bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exact regularized point particle method for multiphase flows in the two-way coupling regime
Authors: Gualtieri P. , Picano F. , Sardina G. , Casciola C. M. 
Published: May 2015

Particulate flows have mainly been studied under the simplifying assumption of a one-way coupling regime where the disperse phase does not modify the carrier fluid. A more complete view of multiphase flows can be gained calling into play two-way coupling effects, i.e. by accounting for the inter-phase momentum exchange, which is certainly relevant at increasing mass loading. In this paper we present a new methodology rigorously designed to capture the inter-phase momentum exchange for particles smaller than the smallest hydrodynamical scale, e.g. the Kolmogorov scale in a turbulent flow. The momentum coupling mechanism exploits the unsteady Stokes flow around a small rigid sphere, where the transient disturbance produced by each particle is evaluated in a closed form. The particles are described as lumped point masses, which would lead to the appearance of singularities. A rigorous regularization procedure is conceived to extract the physically relevant interactions between the particles and the fluid which avoids any ‘ad hoc’ assumption. The approach is suited for high-efficiency implementation on massively parallel machines since the transient disturbance produced by the particles is strongly localized in space. We will show that hundreds of thousands of particles can be handled at an affordable computational cost, as demonstrated by a preliminary application to a particle-laden turbulent shear flow.
Long-Term Multicolour Photometry of the Young Stellar Objects FHO 26, FHO 27, FHO 28, FHO 29, and V1929 Cygni
Authors: Ibryamov S. I. , Semkov E. H. , Peneva S. P. 
Published: May 2015

AbstractResults from long-term multicolour optical photometric observations of the pre-main-sequence stars FHO 26, FHO 27, FHO 28, FHO 29, and V1929 Cyg collected during the period from 1997 June to 2014 December are presented. The objects are located in the dense molecular cloud L935, named ‘Gulf of Mexico’, in the field between the North America and Pelican nebulae. All stars from our study exhibit strong photometric variability in all optical passbands. Using our BVRI observations and data published by other authors, we tried to define the reasons for the observed brightness variations. The presented paper is a part of our long-term photometric study of the young stellar objects in the region of ‘Gulf of Mexico’.
In situ ruminal degradation of phenolic acid, cellulose and hemicellulose in crop brans and husks differing in ferulic and p-coumaric acid patterns
Authors: CAO B. B. , WANG R. , YANG H. J. , JIANG L. S. 
Published: May 2015

SUMMARYLignification-associated phenolic acids are widely distributed in graminaceous plant cell walls. Nylon bags containing maize bran, wheat bran, millet husk and rice husk were incubated in the rumens of five Charolais (♂) × Nanyang (♀) crossbred steers for 6, 12, 24, 36, 48 and 72 h. The in situ ruminal disappearance of ester-linked phenolic acids linearly increased in the brans with increasing incubation time, and the disappearance was greater for ester-linked ferulic acid (FAest) than for ester-linked p-coumaric acid (PCAest). The disappearances of FAest and PCAest were positively correlated with disappearances of neutral detergent fibre (NDF), cellulose and hemicellulose. The effective degradabilities of NDF, cellulose and hemicellulose in the brans were markedly greater than the effective degradabilities of these components in the husks, and were negatively correlated with the contents of Lignin (sa), ether-linked ferulic acid, PCAest and ether-linked p-coumaric acid in both the cereal brans and husks. These findings suggested that breeding forage crops with modified phenolic acid contents could represent an alternative strategy to promote further increases in fibre digestibility of cereal residue feeds for ruminant animals.
A simulation study on the statistical monitoring of condemnation rates from slaughterhouses for syndromic surveillance: an evaluation based on Swiss data
Authors: VIAL F. , THOMMEN S. , HELD L. 
Published: May 2015

