title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1363
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Galantamine plasma concentration and cognitive response in Alzheimer’s disease
link: https://peerj.com/articles/6887
last-modified: 2019-05-02
description: BackgroundGalantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients.MethodsAD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response.ResultsThe total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up.ConclusionsIn the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.
creator: Yi-Ting Lin
creator: Mei-Chuan Chou
creator: Shyh-Jong Wu
creator: Yuan-Han Yang
uri: https://doi.org/10.7717/peerj.6887
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Lin et al.

title: A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast
link: https://peerj.com/articles/6892
last-modified: 2019-05-02
description: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast.
creator: Ricardo A. Scrosati
creator: Julius A. Ellrich
uri: https://doi.org/10.7717/peerj.6892
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Scrosati and Ellrich

title: The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment
link: https://peerj.com/articles/6743
last-modified: 2019-05-01
description: BackgroundThe increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues.MethodsSS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay.ResultsThe initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained unchanged, and the chlorophyll a/b ratio was slightly elevated only after the application of the highest SS and SED dose. The use of SS and SED did not significantly affect TBARS content. APx activity fell after SS or SED application; however, CAT activity tended to increase, but only in the leaves of plants grown in SS-amended soil.DiscussionThe cultivation of cucumber plants reduces PCB concentration in soil amended with SS or SED; however, this effect is more evident in the case of SS. SS application also induced more intensive changes in the activity of enzymes engaged in antioxidative response and oxidative stress markers in plant tissues than SED. The levels of PCB in the SS may have triggered a more severe imbalance between pro- and antioxidative reactions in plants. Cucumber plants appear to be resistant to the presence of toxic substances in SS and SED, and the addition of SS and SED not only acts as a fertilizer, but also protects against accelerated aging.
creator: Anna Wyrwicka
creator: Magdalena Urbaniak
creator: Mirosław Przybylski
uri: https://doi.org/10.7717/peerj.6743
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Wyrwicka et al.

title: Predicting gene expression using DNA methylation in three human populations
link: https://peerj.com/articles/6757
last-modified: 2019-05-01
description: BackgroundDNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples.ResultsWe examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect.ConclusionIn our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for gene expression across individuals with linear regression models. The prediction power potentially varies depending on tissue, cell type, and data sources. In our analyses, the combination of LASSO regression and all probes not excluding any probe on the methylation array provides the best prediction for gene expression.
creator: Huan Zhong
creator: Soyeon Kim
creator: Degui Zhi
creator: Xiangqin Cui
uri: https://doi.org/10.7717/peerj.6757
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Zhong et al.

title: Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids
link: https://peerj.com/articles/6811
last-modified: 2019-05-01
description: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous.
creator: Serjoscha W. Evers
creator: Paul M. Barrett
creator: Roger B. J. Benson
uri: https://doi.org/10.7717/peerj.6811
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Evers et al.

title: Impacts of the invasive shot hole borer (Euwallacea kuroshio) are linked to sewage pollution in southern California: the Enriched Tree Hypothesis
link: https://peerj.com/articles/6812
last-modified: 2019-05-01
description: The Kuroshio Shot Hole Borer (KSHB, Euwallacea kuroshio) and the Polyphagous Shot Hole Borer (E. whitfordiodendrus; Coleoptera: Curculionidae: Scolytinae) have recently invaded southern California and are attacking live trees in commercial agriculture groves, urban parks and native riparian forests. Among native forests the worst impacts observed to date have been in the Tijuana River Valley in south San Diego County, where approximately 30% of the native willows (Salix spp.), or 120,000 trees, have died as a result of a KSHB infestation. This paper examines wood densities, wood moisture contents, KSHB infestation rates, and KSHB-induced mortality rates in two willow species (Salixlasiolepis and S. gooddingii) at sites near and far from sewage input. Comparisons were made on two spatial scales: broadly among sites within San Diego County; and locally among sites within the Tijuana River Valley. The results showed that, on average, willow trees growing closest to sewage pollution had significantly lower wood density, higher wood moisture content, higher KSHB infestation rates, and higher KSHB-induced willow mortality rates than those growing farther away. We present the Enriched Tree Hypothesis to explain the link between sewage pollution and KSHB impacts; it is as follows: (A) Riparian trees subject to nutrient enrichment from frequent sewage pollution grow quickly, and their fast growth results in wood of low density and high moisture content. If attacked by the KSHB, the trunks and branches of these nutrient-enriched trees provide an environment conducive to the fast growth of the symbiotic fungi upon which the KSHB feeds. With an abundant food supply, the KSHB population increases rapidly and the trees are heavily damaged by thousands of KSHB galleries in their trunks and branches. (B) Riparian trees not subject to frequent sewage pollution grow more slowly and have denser, drier wood. Conditions in their trunks and branches are not conducive to the fast growth of the KSHB’s symbiotic fungi. The KSHB generally ignores, or has low abundances in, these slow-growing trees. This new hypothesis explains current patterns of KSHB impact in San Diego County and focuses attention on the important roles of the environment and preexisting conditions of trees in determining the extent of KSHB impact. It highlights the Tijuana River Valley as an unusual site due to high sewage inputs and predicts that the high KSHB-induced willow mortality seen there should not occur in other natural riparian habitats in southern California. Most importantly, by identifying sewage pollution (or nutrient enrichment) as a major risk factor for KSHB impacts, the hypothesis ratchets down the KSHB-threat level for most riparian sites in southern California and directs attention to other nutrient-enriched sites as those most at risk.
creator: John M. Boland
creator: Deborah L. Woodward
uri: https://doi.org/10.7717/peerj.6812
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Boland and Woodward

