bluuebunny/crossref_metadata_2025_split huggingface dataset:
GUMBOS matrices of variable hydrophobicity for matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Al Ghafly Hashim , Siraj Noureen , Das Susmita , Regmi Bishnu P. , Magut Paul K. S. , Galpothdeniya Waduge Indika S. , Murray Kermit K. , Warner Isiah M. 
Published: September 2014

RATIONALEDetection of hydrophobic peptides remains a major obstacle for matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). This stems from the fact that most matrices for MALDI are hydrophilic and therefore have low affinities for hydrophobic peptides. Herein, 1‐aminopyrene (AP) and AP‐derived group of uniform materials based on organic salts (GUMBOS) as novel matrices for MALDI‐MS analyses of peptides were investigated for hydrophobic and hydrophilic peptides.METHODSA number of solid‐phase AP‐based GUMBOS are synthesized with variable hydrophobicity simply by changing the counterions. Structures were confirmed by use of 1H NMR and electrospray ionization mass spectrometry (ESI‐MS). 1‐Octanol/water partition coefficients (Ko/w) were used to measure the hydrophobicity of the matrices. A dried‐droplet method was used for sample preparation. All spectra were obtained using a MALDI‐TOF mass spectrometer in positive ion reflectron mode.RESULTSA series of AP‐based GUMBOS was synthesized including [AP][chloride] ([AP][Cl]), [AP][ascorbate] ([AP][Asc]) and [AP][bis(trifluoromethane)sulfonimide] ([AP][NTf2]). The relative hydrophobicities of these compounds and α‐cyano‐4‐hydroxycinnamic acid (CHCA, a common MALDI matrix) indicated that AP‐based GUMBOS can be tuned to be much more hydrophobic than CHCA. A clear trend is observed between the signal intensities of hydrophobic peptides and hydrophobicity of the matrix.CONCLUSIONSMALDI matrices of GUMBOS with tunable hydrophobicities are easily obtained simply by varying the counterion. We have found that hydrophobic matrix materials are very effective for MALDI determination of hydrophobic peptides and, similarly, the more hydrophilic peptides displayed greater intensity in the more hydrophilic matrix. Copyright © 2014 John Wiley & Sons, Ltd.
An inviscid modal interpretation of the ‘lift-up’ effect
Authors: Roy Anubhab , Subramanian Ganesh 
Published: September 2014

AbstractIn this paper, we give a modal interpretation of the lift-up effect, one of two well-known mechanisms that lead to an algebraic instability in parallel shearing flows, the other being the Orr mechanism. To this end, we first obtain the two families of continuous spectrum modes that make up the complete spectrum for a non-inflectional velocity profile. One of these families consists of modified versions of the vortex-sheet eigenmodes originally found by Case (Phys. Fluids, vol. 3, 1960, pp. 143–148) for plane Couette flow, while the second family consists of singular jet modes first found by Sazonov (Izv. Acad. Nauk SSSR Atmos. Ocean. Phys., vol. 32, 1996, pp. 21–28), again for Couette flow. The two families are used to construct the modal superposition for an arbitrary three-dimensional distribution of vorticity at the initial instant. The so-called non-modal growth that underlies the lift-up effect is associated with an initial condition consisting of rolls, aligned with the streamwise direction, and with a spanwise modulation (that is, a modulation along the vorticity direction of the base-state shearing flow). This growth is shown to arise from an appropriate superposition of the aforementioned continuous spectrum mode families. The modal superposition is then generalized to an inflectional velocity profile by including additional discrete modes associated with the inflection points. Finally, the non-trivial connection between an inviscid eigenmode and the viscous eigenmodes for large but finite Reynolds number, and the relation between the corresponding modal superpositions, is highlighted.
Weak turbulence theory for rotating magnetohydrodynamics and planetary flows
Authors: Galtier Sébastien 
Published: September 2014

