bluuebunny/crossref_metadata_2025_split huggingface dataset:
High spectral purity Kerr frequency comb radio frequency photonic oscillator
Authors: Liang W. , Eliyahu D. , Ilchenko V. S. , Savchenkov A. A. , Matsko A. B. , Seidel D. , Maleki L. 
Published: August 2015

AbstractFemtosecond laser-based generation of radio frequency signals has produced astonishing improvements in achievable spectral purity, one of the basic features characterizing the performance of an radio frequency oscillator. Kerr frequency combs hold promise for transforming these lab-scale oscillators to chip-scale level. In this work we demonstrate a miniature 10 GHz radio frequency photonic oscillator characterized with phase noise better than −60 dBc Hz−1 at 10 Hz, −90 dBc Hz−1 at 100 Hz and −170 dBc Hz−1 at 10 MHz. The frequency stability of this device, as represented by Allan deviation measurements, is at the level of 10−10 at 1–100 s integration time—orders of magnitude better than existing radio frequency photonic devices of similar size, weight and power consumption.
Water impacting on superhydrophobic macrotextures
Authors: Gauthier Anaïs , Symon Sean , Clanet Christophe , Quéré David 
Published: August 2015

AbstractIt has been recently shown that the presence of macrotextures on superhydrophobic materials can markedly modify the dynamics of water impacting them, and in particular significantly reduce the contact time of bouncing drops, compared with what is observed on a flat surface. This finding constitutes a significant step in the maximization of water repellency, since it enables to minimize even further the contact between solid and liquid. It also opens a new axis of research on the design of super-structures to induce specific functions such as anti-freezing, liquid fragmentation and/or recomposition, guiding, trapping and so on. Here we show that the contact time of drops bouncing on a repellent macrotexture takes discrete values when varying the impact speed. This allows us to propose a quantitative analysis of the reduction of contact time and thus to understand how and why macrotextures can control the dynamical properties of bouncing drops.
Fluorogenic Assay for Inhibitors of HIV-1 Protease with Sub-picomolar Affinity
Authors: Windsor Ian W. , Raines Ronald T. 
Published: August 2015

AbstractA fluorogenic substrate for HIV-1 protease was designed and used as the basis for a hypersensitive assay. The substrate exhibits a kcat of 7.4 s−1, KM of 15 μM and an increase in fluorescence intensity of 104-fold upon cleavage, thus providing sensitivity that is unmatched in a continuous assay of HIV-1 protease. These properties enabled the enzyme concentration in an activity assay to be reduced to 25 pM, which is close to the Kd value of the protease dimer. By fitting inhibition data to Morrison’s equation, Ki values of amprenavir, darunavir and tipranavir were determined to be 135, 10 and 82 pM, respectively. This assay, which is capable of measuring Ki values as low as 0.25 pM, is well-suited for characterizing the next generation of HIV-1 protease inhibitors.
Nanocontact Disorder in Nanoelectronics for Modulation of Light and Gas Sensitivities
Authors: Lin Yen-Fu , Chang Chia-Hung , Hung Tsu-Chang , Jian Wen-Bin , Tsukagoshi Kazuhito , Wu Yue-Han , Chang Li , Liu Zhaoping , Fang Jiye 
Published: August 2015

AbstractTo fabricate reliable nanoelectronics, whether by top-down or bottom-up processes, it is necessary to study the electrical properties of nanocontacts. The effect of nanocontact disorder on device properties has been discussed but not quantitatively studied. Here, by carefully analyzing the temperature dependence of device electrical characteristics and by inspecting them with a microscope, we investigated the Schottky contact and Mott’s variable-range-hopping resistances connected in parallel in the nanocontact. To interpret these parallel resistances, we proposed a model of Ti/TiOxin the interface between the metal electrodes and nanowires. The hopping resistance as well as the nanocontact disorder dominated the total device resistance for high-resistance devices, especially at low temperatures. Furthermore, we introduced nanocontact disorder to modulate the light and gas responsivities of the device; unexpectedly, it multiplied the sensitivities compared with the intrinsic sensitivity of the nanowires. Our results improve the collective understanding of electrical contacts to low-dimensional semiconductor devices and will aid performance optimization in future nanoelectronics.
Potential diagnostic value of the umbilical artery as a definition of neural fatty acid status of the fetus during its growth: the umbilical artery as a diagnostic tool
Authors: CRAWFORD M. A. , COSTELOE K. , DOYLE W. , LEIGHFIELD M. J. , LENNON E. A. , MEADOWS N. 
Published: August 2015

