bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two‐Dimensional Spectra of Radar Returns From Sea: 2. Analysis of the Group Line From Experimental Data
Authors: Platzer F. , Saillard M. , Fabbro V. 
Published: October 2019

AbstractWavenumber‐frequency spectra are obtained by performing a two‐dimensional Fourier transform of range‐time normalized radar cross‐section (NRCS) or Doppler velocity maps. In such diagrams, some energy is present at low space‐time frequencies, resulting from the nonlinear behavior of the measured quantity related to the sea surface geometry. This feature is called the group line, since for a narrow‐band wave packet the energy is concentrated along a straight line with group velocity as slope. Which physical nonlinear process generates the group line remains an open question. Breaking waves have been proposed as the most probable contributor. However, numerical simulations from weakly nonlinear surfaces without breaking events and experiments performed at low winds also provide such feature. In a companion paper, a theoretical and numerical analysis has permitted to predict the energy distribution of the group line depending on the kind of nonlinearity. It provides some means to characterize a group line in a rigorous way. In this paper, it is used to analyze the group lines derived from the experimental MARLENE data. The group lines computed from the backscattering amplitude behave as the one of the square of sea surface slopes. The analysis of the Doppler velocities provides similar results, which significantly differ from what is expected if breaking waves are the main contributors and do break at velocities reported in the literature. Our results suggest that the group line mainly reflects the asymptotic behavior of the scattering amplitude at grazing incidence, of which the leading nonlinear term is proportional to the square of surface slope.
The Fraction of Broken Waves in Natural Surf Zones
Authors: Stringari C. E. , Power H. E. 
Published: October 2019

AbstractThis paper presents a novel quantification of the fraction of broken waves (Qb) in natural surf zones using data from seven microtidal, wave‐dominated, sandy Australian beaches.Qbis a critical, but rarely quantified, parameter for parametric surf zone energy dissipation models, which are commonly used as coastal management tools. Here,Qbis quantified using a combination of remote sensing and in situ data. These data and machine learning techniques enable quantification ofQbfor a substantial data set (>330,000 waves). The results show thatQbis a highly variable parameter with a high degree of interbeach and intrabeach variability. Such variability could be correlated to environmental parameters: tidal variations correlated with changes inQbof up to 70% for a given local water depth (h) on a low tide terrace beach, and increased infragravity relative to sea‐swell energy correlated to lower values ofQbat the surf‐swash boundary.Qbalso correlates well with the Australian beach morphodynamic model: For more dissipative beachesQbincreases rapidly in the outer surf zone, whereas for more reflective beachesQbincreases slowly throughout the surf zone. Finally, when comparing data to existing models, three commonly used theoretical formulations forQbare observed to be poor predictors with errors of the order of 40%. Existing theoreticalQbmodels are shown to improve (revised errors of the order of 10%) if the Rayleigh probability distribution that describes the wave height is in these models is replaced by the Weibull distribution.
A Systematic Analysis of the Salinity Effect on Air Bubbles Evolution: Laboratory Experiments in a Breaking Wave Analog
Authors: Harb Charbel , Foroutan Hosein 
Published: October 2019

AbstractThe evolution of air bubbles after breaking waves plays an important role in gas and particle exchange between water bodies and the atmosphere. To improve our understanding of the impacts of salinity on this process, we systematically investigate the effect of salt concentrations ranging from 0 to 40 g/kg on the volume and size distributions of subsurface bubble plumes and surface foams in a laboratory breaking wave analog. Our experimental setup utilizes an intermittent plunging sheet to simulate breaking waves, while two synchronized digital cameras were used to monitor the temporal evolution of bubble plumes and surface foams. We first highlight the importance of plunging sheet intermittency on surface foam evolution. We then show that increasing salinity enhances the entrainment of submillimeter bubbles but has a less significant effect on larger supramillimeter bubbles. We observed that the foam area in saltier waters is consistently higher than that in freshwater throughout the foam decay phase. Furthermore, our investigation of surface bubble sizes shows that salinity has a more distinct effect on smaller (sub 2 mm) than on larger bubbles. This suggests that salinity may have a more pronounced impact on jet than on film drops ejection mechanisms. Finally, we conclude that the change in salinity within the typical oceanographic range is likely not a major factor for bubble‐mediated interactions at the water surface during breaking waves. However, even low‐salt concentrations greatly alter air entrainment characteristics in freshwater systems.
Coulomb-driven single defect engineering for scalable qubits and spin sensors in diamond
Authors: Lühmann Tobias , John Roger , Wunderlich Ralf , Meijer Jan , Pezzagna Sébastien 
Published: October 2019

