bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double‐hybrid density functionals
Authors: Goerigk Lars , Grimme Stefan 
Published: July 2014

Double‐hybrid density functionals (DHDFs) are reviewed in this study. In DHDFs parts of conventional density functional theory (DFT) exchange and correlation are replaced by contributions from nonlocal Fock‐exchange and second‐order perturbative correlation. The latter portion is based on the well‐known MP2 wave‐function approach in which, however, Kohn–Sham orbitals are used to calculate its contribution. First, related methods preceding this idea are reviewed, followed by a thorough discussion of the first modern double‐hybrid B2‐PLYP. Parallels and differences between B2‐PLYP and its various successors are then outlined. This discussion is rounded off with representative thermochemical examples demonstrating that DHDFs belong to the most robust and accurate DFT approaches currently available. This analysis also presents hitherto unpublished results for recently developed DHDFs. Finally, how double‐hybrids can be combined with linear‐response time‐dependent DFT is also outlined and the value of this approach for electronically excited states is shown. WIREs Comput Mol Sci 2014, 4:576–600. doi: 10.1002/wcms.1193This article is categorized under:

Electronic Structure Theory > Density Functional Theory
Computational finance: correlation, volatility, and markets
Authors: Ensor Katherine Bennett , Koev Ginger M. 
Published: July 2014

Financial data by nature are inter‐related and should be analyzed using multivariate methods. Many models exist for the joint analysis of multiple financial instruments. Early models often assumed some type of constant behavior between the instruments over the time period of analysis. But today, time‐varying covariance models are a key component of financial time series analysis leading to a deeper understanding of changing market conditions. Models for covolatility of financial data quickly grow in their complexity and parameters, and 20 years of research offers a variety of solutions to this complexity. After a short introduction of univariate volatility models, this article begins with the basic multivariate formulation for time series covariance modeling and moves to leading time series tools that address this complexity. Coupling these models with regime switching via a Markov process extends the features that can be understood from market behavior. We ground this review in an example of modeling the covariance of securities within sectors and sectors within markets, with dynamics that allow for two different market regimes. Specifically, we simultaneously model individual daily stock data that belong to one of three market sectors and examine the behavior of the market as a whole as well as the behavior of the market sectors over time. A motivation for this characterization concerns portfolio diversification and stock anomalies, and we capture the changing comovement of stocks within and between sectors as market conditions change. For example, some of these market conditions include market crashes or collapses and common external influences. WIREs Comput Stat 2014, 6:326–340. doi: 10.1002/wics.1323This article is categorized under:

Applications of Computational Statistics > Computational Finance
Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Data: Types and Structure > Time Series, Stochastic Processes, and Functional Data
Reinvestigation of Crystal Structure and Non‐Stoichiometry in Copper Hydride, CuH1–x (0 ≤ x ≤ 0.26)
Authors: Auer Henry , Kohlmann Holger 
Published: July 2014

AbstractCopper hydride and deuteride were reinvestigated by X‐ray and neutron powder diffraction, revealing a pronounced phase width with respect to the hydrogen (deuterium) content. Synthesis from aqueous copper(II) sulfate with hypophosphoric acid solutions yields samples with a broad distribution of compositions and variations of up to 6.5 % in unit cell volume. The result is a metrical distortion with (hkl) dependent asymmetry and broadening of powder diffraction reflections. Patterns of such samples were described using a model with five copper hydride (deuteride) phases with different lattice parameters. A method for developing and refining reasonable multiphase models despite high correlation of parameters is described. Simultaneous refinement on X‐ray and neutron powder diffraction on a deuteride sample suggests a statistical occupation of deuterium on less than half of the tetrahedral voids of a hexagonal close packing of copper atoms [P63/mmc, a = 2.9024(5) Å, c = 4.632(2) Å, Cu in 2c, D in 4f with z = 0.6497(8), deuterium occupation 0.368(6)]. The reaction of aqueous copper(II) chloride with sodium boronate solutions yields copper hydride with a stoichiometric composition [P63/mmc, a = 2.8777(3) Å, c = 4.570(1) Å, Cu in 2c, H in 4f with z = 0.640(1), hydrogen occupation 1/2]. The structures are isotypic to ScD0.33 and reveal a surprising analogy to lanthanide hydrides.
Physiological and proteomic analysis of Lactobacillus casei in response to acid adaptation
Authors: Wu Chongde , He Guiqiang , Zhang Juan 
Published: July 2014

