bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes
Authors: Sousa Thiago de Jesus , Parise Doglas , Profeta Rodrigo , Parise Mariana Teixeira Dornelles , Gomide Anne Cybelle Pinto , Kato Rodrigo Bentos , Pereira Felipe Luiz , Figueiredo Henrique Cesar Pereira , Ramos Rommel , Brenig Bertram , Costa da Silva Artur Luiz da , Ghosh Preetam , Barh Debmalya , Góes-Neto Aristóteles , Azevedo Vasco 
Published: November 2019

AbstractThe number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η
Authors: Rechkoblit Olga , Johnson Robert E. , Buku Angeliki , Prakash Louise , Prakash Satya , Aggarwal Aneel K. 
Published: November 2019

AbstractCytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.
On the possibility of a terahertz light emitting diode based on a dressed quantum well
Authors: Mandal S. , Dini K. , Kibis O. V. , Liew T. C. H. 
Published: November 2019

AbstractWe consider theoretically the realization of a tunable terahertz light emitting diode from a quantum well with dressed electrons placed in a highly doped p-n junction. In the considered system the strong resonant dressing field forms dynamic Stark gaps in the valence and conduction bands and the electric field inside the p-n junction makes the QW asymmetric. It is shown that the electrons transiting through the light induced Stark gaps in the conduction band emit photons with energy directly proportional to the dressing field. This scheme is tunable, compact, and shows a fair efficiency.
Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea)
Authors: Shazib Shahed Uddin Ahmed , Vďačný Peter , Slovák Marek , Gentekaki Eleni , Shin Mann Kyoon 
Published: November 2019

AbstractThe ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
Optimal environmental and culture conditions allow the in vitro coexistence of Pseudomonas aeruginosa and Staphylococcus aureus in stable biofilms
Authors: Cendra Maria del Mar , Blanco-Cabra Núria , Pedraz Lucas , Torrents Eduard 
Published: November 2019

AbstractThe coexistence between species that occurs in some infections remains hard to achieve in vitro since bacterial fitness differences eventually lead to a single organism dominating the mixed culture. Pseudomonas aeruginosa and Staphylococcus aureus are major pathogens found growing together in biofilms in disease-affected lungs or wounds. Herein, we tested and analyzed different culture media, additives and environmental conditions to support P. aeruginosa and S. aureus coexistence in vitro. We have unraveled the potential of DMEM to support the growth of these two organisms in mature cocultured biofilms (three days old) in an environment that dampens the pH rise. Our conditions use equal initial inoculation ratios of both strains and allow the stable formation of separate S. aureus microcolonies that grow embedded in a P. aeruginosa biofilm, as well as S. aureus biofilm overgrowth when bovine serum albumin is added to the system. Remarkably, we also found that S. aureus survival is strictly dependent on a well-characterized phenomenon of oxygen stratification present in the coculture biofilm. An analysis of differential tolerance to gentamicin and ciprofloxacin treatment, depending on whether P. aeruginosa and S. aureus were growing in mono- or coculture biofilms, was used to validate our in vitro coculture conditions.
Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy
Authors: Pan Peipei , Weisenberger Daniel J. , Zheng Siyu , Wolf Marie , Hwang David G. , Rose-Nussbaumer Jennifer R. , Jurkunas Ula V. , Chan Matilda F. 
Published: November 2019

AbstractHomeostatic maintenance of corneal endothelial cells is essential for maintenance of corneal deturgescence and transparency. In Fuchs endothelial corneal dystrophy (FECD), an accelerated loss and dysfunction of endothelial cells leads to progressively severe visual impairment. An abnormal accumulation of extracellular matrix (ECM) is a distinctive hallmark of the disease, however the molecular pathogenic mechanisms underlying this phenomenon are not fully understood. Here, we investigate genome-wide and sequence-specific DNA methylation changes of miRNA genes in corneal endothelial samples from FECD patients. We discover that miRNA gene promoters are frequent targets of aberrant DNA methylation in FECD. More specifically,miR-199Bis extensively hypermethylated and its mature transcript miR-199b-5p was previously found to be almost completely silenced in FECD. Furthermore, we find that miR-199b-5p directly and negatively regulates Snai1 and ZEB1, two zinc finger transcription factors that lead to increased ECM deposition in FECD. Taken together, these findings suggest a novel epigenetic regulatory mechanism of matrix protein production by corneal endothelial cells in whichmiR-199Bhypermethylation leads to miR-199b-5p downregulation and thereby the increased expression of its target genes, includingSnai1andZEB1. Our results support miR-199b-5p as a potential therapeutic target to prevent or slow down the progression of FECD disease.
Correlation between macular vessel density and number of intravitreal anti-VEGF agents for macular edema associated with branch retinal vein occlusion
Authors: Tomita Ryo , Iwase Takeshi , Goto Kensuke , Yamamoto Kentaro , Ra Eimei , Terasaki Hiroko 
Published: November 2019

