bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential impacts of insect-induced harvests in the mixed forests of New England
Authors: MacLean Meghan Graham , Holt Jonathan , Borsuk Mark , Markowski-Lindsay Marla , Butler Brett J. , Kittredge David B. , Duveneck Matthew J. , Laflower Danelle , Orwig David A. , Foster David R. , Thompson Jonathan R. 
Published: July 2019

ABSTRACTForest insects and pathogens (FIPs) have significant impacts on U.S. forests, each year affecting an area nearly three times the area of wildfires and timber harvesting combined. We surveyed family forest owners (FFOs) in the northeastern U.S. and 84% of respondents indicated they would harvest in at least one of the presented FIP infestation scenarios. This harvest response represents a potentially significant shift in the timing, extent, and species selection of harvesting in the Northeast. Here we used the landowner survey, regional forest inventory data, and characteristics of the emerald ash borer (EAB, Agrilus planipennis) invasion to examine the potential for a rapidly spreading FIP to alter harvest regimes and affect regional forest conditions. Twenty-five percent of the FFO parcels in the Connecticut River Watershed in New England are likely to be harvested in response to EAB within 10 years. This prediction represents an increase in harvest frequencies, from 2.9%/yr (historically) to 3.7%/yr, on FFO woodlands. At typical harvest intensities, this would result in 13% of the total aboveground biomass removed through these harvests, with 81% of that biomass from species other than ash, creating a forest disturbance that is over twice the magnitude of the disturbance from EAB alone.
Transmembrane 163 (TMEM163) protein effluxes zinc
Authors: Sanchez Vanessa B. , Ali Saima , Escobar Adrian , Cuajungco Math P. 
Published: July 2019

ABSTRACTRecent investigations of rodent Tmem163 suggest that it binds to and transports zinc as a dimer, and that alanine mutagenesis of its two species-conserved aspartate (D123A/D127A) residues proposed to bind zinc perturbs protein function. Direct corroboration, however, is lacking whether it is an influx or efflux transporter in cells. We hypothesized that human TMEM163 is a zinc effluxer based on its predicted protein characteristics. We used cultured human cell lines that either stably or transiently expressed TMEM163, and pre-loaded the cells with zinc to determine transport activity. We found that TMEM163-expressing cells exhibited significant reduction of intracellular zinc levels as evidenced by two zinc-specific fluorescent dyes and radionuclide zinc-65. The specificity of the fluorescence signal was confirmed upon treatment with TPEN, a high-affinity zinc chelator. Multiple sequence alignment and phylogenetic analyses showed that TMEM163 is related to distinct members of the cation diffusion facilitator (CDF) protein family. To further characterize the efflux function of TMEM163, we substituted alanine in two homologous aspartate residues (D124A/D128A) and performed site-directed mutagenesis of several conserved amino acid residues identified as non-synonymous single nucleotide polymorphism (S61R, S95C, S193P, and E286K). We found a significant reduction of zinc efflux upon cellular expression of D124A/D128A or E286K protein variant when compared with wild-type, suggesting that these particular amino acids are important for normal protein function. Taken together, our findings demonstrate that TMEM163 effluxes zinc and should now be designated ZNT11, as a new member of the mammalian CDF family of zinc efflux transporters.
siland: an R package for estimating the spatial influence of landscape
Authors: Carpentier Florence , Martin Olivier 
Published: July 2019

AbstractContextThe spatial distributions of species and populations are both influenced by local variables and by characteristics of surrounding landscapes. Understanding how landscape features spatially structure the frequency of a trait in a population, the abundance of a species or the species’ richness remains difficult specially because the spatial scale effects of the landscape variables are often unknown.ObjectivesHere, we present “siland”, an R package for analyzing the effect of landscape features on georeferenced point observations (described in a Geographic Information System shapefile format).Methods & Results“siland” simultaneously estimates the spatial scales and intensities of landscape variable effects. It does not require any information about the scale of effect. Two methods are available: one is based on focal sample site (Bsiland method, b for buffer) and one is distance weighted using Spatial Influence Function (Fsiland method, f for function). ‘siland’ allows for effects tests, effects maps and models comparison.ConclusionsAdaptable and user-friendly, the “siland” package is a very practical tool to perform landscape analysis.
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Authors: Waardenberg Ashley J. , Field Matt A. 
Published: July 2019