Abstract
The aim of this study was to investigate the acid tolerance response (ATR) in Lactobacillus casei by a combined physiological and proteomic analysis. To optimize the ATR induction, cells were acid adapted for 1 h at different pHs, and then acid challenged at pH 3.5. The result showed that acid adaptation improved acid tolerance, and the highest survival was observed in cells adapted at pH 4.5 for 1 h. Analysis of the physiological data showed that the acid-adapted cells exhibited higher intracellular pH (pHi), intracellular NH4+ content, and lower inner permeability compared with the cells without adaptation. Proteomic analysis was performed upon acid adaptation to different pHs (pH 6.5 vs. pH 4.5) using two-dimensional electrophoresis. A total of 24 proteins that exhibited at least 1.5-fold differential expression were identified. Four proteins (Pgk, LacD, Hpr, and Galm) involved in carbohydrate catabolism and five classic stress response proteins (GroEL, GrpE, Dnak, Hspl, and LCAZH_2811) were up-regulated after acid adaptation at pH 4.5 for 1 h. Validation of the proteomic data was performed by quantitative RT-PCR, and transcriptional regulation of all selected genes showed a positive correlation with the proteomic patterns of the identified proteins. Results presented in this study may be useful for further elucidating the acid tolerance mechanisms and may help in formulating new strategies to improve the industrial performance of this species during acid stress.
Valproic acid attenuates the suppression of acetyl histone H3 and CREB activity in an inducible cell model of Machado–Joseph disease
Authors: Lin X.P. , Feng L. , Xie C.G. , Chen D.B. , Pei Z. , Liang X.L. , Xie Q.Y. , Li X.H. , Pan S.Y. 
Published: July 2014

AbstractMachado–Joseph disease (MJD) is caused by a (CAG)n trinucleotide repeat expansion that is translated into an abnormally long polyglutamine tract. This disease is considered the most common form of spinocerebellar ataxia (SCA). In the present study, we developed stable inducible cell lines (PC12Tet‐On‐Ataxin‐3‐Q28/84) expressing ataxin‐3 with either normal or abnormal CAG repeats under doxycycline control. The expression of acetyl histone H3 and the induction of c‐Fos in response to cAMP were strongly suppressed in cells expressing the protein with the expanded polyglutamine tract. Treatment with valproic acid, a histone deacetylase inhibitor (HDACi), attenuated mutant ataxin‐3‐induced cell toxicity and suppression of acetyl histone H3, phosphorylated cAMP‐responsive element binding protein (p‐CREB) as well as c‐Fos expression. These results indicate that VPA can stimulate the up‐regulation of gene transcription through hyperacetylation. Thus, VPA might have a therapeutic effect on MJD.
Characterization of long non‐coding RNA transcriptome in clear‐cell renal cell carcinoma by next‐generation deep sequencing
Authors: Malouf Gabriel G. , Zhang Jianping , Yuan Ying , Compérat Eva , Rouprêt Morgan , Cussenot Olivier , Chen Yunxin , Thompson Erika J. , Tannir Nizar M. , Weinstein John N. , Valero Vicente , Khayat David , Spano Jean-Philippe , Su Xiaoping 
Published: July 2014

