bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bias in recent miRBase annotations potentially associated with RNA quality issues
Authors: Ludwig Nicole , Becker Meike , Schumann Timo , Speer Timo , Fehlmann Tobias , Keller Andreas , Meese Eckart 
Published: July 2017

AbstractAlthough microRNAs are supposed to be stable in-vivo, degradation processes potentially blur our knowledge on the small oligonucleotides. We set to quantify the effect of degradation on microRNAs in mouse to identify causes for distorted microRNAs patterns. In liver, we found 298, 99 and 8 microRNAs whose expression significantly correlated to RNA integrity, storage time at room temperature and storage time at 4 °C, respectively. Expression levels of 226 microRNAs significantly differed between liver samples with high RNA integrity compared to liver samples with low RNA integrity by more than two-fold. Especially the 157 microRNAs with increased expression in tissue samples with low RNA integrity were most recently added to miRBase. Testing potentially confounding sources, e.g. in-vitro degraded RNA depleted of small RNAs, we detected signals for 350 microRNAs, suggesting cross-hybridization of fragmented RNAs. Therefore, we conclude that especially microRNAs added in the latest miRBase versions might be artefacts due to RNA degradation. The results facilitate differentiation between degradation-resilient microRNAs, degradation-sensitive microRNAs, and likely erroneously annotated microRNAs. The latter were largely identified by NGS but not experimentally validated and can severely bias microRNA biomarker research and impact the value of microRNAs as diagnostic, prognostic or therapeutic tools.
Next Generation Driver for Attosecond and Laser-plasma Physics
Authors: Rivas D. E. , Borot A. , Cardenas D. E. , Marcus G. , Gu X. , Herrmann D. , Xu J. , Tan J. , Kormin D. , Ma G. , Dallari W. , Tsakiris G. D. , Földes I. B. , Chou S.-w. , Weidman M. , Bergues B. , Wittmann T. , Schröder H. , Tzallas P. , Charalambidis D. , Razskazovskaya O. , Pervak V. , Krausz F. , Veisz L. 
Published: July 2017

AbstractThe observation and manipulation of electron dynamics in matter call for attosecond light pulses, routinely available from high-order harmonic generation driven by few-femtosecond lasers. However, the energy limitation of these lasers supports only weak sources and correspondingly linear attosecond studies. Here we report on an optical parametric synthesizer designed for nonlinear attosecond optics and relativistic laser-plasma physics. This synthesizer uniquely combines ultra-relativistic focused intensities of about 1020 W/cm2 with a pulse duration of sub-two carrier-wave cycles. The coherent combination of two sequentially amplified and complementary spectral ranges yields sub-5-fs pulses with multi-TW peak power. The application of this source allows the generation of a broad spectral continuum at 100-eV photon energy in gases as well as high-order harmonics in relativistic plasmas. Unprecedented spatio-temporal confinement of light now permits the investigation of electric-field-driven electron phenomena in the relativistic regime and ultimately the rise of next-generation intense isolated attosecond sources.
Precise detection of circular dichroism in a cluster of nano-helices by photoacoustic measurements
Authors: Benedetti Alessio , Alam Badrul , Esposito Marco , Tasco Vittorianna , Leahu Grigore , Belardini Alessandro , Li Voti Roberto , Passaseo Adriana , Sibilia Concita 
Published: July 2017

AbstractCompact samples of nano-helices built by means of a focused ion beam technology with large bandwidth and high dichroism for circular polarization are promising for the construction of built-in-chip sensors, where the ideal transducer must be sufficiently confined without compromising its filtering ability. Direct all-optical measurements revealed the sample’s dichroic character with insufficient details because of scattering and diffraction interference. On the other hand, photoacoustic measurements resulted to be a possible alternative investigation, since they directly deal with absorbed power and allow to get clear evidences of the differential selection for the two opposite polarization states. Multi-level numerical simulations confirmed the experimental results, proving once again the reliability of photoacoustic technique and the versatility of this class of dichroic artificial materials.
Use of Single-Frequency Impedance Spectroscopy to Characterize the Growth Dynamics of Biofilm Formation in Pseudomonas aeruginosa
Authors: van Duuren Jozef B. J. H. , Müsken Mathias , Karge Bianka , Tomasch Jürgen , Wittmann Christoph , Häussler Susanne , Brönstrup Mark 
Published: July 2017

