
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roberts
  given name: Rebecca L.
author list: Agent
  family name: Wallace
  given name: Mary C.
author list: Agent
  family name: Harrison
  given name: Andrew A.
author list: Agent
  family name: White
  given name: Douglas
author list: Agent
  family name: Dalbeth
  given name: Nicola
author list: Agent
  family name: Stamp
  given name: Lisa K.
author list: Agent
  family name: Ching
  given name: Daniel
author list: Agent
  family name: Highton
  given name: John
author list: Agent
  family name: Merriman
  given name: Tony R.
author list: Agent
  family name: Robinson
  given name: Philip C.
author list: Agent
  family name: Brown
  given name: Matthew A.
author list: Agent
  family name: Stebbings
  given name: Simon M.
doi: 10.7717/peerj.5088
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: © 2018 Roberts et al.
attribution name: Roberts et al.

Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia)
type: item
type: AcademicArticle
description: The planktonic metabolic balance that is the balance between gross primary production (GPP) and community respiration (CR) was determined in Matilda Bay (estuarine) and Woodman Point (coastal) in Perth, Western Australia. The rates of net community production (NCP = GPP – CR) and the ratio between GPP and CR (P/R) were assessed to evaluate whether the metabolic balance in the two coastal locations tends to be net autotrophic (production exceeding community respiration) or net heterotrophic (respiration exceeding production). We also analyzed environmental variability by measuring temperature, salinity, and nutrients and chlorophyll a concentration. Samples were collected biweekly from March 2014 to March 2015. During the study period the metabolic rates were three times higher in Matilda Bay than in Woodman Point. The predominant metabolism was net autotrophic at both sites with P/R ratios >1 in the majority of the sampling dates. In Matilda Bay, the metabolic rates were negatively correlated with salinity denoting river dynamics influence, and positively with chlorophyll a. In Woodman Point only the GPP was positively correlated with chlorophyll a. The positive correlation between P/R ratio and GPP in Matilda Bay and the positive correlations between the metabolic rates and chlorophyll a suggest that factors controlling autotrophic processes are modulating the planktonic metabolic balance in the coastal marine ecosystem in Perth. Significant correlations were found between CR and GPP-standardized to chlorophyll a and water temperature. The net autotrophic metabolic balance indicates that in both ecosystems planktonic communities are acting as a sink of CO2 and as a source of organic matter and oxygen to the system and are able to export organic matter to other ecosystems.
format: application/pdf
format: text/html
creator: Susana Agusti
creator: Lorena Vigoya
creator: Carlos Manuel Duarte
subject: Ecology
subject: Marine Biology
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.5081
publisher: PeerJ Inc.
rights: © 2018 Agusti et al.
abstract: The planktonic metabolic balance that is the balance between gross primary production (GPP) and community respiration (CR) was determined in Matilda Bay (estuarine) and Woodman Point (coastal) in Perth, Western Australia. The rates of net community production (NCP = GPP – CR) and the ratio between GPP and CR (P/R) were assessed to evaluate whether the metabolic balance in the two coastal locations tends to be net autotrophic (production exceeding community respiration) or net heterotrophic (respiration exceeding production). We also analyzed environmental variability by measuring temperature, salinity, and nutrients and chlorophyll a concentration. Samples were collected biweekly from March 2014 to March 2015. During the study period the metabolic rates were three times higher in Matilda Bay than in Woodman Point. The predominant metabolism was net autotrophic at both sites with P/R ratios >1 in the majority of the sampling dates. In Matilda Bay, the metabolic rates were negatively correlated with salinity denoting river dynamics influence, and positively with chlorophyll a. In Woodman Point only the GPP was positively correlated with chlorophyll a. The positive correlation between P/R ratio and GPP in Matilda Bay and the positive correlations between the metabolic rates and chlorophyll a suggest that factors controlling autotrophic processes are modulating the planktonic metabolic balance in the coastal marine ecosystem in Perth. Significant correlations were found between CR and GPP-standardized to chlorophyll a and water temperature. The net autotrophic metabolic balance indicates that in both ecosystems planktonic communities are acting as a sink of CO2 and as a source of organic matter and oxygen to the system and are able to export organic matter to other ecosystems.
bibliographic citation: Agusti et al. (2018) Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia). PeerJ 6:e5081 https://doi.org/10.7717/peerj.5081
date submitted: 2018-02-19
date accepted: 2018-06-04
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Agusti
  given name: Susana
author list: Agent
  family name: Vigoya
  given name: Lorena
author list: Agent
  family name: Duarte
  given name: Carlos Manuel
doi: 10.7717/peerj.5081
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Agusti et al.
attribution name: Agusti et al.

Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease
type: item
type: AcademicArticle
description: The present study comprises the synthesis of a new series of sulfonamides derived from 4-methoxyphenethylamine (1). The synthesis was initiated by the reaction of 1 with 4-methylbenzenesulfonyl chloride (2) in aqueous sodium carbonate solution at pH 9 to yield N-(4-methoxyphenethyl)-4-methylbenzensulfonamide (3).This parent molecule 3 was subsequently treated with various alkyl/aralkyl halides, (4a–j), using N,N-dimethylformamide (DMF) as solvent and LiH as activator to produce a series of new N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides (5a–j). The structural characterization of these derivatives was carried out by spectroscopic techniques like IR, 1H-NMR, and 13C-NMR. The elemental analysis data was also coherent with spectral data of these molecules. The inhibitory effects on acetylcholinesterase and DPPH were evaluated and it was observed that N-(4-Methoxyphenethyl)-4-methyl-N-(2-propyl)benzensulfonamide (5c) showed acetylcholinesterase inhibitory activity 0.075 ± 0.001 (IC50 0.075 ± 0.001 µM) comparable to Neostigmine methylsulfate (IC50 2.038 ± 0.039 µM).The docking studies of synthesized ligands 5a–j were also carried out against acetylcholinesterase (PDBID 4PQE) to compare the binding affinities with IC50 values. The kinetic mechanism analyzed by Lineweaver-Burk plots demonstrated that compound (5c) inhibits the acetylcholinesterase competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (5c) is 2.5 µM. It was also found from kinetic analysis that derivative 5c irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound 5c may serve as lead structure for the design of more potent acetylcholinesterase inhibitors.
format: application/pdf
format: text/html
creator: Muhammad Athar Abbasi
creator: Mubashir Hassan
creator: Aziz-ur-Rehman
creator: Sabahat Zahra Siddiqui
creator: Syed Adnan Ali Shah
creator: Hussain Raza
creator: Sung Yum Seo
subject: Bioinformatics
subject: Neuroscience
subject: Cognitive Disorders
subject: Drugs and Devices
description: doi:10.7717/peerj.4962
publisher: PeerJ Inc.
rights: © 2018 Abbasi et al.
abstract: The present study comprises the synthesis of a new series of sulfonamides derived from 4-methoxyphenethylamine (1). The synthesis was initiated by the reaction of 1 with 4-methylbenzenesulfonyl chloride (2) in aqueous sodium carbonate solution at pH 9 to yield N-(4-methoxyphenethyl)-4-methylbenzensulfonamide (3).This parent molecule 3 was subsequently treated with various alkyl/aralkyl halides, (4a–j), using N,N-dimethylformamide (DMF) as solvent and LiH as activator to produce a series of new N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides (5a–j). The structural characterization of these derivatives was carried out by spectroscopic techniques like IR, 1H-NMR, and 13C-NMR. The elemental analysis data was also coherent with spectral data of these molecules. The inhibitory effects on acetylcholinesterase and DPPH were evaluated and it was observed that N-(4-Methoxyphenethyl)-4-methyl-N-(2-propyl)benzensulfonamide (5c) showed acetylcholinesterase inhibitory activity 0.075 ± 0.001 (IC50 0.075 ± 0.001 µM) comparable to Neostigmine methylsulfate (IC50 2.038 ± 0.039 µM).The docking studies of synthesized ligands 5a–j were also carried out against acetylcholinesterase (PDBID 4PQE) to compare the binding affinities with IC50 values. The kinetic mechanism analyzed by Lineweaver-Burk plots demonstrated that compound (5c) inhibits the acetylcholinesterase competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (5c) is 2.5 µM. It was also found from kinetic analysis that derivative 5c irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound 5c may serve as lead structure for the design of more potent acetylcholinesterase inhibitors.
bibliographic citation: Abbasi et al. (2018) Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease. PeerJ 6:e4962 https://doi.org/10.7717/peerj.4962
date submitted: 2018-02-14
date accepted: 2018-05-20
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abbasi
  given name: Muhammad Athar
author list: Agent
  family name: Hassan
  given name: Mubashir
author list: Agent
  family name: Aziz-ur-Rehman
author list: Agent
  family name: Siddiqui
  given name: Sabahat Zahra
author list: Agent
  family name: Shah
  given name: Syed Adnan Ali
author list: Agent
  family name: Raza
  given name: Hussain
author list: Agent
  family name: Seo
  given name: Sung Yum
doi: 10.7717/peerj.4962
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Abbasi et al.
attribution name: Abbasi et al.

