bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of porous cationic frameworks by crosslinking polyhedral oligomeric silsesquioxane units with N-heterocyclic linkers
Authors: Chen Guojian , Zhou Yu , Wang Xiaochen , Li Jing , Xue Shuang , Liu Yangqing , Wang Qian , Wang Jun 
Published: June 2015

AbstractIn fields of materials science and chemistry, ionic-type porous materials attract increasing attention due to significant ion-exchanging capacity for accessing diversified applications. Facing the fact that porous cationic materials with robust and stable frameworks are very rare, novel tactics that can create new type members are highly desired. Here we report the first family of polyhedral oligomeric silsesquioxane (POSS) based porous cationic frameworks (PCIF-n) with enriched poly(ionic liquid)-like cationic structures, tunable mesoporosities, high surface areas (up to 1,025 m2 g−1) and large pore volumes (up to 0.90 cm3 g−1). Our strategy is designing the new rigid POSS unit of octakis(chloromethyl)silsesquioxane and reacting it with the rigid N-heterocyclic cross-linkers (typically 4,4′-bipyridine) for preparing the desired porous cationic frameworks. The PCIF-n materials possess large surface area, hydrophobic and special anion-exchanging property and thus are used as the supports for loading guest species PMo10V2O405−; the resultant hybrid behaves as an efficient heterogeneous catalyst for aerobic oxidation of benzene and H2O2-mediated oxidation of cyclohexane.
A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia
Authors: Kaliannan Kanakaraju , Wang Bin , Li Xiang-Yong , Kim Kui-Jin , Kang Jing X. 
Published: June 2015

AbstractMetabolic endotoxemia, commonly derived from gut dysbiosis, is a primary cause of chronic low grade inflammation that underlies many chronic diseases. Here we show that mice fed a diet high in omega-6 fatty acids exhibit higher levels of metabolic endotoxemia and systemic low-grade inflammation, while transgenic conversion of tissue omega-6 to omega-3 fatty acids dramatically reduces endotoxemic and inflammatory status. These opposing effects of tissue omega-6 and omega-3 fatty acids can be eliminated by antibiotic treatment and animal co-housing, suggesting the involvement of the gut microbiota. Analysis of gut microbiota and fecal transfer revealed that elevated tissue omega-3 fatty acids enhance intestinal production and secretion of intestinal alkaline phosphatase (IAP), which induces changes in the gut bacteria composition resulting in decreased lipopolysaccharide production and gut permeability and ultimately, reduced metabolic endotoxemia and inflammation. Our findings uncover an interaction between host tissue fatty acid composition and gut microbiota as a novel mechanism for the anti-inflammatory effect of omega-3 fatty acids. Given the excess of omega-6 and deficiency of omega-3 in the modern Western diet, the differential effects of tissue omega-6 and omega-3 fatty acids on gut microbiota and metabolic endotoxemia provide insight into the etiology and management of today’s health epidemics.
Optimizing cell viability in droplet-based cell deposition
Authors: Hendriks Jan , Willem Visser Claas , Henke Sieger , Leijten Jeroen , Saris Daniël B.F. , Sun Chao , Lohse Detlef , Karperien Marcel 
Published: June 2015

AbstractBiofabrication commonly involves the use of liquid droplets to transport cells to the printed structure. However, the viability of the cells after impact is poorly controlled and understood, hampering applications including cell spraying, inkjet bioprinting and laser-assisted cell transfer. Here, we present an analytical model describing the cell viability after impact as a function of the cell-surrounding droplet characteristics. The model connects (1) the cell survival as a function of cell membrane elongation, (2) the membrane elongation as a function of the cell-containing droplet size and velocity and (3) the substrate properties. The model is validated by cell viability measurements in cell spraying, which is a method for biofabrication and used for the treatment of burn wounds. The results allow for rational optimization of any droplet-based cell deposition technology and we include practical suggestions to improve the cell viability in cell spraying.
Light‐emitting diode driver with a combined energy transfer inductor for current balancing control
Authors: Lin Yu‐Liang , Chiu Huang‐Jen , Lo Yu‐Kang , Leng Chung‐Ming 
Published: June 2015

