bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perovskite nickelates as bio-electronic interfaces
Authors: Zhang Hai-Tian , Zuo Fan , Li Feiran , Chan Henry , Wu Qiuyu , Zhang Zhan , Narayanan Badri , Ramadoss Koushik , Chakraborty Indranil , Saha Gobinda , Kamath Ganesh , Roy Kaushik , Zhou Hua , Chubykin Alexander A. , Sankaranarayanan Subramanian K. R. S. , Choi Jong Hyun , Ramanathan Shriram 
Published: April 2019

AbstractFunctional interfaces between electronics and biological matter are essential to diverse fields including health sciences and bio-engineering. Here, we report the discovery of spontaneous (no external energy input) hydrogen transfer from biological glucose reactions into SmNiO3, an archetypal perovskite quantum material. The enzymatic oxidation of glucose is monitored down to ~5 × 10−16 M concentration via hydrogen transfer to the nickelate lattice. The hydrogen atoms donate electrons to the Ni d orbital and induce electron localization through strong electron correlations. By enzyme specific modification, spontaneous transfer of hydrogen from the neurotransmitter dopamine can be monitored in physiological media. We then directly interface an acute mouse brain slice onto the nickelate devices and demonstrate measurement of neurotransmitter release upon electrical stimulation of the striatum region. These results open up avenues for use of emergent physics present in quantum materials in trace detection and conveyance of bio-matter, bio-chemical sciences, and brain-machine interfaces.
Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases
Authors: Fang Wenxia , Sanz Ana Belén , Bartual Sergio Galan , Wang Bin , Ferenbach Andrew T. , Farkaš Vladimír , Hurtado-Guerrero Ramon , Arroyo Javier , van Aalten Daan M. F. 
Published: April 2019

AbstractFungal cell wall synthesis is achieved by a balance of glycosyltransferase, hydrolase and transglycosylase activities. Transglycosylases strengthen the cell wall by forming a rigid network of crosslinks through mechanisms that remain to be explored. Here we study the function of the Aspergillus fumigatus family of five Crh transglycosylases. Although crh genes are dispensable for cell viability, simultaneous deletion of all genes renders cells sensitive to cell wall interfering compounds. In vitro biochemical assays and localisation studies demonstrate that this family of enzymes functions redundantly as transglycosylases for both chitin-glucan and chitin-chitin cell wall crosslinks. To understand the molecular basis of this acceptor promiscuity, we solved the crystal structure of A. fumigatus Crh5 (AfCrh5) in complex with a chitooligosaccharide at the resolution of 2.8 Å, revealing an extensive elongated binding cleft for the donor (−4 to −1) substrate and a short acceptor (+1 to +2) binding site. Together with mutagenesis, the structure suggests a “hydrolysis product assisted” molecular mechanism favouring transglycosylation over hydrolysis.
Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm
Authors: Kubota Sho , Tokunaga Kenji , Umezu Tomohiro , Yokomizo-Nakano Takako , Sun Yuqi , Oshima Motohiko , Tan Kar Tong , Yang Henry , Kanai Akinori , Iwanaga Eisaku , Asou Norio , Maeda Takahiro , Nakagata Naomi , Iwama Atsushi , Ohyashiki Kazuma , Osato Motomi , Sashida Goro 
Published: April 2019

AbstractBlastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive subtype of acute leukemia, the cell of origin of which is considered to be precursors of plasmacytoid dendritic cells (pDCs). Since translocation (6;8)(p21;q24) is a recurrent anomaly for BPDCN, we demonstrate that a pDC-specific super-enhancer of RUNX2 is associated with the MYC promoter due to t(6;8). RUNX2 ensures the expression of pDC-signature genes in leukemic cells, but also confers survival and proliferative properties in BPDCN cells. Furthermore, the pDC-specific RUNX2 super-enhancer is hijacked to activate MYC in addition to RUNX2 expression, thereby promoting the proliferation of BPDCN. We also demonstrate that the transduction of MYC and RUNX2 is sufficient to initiate the transformation of BPDCN in mice lacking Tet2 and Tp53, providing a model that accurately recapitulates the aggressive human disease and gives an insight into the molecular mechanisms underlying the pathogenesis of BPDCN.
Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm
Authors: Gladstein Scott , Almassalha Luay M. , Cherkezyan Lusik , Chandler John E. , Eshein Adam , Eid Aya , Zhang Di , Wu Wenli , Bauer Greta M. , Stephens Andrew D. , Morochnik Simona , Subramanian Hariharan , Marko John F. , Ameer Guillermo A. , Szleifer Igal , Backman Vadim 
Published: April 2019