AbstractA weak turbulence theory is derived for magnetohydrodynamics (MHD) under rapid rotation and in the presence of a uniform large-scale magnetic field which is associated with a constant Alfvén velocity $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}{\boldsymbol {b}}_{{0}}$. The angular velocity ${\boldsymbol{\Omega}}_{{0}}$ is assumed to be uniform and parallel to ${\boldsymbol {b}}_{{0}}$. Such a system exhibits left and right circularly polarized waves which can be obtained by introducing the magneto-inertial length $d \equiv b_0/\varOmega _0$. In the large-scale limit ($kd \to 0$, with $k$ being the wavenumber) the left- and right-handed waves tend to the inertial and magnetostrophic waves, respectively, whereas in the small-scale limit ($kd \to + \infty $) pure Alfvén waves are recovered. By using a complex helicity decomposition, the asymptotic weak turbulence equations are derived which describe the long-time behaviour of weakly dispersive interacting waves via three-wave interaction processes. It is shown that the nonlinear dynamics is mainly anisotropic, with a stronger transfer perpendicular than parallel to the rotation axis. The general theory may converge to pure weak inertial/magnetostrophic or Alfvén wave turbulence when the large- or small-scale limits are taken, respectively. Inertial wave turbulence is asymptotically dominated by the kinetic energy/helicity, whereas the magnetostrophic wave turbulence is dominated by the magnetic energy/helicity. For both regimes, families of exact solutions are found for the spectra, which do not correspond necessarily to a maximal helicity state. It is shown that the hybrid helicity exhibits a cascade whose direction may vary according to the scale $k_f$ at which the helicity flux is injected, with an inverse cascade if $k_fd < 1$ and a direct cascade otherwise. The theory is relevant to the magnetostrophic dynamo, whose main applications are the Earth and the giant planets, such as Jupiter and Saturn, for which a small (${\sim }10^{-6}$) Rossby number is expected.
Spectral analogues of the law of the wall, the defect law and the log law
Authors: Zúñiga Zamalloa Carlo , Ng Henry Chi-Hin , Chakraborty Pinaki , Gioia Gustavo 
Published: September 2014

AbstractUnlike the classical scaling relations for the mean-velocity profiles of wall-bounded uniform turbulent flows (the law of the wall, the defect law and the log law), which are predicated solely on dimensional analysis and similarity assumptions, scaling relations for the turbulent-energy spectra have been informed by specific models of wall turbulence, notably the attached-eddy hypothesis. In this paper, we use dimensional analysis and similarity assumptions to derive three scaling relations for the turbulent-energy spectra, namely the spectral analogues of the law of the wall, the defect law and the log law. By design, each spectral analogue applies in the same spatial domain as the attendant scaling relation for the mean-velocity profiles: the spectral analogue of the law of the wall in the inner layer, the spectral analogue of the defect law in the outer layer and the spectral analogue of the log law in the overlap layer. In addition, as we are able to show without invoking any model of wall turbulence, each spectral analogue applies in a specific spectral domain (the spectral analogue of the law of the wall in the high-wavenumber spectral domain, where viscosity is active, the spectral analogue of the defect law in the low-wavenumber spectral domain, where viscosity is negligible, and the spectral analogue of the log law in a transitional intermediate-wavenumber spectral domain, which may become sizable only at ultra-high$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathit{Re}_{\tau }$), with the implication that there exist model-independent one-to-one links between the spatial domains and the spectral domains. We test the spectral analogues using experimental and computational data on pipe flow and channel flow.
Pressure forces on sediment particles in turbulent open-channel flow: a laboratory study
Authors: Amir Mohammad , Nikora Vladimir I. , Stewart Mark T. 
Published: September 2014

