bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased survival of cirrhotic patients with septic shock
Authors: Sauneuf Bertrand , Champigneulle Benoit , Soummer Alexis , Mongardon Nicolas , Charpentier Julien , Cariou Alain , Chiche Jean-Daniel , Mallet Vincent , Mira Jean-Paul , Pène Frédéric 
Published: April 2013

Abstract
Introduction
The overall outcome of septic shock has been recently improved. We sought to determine whether this survival gain extends to the high-risk subgroup of patients with cirrhosis.

Methods
Cirrhotic patients with septic shock admitted to a medical intensive care unit (ICU) during two consecutive periods (1997-2004 and 2005-2010) were retrospectively studied.

Results
Forty-seven and 42 cirrhotic patients presented with septic shock in 1997-2004 and 2005-2010, respectively. The recent period differed from the previous one by implementation of adjuvant treatments of septic shock including albumin infusion as fluid volume therapy, low-dose glucocorticoids, and intensive insulin therapy. ICU and hospital survival markedly improved over time (40% in 2005-2010 vs. 17% in 1997-2004, P = 0.02 and 29% in 2005-2010 vs. 6% in 1997-2004, P = 0.009, respectively). Furthermore, this survival gain in the latter period was sustained for 6 months (survival rate 24% in 2005-2010 vs. 6% in 1997-2004, P = 0.06). After adjustment with age, the liver disease stage (Child-Pugh score), and the critical illness severity score (SOFA score), ICU admission between 2005 and 2010 remained an independent favorable prognostic factor (odds ratio (OR) 0.09, 95% confidence interval (CI) 0.02-0.4, P = 0.004). The stage of the underlying liver disease was also independently associated with hospital mortality (Child-Pugh score: OR 1.42 per point, 95% CI 1.06-1.9, P = 0.018).

Conclusions
In the light of advances in management of both cirrhosis and septic shock, survival of such patients substantially increased over recent years. The stage of the underlying liver disease and the related therapeutic options should be included in the decision-making process for ICU admission.
Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish
Authors: Yao Zizhen , Farr, Gist H. , Tapscott Stephen J. , Maves Lisa 
Published: April 2013

Summary
The basic helix–loop–helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes, including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets, in particular fast-twitch muscle differentiation genes, thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast-twitch muscle-specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber-type regulator, Prdm1a, a SET-domain DNA-binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype, early and increased fast muscle differentiation, is the opposite of the Pbx-null phenotype, delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes, we used RNA-seq analysis to globally assess gene expression in zebrafish embryos with single- and double-losses-of-function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4-MO;prdm1a−/− embryos, suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However, other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus, our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program.
The Rho-GEF Trio regulates a novel pro-inflammatory pathway through the transcription factor Ets2
Authors: Van Rijssel Jos , Timmerman Ilse , Van Alphen Floris P. J. , Hoogenboezem Mark , Korchynskyi Olexandr , Geerts Dirk , Geissler Judy , Reedquist Kris A. , Niessen Hans W. M. , Van Buul Jaap D. 
Published: April 2013

SummaryInflammation is characterized by endothelium that highly expresses numerous adhesion molecules to trigger leukocyte extravasation. Central to this event is increased gene transcription. Small Rho-GTPases not only control the actin cytoskeleton, but are also implicated in gene regulation. However, in inflammation, it is not clear how this is regulated. Here, we show that the guanine-nucleotide exchange factor Trio expression is increased upon inflammatory stimuli in endothelium. Additionally, increased Trio expression was found in the vessel wall of rheumatoid arthritis patients. Trio silencing impaired VCAM-1 expression. Finally, we excluded that Trio-controlled VCAM-1 expression used the classical NFκB or MAP-kinase pathways, but rather acts on the transcriptional level by increasing phosphorylation and nuclear translocalization of Ets2. These data implicate Trio in regulating inflammation and provide novel targets for therapeutic purposes to treat inflammatory diseases such as rheumatoid arthritis.
Evidence against a germ plasm in the milkweed bugOncopeltus fasciatus, a hemimetabolous insect
Authors: Ewen-Campen Ben , Jones Tamsin E. M. , Extavour Cassandra G. 
Published: April 2013

