bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical characterization of surface adlayers and their compositional demixing at the nanoscale
Authors: Xiang Limin , Wojcik Michal , Kenny Samuel J. , Yan Rui , Moon Seonah , Li Wan , Xu Ke 
Published: April 2018

AbstractUnder ambient conditions, the behavior of a solid surface is often dominated by a molecularly thin adsorbed layer (adlayer) of small molecules. Here we develop an optical approach to unveil the nanoscale structure and composition of small-molecule adlayers on glass surfaces through spectrally resolved super-resolution microscopy. By recording the images and emission spectra of millions of individual solvatochromic molecules that turn fluorescent in the adlayer phase, we obtain ~30 nm spatial resolution and achieve concurrent measurement of local polarity. This allows us to establish that the adlayer dimensionality gradually increases through a sequence of 0D (nanodroplets), 1D (nano-lines), and 2D (films) for liquids of increasing polarity. Moreover, we find that in adlayers, a solution of two miscible liquids spontaneously demixes into nanodroplets of different compositions that correlate strongly with droplet size and location. We thus reveal unexpectedly rich structural and compositional behaviors of surface adlayers at the nanoscale.
Disclosing the temperature of columnar jointing in lavas
Authors: Lamur Anthony , Lavallée Yan , Iddon Fiona E. , Hornby Adrian J. , Kendrick Jackie E. , von Aulock Felix W. , Wadsworth Fabian B. 
Published: April 2018

AbstractColumnar joints form by cracking during cooling-induced contraction of lava, allowing hydrothermal fluid circulation. A lack of direct observations of their formation has led to ambiguity about the temperature window of jointing and its impact on fluid flow. Here we develop a novel thermo-mechanical experiment to disclose the temperature of columnar jointing in lavas. Using basalts from Eyjafjallajökull volcano (Iceland) we show that contraction during cooling induces stress build-up below the solidus temperature (980 °C), resulting in localised macroscopic failure between 890 and 840 °C. This temperature window for incipient columnar jointing is supported by modelling informed by mechanical testing and thermal expansivity measurements. We demonstrate that columnar jointing takes place well within the solid state of volcanic rocks, and is followed by a nonlinear increase in system permeability of <9 orders of magnitude during cooling. Columnar jointing may promote advective cooling in magmatic-hydrothermal environments and fluid loss during geothermal drilling and thermal stimulation.
Self-cleaning and surface chemical reactions during hafnium dioxide atomic layer deposition on indium arsenide
Authors: Timm Rainer , Head Ashley R. , Yngman Sofie , Knutsson Johan V. , Hjort Martin , McKibbin Sarah R. , Troian Andrea , Persson Olof , Urpelainen Samuli , Knudsen Jan , Schnadt Joachim , Mikkelsen Anders 
Published: April 2018

AbstractAtomic layer deposition (ALD) enables the ultrathin high-quality oxide layers that are central to all modern metal-oxide-semiconductor circuits. Crucial to achieving superior device performance are the chemical reactions during the first deposition cycle, which could ultimately result in atomic-scale perfection of the semiconductor–oxide interface. Here, we directly observe the chemical reactions at the surface during the first cycle of hafnium dioxide deposition on indium arsenide under realistic synthesis conditions using photoelectron spectroscopy. We find that the widely used ligand exchange model of the ALD process for the removal of native oxide on the semiconductor and the simultaneous formation of the first hafnium dioxide layer must be significantly revised. Our study provides substantial evidence that the efficiency of the self-cleaning process and the quality of the resulting semiconductor–oxide interface can be controlled by the molecular adsorption process of the ALD precursors, rather than the subsequent oxide formation.
Understanding the adsorption process in ZIF-8 using high pressure crystallography and computational modelling
Authors: Hobday Claire L. , Woodall Christopher H. , Lennox Matthew J. , Frost Mungo , Kamenev Konstantin , Düren Tina , Morrison Carole A. , Moggach Stephen A. 
Published: April 2018