title: ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean
link: https://peerj.com/articles/6842
last-modified: 2019-05-01
description: Recently, Caribbean coasts have experienced atypical massive arrivals of pelagic Sargassum with negative consequences both ecologically and economically. Based on deep learning techniques, this study proposes a novel algorithm for floating and accumulated pelagic Sargassum detection along the coastline of Quintana Roo, Mexico. Using convolutional and recurrent neural networks architectures, a deep neural network (named ERISNet) was designed specifically to detect these macroalgae along the coastline through remote sensing support. A new dataset which includes pixel values with and without Sargassum was built to train and test ERISNet. Aqua-MODIS imagery was used to build the dataset. After the learning process, the designed algorithm achieves a 90% of probability in its classification skills. ERISNet provides a novel insight to detect accurately algal blooms arrivals.
creator: Javier Arellano-Verdejo
creator: Hugo E. Lazcano-Hernandez
creator: Nancy Cabanillas-Terán
uri: https://doi.org/10.7717/peerj.6842
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Arellano-Verdejo et al.

title: Manganese affects the growth and metabolism of Ganoderma lucidum based on LC-MS analysis
link: https://peerj.com/articles/6846
last-modified: 2019-05-01
description: BackgroundAs a metal-enriched edible fungus, Ganoderma lucidum is capable of adsorbing manganese effectively. And the manganese ion is demonstrated to play an important role in the synthesis of manganese peroxidase (Mnp) and other physiological activities during G. lucidum growth. Recently, the influence of manganese on the metabolites of G. lucidum fruiting bodies can be revealed through metabonomics technique.MethodsIn this study, we uncovered the changes between the control and 200 mg/kg Mn-treated fruiting bodies with liquid chromatography coupled to mass spectrometry (LC-MS).ResultsThe mycelial growth rate, dry yield, Mnp activity , total polysaccharide content, triterpenoid content, and total manganese content in the mature fruiting bodies of G. lucidum changed between the control and different Mn-treated groups. Based on LC-MS method, a total of 16 significantly different metabolites were obtained and identified, among which, five presented significantly down-regulated and 11 up-regulated in Mn-treated samples. The metabolites chavicol and palmitoylethanolamide were particularly significantly up-regulated, and were found the strong promotion relationship. Dependent on the MetPA database, four KEGG pathways were detected and glycerophospholipid metabolism was most impacted, in which, choline was involved in.DiscussionThe added manganese ion in the substrate enhanced Mnp activities, and consequently promoted the mycelial growth, yield , metabolites in the fruiting bodies including triterpenoids, total manganese, chavicol, etc. Our finding can provide a theoretical reference to regulation of manganese on the physiological metabolism of G. lucidum.
creator: Bo Zhang
creator: Jie Zhou
creator: Qiang Li
creator: Bingcheng Gan
creator: Weihong Peng
creator: Xiaoping Zhang
creator: Wei Tan
creator: Lin Jiang
creator: Xiaolin Li
uri: https://doi.org/10.7717/peerj.6846
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Zhang et al.

title: A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis
link: https://peerj.com/articles/6857
last-modified: 2019-05-01
description: Recent years saw a growing interest in predicting antibiotic resistance from whole-genome sequencing data, with promising results obtained for Staphylococcus aureus and Mycobacterium tuberculosis. In this work, we gathered 6,574 sequencing read datasets of M. tuberculosis public genomes with associated antibiotic resistance profiles for both first and second-line antibiotics. We performed a systematic evaluation of TBProfiler and Mykrobe, two widely recognized softwares allowing to predict resistance in M. tuberculosis. The size of the dataset allowed us to obtain confident estimations of their overall predictive performance, to assess precisely the individual predictive power of the markers they rely on, and to study in addition how these softwares behave across the major M. tuberculosis lineages. While this study confirmed the overall good performance of these tools, it revealed that an important fraction of the catalog of mutations they embed is of limited predictive power. It also revealed that these tools offer different sensitivity/specificity trade-offs, which is mainly due to the different sets of mutation they embed but also to their underlying genotyping pipelines. More importantly, it showed that their level of predictive performance varies greatly across lineages for some antibiotics, therefore suggesting that the predictions made by these softwares should be deemed more or less confident depending on the lineage inferred and the predictive performance of the marker(s) actually detected. Finally, we evaluated the relevance of machine learning approaches operating from the set of markers detected by these softwares and show that they present an attractive alternative strategy, allowing to reach better performance for several drugs while significantly reducing the number of candidate mutations to consider.
creator: Pierre Mahé
creator: Meriem El Azami
creator: Philippine Barlas
creator: Maud Tournoud
uri: https://doi.org/10.7717/peerj.6857
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Mahé et al.

title: A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling
link: https://peerj.com/articles/6863
last-modified: 2019-05-01
description: The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability.Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases.This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.
creator: Małgorzata Dudkiewicz
creator: Krzysztof Pawłowski
uri: https://doi.org/10.7717/peerj.6863
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Dudkiewicz and Pawłowski