SummaryPrimordial germ cell (PGC) formation in holometabolous insects like Drosophila melanogaster relies on maternally synthesised germ cell determinants that are asymmetrically localised to the oocyte posterior cortex. Embryonic nuclei that inherit this “germ plasm” acquire PGC fate. In contrast, historical studies of basally branching insects (Hemimetabola) suggest that a maternal requirement for germ line genes in PGC specification may be a derived character confined principally to Holometabola. However, there have been remarkably few investigations of germ line gene expression and function in hemimetabolous insects. Here we characterise PGC formation in the milkweed bug Oncopeltus fasciatus, a member of the sister group to Holometabola, thus providing an important evolutionary comparison to members of this clade. We examine the transcript distribution of orthologues of 19 Drosophila germ cell and/or germ plasm marker genes, and show that none of them localise asymmetrically within Oncopeltus oocytes or early embryos. Using multiple molecular and cytological criteria, we provide evidence that PGCs form after cellularisation at the site of gastrulation. Functional studies of vasa and tudor reveal that these genes are not required for germ cell formation, but that vasa is required in adult males for spermatogenesis. Taken together, our results provide evidence that Oncopeltus germ cells may form in the absence of germ plasm, consistent with the hypothesis that germ plasm is a derived strategy of germ cell specification in insects.
Annulation of 2H-Pyran onto 1-Oxa- or 1-Azacyclohexane-2,4-diones and Their Analogues via Sequential Condensation with α-Substituted Enals and 6π-Electrocyclization
Authors: Hossain Md Imran , Shaban Elkhabiry , Ikemi Taku , Peng Wei , Kawafuchi Hiroyuki , Inokuchi Tsutomu 
Published: April 2013

Abstract
2H-Pyrans are constructed on a 1-oxa- or 1-azacyclohexane-2,4-dione core via Knoevenagel condensation with enals followed by 6π-electrocyclization, which are readily catalyzed with ethylenediammonium diacetate. This formal [3 + 3] strategy constitutes C–O and C–C bond making and the diastereomer formation is circumvented using 6,6-disubstitution with the same aryl group in the 1-oxacyclohexane-2,4-diones. This facile methodology significantly advances the access to polysubstituted bicyclic 2H-pyrans with a versatile substrate choice and improved stability of the product.
Crystal structure of (E)-2-(1-(2,4-dihydroxyphenyl)ethylidene)hydrazinecarbothioamide, C9H11N3O2S
Authors: Xu Suo-Ping , Feng Li 
Published: April 2013

Abstract C9H11N3O2S, monoclinic, C2/c (no. 15), a = 20.900(2) Å, b = 7.9290(8) Å, c = 13.248(1) Å, β = 100.209(1)°, V = 2160.7 Å3, Z = 8, Rgt(F) = 0.0460, wRref(F2) = 0.1669, T = 298 K.
Crystal structure of 1-[2-n-butyl-5-formyl-3-thienyl]-2-[2-cyano-1,5- dimethyl-4-pyrryl]-3,3,4,4,5,5-hexafluoro-cyclopent-1-ene, C21H18F6N2OS
Authors: He Shanghua , Fan Congbin 
Published: April 2013

Abstract C21H18F6N2OS, monoclinic, P21/c (no. 14), a = 9.331(1) Å, b = 20.492(2) Å, c = 11.998(1) Å, β = 108.748(1)°, V = 2172.4 Å3, Z = 4, Rgt(F) = 0.0710, wRref(F2) = 0.2198, T = 296 K.
Crystal structure of bis((dimethylphosphoryl)methanaminium)hexachloridostannate( IV), C6H22Cl6N2O2P2Sn
Authors: Lambertz Charlotte , Luppa Anne , Reiss Guido J. 
Published: April 2013

Abstract C6H22Cl6N2O2P2Sn, monoclinic, P21/c (no. 14), a = 6.8425(1) Å, b = 14.0497(2) Å, c = 9.9977(2) Å, β = 104.521(2)°, V = 930.4 Å3, Z = 2, Rgt(F) = 0.0145, wRref(F2) = 0.0347, T = 105 K.
Investigation of Template Releasing Energy in Nanoimprint Lithography
Authors: Nishino Tomoki , Fujikawa Norihiro , Kawata Hiroaki , Hirai Yoshihiko 
Published: April 2013