Summary
Low birth weight (LBW) is associated with handicaps, the most prevelant of which affect the brain or its sensory attributes and have a life long impact. We have therefore been interested in nutrition and fetal growth and have studied the relationship between maternal diet and the outcome of pregnancy.
Essential fatty acids are methylene-interrupted, polyenoic fatty acids that are required for cell membrane structure, integrity and function. Some 60% of the structural material of the brain and nervous system is lipid and it uses 20- and 22-carbon-chain-length polyenoic acids specifically in sites of signal transduction and high activity (Fig. 1).
We have been interested in the acquisition of these fatty acids during fetal growth and along with deficits of several nutrients found low intakes of essential fatty acids (EFA) in the mothers of LBW babies. In order to test this food intake data we have analysed the lipids of the umbilical artery as representative of fetal tissue.
We found surprisingly high proportions of the n − 9 eicosatrienoic acid (20:3, n − 9) and docosatrienoic acid (22:3, n − 9). The 20:3, n − 9 is known as the Mead acid and is recognized as a biochemical index of EFA deficiency [1,2]. The 20:3, n − 9/2:4, n − 6 ratio has been used as a biochemical test of general EFA deficiency and the 22:5, n − 6/ 22:4, n − 6 ratio as a marker of docosahexaenoic or n − 3 deficiency. Both ratios were unusually high. Further analysis of 14 babies of different birth weights produced highly significant Pearson correlation coefficients between birth weights and head circumferences, and these two indices, which were negative, and greater in the ethanolamine phosphoglycerides than in the choline phosphoglycerides of the umbilical artery.
The ethanolamine phosphoglycerides are inner membrane lipids and therefore the presence of the Mead acid and high levels of 22:5, n − 6 are statements about the biochemical history of the individual fetus. These indices may therefore have a diagnostic value as a measure of the nutritional status of the fetus during its growth. Because they describe the status of fatty acids specifically used for neural tissue growth, this diagnostic tool has a potential, which needs now to be tested, for assessing risk of neural deficits or damage in, for example, LBW and premature infants.
KATP channels and insulin secretion: a key role in health and disease
Authors: Ashcroft F.M. 
Published: August 2015

This review summarizes advances in our understanding of the structure and function of the ATP-sensitive potassium (KATP) channel of the pancreatic β-cell that have been made over the last 5 years. It discusses recent structural studies of the octameric KATP channel complex and studies of the regulation of KATP channel activity by nucleotides. It then considers the molecular mechanism by which gain-of-function mutations in the Kir6.2 subunit of the KATP channel reduce channel inhibition by ATP and thereby lead to neonatal diabetes, and how identification of these mutations has led to changes in therapy. Finally, it illustrates how mouse models of glucose intolerance or diabetes can provide fresh insight into β-cell function, using the C57BL/6J mouse, whose glucose intolerance arises from mutations in nicotinamide nucleotide transhydrogenase, as an example.
Modelling FUSopathies: focus on protein aggregation
Authors: Shelkovnikova Tatyana A. 
Published: August 2015

