bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of the relationship between the level of anxiety declared by MRI patients in the STAI questionnaire and their respiratory rate acquired by a fibre-optic sensor system
Authors: Dziuda Łukasz , Zieliński Piotr , Baran Paulina , Krej Mariusz , Kopka Lech 
Published: March 2019

AbstractMagnetic resonance imaging (MRI) patients often experience anxiety-related respiratory disorders, including hyperventilation, but their respiratory indicators are not routinely monitored during scanning. Free from metal parts and immune to electromagnetic radiation, fibre-optic sensors have the potential to better control the patient’s condition by providing continuous non-invasive monitoring of the respiratory rate (RR). The study was purposed to assess the relationship between anxiety in MRI patients and their RR acquired by a fibre-optic sensor system. Forty-four subjects were involved in the study. The mean RR values recorded for 2 minutes immediately after the beginning and immediately before the end of the scanning were assessed relative to the State-Trait Anxiety Inventory (STAI) X-1 scores obtained immediately before and immediately after the scanning, respectively. A growth mixture model analysis was performed to statistically differentiate two groups of subjects according to the trends in repeated measures of RR. A significant lowering of the anxiety state was observed in the group characterised by a decrease in RR, whereas essentially no change in anxiety level was observed in the group with a stable RR. The t-test showed significant differences in changes in anxiety between these groups (t(39) = −2.349, p = 0.012, Cohen’s d = 2.13).
Featherweight long read alignment using partitioned reference indexes
Authors: Gamaarachchi Hasindu , Parameswaran Sri , Smith Martin A. 
Published: March 2019

AbstractThe advent of Nanopore sequencing has realised portable genomic research and applications. However, state of the art long read aligners and large reference genomes are not compatible with most mobile computing devices due to their high memory requirements. We show how memory requirements can be reduced through parameter optimisation and reference genome partitioning, but highlight the associated limitations and caveats of these approaches. We then demonstrate how these issues can be overcome through an appropriate merging technique. We incorporated multi-index merging into the Minimap2 aligner and demonstrate that long read alignment to the human genome can be performed on a system with 2 GB RAM with negligible impact on accuracy.
Dynamic flood modeling essential to assess the coastal impacts of climate change
Authors: Barnard Patrick L. , Erikson Li H. , Foxgrover Amy C. , Hart Juliette A. Finzi , Limber Patrick , O’Neill Andrea C. , van Ormondt Maarten , Vitousek Sean , Wood Nathan , Hayden Maya K. , Jones Jeanne M. 
Published: March 2019

AbstractCoastal inundation due to sea level rise (SLR) is projected to displace hundreds of millions of people worldwide over the next century, creating significant economic, humanitarian, and national-security challenges. However, the majority of previous efforts to characterize potential coastal impacts of climate change have focused primarily on long-term SLR with a static tide level, and have not comprehensively accounted for dynamic physical drivers such as tidal non-linearity, storms, short-term climate variability, erosion response and consequent flooding responses. Here we present a dynamic modeling approach that estimates climate-driven changes in flood-hazard exposure by integrating the effects of SLR, tides, waves, storms, and coastal change (i.e. beach erosion and cliff retreat). We show that for California, USA, the world’s 5th largest economy, over $150 billion of property equating to more than 6% of the state’s GDP and 600,000 people could be impacted by dynamic flooding by 2100; a three-fold increase in exposed population than if only SLR and a static coastline are considered. The potential for underestimating societal exposure to coastal flooding is greater for smaller SLR scenarios, up to a seven-fold increase in exposed population and economic interests when considering storm conditions in addition to SLR. These results highlight the importance of including climate-change driven dynamic coastal processes and impacts in both short-term hazard mitigation and long-term adaptation planning.
Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model
Authors: Mishra Priyanka , Ngo Jessica , Ashkani Jahanshah , Pio Frederic 
Published: March 2019

AbstractThe genetic model organism,Caenorhabditis elegans(C.elegans), shares many genes with humans and is the best-annotated of the eukaryotic genome. Therefore, the identification of new genes and pathways is unlikely. Nevertheless, host-pathogen interaction studies from viruses, recently discovered in the environment, has created new opportunity to discover these pathways. For example, the exogenous RNAi response inC.elegansby the Orsay virus as seen in plants and other eukaryotes is not systemic and transgenerational, suggesting different RNAi pathways between these organisms. Using a bioinformatics meta-analysis approach, we show that the top 17 genes differentially-expressed duringC. elegansinfection by Orsay virus are functionally uncharacterized genes. Furthermore, functional annotation using similarity search and comparative modeling, was able to predict folds correctly, but could not assign easily function to the majority. However, we could identify gene expression studies that showed a similar pattern of gene expression related to toxicity, stress and immune response. Those results were strengthened using protein-protein interaction network analysis. This study shows that novel molecular pathway components, of viral innate immune response, can be identified and provides models that can be further used as a framework for experimental studies. Whether these features are reminiscent of an ancient mechanism evolutionarily conserved, or part of a novel pathway, remain to be established. These results reaffirm the tremendous value of this approach to broaden our understanding of viral immunity inC.elegans.
Blue carbon potential of coastal wetland restoration varies with inundation and rainfall
Authors: Negandhi Karita , Edwards Grant , Kelleway Jeffrey J. , Howard Dean , Safari David , Saintilan Neil 
Published: March 2019