AbstractExtensive evaluation of RNA-seq methods have demonstrated that no single algorithm consistently outperforms all others. Removal of unwanted variation (RUV) has also been proposed as a method for stabilizing differential expression (DE) results. Despite this, it remains a challenge to run multiple RNA-seq algorithms to identify significant differences common to multiple algorithms, whilst also integrating and assessing the impact of RUV into all algorithms. consensusDE was developed to automate the process of identifying significant DE by combining the results from multiple algorithms with minimal user input and with the option to automatically integrate RUV. consensusDE only requires a table describing the sample groups, a directory containing BAM files or preprocessed count tables and an optional transcript database for annotation. It supports merging of technical replicates, paired analyses and outputs a compendium of plots to guide the user in subsequent analyses. Herein, we also assess the ability of RUV to improve DE stability when combined with multiple algorithms through application to real and simulated data. We find that, although RUV demonstrated improved FDR in a setting of low replication, the effect was algorithm specific and diminished with increased replication, reinforcing increased replication for recovery of true DE genes. We finish by offering some rules and considerations for the application of RUV in a consensus-based setting.consensusDE is freely available, implemented in R and available as a Bioconductor package, under the GPL-3 license, along with a comprehensive vignette describing functionality: http://bioconductor.org/packages/consensusDE/
Cross-species Functional Alignment Reveals Evolutionary Hierarchy Within the Connectome
Authors: Xu Ting , Nenning Karl-Heinz , Schwartz Ernst , Hong Seok-Jun , Vogelstein Joshua T. , Fair Damien A. , Schroeder Charles E. , Margulies Daniel S. , Smallwood Jonny , Milham Michael P. , Langs Georg 
Published: July 2019

AbstractEvolution provides an important window into how cortical organization shapes function and vice versa. The complex mosaic of changes in brain morphology and functional organization that have shaped the mammalian cortex during evolution, complicates attempts to chart cortical differences across species. It limits our ability to fully appreciate how evolution has shaped our brain, especially in systems associated with unique human cognitive capabilities that lack anatomical homologues in other species. Here, we demonstrate a function-based method for cross-species cortical alignment that leverages recent advances in understanding cortical organization and that enables the quantification of homologous regions across species, even when their location is decoupled from anatomical landmarks. Critically, our method establishes that cross-species similarity in cortical organization decreases with geodesic distance from unimodal systems, and culminates in the most pronounced changes in posterior regions of the default network (angular gyrus, posterior cingulate and middle temporal cortices). Our findings suggest that the establishment of the default network, as the apex of a cognitive hierarchy, as is seen in humans, is a relatively recent evolutionary adaptation. They also highlight functional changes in regions such as the posterior cingulate cortex and angular gyrus as key influences on uniquely human features of cognition.
Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats
Authors: Weisbecker Vera , Guillerme Thomas , Speck Cruise , Sherratt Emma , Abraha Hyab Mehari , Sharp Alana C. , Terhune Claire E. , Collins Simon , Johnston Steve , Panagiotopoulou Olga 
Published: July 2019

AbstractBackgroundWithin-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, shape variation should not be dominated by allometry; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues.ResultsWe assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of thre species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus.DiscussionOur results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraint act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation
Authors: Li Feng , Upadhyaya Narayana M. , Sperschneider Jana , Matny Oadi , Nguyen-Phuc Hoa , Mago Rohit , Raley Castle , Miller Marisa E. , Silverstein Kevin A.T. , Henningsen Eva , Hirsch Cory D. , Visser Botma , Pretorius Zacharias A. , Steffenson Brian J. , Schwessinger Benjamin , Dodds Peter N. , Figueroa Melania 
Published: July 2019

AbstractParasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here we show that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis revealed that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or reassortment. Generation of genetic variation by nuclear exchange may favour the evolution of dikaryotism by providing an advantage over diploidy.
Diversity and some bioactivities of soil actinomycetes from southwestern China
Authors: Jiang Yi , Li Guiding , Li Qinyuan , Zhang Kun , Jiang Longqian , Chen Xiu , Jiang Chenglin 
Published: July 2019