AbstractImpedance spectroscopy has been applied in prokaryotic and eukaryotic cytometry as a label-free method for the investigation of adherent cells. In this paper, its use for characterizing the growth dynamics of P. aeruginosa biofilms is described and compared to crystal violet staining and confocal microscopy. The method allows monitoring the growth of biofilm-forming P. aeruginosa in a continuous and label-free manner over a period of 72 h in a 96 well plate format. Impedance curves obtained for P. aeruginosa PA14 wild type and mutant strains with a transposon insertion in pqsA and pelA genes exhibited distinct phases. We propose that the slope of the declining curve following a maximum at ca. 35–40 h is a measure of biofilm formation. Transplant experiments with P. aeruginosa biofilms and paraffin suggest that the impedance also reflects pellicle formation at the liquid-air interface, a barely considered contributor to impedance. Finally, the impairment of biofilm formation upon treatment of cultures with L-arginine and with ciprofloxacin, tobramycin and meropenem was studied by single frequency impedance spectroscopy. We suggest that these findings qualify impedance spectroscopy as an additional technique to characterize biofilm formation and its modulation by small molecule drugs.
Development of sodium acetate trihydrate-ethylene glycol composite phase change materials with enhanced thermophysical properties for thermal comfort and therapeutic applications
Authors: Kumar Rohitash , Vyas Sumita , Kumar Ravindra , Dixit Ambesh 
Published: July 2017

AbstractThe heat packs using phase change materials (PCMs) are designed for possible applications such as body comfort and medical applications under adverse situations. The development and performance of such heat packs rely on thermophysical properties of PCMs such as latent heat, suitable heat releasing temperature, degree of supercooling, effective heat releasing time, crystallite size, stability against spontaneous nucleation in metastable supercooled liquid state and thermal stability during heating and cooling cycles. Such PCMs are rare and the available PCMs do not exhibit such properties simultaneously to meet the desired requirements. The present work reports a facile approach for the design and development of ethylene glycol (EG) and aqueous sodium acetate trihydrate (SAT) based composite phase change materials, showing these properties simultaneously. The addition of 2–3 wt% EG in aqueous SAT enhances the softness of SAT crystallites, its degree of supercooling and most importantly the effective heat releasing time by ~10% with respect to aqueous SAT material. In addition, the maximum heat releasing temperature of aqueous SAT has been tailored from 56.5 °C to 55 °C, 54.9 °C, 53.5 °C, 51.8 °C and 43.2 °C using 2%, 3%, 5%, 7% and 10 wt% EG respectively, making the aqueous SAT-EG composite PCMs suitable for desired thermal applications.
Temperature dependent giant resistance anomaly in LaAlO3/SrTiO3 nanostructures
Authors: Minhas M. Z. , Müller A. , Heyroth F. , Blaschek H. H. , Schmidt G. 
Published: July 2017

AbstractThe resistance of the electron gas (2DEG) at the interface between the two band insulators LaAlO3 (LAO) and SrTiO3 (STO) typically drops monotonically with temperature and R/T curves during cooling and warm-up look identical for large area structures. Here we show that if the LAO/STO is laterally restricted by nanopatterning the resistance exhibits a temperature anomaly. Warming up nanostructures from low temperatures leads to one or two pronounced resistance peaks between 50 and 100 K not observed for larger dimensions. During cool-down current filaments emerge at the domain walls that form during a structural phase transition of the STO substrate. During warm-up the reverse phase transition can interrupt filaments before the sheet conductivity which dominates at higher temperature is reestablished. Due to the limited number of filaments in a nanostructure this process can result in a complete loss of conductance. As a consequence of these findings the transport physics extracted from experiments in small and large area LAO/STO structures may need to be reconsidered.
Clustering on Magnesium Surfaces – Formation and Diffusion Energies
Authors: Chu Haijian , Huang Hanchen , Wang Jian 
Published: July 2017

AbstractThe formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and $$\{\bar{1}011\}$$
{

1
¯

011
}
. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a $$\{\bar{1}011\}$$
{

1
¯

011
}
, clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface $$\{\bar{1}011\}$$
{

1
¯

011
}
is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.
Genotype by random environmental interactions gives an advantage to non-favored minor alleles
Authors: Mahdipour-Shirayeh A. , Darooneh A. H. , Long A. D. , Komarova N. L. , Kohandel M. 
Published: July 2017

