bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of computational methods in transcriptome-wide alternative splicing analysis
Authors: Wang Jianbo , Ye Zhenqing , Huang Tim H.-M. , Shi Huidong , Jin Victor 
Published: February 2015

AbstractAlternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.
Quantitative biomechanical comparison of ankle fracture casting methods
Authors: Shipman Alastair , Alsousou Joseph , Keene David J. , Dyson Igor N. , Lamb Sarah E. , Willett Keith M. , Thompson Mark S. 
Published: February 2015

AbstractThe incidence of ankle fractures is increasing rapidly due to the ageing demographic. In older patients with compromised distal circulation, conservative treatment of fractures may be indicated. High rates of malunion and complications due to skin fragility motivate the design of novel casting systems, but biomechanical stability requirements are poorly defined. This article presents the first quantitative study of ankle cast stability and hypothesises that a newly proposed close contact cast (CCC) system provides similar biomechanical stability to standard casts (SC). Two adult mannequin legs transected at the malleoli, one incorporating an inflatable model of tissue swelling, were stabilised with casts applied by an experienced surgeon. They were cyclically loaded in torsion, measuring applied rotation angle and resulting torque. CCC stiffness was equal to or greater than that of SC in two measures of ankle cast resistance to torsion. The effect of swelling reduction at the ankle site was significantly greater on CCC than on SC. The data support the hypothesis that CCC provides similar biomechanical stability to SC and therefore also the clinical use of CCC. They suggest that more frequent re-application of CCC is likely required to maintain stability following resolution of swelling at the injury site.
Combining antibody tests and taking into account antibody levels improves serologic diagnosis of celiac disease
Authors: Oyaert Matthijs , Vermeersch Pieter , De Hertogh Gert , Hiele Martin , Vandeputte Nathalie , Hoffman Ilse , Bossuyt Xavier 
Published: February 2015

AbstractThe European Society for Pediatric Gastroenterology and Nutrition states that if IgA anti-tissue transglutaminase (tTG) exceeds 10 times the upper limit of normal (ULN), there is the possibility to diagnose celiac disease (CD) without duodenal biopsy, if supported by anti-endomysium testing and human leukocyte antigen (HLA) typing. We aimed to evaluate whether combining IgA tTG and IgG anti-deamidated gliadin peptide (DGP) antibody testing and taking into account the antibody levels improves clinical interpretation.We calculated likelihood ratios for various test result combinations using data obtained from newly diagnosed CD patients (n=156) [13 children <2 years, 45 children between 2 and 16 years, and 98 adults (>16 years)] and 974 disease controls. All patients and controls underwent duodenal biopsy. IgA anti-tTG and IgG anti-DGP assays were from Thermo Fisher and Inova.Likelihood ratios for CD markedly increased with double positivity and increasing antibody levels of IgA anti-tTG and IgG anti-DGP. Patients with double positivity and high antibody levels (>3 times, >10 times ULN) had a high probability for having CD (likelihood ratio ≥649 for >3 times ULN and ∞ for >10 times ULN). The fraction of CD patients with double positivity and high antibody levels was 59%–67% (depending on the assay) for >3 ULN and 33%–36% (depending on the assay) for >10 ULN, respectively. This fraction was significantly higher in children with CD than in adults.Combining IgG anti-DGP with IgA anti-tTG and defining thresholds for antibody levels improves the serologic diagnosis of CD.
Methods to identify saline-contaminated electrolyte profiles
Authors: Patel Devin K. , Naik Rishi D. , Boyer Richard B. , Wikswo John , Vasilevskis Eduard E. 
Published: February 2015