IntroductionLong non‐coding RNA (lncRNA) have proven to play key roles in cell physiology from nuclear organization and epigenetic remodeling to post‐transcriptional regulation. Last decade, gene expression based‐classifications have been developed in clear‐cell renal cell carcinoma (ccRCC) to identify distinct subtypes of disease and predict patient's outcome. However, there are no current lncRNA comprehensive characterizations in ccRCC.Patients and methodsRNA‐sequencing profiles of 475 primary ccRCC samples from the Cancer Genome Atlas (TCGA) were used to assess expressed lncRNA and identify lncRNA‐based classification. In addition, integrative analysis was performed to correlate tumor subtypes with copy‐number alterations and somatic mutations.ResultsUsing stringent criteria, we identified 1934 expressed lncRNA and assessed their chromatin marks. Unsupervised clustering unravels four lncRNA subclasses in ccRCC associated with distinct clinicopathological and genomic features of this disease. Cluster C2 (23.4%) defines the most aggressive tumours, with the highest Fuhrman grade and stage and the worst overall survival time. Furthermore, cluster C2 is enriched for 9p deletion and chromatin remodeler BAP1 somatic mutations. Interestingly, cluster C4 (7.8%) is related to a tumor subtype arising from the distal tubules of the nephron. Consistent with its distinct ontogeny, cluster C4 is devoid of classical alterations seen in ccRCC, bears frequent 1p deletion and 17q gain, and is enriched for MiTF/TFE translocations. In addition, reexaminations of copy‐number data from one side and tumor histology by pathologists from the other side reveal misclassified tumors within C4 cluster including chromophobe RCC and clear cell papillary RCC.ConclusionThis study establishes a foundation for categorizing lncRNA subclasses, which may contribute to understand tumor ontogeny and help predicting patients' outcome in ccRCC.
Spot-on™ Technology for Low Volume Liquid Handling
Authors: Shvets I.V. , Makarov S. , Franken C. , Shvets A. , Sweeney D. , Osing J. 
Published: July 2014

The article describes the new proprietary spot-on™ technology developed by Allegro Technologies, Ltd., for nanolitre and microlitre dispensing of liquids for the drug discovery, genomics and proteomics industries. We analyze the requirements of the drug discovery industry for low volume liquid handling technologies and briefly summarize some the more common technologies currently available. A detailed description is provided of the new spot-on™ technology in terms of function and operation as well as the relevant features and potential benefits to using this new method of nanolitre dispensing.
ACTUARIAL FAIRNESS AND SOLIDARITY IN POOLED ANNUITY FUNDS
Authors: Donnelly Catherine 
Published: July 2014

AbstractVarious types of structures that enable a group of individuals to pool their mortality risk have been proposed in the literature. Collectively, the structures are called pooled annuity funds. Since the pooled annuity funds propose different methods of pooling mortality risk, we investigate the connections between them and find that they are genuinely different for a finite heterogeneous membership profile. We discuss the importance of actuarial fairness, defined as the expected benefits equalling the contributions for each member, in the context of pooling mortality risk and comment on whether actuarial unfairness can be seen as solidarity between members. We show that, with a finite number of members in the fund, the group self-annuitization scheme is not actuarially fair: some members subsidize the other members. The implication is that the members who are subsidizing the others may obtain a higher expected benefit by joining a fund with a more favorable membership profile. However, we find that the subsidies are financially significant only for very small or highly heterogeneous membership profiles.
Wavefront measurement techniques used in high power lasers
Authors: Wang Haiyan , Liu Cheng , He Xiaoliang , Pan Xingchen , Zhou Shenlei , Wu Rong , Zhu Jianqiang 
Published: July 2014

AbstractThe properties of a series of phase measurement techniques, including interferometry, the Hartmann–Shack wavefront sensor, the knife-edge technique, and coherent diffraction imaging, are summarized and their performance in high power laser applications is compared. The advantages, disadvantages, and application ranges of each technique are discussed.
Cyclic homology, Serre's local factors and λ-operations
Authors: Connes Alain , Consani Caterina 
Published: July 2014

AbstractWe show that for a smooth, projective variety X defined over a number field K, cyclic homology with coefficients in the ring , provides the right theory to obtain, using λ-operations, Serre's archimedean local factors of the complex L-function of X as regularized determinants.
Effects of radiation in turbulent channel flow: analysis of coupled direct numerical simulations
Authors: Vicquelin R. , Zhang Y. F. , Gicquel O. , Taine J. 
Published: July 2014