The discovery of a causative link between dysfunction of a number of RNA-binding proteins with prion-like domains and the development of certain (neuro)degenerative diseases has completely changed our perception of molecular mechanisms instigating pathological process in these disorders. Irreversible aggregation of these proteins is a crucial pathogenic event delineating a type of proteinopathy. FUS (fused in sarcoma) is a prototypical member of the class, and studies into the causes and consequences of FUSopathies have been instrumental in characterizing the processes leading to deregulation of RNA metabolism in neurodegeneration. In vivo models of FUSopathy have provided critical insights into the mechanisms of FUS toxicity and clues on the role of non-amyloid aggregates, which are hallmarks of these diseases. The present review summarizes the data on FUS aggregation signatures in available model organisms on the basis of overexpression of FUS variants.
Beamspace reduced‐dimension space–time adaptive processing for multiple‐input multiple‐output radar based on maximum cross‐correlation energy
Authors: Zhang Wei , He Zishu , Li Jun , Li Chaohai 
Published: August 2015

A new method for selecting auxiliary channels in reduced‐dimension space–time adaptive processing (STAP) based on maximum cross‐correlation energy has been proposed for airborne multiple‐input multiple‐output radar. It is demonstrated that the proposed algorithm can achieve the same output signal‐to‐interference–noise ratio (SINR) performance as the multistage multiple‐beam STAP algorithm which can assure the optimal performance when the number of auxiliary channels is fixed, but the auxiliary channels selecting process of the proposed algorithm is extremely simplified. Hence, the computation complexity is reduced dramatically. Practical considerations dictate that only the minimum number of auxiliary channels [(adaptive degrees of freedom (DoFs)] is required to achieve the desired array performance. The proposed approach can achieve the desired output signal‐to‐interference–noise performance with the minimum number of auxiliary channels. Consequently, the proposed approach can reduce the requirement of the sample support dramatically. It is demonstrated that the SINR loss will be <3 dB when only one channel is selected as the auxiliary channel. Generally, two to three channels are enough even when the clutter covariance matrix is unknown. This will be more obvious advantage when the number of independent and identically distributed secondary samples is limited. The reduction in DoFs can make the proposed approach more suitable for the practical clutter environments.
Facile method to prepare copper‐doped LiNbO3 nanocrystals
Authors: Liu Xiaobin , Que Wenxiu , Xing Yonglei , He Zuoli , He Yucheng 
Published: August 2015

A facile method to prepare copper‐doped LiNbO3 nanocrystalline is reported. It should be mentioned here that the harmless citric acid plays a key role in soluble niobate at first and in the formation of the uniform gel. A detail thermal behaviour of the as‐obtained gel was investigated by thermogravimetry and differential thermal analysis. The crystal structure, elemental composition and microstructural properties were characterised by X‐ray diffraction analysis, X‐ray photoelectron spectroscopy and scanning electron microscopy. Results indicate that a pure phase similar to LiNbO3, which has the cell parameters of a = b = 5.150(5) Å and c = 13.896(9) Å, can be obtained at a low temperature (∼550°C) and the mean particle size of the as‐synthesised nanocrystalline is about 40 nm.
Evolution of Dissipative Anisotropic Expansion-Free Axial Fluids
Authors: Sharif M. , Nasir Zunaira 
Published: August 2015

Abstract
A general study of non-static restricted class of axial system with anisotropic dissipative expansion-free fluid under geodesic condition is carried out. It is found that expansion-free model must be dissipative under geodesic condition to preserve axial symmetry. We also investigate this system without geodesic condition. Finally, the role of dissipation is explored via transport equation.
New Agegraphic Pilgrim Dark Energy in f(T, TG
) Gravity
Authors: Jawad Abdul , Debnath Ujjal 
Published: August 2015

Abstract
In this work, we briefly discuss a novel class of modified gravity like f(T, TG) gravity. In this background, we assume the new agegraphic version of pilgrim dark energy and reconstruct f(T, TG) models for two specific values of s. We also discuss the equation of state parameter, squared speed of sound and wDE-w′DE plane for these reconstructed f(T, TG) models. The equation of state parameter provides phantom-like behavior of the universe. The wDE-w′DE plane also corresponds to ΛCDM limit, thawing and freezing regions for both models.
The Analytical Parametrization of Fusion Barrier by Using the Skyrme Energy-Density Function Model
Authors: Zanganeh V. , Mirzaei M. , Wang N. 
Published: August 2015