ABSTRACTTo investigate template releasing process in nanoimprint lithography, template releasing energy (i.e. surface energy between the template and the resist polymer) in various releasing conditions is evaluated using multi-axial controlled releasing system. The releasing energy is in proportion to the surface free energy of the template, but does not depend on the velocity of releasing. Also, a peeling mode where the template is released from a single side and a lift-off mode where the template is removed in the perpendicular direction to the resist are examined. The result shows that the releasing energy by peeling mode is lower than that by lift-off modes.
Computational Study on Polymer Filling Process in Nanoimprint Lithography for Bi-Layered Resist
Authors: Araki Kosei , Yasuda Masaaki , Horiba Akira , Kawata Hiroaki , Hirai Yoshihiko 
Published: April 2013

ABSTRACTA molecular dynamics simulation was performed to study the polymer filling process in nanoimprint lithography for a bi-layered resist. The bi-layered resist consisted of PMMA resins with different molecular weights. When the mold cavity size became smaller than the polymer size of the top layer resist, the required force to fill the cavity became large. The molecular weight of the top layer dominated the filling characteristics in the bi-layered resist process.
Read Back of Stored Data in Non Volatile Memory Devices by Scanning Capacitance Microscopy
Authors: Dhar Rudra S. , Dixon-Warren St.J. , Kawaliye Mohamed A. , Campbell Jeff , Green Mike , Ban Dayan 
Published: April 2013

ABSTRACTThis report outlines a methodology for reading back different electrical charges, from Non Volatile Memory (NVM) based Flash devices. The charge is stored in the floating gates (FGs) of the transistors. Reading back these charges in the form of logic levels of “1 bit (1b)” and “0 bit (0b)” without deleting the information from the device was the goal. Scanning Capacitance Microscopy (SCM) with ∼50-100 nm spatial resolution was used, to directly probe the charge on Floating Gate Transistor (FGT) channels. Transistor charge values (ON/OFF or “1b/0b”) are measured. Both the sample preparation and SCM probing methods are discussed. The application has been demonstrated with SanDisk based 64 MB NAND Flash memory device.
Heteroepitaxial bonding of Si for hybrid photonic devices
Authors: Le Bourhis Eric , Talneau Anne , Sagnes Isabelle , Patriarche Gilles , Largeau Ludovic , Troadec David 
Published: April 2013

ABSTRACTNew fabrication routes for hybrid photonic devices are explored. We report on silicon bonding to III-V semi-conducteurs e.g. Si/InP for emission/amplification function. The materials have been bonded to silicon since it can be nanostructured to obtain optical guides. The bonded surfaces are of the order of ∼ 1 cm2. Special attention has been paid to the surface preparation. The obtained structure has been characterized employing XRD while the mechanical response and interface strength have been investigated employing instrumented nanoindentation.
Higher order alignment tensors for continuum dislocation dynamics
Authors: Hochrainer Thomas 
Published: April 2013

ABSTRACTDislocation density based modeling of crystal plasticity remains one of the central challenges in multi scale materials modeling. A dislocation based theory requires sufficiently rich dislocation density measures which are capable of predicting their own evolution. Continuum dislocation dynamics is based on a higher dimensional dislocation density tensor comprised of two distribution functions on the space of local orientations, which are the density of dislocations per orientation and the density of dislocation curvature per orientation. We propose to expand these functions into series of symmetric tensors (alignment tensors), to be used in dislocation based theories without extra dimensions. The first two terms in the expansion of the density define the total dislocation density and the Kröner-Nye tensor. The first term in the expansion of the curvature density, the scalar total curvature density, turns out to be a conserved quantity; the integral of which corresponds to the total number of dislocations. The content of the next higher order tensors is discussed.
Effect of Carbon Impurity Content on Microstructural Evolution in Neutron-Irradiated Alpha Iron: Cluster Dynamics Modeling
Authors: Abe Yosuke , Tsuru Tomohito , Jitsukawa Shiro 
Published: April 2013