AbstractFixation probability, the probability that the frequency of a newly arising mutation in a population will eventually reach unity, is a fundamental quantity in evolutionary genetics. Here we use a number of models (several versions of the Moran model and the haploid Wright-Fisher model) to examine fixation probabilities for a constant size population where the fitness is a random function of both allelic state and spatial position, despite neither allele being favored on average. The concept of fitness varying with respect to both genotype and environment is important in models of cancer initiation and progression, bacterial dynamics, and drug resistance. Under our model spatial heterogeneity redefines the notion of neutrality for a newly arising mutation, as such mutations fix at a higher rate than that predicted under neutrality. The increased fixation probability appears to be due to rare alleles having an advantage. The magnitude of this effect can be large, and is an increasing function of the spatial variance and skew in fitness. The effect is largest when the fitness values of the mutants and wild types are anti-correlated across environments. We discuss results for both a spatial ring geometry of cells (such as that of a colonic crypt), a 2D lattice and a mass-action (complete graph) arrangement.
High-throughput Identification and Characterization of Two-dimensional Materials using Density functional theory
Authors: Choudhary Kamal , Kalish Irina , Beams Ryan , Tavazza Francesca 
Published: July 2017

AbstractWe introduce a simple criterion to identify two-dimensional (2D) materials based on the comparison between experimental lattice constants and lattice constants mainly obtained from Materials-Project (MP) density functional theory (DFT) calculation repository. Specifically, if the relative difference between the two lattice constants for a specific material is greater than or equal to 5%, we predict them to be good candidates for 2D materials. We have predicted at least 1356 such 2D materials. For all the systems satisfying our criterion, we manually create single layer systems and calculate their energetics, structural, electronic, and elastic properties for both the bulk and the single layer cases. Currently the database consists of 1012 bulk and 430 single layer materials, of which 371 systems are common to bulk and single layer. The rest of calculations are underway. To validate our criterion, we calculated the exfoliation energy of the suggested layered materials, and we found that in 88.9% of the cases the currently accepted criterion for exfoliation was satisfied. Also, using molybdenum telluride as a test case, we performed X-ray diffraction and Raman scattering experiments to benchmark our calculations and understand their applicability and limitations. The data is publicly available at the website http://www.ctcms.nist.gov/~knc6/JVASP.html.
Free-of-Acrylamide SDS-based Tissue Clearing (FASTClear) for three dimensional visualization of myocardial tissue
Authors: Perbellini Filippo , Liu Alan K. L. , Watson Samuel A. , Bardi Ifigeneia , Rothery Stephen M. , Terracciano Cesare M. 
Published: July 2017

AbstractSeveral pathologic conditions of the heart lead to cardiac structural remodelling. Given the high density and the opaque nature of the myocardium, deep three dimensional (3D) imaging is difficult to achieve and structural analysis of pathological myocardial structure is often limited to two dimensional images and of thin myocardial sections. Efficient methods to obtain optical clearing of the tissue for 3D visualisation are therefore needed. Here we describe a rapid, simple and versatile Free-of-Acrylamide SDS-based Tissue Clearing (FASTClear) protocol specifically designed for cardiac tissue. With this method 3D information regarding collagen content, collagen localization and distribution could be easily obtained across a whole 300 µm-thick myocardial slice. FASTClear does not induce structural or microstructural distortion and it can be combined with immunostaining to identify the micro- and macrovascular networks. In summary, we have obtained decolorized myocardial tissue suitable for high resolution 3D imaging, with implications for the study of complex cardiac tissue structure and its changes during pathology.
Deficient Vitamin E Uptake During Development Impairs Neural Tube Closure in Mice Lacking Lipoprotein Receptor SR-BI
Authors: Santander Nicolás , Lizama Carlos , Parga María José , Quiroz Alonso , Pérez Druso , Echeverría Guadalupe , Ulloa Lorena , Palma Verónica , Rigotti Attilio , Busso Dolores 
Published: July 2017

AbstractSR-BI is the main receptor for high density lipoproteins (HDL) and mediates the bidirectional transport of lipids, such as cholesterol and vitamin E, between these particles and cells. During early development, SR-BI is expressed in extraembryonic tissue, specifically in trophoblast giant cells in the parietal yolk sac. We previously showed that approximately 50% of SR-BI−/− embryos fail to close the anterior neural tube and develop exencephaly, a perinatal lethal condition. Here, we evaluated the role of SR-BI in embryonic vitamin E uptake during murine neural tube closure. Our results showed that SR-BI−/− embryos had a very low vitamin E content in comparison to SR-BI+/+ embryos. Whereas SR-BI−/− embryos with closed neural tubes (nSR-BI−/−) had high levels of reactive oxygen species (ROS), intermediate ROS levels between SR-BI+/+ and nSR-BI−/− embryos were detected in SR-BI−/− with NTD (NTD SR-BI−/−). Reduced expression of Pax3, Alx1 and Alx3 genes was found in NTD SR-BI−/− embryos. Maternal α-tocopherol dietary supplementation prevented NTD almost completely (from 54% to 2%, p < 0.001) in SR-BI−/− embryos and normalized ROS and gene expression levels. In sum, our results suggest the involvement of SR-BI in the maternal provision of embryonic vitamin E to the mouse embryo during neural tube closure.
Spatiotemporal expression profiling of long intervening noncoding RNAs in Caenorhabditis elegans
Authors: Liu Weihong , Yu Enchao , Chen Siyu , Ma Xiaopeng , Lu Yiwen , Liu Xiao 
Published: July 2017

