title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1354 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Application of dynamic expansion tree for finding large network motifs in biological networks link: https://peerj.com/articles/6917 last-modified: 2019-05-17 description: Network motifs play an important role in the structural analysis of biological networks. Identification of such network motifs leads to many important applications such as understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families, and protein function annotation. However, identification of large network motifs is a challenging task as it involves the graph isomorphism problem. Although this problem has been studied extensively in the literature using different computational approaches, still there is a lot of scope for improvement. Motivated by the challenges involved in this field, an efficient and scalable network motif finding algorithm using a dynamic expansion tree is proposed. The novelty of the proposed algorithm is that it avoids computationally expensive graph isomorphism tests and overcomes the space limitation of the static expansion tree (SET) which makes it enable to find large motifs. In this algorithm, the embeddings corresponding to a child node of the expansion tree are obtained from the embeddings of a parent node, either by adding a vertex or by adding an edge. This process does not involve any graph isomorphism check. The time complexity of vertex addition and edge addition are O(n) and O(1), respectively. The growth of a dynamic expansion tree (DET) depends on the availability of patterns in the target network. Pruning of branches in the DET significantly reduces the space requirement of the SET. The proposed algorithm has been tested on a protein–protein interaction network obtained from the MINT database. The proposed algorithm is able to identify large network motifs faster than most of the existing motif finding algorithms. creator: Sabyasachi Patra creator: Anjali Mohapatra uri: https://doi.org/10.7717/peerj.6917 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Patra and Mohapatra title: Moderating factors influence the relative age effect in Australian cricket link: https://peerj.com/articles/6867 last-modified: 2019-05-17 description: BackgroundThe relative age effect is a commonly occurring phenomenon whereby there is a tendency for relatively older players to be over-represented during high level competitions. This effect is often seen to diminish as player’s age, however, there has been far less investigation on other potential moderating factors.MethodThis study investigated the impact of the relative age effect, and potential moderating factors, within the talent selection process of Australian cricket. Relative age distribution of 2,415 male and female junior and senior state level cricket players, who played in the Junior National Championships or State competition (senior level) between 2011 and 2015, were analysed.ResultsPlayers born in the first quartile of the cricket season were significantly over-represented in both male Under-15, Under-17, Under-19 and female Under-15 and Under-18 levels. However, there was no significant difference at the senior state level for either male or female cricketers. Further investigation of the relative age effect in the junior talent pathway revealed that male all-rounders, batters and pace bowlers, and female all-rounders and batters, born in first quartile were over-represented. Right-handed batters and bowlers were also influenced by the relative age effect at all Junior National levels, while left-handed batters and bowlers were only influenced at the Under-15 and Under-17 levels. These results highlight the impact relative age has on junior cricket talent pathways, including sex, age, handedness and primary skills. Only state level, and left-handedness at the Under-19 level, were unaffected by relative age.DiscussionThe findings of this study highlight the influence of relative age effects for both male and female junior cricket players. Interestingly, there may be an advantage to being left-handed that is more prevalent at the older (male Under-19; female Under-18) age levels. creator: Jonathan D. Connor creator: Ian Renshaw creator: Kenji Doma uri: https://doi.org/10.7717/peerj.6867 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Connor et al. title: Cmah deficiency may lead to age-related hearing loss by influencing miRNA-PPAR mediated signaling pathway link: https://peerj.com/articles/6856 last-modified: 2019-05-17 description: BackgroundPrevious evidence has indicated CMP-Neu5Ac hydroxylase (Cmah) disruption inducesaging-related hearing loss (AHL). However, its function mechanisms remain unclear. This study was to explore the mechanisms of AHL by using microarray analysis in the Cmah deficiency animal model.MethodsMicroarray dataset GSE70659 was available from the Gene Expression Omnibus database, including cochlear tissues from wild-type and Cmah-null C57BL/6J mice with old age (12 months, n = 3). Differentially expressed genes (DEGs) were identified using the Linear Models for Microarray data method and a protein–protein interaction (PPI) network was constructed using data from the Search Tool for the Retrieval of Interacting Genes database followed by module analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery. The upstream miRNAs and potential small-molecule drugs were predicted by miRwalk2.0 and Connectivity Map, respectively.ResultsA total of 799 DEGs (449 upregulated and 350 downregulated) were identified. Upregulated DEGs were involved in Cell adhesion molecules (ICAM1, intercellular adhesion molecule 1) and tumor necrosis factor (TNF) signaling pathway (FOS, FBJ osteosarcoma oncogene; ICAM1), while downregulated DEGs participated in PPAR signaling pathway (PPARG, peroxisome proliferator-activated receptor gamma). A PPI network was constructed, in which FOS, ICAM1 and PPARG were ranked as hub genes and PPARG was a transcription factor to regulate other target genes (ICAM1, FOS). Function analysis of two significant modules further demonstrated PPAR signaling pathway was especially important. Furthermore, mmu-miR-130b-3p, mmu-miR-27a-3p, mmu-miR-27b-3p and mmu-miR-721 were predicted to regulate PPARG. Topiramate were speculated to be a potential small-molecule drug to reverse DEGs in AHL.ConclusionsPPAR mediated signaling pathway may be an important mechanism for AHL. Downregulation of the above miRNAs and use of topiramate may be potential treatment strategies for ALH by upregulating PPARG. creator: Juhong Zhang creator: Na Wang creator: Anting Xu uri: https://doi.org/10.7717/peerj.6856 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: A new balaenopterid whale from the late Miocene of the Southern North Sea Basin and the evolution of balaenopterid diversity (Cetacea, Mysticeti) link: https://peerj.com/articles/6915 last-modified: 2019-05-17 description: BackgroundBalaenopterid mysticetes represent the most successful family-rank group of this clade. Their evolutionary history is characterized by a rich fossil record but the origin of the living genera is still largely not understood. Recent discoveries in the southern border of the North Sea revealed a number of well preserved fossil balaenopterid whales that may help resolving this problem. In particular, skull NMR 14035 shares morphological characters with the living humpback whale, Megaptera novaeangliae and, for this reason, its characteristics are investigated here.MethodsThe comparative anatomical analysis of the new specimen formed the basis of a new phylogenetic analysis of the Mysticeti based on a matrix including 350 morphological character states scored for 82 Operational Taxonomic Units. The stratigraphic age of the specimen was determined based on the analysis of the dinocyst assemblage recovered in the associated sediment. We assessed clade diversity in Balaenopteridae by counting the numbers of clades in given time intervals and then plotted the results.ResultsNehalaennia devossi n. gen. et sp. is described for the first time from the late Tortonian (8.7–8.1 Ma) of the Westerschelde (The Netherlands). This new taxon belongs to Balaenopteridae and shows a surprisingly high number of advanced characters in the skull morphology. Nehalaennia devossi is compared to a large sample of balaenopterid mysticetes and a phylogenetic analysis placed it as the sister group of a clade including the genus Archaebalaenoptera. The inclusion of this fossil allowed to propose a phylogenetic hypothesis for Balaenopteridae in which (1) Eschrichtiidae (gray whales) represents a family of its own, (2) Balaenopteridae + Eschrichtiidae form a monophyletic group (superfamily Balaenopteroidea), (3) Cetotheriidae is the sister group of Balaenopteroidea, (4) living Balaenoptera species form a monophyletic group and (5) living M. novaeangliae is the sister group of Balaenoptera. Our work reveals a complex phylogenetic history of Balaenopteridae and N. devossi informs us about the early morphological transformations in this family. Over time, this family experienced a number of diversity pulses suggesting that true evolutionary radiations had taken place. The paleoecological drivers of these pulses are then investigated. creator: Michelangelo Bisconti creator: Dirk K. Munsterman creator: Klaas Post uri: https://doi.org/10.7717/peerj.6915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bisconti et al. title: Genotypic analyses and virulence characterization of Glaesserella parasuis isolates from Taiwan link: https://peerj.com/articles/6960 last-modified: 2019-05-17 description: BackgroundGlaesserella (Haemophilus) parasuis (G. parasuis) causes severe economic losses in the swine industry. Multiple G. parasuis strains can exist in single animals. Typing techniques are required for identifying G. parasuis isolates. Different strains within a serovar display varying virulence. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) can assess the heterogeneity. The group 1 virulence-associated trimeric autotransporters (vtaA) gene is an indicator of virulence. The aim of this study was to characterize Taiwanese G. parasuis isolates via molecular serotyping, vtaA PCR and ERIC-PCR.MethodsOne hundred and forty-five strains were collected between November 2013 and March 2017 in Taiwan and further examined by molecular serotyping, vtaA PCR and ERIC-PCR.ResultsThe dendrogram revealed heterogeneous genetic diversity within many clusters. Partial correlation between the ERIC-PCR clusters of different strains, serovars and lesion patterns was observed. Twelve herds (8.3%) infected with more than one strain. Group 1 vtaA positive rate reached 98.6%.DiscussionThis study showed the high genetic diversity of G. parasuis in Taiwan by a high discriminatory capability of ERIC-PCR. Group 1 vtaA commonly exists in G. parasuis isolates and may play important roles in the pathogenesis of Taiwanese G. parasuis isolates. creator: Wei-Hao Lin creator: Hsing-Chun Shih creator: Chuen-Fu Lin creator: Cheng-Yao Yang creator: Chao-Nan Lin creator: Ming-Tang Chiou uri: https://doi.org/10.7717/peerj.6960 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep link: https://peerj.com/articles/6961 last-modified: 2019-05-17 description: Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented by Nitrosopumilus were dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered. creator: Guojie Cui creator: Jun Li creator: Zhaoming Gao creator: Yong Wang uri: https://doi.org/10.7717/peerj.6961 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cui et al. title: Adsorption of thallium(I) on rutile nano-titanium dioxide and environmental implications link: https://peerj.com/articles/6820 last-modified: 2019-05-16 description: Rutile nano-titanium dioxide (RNTD) characterized by loose particles with diameter in 20–50 nm has a very large surface area for adsorption of Tl, a typical trace metal that has severe toxicity. The increasing application of RNTD and widespread discharge of Tl-bearing effluents from various industrial activities would increase the risk of their co-exposure in aquatic environments. The adsorption behavior of Tl(I) (a prevalent form of Tl in nature) on RNTD was studied as a function of solution pH, temperature, and ion strength. Adsorption isotherms, kinetics, and thermodynamics for Tl(I) were also investigated. The adsorption of Tl(I) on RNTD started at very low pH values and increased abruptly, then maintained at high level with increasing pH >9. Uptake of Tl(I) was very fast on RNTD in the first 15 min then slowed down. The adsorption of Tl(I) on RNTD was an exothermic process; and the adsorption isotherm of Tl(I) followed the Langmuir model, with the maximum adsorption amount of 51.2 mg/g at room temperature. The kinetics of Tl adsorption can be described by a pseudo-second-order equation. FT-IR spectroscopy revealed that -OH and -TiOO-H play an important role in the adsorption. All these results indicate that RNTD has a fast adsorption rate and excellent adsorption amount for Tl(I), which can thus alter the transport, bioavailability and fate of Tl(I) in aqueous environment. creator: Weilong Zhang creator: Yang Wu creator: Jin Wang creator: Juan Liu creator: Haifeng Lu creator: Shuijing Zhai creator: Qiaohui Zhong creator: Siyu Liu creator: Wanying Zhong creator: Chunling Huang creator: Xiaoxiang Yu creator: Wenhui Zhang creator: Yongheng Chen uri: https://doi.org/10.7717/peerj.6820 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Incorporating acoustic objectives into Forest Management Planning when sensitive bird species are relevant link: https://peerj.com/articles/6922 last-modified: 2019-05-16 description: BackgroundThe potentially negative effects of timber harvesting on biodiversity and habitat conservation leads to the consideration of a wide range of restrictions to forest logging in natural areas. In particular, high noise levels produced by forest machinery present a challenge to developing sustainable forest management plans. The Cinereous vulture (Aegypius monachus), the largest bird of prey whose nests are located in mature trees, is considered to be appropriate as an indicator species for environment-friendly forest planning. In this work, we evaluated spatially differences in sound propagation between stands. We hypothesized that differences due to the influence of orography in mountainous forests would allow the relaxation of spatial and temporary restrictions to timber logging, without causing any great disturbance at nesting sites of sensitive species.MethodsOur study was conducted in a Scots pine (Pinus sylvestris) forest of Spain, where an important colony of the Western European population of Cinereous vulture is located. We built 62 noise maps to characterize noise pollution due to tree logging at planning level. We modeled two different scenarios, in order to characterize; (i) the effect of a chainsaw operator during a complete cycle for felling a tree (Scenario 1), and (ii) the effect of the peak level produced by the breaking noise emitted by the trunk of the tree and its impact on the ground (Scenario 2). A strategy of three logical steps was designed; (i) landscape-scale analysis of noise propagation in stands, (ii) hierarchical cluster analysis of stands, (iii) assessment of the potentially significant influence of noise management in timber harvesting.ResultsThe minimum distance (DIST) from chainsaw operator sites to the 40 dB(A) contour lines was the only variable that had a significant influence on the clustering results. On the other hand, mean values of a newly proposed metric called average radius or radial distance (ARD) oscillated between 174 m in cluster #1 (Scenario 1) and 407 m in cluster #2 (Scenario 2).DiscussionOur results highlight the convenience of considering noise modeling tools at a forest planning level in order to address the compatibility of