AbstractThere is a growing interest in how the management of ‘blue carbon’ sequestered by coastal wetlands can influence global greenhouse gas (GHG) budgets. A promising intervention is through restoring tidal exchange to impounded coastal wetlands for reduced methane (CH4) emissions. We monitored an impounded wetland’s GHG flux (CO2and CH4) prior to and following tidal reinstatement. We found that biogeochemical responses varied across an elevation gradient. The low elevation zone experienced a greater increase in water level and an associated greater marine transition in the sediment microbial community (16 S rRNA) than the high elevation zone. The low elevation zone’s GHG emissions had a reduced sustained global warming potential of 264 g m−2yr−1CO2-e over 100 years, and it increased to 351 g m−2yr−1with the removal of extreme rain events. However, emission benefits were achieved through a reduction in CO2emissions, not CH4emissions. Overall, the wetland shifted from a prior CH4sink (−0.07 to −1.74 g C m−2yr−1) to a variable sink or source depending on the elevation site and rainfall. This highlights the need to consider a wetland’s initial GHG emissions, elevation and future rainfall trends when assessing the efficacy of tidal reinstatement for GHG emission control.
Profibrotic epithelial phenotype: a central role for MRTF and TAZ
Authors: Bialik Janne Folke , Ding Mei , Speight Pam , Dan Qinghong , Miranda Maria Zena , Di Ciano-Oliveira Caterina , Kofler Michael M. , Rotstein Ori D. , Pedersen Stine F. , Szászi Katalin , Kapus András 
Published: March 2019

AbstractEpithelial injury is a key initiator of fibrosis but - in contrast to the previous paradigm - the epithelium in situ does not undergo wide-spread epithelial-mesenchymal/myofibroblast transition (EMT/EMyT). Instead, it assumes a Profibrotic Epithelial Phenotype (PEP) characterized by fibrogenic cytokine production. The transcriptional mechanisms underlying PEP are undefined. As we have shown that two RhoA/cytoskeleton-regulated transcriptional coactivators, Myocardin-related transcription factor (MRTF) and TAZ, are indispensable for EMyT, we asked if they might mediate PEP as well. Here we show that mechanical stress (cyclic stretch) increased the expression of transforming growth factor-β1 (TGFβ1), connective tissue growth factor (CTGF), platelet-derived growth factor and Indian Hedgehog mRNA in LLC-PK1 tubular cells. These responses were mitigated by siRNA-mediated silencing or pharmacological inhibition of MRTF (CCG-1423) or TAZ (verteporfin). RhoA inhibition exerted similar effects. Unilateral ureteral obstruction, a murine model of mechanically-triggered kidney fibrosis, induced tubular RhoA activation along with overexpression/nuclear accumulation of MRTF and TAZ, and increased transcription of the above-mentioned cytokines. Laser capture microdissection revealed TAZ, TGFβ1 and CTGF induction specifically in the tubular epithelium. CCG-1423 suppressed total renal and tubular expression of these proteins. Thus, MRTF regulates epithelial TAZ expression, and both MRTF and TAZ are critical mediators of PEP-related epithelial cytokine production.
Adhesive protein-mediated cross-talk between Candida albicans and Porphyromonas gingivalis in dual species biofilm protects the anaerobic bacterium in unfavorable oxic environment
Authors: Bartnicka Dominika , Karkowska-Kuleta Justyna , Zawrotniak Marcin , Satała Dorota , Michalik Kinga , Zielinska Gabriela , Bochenska Oliwia , Kozik Andrzej , Ciaston Izabela , Koziel Joanna , Dutton Lindsay C. , Nobbs Angela H. , Potempa Barbara , Baster Zbigniew , Rajfur Zenon , Potempa Jan , Rapala-Kozik Maria 
Published: March 2019

