bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Statistical Model of Cell Wall Dynamics during Expansive Growth
Authors: Sridhar S. Lalitha , Ortega J.K.E. , Vernerey F.J. 
Published: June 2018

ABSTRACTExpansive growth is a process by which walled cells found in plants, algae and fungi, use turgor pressure to mediate irreversible wall deformation and regulate their shape and volume. The molecular structure of the primary cell wall must therefore be able to perform multiple function simultaneously such as providing structural support by a combining elastic and irreversible deformation and facilitate the deposition of new material during growth. This is accomplished by a network of microfibrils and tethers composed of complex polysaccharides and proteins that are able to dynamically mediate the network topology via constant detachment and reattachment events. Global biophysical models such as those of Lockhart and Ortega have provided crucial macroscopic understanding of the expansive growth process, but they lack the connection to molecular processes that trigger network rearrangements in the wall. In this context, we propose a statistical approach that describes the population behavior of tethers that have elastic properties and the ability to break and re-form in time. Tether properties such as bond lifetimes and stiffness, are then shown to govern global cell wall mechanics such as creep and stress relaxation. The model predictions are compared with experiments of stress relaxation and turgor pressure step-up from existing literature, for the growing cells of incised pea (Pisum sativus L.), algaeChara corallinaand the sporangiophores of the fungus,Phycomyces blakesleeanus. The molecular parameters are estimated from fits to experimental measurements combined with the information on the dimensionless number Πpethat is unique to each species. To our knowledge, this research is the first attempt to use a statistical approach to model the cell wall during expansive growth and we believe it will provide a better understanding of the cell wall dynamics at a molecular level.
Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data
Authors: Webster Timothy H. , Couse Madeline , Grande Bruno M. , Karlins Eric , Phung Tanya N. , Richmond Phillip A. , Whitford Whitney , Sayres Melissa A. Wilson 
Published: June 2018

AbstractMammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. This sequence homology can cause the mismapping of short sequencing reads derived from the sex chromosomes and affect variant calling and other downstream analyses. Understanding and correcting this problem is critical for medical genomics and population genomic inference. Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that: (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We show how these metrics can be used to identify XX and XY individuals across diverse sequencing experiments, including low and high coverage whole genome sequencing, and exome sequencing. We also show that XYalign corrects mismapped reads on the sex chromosomes, resulting in more accurate variant calling. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other use cases including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3).
New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract
Authors: Escapa Isabel F. , Chen Tsute , Huang Yanmei , Gajare Prasad , Dewhirst Floyd E. , Lemon Katherine P. 
Published: June 2018

ABSTRACTThe expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most NextGeneration sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus and mouth. Using Minimum Entropy Decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, one of these 19 belonged to a currently uncultivated genus. Fourth, for 94% of the participants, two to ten species constituted 90% of their sequences, indicating nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies.IMPORTANCEThe eHOMD (ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes, and the individual microbes, in health and disease of body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus and mouth, and the lower respiratory tract. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (1) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (2) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (3) reference genomes to facilitate metagenomic, metatranscriptomic and proteomic studies and (4) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.
Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems
Authors: Paver Sara F. , Muratore Daniel J. , Newton Ryan J. , Coleman Maureen L. 
Published: June 2018

AbstractMarine and freshwater microbial communities are phylogenetically distinct and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing datasets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages; at the same time, however, many shared taxa were observed in both environments. Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between marine and freshwater sample pairs. Gammaproteobacteria and Alphaproteobacteria contained the highest number of Minimum Entropy Decomposition nodes shared by marine and freshwater samples. Shared nodes included lineages of the abundant alphaproteobacterial group SAR11 that have not previously been reported in 16S rRNA gene surveys of freshwater lakes. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Lineages with a high degree of shared taxa or habitat-specific diversification represent targets for genome-scale investigations into microbial adaptations and evolutionary innovations. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may have novel adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.ImportanceThe distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated datasets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed phyla and proteobacterial classes inferred to include more or less recent transitions across habitat types as well as specific lineages that are shared by marine and freshwater environments at the level of 16S rRNA sequence types. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
A metapopulation model of the spread of the Devil Facial Tumour Disease predicts the long term collapse of its host but not its extinction
Authors: Siska Veronika , Eriksson Anders , Mehlig Bernhard , Manica Andrea 
Published: June 2018

