title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1622
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: A new ICA-based fingerprint method for the automatic removal of physiological artifacts from EEG recordings
link: https://peerj.com/articles/4380
last-modified: 2018-02-23
description: BackgroundEEG may be affected by artefacts hindering the analysis of brain signals. Data-driven methods like independent component analysis (ICA) are successful approaches to remove artefacts from the EEG. However, the ICA-based methods developed so far are often affected by limitations, such as: the need for visual inspection of the separated independent components (subjectivity problem) and, in some cases, for the independent and simultaneous recording of the inspected artefacts to identify the artefactual independent components; a potentially heavy manipulation of the EEG signals; the use of linear classification methods; the use of simulated artefacts to validate the methods; no testing in dry electrode or high-density EEG datasets; applications limited to specific conditions and electrode layouts.MethodsOur fingerprint method automatically identifies EEG ICs containing eyeblinks, eye movements, myogenic artefacts and cardiac interference by evaluating 14 temporal, spatial, spectral, and statistical features composing the IC fingerprint. Sixty-two real EEG datasets containing cued artefacts are recorded with wet and dry electrodes (128 wet and 97 dry channels). For each artefact, 10 nonlinear SVM classifiers are trained on fingerprints of expert-classified ICs. Training groups include randomly chosen wet and dry datasets decomposed in 80 ICs. The classifiers are tested on the IC-fingerprints of different datasets decomposed into 20, 50, or 80 ICs. The SVM performance is assessed in terms of accuracy, False Omission Rate (FOR), Hit Rate (HR), False Alarm Rate (FAR), and sensitivity (p). For each artefact, the quality of the artefact-free EEG reconstructed using the classification of the best SVM is assessed by visual inspection and SNR.ResultsThe best SVM classifier for each artefact type achieved average accuracy of 1 (eyeblink), 0.98 (cardiac interference), and 0.97 (eye movement and myogenic artefact). Average classification sensitivity (p) was 1 (eyeblink), 0.997 (myogenic artefact), 0.98 (eye movement), and 0.48 (cardiac interference). Average artefact reduction ranged from a maximum of 82% for eyeblinks to a minimum of 33% for cardiac interference, depending on the effectiveness of the proposed method and the amplitude of the removed artefact. The performance of the SVM classifiers did not depend on the electrode type, whereas it was better for lower decomposition levels (50 and 20 ICs).DiscussionApart from cardiac interference, SVM performance and average artefact reduction indicate that the fingerprint method has an excellent overall performance in the automatic detection of eyeblinks, eye movements and myogenic artefacts, which is comparable to that of existing methods. Being also independent from simultaneous artefact recording, electrode number, type and layout, and decomposition level, the proposed fingerprint method can have useful applications in clinical and experimental EEG settings.
creator: Gabriella Tamburro
creator: Patrique Fiedler
creator: David Stone
creator: Jens Haueisen
creator: Silvia Comani
uri: https://doi.org/10.7717/peerj.4380
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Tamburro et al.

title: MIA-Clustering: a novel method for segmentation of paleontological material
link: https://peerj.com/articles/4374
last-modified: 2018-02-23
description: Paleontological research increasingly uses high-resolution micro-computed tomography (μCT) to study the inner architecture of modern and fossil bone material to answer important questions regarding vertebrate evolution. This non-destructive method allows for the measurement of otherwise inaccessible morphology. Digital measurement is predicated on the accurate segmentation of modern or fossilized bone from other structures imaged in μCT scans, as errors in segmentation can result in inaccurate calculations of structural parameters. Several approaches to image segmentation have been proposed with varying degrees of automation, ranging from completely manual segmentation, to the selection of input parameters required for computational algorithms. Many of these segmentation algorithms provide speed and reproducibility at the cost of flexibility that manual segmentation provides. In particular, the segmentation of modern and fossil bone in the presence of materials such as desiccated soft tissue, soil matrix or precipitated crystalline material can be difficult. Here we present a free open-source segmentation algorithm application capable of segmenting modern and fossil bone, which also reduces subjective user decisions to a minimum. We compare the effectiveness of this algorithm with another leading method by using both to measure the parameters of a known dimension reference object, as well as to segment an example problematic fossil scan. The results demonstrate that the medical image analysis-clustering method produces accurate segmentations and offers more flexibility than those of equivalent precision. Its free availability, flexibility to deal with non-bone inclusions and limited need for user input give it broad applicability in anthropological, anatomical, and paleontological contexts.
creator: Christopher J. Dunmore
creator: Gert Wollny
creator: Matthew M. Skinner
uri: https://doi.org/10.7717/peerj.4374
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Dunmore et al.

title: Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound
link: https://peerj.com/articles/4275
last-modified: 2018-02-23
description: Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic–terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness) from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable.
creator: Timothy S. Lee
creator: Jason D. Toft
creator: Jeffery R. Cordell
creator: Megan N. Dethier
creator: Jeffrey W. Adams
creator: Ryan P. Kelly
uri: https://doi.org/10.7717/peerj.4275
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Lee et al.