This study proposes a two‐channel light‐emitting diode (LED) backlight driver specifically for liquid crystal display monitor application that utilises an integrated magnetic component: a combined energy transfer inductor for current balancing. The integrated magnetic component has two functions: as a boost inductor and as a differential‐mode current balance transformer. Under proper design and arrangement, all of the windings are wound on a single UU‐core. This scheme uses leakage inductance as boost inductor for energy transfer and mutual inductance as differential mode transformer for output current balancing. By introducing the magnetic component, power density is increased whereas the overall cost and volume of the magnetic components are reduced in comparison with those values under conventional topology. The operating principles and design considerations of the proposed LED driver were analysed. A 10 W prototype converter with a two‐channel LED string was developed to verify the feasibility of the proposed driver. Experimental results show that the proposed LED driver provides an equal current for a two‐channel LED string.
Peritoneal Pigmentation in Purebred and Hybrid River Herring
Authors: Berlinsky David L. , DiMaggio Matthew A. , Breton Timothy S. , Walsh Jennifer , Kovach Adrienne I. 
Published: June 2015

AbstractRiver herring (Alewives Alosa pseudoharengus and Blueback Herring A. aestivalis [bluebacks]) are congeneric, anadromous clupeid fishes that hybridize in areas of sympatry. Peritoneal pigmentation is the most diagnostic characteristic used to distinguish the species, but pigmentation has not been examined in hybrids. We developed a molecular‐based assay to distinguish purebred river herring species from F1 hybrids and compared the peritoneal pigmentation among captive‐raised purebred and hybrid individuals. Both wild‐caught Alewife and blueback females tank‐spawned with conspecific and congeneric males, but Alewives required exogenous hormone administration. Larvae of both species and hybrids were raised for ∼290 d posthatch, and peritoneal pigmentation was quantified. A nuclear gene (rag2) restriction fragment length polymorphism assay was used for species and hybrid identification. The peritoneal pigmentation was significantly darker in hatchery‐spawned bluebacks than in Alewives, and hybrids exhibited consistent, intermediate expression. Adult individuals collected from the wild, however, exhibited darker (Alewives) or more variable (bluebacks) peritoneal coloration than their respective, captive‐reared juveniles. These results indicated that peritoneal pigmentation alone is insufficient for diagnostic river herring species identification and should be coupled with genetic assays.
Compatible Lie Bialgebras*
Authors: Wu Ming-Zhong , Bai Cheng-Ming 
Published: June 2015

Abstract
A compatible Lie algebra is a pair of Lie algebras such that any linear combination of the two Lie brackets is a Lie bracket. We construct a bialgebra theory of compatible Lie algebras as an analogue of a Lie bialgebra. They can also be regarded as a “compatible version” of Lie bialgebras, that is, a pair of Lie bialgebras such that any linear combination of the two Lie bialgebras is still a Lie bialgebra. Many properties of compatible Lie bialgebras as the “compatible version” of the corresponding properties of Lie bialgebras are presented. In particular, there is a coboundary compatible Lie bialgebra theory with a construction from the classical Yang–Baxter equation in compatible Lie algebras as a combination of two classical Yang–Baxter equations in Lie algebras. Furthermore, a notion of compatible pre-Lie algebra is introduced with an interpretation of its close relation with the classical Yang–Baxter equation in compatible Lie algebras which leads to a construction of the solutions of the latter. As a byproduct, the compatible Lie bialgebras fit into the framework to construct non-constant solutions of the classical Yang–Baxter equation given by Golubchik and Sokolov.
Solving the Generalized Higgs Model from the Generalized CRS Model*
Authors: Song Ci , Li Yan , Chen Jing-Ling 
Published: June 2015

AbstractIn this paper, we reveal a direct relation between the generalized one-dimensional Carinena–Ranada–Santander (CRS) model and the radial part of two-dimensional generalized Higgs model. By this relation, we construct a series of quasi-exactly solutions for the two-dimensional Higgs model from a solved generalized CRS model.
Solutions and Continuum Limits of Two Semi-Discrete Lattice Potential Korteweg-de Vries Equations*
Authors: Wu Hua , Pan Jia-Jia , Zhang Da-Jun 
Published: June 2015