AbstractWith the natural medicine exploring, the actinomycetes (actinobacteria) have gotten more and more recognition. 815 soil samples were collected from six areas in the southwestern China. 7063 purified strains of actinomycetes were isolated from these samples by using four media. The 16S rRNA gene sequences of 1998 selected strains of the 7063 were determined, and the phylogenetic analysis was carried out. The diversity of actinomycetes is analyzed. Total 33 genera of actinomycetes as the purified cultivation were identified from these soil samples. 14, 13, 5, 9 and 26 genera of actinobacteria were identified from E, A, B, D, C and F area respectively, and the communities of actinomycetes are very different from each other. The diversity of Xishuangbanna (F area) is the richest, and 26 genera were isolated. That of Emei and Qingcheng Mountain (C area) is monotone, and only five genera were isolated. 158 of 1998 strains (7.9 %) are possible new species. Antimicrobial activities of 1070 selected strains against 11 bacteria and fungi were tested using agar well diffusion method, and biosynthetic genes of type I and II polyketide synthases (PKS I, PKS II), nonribosomal peptide synthase (NRPS) and polygene cytochrome P450 hydroxylase (CYP) of 1036 selected strains were detected by PCR. High rate of antimicrobial activity and the four antibiotic biosynthetic genes existed in these actinomycetes. Results of this study indicates that firstly more unknown actinomycetes can be obtained from soil samples, specially primeval tropical forests. Second, isolation methods for actinomycetes must be continually improved and improved.ImportanceFirst, discarding repeat of a mass of known microbes and compounds is very difficult. Second, pharmaceuticals development can still not overtake the increase of resistance of pathogens to antibiotics, and new diseases continuously and fleetly occur. Soil actinomycetes of these regions are researched few by microbiologist yet. In order to get much more unknown actinomycetes for discovery of new bioactive metabolites, the actinomycetes of forest soil in southwestern China were isolated and identified. Anti-microbial activities and synthetic gene clusters’ of four kinds of antibiotics of some selected strains were detected.
Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily)
Authors: Catalano Giulio , Lo Vetro Domenico , Fabbri Pier Francesco , Mallick Swapan , Reich David , Rohland Nadin , Sineo Luca , Mathieson Iain , Martini Fabio 
Published: July 2019

AbstractGrotta d’Oriente, a small coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. The individual known as Oriente C was found in the lower portion of an anthropogenic deposit containing typical local Late Upper Palaeolithic (Late Epigravettian) stone assemblages. Two radiocarbon dates on charcoal from the deposit containing the burial are consistent with the archaeological context and refer Oriente C to a period spanning about 14,200-13,800 cal. BP. Anatomical features are close to those of Late Upper Palaeolithic populations of the Mediterranean and show strong affinity with Palaeolithic individuals of San Teodoro. Here we present new ancient DNA data from Oriente C. Our results, confirming previous genetic analysis, suggest a substantial genetic homogeneity among Late Epigravettian hunter-gatherer populations of Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the Last Glacial Maximum (LGM).
Theory of antiparallel microtubule overlap stabilization by motors and diffusible crosslinkers
Authors: Lera-Ramirez Manuel , Nédélec François J. 
Published: July 2019

AbstractAntiparallel microtubule bundles are essential structural elements of many cytoskeletal structures, for instance the mitotic spindle. In such bundles, neighbouring microtubules are bonded by specialised crosslinkers of the Ase1/PRC1/MAP65 family that can diffuse longitudinally along microtubules. Similarly, some kinesin motors implicated in bundle formation have a diffusible tail allowing them to slide passively along microtubules. We develop here a theory of two microtubules connected by motors and diffusible connectors, in different configurations that can be realized experimentally. In all cases, the microtubule sliding speed derived analytically is validated by stochastic simulations and used to discuss recent experimental results, such as force generation by kinesin-14, and overlap stabilization by Ase1. Some systems can produce steady overlaps that are determined by the density of crosslinkers on the microtubule lattice. This property naturally leads to robust coordination between sliding and growth in dynamic bundles of microtubules, an essential property in mitosis.
Construct a molecular associations network to systematically understand intermolecular associations inHumancells
Authors: Yi Hai-Cheng , You Zhu-Hong , Guo Zhen-Hao 
Published: July 2019