AbstractWe evaluated whether the reduction of macular vessel density was correlated with the number of intravitreal injections of anti-vascular endothelial growth factor (VEGF) agents in eyes with a branch retinal vein occlusion (BRVO). The mean vessel density was determined by optical coherence tomography angiography in 29 eyes with macular edema associated with a BRVO. Our results showed that the mean vessel density in the group that had a resolution of the macular edema after one anti-VEGF injection was significantly higher than group that had a recurrence of the macular edema (P = 0.028). Single regression analysis showed that the number of intravitreal injections was significantly correlated with the reduction of the modified vessel density (r = −0.421, P = 0.023) and systemic hypertension (r = 0.377, P = 0.044). Multiple stepwise regression analysis showed that the reduction of the modified vessel density (β = −0.442, P = 0.009) and hypertension (β = 0.403, P = 0.016) were independent factors associated with the number of intravitreal injections. We conclude that the vessel density reduction can be used to predict whether recurrences of the macular edema will develop after the initial anti-VEGF injection in eyes with macular edema associated with a BRVO.
Gradual and selective trace-element enrichment in slab-released fluids at sub-arc depths
Authors: Ferrando Simona , Petrelli Maurizio , Frezzotti Maria Luce 
Published: November 2019

AbstractThe geochemical signature of magmas generated at convergent margins greatly depends on the nature of fluids and melts released during subduction. While major- and trace-elements transport capacity of ultrahigh pressure (UHP) hydrous-silicate melts has been investigated, little is known about solute enrichment and fractionation in UHP (>3.5–4 GPa) solute-rich aqueous fluids released along colder geothermal gradients. Here, we performed in situ LA-ICP-MS trace-element analyses on selected UHP prograde-to-peak fluid inclusions trapped in a kyanite-bearing quartzite from Sulu (China). The alkali-aluminosilicate-rich aqueous fluid released from the meta-sediments by dehydration reactions is enriched in LILE, U, Th, Sr, and REE. Inclusions trapped at increasing temperature (and pressure) preserve a gradual and selective trace-element enrichment resulting from the progressive dissolution of phengite and carbonate and the partial dissolution of allanite/monazite. We show that, at the investigated P-T conditions, aqueous fluids generated by dissolution of volatile-bearing minerals fractionate trace-element distinctly from hydrous-silicate melts, regardless of the source lithology. The orogenic/post-orogenic magmas generated in a mantle enriched by metasomatic processes involving either solute-rich aqueous fluids or hydrous-silicate melts released by the slab at UHP conditions can preserve evidence of the nature of these agents.
Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity
Authors: Imanishi Ichiro , Nicolas Aurélie , Caetano Ana-Carolina Barbosa , Castro Thiago Luiz de Paula , Tartaglia Natayme Rocha , Mariutti Ricardo , Guédon Eric , Even Sergine , Berkova Nadia , Arni Raghuvir K. , Seyffert Nubia , Azevedo Vasco , Nishifuji Koji , Le Loir Yves 
Published: November 2019