Abstract
We derive bilinear forms and Casoratian solutions for two semi-discrete potential Korteweg-de Vries equations. Their continuum limits go to the counterparts of the continuous potential Korteweg-de Vries equation.
Explicit Relations of Physical Potentials Through Generalized Hypervirial and Kramers' Recurrence Relations*
Authors: Sun Guo-Hua , Dong Shi-Hai 
Published: June 2015

Abstract
Based on a Hamiltonian identity, we study one-dimensional generalized hypervirial theorem, Blanchard-like (non-diagonal case) and Kramers' (diagonal case) recurrence relations for arbitrary xκ which is independent of the central potential V(x). Some significant results in diagonal case are obtained for special κ in xκ (κ ≥ 2). In particular, we find the orthogonal relation 〈n1 | n2〉 = δn1n2
(κ = 0), 〈n1 | V′ (x)|n2〉 = (En1
− En2
)2〈n1 | x | n2〉 (κ = 1), En = 〈n | V′ (x)x/2|n〉 + 〈n | V (x)|n〉 (κ = 2) and −4En〈n| x|n〉 + 〈n|V′(x)x2|n〉 + 4〈n|V(x)x|n〉 = 0 (κ = 3). The latter two formulas can be used directly to calculate the energy levels. We present useful explicit relations for some well known physical potentials without requiring the energy spectra of quantum system.
Coherent Destruction of Tunneling of Bosons with Effective Three-Body Interactions*
Authors: Niu Zhen-Xia , Yu Zi-Fa , Xue Ju-Kui 
Published: June 2015

Abstract
The tunneling dynamics of dilute boson gases with three-body interactions in a periodically driven double wells are investigated both theoretically and numerically. In our findings, when the system is with only repulsive two-body interactions or only three-body interactions, the tunneling will be suppressed; while in the case of the coupling between two- and three-body interactions, the tunneling can be either suppressed or enhanced. Particularly, when attractive three-body interactions are twice large as repulsive two-body interactions, CDT occurs at isolated points of driving force, which is similar to the linear case. Considering different interaction, the system can experience different transformation from coherent tunneling to coherent destruction of tunneling (CDT). The quasi-energy of the system as the function of the periodically driving force shows a triangular structure, which provides a deep insight into the tunneling dynamics of the system.
f (T) Non-linear Massive Gravity and the Cosmic Acceleration*
Authors: Wu You , Chen Zu-Cheng , Wang Jia-Xin , Wei Hao 
Published: June 2015

Abstract
Inspired by the f (R) non-linear massive gravity, we propose a new kind of modified gravity model, namely f (T) non-linear massive gravity, by adding the dRGT mass term reformulated in the vierbein formalism, to the f (T) theory. We then investigate the cosmological evolution of f (T) massive gravity, and constrain it by using the latest observational data. We find that it slightly favors a crossing of the phantom divide line from the quintessence-like phase (wde > −1) to the phantom-like one (wde < −1) as redshift decreases.
First-Principles GGA+U Study of Intermediate-Band Characters from Zn1−x
M
x
O (M = 3d Transition-Metal) Alloys Suitable for High Efficiency Solar Cell*
Authors: Wu Kong-Ping , Lu Kai-Lin , Jiang Jian-Hui , Gu Shu-Lin , Tang Kun , Ye Jian-Dong , Zhu Shun-Ming , Zhang Rong , Zheng You-Dou 
Published: June 2015

