bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Methylation Profiling Distinguishes Three Clusters of Breast Cancer Cell Lines
Authors: Zheng Siyuan , Zhao Zhongming 
Published: May 2012

AbstractMethylation change plays an important role in many cellular systems, including cancer development. During recent years, genome‐wide or large‐scale methylation data has become available thanks to rapid advances in high‐throughput biotechnologies. So far, researchers have always used gene expression profiling to study disease subtypes and related therapies. In this study, we investigated methylation profiles in 30 breast cancer cell lines using methylation data generated by microarray technologies. Strong variation of the number of methylation peaks was found among these 30 cell lines; however, more peaks were found in the upstream regions than in downstream regions of genes. We further grouped the methylation profiles of these cell lines into three consensus clusters. Finally, we performed an integrative analysis of breast cancer cell lines using both methylation and gene‐expression profiling data. There was no significant correlation between methylation‐profiling subtypes and gene‐expression profiling subtypes, suggesting the complex nature of methylation in the regulation of gene expression. However, we found basal B cell lines appeared exclusively in two methylation clusters. Although these results are preliminary, this study suggests that methylation profiling might be promising in disease subtype classification and the development of therapeutic strategies.
A Core Process in Receptor Function, General Anesthesia, Sleep, and Aging
Authors: Kier Lemont B. , Slattum Patricia W. 
Published: May 2012

AbstractThe diffusion of ligands and proteins was proposed to be guided by chreodes in water organized by protein‐surface side chains with varying hydropathic states. These chreodes are proposed to be the target of volatile general anesthetic agents. The similarity between this effect and sleep deprivation leads to a proposal of an external agent responsible for sleep. This agent is elemental nitrogen. An extension of this effect is the concept that elemental nitrogen is a core factor in aging.
A New Era of the Vaginal Microbiome: Advances Using Next‐Generation Sequencing
Authors: Fettweis Jennifer M. , Serrano Myrna G. , Girerd Philippe H. , Jefferson Kimberly K. , Buck Gregory A. 
Published: May 2012

AbstractUntil recently, bacterial species that inhabit the human vagina have been primarily studied using organism‐centric approaches. Understanding how these bacterial species interact with each other and the host vaginal epithelium is essential for a more complete understanding of vaginal health. Molecular approaches have already led to the identification of uncultivated bacterial taxa associated with bacterial vaginosis. Here, we review recent studies of the vaginal microbiome and discuss how culture‐independent approaches, such as applications of next‐generation sequencing, are advancing the field and shifting our understanding of how vaginal health is defined. This work may lead to improved diagnostic tools and treatments for women who suffer from, or are at risk for, vaginal imbalances, pregnancy complications, and sexually acquired infections. These approaches may also transform our understanding of how host genetic factors, physiological conditions (e.g., menopause), and environmental exposures (e.g., smoking, antibiotic usage) influence the vaginal microbiome.
Identification of Metabolic Changes in Genetically Unstable Stem Cells by Using Model Analysis of Gene Expression
Authors: Vanee Niti , Roberts Seth B. , Riggs Marion Joe , Rao Raj R. , Fong Stephen S. 
Published: May 2012

AbstractStem‐cell research seeks to address many different questions related to fundamental stem‐cell function with the ultimate goal of being able to control and utilize stem cells for a broad range of therapeutic needs. While a large amount of work is focused on discovering and controlling differentiation mechanisms in stem cells, an equally interesting and important area of work is to understand the basics of stem‐cell propagation and self‐renewal. With high‐throughput genomics and transcriptomic information on hand, it is becoming possible to address some of the detailed mechanistic processes occurring in stem cells, though interpretation of these data is often difficult. In this work, stem cells with genetic abnormalities were compared to genetically normal stem cells using gene‐expression array data integrated with a large‐scale metabolic model to help interpret changes in metabolism resulting in the identification of several metabolic pathways that were different in the normal and abnormal cells.
Synthesis, Structure, Properties, and Application of a Carbazole‐Based Diaza[7]helicene in a Deep‐Blue‐Emitting OLED
Authors: Shi Longqiang , Liu Zhi , Dong Guifang , Duan Lian , Qiu Yong , Jia Jiong , Guo Wei , Zhao Dan , Cui Deliang , Tao Xutang 
Published: May 2012