AbstractA key aim of post-genomic biomedical research is to systematically integrate and model all molecules and their interactions in living cells. Existing research usually only focusing on the associations between individual or very limited type of molecules. But the interactions between molecules shouldn’t be isolated but interconnected and influenced. In this study, we revealed, constructed and analyzed a large-scale molecular association network of multiple biomolecules inhumancells by modeling all associations among lncRNA, miRNA, protein, circRNA, microbe, drug, and disease, in which various associations are interconnected and any type of associations can be predicted. More specifically, we defined the molecular associations network and constructed a molecular associations dataset containing 105546 associations. Then, each node is represented by its attribute feature and network embedding learned by Structural Deep Network Embedding. Moreover, Random Forest is trained to predict any kind of associations. And we compared the features and classifiers under five-fold cross-validation. Our method achieves a remarkable performance on entire molecular associations network with an AUC of 0.9552 and an AUPR of 0.9338. To further evaluate the performance of our method, a case study for predicting lncRNA-protein interactions was executed. The experimental results demonstrate that the systematic insight for understanding the synergistic interactions between various molecules and complex diseases. It is anticipated that this work can bring beneficial inspiration and advance related systems biology and biomedical research.Author SummaryThe interactions between the various biomolecules in the cells should not be isolated, but interconnected and influenced. There have been many valuable studies on the interactions between two individual molecules. Based on a systematic and holistic perspective, we revealed and constructed a large-scale molecular associations network by combining various associations in human living cells, including miRNA-lncRNA association, miRNA-disease association, miRNA-protein interaction, lncRNA-disease association, protein-protein interaction, protein-disease association, drug-protein interaction, drug-disease interaction, and lncRNA-protein interaction. To model and analyze this molecular associations network, we employed the network representation learning model to learn how to represent the node. Each node in the network can be represented by network embedding and its own attribute information. Any node can be classified. And any type of the associations in this network can be predicted, which can be considered as link prediction task. Our work provides a new systematic view and conceptual framework to understand complex diseases and life activities. It is anticipated that our study can advance related biological macromolecules, systems biology and biomedical research, and bring some meaningful inspiration.
Genome wide identification of NAC transcription factors and their role in abiotic stress tolerance in Chenopodium quinoa
Authors: Alshareef Nouf Owdah , Rey Elodie , Khoury Holly , Tester Mark , Schmöckel Sandra M. 
Published: July 2019

AbstractChenopodium quinoa Willd. (quinoa) is a pseudocereal with high nutritional value and relatively high tolerance to several abiotic stresses, including water deficiency and salt stress, making it a suitable plant for the study of mechanisms of abiotic stress tolerance. NAC (NAM, ATAF and CUC) transcription factors are involved in a range of plant developmental processes and in the response of plants to biotic and abiotic stresses. In the present study, we perform a genome-wide comprehensive analysis of the NAC transcription factor gene family in quinoa. In total, we identified 107 quinoa NAC transcription factor genes, distributed equally between sub-genomes A and B. They are phylogenetically clustered into two major groups and 18 subgroups. Almost 75% of the identified CqNAC genes were duplicated two to seven times and the remaining 25% of the CqNAC genes were found as a single copy. We analysed the transcriptional responses of the identified quinoa NAC TF genes in response to various abiotic stresses. The transcriptomic data revealed 28 stress responsive CqNAC genes, where their expression significantly changed in response to one or more abiotic stresses, including salt, water deficiency, heat and phosphate starvation. Among these stress responsive NACs, some were previously known to be stress responsive in other species, indicating their potentially conserved function in response to abiotic stress across plant species. Six genes were differentially expressed specifically in response to phosphate starvation but not to other stresses, and these genes may play a role in controlling plant responses to phosphate deficiency. These results provide insights into quinoa NACs that could be used in the future for genetic engineering or molecular breeding.
Additional analytical support for a new method to compute the likelihood of diversification models
Authors: Laudanno Giovanni , Haegeman Bart , Etienne Rampal S. 
Published: July 2019

AbstractMolecular phylogenies have been increasingly recognized as an important source of information on species diversification. For many models of macro-evolution, analytical likelihood formulas have been derived to infer macro-evolutionary parameters from phylogenies. A few years ago, a general framework to numerically compute such likelihood formulas was proposed, which accommodates models that allow speciation and/or extinction rates to depend on diversity. This framework calculates the likelihood as the probability of the diversification process being consistent with the phylogeny from the root to the tips. However, while some readers found the framework presented in Etienne et al. (2012) convincing, others still questioned it (personal communication), despitenumericalevidence that for special cases the framework yields the same (i.e. within double precision) numerical value for the likelihood as analytical formulas do that were independently derived for these special cases. Here we proveanalyticallythat the likelihoods calculated in the new framework are correct for all special cases with known analytical likelihood formula. Our results thus add substantial mathematical support for the overall coherence of the general framework.