AbstractWith providers becoming more selective in ordering daily chemistry profiles, it is critical that profiles ordered are accurate. Contaminated electrolyte profiles are an overlooked and potentially dangerous source of inaccurate clinical data. This study aimed to develop a method to accurately identify electrolyte profiles contaminated with normal saline to prevent reporting of erroneous measurements.We conducted a retrospective cohort study of 76,497 electrolyte profiles from 5032 patients in a deidentified clinical database of all patients in the electronic medical record at Vanderbilt University Medical Center. Five methods to identify errors in quantification based on either deviations from observed concentration distributions or expected numerical changes from saline contamination were developed and tested. Potentially contaminated measurements were validated based on changes in electrolyte concentrations observed in the subsequent sample.Identification of erroneous electrolyte profiles based on absolute and percent deviations from normal variation rarely resulted in >50% of identified samples validated as contaminated. A targeted methodology based on expected changes in calcium and chloride concentrations due to saline contamination validated approximately 80% of identified samples when higher thresholds for changes in electrolyte concentration were used and 50% of identified samples when lower thresholds were used.Targeted methodology based on changes in chloride and calcium successfully identified electrolyte profiles suspicious for contamination. Implementation of this methodology could prevent misinterpretation of a patient’s clinical course, inappropriate interventions, and unwarranted changes in treatment strategy.
Downregulation of sphingosine 1-phosphate (S1P) receptor 1 by dexamethasone inhibits S1P-induced mesangial cell migration
Authors: Koch Alexander , Jäger Manuel , Völzke Anja , Grammatikos Georgios , zu Heringdorf Dagmar Meyer , Huwiler Andrea , Pfeilschifter Josef 
Published: February 2015

Abstract
Sphingosine 1-phosphate (S1P) is generated by sphingosine kinase (SK)-1 and -2 and acts mainly as an extracellular ligand at five specific receptors, denoted S1P1–5. After activation, S1P receptors regulate important processes in the progression of renal diseases, such as mesangial cell migration and survival. Previously, we showed that dexamethasone enhances SK-1 activity and S1P formation, which protected mesangial cells from stress-induced apoptosis. Here we demonstrate that dexamethasone treatment lowered S1P1 mRNA and protein expression levels in rat mesangial cells. This effect was abolished in the presence of the glucocorticoid receptor antagonist RU-486. In addition, in vivo studies showed that dexamethasone downregulated S1P1 expression in glomeruli isolated from mice treated with dexamethasone (10 mg/kg body weight). Functionally, we identified S1P1 as a key player mediating S1P-induced mesangial cell migration. We show that dexamethasone treatment significantly lowered S1P-induced migration of mesangial cells, which was again reversed in the presence of RU-486. In summary, we suggest that dexamethasone inhibits S1P-induced mesangial cell migration via downregulation of S1P1. Overall, these results demonstrate that dexamethasone has functional important effects on sphingolipid metabolism and action in renal mesangial cells.
The Cross-Border Impact of Political Violence
Authors: Al-Ississ Mohamad 
Published: February 2015

AbstractThis paper documents the reallocation of financial and economic resources after political violence to other countries. It analyzes the impact of 66 political violence events that took place in 32 countries on 57 stock exchanges over a period of 20 years. Using the event study methodology, this paper is the first to document a positive financial impact from political violence in other countries. The results show that in globally integrated markets, the substitution of financial and economic activities away from afflicted countries magnifies their losses. On average over a 20 day window, event countries suffered a 2.9% drop in stock valuation while other countries picked a windfall of 0.8%. Additionally, the paper investigates the geographic, economic, and risk determinants of this cross-border flow of capital.
High Resolution Microwave Spectroscopy of Ethyl Vinyl Ether: Accurate Determination of the Methyl Top Internal Rotation Barrier
Authors: Dreizler H. , Hansen N. 
Published: February 2015

Abstract
We have performed an investigation of the internal rotation of the methyl group in trans-cis ethyl vinyl ether by using molecular beam-Fourier transform Microwave (MB-FTMW) spectroscopy. Rotational spectra (up to J = 20) were recorded in the frequency region 4-19 GHz. Due to the internal rotation of the methyl group, some rotational transitions were split and the torsional barrier could be determined to V3 (CH3) = 1074.4(4) cm-1 .
Complete Integrability Prolongation Structure and Backlund Transformation for the Konno-Onno Equation
Authors: Das Chandan Kr. , Chowdhury A. Roy 
Published: February 2015

Abstract
Painleve analysis is used to study the complete integrability of the recently proposed Konno-Onno equation, which also leads to a general form of solutions of the system. An independent study, using the prolongation theory, gives the explicit form of the Lax pair which is then used to obtain the Backlund transformation connecting two sets of solutions of the system. The existence of the Lax pair and the positive result of the Painleve test indicate the complete integrability of the system
Ionic Conductivity of Poorly Crystalline Apatite: Effect of Maturation
Authors: Bensaoud A. , Bouhaouss A. , Ferhat M. 
Published: February 2015