SUMMARYSyndromic surveillance (SyS) systems currently exploit various sources of health-related data, most of which are collected for purposes other than surveillance (e.g. economic). Several European SyS systems use data collected during meat inspection for syndromic surveillance of animal health, as some diseases may be more easily detected post-mortem than at their point of origin or during the ante-mortem inspection upon arrival at the slaughterhouse. In this paper we use simulation to evaluate the performance of a quasi-Poisson regression (also known as an improved Farrington) algorithm for the detection of disease outbreaks during post-mortem inspection of slaughtered animals. When parameterizing the algorithm based on the retrospective analyses of 6 years of historic data, the probability of detection was satisfactory for large (range 83–445 cases) outbreaks but poor for small (range 20–177 cases) outbreaks. Varying the amount of historical data used to fit the algorithm can help increasing the probability of detection for small outbreaks. However, while the use of a 0·975 quantile generated a low false-positive rate, in most cases, more than 50% of outbreak cases had already occurred at the time of detection. High variance observed in the whole carcass condemnations time-series, and lack of flexibility in terms of the temporal distribution of simulated outbreaks resulting from low reporting frequency (monthly), constitute major challenges for early detection of outbreaks in the livestock population based on meat inspection data. Reporting frequency should be increased in the future to improve timeliness of the SyS system while increased sensitivity may be achieved by integrating meat inspection data into a multivariate system simultaneously evaluating multiple sources of data on livestock health.
Centrin-2 (Cetn2) mediated regulation of FGF/FGFR gene expression in Xenopus
Authors: Shi Jianli , Zhao Ying , Vonderfecht Tyson , Winey Mark , Klymkowsky Michael W. 
Published: May 2015

AbstractCentrins (Cetns) are highly conserved, widely expressed and multifunctional Ca2+-binding eukaryotic signature proteins best known for their roles in ciliogenesis and as critical components of the global genome nucleotide excision repair system. Two distinct Cetn subtypes, Cetn2-like and Cetn3-like, have been recognized and implicated in a range of cellular processes. In the course of morpholino-based loss of function studies in Xenopus laevis, we have identified a previously unreported Cetn2-specific function, namely in fibroblast growth factor (FGF) mediated signaling, specifically through the regulation of FGF and FGF receptor RNA levels. Cetn2 was found associated with the RNA polymerase II binding sites of the Cetn2-regulated FGF8 and FGFR1a genes, but not at the promoter of a gene (BMP4) whose expression was altered indirectly in Cent2 morphant embryos. These observations point to a previously unexpected role of Cetn2 in the regulation of gene expression and embryonic development.
Exploiting lipopolysaccharide-induced deformation of lipid bilayers to modify membrane composition and generate two-dimensional geometric membrane array patterns
Authors: Adams Peter G. , Swingle Kirstie L. , Paxton Walter F. , Nogan John J. , Stromberg Loreen R. , Firestone Millicent A. , Mukundan Harshini , Montaño Gabriel A. 
Published: May 2015

AbstractSupported lipid bilayers have proven effective as model membranes for investigating biophysical processes and in development of sensor and array technologies. The ability to modify lipid bilayers after their formation and in situ could greatly advance membrane technologies, but is difficult via current state-of-the-art technologies. Here we demonstrate a novel method that allows the controlled post-formation processing and modification of complex supported lipid bilayer arrangements, under aqueous conditions. We exploit the destabilization effect of lipopolysaccharide, an amphiphilic biomolecule, interacting with lipid bilayers to generate voids that can be backfilled to introduce desired membrane components. We further demonstrate that when used in combination with a single, traditional soft lithography process, it is possible to generate hierarchically-organized membrane domains and microscale 2-D array patterns of domains. Significantly, this technique can be used to repeatedly modify membranes allowing iterative control over membrane composition. This approach expands our toolkit for functional membrane design, with potential applications for enhanced materials templating, biosensing and investigating lipid-membrane processes.
Universal dependence of the spin wave band structure on the geometrical characteristics of two-dimensional magnonic crystals
Authors: Tacchi S. , Gruszecki P. , Madami M. , Carlotti G. , Kłos J. W. , Krawczyk M. , Adeyeye A. , Gubbiotti G. 
Published: May 2015