AbstractA carbazole‐based diaza[7]helicene, 2,12‐dihexyl‐2,12‐diaza[7]helicene (1), was synthesized by a photochemical synthesis and its use as a deep‐blue dopant emitter in an organic light‐emitting diode (OLED) was examined. Compound 1 exhibited good solubility and excellent thermal stability with a high decomposition temperature (Td=372.1 °C) and a high glass‐transition temperature (Tg, up to 203.0 °C). Single‐crystal structural analysis of the crystalline clathrate (1)2⋅cyclohexane along with a theoretical investigation revealed a non‐planar‐fused structure of compound 1, which prevented the close‐packing of molecules in the solid state and kept the molecule in a good amorphous state, which allowed the optimization of the properties of the OLED. A device with a structure of ITO/NPB (50 nm)/CBP:5 % 1 (30 nm)/BCP (20 nm)/Mg:Ag (100 nm)/Ag (50 nm) showed saturated blue light with Commission Internationale de L’Eclairage (CIE) coordinates of (0.15, 0.10); the maximum luminance efficiency and brightness were 0.22 cd A−1 (0.09 Lm W−1) and 2365 cd m−2, respectively. This new class of helicenes, based on carbazole frameworks, not only opens new possibilities for utilizing helicene derivatives in deep‐blue‐emitting OLEDs but may also have potential applications in many other fields, such as molecular recognition and organic nonlinear optical materials.
An efficient algorithm for mapping imaging data to 3D unstructured grids in computational biomechanics
Authors: Einstein Daniel R. , Kuprat Andrew P. , Jiao Xiangmin , Carson James P. , Einstein David M. , Jacob Richard E. , Corley Richard A. 
Published: May 2012

SUMMARYGeometries for organ scale and multiscale simulations of organ function are now routinely derived from imaging data. However, medical images may also contain spatially heterogeneous information other than geometry that are relevant to such simulations either as initial conditions or in the form of model parameters. In this manuscript, we present an algorithm for the efficient and robust mapping of such data to imaging‐based unstructured polyhedral grids in parallel. We then illustrate the application of our mapping algorithm to three different mapping problems: (i) the mapping of MRI diffusion tensor data to an unstructured ventricular grid; (ii) the mapping of serial cyrosection histology data to an unstructured mouse brain grid; and (iii) the mapping of computed tomography‐derived volumetric strain data to an unstructured multiscale lung grid. Execution times and parallel performance are reported for each case. Copyright © 2012 John Wiley & Sons, Ltd.
General‐purpose computation on GPUs for high performance cloud computing
Authors: Expósito Roberto R. , Taboada Guillermo L. , Ramos Sabela , Touriño Juan , Doallo Ramón 
Published: May 2012

SUMMARYCloud computing is offering new approaches for High Performance Computing (HPC) as it provides dynamically scalable resources as a service over the Internet. In addition, General‐Purpose computation on Graphical Processing Units (GPGPU) has gained much attention from scientific computing in multiple domains, thus becoming an important programming model in HPC. Compute Unified Device Architecture (CUDA) has been established as a popular programming model for GPGPUs, removing the need for using the graphics APIs for computing applications. Open Computing Language (OpenCL) is an emerging alternative not only for GPGPU but also for any parallel architecture. GPU clusters, usually programmed with a hybrid parallel paradigm mixing Message Passing Interface (MPI) with CUDA/OpenCL, are currently gaining high popularity. Therefore, cloud providers are deploying clusters with multiple GPUs per node and high‐speed network interconnects in order to make them a feasible option for HPC as a Service (HPCaaS). This paper evaluates GPGPU for high performance cloud computing on a public cloud computing infrastructure, Amazon EC2 Cluster GPU Instances (CGI), equipped with NVIDIA Tesla GPUs and a 10 Gigabit Ethernet network. The analysis of the results, obtained using up to 64 GPUs and 256‐processor cores, has shown that GPGPU is a viable option for high performance cloud computing despite the significant impact that virtualized environments still have on network overhead, which still hampers the adoption of GPGPU communication‐intensive applications. Copyright © 2012 John Wiley & Sons, Ltd.
Exact capacity analysis of multi‐relay multiuser cooperative networks based on two‐step selection
Authors: Guo Weidong , Liu Ju , Liu Yuxi , Zheng Lina , Zhang Guowei 
Published: May 2012

SUMMARYThis paper advocates the capacity analysis of an amplify‐and‐forward cooperative communication system model in multi‐relay multiuser networks. A two‐step selection scheme is adopted, and both relay and user selection are based on the outdated channel state information. Exact expression of channel capacity for independent, but not necessarily identically distributed, Rayleigh fading channels is derived. Finally, simulations are carried out to verify the correctness of theoretical analysis and illustrate the effect of parameters on the performance. Results show that although the performance of our scheme is inferior to the optimal joint selection scheme, it is still a practical scheme because its complexity is much lower than that of the optimal scheme. Copyright © 2012 John Wiley & Sons, Ltd.
Circadian expression of the presynaptic active zone protein bruchpilot in the lamina of Drosophila melanogaster
Authors: Górska‐Andrzejak Jolanta , Makuch Renata , Stefan Joanna , Görlich Alicja , Semik Danuta , Pyza Elzbieta 
Published: May 2012