Abstract
This study deals with the effect of maturation on the ionic conduction of poorly crystalline synthetic apatite. The tendency of this materials to crystallise during maturation is accompanied by an improvement of its ionic conductivity σ. At room temperature, σ increased by a factor of 300 after 50 days of maturation. The frequency dependence of the ionic conductivity was attenuated gradually during maturation. These results are explained by the short-range organisation of sites with time, and by the fact that the translational movement of the mobile ions becomes less hindered as the material matures.
Liquid Crystals in Binary Systems of Lead Decanoate with Zinc or Cadmium Decanoate
Authors: T. A. Mirnaya , Sudovtsova L. S. , Yaremchuk G. G. 
Published: February 2015

Abstract
The phase transition temperatures were determined by differential thermal analysis and hot stage polarization microscopy between room temperature and the isotropic liquid region for the binary systems of lead (II) decanoate with zinc (II) or cadmium (II) decanoate. The boundaries of the liquid crystal formation in these systems were found.
Laser Compression and Ignition of Z-Pinch Magnetized Dense Fusion Targets
Authors: Winterberg F. 
Published: February 2015

Abstract
With thin wire multimegampere shear flow stabilized fast z-pinch discharges, magnetic fields of hundreds of megagauss can be reached in the vicinity of the discharge channel. Then, if by laser-ablation-propulsion pieces of solid DT are simultaneously shot onto the discharge channel from several sides, the DT is compressed upon impact to high densities, with the magnetic field acting as a cushion to make the compression isentropic. The highly compressed and magnetized DT target can then be ignited at one point by a pulsed laser beam launching a thermonuclear detonation wave propagating along the discharge channel. Estimates indicate thermonuclear gains large in comparison to hohlraum targets.
Molecular Ordering of 4-Acetyl-2'-Nitrobiphenyl - A Computational Analysis
Authors: Ojha Durga Prasad 
Published: February 2015

Abstract
The molecular ordering of some biphenyl derivatives like 4-acetyl-2'-nitrobiphenyl (ANBP), 4-nitro-2-biphenylamine (NBPA) and 4-acetyl-3'-chlorobiphenyl (ACBP) has been examined using basic con-cepts of quantum mechanics and intermolecular forces. The CNDO/2 method has been employed to compute the net atomic charge and atomic dipole components at each atomic centre. The modified Ray-leigh-Schrödinger perturbation theory along with the multicentred-multipole expansion method has been employed to evaluate long-range interactions while a '6-exp' potential function has been assumed for short-range interactions. Accuracies upto 0.1 A in translation and 1° in rotation have been achieved. Probability of occurrence of a particular configuration has been calculated using MB-statistics. On the basis of stacking and in-plane interaction energy calculations, all possible geometrical arrangements between molecular pairs have been considered and a most favorable configuration of pairing has been obtained. A comparative picture of molecular parameters like total energy, binding energy, total dipole moment etc. has been given. An attempt has been made to develop a molecular model correlated with the liquid crystalline property exhibited by this class of molecules.
Molecular Ordering in Liquid Crystalline EMBAC. A Quantum Mechanical Study
Authors: Ojha Durga Prasad 
Published: February 2015

Abstract
Molecular ordering in a liquid crystal, ethyl 4-(4'-methoxybenzylidene amino) cinnamate (EMBAC) has been studied by intermolecular interaction energy calculations. The CNDO/2 method has been employed to compute the atomic charge and atomic dipole at each atomic centre. The modified Rayleigh-Schrödinger perturbation theory along with the multicentered-multipole expansion method have been employed to evaluate the long-range intermolecular interactions, while a '6-exp' potential function has been assumed for the short-range interactions. On the basis of stacking, in-plane, and terminal interaction energy calculations all possible geometrical arrangements of a molecular pair have been considered, and the most favourable configuration of the pair has been obtained. Molecular parameters like total energy, binding energy and total dipole moment have been given. Results are discussed in the light of those obtained for the nematogens 4-(4'-ethoxyphenylazo) phenyl valerate (EPPV) and 4,4'-di-n-propoxy-azoxybenzene (DPAB). An attempt is made to explain the liquid crystalline behavior of these liquid crystals and thereby develop a molecular model for liquid crystallinity.
Molecular Ordering of a Nematic Liquid Crystal in a Dielectric Medium
Authors: Ojha Durga Prasad , Rajeswari B. Raja , Pisipati V. G. K. M. 
Published: February 2015