AbstractThe Devil Facial Tumour Disease (DFTD), a unique case of a transmissible cancer, had a devastating effect on its host, the Tasmanian Devil. Current estimates of its density are at roughly 20% of the pre-disease state, and single-population epidemiological models have predicted the likely extinction of the host. Here we take advantage of extensive surveys across Tasmania providing data on the spatial and temporal spread of DFTD, and investigate the dynamics of this host-pathogen system using a spatial metapopulation model. We first confirm a most likely origin of DFTD in the north-east corner of the island, and then use the inferred dynamics to predict the fate of the species. We find that our medium-term predictions match additional data not used for fitting, and that on the longterm, Tasmanian Devils are predicted to coexist with the tumour. The key process allowing persistence is the repeated reinvasion of extinct patches from neighbouring areas where the disease has flared up and died out, resulting in a dynamic equilibrium with different levels of spatial heterogeneity. However, this dynamic equilibrium is predicted to keep this apex predator at about 9 % of its original density, with possible dramatic effects on the Tasmanian ecosystem.
Aerobic removal of microcystin-LR by a novel native effective bacterial community designated as YFMCD4 isolated from Lake Taihu
Authors: Yang Fei , Guo Jian , Huang Feiyu , Massey Isaac Yaw , Huang Ruixue , Ding Ping , Zeng Weiming 
Published: June 2018

AbstractMicrocystins (MCs) are a group of monocyclic heptapeptide hepatotoxins produced by species of cyanobacteria. MC-LR is the most toxic and frequently detected MCs variant in water, which poses a great threat to the natural ecosystem and public health. It’s important to seek environment-friendly and cost-efficient methods to remove MC-LR. To investigate the MC-degrading capacities of a novel indigenous bacterial community designated as YFMCD4 and the influence of environmental factors including various temperatures, MC concentrations and pH on the MC-degrading activities, the concentration of MC-LR was measured by high performance liquid chromatography. In addition, the MC-degrading mechanism containing the degradation pathway and products of YFMCD4 was studied using HPLC coupled with an ultra-high resolution LTQ Orbitrap Velos Pro ETD mass spectrometry equipped with electrospray ionization interface. The data showed MC-LR can be removed at the maximum rate of 0.5 µg/(ml·h) by YFMCD4 containingAlcaligenes faecalisandStenotrophomonas acidaminiohila. The MC-degrading rates of YFMCD4 were significantly affected by different temperatures, pH and MC-LR concentrations. Two intermediates of a tetrapeptide and Adda appeared in the degradation process. These results illustrate that the novel bacterial community YFMCD4 can remove MC-LR effectively and completely, which indicates YFMCD4 possesses a significant potential to be used in bioremediation of water bodies contaminated by MC-LR.
High-fat diet suppresses the positive effect of creatine supplementation on skeletal muscle function by reducing protein expression of IGF-PI3K-AKT-mTOR pathway
Authors: Ferretti Renato , Moura Eliezer Guimarães , Carvalho dos Santos Veridiana , Caldeira Eduardo José , Conte Marcelo , Matsumura Cintia Yuri , Pertille Adriana , Mosqueira Matias 
Published: June 2018

AbstractHigh-fat (HF) diets in combination with sedentary lifestyle represent one of the major public health concerns predisposing to obesity and diabetes leading to skeletal muscle atrophy, decreased fiber diameter and muscle mass with accumulation of fat tissue resulting in loss of muscle strength. One strategy to overcome the maleficent effects of HF diet is resistance training, a strategy used to improve muscle mass, reverting the negative effects on obesity-related changes in skeletal muscle. Together with resistance training, supplementation with creatine monohydrate (CrM) in the diet has been used to improve muscle mass and strength. Creatine is a non-essential amino acid that is directly involved in the cross-bridge cycle providing a phosphate group to ADP during the initiation of muscle contraction. Besides its antioxidant and anti-inflammatory effects CrM also upregulates IGF-1 resulting in hyperthophy with an increase in muscle function. However, it is unknown whether CrM supplementation during resistance training would revert the negative effects of high-fat diet on the muscle performance. During 8 weeks we measured muscle performance to climb a 1.1m and 80° ladder with increasing load on trained rats that had received standard diet or high-fat diet, supplemented or not with CrM. We observed that the CrM supplementation up-regulated IGF-1 and phospho-AKT protein levels, suggesting an activation of the IGF1-PI3K-Akt/PKB-mTOR pathway. Moreover, despite the CrM supplementation, HF diet down-regulated several proteins of the IGF1-PI3K-Akt/PKB-mTOR pathway, suggesting that diet lipid content is crucial to maintain or improve muscle function during resistance training.
Facility delivery and postnatal care services use among mothers who attended four or more antenatal care visits in Ethiopia: further analysis of the 2016 Demographic and Health Survey
Authors: Fekadu Gedefaw Abeje , Getahun Fentie Ambaw , Kidanie Seblewongiel Ayenalem 
Published: June 2018