AbstractThe role of radiative energy transfer in turbulent boundary layers is carefully analysed, focusing on the effect on temperature fluctuations and turbulent heat flux. The study is based on direct numerical simulations (DNS) of channel flows with hot and cold walls coupled to a Monte-Carlo method to compute the field of radiative power. In the conditions studied, the structure of the boundary layers is strongly modified by radiation. Temperature fluctuations and turbulent heat flux are reduced, and new radiative terms appear in their respective balance equations. It is shown that they counteract turbulence production terms. These effects are analysed under different conditions of Reynolds number and wall temperature. It is shown that collapsing of wall-scaled profiles is not efficient when radiation is considered. This drawback is corrected by the introduction of a radiation-based scaling. Finally, the significant impact of radiation on turbulent heat transfer is studied in terms of the turbulent Prandtl number. A model for this quantity, based on the new proposed scaling, is developed and validated.
Inertial wave dynamics in a rotating liquid metal
Authors: Vogt Tobias , Räbiger Dirk , Eckert Sven 
Published: July 2014

AbstractThe dynamics of free and forced inertial waves inside cylinders of different aspect ratios ($\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}A=H_0/2R_0$) were investigated experimentally in this study. The liquid metal GaInSn was chosen as the fluid in order to enable a contactless stimulation of the flow by means of alternating electromagnetic fields. A rotating magnetic field generates the rotating motion of the liquid, whereas periodic modulations of the field strength and short pulses excite specific wave modes. Ultrasound Doppler velocimetry was used to record the flow structure and to identify inertial waves in the set-up. Our experiments demonstrate selective excitation of different inertial wave modes by deliberate variation of the magnetic field parameters. Furthermore, it was found that turbulent perturbations in the boundary layers of the swirling flow are able to induce an inertial wave mode that survives over a long time. Experiments at the fundamental resonance have shown that multiple harmonic wave modes appeared simultaneously. The measured inertial wave frequencies were compared to the predictions of the linear inviscid theory.
Large-eddy simulation of turbulence and particle dispersion inside the canopy roughness sublayer
Authors: Pan Ying , Chamecki Marcelo , Isard Scott A. 
Published: July 2014

AbstractModelling the dispersion of small particles such as fungal spores, pollens and small seeds inside and above plant canopies is important for many applications. Transport of these particles is driven by strongly inhomogeneous and non-Gaussian turbulent flows inside the canopy roughness sublayer, the region that extends from the ground to approximately three canopy heights. A large-eddy simulation (LES) approach is refined to study particle dispersion within and above the canopy region. Effects of plant reconfiguration are parameterized through a velocity-dependent drag coefficient, which is shown to be critical for accurate reproduction of velocity statistics and mean spore concentrations. The model yields predictions of turbulence statistics that are in good agreement with measurements. This is particularly true of the stress fractions carried by strong events, as revealed by standard quadrant analysis of the resolved velocity fluctuations, which is a known weakness of earlier LES studies of canopy flow using a constant drag coefficient. Experimental data on spore dispersal inside and above a maize canopy are reproduced successfully as well. Characteristics of the particle plume are analysed using LES results, and a pre-existing theoretical framework is adapted to model particle dispersal above the canopy. The results suggest that the plume above the canopy can be approximated using a simple analytical solution if the fraction of spores that escape the canopy region is known. Source height and gravitational settling have strong effects on the plume inside the canopy region and consequently determine the escape fraction. These effects are parameterized in the theoretical model by using the escape fraction to rescale the source strength.
Diet quality score is a predictor of type 2 diabetes risk in women: The Australian Longitudinal Study on Women's Health
Authors: Alhazmi Amani , Stojanovski Elizabeth , McEvoy Mark , Brown Wendy , Garg Manohar L. 
Published: July 2014