Abstract
A computational analysis of the molecular ordering of 4-(4'-ethoxyphenylazo) phenyl hexanoate (EPPH) has ben carried out on the basis of intermolecular interaction energy calculations. The CNDO/2 method has been employed to evaluate the net atomic charge ad atomic dipole moment components at each atomic centre of the molecule. A modified Rayleigh-Schrödinger perturbation theory alongwith a multicentered-multipole expansion method has been employed to evaluate long-range intermolecular interactions, while a "6-exp" potential function has been assumed for short-range interactions, and corresponding probabilities have been calculated in a dielectric medium (benzene) using the Maxwell-Boltzmann formula. Further, the flexibility of various configurations has been studied in terms of variations of the probability due to departure from the most probable configuration. All possible geometrical arrangements between molecular pairs have been considered during stacking, in-plane and terminal interactions, and the most favourable configuration of the paring has been obtained. It has been observed that in a dielectric medium the probabilities are redistributed and there is a considerable rise in the prob-ability of interactions although the order of preference remains the same. An attempt has been made to explain the nematogenic behaviour of liquid crystals and thereby develop a molecular model for liquid crystallinity. Results have been discussed in the light of those obtained for other nematogens like EPPV [4-(4'-ethoxyphenylazo) phenyl valerate] and DPAB [4-4'-di-n-propoxy-azoxybenzene],
Effect of Modulation on Thermal Convection Instability
Authors: Bhatia P. K. , Bhadauria B. S. 
Published: February 2015

Abstract
The linear stability problem for a fluid in a classic Benard configuration is considered. The applied temperature gradient is the sum of a steady component and a time-dependent periodic component. Only infinitesimal disturbances are considered. The time-dependent perturbation is expressed in Fourier series. The shift in critical Rayleigh number is calculated and the modulating effect of the oscillatory temperature gradient on the stability of the fluid layer is examined. Some comparison is made with known results.
Surface Properties and Concentration Fluctuations in Sn-based Molten Alloys
Authors: Prasad L. C. , Singh V. N. 
Published: February 2015

Abstract
A simple model based on the concept of a layered structure near the interface has been used to investigate the surface tension and surface segregation of SnPb and SnZn molten alloys. With increasing concentration of Sn, the surface tension (σ) of SnPb alloys has been found to increase, while a of SnZn alloys decreases, σ of both systems is smaller than the ideal value ΣCiσi. Our study reveals that both in SnPb and SnZn alloys the heavier atoms segregate towards the surface. The degree of segregation in SnZn alloys is greater than that in SnPb alloys. The Cahn-Hillard phenomenological model for the surface of pure liquids has been extended to binary molten mixtures and applied to the above systems. An attempt has been made to establish a link between the surface tension and the bulk properties such as concentration fluctuations in the long wavelength limit [Scc (0)] and isothermal compressibility (λT). The impact of the very sensitive bulk parameter Scc(0) has been examined. Reasonable agreement between our model and the experiment is observed for binary molten alloys such as SnPb in which the segregation is small, while for the SnZn alloys, in which the segregation is quite large, the agreement is not satisfactory.
The Number of High-Energy Bands in the Photoelectron Spectrum of Alkanes
Authors: Merris Russell , Gutman Ivan 
Published: February 2015

Abstract
It was observed that within the Bieri-Dill-Heilbronner-Schmelzer model for the calculation of the ion-ization energies of alkanes CnH2n+2, there are exactly n C2s -electron energy levels lying below the degenerate α-ß manifold. We now show that, indeed, this regularity is obeyed by practically all alkane species. Exceptions do exist, but they must possess a (chemically infeasible) group of more than six mutually connected quaternary carbon atoms.
H NMR Study of Ionic Motions in High Temperature Solid Phases of (CH3NH3)2ZnCl4
Authors: Ishida Hiroyuki 
Published: February 2015