AbstractQubits based on colour centres in diamond became a prominent system for solid-state quantum information processing and sensing. But the deterministic creation of qubits and the control of their environment are still critical issues, preventing the development of a room-temperature quantum computer. We report on the high creation yield of NV centres of 75% (a tenfold enhancement) by charge-assisted defect engineering, together with an improvement of their spin coherence. The method strongly favours the formation and negative charge state of the NV centres with respect to intrinsic diamond, while it hinders the formation of competing and perturbing defects such as di-vacancies or NVH complexes. We evidence spectrally the charge state tuning of the implantation-induced vacancies from V0 to V−, key element of this Coulomb-driven engineering. The generality of the method is demonstrated using several donors (phosphorous, oxygen and sulphur) and applying it to other centres (SnV and MgV) in diamond.
Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca2+-bound nhTMEM16
Authors: Khelashvili George , Falzone Maria E. , Cheng Xiaolu , Lee Byoung-Cheol , Accardi Alessio , Weinstein Harel 
Published: October 2019

AbstractBoth lipid and ion translocation by Ca2+-regulated TMEM16 transmembrane proteins utilizes a membrane-exposed hydrophilic groove. Several conformations of the groove are observed in TMEM16 protein structures, but how these conformations form, and what functions they support, remains unknown. From analyses of atomistic molecular dynamics simulations of Ca2+-bound nhTMEM16 we find that the mechanism of a conformational transition of the groove from membrane-exposed to occluded from the membrane involves the repositioning of transmembrane helix 4 (TM4) following its disengagement from a TM3/TM4 interaction interface. Residue L302 is a key element in the hydrophobic TM3/TM4 interaction patch that braces the open-groove conformation, which should be changed by an L302A mutation. The structure of the L302A mutant determined by cryogenic electron microscopy (cryo-EM) reveals a partially closed groove that could translocate ions, but not lipids. This is corroborated with functional assays showing severely impaired lipid scrambling, but robust channel activity by L302A.
Synthetic asters as elastic and radial skeletons
Authors: Xie Qingqiao , Chen Xixi , Wu Tianli , Wang Tiankuo , Cao Yi , Granick Steve , Li Yuchao , Jiang Lingxiang 
Published: October 2019

AbstractThe radial geometry with rays radiated from a common core occurs ubiquitously in nature for its symmetry and functions. Herein, we report a class of synthetic asters with well-defined core-ray geometry that can function as elastic and radial skeletons to harbor nano- and microparticles. We fabricate the asters in a single, facile, and high-yield step that can be readily scaled up; specifically, amphiphilic gemini molecules self-assemble in water into asters with an amorphous core and divergently growing, twisted crystalline ribbons. The asters can spontaneously position microparticles in the cores, along the radial ribbons, or by the outer rims depending on particle sizes and surface chemistry. Their mechanical properties are determined on single- and multiple-aster levels. We further maneuver the synthetic asters as building blocks to form higher-order structures in virtue of aster-aster adhesion induced by ribbon intertwining. We envision the astral structures to act as rudimentary spatial organizers in nanoscience for coordinated multicomponent systems, possibly leading to emergent, synergistic functions.
In situ nuclear-glass corrosion under geological repository conditions
Authors: Debure Mathieu , Linard Yannick , Martin Christelle , Claret Francis 
Published: October 2019

AbstractSilicate glasses are durable materials but laboratory experiments reveal that elements that derive from their environment may induce high corrosion rates and reduce their capacity to confine high-level radioactive waste. This study investigates nuclear-glass corrosion in geological media using an in situ diffusion experiment and multi-component diffusion modelling. The model highlights that the pH imposed by the Callovo–Oxfordian (COx) claystone host rock supports secondary-phase precipitation and increases glass corrosion compared with pure water. Elements from the COx rock (mainly Mg and Fe) form secondary phases with Si provided by the glass, which delay the establishment of a passivating interface. The presence of elements (Mg and Fe) that sustain glass alteration does not prevent a significant decrease in the glass-alteration rate, mainly due to the limited species transport that drives system reactivity. These improvements in the understanding of glass corrosion in its environment provide further insights for predictive modelling over larger timescales and space.
ColPortal, an integrative multiomic platform for analysing epigenetic interactions in colorectal cancer
Authors: Esteban-Gil Angel , Pérez-Sanz Fernando , García-Solano José , Alburquerque-González Begoña , Parreño-González María Antonia , Legaz-García María del Carmen , Fernández-Breis Jesualdo Tomás , Rodriguez-Braun Edith , Pimentel Paola , Tuomisto Anne , Mäkinen Markus , Slaby Ondrej , Conesa-Zamora Pablo 
Published: October 2019

AbstractColorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. Different pathological pathways and molecular drivers have been described and some of the associated markers are used to select effective anti-neoplastic therapy. More recent evidence points to a causal role of microbiota and altered microRNA expression in CRC carcinogenesis, but their relationship with pathological drivers or molecular phenotypes is not clearly established. Joint analysis of clinical and omics data can help clarify such relations. We present ColPortal, a platform that integrates transcriptomic, microtranscriptomic, methylomic and microbiota data of patients with colorectal cancer. ColPortal also includes detailed information of histological features and digital histological slides from the study cases, since histology is a morphological manifestation of a complex molecular change. The current cohort consists of Caucasian patients from Europe. For each patient, demographic information, location, histology, tumor staging, tissue prognostic factors, molecular biomarker status and clinical outcomes are integrated with omics data. ColPortal allows one to perform multiomics analyses for groups of patients selected by their clinical data.
STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
Authors: Gomez-Cabrero David , Tarazona Sonia , Ferreirós-Vidal Isabel , Ramirez Ricardo N. , Company Carlos , Schmidt Andreas , Reijmers Theo , Paul Veronica von Saint , Marabita Francesco , Rodríguez-Ubreva Javier , Garcia-Gomez Antonio , Carroll Thomas , Cooper Lee , Liang Ziwei , Dharmalingam Gopuraja , van der Kloet Frans , Harms Amy C. , Balzano-Nogueira Leandro , Lagani Vincenzo , Tsamardinos Ioannis , Lappe Michael , Maier Dieter , Westerhuis Johan A. , Hankemeier Thomas , Imhof Axel , Ballestar Esteban , Mortazavi Ali , Merkenschlager Matthias , Tegner Jesper , Conesa Ana 
Published: October 2019

AbstractMulti-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
The Personal Genome Project-UK, an open access resource of human multi-omics data
Authors: Chervova Olga , Conde Lucia , Guerra-Assunção José Afonso , Moghul Ismail , Webster Amy P. , Berner Alison , Larose Cadieux Elizabeth , Tian Yuan , Voloshin Vitaly , Jesus Tiago F. , Hamoudi Rifat , Herrero Javier , Beck Stephan 
Published: October 2019

AbstractIntegrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.
High-speed and Large-scale Privacy Amplification Scheme for Quantum Key Distribution
Authors: Tang Bang-Ying , Liu Bo , Zhai Yong-Ping , Wu Chun-Qing , Yu Wan-Rong 
Published: October 2019

AbstractState-of-art quantum key distribution (QKD) systems are performed with several GHz pulse rates, meanwhile privacy amplification (PA) with large scale inputs has to be performed to generate the final secure keys with quantified security. In this paper, we propose a fast Fourier transform (FFT) enhanced high-speed and large-scale (HiLS) PA scheme on commercial CPU platform without increasing dedicated computational devices. The long input weak secure key is divided into many blocks and the random seed for constructing Toeplitz matrix is shuffled to multiple sub-sequences respectively, then PA procedures are parallel implemented for all sub-key blocks with correlated sub-sequences, afterwards, the outcomes are merged as the final secure key. When the input scale is 128 Mb, our proposed HiLS PA scheme reaches 71.16 Mbps, 54.08 Mbps and 39.15 Mbps with the compression ratio equals to 0.125, 0.25 and 0.375 respectively, resulting achievable secure key generation rates close to the asymptotic limit. HiLS PA scheme can be applied to 10 GHz QKD systems with even larger input scales and the evaluated throughput is around 32.49 Mbps with the compression ratio equals to 0.125 and the input scale of 1 Gb, which is ten times larger than the previous works for QKD systems. Furthermore, with the limited computational resources, the achieved throughput of HiLS PA scheme is 0.44 Mbps with the compression ratio equals to 0.125, when the input scale equals up to 128 Gb. In theory, the PA of the randomness extraction in quantum random number generation (QRNG) is same as the PA procedure in QKD, and our work can also be efficiently performed in high-speed QRNG.
A Clearing Technique to Enhance Endogenous Fluorophores in Skin and Soft Tissue
Authors: Foster Deshka S. , Nguyen Alan T. , Chinta Malini , Salhotra Ankit , Jones R. Ellen , Mascharak Shamik , Titan Ashley L. , Ransom R. Chase , da Silva Oscar L. , Foley Eliza , Briger Emma , Longaker Michael T. 
Published: October 2019