AbstractAn experimental investigation into the fluctuating pressure acting on sediment particles on the bed of an open-channel flow was carried out in a large laboratory flume for a range of flow depths and bed slopes. The pressure measurements were made using 23 spherical particles instrumented with differential pressure sensors. These measurements were complemented with simultaneous measurements of the velocity field using high-resolution stereoscopic particle image velocimetry. The pressure statistics show that the standard deviations of the drag and lift fluctuations vary from 2.0 to 2.6 and from 2.5 to 3.4 times the wall shear stress, respectively, and are dependent on relative submergence and flow Reynolds number. The skewness is positive for the drag fluctuations and negative for the lift fluctuations. The kurtosis values of both drag and lift fluctuations increase with particle submergence. The two-particle correlation between drag and lift fluctuations is found to be relatively weak compared to the two-point drag–drag and lift–lift correlations. The pressure cross-correlations between particles separated in the longitudinal direction exhibit maxima at certain time delays corresponding to the convection velocities varying from 0.64 to 0.72 times the bulk flow velocity, being very close to the near-bed eddy convection velocities. The temporal autocorrelation of drag fluctuations decays much faster than that for the lift fluctuations; as a result, the temporal scales of lift fluctuations are 3–6 times that of drag fluctuations. The spatial and temporal scales of both drag and lift fluctuations show dependence on flow depth and bed slope. The spectral behaviour of both drag and lift fluctuations is also assessed. A $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}f^{-11/3}$ slope is observed for the spectra of the drag fluctuations over the majority of the frequency range, whereas the lift spectra suggest two scaling ranges, following a $f^{-11/3}$ slope at high frequencies and $f^{-5/3}$ behaviour at lower frequencies.
Parametric subharmonic instability of internal waves: locally confined beams versus monochromatic wavetrains
Authors: Karimi Hussain H. , Akylas T. R. 
Published: September 2014

AbstractInternal gravity wavetrains in continuously stratified fluids are generally unstable as a result of resonant triad interactions which, in the inviscid limit, amplify short-scale perturbations with frequency equal to one half of that of the underlying wave. This so-called parametric subharmonic instability (PSI) has been studied extensively for spatially and temporally monochromatic waves. Here, an asymptotic analysis of PSI for time-harmonic plane waves with locally confined spatial profile is made, in an effort to understand how such wave beams differ, in regard to PSI, from monochromatic plane waves. The discussion centres upon a system of coupled evolution equations that govern the interaction of a small-amplitude wave beam with short-scale subharmonic wavepackets in a nearly inviscid uniformly stratified Boussinesq fluid. For beams with general localized profile, it is found that triad interactions are not strong enough to bring about instability in the limited time that subharmonic perturbations overlap with the beam. On the other hand, for quasi-monochromatic wave beams whose profile comprises a sinusoidal carrier modulated by a locally confined envelope, PSI is possible if the beam is wide enough. In this instance, a stability criterion is proposed which, under given flow conditions, provides the minimum number of carrier wavelengths a beam of small amplitude must comprise for instability to arise.
Finger millet bran supplementation alleviates obesity-induced oxidative stress, inflammation and gut microbial derangements in high-fat diet-fed mice
Authors: Murtaza Nida , Baboota Ritesh K. , Jagtap Sneha , Singh Dhirendra P. , Khare Pragyanshu , Sarma Siddhartha M. , Podili Koteswaraiah , Alagesan Subramanian , Chandra T. S. , Bhutani K. K. , Boparai Ravneet K. , Bishnoi Mahendra , Kondepudi Kanthi Kiran 
Published: September 2014

Several epidemiological studies have shown that the consumption of finger millet (FM) alleviates diabetes-related complications. In the present study, the effect of finger millet whole grain (FM-WG) and bran (FM-BR) supplementation was evaluated in high-fat diet-fed LACA mice for 12 weeks. Mice were divided into four groups: control group fed a normal diet (10 % fat as energy); a group fed a high-fat diet; a group fed the same high-fat diet supplemented with FM-BR; a group fed the same high-fat diet supplemented with FM-WG. The inclusion of FM-BR at 10 % (w/w) in a high-fat diet had more beneficial effects than that of FM-WG. FM-BR supplementation prevented body weight gain, improved lipid profile and anti-inflammatory status, alleviated oxidative stress, regulated the expression levels of several obesity-related genes, increased the abundance of beneficial gut bacteria (Lactobacillus, Bifidobacteria and Roseburia) and suppressed the abundance of Enterobacter in caecal contents (P≤ 0·05). In conclusion, FM-BR supplementation could be an effective strategy for preventing high-fat diet-induced changes and developing FM-BR-enriched functional foods.
Endolymphatic hydrops and Ménière's disease: a lesion meta-analysis
Authors: Pender D J 
Published: September 2014