AbstractThe oral cavity contains different types of microbial species that colonize human host via extensive cell-to-cell interactions and biofilm formation. Candida albicans—a yeast-like fungus that inhabits mucosal surfaces—is also a significant colonizer of subgingival sites in patients with chronic periodontitis. It is notable however that one of the main infectious agents that causes periodontal disease is an anaerobic bacterium—Porphyromonas gingivalis. In our study, we evaluated the different strategies of both pathogens in the mutual colonization of an artificial surface and confirmed that a protective environment existed for P. gingivalis within developed fungal biofilm formed under oxic conditions where fungal cells grow mainly in their filamentous form i.e. hyphae. A direct physical contact between fungi and P. gingivalis was initiated via a modulation of gene expression for the major fungal cell surface adhesin Als3 and the aspartic proteases Sap6 and Sap9. Proteomic identification of the fungal surfaceome suggested also an involvement of the Mp65 adhesin and a “moonlighting” protein, enolase, as partners for the interaction with P. gingivalis. Using mutant strains of these bacteria that are defective in the production of the gingipains—the proteolytic enzymes that also harbor hemagglutinin domains—significant roles of these proteins in the formation of bacteria-protecting biofilm were clearly demonstrated.
Histone acetylation determines transcription of atypical protein kinases in rat neurons
Authors: Borodinova Anastasia A. , Kuznetsova Maria A. , Alekseeva Victoria S. , Balaban Pavel M. 
Published: March 2019

AbstractIt is widely accepted that memory consolidation requires de-novo transcription of memory-related genes. Epigenetic modifications, particularly histone acetylation, may facilitate gene transcription, but their potential molecular targets are poorly characterized. In the current study, we addressed the question of epigenetic control of atypical protein kinases (aPKC) that are critically involved in memory consolidation and maintenance. We examined the patterns of expression of two aPKC genes (Prkci and Prkcz) in rat cultured cortical neurons treated with histone deacetylase inhibitors. Histone hyperacetylation in the promoter region of Prkci gene elicited direct activation of transcriptional machinery, resulting in increased production of PKCλ mRNA. In parallel, histone hyperacetylation in the upstream promoter of Prkcz gene led to appearance of the corresponding PKCζ transcripts that are almost absent in the brain in resting conditions. In contrast, histone hyperacetylation in the downstream promoter of Prkcz gene was accompanied by a decreased expression of the brain-specific PKMζ products. We showed that epigenetically-triggered differential expression of PKMζ and PKCζ mRNA depended on protein synthesis. Summarizing, our results suggest that genes, encoding memory-related aPKC, may represent the molecular targets for epigenetic regulation through posttranslational histone modifications.
Sanitization Efficacy of Slightly Acidic Electrolyzed Water against pure cultures of Escherichia coli, Salmonella enterica, Typhimurium, Staphylococcus aureus and Bacillus cereus spores, in Comparison with Different Water Hardness
Authors: Kim Hyun-Ji , Tango Charles Nkufi , Chelliah Ramachandran , Oh Deog-Hwan 
Published: March 2019

AbstractThe Influence of water source on the production of slightly acidic electrolyzed water (SAEW) and its sanitization efficacy were investigated. Two different water sources (tap water (TW) and underground water (UGW)) were applied to produce slightly acidic electrolyzed water (SAEW) at same setting current, with similar electrolyte flow rate (EFR) and concentration. Properties of SAEW were evaluated based on pH, Available chlorine concentration (ACC) and oxidation-reduction potential (ORP). Methods for the optimization of SAEW production process was examined to obtain high ACC value by implanting different types of electrolytes. Effect of ACC and pH of SAEW were evaluated in vitro towards inactivate foodborne pathogens. The results indicated that TW with hardness of 29 ppm produced effectively SAEW than through UGW (12 ppm) using electrolytes. Likewise, low water hardness could be reinforced by combining HCL with a salt (NaCl or KCL). The optimized SAEW production system was determined at 4% HCl + 2.0 M KCL with EFR of 2 mL/min and 4% HCl + 3.0 M KCL with EFR of 2 mL/min resulting in higher ACC value of 56.5 and 65.5 ppm, respectively using TW. Pathogenic vegetative cells were completely inactivated within 1 min of treatment in SAEW with 20 ppm. Viability observations using Confocal and TEM Microscopy, Flow cytometry, and antimicrobial activity were carried out to confirm the sanitizing effect and cell membrane disruption. Based on the experimental results obtained, it provides a foundation for future advancement towards commercial application of SAEW in the food and agricultural industries.
Defects, dopants and Mg diffusion in MgTiO3
Authors: Kuganathan Navaratnarajah , Iyngaran Poobalasuntharam , Vovk Ruslan , Chroneos Alexander 
Published: March 2019