AbstractUnderstanding the relationship between intracellular motion and macromolecular structure remains a challenge in biology. Macromolecular structures are assembled from numerous molecules, some of which cannot be labeled. Most techniques to study motion require potentially cytotoxic dyes or transfection, which can alter cellular behavior and are susceptible to photobleaching. Here we present a multimodal label-free imaging platform for measuring intracellular structure and macromolecular dynamics in living cells with a sensitivity to macromolecular structure as small as 20 nm and millisecond temporal resolution. We develop and validate a theory for temporal measurements of light interference. In vitro, we study how higher-order chromatin structure and dynamics change during cell differentiation and ultraviolet (UV) light irradiation. Finally, we discover cellular paroxysms, a near-instantaneous burst of macromolecular motion that occurs during UV induced cell death. With nanoscale sensitive, millisecond resolved capabilities, this platform could address critical questions about macromolecular behavior in live cells.
Orbitally driven giant thermal conductance associated with abnormal strain dependence in hydrogenated graphene-like borophene
Authors: He Jia , Li Dengfeng , Ying Yan , Feng Chunbao , He Junjie , Zhong Chengyong , Zhou Hangbo , Zhou Ping , Zhang Gang 
Published: April 2019

AbstractHeat energy in solids is carried by phonons and electrons. However, in most two-dimensional (2D) materials, the contribution from electrons to total thermal conduction is much lower than that for phonons. In this work, through first-principles calculations combined with non-equilibrium Green’s function theory, we studied electron and phonon thermal conductance in recently synthesized 2D hydrogen boride. The hexagonal boron network with bridging hydrogen atoms is suggested to exhibit comparable lattice thermal conductance (4.07 nWK−1 nm−2) as graphene (4.1 nWK−1 nm−2), and similar electron thermal conductance (3.6 nWK−1 nm−2), which is almost ten times that of graphene. As a result, total thermal conductance of 2D hydrogen boride is about two-fold of graphene, being the highest value in all known 2D materials. Moreover, tensile strain along the armchair direction leads to an increase in carrier density, significantly increasing electron thermal conductance. The increase in electron thermal conductance offsets the reduction in phonon thermal conductance, contributing to an abnormal increase in thermal conductance. We demonstrate that the high electron density governs extraordinarily high thermal conductance in 2D hydrogen boride, distinctive among 2D materials.
A data citation roadmap for scholarly data repositories
Authors: Fenner Martin , Crosas Mercè , Grethe Jeffrey S. , Kennedy David , Hermjakob Henning , Rocca-Serra Phillippe , Durand Gustavo , Berjon Robin , Karcher Sebastian , Martone Maryann , Clark Tim 
Published: April 2019

AbstractThis article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles, a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Expert Group, as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH-funded BioCADDIE (https://biocaddie.org) project. The roadmap makes 11 specific recommendations, grouped into three phases of implementation: a) required steps needed to support the Joint Declaration of Data Citation Principles, b) recommended steps that facilitate article/data publication workflows, and c) optional steps that further improve data citation support provided by data repositories. We describe the early adoption of these recommendations 18 months after they have first been published, looking specifically at implementations of machine-readable metadata on dataset landing pages.
A Multi-Trait Approach Identified Genetic Variants Including a Rare Mutation in RGS3 with Impact on Abnormalities of Cardiac Structure/Function
Authors: Yazdani Akram , Yazdani Azam , Méndez Giráldez Raúl , Aguilar David , Sartore Luca 
Published: April 2019

AbstractHeart failure is a major cause for premature death. Given the heterogeneity of the heart failure syndrome, identifying genetic determinants of cardiac function and structure may provide greater insights into heart failure. Despite progress in understanding the genetic basis of heart failure through genome wide association studies, the heritability of heart failure is not well understood. Gaining further insights into mechanisms that contribute to heart failure requires systematic approaches that go beyond single trait analysis. We integrated a Bayesian multi-trait approach and a Bayesian networks for the analysis of 10 correlated traits of cardiac structure and function measured across 3387 individuals with whole exome sequence data. While using single-trait based approaches did not find any significant genetic variant, applying the integrative Bayesian multi-trait approach, we identified 3 novel variants located in genes, RGS3, CHD3, and MRPL38 with significant impact on the cardiac traits such as left ventricular volume index, parasternal long axis interventricular septum thickness, and mean left ventricular wall thickness. Among these, the rare variant NC_000009.11:g.116346115C > A (rs144636307) in RGS3 showed pleiotropic effect on left ventricular mass index, left ventricular volume index and maximal left atrial anterior-posterior diameter while RGS3 can inhibit TGF-beta signaling associated with left ventricle dilation and systolic dysfunction.
Plastic waste interferes with chemical communication in aquatic ecosystems
Authors: Trotter B. , Ramsperger A. F. R. M. , Raab P. , Haberstroh J. , Laforsch C. 
Published: April 2019