AbstractFluorescent proteins are used extensively in transgenic animal models to label and study specific cell and tissue types. Expression of these proteins can be imaged and analyzed using fluorescent and confocal microscopy. Conventional confocal microscopes cannot penetrate through tissue more than 4–6 μm thick. Tissue clearing procedures overcome this challenge by rendering thick specimens into translucent tissue. However, most tissue clearing techniques do not satisfactorily preserve expression of endogenous fluorophores. Using simple adjustments to the BABB (Benzoic Acid Benzyl Benzoate) clearing methodology, preservation of fluorophore expression can be maintained. Modified BABB tissue clearing is a reliable technique to clear skin and soft tissue specimens for the study of dermal biology, wound healing and fibrotic pathologies.
Experimental characterisation of the bound acoustic surface modes supported by honeycomb and hexagonal hole arrays
Authors: Starkey Timothy A. , Kyrimi Vicky , Ward Gareth P. , Sambles J. Roy , Hibbins Alastair P. 
Published: October 2019

AbstractThe Dirac point and associated linear dispersion exhibited in the band structure of bound (non-radiative) acoustic surface modes supported on a honeycomb array of holes is explored. An aluminium plate with a honeycomb lattice of periodic sub-wavelength perforations is characterised by local pressure field measurements above the sample surface to obtain the full band-structure of bound modes. The local pressure fields of the bound modes at the K and M symmetry points are imaged, and the losses at frequencies near the Dirac frequency are shown to increase monotonically as the mode travels through the K point at the Dirac frequency on the honeycomb lattice. Results are contrasted with those from a simple hexagonal array of similar holes, and both experimentally obtained dispersion relations are shown to agree well with the predictions of a numerical model.
MC-SleepNet: Large-scale Sleep Stage Scoring in Mice by Deep Neural Networks
Authors: Yamabe Masato , Horie Kazumasa , Shiokawa Hiroaki , Funato Hiromasa , Yanagisawa Masashi , Kitagawa Hiroyuki 
Published: October 2019

AbstractAutomated sleep stage scoring for mice is in high demand for sleep research, since manual scoring requires considerable human expertise and efforts. The existing automated scoring methods do not provide the scoring accuracy required for practical use. In addition, the performance of such methods has generally been evaluated using rather small-scale datasets, and their robustness against individual differences and noise has not been adequately verified. This research proposes a novel automated scoring method named “MC-SleepNet”, which combines two types of deep neural networks. Then, we evaluate its performance using a large-scale dataset that contains 4,200 biological signal records of mice. The experimental results show that MC-SleepNet can automatically score sleep stages with an accuracy of 96.6% and kappa statistic of 0.94. In addition, we confirm that the scoring accuracy does not significantly decrease even if the target biological signals are noisy. These results suggest that MC-SleepNet is very robust against individual differences and noise. To the best of our knowledge, evaluations using such a large-scale dataset (containing 4,200 records) and high scoring accuracy (96.6%) have not been reported in previous related studies.
C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1
Authors: Akhoon Bashir A. , Gupta Shishir K. , Tiwari Sudeep , Rathor Laxmi , Pant Aakanksha , Singh Nivedita , Gupta Shailendra K. , Dandekar Thomas , Pandey Rakesh 
Published: October 2019

AbstractProtein-protein interaction (PPI) studies are gaining momentum these days due to the plethora of various high-throughput experimental methods available for detecting PPIs. Proteins create complexes and networks by functioning in harmony with other proteins and here in silico network biology hold the promise to reveal new functionality of genes as it is very difficult and laborious to carry out experimental high-throughput genetic screens in living organisms. We demonstrate this approach by computationally screening C. elegans conserved homologs of already reported human tumor suppressor and aging associated genes. We select by this nhr-6, vab-3 and gst-23 as predicted longevity genes for RNAi screen. The RNAi results demonstrated the pro-longevity effect of these genes. Nuclear hormone receptor nhr-6 RNAi inhibition resulted in a C. elegans phenotype of 23.46% lifespan reduction. Moreover, we show that nhr-6 regulates oxidative stress resistance in worms and does not affect the feeding behavior of worms. These findings imply the potential of nhr-6 as a common therapeutic target for aging and cancer ailments, stressing the power of in silico PPI network analysis coupled with RNAi screens to describe gene function.