AbstractExfoliative toxins (ETs) are secreted virulence factors produced by staphylococci. These serine proteases specifically cleave desmoglein 1 (Dsg1) in mammals and are key elements in staphylococcal skin infections. We recently identified a newetgene inS. aureusO46, a strain isolated from ovine mastitis. In the present study, we characterized the newetgene at a genetic level and the enzymatic activity of the deduced protein. TheS. aureusO46 genome was re-assembled, annotated and compared with other publicly availableS. aureusgenomes. The deduced amino acid sequence of the newetgene shared 40%, 53% and 59% sequence identity to those of ETA, ETB and ETD, respectively. The newetgene shared the same genetic vicinity and was similar in otherS. aureusstrains bearing this gene. The recombinant enzyme of the newetgene caused skin exfoliationin vivoin neonatal mice. The newet-gene was thus namedete, encoding a new type (type E) of exfoliative toxin. We showed that ETE degraded the extracellular segments of Dsg1 in murine, ovine and caprine epidermis, as well as in ovine teat canal epithelia, but not that in bovine epidermis. We further showed that it directly hydrolyzed human and swine Dsg1 as well as murine Dsg1α and Dsg1β, but not canine Dsg1 or murine Dsg1γ. Molecular modeling revealed a correlation between the preferred orientation of ETE docking on its Dsg1 cleavage site and species-specific cleavage activity, suggesting that the docking step preceding cleavage accounts for the ETE species-specificity. This new virulence factor may contribute to the bacterial colonization on the stratified epithelia in certain ruminants with mastitis.
Effect of Si and C additions on the reaction mechanism and mechanical properties of FeCrNiCu high entropy alloy
Authors: Wu Hao , Huang Sirui , Qiu Huan , Zhu Heguo , Xie Zonghan 
Published: November 2019

AbstractFeCrNiCu based high entropy alloy matrix composites were fabricated with addition of Si and C by vacuum electromagnetic induction melting. The primary goal of this research was to analyze the reaction mechanism, microstructure, mechanical properties at room temperature and strengthening mechanism of the composites with addition of Si and C. The reaction mechanism of powders containing (Si, Ni and C) was analyzed, only one reaction occurred (i.e., Si + C → SiC) and its activation energy is 1302.8 kJ/mol. The new composites consist of a face centered cubic (FCC) structured matrix reinforced by submicron sized SiC particles. The addition of Si and C enhances the hardness from 351.4 HV to 626.4 HV and the tensile strength from 565.5 MPa to 846.0 MPa, accompanied by a slight decrease in the plasticity. The main strengthening mechanisms of SiC/FeCrNiCu composites were discussed based on dislocation strengthening, load bearing effect, Orowan mechanism and solid solution hardening, whose contributions to the tensile strength increase are 58.6%, 6.3%, 14.3% and 20.8%, respectively.
Induction of detrusor underactivity by extensive vascular endothelial damages of iliac arteries in a rat model and its pathophysiology in the genetic levels
Authors: Kim Myong , Yu Hwan Yeul , Ju Hyein , Shin Jung Hyun , Kim Aram , Lee Jaehoon , Ryu Chae-Min , Yun HongDuck , Lee Seungun , Lim Jisun , Heo Jinbeom , Shin Dong-Myung , Choo Myung-Soo 
Published: November 2019

AbstractWe tried to establish a reliable detrusor underactivity (DUA) rat model and to investigate pathophysiology of chronic bladder ischemia (CBI) on voiding behavior and bladder function. Adult male rats were divided into five groups. The arterial injury (AI) groups (AI-10, AI-20, AI-30) underwent vascular endothelial damage (VED) of bilateral iliac arteries (with 10, 20, and 30 bilateral repetitions of injury, respectively) and received a 1.25% cholesterol diet. The sham group underwent sham operation and received the same diet. Controls received a regular diet. After 8 weeks, all rats underwent unanesthetized cystometrogram. Bladder tissues were processed for organ bath investigation, immunohistochemistry staining, and genome-wide gene expression analysis. Awake cystometry analysis showed that frequency of voiding contractions and micturition pressure were lower in the AI-30 group than in sham group (p < 0.01). Contractile responses to various stimuli were lower in AI-20 and AI-30 groups (both p < 0.001). In the AI-20 and AI-30 groups, atherosclerotic occlusion in the iliac arteries, tissue inflammation, fibrosis, denervation, and apoptosis of bladder muscle were prominent compared to the sham. Mechanistically, the expression of purinergic receptor P2X-1 was reduced in the AI-30 group, and the genome-wide gene expression analysis revealed that genes related to IL-17 and HIF-1 signaling pathways including INF-γ receptor-1 and C-X-C motif chemokine ligand-2 were upregulated in the CBI-induced DUA rat model. A rat model of progressive VED successfully induced DUA. Abnormal tissue inflammation, fibrosis, denervation, and bladder muscle tissue apoptosis may be involved in CBI-induced DUA pathophysiology.
Visualization of epithelial-mesenchymal transition in an inflammatory microenvironment–colorectal cancer network
Authors: Ieda Takeshi , Tazawa Hiroshi , Okabayashi Hiroki , Yano Shuya , Shigeyasu Kunitoshi , Kuroda Shinji , Ohara Toshiaki , Noma Kazuhiro , Kishimoto Hiroyuki , Nishizaki Masahiko , Kagawa Shunsuke , Shirakawa Yasuhiro , Saitou Takashi , Imamura Takeshi , Fujiwara Toshiyoshi 
Published: November 2019