AbstractIn the emerging field of magnon-spintronics, spin waves are exploited to encode, carry and process information in materials with periodic modulation of their magnetic properties, named magnonic crystals. These enable the redesign of the spin wave dispersion, thanks to its dependence on the geometric and magnetic parameters, resulting in the appearance of allowed and forbidden band gaps for specific propagation directions. In this work, we analyze the spin waves band structure of two-dimensional magnonic crystals consisting of permalloy square antidot lattices with different geometrical parameters. We show that the frequency of the most intense spin-wave modes, measured by Brillouin light scattering, exhibits a universal dependence on the aspect ratio (thickness over width) of the effective nanowire enclosed between adjacent rows of holes. A similar dependence also applies to both the frequency position and the width of the main band gap of the fundamental (dispersive) mode at the edge of the first Brillouin zone. These experimental findings are successfully explained by calculations based on the plane-wave method. Therefore, a unified vision of the spin-waves characteristics in two-dimensional antidot lattices is provided, paving the way to the design of tailored nanoscale devices, such as tunable magnonic filters and phase-shifters, with predicted functionalities.
SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains
Authors: Huang Yong-Heng , Jankowski Aleksander , Cheah Kathryn S. E. , Prabhakar Shyam , Jauch Ralf 
Published: May 2015

AbstractThe SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins.
A transcription and translation-coupled DNA replication system using rolling-circle replication
Authors: Sakatani Yoshihiro , Ichihashi Norikazu , Kazuta Yasuaki , Yomo Tetsuya 
Published: May 2015

AbstractAll living organisms have a genome replication system in which genomic DNA is replicated by a DNA polymerase translated from mRNA transcribed from the genome. The artificial reconstitution of this genome replication system is a great challenge in in vitro synthetic biology. In this study, we attempted to construct a transcription- and translation-coupled DNA replication (TTcDR) system using circular genomic DNA encoding phi29 DNA polymerase and a reconstituted transcription and translation system. In this system, phi29 DNA polymerase was translated from the genome and replicated the genome in a rolling-circle manner. When using a traditional translation system composition, almost no DNA replication was observed, because the tRNA and nucleoside triphosphates included in the translation system significantly inhibited DNA replication. To minimize these inhibitory effects, we optimized the composition of the TTcDR system and improved replication by approximately 100-fold. Using our system, genomic DNA was replicated up to 10 times in 12 hours at 30 °C. This system provides a step toward the in vitro construction of an artificial genome replication system, which is a prerequisite for the construction of an artificial cell.
Morphological and molecular characterization of a sexually reproducing colony of the booklouse Liposcelis bostrychophila (Psocodea: Liposcelididae) found in Arizona
Authors: Yang Qianqian , Kučerová Zuzana , Perlman Steve J. , Opit George P. , Mockford Edward L. , Behar Adi , Robinson Wyatt E. , Stejskal Václav , Li Zhihong , Shao Renfu 
Published: May 2015

AbstractThe booklouse,Liposcelis bostrychophila, is a worldwide pest of stored products. For decades, only thelytokous parthenogenetic reproduction was documented inL. bostrychophila. MaleL. bostrychophilawere first found in Hawaii in 2002. In 2009, a sexual strain was found in Arizona. We examined the morphology of both males and females of the Arizona strain and compared the Arizona sexual strain with the Hawaii sexual strain and the parthenogenetic strains ofL. bostrychophila. The sexual and parthenogenetic strains show some differences in eye morphology. To examine the relationship between sexual and asexual lineages, we sequenced the mitochondrial12Sand16Sribosomal RNA genes of males and females from the Arizona strain. Phylogenetic analyses ofL. bostrychophilaindividuals revealed that: 1) the sexually reproducing colony found in Arizona contains two closely related mitochondrial DNA haplotypes – one present in only females and the other in both males and females; and 2) the Arizona sexual strain was most closely related to a parthenogenetic strain in Illinois. We detectedRickettsiain all of the parthenogenetic individuals we checked but not in any Arizona sexual individuals. Further evidence is required to establish whether the presence ofRickettsiais linked to asexual reproduction inLiposcelis.
Topological nature and the multiple Dirac cones hidden in Bismuth high-Tc superconductors
Authors: Li Gang , Yan Binghai , Thomale Ronny , Hanke Werner 
Published: May 2015