AbstractEnvironmental pollution with plastic waste has gained increasing attention, as the contamination of aquatic habitats poses a challenge to these ecosystems. Plastic waste has direct negative effects on animals such as reduced growth rate, fecundity or life span. However, the indirect effects of plastic waste, which has the ability to sorb chemicals from the surrounding media, on chemical communication have yet to be investigated. Chemical communication is crucial for aquatic organisms, e.g., to avoid predation. The planktonic water flea Daphnia (Crustacea), an important link between trophic levels, relies on info-chemicals (kairomones) to assess its current predation risk and to form inducible defences. We show that plastic waste, composed of high-density polyethylene (HDPE) and polyethylene terephthalate (PET) interferes with the formation of inducible defences in Daphnia longicephala when exposed to a combination of kairomones of Notonecta glauca and plastic waste. D. longicephala shows a reduction in all defensive traits, including body length, crest width and time until primiparity, compared to exposure to solely kairomone conditioned media. Plastic waste in the absence of kairomones had no effect on defensive traits. Since it is vital to adjust these defences to the current predation risk, any misperception can have far-reaching ecological consequences. Therefore, plastic waste can have indirect effects on organisms, which may manifest at the community level.
Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity
Authors: Khanna Kanika , Jamwal Vijay Lakshmi , Gandhi Sumit G. , Ohri Puja , Bhardwaj Renu 
Published: April 2019

AbstractPlant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.
Roles of cellular heterogeneity, intrinsic and extrinsic noise in variability of p53 oscillation
Authors: Wang Dao-Guang , Wang Shaobing , Huang Bo , Liu Feng 
Published: April 2019

AbstractThe p53 protein is a key mediator of the cellular response to various stress signals. In response to DNA damage, the concentration of p53 can temporally oscillate with fluctuations in both the amplitude and period. The underlying mechanism for p53 variability is not fully understood. Here, we construct a core regulatory network of p53 dynamics comprising the ATM-p53-Wip1 and p53-Mdm2 negative feedback loops. We dissect the contributions of cellular heterogeneity, intrinsic noise, and multiple forms of extrinsic noise to p53 variability in terms of the coefficients of variation of four quantities. Cellular heterogeneity greatly determines the fraction of oscillating cells among a population of isogenic cells. Intrinsic noise—fluctuation in biochemical reactions–has little impact on p53 variability given large amounts of molecules, whereas extrinsic colored noise with proper strength and correlation time contributes much to oscillatory variability in individual cells. With the three sources of noise combined, our results reproduce the experimental observations, suggesting that the long correlation time of colored noise is essential to p53 variability. Compared with previous studies, the current work reveals both the individual and integrated effects of distinct noise sources on p53 variability. This study provides a framework for exploring the variability in oscillations in cellular signaling pathways.
Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations
Authors: Filppula Anne M. , Parvizi Rezvan , Mateus André , Baranczewski Pawel , Artursson Per 
Published: April 2019

AbstractThe clinical impact of drug-drug interactions based on time-dependent inhibition of cytochrome P450 (CYP) 3A4 has often been overpredicted, likely due to use of improper inhibitor concentration estimates at the enzyme. Here, we investigated if use of cytosolic unbound inhibitor concentrations could improve predictions of time-dependent drug-drug interactions. First, we assessed the inhibitory effects of ten time-dependent CYP3A inhibitors on midazolam 1′-hydroxylation in human liver microsomes. Then, using a novel method, we determined the cytosolic bioavailability of the inhibitors in human hepatocytes, and used the obtained values to calculate their concentrations at the active site of the enzyme, i.e. the cytosolic unbound concentrations. Finally, we combined the data in mechanistic static predictions, by considering different combinations of inhibitor concentrations in intestine and liver, including hepatic concentrations corrected for cytosolic bioavailability. The results were then compared to clinical data. Compared to no correction, correction for cytosolic bioavailability resulted in higher accuracy and precision, generally in line with those obtained by more demanding modelling. The best predictions were obtained when the inhibition of hepatic CYP3A was based on unbound maximal inhibitor concentrations corrected for cytosolic bioavailability. Our findings suggest that cytosolic unbound inhibitor concentrations improves predictions of time-dependent drug-drug interactions for CYP3A.
Comparison of a personalized breast dosimetry method with standard dosimetry protocols
Authors: Salomon Elisabeth , Homolka Peter , Semturs Friedrich , Figl Michael , Gruber Michael , Hummel Johann 
Published: April 2019