AbstractSome porous crystalline solids change their structure upon guest inclusion. Unlocking the potential of these solids for a wide variety of applications requires full characterisation of the response to adsorption and the underlying framework–guest interactions. Here, we introduce an approach to understanding gas uptake in porous metal-organic frameworks (MOFs) by loading liquefied gases at GPa pressures inside the Zn-based framework ZIF-8. An integrated experimental and computational study using high-pressure crystallography, grand canonical Monte Carlo (GCMC) and periodic DFT simulations has revealed six symmetry-independent adsorption sites within the framework and a transition to a high-pressure phase. The cryogenic high-pressure loading method offers a different approach to obtaining atomistic detail on guest molecules. The GCMC simulations provide information on interaction energies of the adsorption sites allowing to classify the sites by energy. DFT calculations reveal the energy barrier of the transition to the high-pressure phase. This combination of techniques provides a holistic approach to understanding both structural and energetic changes upon adsorption in MOFs.
LRH-1 agonism favours an immune-islet dialogue which protects against diabetes mellitus
Authors: Cobo-Vuilleumier Nadia , Lorenzo Petra I. , Rodríguez Noelia García , Herrera Gómez Irene de Gracia , Fuente-Martin Esther , López-Noriega Livia , Mellado-Gil José Manuel , Romero-Zerbo Silvana-Yanina , Baquié Mathurin , Lachaud Christian Claude , Stifter Katja , Perdomo German , Bugliani Marco , De Tata Vincenzo , Bosco Domenico , Parnaud Geraldine , Pozo David , Hmadcha Abdelkrim , Florido Javier P. , Toscano Miguel G. , de Haan Peter , Schoonjans Kristina , Sánchez Palazón Luis , Marchetti Piero , Schirmbeck Reinhold , Martín-Montalvo Alejandro , Meda Paolo , Soria Bernat , Bermúdez-Silva Francisco-Javier , St-Onge Luc , Gauthier Benoit R. 
Published: April 2018

AbstractType 1 diabetes mellitus (T1DM) is due to the selective destruction of islet beta cells by immune cells. Current therapies focused on repressing the immune attack or stimulating beta cell regeneration still have limited clinical efficacy. Therefore, it is timely to identify innovative targets to dampen the immune process, while promoting beta cell survival and function. Liver receptor homologue-1 (LRH-1) is a nuclear receptor that represses inflammation in digestive organs, and protects pancreatic islets against apoptosis. Here, we show that BL001, a small LRH-1 agonist, impedes hyperglycemia progression and the immune-dependent inflammation of pancreas in murine models of T1DM, and beta cell apoptosis in islets of type 2 diabetic patients, while increasing beta cell mass and insulin secretion. Thus, we suggest that LRH-1 agonism favors a dialogue between immune and islet cells, which could be druggable to protect against diabetes mellitus.
Decoding the influence of anticipatory states on visual perception in the presence of temporal distractors
Authors: van Ede Freek , Chekroud Sammi R. , Stokes Mark G. , Nobre Anna C. 
Published: April 2018

AbstractAnticipatory states help prioritise relevant perceptual targets over competing distractor stimuli and amplify early brain responses to these targets. Here we combine electroencephalography recordings in humans with multivariate stimulus decoding to address whether anticipation also increases the amount of target identity information contained in these responses, and to ask how targets are prioritised over distractors when these compete in time. We show that anticipatory cues not only boost visual target representations, but also delay the interference on these target representations caused by temporally adjacent distractor stimuli—possibly marking a protective window reserved for high-fidelity target processing. Enhanced target decoding and distractor resistance are further predicted by the attenuation of posterior 8–14 Hz alpha oscillations. These findings thus reveal multiple mechanisms by which anticipatory states help prioritise targets from temporally competing distractors, and they highlight the potential of non-invasive multivariate electrophysiology to track cognitive influences on perception in temporally crowded contexts.
Deciphering the dark proteome of Chikungunya virus
Authors: Singh Ankur , Kumar Ankur , Yadav Rakhi , Uversky Vladimir N. , Giri Rajanish 
Published: April 2018