AbstractRecent theoretical studies employing density-functional theory have predicted BaBiO3 (when doped with electrons) and YBiO3 to become a topological insulator (TI) with a large topological gap (~0.7 eV). This, together with the natural stability against surface oxidation, makes the Bismuth-Oxide family of special interest for possible applications in quantum information and spintronics. The central question, we study here, is whether the hole-doped Bismuth Oxides, i.e. Ba1-xKxBiO3 and BaPb1-xBixO3, which are “high-Tc” bulk superconducting near 30 K, additionally display in the further vicinity of their Fermi energy EF a topological gap with a Dirac-type of topological surface state. Our electronic structure calculations predict the K-doped family to emerge as a TI, with a topological gap above EF. Thus, these compounds can become superconductors with hole-doping and potential TIs with additional electron doping. Furthermore, we predict the Bismuth-Oxide family to contain an additional Dirac cone below EF for further hole doping, which manifests these systems to be candidates for both electron- and hole-doped topological insulators.
Exercise intolerance and developmental delay associated with a novel mitochondrial ND5 mutation
Authors: Fang Hezhi , Shi Hao , Li Xiyuan , Sun Dayan , Li Fengjie , Li Bin , Ding Yuan , Ma Yanyan , Liu Yupeng , Zhang Yao , Shen Lijun , Bai Yidong , Yang Yanling , Lu Jianxin 
Published: May 2015

AbstractThe aim of this study was to evaluate the contribution of mitochondrial DNA (mtDNA) mutations in oxidative phosphorylation (OXPHOS) deficiency. The complete mitochondrial genomes of 41 families with OXPHOS deficiency were screened for mutations. Mitochondrial functional analysis was then performed in primary and cybrid cells containing candidate mutations identified during the screening. A novel mitochondrial NADH dehydrogenase 5 (ND5) m.12955A > G mutation was identified in a patient with exercise intolerance and developmental delay. A biochemical analysis revealed deficiencies in the activity of complex I (NADH:quinone oxidoreductase) and IV (cytochrome c oxidase) of this patient. Defects in complexes I and IV were confirmed in transmitochondrial cybrid cells containing the m.12955A > G mutation, suggesting that this mutation impairs complex I assembly, resulting in reduced stability of complex IV. Further functional investigations revealed that mitochondria with the m.12955A > G mutation exhibited lower OXPHOS coupling respiration and adenosine triphosphate (ATP) generation. In addition, the cytotoxic effects, determined as reactive oxygen species (ROS) and lactate levels in the present study, increased in the cells carrying a higher m.12955A > G mutant load. In conclusion, we identified m.12955A > G as a mitochondrial disease-related mutation. Therefore, screening of m.12955A > G is advised for the diagnosis of patients with mitochondrial disease.
Ion adsorption-induced wetting transition in oil-water-mineral systems
Authors: Mugele Frieder , Bera Bijoyendra , Cavalli Andrea , Siretanu Igor , Maestro Armando , Duits Michel , Cohen-Stuart Martien , van den Ende Dirk , Stocker Isabella , Collins Ian 
Published: May 2015