AbstractAverage glandular dose (AGD) in digital mammography crucially depends on the estimation of breast glandularity. In this study we compared three different methods of estimating glandularities according to Wu, Dance and Volpara with respect to resulting AGDs. Exposure data from 3050 patient images, acquired with a GE Senographe Essential constituted the study population of this work. We compared AGD (1) according to Dance et al. applying custom g, c, and s factors using HVL, breast thickness, patient age and incident air kerma (IAK) from the DICOM headers; (2) according to Wu et al. as determined by the GE system; and (3) AGD derived with the Dance model with personalized c factors using glandularity determined with the Volpara (Volpara Solutions, Wellington, New Zealand) software (Volpare AGD). The ratios of the resulting AGDs were analysed versus parameters influencing dose. The highest deviation between the resulting AGDs was found in the ratio of GE AGD to Volpara AGD for breast thicknesses between 20 and 40 mm (ratio: 0.80). For thicker breasts this ratio is close to one (1 ± 0.02 for breast thicknesses >60 mm). The Dance to Volpara ratio was between 0.86 (breast thickness 20–40 mm) and 0.99 (>80 mm), and Dance/GE AGD was between 1.07 (breast thickness 20–40 mm) and 0.98 (41–60, and >80 mm). Glandularities by Volpara were generally smaller than the one calculated with the Dance method. This effect is most pronounced for small breast thickness and older ages. Taking the considerable divergences between the AGDs from different methods into account, the selection of the method should by done carefully. As the Volpara method provides an analysis of the individual breast tissue, while the Wu and the Dance methods use look up tables and custom parameter sets, the Volpara method might be more appropriate if individual ADG values are sought. For regulatory purposes and comparison with diagnostic reference values, the method to be used needs to be defined exactly and clearly be stated. However, it should be accepted that dose values calculated with standardized models, like AGD and also effective dose, are afflicted with a considerable uncertainty budgets that need to be accounted for in the interpretation of these values.
First Trimester Circulating MicroRNA Biomarkers Predictive of Subsequent Preterm Delivery and Cervical Shortening
Authors: Cook Joanna , Bennett Phillip R. , Kim Sung Hye , Teoh Tiong Ghee , Sykes Lynne , Kindinger Lindsay M. , Garrett Alice , Binkhamis Reem , MacIntyre David A. , Terzidou Vasso 
Published: April 2019

AbstractPreterm birth (PTB) is the leading cause of infant death and disability worldwide. The onset of preterm uterine contractions is preceded by asymptomatic cervical remodelling and ripening, which can be seen on trans-vaginal ultrasound as cervical shortening. This study aimed to identify plasma miRNA biomarkers that predict preterm birth and/or cervical shortening. We collected serial plasma samples from pregnant women prospectively from 12 to 22 weeks gestation. The nCounter miRNA assay was used to identify differentially expressed miRNAs associated with spontaneous PTB and/or cervical shortening (n = 16 term no short, n = 13 preterm, n = 24 short). Predictive values of the miRNA biomarkers were confirmed in an independent validation cohort consisting of 96 women who delivered at term, 14 preterm and 21 early cervical shortening at <20 weeks gestation. Nine miRNAs (hsa-let-7a-5p, hsa-miR-374a-5p, hsa-miR-15b-5p, hsa-miR-19b-3p, hsa-miR-23a-3p, hsa-miR-93-5p, hsa-miR-150-5p, hsa-miR-185-5p and hsa-miR-191-5p) were differentially expressed (P < 0.001) in women subsequently experiencing PTB or cervical shortening. Hsa-miR-150-5p had the strongest ability to predict PTB (AUC = 0.8725) and cervical shortening (AUC = 0.8514). Plasma miRNAs in the first trimester can predict PTB and cervical shortening in women at risk of preterm delivery. This is a key period in pregnancy when early identification of PTB risk allows time to deliver outcome-modifying interventions.
Histological Chorioamnionitis Induces Differential Gene Expression in Human Cord Blood Mononuclear Leukocytes from Term Neonates
Authors: Gayen nee’ Betal Suhita , Murthy Swati , Favara Michael , Fong Gina , Chan Joanna S. Y. , Addya Sankar , Shaffer Thomas H. , Greenspan Jay , Bhandari Vineet , Rahman Irfan , Aghai Zubair H. 
Published: April 2019

AbstractHistological chorioamnionitis (HCA) is an infection of fetal membranes and complicates 5.2% to 28.5% of all live births. HCA is associated with increased mortality and morbidity in both premature and term neonates. Exposure to HCA may have long-term consequences, including an increased risk for allergic disorders and asthma later in childhood, the mechanism(s) of which are still not yet well understood. The objective of this study was to determine the mRNA transcriptome of cord blood mononuclear leukocytes from term neonates to identify key genes and pathways involved in HCA. We found 366 differentially expressed probe IDs with exposure to HCA (198 upregulated, 168 downregulated). These transcriptomes included novel genes and pathways associated with exposure to HCA. The differential gene expression included key genes regulating inflammatory, immune, respiratory and neurological pathways, which may contribute to disorders in those pathways in neonates exposed to HCA. Our data may lead to understanding of the role of key genes and pathways identified on the long-term sequelae related to exposure to HCA, as well as to identifying potential markers and therapies to prevent HCA-associated complications.