AbstractObjective:To determine whether the distribution of membrane lesions associated with Ménière's disease is random, as might be expected from a pervasive process such as hydrops, or orderly, as might be expected if membrane resistance is graded.Method:A meta-analysis of temporal bone reports on 184 specimens demonstrating endolymphatic hydrops was undertaken to determine membrane lesion evolution and distribution.Results:Lesion distribution was found to be orderly and cochleocentric. No random scattershot lesions were reported in any study. Disease always started in the cochlear apex, even in non-symptomatic cases, and then involved the saccule, utricle, ampullae and canal system in that precise sequence as the disease progressed.Conclusion:The orderly lesion progression in the otopathology associated with Ménière's disease suggests that the hydropic process has a graded non-random effect on the labyrinth. These findings suggest a pathological staging system that may be useful in temporal bone evaluation.
Additional modes in a waveguide system of zero-index-metamaterials with defects
Authors: Fu Yangyang , Xu Yadong , Chen Huanyang 
Published: September 2014

AbstractZero-index-metamaterials (ZIM) have drawn much attention due to their intriguing properties and novel applications. Particularly, in a parallel plated ZIM waveguide system with defects, total reflection or transmission of wave can be achieved by adjusting the properties of defects. This effect has been explored extensively in different types of ZIM (e.g., epsilon-near-zero metamaterials, matched impedance ZIM, or anisotropic ZIM). Almost all previous literatures showed that only monopole modes are excited inside the defects if they are in circular cylinder shapes. However, the underlying physics for excited modes inside defects is wrongly ignored. In this work, we uncover that additional modes could be excited by theoretical analysis, which is important as it will correct the current common perception. For the case of matched impedance zero-index metamaterials (MIZIM), the additional dipole modes can be excited inside the defects when total transmission occurs. Moreover, we also observe the same results in Dirac-cone-like photonic crystals which have been demonstrated theoretically and experimentally to function as MIZIM. For another case of epsilon-near-zero metamaterials (ENZ), we find that additional higher order modes (e.g., tri-pole) can be excited inside the defects when total transmission happens. Numerical simulations are performed to verify our finding regarding the additional modes.
Double Charge Ordering States and Spin Ordering State Observed in a RFe2O4 System
Authors: Sun Fei , Wang Rui , Aku-Leh C. , Yang H. X. , He Rui , Zhao Jimin 
Published: September 2014

AbstractCharge, spin and lattice degrees of orderings are of great interest in the layered quantum material RFe2O4 (R = Y, Er, Yb, Tm and Lu) system. Recently many unique properties have been found using various experimental methods. However so far the nature of the two-dimensional (2D) charge ordering (CO) state is not clear and no observation of its fine structure in energy has been reported. Here we report unambiguous observation of double 2D CO states at relatively high temperature in a polycrystalline Er0.1Yb0.9Fe2O4 using Raman scattering. The energy gaps between the 3D and the double 2D states are 170 meV (41.2 THz) and 193 meV (46.6 THz), respectively. We also observed a spin ordering (SO) state at below 210 K with characteristic energy of 45 meV (10.7 THz). Our investigation experimentally identified new fine structures of quantum orders in the system, which also extends the capability of optical methods in investigating other layered quantum materials.
Existence and symmetry of positive ground states for a doubly critical Schrödinger system
Authors: Chen Zhijie , Zou Wenming 
Published: September 2014

We study the following doubly critical Schrödinger system:
\[

{

−
Δ
u
−

λ
1

|

x

|

2

u
=

u

2
∗

−
1

+
ν
α

u

α
−
1

v
β

,

x
∈

R

N

,

−
Δ
v
−

λ
2

|

x

|

2

v
=

v

2
∗

−
1

+
ν
β

u

α

v

β
−
1

,

x
∈

R

N

,

u
,

v
∈

D

1
,
2

(

R

N

)
,

u
,

v
>
0

in

R

N

∖
{
0
}

,

\begin {cases}-\Delta u -\frac {\lambda _1}{|x|^2}u=u^{2^\ast -1}+ \nu \alpha u^{\alpha -1}v^\beta , \quad x\in \mathbb {R}^N,\\ -\Delta v -\frac {\lambda _2}{|x|^2}v=v^{2^\ast -1} + \nu \beta u^{\alpha }v^{\beta -1}, \quad x\in \mathbb {R}^N,\\ u,\, v\in D^{1, 2}(\mathbb {R}^N),\quad u,\, v>0\,\,\hbox {in $\mathbb {R}^N\setminus \{0\}$},\end {cases}