AbstractChikungunya virus (CHIKV) is a mosquito-borne alphavirus. The outbreak of CHIKV infection has been seen in many tropical and subtropical regions of the biosphere. Current reports evidenced that after outbreaks in 2005–06, the fitness of this virus propagating in Aedes albopictus enhanced due to the epistatic mutational changes in its envelope protein. In our study, we evaluated the prevalence of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) in CHIKV proteome. IDPs/IDPRs are known as members of a ‘Dark Proteome’ that defined as a set of polypeptide segments or whole protein without unique three-dimensional structure within the cellular milieu but with significant biological functions, such as cell cycle regulation, control of signaling pathways, and maintenance of viral proteomes. However, the intrinsically disordered aspects of CHIKV proteome and roles of IDPs/IDPRs in the pathogenic mechanism of this important virus have not been evaluated as of yet. There are no existing reports on the analysis of intrinsic disorder status of CHIKV. To fulfil this goal, we have analyzed the abundance and functionality of IDPs/IDPRs in CHIKV proteins, involved in the replication and maturation. It is likely that these IDPs/IDPRs can serve as novel targets for disorder based drug design.
Causal Pathways from Blood Pressure to Larger QRS Amplitudes: a Mendelian Randomization Study
Authors: Van Der Ende M. Yldau , Hendriks Tom , Van Veldhuisen Dirk J. , Snieder Harold , Verweij Niek , Van Der Harst Pim 
Published: April 2018

AbstractAbnormal QRS duration and amplitudes on the electrocardiogram are indicative of cardiac pathology and are associated with adverse outcomes. The causal nature of these associations remains uncertain and could be due to QRS abnormalities being a symptom of cardiac damage rather than a factor on the causal pathway. By performing Mendelian randomization (MR) analyses using summary statistics of genome wide association study consortia with sample sizes between 20,687 and 339,224 individuals, we aimed to determine which cardiovascular risk factors causally lead to changes in QRS duration and amplitude (Sokolow-Lyon, Cornell and 12-leadsum products). Additionally, we aimed to determine whether QRS traits have a causal relationship with mortality and longevity. We performed inverse-variance weighted MR as main analyses and MR-Egger regression and weighted median estimation as sensitivity analyses. We found evidence for a causal relationship between higher blood pressure and larger QRS amplitudes (systolic blood pressure on Cornell: 55SNPs, causal effect estimate per 1 mmHg = 9.77 millimeters·milliseconds (SE = 1.38,P = 1.20 × 10−12) and diastolic blood pressure on Cornell: 57SNPs, causal effect estimate per 1 mmHg = 14.89 millimeters·milliseconds (SE = 1.82,P = 3.08 × 10−16), but not QRS duration. Genetically predicted QRS traits were not associated with longevity, suggesting a more prominent role of acquired factors in explaining the well-known link between QRS abnormalities and outcome.
Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood
Authors: Lietzén Niina , Cheng Lu , Moulder Robert , Siljander Heli , Laajala Essi , Härkönen Taina , Peet Aleksandr , Vehtari Aki , Tillmann Vallo , Knip Mikael , Lähdesmäki Harri , Lahesmaa Riitta 
Published: April 2018

AbstractChildren develop rapidly during the first years of life, and understanding the sources and associated levels of variation in the serum proteome is important when using serum proteins as markers for childhood diseases. The aim of this study was to establish a reference model for the evolution of a healthy serum proteome during early childhood. Label-free quantitative proteomics analyses were performed for 103 longitudinal serum samples collected from 15 children at birth and between the ages of 3–36 months. A flexible Gaussian process-based probabilistic modelling framework was developed to evaluate the effects of different variables, including age, living environment and individual variation, on the longitudinal expression profiles of 266 reliably identified and quantified serum proteins. Age was the most dominant factor influencing approximately half of the studied proteins, and the most prominent age-associated changes were observed already during the first year of life. High inter-individual variability was also observed for multiple proteins. These data provide important details on the maturing serum proteome during early life, and evaluate how patterns detected in cord blood are conserved in the first years of life. Additionally, our novel modelling approach provides a statistical framework to detect associations between covariates and non-linear time series data.
The local and global climate forcings induced inhomogeneity of Indian rainfall
Authors: Nair P. J. , Chakraborty A. , Varikoden H. , Francis P. A. , Kuttippurath J. 
Published: April 2018