The present study aimed to determine the ability of two diet quality scores to predict the incidence of type 2 diabetes in women. The study population comprised a nationally representative sample of 8370 Australian middle-aged (45–50 years) women participating in the ALSWH (Australian Longitudinal Study on Women's Health), who were free of diabetes and completed FFQ at baseline. The associations between the Australian Recommended Food Score (ARFS) and Dietary Guideline Index (DGI) with type 2 diabetes risk were assessed using multiple logistic regression models, adjusting for sociodemographic characteristics, lifestyle factors and energy intake. During 6 years of follow-up, 311 incident cases of type 2 diabetes were reported. The DGI score was inversely associated with type 2 diabetes risk (OR comparing the highest with the lowest quintile of DGI was 0·51; 95 % CI 0·35, 0·76; P for trend = 0·01). There was no statistically significant association between the ARFS and type 2 diabetes risk (OR comparing the highest with the lowest quintile of ARFS was 0·99; 95 % CI 0·68, 1·43; P for trend = 0·42). The results of the present prospective study indicate that the DGI score, which assesses compliance with established dietary guidelines, is predictive of type 2 diabetes risk in Australian women. The risk of type 2 diabetes among women in the highest quintile of DGI was approximately 50 % lower than that in women in the lowest quintile. The ARFS was not significantly predictive of type 2 diabetes.
Dietary isoflavone intake is not statistically significantly associated with breast cancer risk in the Multiethnic Cohort
Authors: Morimoto Yukiko , Maskarinec Gertraud , Park Song-Yi , Ettienne Reynolette , Matsuno Rayna K. , Long Camonia , Steffen Alana D. , Henderson Brian E. , Kolonel Laurence N. , Le Marchand Loïc , Wilkens Lynne R. 
Published: July 2014

Given the high intake levels of soya and low incidence rates of breast cancer in Asian countries, isoflavones, substances with an oestrogen-like structure occurring principally in soyabeans, are postulated to be cancer protective. In the present study, we examined the association of dietary isoflavone intake with breast cancer risk in 84 450 women (896 in situ and 3873 invasive cases) who were part of the Multiethnic Cohort (Japanese Americans, whites, Latinos, African Americans and Native Hawaiians) with a wide range of soya intake levels. The absolute levels of dietary isoflavone intake estimated from a baseline FFQ were categorised into quartiles, with the highest quartile being further subdivided to assess high dietary intake. The respective intake values for the quartiles (Q1, Q2, Q3, and lower and upper Q4) were 0– < 3·2, 3·2– < 6·7, 6·7– < 12·9, 12·9– < 20·3, and 20·3–178·7 mg/d. After a mean follow-up period of 13 years, hazard ratios (HR) and 95 % CI were calculated using Cox regression models stratified by age and adjusted for known confounders. Linear trends were tested by modelling continuous variables of interest assigned the median value within the corresponding quartile. No statistically significant association was observed between dietary isoflavone intake and overall breast cancer risk (HR for upper Q4 v. Q1: 0·96 (95 % CI 0·85, 1·08); P trend = 0·40). While the test for interaction was not significant (P= 0·14), stratified analyses suggested possible ethnic/racial differences in risk estimates, indicating that higher isoflavone intakes may be protective in Latina, African American and Japanese American women. These results are in agreement with those of previous meta-analyses showing no protection of isoflavones at low intake levels, but suggesting inverse associations in populations consuming high amounts of soya.
Is there an excess of significant findings in published studies of psychotherapy for depression?
Authors: Flint J. , Cuijpers P. , Horder J. , Koole S. L. , Munafò M. R. 
Published: July 2014

BackgroundMany studies have examined the efficacy of psychotherapy for major depressive disorder (MDD) but publication bias against null results may exist in this literature. However, to date, the presence of an excess of significant findings in this literature has not been explicitly tested.MethodWe used a database of 1344 articles on the psychological treatment of depression, identified through systematic search in PubMed, PsycINFO, EMBASE and the Cochrane database of randomized trials. From these we identified 149 studies eligible for inclusion that provided 212 comparisons. We tested for an excess of significant findings using the method developed by Ioannidis and Trikalinos (2007), and compared the distribution of p values in this literature with the distribution in the antidepressant literature, where publication bias is known to be operating.ResultsThe average statistical power to detect the effect size indicated by the meta-analysis was 49%. A total of 123 comparisons (58%) reported a statistically significant difference between treatment and control groups, but on the basis of the average power observed, we would only have expected 104 (i.e. 49%) to do so. There was therefore evidence of an excess of significance in this literature (p = 0.010). Similar results were obtained when these analyses were restricted to studies including a cognitive behavioural therapy (CBT) arm. Finally, the distribution of p values for psychotherapy studies resembled that for published antidepressant studies, where publication bias against null results has already been established.ConclusionsThe small average size of individual psychotherapy studies is only sufficient to detect large effects. Our results indicate an excess of significant findings relative to what would be expected, given the average statistical power of studies of psychotherapy for major depression.