AbstractThe relative wettability of oil and water on solid surfaces is generally governed by a complex competition of molecular interaction forces acting in such three-phase systems. Herein, we experimentally demonstrate how the adsorption of in nature abundant divalent Ca2+ cations to solid-liquid interfaces induces a macroscopic wetting transition from finite contact angles (≈10°) with to near-zero contact angles without divalent cations. We developed a quantitative model based on DLVO theory to demonstrate that this transition, which is observed on model clay surfaces, mica, but not on silica surfaces nor for monovalent K+ and Na+ cations is driven by charge reversal of the solid-liquid interface. Small amounts of a polar hydrocarbon, stearic acid, added to the ambient decane synergistically enhance the effect and lead to water contact angles up to 70° in the presence of Ca2+. Our results imply that it is the removal of divalent cations that makes reservoir rocks more hydrophilic, suggesting a generalizable strategy to control wettability and an explanation for the success of so-called low salinity water flooding, a recent enhanced oil recovery technology.
Live Cell Characterization of DNA Aggregation Delivered through Lipofection
Authors: Mieruszynski Stephen , Briggs Candida , Digman Michelle A. , Gratton Enrico , Jones Mark R 
Published: May 2015

AbstractDNA trafficking phenomena, such as information on where and to what extent DNA aggregation occurs, have yet to be fully characterised in the live cell. Here we characterise the aggregation of DNA when delivered through lipofection by applying the Number and Brightness (N&B) approach. The N&B analysis demonstrates extensive aggregation throughout the live cell with DNA clusters in the extremity of the cell and peri-nuclear areas. Once within the nucleus aggregation had decreased 3-fold. In addition, we show that increasing serum concentration of cell media results in greater cytoplasmic aggregation. Further, the effects of the DNA fragment size on aggregation was explored, where larger DNA constructs exhibited less aggregation. This study demonstrates the first quantification of DNA aggregation when delivered through lipofection in live cells. In addition, this study has presents a model for alternative uses of this imaging approach, which was originally developed to study protein oligomerization and aggregation.
Three-dimensional cage-like microscaffolds for cell invasion studies
Authors: Spagnolo Barbara , Brunetti Virgilio , Leménager Godefroy , De Luca Elisa , Sileo Leonardo , Pellegrino Teresa , Paolo Pompa Pier , De Vittorio Massimo , Pisanello Ferruccio 
Published: May 2015

AbstractCancer cell motility is one of the major events involved in metastatic process. Tumor cells that disseminate from a primary tumor can migrate into the vascular system and, being carried by the bloodstream, transmigrate across the endothelium, giving rise to a new tumor site. However, during the invasive process, tumor cells must pass through the extracellular matrix, whose structural and mechanical properties define the parameters of the migration process. Here, we propose 3D-complex cage-like microstructures, realized by two-photon (TP) direct laser writing (DLW), to analyze cell migration through pores significantly smaller than the cell nucleus. We found that the ability to traverse differently sized pores depends on the metastatic potential and on the invasiveness of the cell lines, allowing to establish a pore-area threshold value able to discriminate between non-tumorigenic and tumorigenic human breast cells.
The Local CNP/GC-B system in growth plate is responsible for physiological endochondral bone growth
Authors: Nakao Kazumasa , Osawa Kenji , Yasoda Akihiro , Yamanaka Shigeki , Fujii Toshihito , Kondo Eri , Koyama Noriaki , Kanamoto Naotetsu , Miura Masako , Kuwahara Koichiro , Akiyama Haruhiko , Bessho Kazuhisa , Nakao Kazuwa 
Published: May 2015

AbstractRecent studies revealed C-type natriuretic peptide (CNP) and its receptor, guanylyl cyclase-B (GC-B) are potent stimulators of endochondral bone growth. As they exist ubiquitously in body, we investigated the physiological role of the local CNP/GC-B in the growth plate on bone growth using cartilage-specific knockout mice. Bones were severely shorter in cartilage-specific CNP or GC-B knockout mice and the extent was almost the same as that in respective systemic knockout mice. Cartilage-specific GC-B knockout mice were shorter than cartilage-specific CNP knockout mice. Hypertrophic chondrocyte layer of the growth plate was drastically reduced and proliferative chondrocyte layer, along with the proliferation of chondrocytes there, was moderately reduced in either cartilage-specific knockout mice. The survival rate of cartilage-specific CNP knockout mice was comparable to that of systemic CNP knockout mice. The local CNP/GC-B system in growth plate is responsible for physiological endochondral bone growth and might further affect mortality via unknown mechanisms.