ABSTRACTCluster dynamics (CD) modeling has been used to estimate the long-term evolution of point defect (PD) clusters. However, previous studies have often simplified the governing equations by assuming the maximum size of mobile self-interstitial atom (SIA) clusters and by ignoring the one-dimensional (1D) reaction kinetics of SIA loops. They have also conducted parameter fittings, such as the clustered fraction and the maximum size of clusters produced by collision cascade, to reproduce experimental data. In this study, in addition to modeling the 1D motion of SIA loops in the framework of the production bias model (PBM), reaction rates associated with carbon impurity atoms present in alpha iron were formulated to consider the trapping effect of one-dimensionally migrating SIA loops by a vacancy-carbon (V-C) complex that was shown to have strong bindings with SIA loops by previous atomistic simulations. Calculations results for neutron-irradiated alpha iron showed that the developed CD model can successfully reproduce the saturation trend of the number density of immobile SIA loops in contrast to the prediction using a model without the trapping effect.
Modeling the Low Cycle Fatigue in Copper Single Crystal: Multiscale Dislocation Dynamics Simulations
Authors: Kattoura Micheal , Shehadeh Mutasem 
Published: April 2013

ABSTRACTMultiscale dislocation dynamics plasticity (MDDP) model is used to investigate the evolution of dislocation microstructure in copper single crystals subjected to low cycle fatigue loading. Half cycle total plastic strain simulations are carried out at strain amplitudes ranging from 1×10-3 to 8×10-3. The initial hardening is investigated and the micro-structural cause behind it is presented. In addition, the loading history is presented and the effect of the initial micro-structure and dislocation distribution on the hardening behavior is studied. In addition, the evolution of the microstructures is examined. In depth analyses of the dislocation microstructures show that: 1) dislocation planes that are parallel and very close to each other are formed, 2) these walls contain dipoles that keep on zipping and unzipping during the first few cycles until they reach some stable zipping configuration. We can see that the hardening rate decreases with the increase of the number of cycles where we have large hardening rate in the first cycles then we reach to somehow constant stress. Our results are qualitatively in good agreement with recent experimental results of low cycle fatigue deformation.
Application of TDGL Model to B2 Type Ordering with Two Step Phase Separation in Fe-Ni-Al Alloys
Authors: Oguma Ryuichiro , Matsumura Syo , Doi Minoru , Hata Satoshi , Ogata Keisuke 
Published: April 2013

ABSTRACTFormation of domain structures in two-step phase separation in Fe-based Fe-Ni-Al alloys are investigated by applying a time-dependent Ginzburg-Landau (TDGL) model. The present authors recently developed a TDGL formulation for ordering processes of B2 and D03 in binary alloys, taking into account the symmetrical relationships between these ordered phases. In this formulation, multiple types of variants of the structures are represented by three order parameters which can be measured independently through crystal structure factors. Mean-field free energies are defined in a form of Landau type expansion with the order parameters and a composition parameter. Interfacial energies due to local variations of degrees of order and composition are given in a gradient square approximation. Kinetic equations for time-evolution of the order parameters and the composition one are derived from the Ginzburg-Landau type potential consisting of the mean-field free energies and the interfacial energy terms. On the other hand, coauthors have investigated domain structures in two-step phase separation of Fe-based Fe-Ni-Al alloys. The evolution of three-dimensional domain structures and composition profiles has been analyzed by electron tomography imaging and energy-dispersive X-ray spectroscopy. In this work the authors performed three-dimensional numerical simulations assuming the thermal processing. The results of the simulations well reproduced the characteristics of the micro-structures obtained from the observations.
About an analytical verification of quasi-continuum methods with Γ-convergence techniques
Authors: Schäffner Mathias , Schlömerkemper Anja 
Published: April 2013

