bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved prediction of chronological age from DNA methylation limits it as a biomarker of ageing
Authors: Zhang Qian , Vallerga Costanza L. , Walker Rosie M , Lin Tian , Henders Anjali K. , Montgomery Grant W. , He Ji , Fan Dongsheng , Fowdar Javed , Kennedy Martin , Pitcher Toni , Pearson John , Halliday Glenda , Kwok John B. , Hickie Ian , Lewis Simon , Anderson Tim , Silburn Peter A. , Mellick George D. , Harris Sarah E. , Redmond Paul , Murray Alison D. , Porteous David J. , Haley Christopher S. , Evans Kathryn L. , McIntosh Andrew M. , Yang Jian , Gratten Jacob , Marioni Riccardo E. , Wray Naomi R. , Deary Ian J. , McRae Allan F. , Visscher Peter M. 
Published: May 2018

AbstractDNA methylation is associated with age. The deviation of age predicted from DNA methylation from actual age has been proposed as a biomarker for ageing. However, a better prediction of chronological age implies less opportunity for biological age. Here we used 13,661 samples (from blood and saliva) in the age range of 2 to 104 years from 14 cohorts measured on Illumina HumanMethylation450/EPIC arrays to perform prediction analyses. We show that increasing the sample size achieves a smaller prediction error and higher correlations in test datasets. We demonstrate that smaller prediction errors provide a limit to how much variation in biological ageing can be captured by methylation and provide evidence that age predictors from small samples are prone to confounding by cell composition. Our predictor shows a similar or better performance in non-blood tissues including saliva, endometrium, breast, liver, adipose and muscle, compared with Horvath’s across-tissue age predictor.
Effect of eco-remediation and microbial community using multilayer solar planted floating island (MS-PFI) in the drainage channel
Authors: Sun Zhen , Xie Dongge , Jiang Xiran , Fu Guihong , Xiao Dongxue , Zheng Liang 
Published: May 2018

AbstractA multilayer solar planted floating island (MS-PFI) planted with Eichhornia crassipes are potential alternatives to traditional PFI. The highest removal rates of suspended solids, total nitrogen, total phosphorus, ammonia nitrogen and chemical oxygen demand was 86%, 75%, 80%, 95% and 84%, respectively. Proteobacteria (average 43.4% of total sequences) and Actinobacteria (19.9%) were the dominant phyla. Numerous genus had obvious differences between influent and effluent water, for instance, 13, 12 and 7 % in effluent water were assigned to the hgcl_clade, Norank_c_Cyanobacteria, and Rhizorhapis, while their relative abundances were decreased to 5, 3 and 0 %. In contrast, a distinct increase among Flavobacterium (10%), Limnohabitans (7%), Alpinimonas (4%), norank_p_Saccharibacteria (4%), Erwinia (3%) after MS-PFI treatment. MS-PFI brings various bacteria involved in contaminant degradation and nutrient removal in biological wastewater treatment systems. An amount of ¥ 1,843 was totally inputted to construct floating bed, which was rarely needed operation and maintenance costs.ImportanceIn-situ micro-polluted water ecological remediation, microorganisms and plants are effective to improve environmental quality and provide essential ecosystem services. Recently, we invent a new multilayer solar with an excellent pollutant removal efficiency. Microbes can decompose or mineralize organic matter effectively, also provide food for aquatic animals and increase nutrients or substances for plants, it is an important part of biogeochemical cycles and energy flows in aquatic ecological systems. However, few study explain the bacteria diversity and its responses between influent and effluent water in a planted floating island. The significance of our study is in identifying-in greater detail-the responses of bacteria in the new MS-PFI. This will greatly enhance our knowledge of bacteria communities, and can be widely used in micro-polluted water remediation.
Interleukin-17A Secreted from the Lung–infiltrating T Helper 17 Cells Renders Protective Immunity to PulmonaryCryptococcus neoformansInfection
Authors: Movahed Elaheh , Yi Tan Grace Min , Cheong Heng Choon , Qin Lee Chalystha Yie , Cheok Yi Ying , Tay Sun Tee , Chong Pei Pei , Wong Won Fen , Looi Chung Yeng 
Published: May 2018