AbstractIndia is home for more than a billion people and its economy is largely based on agrarian society. Therefore, rainfall received not only decides its livelihood, but also influences its water security and economy. This situation warrants continuous surveillance and analysis of Indian rainfall. These kinds of studies would also help forecasters to better tune their models for accurate weather prediction. Here, we introduce a new method for estimating variability and trends in rainfall over different climate regions of India. The method based on multiple linear regression helps to assess contributions of different remote and local climate forcings to seasonal and regional inhomogeneity in rainfall. We show that the Indian Summer Monsoon Rainfall (ISMR) variability is governed by Eastern and Central Pacific El Niño Southern Oscillation, equatorial zonal winds, Atlantic zonal mode and surface temperatures of the Arabian Sea and Bay of Bengal, and the North East Monsoon Rainfall variability is controlled by the sea surface temperature of the North Atlantic and extratropial oceans. Also, our analyses reveal significant positive trends (0.43 mm/day/dec) in the North West for ISMR in the 1979–2017 period. This study cautions against the significant changes in Indian rainfall in a perspective of global climate change.
Lagged influence of Atlantic and Pacific climate patterns on European extreme precipitation
Authors: Tabari Hossein , Willems Patrick 
Published: April 2018

AbstractThe risk of European extreme precipitation and flooding as an economic and humanitarian disaster is modulated by large-scale atmospheric processes that operate over (multi-)decadal periods and transport huge quantities of moisture inland from the oceans. Yet the previous studies for better understanding of extreme precipitation variability and its skillful seasonal prediction are far from comprehensive. Here we show that the winter North Atlantic Oscillation (NAO) and, to a lesser extent, winter ENSO signal have a controlling influence not only concurrently on European extreme precipitation anomaly in winter, but in a delayed way on the extremes in the following seasons. In a similar pattern, there is a strong footprint of summer atmospheric circulations over the Mediterranean Sea on summer extreme precipitation and with 1-, 2- and 3-season lags on the following autumn, winter and spring extremes. The combined influences of the different atmospheric circulation patterns mark a significant step forward for an improved predictability of European extreme precipitation in the state-of-the-art seasonal prediction systems.
A cell surface display fluorescent biosensor for measuring MMP14 activity in real-time
Authors: Braun Alexander , Farber Matthew J. , Klase Zachary A. , Berget Peter B. , Myers Kenneth A. 
Published: April 2018

AbstractDespite numerous recent advances in imaging technologies, one continuing challenge for cell biologists and microscopists is the visualization and measurement of endogenous proteins as they function within living cells. Achieving this goal will provide a tool that investigators can use to associate cellular outcomes with the behavior and activity of many well-studied target proteins. Here, we describe the development of a plasmid-based fluorescent biosensor engineered to measure the location and activity of matrix metalloprotease-14 (MMP14). The biosensor design uses fluorogen-activating protein technology coupled with a MMP14-selective protease sequence to generate a binary, “switch-on” fluorescence reporter capable of measuring MMP14 location, activity, and temporal dynamics. The MMP14-fluorogen activating protein biosensor approach is applicable to both short and long-term imaging modalities and contains an adaptable module that can be used to study many membrane-bound proteases. This MMP14 biosensor promises to serve as a tool for the advancement of a broad range of investigations targeting MMP14 activity during cell migration in health and disease.
Discovery of the World’s Smallest Terrestrial Pteridophyte
Authors: Patel Mitesh , Reddy Mandadi Narsimha 
Published: April 2018

AbstractOphioglossum L. commonly known as “adder’s tongue fern”, has been of great interest due to the highest number of chromosomes in any organism so far known in biological world. Here, a new species of adder’s tongue fern has been discovered and reported from Western Ghats of India. It is prominently distinct from the other known taxa in Ophioglossaceae family. Phylogenetic analysis of three chloroplast DNA (cpDNA) regions (trnL-F, rbcL and psbA-trnH) unambiguously designate this adder’s tongue fern as the distinct lineage and is sister to the clade containing O. parvifolium and O. nudicaule. Azolla caroliniana – an aquatic fern (average size, 0.5–1.5 cm), is the smallest fern on the earth. Our discovery discloses a new species of adder’s tongue fern and ranking it among the smallest terrestrial fern in the world, attaining an average size of only 1–1.2 cm.
Alternative SNP detection platforms, HRM and biosensors, for varietal identification in Vitis vinifera L. using F3H and LDOX genes
Authors: Gomes Sónia , Castro Cláudia , Barrias Sara , Pereira Leonor , Jorge Pedro , Fernandes José R. , Martins-Lopes Paula 
Published: April 2018