ABSTRACTQuasi-continuum (QC) methods are computational techniques, which reduce the complexity of atomistic simulations in a static setting while keeping information on small-scale structures and effects. The main idea is to couple atomistic and continuum models and thus to obtain quite detailed but still not too expensive numerical simulations.We aim at a mathematically rigorous verification of QC methods by means of discrete to continuum limits. In this article we present our first results for the so-called quasi-nonlocal QC method in the context of fracture mechanics. To this end we start from a one-dimensional chain of atoms with nearest and next-to-nearest neighbour interactions of Lennard-Jones type. This is considered as a fully atomistic model of which the Γ-limits (of zeroth and first order) for an infinite number of atoms are known [7].The QC models we construct are equal to this fully atomistic model in the atomistic region; in the continuum regime we approximate the next-to-nearest neighbour interactions by some nearest neighbour potential which is related to the so-called Cauchy-Born rule. Further we choose certain representative atoms in order to coarsen the mesh in the continuum region. It turns out that the selection of the representative atoms is crucial and influences the Γ-limits.We regard a QC model as good if the Γ-limits of zeroth and first order or at least their minimal values and minimizers are the same as those of the fully atomistic model. Our analysis shows that, while in an elastic regime only the size of the atomistic region matters, in the case of fracture a proper choice of the representative atoms is an essential ingredient.
Effects of External Stresses on the Martensitic Transformation in a 3D Polycrystalline Material Using the Phase Field Method
Authors: Malik Amer , Amberg Gustav , Ågren John 
Published: April 2013

ABSTRACTIn the current study an elasto-plastic phase field (PF) model, based on the PF microelasticity theory proposed by A.G. Khachaturyan, is used to investigate the effects of external stresses on the evolution of martensitic microstructure in a Fe-0.3%C polycrystalline alloy. The current model is improved to include the effects of grain boundaries in a polycrystalline material. The evolution of plastic deformation is governed by using a time dependent Ginzburg-Landau equation, solving for the minimization of the shear strain energy. PF simulations are performed in 2D and 3D to study the effects of tension, compression and shear on the martensitic transformation. It has been found that external stresses cause an increase in the volume fraction of the martensitic phase if they add to the net effect of the transformation strains, and cause a decrease otherwise. It has been concluded that the stress distribution and the evolution of martensitic microstructure can be predicted with the current model in a polycrystalline material under applied stresses.
Numerical study of the liquid-solid interface properties for binary alloys using phase-field crystal approach
Authors: Choudhary Muhammad Ajmal , Kundin Julia , Emmerich Heike 
Published: April 2013

ABSTRACTThe phase-field crystal (PFC) method has emerged as a promising technique to simulate the evolution of crystalline patterns with atomistic resolution on mesoscopic time scales. We use a 2D PFC model based on Elder et al. [Phy. Rev. B 75, 064107 (2007)] to perform a systematic analysis of a liquid-solid interface for a binary alloy system. We propose the method of determining interfacial energies for a curved liquid-solid interface by stabilizing the circular solid seed in the surrounding liquid phase and the liquid droplet in the solid phase for various seed sizes in a finite system. We also investigate the impact of model parameters on the resulting interface energies. The interface energies are computed with various system sizes in order to study the system size effects. In particular, we compare the simulation results in the form of the interface energy as a function of radius with the existing theories.
Computer-aided Analysis of Micromechanics and Damage of Composite Materials Based on Multiscale Homogenization Method
Authors: Dimitrienko Yuriy I. , Sokolov Alexandr P. , Shpakova Yulia V. 
Published: April 2013

ABSTRACTResults of finite element analysis of linked two and three scale levels tasks are presented. Fields of components of stress concentration tensor function for several models of unit cells of textile composite materials are presented too. Comparison of experimental and computational results of obtained effective properties was carried out and results of this research are introduced. The basis of this phenomenological approaches was made by Prof. N.S. Bahvalov and Prof. B.E. Pobedriya in 80's and finally this method was renovated by Prof. Yu.I. Dimitrienko at Bauman Moscow State Technical University at «Computational mathematics and mathematical physics» department. Computational procedures and program implementation was made using object-oriented design and C/C++ language by A.P. Sokolov. All computational results have been performed using new-developed distributed high-perfomance software system GCD. Multiscale homogenization method was applied for single macroscopic level of composite construction and several connected microscopic levels. The task of stress-strain determination of composite construction was stated automatically by means of automatically defined plan based on certain computational problems. Architecture of software system and finite-element subsystem were developed too. Several practically important tasks were solved and some of its results are attached.