ABSTRACTIL-17A has emerged as a key player in the pathologies of inflammation, autoimmune disease, and immunity to microbes since its discovery two decades ago. In this study, we aim to elucidate the activity of IL-17A in the protection againstCryptococcus neoformans, an opportunistic fungus that causes fatal meningoencephalitis among AIDS patients. For this purpose, we examined ifC. neoformansinfection triggers IL-17A secretion in thein vitrosetting using RAW264.7 murine macrophage cells, andin vivousing wildtype C57BL/6 mice. In addition, an enhanced green fluorescence protein (eGFP) reporter and a knockout (KO) mouse models were used to track the source of IL-17A secretion and explore the protective function of IL-17A, respectively. Our findings showed that bothin vivoandin vitromodels ofC. neoformansinfection demonstrated induction of abundant IL-17A secretion. By examining the lung bronchoalveolar lavage fluid (BALF), mediastinal lymph node (mLN) and spleen of the IL-17A– EGFP reporter mice, we showed that intranasal inoculation withC. neoformanspromoted leukocytes lung infiltration. A large proportion (~50%) of the infiltrated CD4+helper T cell population secreted EGFP, indicating vigorous TH17 activity in theC. neoformans–infected lung. The infection study in IL-17A–KO mice, on the other hand, revealed that absence of IL-17A marginally boosted fungal burden in the lung and accelerated the mouse death. Therefore, our data suggest that IL-17A, released predominantly from TH17 cellsin vivo, is essential in providing a protective immunity againstC. neoformansinfection.
The community and ecosystem consequences of intraspecific diversity: a meta-analysis
Authors: Raffard Allan , Santoul Frédéric , Cucherousset Julien , Blanchet Simon 
Published: May 2018

ABSTRACTUnderstanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity–ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within-species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non-linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity–function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within-species biodiversity for understanding ecological dynamics.
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
Authors: Sherman Thomas D , Kagohara Luciane T , Cao Raymon , Cheng Raymond , Satriano Matthew , Considine Michael , Krigsfeld Gabriel , Ranaweera Ruchira , Tang Yong , Jablonski Sandra A , Stein-O’Brien Genevieve , Gaykalova Daria A , Weiner Louis M , Chung Christine H , Fertig Elana J 
Published: May 2018

AbstractBioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The absence of a known ground truth of the dynamics of molecular changes challenges benchmarking their performance on real data. Realistic simulated time-course datasets are essential to assess the performance of time course bioinformatics algorithms. We develop an R/Bioconductor package, CancerInSilico, to simulate bulk and single cell transcriptional data from a known ground truth obtained from mathematical models of cellular systems. This package contains a general R infrastructure for running cell-based models and simulating gene expression data based on the model states. We show how to use this package to simulate a gene expression data set and consequently benchmark analysis methods on this data set with a known ground truth. The package is freely available via Bioconductor: http://bioconductor.org/packages/CancerInSilico/
LFAQ: towards unbiased label-free absolute protein quantification by predicting peptide quantitative factors
Authors: Chang Cheng , Gao Zhiqiang , Ying Wantao , Zhao Yan , Fu Yan , Wu Songfeng , Li Mengjie , Wang Guibin , Qian Xiaohong , Zhu Yunping , He Fuchu 
Published: May 2018

AbstractMass spectrometry (MS) has become a prominent choice for large-scale absolute protein quantification, but its quantification accuracy still has substantial room for improvement. A crucial issue is the bias between the peptide MS intensity and the actual peptide abundance, i.e., the fact that peptides with equal abundance may have different MS intensities. This bias is mainly caused by the diverse physicochemical properties of peptides. Here, we propose a novel algorithm for label-free absolute protein quantification, LFAQ, which can correct the biased MS intensities by using the predicted peptide quantitative factors for all identified peptides. When validated on datasets produced by different MS instruments and data acquisition modes, LFAQ presented accuracy and precision superior to those of existing methods. In particular, it reduced the quantification error by an average of 46% for low-abundance proteins.
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of theMethanomassiliicoccales
Authors: Speth Daan R. , Orphan Victoria J. 
Published: May 2018

AbstractOver the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an understudied environmental clade of theMethanomassiliicoccales. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
Small females prefer small males: size assortative mating in Aedes aegypti mosquitoes
Authors: Callahan Ashley G. , Ross Perran A. , Hoffmann Ary A. 
Published: May 2018

AbstractWith Aedes aegypti mosquitoes now being released in field programs aimed at disease suppression, there is interest in identifying factors influencing the mating and invasion success of released mosquitoes. One factor that can increase release success is size: released males may benefit competitively from being larger than their field counterparts. However, there could be a risk in releasing only large males if small field females avoid these males and instead prefer small males. Here we investigate this risk by evaluating mating success for mosquitoes differing in size. We measured mating success indirectly by coupling size with Wolbachia-infected or uninfected mosquitoes and scoring cytoplasmic incompatibility as a way of estimating relative mating success. Large females showed no evidence of a mating preference, whereas small males were relatively more successful than large males when mating with small females, exhibiting an advantage of around 20-25%. Because field females typically encompass a wide range of sizes while laboratory reared (and released) males typically fall into a narrow size range of large mosquitoes, these patterns can influence the success of release programs which rely on cytoplasmic incompatibility to suppress populations and initiate replacement invasions. Releases could include some small males generated under low food or crowded conditions to counter this issue, although this would need to be weighed against issues associated with costs of producing males of various size classes.
HIV protease inhibitor Saquinavir inhibits toll-like receptor 4 activation by targeting receptor dimerization
Authors: Peng Cheng , Deng Gang , Wang Yong , Abdulwahab Alzahrani Walid , Luo Hongwu , Huang Feizhou , Xu Hongbo 
Published: May 2018