AbstractTo better understand the biological function of long noncoding RNAs, it is critical to determine their spatiotemporal expression patterns. We generated transgenic reporter strains for 149 out of the 170 annotated C. elegans long intervening noncoding RNAs (lincRNAs) and profiled their temporal activity. For the 68 lincRNAs with integrated reporter lines, we profiled their expression at the resolution of single cells in L1 larvae, and revealed that the expression of lincRNAs is more specific, heterogeneous and at lower level than transcription factors (TFs). These expression patterns can be largely attributed to transcriptional regulation because they were observed in assays using reporters of promoter activity. The spatial expression patterns of the 68 lincRNAs were further examined in 18 tissue categories throughout eight developmental stages. We compared the expression dynamics of lincRNAs, miRNAs and TFs during development. lincRNA and miRNA promoters are less active at embryo stage than those of TFs, but become comparable to TFs after embryogenesis. Finally, the lincRNA gene set shows a similar tissue distribution to that of miRNAs and TFs. We also generated a database, CELE, for the storage and retrieval of lincRNA reporter expression patterns and other relevant information. The data and strains described here will provide a valuable guide and resource for future functional exploration of C. elegans lincRNAs.
Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics
Authors: Hosokawa Masahito , Nishikawa Yohei , Kogawa Masato , Takeyama Haruko 
Published: July 2017

AbstractMassively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.
An ant-coccid mutualism affects the behavior of the parasitoid Aenasius bambawalei, but not that of the ghost ant Tetramorium bicarinatum
Authors: Huang Jun , Zhang Peng-Jun , Zhang Juan , Tang Ya-Yuan 
Published: July 2017

AbstractMutualisms between honeydew-producing insects and ants change the emission of volatiles from plants, but whether such changes alter the behaviors of ants that tend honeydew-producing insects or wasps that parasitize honeydew-producing insects remain unknown. This study compared the behavioral responses of the ant Tetramorium bicarinatum and the parasitoid wasp Aenasius bambawalei to odors from cotton plants infested with the mealybug Phenacoccus solenopsis or infested with the mealybug and the ant, which tends the mealybug. The ant could not distinguish between the volatiles from plants infested with the mealybug alone and those from plants infested with the mealybug and the ant. Likewise, naïve wasps failed to distinguish between volatiles from the two treatments. In contrast, experienced wasps preferred volatiles from plants infested with the mealybug and the ant. Volatile analysis showed that the amounts of MeSA were increased and those of methyl nicotinate were decreased when plants were infested by the mealybug and the ant rather than when plants were uninfested or were infested by the mealybug alone. Thus, the mutualism between the mealybug and ant changed the volatiles emitted by cotton plants such that the attraction of A. bambawalei (but not that of the ant) to the plants was increased.
Genotypic variability based association identifies novel non-additive loci DHCR7 and IRF4 in sero-negative rheumatoid arthritis
Authors: Wei Wen-Hua , Viatte Sebastien , Merriman Tony R. , Barton Anne , Worthington Jane 
Published: July 2017

AbstractSero-negative rheumatoid arthritis (RA) is a highly heterogeneous disorder with only a few additive loci identified to date. We report a genotypic variability-based genome-wide association study (vGWAS) of six cohorts of sero-negative RA recruited in Europe and the US that were genotyped with the Immunochip. A two-stage approach was used: (1) a mixed model to partition dichotomous phenotypes into an additive component and non-additive residuals on the liability scale and (2) the Levene’s test to assess equality of the residual variances across genotype groups. The vGWAS identified rs2852853 (P = 1.3e-08, DHCR7) and rs62389423 (P = 1.8e-05, near IRF4) in addition to two previously identified loci (HLA-DQB1 and ANKRD55), which were all statistically validated using cross validation. DHCR7 encodes an enzyme important in cutaneous synthesis of vitamin D and DHCR7 mutations are believed to be important for early humans to adapt to Northern Europe where residents have reduced ultraviolet-B exposure and tend to have light skin color. IRF4 is a key locus responsible for skin color, with a vitamin D receptor-binding interval. These vGWAS results together suggest that vitamin D deficiency is potentially causal of sero-negative RA and provide new insights into the pathogenesis of the disorder.