Abstract
Using the skyrme energy density formalism, a pocket formula is introduced for barrier heights and positions of 95 fusion reactions (48 ≤ ZP ZT ≤ 1520) with respect to the charge and mass numbers of the interacting nuclei. It is shown that the parameterized values of RB and VB are able to reproduce the corresponding experimental data with good accuracy. Moreover, the absolute errors of our formulas are less than those obtained using the analytical parametrization forms of the fusion barrier based on the proximity versions. The ability of the parameterized forms of the barrier heights and its positions to reproduce the experimental data of the fusion cross section have been analyzed using the Wong model.
Hopf Bifurcation in a New Four-Dimensional Hyperchaotic System*
Authors: Li Xin , Yan Zhen-Ya 
Published: August 2015

AbstractIn this paper, the Hopf bifurcation in a new hyperchaotic system is studied. Based on the first Lyapunov coefficient theory and symbolic computation, the conditions of supercritical and subcritical bifurcation in the new hyperchaotic system are obtained. Numerical simulations are used to illustrate some main results.
Structural, Elastic, and Electronic Properties of a New Phase of Carbon*
Authors: Xing Meng-Jiang , Li Bin-Hua , Yu Zheng-Tao , Chen Qi 
Published: August 2015

Abstract
Based on density function theory with the ultrasoft pseudopotential scheme in the frame of the local density approximation and the generalized gradient approximation, the structural, elastic, and electronic properties of carbon with P2221 phase have been systematically studied in this paper. The calculated results show that the P2221 phase of carbon is mechanically stable and dynamically stable at ambient pressure. The anisotropy studies of Young's modulus, Poisson's ratio, shear anisotropic factor, the percentage of elastic anisotropy for bulk modulus, the percentage of elastic anisotropy for shear modulus and the universal anisotropic index show that P2221 phase of carbon exhibits anisotropy. In addition, P2221 phase is an indirect semiconductor with bandgap of 3.423 eV. But, the band gap of P2221 phase for carbon increase with increasing pressure.
Structural and Optical Properties of Point Defects in α-SiO2 Cluster*
Authors: Liu Meng , Lu Peng-Fei , Yang Yang , Wu Li-Yuan , Su Rui , Chen Jun 
Published: August 2015

Abstract
First-principles methods based on the density functional theory (DFT) are used in order to calculate the structural and optical properties of α-SiO2 cluster with the non-bridging oxygen hole centers (NBOHC) and NBOHC-E' defects. We clarify the stable structure of the NBOHC-E' point defects for the first time using the functional B3LYP, which is also tested to investigate the influence of electronic properties. The calculation is carried out for cluster configurations extracted from supercell. The results of optical absorption peak for Si2O7H6 and Si5O16H12 with NBOHC-E' defects are found at 2.66 eV, which is higher than the often observed OA peak at 2.0 eV for the NBOHC defect in α-SiO2. The overall absorption spectra are in qualitative agreement with the experiment.
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments
Authors: Kosugi Shunichi , Hirakawa Hideki , Tabata Satoshi 
Published: August 2015

Abstract
Motivation: Genome assemblies generated with next-generation sequencing (NGS) reads usually contain a number of gaps. Several tools have recently been developed to close the gaps in these assemblies with NGS reads. Although these gap-closing tools efficiently close the gaps, they entail a high rate of misassembly at gap-closing sites.
Results: We have found that the assembly error rates caused by these tools are 20–500-fold higher than the rate of errors introduced into contigs by de novo assemblers. We here describe GMcloser, a tool that accurately closes these gaps with a preassembled contig set or a long read set (i.e. error-corrected PacBio reads). GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency.
Availability and implementation: GMcloser and an accompanying tool (GMvalue) for evaluating the assembly and correcting misassemblies except SNPs and short indels in the assembly are available at https://sourceforge.net/projects/gmcloser/.
Contact: shunichi.kosugi@riken.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring linkage disequilibrium
Authors: Baird Stuart J. E. 
Published: August 2015

Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignoreLDat our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 ‘independent witnesses’ of the evolutionary process. If instead, we sample variation at 1000 loci, many areboundto be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that evenLDcreated far in the past will not have dissipated, so wecannottreat the 1000 loci as independent witnesses (Barton). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us aboutLDgenerating events far in the past, for example human/Neanderthal admixture (Fuet al.). With increased marker density, biologists must increase their awareness ofLDand, in this issue of Molecular Ecology Resources, Kemppainenet al. () make software available that can only help in this process:LDna allows patterns ofLDin a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understandingLD.
Guidelines for the Reporting of Treatment Trials for Alcohol Use Disorders
Authors: Witkiewitz Katie , Finney John W. , Harris Alex H. S. , Kivlahan Daniel R. , Kranzler Henry R. 
Published: August 2015

BackgroundThe primary goals in conducting clinical trials of treatments for alcohol use disorders (AUDs) are to identify efficacious treatments and determine which treatments are most efficacious for which patients. Accurate reporting of study design features and results is imperative to enable readers of research reports to evaluate to what extent a study has achieved these goals. Guidance on quality of clinical trial reporting has evolved substantially over the past 2 decades, primarily through the publication and widespread adoption of the Consolidated Standards of Reporting Trials statement. However, there is room to improve the adoption of those standards in reporting the design and findings of treatment trials for AUD.MethodsThis paper provides a narrative review of guidance on reporting quality in AUD treatment trials.ResultsDespite improvements in the reporting of results of treatment trials for AUD over the past 2 decades, many published reports provide insufficient information on design or methods.ConclusionsThe reporting of alcohol treatment trial design, analysis, and results requires improvement in 4 primary areas: (i) trial registration, (ii) procedures for recruitment and retention, (iii) procedures for randomization and intervention design considerations, and (iv) statistical methods used to assess treatment efficacy. Improvements in these areas and the adoption of reporting standards by authors, reviewers, and editors are critical to an accurate assessment of the reliability and validity of treatment effects. Continued developments in this area are needed to move AUD treatment research forward via systematic reviews and meta‐analyses that maximize the utility of completed studies.
Habitat‐specific population trajectories in boreal waterbirds: alarming trends and bioindicators for wetlands
Authors: Lehikoinen A. , Rintala J. , Lammi E. , Pöysä H. 
Published: August 2015

AbstractIdentification of conservation priorities is a fundamental issue for successful nature conservation. This can be done by looking at population trends of species in different habitats. Boreal zone is the key breeding area for manyEurasian waterbirds. Wetlands of the boreal zone can be roughly classified into two different groups: nutrient‐poor oligotrophic and nutrient‐rich eutrophic water ecosystems. Earlier work has shown that eutrophic lake‐specialist species have declined compared with generalists and species preferring oligotrophic lakes. However, it is not known if species that live in both habitats show habitat‐specific population trends. We used monitoring data of breeding waterbirds inFinland from 1986 to 2013 to evaluate habitat‐specific population trends in five generalist duck species, which mostly overwinter in the coastal waters of West Europe. Population trend of tufted duck was highly significantly more positive in oligotrophic wetlands compared with populations in eutrophic wetlands, and two other species had similar but weaker effects. In addition, we established bird population state indicators for oligotrophic and eutrophic water ecosystems inFinland. The indicators revealed that the populations in eutrophic wetlands have on average halved since early 1990s. The populations in oligotrophic wetlands have remained stable, except a moderate decline since the late 2000s. Our findings support the idea that the waterbird populations of the eutrophic wetlands are in serious trouble. This is likely due to over‐eutrophication of these ecosystems. Conservation and management actions should be urgently taken to halt the loss of biodiversity in these globally threatened freshwater ecosystems.