ABSTRACTToll like receptor 4 (TLR4) is crucial in induction of innate immune response through recognition of invading pathogens or endogenous alarming molecules.Ligand-induced dimerization of TLR4 is required for the activation of downstream signaling pathways. TLR4 dimerization induces the activation of NF-kB and IRF3 through MyD88- or TRIF-dependent pathways. Saquinavir (SQV), a FDA-approved HIV protease inhibitor, has been shown to suppress the activation of NF-kB induced by HMGB1 by blocking TLR4-MyD88 association in proteasome-independent pathway. However, it remains nknown whether SQV is a HMGB1-specific and MyD88-dependent TLR4 signaling inhibitor and which precise signaling element of TLR4 is targeted by SQV. Our results showed that SQV inhibits both MyD88- and TRIF-dependent pathways in response to LPS, a critical sepsis inducer and TLR4 agonist, leading to downregulation of NF-kB and IRF3. SQV did not suppress MyD88-dependent pathway triggered by TLR1/2 agonist Pam3csk4. In the only TRIF-dependent pathway, SQV did not attenuate IRF3 activation induced by TLR3 agonist Poly(I:C). Furthermore, dimerization of TLR4 induced by LPS and HMGB1 was decreased by SQV. These results suggest that TLR4 receptor complex is the molecular target of SQV and shed light on that TLR4-mediated inmune responses and consequent risk for uncontrolled inflammation could be modulated by FDA-approved drug SQV.
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Authors: Arredondo-Alonso Sergio , Rogers Malbert R. C. , Braat Johanna C. , Verschuuren T. D. , Top Janetta , Corander Jukka , Willems Rob J.L. , Schürch Anita C. 
Published: May 2018

AbstractAssembly of bacterial short-read whole genome sequencing (WGS) data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Long-read sequencing has emerged as a solution to resolve plasmid structures and to obtain complete genomes for most bacterial species. This information can be used to generate and label datasets from short-read based contigs as plasmid- or chromosome-derived. We investigated the use of several popular machine learning methods to classify short-read contigs with known plasmid- or chromosome-origin from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. Based on resulting F1-scores we selected support-vector machine (SVM) models as best classifier for all three bacterial species (F1-score E. faecium = 0.94, F1-score K. pneumoniae = 0.90, F1-score E. coli = 0.76), which outperformed other existing plasmid tools using an independent set of isolates (precision E. faecium = 0.92, precision K. pneumoniae = 0.86, precision E. coli = 0.82). We demonstrated the scalability of our model by accurately predicting the plasmidome of a large collection of 1,644 E. faecium isolates with only short-read WGS available using a standard laptop with a single core. A low number of false positive predicted sequences suggests that the assignment of a particular gene of interest as plasmid- or chromosome-encoded by the models is plausible. The SVM classifiers are publicly available as a new R package called ‘mlplasmids’ at https://gitlab.com/sirarredondo/mlplasmids under the GNU General Public License v3.0. We additionally developed a graphical-user interface using the Shiny package which can be accessed at https://sarredondo.shinyapps.io/mlplasmids/. Single genomes can easily be predicted by uploading genome assemblies. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.
Cell adhesion promoted by a unique Shigella IpaA vinculin- and talin-binding site
Authors: Valencia-Gallardo Cesar , Bou-Nader Charles , Aguilar Daniel , Carayol Nathalie , Quenech’Du Nicole , Pecqueur Ludovic , Park HaJeung , Fontecave Marc , Izard Tina , Van Nhieu Guy Tran 
Published: May 2018