AbstractThe wine sector requires quick and reliable methods for Vitis vinifera L. varietal identification. The number of V. vinifera varieties is estimated in about 5,000 worldwide. Single Nucleotide Polymorphisms (SNPs) represent the most basic and abundant form of genetic sequence variation, being adequate for varietal discrimination. The aim of this work was to develop DNA-based assays suitable to detect SNP variation in V. vinifera, allowing varietal discrimination. Genotyping by sequencing allowed the detection of eleven SNPs on two genes of the anthocyanin pathway, the flavanone 3-hydroxylase (F3H, EC: 1.14.11.9), and the leucoanthocyanidin dioxygenase (LDOX, EC 1.14.11.19; synonym anthocyanidin synthase, ANS) in twenty V. vinifera varieties. Three High Resolution Melting (HRM) assays were designed based on the sequencing information, discriminating five of the 20 varieties: Alicante Bouschet, Donzelinho Tinto, Merlot, Moscatel Galego and Tinta Roriz. Sanger sequencing of the HRM assay products confirmed the HRM profiles. Three probes, with different lengths and sequences, were used as bio-recognition elements in an optical biosensor platform based on a long period grating (LPG) fiber optic sensor. The label free platform detected a difference of a single SNP using genomic DNA samples. The two different platforms were successfully applied for grapevine varietal identification.
Defective immuno- and thymoproteasome assembly causes severe immunodeficiency
Authors: Treise Irina , Huber Eva M. , Klein-Rodewald Tanja , Heinemeyer Wolfgang , Grassmann Simon A. , Basler Michael , Adler Thure , Rathkolb Birgit , Helming Laura , Andres Christian , Klaften Matthias , Landbrecht Christina , Wieland Thomas , Strom Tim M. , McCoy Kathy D. , Macpherson Andrew J. , Wolf Eckhard , Groettrup Marcus , Ollert Markus , Neff Frauke , Gailus-Durner Valerie , Fuchs Helmut , Hrabě de Angelis Martin , Groll Michael , Busch Dirk H. 
Published: April 2018

AbstractBy N-ethyl-N-nitrosourea (ENU) mutagenesis, we generated the mutant mouse line TUB6 that is characterised by severe combined immunodeficiency (SCID) and systemic sterile autoinflammation in homozygotes, and a selective T cell defect in heterozygotes. The causative missense point mutation results in the single amino acid exchange G170W in multicatalytic endopeptidase complex subunit-1 (MECL-1), the β2i-subunit of the immuno- and thymoproteasome. Yeast mutagenesis and crystallographic data suggest that the severe TUB6-phenotype compared to the MECL-1 knockout mouse is caused by structural changes in the C-terminal appendage of β2i that prevent the biogenesis of immuno- and thymoproteasomes. Proteasomes are essential for cell survival, and defective proteasome assembly causes selective death of cells expressing the mutant MECL-1, leading to the severe immunological phenotype. In contrast to the immunosubunits β1i (LMP2) and β5i (LMP7), mutations in the gene encoding MECL-1 have not yet been assigned to human disorders. The TUB6 mutant mouse line exemplifies the involvement of MECL-1 in immunopathogenesis and provides the first mouse model for primary immuno- and thymoproteasome-associated immunodeficiency that may also be relevant in humans.
Scalability assessment of Group-IV mono-chalcogenide based tunnel FET
Authors: Brahma Madhuchhanda , Kabiraj Arnab , Saha Dipankar , Mahapatra Santanu 
Published: April 2018

AbstractSelection of appropriate channel material is the key to design high performance tunnel field effect transistor (TFET), which promises to outperform the conventional metal oxide semiconductor field effect transistor (MOSFET) in ultra-low energy switching applications. Recently discovered atomically thin GeSe, a group IV mono-chalcogenide, can be a potential candidate owing to its direct electronic band gap and low carrier effective mass. In this work we employ ballistic quantum transport model to assess the intrinsic performance limit of monolayer GeSe-TFET. We first study the electronic band structure by regular and hybrid density functional theory and develop two band k · p hamiltonian for the material. We find that the complex band wraps itself within the conduction band and valence band edges and thus signifies efficient band to band tunneling mechanism. We then use the k · p hamiltonian to calculate self-consistent solution of the transport equations within the non-equilibrium Green’s function formalism and the Poisson’s equation based electrostatic potential. Keeping the OFF-current fixed at 10 pA/μm we investigate different static and dynamic performance metrics (ON current, energy and delay) under three different constant-field scaling rules: 40, 30 and 20 nm/V. Our study shows that monolayer GeSe-TFET is scalable till 8 nm while preserving ON/OFF current ratio higher than 104.