forest logging and the necessity of protecting nature. We found that spatial propagation of noise made by chainsaws at felling sites does not differ between stands even in a mountainous terrain, contrary to what we initially hypothesized. However, temporary logging restrictions could be excluded in about 36% of the current conditioned management areas according to ARD results in Scenario 2 (400 m). This proposal could be based on a sound pressure level (in decibels) criteria instead of conventional buffer protection distance criteria. In addition, it is suggested that the current size of restricted management areas could be generally extended from a 100 m radius to a 200 m one around the Cinereous vulture nest sites. creator: Carlos Iglesias-Merchan creator: Esther Ortiz-Urbina creator: Marta Ezquerro creator: Luis Diaz-Balteiro uri: https://doi.org/10.7717/peerj.6922 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Iglesias-Merchan et al. title: Towards a distributed connectionist account of cognates and interlingual homographs: evidence from semantic relatedness tasks link: https://peerj.com/articles/6725 last-modified: 2019-05-16 description: BackgroundCurrent models of how bilinguals process cognates (e.g., “wolf”, which has the same meaning in Dutch and English) and interlingual homographs (e.g., “angel”, meaning “insect’s sting” in Dutch) are based primarily on data from lexical decision tasks. A major drawback of such tasks is that it is difficult—if not impossible—to separate processes that occur during decision making (e.g., response competition) from processes that take place in the lexicon (e.g., lateral inhibition). Instead, we conducted two English semantic relatedness judgement experiments.MethodsIn Experiment 1, highly proficient Dutch–English bilinguals (N = 29) and English monolinguals (N = 30) judged the semantic relatedness of word pairs that included a cognate (e.g., “wolf”–“howl”; n = 50), an interlingual homograph (e.g., “angel”–“heaven”; n = 50) or an English control word (e.g., “carrot”–“vegetable”; n = 50). In Experiment 2, another group of highly proficient Dutch–English bilinguals (N = 101) read sentences in Dutch that contained one of those cognates, interlingual homographs or the Dutch translation of one of the English control words (e.g., “wortel” for “carrot”) approximately 15 minutes prior to completing the English semantic relatedness task.ResultsIn Experiment 1, there was an interlingual homograph inhibition effect of 39 ms only for the bilinguals, but no evidence for a cognate facilitation effect. Experiment 2 replicated these findings and also revealed that cross-lingual long-term priming had an opposite effect on the cognates and interlingual homographs: recent experience with a cognate in Dutch speeded processing of those items 15 minutes later in English but slowed processing of interlingual homographs. However, these priming effects were smaller than previously observed using a lexical decision task.ConclusionAfter comparing our results to studies in both the bilingual and monolingual domain, we argue that bilinguals appear to process cognates and interlingual homographs as monolinguals process polysemes and homonyms, respectively. In the monolingual domain, processing of such words is best modelled using distributed connectionist frameworks. We conclude that it is necessary to explore the viability of such a model for the bilingual case.Data, scripts, materials and pre-registrations.Experiment 1: http://www.osf.io/ndb7p; Experiment 2: http://www.osf.io/2at49. creator: Eva D. Poort creator: Jennifer M. Rodd uri: https://doi.org/10.7717/peerj.6725 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Poort and Rodd title: Facial flatness indices: application in orthodontics link: https://peerj.com/articles/6889 last-modified: 2019-05-16 description: Facial flatness indices have been used in anthropology to discern differences among populations. They were evaluated on skulls from around the world.Aims(1) to evaluate the use of facial flatness indices in orthodontics and (2) to assess their variation among malocclusions, age and sex.Materials and MethodsA total of 322 cone beam computed tomography radiographs were digitized and three facial indices (frontal, simotic and zygomaxillary) along with three transverse distances (fmo1–fmo2, zma1–zma2 and n1–n2) were assessed and compared between different groups.ResultsThe zygomaxillary index was increased in Class II (32.6 ± 0.42; p < 0.001) and decreased in Class III malocclusions (29.4 ± 0.66; p < 0.001) compared to Class I (31.18 ± 0.3; p < 0.001). The frontal and nasal flatness are not characteristic features of any of the sagittal malocclusions. Facial flatness indices did not differ between males and females and between growing and non-growing patients.ConclusionThe position of subspinale point (A point) forward or backward relative to the zygomaxillary width is a factor of assessment of facial flatness. The zygomaxillary index could be helpful in weighting proportionally the width of the maxilla (expansion) relative to its sagittal position in Class II and Class III malocclusions. creator: Chimène Chalala creator: Maria Saadeh creator: Fouad Ayoub uri: https://doi.org/10.7717/peerj.6889 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chalala et al.