\]
where

N
≥
3

N\ge 3

,

λ
1

,

λ
2

∈
(
0
,

(
N
−
2

)
2

4

)

\lambda _1, \lambda _2\in (0, \frac {(N-2)^2}{4})

,

2
∗

=

2
N

N
−
2

2^\ast =\frac {2N}{N-2}

and

α
>
1
,
β
>
1

\alpha >1, \beta >1

satisfying

α
+
β
=

2
∗

\alpha +\beta =2^\ast

. This problem is related to coupled nonlinear Schrödinger equations with critical exponent for Bose-Einstein condensate. For different ranges of

N
N

,

α
\alpha

,

β
\beta

and

ν
>
0

\nu >0

, we obtain positive ground state solutions via some quite different variational methods, which are all radially symmetric. It turns out that the least energy level depends heavily on the relations among

α
,

β

\alpha , \,\beta

and

2
2

. Besides, for sufficiently small

ν
>
0

\nu >0

, positive solutions are also obtained via a variational perturbation approach. Note that the Palais-Smale condition cannot hold for any positive energy level, which makes the study via variational methods rather complicated.
Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity
Authors: Chen Xiang , Shi Shao-Ping , Suo Sheng-Bao , Xu Hao-Dong , Qiu Jian-Ding 
Published: September 2014

Abstract
Motivation: Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes through highly dynamic and complex signaling pathways. Large-scale comparative phosphoproteomic studies have frequently been done on whole cells or organs by conventional bottom-up mass spectrometry approaches, i.e at the phosphopeptide level. Using this approach, there is no way to know from where the phosphopeptide signal originated. Also, as a consequence of the scale of these studies, important information on the localization of phosphorylation sites in subcellular compartments (SCs) is not surveyed.
Results: Here, we present a first account of the emerging field of subcellular phosphoproteomics where a support vector machine (SVM) approach was combined with a novel algorithm of discrete wavelet transform (DWT) to facilitate the identification of compartment-specific phosphorylation sites and to unravel the intricate regulation of protein phosphorylation. Our data reveal that the subcellular phosphorylation distribution is compartment type dependent and that the phosphorylation displays site-specific sequence motifs that diverge between SCs.
Availability and implementation: The method and database both are available as a web server at: http://bioinfo.ncu.edu.cn/SubPhos.aspx .
Contact: jdqiu@ncu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Using population data for assessing next-generation sequencing performance
Authors: Houniet Darren T. , Rahman Thahira J. , Al Turki Saeed , Hurles Matthew E. , Xu Yaobo , Goodship Judith , Keavney Bernard , Santibanez Koref Mauro 
Published: September 2014

Abstract
Motivation : During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their output. This requires approaches to assess the performance of different methods. Traditionally, criteria such as comparison with microarray data or a number of known polymorphic sites have been used. Here we expand such approaches, developing a maximum likelihood framework and using it to estimate the sensitivity and specificity of whole-exome sequencing data.
Results : Using whole-exome sequencing data for a panel of 19 individuals, we show that estimated sensitivity and specificity are similar to those calculated using microarray data as a reference. We explore the effect of frequency misspecification arising from using an inappropriately selected population and find that, although the estimates are affected, the rankings across procedures remain the same.
Availability and implementation : An implementation using Perl and R can be found at busso.ncl.ac.uk (Username: igm101; Password: Z1z1nts).
Contact : Darren.Houniet@ogt.com ; mauro.santibanez-koref@newcastle.ac.uk
Making novel proteins from pseudogenes
Authors: Shidhi P. R. , Suravajhala Prashanth , Nayeema Aysha , Nair Achuthsankar S. , Singh Shailja , Dhar Pawan K. 
Published: September 2014

Abstract
Motivation: Recently, we made synthetic proteins from non-coding DNA of Escherichia coli . Encouraged by this, we asked: can we artificially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes?
Results: To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indicated interesting molecular and cellular functional roles for pseudogene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, transport and binding. Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases.
Impact: To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.
Contact: pawan.dhar@snu.edu.in
Supplementary information: Supplementary data are available at Bioinformatics online.