Abstract
The electronic structure characters are calculated for the Zn1−xMxO alloys with some Zn atoms in ZnO substituted by 3d transition-metal atoms (M), in order to find out which of these alloys could provide an intermediate band material used for fabricating high efficiency solar cell. Especially, among of these alloys, the electronic structure character and optical performance of Zn1−xCrxO alloys clearly show an intermediate band filled partially and isolated from the VB and the CB in energy band structure of ZnO host, and the intermediate band characters can be preserved with increasing Cr concentrations no more than 8.33% in Zn1−xCrxO alloys, at the same time, the ratio 0.52 of Eg
FC to Eg
VF in Zn1−xCrxO, (x = 4.16%) alloy is closest to the optimal ratio of 0.57. Besides, compared to the ZnO, the optical absorption does indicate a great improved absorption below the calculated band gap of the ZnO and an enhancement of the optical absorption in the whole solar spectral energy range.
DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts
Authors: Lee Donghyung , Bigdeli T. Bernard , Williamson Vernell S. , Vladimirov Vladimir I. , Riley Brien P. , Fanous Ayman H. , Bacanu Silviu-Alin 
Published: June 2015

AbstractMotivation: To increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts.Results: To decrease computational and access requirements for the analysis of cosmopolitan cohorts, we propose DISTMIX, which extends DIST capabilities to the analysis of mixed ethnicity cohorts. The method uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistics at measured SNPs and estimated/user-specified ethnic proportions. Simulations show that the proposed method adequately controls the Type I error rates. The 1000 Genomes panel imputation of summary statistics from the ethnically diverse Psychiatric Genetic Consortium Schizophrenia Phase 2 suggests that, when compared to genotype imputation methods, DISTMIX offers comparable imputation accuracy for only a fraction of computational resources.Availability and implementation: DISTMIX software, its reference population data, and usage examples are publicly available at http://code.google.com/p/distmix.Contact: dlee4@vcu.eduSupplementary information: Supplementary Data are available at Bioinformatics online.
UniAlign: protein structure alignment meets evolution
Authors: Zhao Chunyu , Sacan Ahmet 
Published: June 2015

Abstract
Motivation: During the evolution, functional sites on the surface of the protein as well as the hydrophobic core maintaining the structural integrity are well-conserved. However, available protein structure alignment methods align protein structures based solely on the 3D geometric similarity, limiting their ability to detect functionally relevant correspondences between the residues of the proteins, especially for distantly related homologous proteins.
Results: In this article, we propose a new protein pairwise structure alignment algorithm (UniAlign) that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles and residue conservation. We define a per-residue score (UniScore) as a weighted sum of these and other features and develop an iterative optimization procedure to search for an alignment with the best overall UniScore. Our extensive experiments on CDD, HOMSTRAD and BAliBASE benchmark datasets show that UniAlign outperforms commonly used structure alignment methods. We further demonstrate UniAlign's ability to develop family-specific models to drastically improve the quality of the alignments.
Availability and implementation: UniAlign is available as a web service at: http://sacan.biomed.drexel.edu/unialign
Contact: ahmet.sacan@drexel.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated profiling of individual cell–cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING)
Authors: Merouane Amine , Rey-Villamizar Nicolas , Lu Yanbin , Liadi Ivan , Romain Gabrielle , Lu Jennifer , Singh Harjeet , Cooper Laurence J.N. , Varadarajan Navin , Roysam Badrinath 
Published: June 2015

Abstract
Motivation: There is a need for effective automated methods for profiling dynamic cell–cell interactions with single-cell resolution from high-throughput time-lapse imaging data, especially, the interactions between immune effector cells and tumor cells in adoptive immunotherapy.
Results: Fluorescently labeled human T cells, natural killer cells (NK), and various target cells (NALM6, K562, EL4) were co-incubated on polydimethylsiloxane arrays of sub-nanoliter wells (nanowells), and imaged using multi-channel time-lapse microscopy. The proposed cell segmentation and tracking algorithms account for cell variability and exploit the nanowell confinement property to increase the yield of correctly analyzed nanowells from 45% (existing algorithms) to 98% for wells containing one effector and a single target, enabling automated quantification of cell locations, morphologies, movements, interactions, and deaths without the need for manual proofreading. Automated analysis of recordings from 12 different experiments demonstrated automated nanowell delineation accuracy &gt;99%, automated cell segmentation accuracy &gt;95%, and automated cell tracking accuracy of 90%, with default parameters, despite variations in illumination, staining, imaging noise, cell morphology, and cell clustering. An example analysis revealed that NK cells efficiently discriminate between live and dead targets by altering the duration of conjugation. The data also demonstrated that cytotoxic cells display higher motility than non-killers, both before and during contact.
Contact: broysam@central.uh.edu or nvaradar@central.uh.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A NuSTAR observation of disc reflection from close to the neutron star in 4U 1608–52
Authors: Degenaar N. , Miller J. M. , Chakrabarty D. , Harrison F. A. , Kara E. , Fabian A. C. 
Published: June 2015