title: In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein
link: https://peerj.com/articles/4396
last-modified: 2018-02-22
description: African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780.1), an open reading frame found in all ASFV strains. Sequence-based profiling and hidden Markov model search methods were used to identify remote pB263R homologs. Iterative Threading ASSEmbly Refinement (I-TASSER) was used to model the three-dimensional structure of pB263R. The posterior probability of fold family assignment was calculated using TM-fold, and biological function was assigned using TM-site, RaptorXBinding, Gene Ontology, and TM-align. Our results suggests that pB263R has the features of a TATA-binding protein and is thus likely to be involved in viral gene transcription.
creator: Dickson Kinyanyi
creator: George Obiero
creator: George F.O. Obiero
creator: Peris Amwayi
creator: Stephen Mwaniki
creator: Mark Wamalwa
uri: https://doi.org/10.7717/peerj.4396
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Kinyanyi et al.

title: Genome-Enhanced Detection and Identification (GEDI) of plant pathogens
link: https://peerj.com/articles/4392
last-modified: 2018-02-22
description: Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
creator: Nicolas Feau
creator: Stéphanie Beauseigle
creator: Marie-Josée Bergeron
creator: Guillaume J. Bilodeau
creator: Inanc Birol
creator: Sandra Cervantes-Arango
creator: Braham Dhillon
creator: Angela L. Dale
creator: Padmini Herath
creator: Steven J.M. Jones
creator: Josyanne Lamarche
creator: Dario I. Ojeda
creator: Monique L. Sakalidis
creator: Greg Taylor
creator: Clement K.M. Tsui
creator: Adnan Uzunovic
creator: Hesther Yueh
creator: Philippe Tanguay
creator: Richard C. Hamelin
uri: https://doi.org/10.7717/peerj.4392
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: 16S rRNA gene sequencing reveals effects of photoperiod on cecal microbiota of broiler roosters
link: https://peerj.com/articles/4390
last-modified: 2018-02-22
description: Photoperiod is an important factor in stimulating broiler performance in commercial poultry practice. However, the mechanism by which photoperiod affects the performance of broiler chickens has not been adequately explored. The current study evaluated the effects of three different photoperiod regimes (short day (LD) = 8 h light, control (CTR) = 12.5 h light, and long day (SD) = 16 h light) on the cecal microbiota of broiler roosters by sequencing bacterial 16S rRNA genes. At the phylum level, the dominant bacteria were Firmicutes (CTR: 68%, SD: 69%, LD: 67%) and Bacteroidetes (CTR: 25%, SD: 26%, and LD: 28%). There was a greater abundance of Proteobacteria (p < 0.01) and Cyanobacteria (p < 0.05) in chickens in the LD group than in those in the CTR group. A significantly greater abundance of Actinobacteria was observed in CTR chickens than in SD and LD chickens (p < 0.01). The abundance of Deferribacteres was significantly higher in LD chickens than in SD chickens (p < 0.01). Fusobacteria and Proteobacteria were more abundant in SD chickens than in CTR and LD chickens. The predicted functional properties indicate that cellular processes may be influenced by photoperiod. Conversely, carbohydrate metabolism was enhanced in CTR chickens as compared to that in SD and LD chickens. The current results indicate that different photoperiod regimes may influence the abundance of specific bacterial populations and then contribute to differences in the functional properties of gut microbiota of broiler roosters.
creator: Jun Wang
creator: Lucky T. Nesengani
creator: Yongsheng Gong
creator: Yujiang Yang
creator: Wenfa Lu
uri: https://doi.org/10.7717/peerj.4390
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Wang et al.

title: Evolutionary radiation of earless frogs in the Andes: molecular phylogenetics and habitat shifts in high-elevation terrestrial breeding frogs
link: https://peerj.com/articles/4313
last-modified: 2018-02-22
description: The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae) living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of Phrynopus that includes 24 nominal species. Our phylogeny includes Phrynopus peruanus, the type species of the genus, and 10 other species for which genetic data were previously unavailable. We found strong support for monophyly of Phrynopus, and that two nominal species—Phrynopus curator and Phrynopus nicoleae—are junior synonyms of Phrynopus tribulosus. Using X-ray computed tomography (CT) imaging, we demonstrate that the absence of external hearing structures is associated with complete loss of the auditory skeletal elements (columella) in at least one member of the genus. We mapped the tympanum condition on to a species tree to infer whether the loss of hearing structures took place once or multiple times. We also assessed whether tympanum condition, body size, and body shape are associated with the elevational distribution and habitat use. We identified a single evolutionary transition that involved the loss of both the tympanic membrane and tympanic annulus, which in turn is correlated with the absence of advertisement calls. We also identified several species pairs where one species inhabits the Andean grassland and the other montane forest. When accounting for phylogenetic relatedness among species, we detected a significant pattern of increasing body size with increasing elevation. Additionally, species at higher elevations tend to develop shorter limbs, shorter head, and shorter snout than species living at lower elevations. Our findings strongly suggest a link between ecological divergence and morphological diversity of terrestrial breeding frogs living in montane gradients.
creator: Rudolf von May
creator: Edgar Lehr
creator: Daniel L. Rabosky
uri: https://doi.org/10.7717/peerj.4313
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 von May et al.