AbstractDuring Shigella cell invasion, the IpaA effector targets the focal adhesion protein vinculin through three vinculin-binding sites (VBSs). Here, we report that IpaA VBS3 also binds to talin. The 2.5 Å resolution crystal structure indicates that IpaA VBS3 forms a tightly folded α-helical bundle with talin H1-H4, contrasting with bundle unraveling upon vinculin interaction. High-affinity binding of Ipa VBS3 to talin H1-H4 requires a core of hydrophobic residues conserved in vinculin binding and a pair of electrostatic interactions accounting for talin binding specificity. IpaA VBS3 does not bind to talin H1-H5 suggesting the targeting of partially activated stretched talin but not inactive talin. Consistently, IpaA VBS3 labeled filopodial and nascent adhesions and regulated their formation through talin binding. In addition, talin-binding by IpaA VBS3 was required for bacterial capture by filopodia during Shigella invasion and for the stabilization of focal adhesions in infected cells. These findings point to the functional diversity of VBSs and a critical role for talin-binding by Shigella IpaA VBS3 and possibly talin VBSs in the regulation of adhesion structures.
Lack of negative density-dependence regulation in a dominant oak tree from a neotropical highland forest
Authors: Calderón-Sanou Irene , Ríos Luis Diego , Cascante-Marín Alfredo , Barrantes Gilbert , Fuchs Eric J. 
Published: May 2018

AbstractConspecific negative density-dependence(CNDD) is one of the main mechanisms proposed to regulate species coexistence. Tropical highland forests, in contrast to diverse lowland forests, are commonly dominated by a few tree species. Testing the importance of density-dependence effects on seedling establishment of dominant trees may provide insights on the mechanisms regulating population dynamics and forest composition of tropical highlands. We tested the importance of CNDD regulation on seedling survival and recruitment ofQuercus costaricensis, a monodominant oak in the Talamanca highland forests of Costa Rica. We used spatial statistics and generalized linear mixed models to test the effects of conspecific density, distance to the nearest adult, density ofChusqueabamboo shoots, and herbivory on the annual survival probability of 3538 seedlings between 2014 and 2017. We did not find any effect of CNDD on seedling survival. However, bamboo density and herbivory both significantly decreased seedling survival. All seedlings had signs of herbivory and predator satiation may explain the lack of density dependent regulation in this species. We argue that the lack of intraspecific density regulation at the seedling stage may explain the dominance ofQ. costaricensisin the highland forests of Costa Rica. Local density of this endemic oak is instead regulated by herbivory and the density ofChusquea.
Taxonomy, phylogeny and biogeography of African spurfowls (Galliformes, Phasianidae, Coturnicinae,Pternistisspp.)
Authors: Mandiwana-Neudani Tshifhiwa G. , Little Robin M. , Crowe Timothy M. , Bowie Rauri C.K. 
Published: May 2018

AbstractDuring much of the 20thCentury, partridge/quail-like, Afro-Asian phasianine birds referred to commonly as African spurfowls, francolins and/or partridges had a tortuous taxonomic history. Because of striking autapomorphic differences in plumage, vocalizations and ecology in some of these taxa, as many as nine genera and nearly 200 clinal and/or idiosyncratic subspecies, embedded within a polyphyletic Perdicinae, were recognized. In 1963, two clades, 28 ‘francolin’ and ‘spurfowl’ species (fisantein Afrikaans) and 13 Afro-Asiatic ‘francolins’ and ‘partridges’ (patrysein Afrikaans), were combined into a single genus (Francolinus) – the largest within the Galliformes – comprising about 100 subspecies. Furthermore,fisanteandpatrysewere partitioned into several unnamed “Groups” and four “Unplaced” species. Here, we use morphological, behavioural and DNA evidence to produce: a comprehensive revision of the taxonomy and phylogeny of thefisanteclade; a stable classification system for tis component taxa; and hypotheses vis-à-vis eco-biogeographical processes that promoted their speciation and cladogenesis. We shiftFrancolinusspp. sensu stricto (members of the Spotted Group) and the Unplaced ‘Francolinus’ gularisfrom thefisanteclade to thepatryse[discussed in Mandiwana-Neudani et al., in review]. An Unplacedfisant, ‘F.’ nahani, is linked withPtilopachus petrosus(another African endemic ‘partridge‘) within the Odontophoridae (New World ‘Quails‘). We recognize 25 species of fisante (hereafter spurfowls), including seven with subspecies. They comprise 34 terminal taxa placed within a single genus,Pternistis, sister toAmmoperdixandPerdiculaspp.,Coturnix‘quails’ andAlectoris‘partridges‘, within the now monophyletic Coturnicinae. Only one of four putative Groups of spurfowls, the Bare-throated Group, is monophyletic. The other three Groups (Montane, Scaly and Vermiculated) are para- or polyphyletic. Several species pairs of spurfowls, most notablyP. aferandcranchii, hybridize in para/sympatry. One Bare-throated spurfowl,P. rufopictus, may be the product of stabilized hybridization betweenP. aferand/orcranchiiandP. leucoscepus.