AbstractIntroductionIn Ethiopia, many mothers who attend the recommended number of antenatal care visits fail to use facility delivery and postnatal care services. This study identifies factors associated with facility delivery and use of postnatal care among mothers who had four or more antenatal care visits, using data from the 2016 Ethiopian Demographic and Health Survey (EDHS).MethodsTo identify factors associated with facility delivery, we studied background and service-related characteristics among 2,415 mothers who attended four or more antenatal care visits for the most recent birth. In analyzing factors associated with postnatal care within 42 days after delivery, the study included 1,055 mothers who attended four or more antenatal care visits and delivered at home. We focused on women who delivered at home because women who deliver at a health facility are more likely also to receive postnatal care as well. A multivariable logistic regression model was fitted for each outcome to find significant associations between facility delivery and use of postnatal care.ResultsFifty-six percent of women who had four or more antenatal care visits delivered at a health facility, while 44% delivered at home. Mothers with secondary or above level of education, urban residents, women in the richest wealth quintile, and women who were working at the time of interview had higher odds of delivering in a health facility. High birth order was associated with a lower likelihood of health facility delivery. Among women who delivered at home, only 8% received postnatal care within 42 days after delivery. Quality of antenatal care as measured by the content of care received during antenatal care visits stood out as an important factor that influences both facility delivery and postnatal care. Among mothers who attended four or more antenatal care visits and delivered at home, the content of care received during ANC visits was the only factor that showed a statistically significant association with receiving postnatal care.ConclusionsThe more antenatal care components a mother receives, the higher her probability of delivering at a health facility and of receiving postnatal care. The health care system needs to increase the quality of antenatal care provided to mothers because receiving more components of antenatal care is associated with increased health facility delivery and postnatal care. Further research is recommended to identify other reasons why many women do not use facility delivery and postnatal care services even after attending four or more antenatal care visits.
Mutations in nucleoporinNUP88cause lethal neuromuscular disorder
Authors: Bonnin Edith , Cabochette Pauline , Filosa Alessandro , Jühlen Ramona , Komatsuzaki Shoko , Hezwani Mohammed , Dickmanns Achim , Martinelli Valérie , Vermeersch Marjorie , Supply Lynn , Martins Nuno , Pirenne Laurence , Ravenscroft Gianina , Lombard Marcus , Port Sarah , Spillner Christiane , Janssens Sandra , Roets Ellen , Dorpe Jo Van , Lammens Martin , Kehlenbach Ralph H. , Ficner Ralf , Laing Nigel , Hoffmann Katrin , Vanhollebeke Benoit , Fahrenkrog Birthe 
Published: June 2018

AbstractNucleoporins build the nuclear pore complex (NPC), which, as sole gate for nuclear-cytoplasmic exchange, are of outmost importance for normal cell function. Defects in the process of nucleocytoplasmic transport or in its machinery have been frequently described in human diseases, such as cancer and neurodegenerative disorders, but only in a few cases of developmental disorders. Here we report biallelic mutations in the nucleoporinNUP88as a novel cause of lethal fetal akinesia deformation sequence (FADS) in two families. FADS comprises a spectrum of clinically and genetically heterogeneous disorders with congenital malformations related to impaired fetal movement. We show that genetic disruption ofnup88in zebrafish results in pleiotropic developmental defects reminiscent of those seen in affected human fetuses, including locomotor defects as well as defects at neuromuscular junctions. Phenotypic alterations become visible at distinct developmental stages, both in affected human fetuses and in zebrafish, whereas early stages of development are apparently normal. The zebrafish phenotypes caused by nup88 deficiency are only rescued by expressing wild-type nup88 and not the disease-linked mutant forms of nup88. Furthermore, using human and mouse cell lines as well as immunohistochemistry on fetal muscle tissue, we demonstrate that NUP88 depletion affects rapsyn, a key regulator of the muscle nicotinic acetylcholine receptor at the neuromuscular junction. Together, our studies provide the first characterization of NUP88 in vertebrate development, expand our understanding of the molecular events causing FADS, and suggest that variants inNUP88should be investigated in cases of FADS.
Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia
Authors: Arias Leonardo , Schröder Roland , Hübner Alexander , Barreto Guillermo , Stoneking Mark , Pakendorf Brigitte 
Published: June 2018

ABSTRACTHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Authors: Didelot Xavier , Croucher Nicholas J , Bentley Stephen D , Harris Simon R , Wilson Daniel J 
Published: June 2018

ABSTRACTThe sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-steps approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download athttps://github.com/xavierdidelot/BactDating.