Abstract
The reorientation of the tetrahedral complex anion ZnCl4
2- and the self-diffusion of the cation in (CH3NH3)2ZnCl4 were studied by 1H NMR spin-lattice relaxation time (1H T1) experiments. In the second highest-temperature phase, the temperature dependence of 1H T1 observed at 8.5 MHz could be explained by a magnetic dipolar-electric quadrupolar cross relaxation between 1H and chlorine nuclei, and the activation energy of the anion motion was determined to be 105 kJ mol -1 . In the highest-temperature phase, the activation energy of the self-diffusion of the cation was determined to be 58 kJ mol -1 from the temperature and frequency dependence of 1H T1
Electronic Energy Partitioning in the Reactions of Metastable Mg*(3PJ) Atoms with F2, Cl2, Br2, I2, ICl, IBr
Authors: Kierzkowski P. , Pranszke B. , Kowalski A. , Menzinger M. 
Published: February 2015

Abstract
Chemiluminescent reactions of metastable Mg*(3PJ) atoms with F2 , Cl2 , Br2 , I2 , IC1, IBr molecules were studied in a beam-gas experiment. For all homonuclear targets the MgX(A 2Π -X 2Σ+) emission was observed, but for IC1 and IBr reactants the Mgl(A-X) emission was absent and only MgCl(A-X) or MgBr(A-X) spectra were found. In addition, for the I2 , IBr, IC1, Br2 reactions, broad pseudocontinua extend from above 400 nm into the infrared. These pseudocontinua are ten-tatively attributed to the Mgl, MgBr (B' 2Σ+ -X2Σ+) transition. The total attenuation cross sections, chemiluminescence cross sections and quantum yields were measured. The quantum yields are all below 5%. The results are analyzed using information theory. The low yields for the Mg* + F2 system are explained by a barrier in the entrance channel. For other reactions the low yields are most probably caused by predissociation of the MgX*(A 2Π) products
Hole Injection Sequence in BaCuO2 as Seen by XANES
Authors: Morgante Norberto , Ghigna Paolo , Spinolo Giorgio 
Published: February 2015

Abstract
Cu-LIII in XANES data collected on Ba0.98CuO1.98+δ samples with different oxygen content are reported. The near-edge structures are discussed together with previous conductivity measurements, and an estimate of the hole density evolution with oxygen doping is given. The reported results give evidence of the increase with δ of the localization of doping holes on oxygen atoms
Polymerie Structures in Aluminium and Gallium Halides
Authors: Akdeniz Z. , Çaliskana M. , Tosib M. P. 
Published: February 2015

54a,
The anionic species (Aln X3n + 1) − with X = CI or Br and n ≥ 1 have been recognized for a number of years to form in acidic liquid mixtures of aluminium chloride or bromide with the corresponding halides of alkali or organic cations, in relative proportions which vary with the composition of the mixture. In this work we evaluate the structure and the energetics of such polymeric series in a comparative study of Al and Ga compounds. To this end we first extend an earlier study of the ionic interactions in the Al2Cl6 molecule [Z. Akdeniz and M. P. Tosi, Z. Naturforsch. 180 (1999)] to determine microscopic ionic models for Ga2Cl6, Al2Br6, and Ga2Br6. The models are then used (i) to evaluate the polymeric clusters for n ≤ 4 in the two trivalent-metal chlorides, and (ii) to explore the potential-energy hypersurface of alkali counterions in the case n = 2. We present tests of the results against available data and an evaluation of the convergence of the energy of the polymeric series towards a value of about 0.5 eV per monomer.
Influence of Conformational Equilibria upon the Self-Diffusion of the Conformers in Neat Liquids
Authors: Chen Liuping , Lüdemann Hans-Dietrich 
Published: February 2015

Abstract
The self-diffusion coefficients D of the isomers of liquid N-isopropyl-N-methylacetamide (IPMAA) and acetylacetone (AC AC) are studied as functions of temperature. For AC AC also pressure dependent studies were undertaken. In IPMAA the eis and trans conformers have almost identical D. In liquid ACAC, DKclo is always smaller than Denol , this difference being 15% around 300 K.