Abstract
Studying the reflection of X-rays off the inner edge of the accretion disc in a neutron star low-mass X-ray binary allows us to investigate the accretion geometry and to constrain the radius of the neutron star. We report on a NuSTAR observation of 4U 1608–52 obtained during a faint outburst in 2014 when the neutron star, which has a known spin frequency of ν = 620 Hz, was accreting at ≃1–2 per cent of the Eddington limit. The 3–79 keV continuum emission was dominated by a Γ ≃ 2 power law, with an ≃1–2 per cent contribution from a kTbb ≃ 0.3–0.6 keV blackbody component. The high-quality NuSTAR spectrum reveals the hallmarks of disc reflection; a broad iron-line peaking near 7 keV and a Compton back-scattering hump around ≃20–30 keV. Modelling the disc reflection spectrum points to a binary inclination of i ≃30°–40° and a small ‘coronal’ height of h ≲8.5GM/c2. Furthermore, our spectral analysis suggests that the inner disc radius extended to Rin ≃ 7–10GM/c2, close to the innermost stable circular orbit. This constrains the neutron star radius to R ≲21 km and the redshift from the stellar surface to z ≳0.12, for a mass of M = 1.5 M⊙ and a spin parameter of a = 0.29.
Luminosity and spin-period evolution of GX 304−1 during outbursts from 2009 to 2013 observed with the MAXI/GSC, RXTE/PCA, and Fermi/GBM
Authors: Sugizaki Mutsumi , Yamamoto Takayuki , Mihara Tatehiro , Nakajima Motoki , Makishima Kazuo 
Published: June 2015

Abstract
A report is made on the luminosity and pulse period evolution of the Be binary X-ray pulsar GX 304−1 during a series of outbursts from 2009 to 2013 observed by MAXI/GSC, RXTE/PCA, and Fermi/GBM. In total, 12 outbursts repeated by ∼ 132.2 d were observed, which is consistent with the X-ray periodicity of this object observed in the 1970s. These 12 outbursts, together with those in the 1970s, were all found to recur with a well-defined period of 132.189 ± 0.02 d, which can be identified with the orbital period. The pulse period of ∼ 275 s, obtained from the RXTE/PCA and Fermi/GBM data, apparently exhibited a periodic modulation synchronized with the outburst period, suggesting the pulsar orbital motion, which is superposed on a secular spin-up trend throughout the entire active phase. The observed pulse period changes were successfully represented by a model composed of the binary orbital modulation and pulsar spin up caused by mass accretion through an accretion disk. The orbital elements obtained from the best-fit model, including the projected orbital semi-major axis ax sin i ≃ 500–600 light-s and an eccentricity e ≃ 0.5, are typical of Be binary X-ray pulsars.
Discrete Distributional Differential Expression (D3E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data
Authors: Delmans Mihails , Hemberg Martin 
Published: June 2015

AbstractThe advent of high throughput RNA-seq at the single-cell level has opened up new opportunities to elucidate the heterogeneity of gene expression. One of the most widespread applications of RNA-seq is to identify genes which are differentially expressed between two experimental conditions. Here, we present a discrete, distributional method for differential gene expression (D3E), a novel algorithm specifically designed for single-cell RNA-seq data. We use synthetic data to evaluate D3E, demonstrating that it can detect changes in expression, even when the mean level remains unchanged. Since D3E is based on an analytically tractable stochastic model, it provides additional biological insights by quantifying biologically meaningful properties, such as the average burst size and frequency. We use D3E to investigate experimental data, and with the help of the underlying model, we directly test hypotheses about the driving mechanism behind changes in gene expression.