AbstractEpithelial-mesenchymal transition (EMT) is a biological process by which epithelial cells acquire mesenchymal characteristics. In malignant tumors, EMT is crucial for acquisition of a mesenchymal phenotype with invasive and metastatic properties, leading to tumor progression. An inflammatory microenvironment is thought to be responsible for the development and progression of colorectal cancer (CRC); however, the precise role of inflammatory microenvironments in EMT-related CRC progression remains unclear. Here, we show the spatiotemporal visualization of CRC cells undergoing EMT using a fluorescence-guided EMT imaging system in which the mesenchymal vimentin promoter drives red fluorescent protein (RFP) expression. An inflammatory microenvironment including TNF-α, IL-1β, and cytokine-secreting inflammatory macrophages induced RFP expression in association with the EMT phenotype in CRC cells.In vivoexperiments further demonstrated the distribution of RFP-positive CRC cells in rectal and metastatic tumors. Our data suggest that the EMT imaging system described here is a powerful tool for monitoring EMT in inflammatory microenvironment–CRC networks.
The Replication-Transmission Relativity Theory for Multiscale Modelling of Infectious Disease Systems
Authors: Garira Winston 
Published: November 2019

AbstractIt is our contention that for multiscale modelling of infectious disease systems to evolve and expand in scope, it needs to be founded on a theory. Such a theory would improve our ability to describe infectious disease systems in terms of their scales and levels of organization, and their inter-relationships. In this article we present a relativistic theory for multiscale modelling of infectious disease systems, that can be considered as an extension of the relativity principle in physics, called the replication-transmission relativity theory. This replication-transmission relativity theory states that at any level of organization of an infectious disease system there is no privileged/absolute scale which would determine, disease dynamics, only interactions between the microscale and macroscale. Such a relativistic theory provides a scientific basis for a systems level description of infectious disease systems using multiscale modelling methods. The central idea of this relativistic theory is that at every level of organization of an infectious disease system, the reciprocal influence between the microscale and the macroscale establishes a pathogen replication-transmission multiscale cycle. We distinguish two kinds of reciprocal influence between the microscale and the macroscale based on systematic differences in their conditions of relevancy. Evidence for the validity of the replication-transmission relativity theory is presented using a multiscale model of hookworm infection that is developed at host level when the relationship between the microscale and the macroscale is described by one of the forms of reciprocal influence.
Facile Recoverable and Reusable Macroscopic Alumina Supported Ni-based Catalyst for Efficient Hydrogen Production
Authors: Teo Siow Hwa , Yap Davin Kin Yew , Mansir Nasar , Islam Aminul , Taufiq-Yap Yun Hin 
Published: November 2019

AbstractA γ-NA5 catalyst in the form of pellet was first to be reported and was pioneering in gasification to accelerate the production of syngas through biomass (palm empty fruit brunch) conversion. The synthesised γ-NA5 pellet possesses a high surface area of 212.32 m2 g−1, which renders more active sites for hydrocarbon cracking, subsequently leading to high H2 production (0.0716 m3 kg−1). Additionally, the pellet exhibits remarkable reversibility and reusability with 91% H2 production efficiency being retained after five consecutive gasification cycles. Distinctively, the feature of the synthesised γ-NA5 pellet from the conventional powder-like catalyst is that it eases the separation of the used catalyst from the biomass ash, and subsequently facilitates regeneration solely by calcination process. The loading of 20 wt.% optimised amount of catalyst itself has successfully shorten the completion of gasification process up to 135 min, which is highly feasible for a large scale industrial usage after considering the cost of the catalyst, facile preparation method, and catalyst’s effectiveness towards gasification.
Niche partitioning of microbial communities in riverine floodplains
Authors: Peipoch Marc , Miller Scott R. , Antao Tiago R. , Valett H. Maurice 
Published: November 2019

AbstractRiverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H’: 2.8–4.1) nor β (Sørensen: 0.3–0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.