A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan
type: item
type: AcademicArticle
description: A fossil whale from the Hikatagawa Formation (Middle Miocene, 15.2–11.5 Ma) of Hokkaido, Japan is described as a new genus and species Taikicetus inouei and its phylogenetic position is examined. Consistent with the result of Marx, Lambert & de Muizon (2017), the Cetotheriidae form a clade with the Balaenopteroidea, and “a clade comprising Isanacetus, Parietobalaena and related taxa” is located basal to the Balaenopteroidea + Cetotheriidae clade. Taikicetus inouei is placed in the clade with most of members of “Cetotheres” sensu lato comprising Isanacetus, Parietobalaena and related taxa. Taikicetus inouei can be distinguished from the other members of “Cetotheres” sensu lato in having an anteriorly swollen short zygomatic process, high triangular coronoid process, and angular process, which does not reach as far posterior as the mandibular condyle. Taikicetus inouei is only record of “Cetotheres” sensu lato from Hokkaido, Japan and the northern-most records of “Cetotheres” sensu lato in Japan.
format: application/pdf
format: text/html
creator: Yoshihiro Tanaka
creator: Tatsuro Ando
creator: Hiroshi Sawamura
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.4934
publisher: PeerJ Inc.
rights: © 2018 Tanaka et al.
abstract: A fossil whale from the Hikatagawa Formation (Middle Miocene, 15.2–11.5 Ma) of Hokkaido, Japan is described as a new genus and species Taikicetus inouei and its phylogenetic position is examined. Consistent with the result of Marx, Lambert & de Muizon (2017), the Cetotheriidae form a clade with the Balaenopteroidea, and “a clade comprising Isanacetus, Parietobalaena and related taxa” is located basal to the Balaenopteroidea + Cetotheriidae clade. Taikicetus inouei is placed in the clade with most of members of “Cetotheres” sensu lato comprising Isanacetus, Parietobalaena and related taxa. Taikicetus inouei can be distinguished from the other members of “Cetotheres” sensu lato in having an anteriorly swollen short zygomatic process, high triangular coronoid process, and angular process, which does not reach as far posterior as the mandibular condyle. Taikicetus inouei is only record of “Cetotheres” sensu lato from Hokkaido, Japan and the northern-most records of “Cetotheres” sensu lato in Japan.
bibliographic citation: Tanaka et al. (2018) A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan. PeerJ 6:e4934 https://doi.org/10.7717/peerj.4934
date submitted: 2018-02-27
date accepted: 2018-05-18
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanaka
  given name: Yoshihiro
author list: Agent
  family name: Ando
  given name: Tatsuro
author list: Agent
  family name: Sawamura
  given name: Hiroshi
doi: 10.7717/peerj.4934
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: © 2018 Tanaka et al.
attribution name: Tanaka et al.

Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification
type: item
type: AcademicArticle
description: Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.
format: application/pdf
format: text/html
creator: Sandra Smieszek
creator: Sabrina L. Mitchell
creator: Eric H. Farber-Eger
creator: Olivia J. Veatch
creator: Nicholas R. Wheeler
creator: Robert J. Goodloe
creator: Quinn S. Wells
creator: Deborah G. Murdock
creator: Dana C. Crawford
subject: Bioinformatics
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.5149
publisher: PeerJ Inc.
rights: © 2018 Smieszek et al.
abstract: Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.
bibliographic citation: Smieszek et al. (2018) Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification. PeerJ 6:e5149 https://doi.org/10.7717/peerj.5149
date submitted: 2017-11-20
date accepted: 2018-06-12
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smieszek
  given name: Sandra
author list: Agent
  family name: Mitchell
  given name: Sabrina L.
author list: Agent
  family name: Farber-Eger
  given name: Eric H.
author list: Agent
  family name: Veatch
  given name: Olivia J.
author list: Agent
  family name: Wheeler
  given name: Nicholas R.
author list: Agent
  family name: Goodloe
  given name: Robert J.
author list: Agent
  family name: Wells
  given name: Quinn S.
author list: Agent
  family name: Murdock
  given name: Deborah G.
author list: Agent
  family name: Crawford
  given name: Dana C.
doi: 10.7717/peerj.5149
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Smieszek et al.
attribution name: Smieszek et al.

Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015
type: item
type: AcademicArticle
description: Background Influenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data. Methods The official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error. Results In total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data. Conclusions The results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM r…
format: application/pdf
format: text/html
creator: Feng Liang
creator: Peng Guan
creator: Wei Wu
creator: Desheng Huang
subject: Health Policy
subject: Infectious Diseases
description: doi:10.7717/peerj.5134
publisher: PeerJ Inc.
rights: © 2018 Liang et al.
abstract: Background Influenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data. Methods The official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error. Results In total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data. Conclusions The results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM r…
bibliographic citation: Liang et al. (2018) Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015. PeerJ 6:e5134 https://doi.org/10.7717/peerj.5134
date submitted: 2018-04-05
date accepted: 2018-06-08
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Feng
author list: Agent
  family name: Guan
  given name: Peng
author list: Agent
  family name: Wu
  given name: Wei
author list: Agent
  family name: Huang
  given name: Desheng
doi: 10.7717/peerj.5134
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Liang et al.
attribution name: Liang et al.

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