AbstractMagnesium titanate is technologically important due to its excellent dielectric properties required in wireless communication system. Using atomistic simulation based on the classical pair potentials we study the defect chemistry, Mg and O diffusion and a variety of dopant incorporation at Mg and Ti sites. The defect calculations suggest that cation anti-site defect is the most favourable defect process. The Mg Frenkel is the second most favourable intrinsic defect though the formation energy is highly endoergic. Higher overall activation energies (>3 eV) are observed for oxygen migration compared to those observed for magnesium (0.88 eV). Dopant substitution energies for a range of cations with charges varying from +2 to +4 were examined. Divalent dopants (Mn2+, Fe2+, Co2+, Ca2+ and Zn2+) on the Mg site exhibit low solution energies. Trivalent dopants prefer to occupy Mg site though their solution energies are high. Exothermic solution energies calculated for tetravalent dopants (Ge4+ and Si4+) on the Ti site suggest the necessity of experimental verification.
Phosphorus source driving the soil microbial interactions and improving sugarcane development
Authors: Gumiere Thiago , Rousseau Alain N. , da Costa Diogo Paes , Cassetari Alice , Cotta Simone Raposo , Andreote Fernando Dini , Gumiere Silvio J. , Pavinato Paulo Sergio 
Published: March 2019

AbstractThe world demand for phosphate has gradually increased over the last decades, currently achieving alarming levels considering available rock reserves. The use of soil microorganisms, such as arbuscular mycorrhizal fungi (AMF), has been suggested as a promising alternative to improve phosphorus-use efficiency. However, the effect of the source of phosphorus on the interactions within the soil microbial community remains unclear. Here, we evaluated the links between the total dry matter content of sugarcane and the interactions within the soil microbial community under different phosphate sources, with/without AMF inoculation. The phosphate sources were Simple Superphosphate (SS, 18% of P2O5), Catalão rock phosphate (CA, 2.93% of P2O5) and Bayovar rock phosphate (BA, 14% of P2O5). The results indicated that the BA source led to the largest total dry matter content. The phosphate source affected total dry matter and the structure of the soil microbial communities. The bacterial interactions increased across sources with high percentage of P2O5, while the fungal interactions decreased. The interactions between bacterial and fungal microorganisms allowed to identify the percentage of P2O5 resulting in the highest total sugarcane dry matter. Our findings suggested the soil microbial interactions as a potential microbial indicator helping to improve the agricultural management.
Metatranscriptomic exploration of microbial functioning in clouds
Authors: Amato Pierre , Besaury Ludovic , Joly Muriel , Penaud Benjamin , Deguillaume Laurent , Delort Anne-Marie 
Published: March 2019

AbstractClouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.
Model systems inform rare disease diagnosis, therapeutic discovery and pre-clinical efficacy
Authors: Enikanolaiye Adebola , Justice Monica J. 
Published: March 2019

Abstract
Model systems have played a large role in understanding human diseases and are instrumental in taking basic research findings to the clinic; however, for rare diseases, model systems play an even larger role. Here, we outline how model organisms are crucial for confirming causal associations, understanding functional mechanisms and developing therapies for disease. As diseases that have been studied extensively through genetics and molecular biology, cystic fibrosis and Rett syndrome are portrayed as primary examples of how genetic diagnosis, model organism development and therapies have led to improved patient health. Considering which model to use, yeast, worms, flies, fish, mice or larger animals requires a careful evaluation of experimental genetic tools and gene pathway conservation. Recent advances in genome editing will aid in confirming diagnoses and developing model systems for rare disease. Genetic or chemical screening for disease suppression may reveal functional pathway members and provide candidate entry points for developing therapies. Model organisms may also be used in drug discovery and as preclinical models as a prelude to testing treatments in patient populations. Now, model organisms will increasingly be used as platforms for understanding variation in rare disease severity and onset, thereby informing therapeutic intervention.
The Collaborative Network Approach: a model for advancing patient-centric research for Castleman disease and other rare diseases
Authors: Zuccato Mary , Shilling Dustin , Fajgenbaum David C. 
Published: March 2019

Abstract
There are ∼7000 rare diseases affecting 30 000 000 individuals in the U.S.A. 95% of these rare diseases do not have a single Food and Drug Administration-approved therapy. Relatively, limited progress has been made to develop new or repurpose existing therapies for these disorders, in part because traditional funding models are not as effective when applied to rare diseases. Due to the suboptimal research infrastructure and treatment options for Castleman disease, the Castleman Disease Collaborative Network (CDCN), founded in 2012, spearheaded a novel strategy for advancing biomedical research, the ‘Collaborative Network Approach’. At its heart, the Collaborative Network Approach leverages and integrates the entire community of stakeholders — patients, physicians and researchers — to identify and prioritize high-impact research questions. It then recruits the most qualified researchers to conduct these studies. In parallel, patients are empowered to fight back by supporting research through fundraising and providing their biospecimens and clinical data. This approach democratizes research, allowing the entire community to identify the most clinically relevant and pressing questions; any idea can be translated into a study rather than limiting research to the ideas proposed by researchers in grant applications. Preliminary results from the CDCN and other organizations that have followed its Collaborative Network Approach suggest that this model is generalizable across rare diseases.