title: Functional outcomes and quality of life after a 6-month early intervention program for oral cancer survivors: a single-arm clinical trial
link: https://peerj.com/articles/4419
last-modified: 2018-02-21
description: BackgroundAdvanced treatment of oral cancer increases survival rates; however, it also increases the risk of developing shoulder dysfunction, dysphagia, oral dysfunction, donor site morbidity and psychological issues. This single-arm preliminary pilot study aims to explore the effects of a six-month early intervention program following reconstructive surgery in oral cancer survivors.MethodsA total of 65 participants were analyzed following reconstructive surgery. Outcome measurements were taken during the first visit, and at one, three and six months after reconstructive surgery.ResultsScapular muscle strength and shoulder range of motion progressively improved during the 6-month follow-up. The mean Disability of the Arms, Shoulder and Hand (DASH) score showed significant improvement at 1 month (p < .001). Health related QoL showed significant differences between baseline and 6-months post-surgery scores on global health and on most of the function and symptom scales. The predicted return-to-work rate was 80% at one year after the operation. Return-to-work rate differs in different vocational types, with a higher rate of return in the skilled or semi-skilled (87.5%) and self-employed (86.7%). ConclusionsWe suggest that early integrated intervention program with a follow-up of at least six months following reconstructive surgery may help develop and identify intervention guidelines and goals in the initial six months of treatment following neck dissection in oral cancer survivors.
creator: Yueh-Hsia Chen
creator: Wei-An Liang
creator: Chung-Yin Hsu
creator: Siang-Lan Guo
creator: Shwu-Huei Lien
creator: Hsiao-Jung Tseng
creator: Yuan-Hung Chao
uri: https://doi.org/10.7717/peerj.4419
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Chen et al.

title: Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition
link: https://peerj.com/articles/4416
last-modified: 2018-02-21
description: Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine (n = 24) and Saanen (n = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13. The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) (P < 0.05). The results showed that four SNPs rs671391101 (GHRHR), rs640582069 (IL1RN) rs635583012 (SOCS3) and rs635969404 (IL15RA) out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the GHRHR, IL1RN, SOCS3, and IL15RA genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.
creator: Szilvia Kusza
creator: Ludovic Toma Cziszter
creator: Daniela Elena Ilie
creator: Maria Sauer
creator: Ioan Padeanu
creator: Dinu Gavojdian
uri: https://doi.org/10.7717/peerj.4416
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Kusza et al.

title: Fruit and vegetable consumption and anemia among adult non-pregnant women: Ghana Demographic and Health Survey
link: https://peerj.com/articles/4414
last-modified: 2018-02-21
description: BackgroundAnemia is the most widely prevalent form of micronutrient deficiency that affects over a quarter of the global population. Evidence suggests that the burden of anemia is higher in the developing countries with women of reproductive age and children being the most at-risk groups. The most common causes are believed to be malnutrition and low bioavailability of micronutrients, which usually result from poor dietary habits and inadequate intake of food rich in micronutrients such as fresh fruits and vegetables. Regular consumption of F&V was shown to have protective effect against NCDs; however, evidence on this protective effect against micronutrient deficiency diseases are limited.Objectives(1) To measure the prevalence of anemia among adult non-pregnant women in Ghana, and (2) to investigate if there is any cross-sectional relationship between F&V consumption and anemia.MethodsThis is a cross-sectional study based on data extracted from the Ghana Demographic and Health Survey, 2008. Subjects were 4,290 non-pregnant women aged between 15 and 49 years. Hemoglobin levels were measured by HemoCue® hemoglobin-meter. Association between anemia and F&V consumption was assessed by multivariable regression methods.ResultsFindings indicate that well over half (57.9%) of the women were suffering from anemia of some level. The percentage of women consuming at least five servings of fruits and vegetables a day were 5.4% and 2.5% respectively. Results of multivariable analysis indicated that among urban women, consumption of <5 servings fruits/day was associated with significantly higher odds of severe [AOR = 9.27; 95% CI [5.15–16.70]] and moderate anemia [AOR = 6.63; 95% CI [4.21–10.44]], and consumption of <5 servings of vegetables/day was associated with higher odds of moderate anemia [AOR = 2.39; 95% CI [1.14–5.02]] compared with those who consumed >5 servings/day.ConclusionThe findings indicate that urban women who did not maintain WHO recommended level of F&V consumption bear a significantly higher likelihood of being moderate to severely anemic.
creator: Bishwajit Ghose
creator: Sanni Yaya
uri: https://doi.org/10.7717/peerj.4414
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Ghose and Yaya