AbstractIn the fly's visual system, the morphology of cells and the number of synapses change during the day. In the present study we show that in the first optic neuropil (lamina) of Drosophila melanogaster, a presynaptic active zone protein Bruchpilot (BRP) exhibits a circadian rhythm in abundance. In day/night (or light/dark, LD) conditions the level of BRP increases two times, in the morning and in the evening. The same pattern of changes in the BRP level was detected in whole brain homogenates, thus indicating that the majority of synapses in the brain peaks twice during the day. However, these two peaks in BRP abundance, measured as the fluorescence intensity of immunolabeling, seem to be regulated differently. The peak in the morning is predominantly regulated by light and involves the transduction pathway in the retina photoreceptors. This peak is present neither in wild‐type Canton‐S flies in constant darkness (DD), nor in norpA7 phototransduction mutant in LD. However, it also depends on the clock gene per, because it is abolished in the per0 arrhythmic mutant. In turn, the peak of BRP in the evening is endogenously regulated by an input from the pacemaker located in the brain. This peak is present in Canton‐S flies in DD, as well as in the norpA7 mutant in LD, but is absent in per01, tim,01 and cry01 mutants in LD. In addition both peaks seem to depend on clock gene‐expressing photoreceptors and glial cells of the visual system. © 2012 Wiley Periodicals, Inc. Develop Neurobiol, 2013
A Cyano‐Bridged Vanadium–Niobium Bimetal Assembly Exhibiting a High Curie Temperature of 210 K (Eur. J. Inorg. Chem. 16/2012)
Authors: Imoto Kenta , Takemura Miho , Tokoro Hiroko , Ohkoshi Shin‐ichi 
Published: May 2012

AbstractThe front cover picture shows a schematic representation of the coordination network and the temperature dependence of magnetization of a cyano‐bridged V–Nb bimetal assembly, K0.59VII1.59VIII0.41[NbIV(CN)8]·(SO4)0.50·6.9H2O. This compound exhibits ferrimagnetism with a high Curie temperature (TC) of 210�K. This temperature is the highest TC value among those of octacyano‐bridged bimetal assemblies. The Short Communication by S. Ohkoshi et al. on p. 2649 ff. demonstrates that the increase in the superexchange pathways of VII–NC–NbIV contributes to the achievement of the high TC value. magnified image
Thermolysis of 3,3,5,5‐Tetramethyl‐1,2,4‐trithiolane 1‐Oxide: First Matrix Isolation of the HOSS· Radical
Authors: Reisenauer Hans Peter , Mloston Grzegorz , Romanski Jaroslaw , Schreiner Peter R. 
Published: May 2012

AbstractFlash vacuum pyrolysis of 3,3,5,5‐tetramethyl‐1,2,4‐trithiolane 1‐oxide performed at 700 °C yields the 1‐oxatrisulfan‐3‐yl radical (HOSS·) along with disulfur monoxide (S2O) and diisopropyl sulfide, which were isolated in argon matrices at 10 K. Upon irradiation with UV light, the 1‐oxatrisulfan‐3‐yl radical undergoes isomerization to the 1‐oxatrisulfan‐1‐yl radical (HSSO·). Both radicals were identified by comparison of their computed and experimental IR and UV/Vis spectra. In addition, density functional theory (DFT) computations offer a plausible explanation of the most likely reaction mechanism, suggesting that the initial step is a 1,3‐H shift with simultaneous ring opening. A 1‐oxatrisulfane derivative formed thereby undergoes fragmentations via a radical and a competitive concerted pathway leading to the observed final products. The same mechanism also governs the thermal fragmentation of di‐tert‐butyl disulfide S‐oxide. Its pyrolysis at 700 °C affords an analogous set of products, including the 1‐oxatrisulfan‐3‐yl radical (HOSS·) as the key intermediate.
C3v‐Symmetrical Tribenzotriquinacenes Bearing Six Benzylic Tentacle Groups at the Molecular Periphery
Authors: Mughal Ehsan Ullah , Kuck Dietmar 
Published: May 2012

AbstractThe synthesis and characterization of several C3v‐symmetrically extended tribenzotriquinacenes (TBTQs) bearing six benzylic C1‐tentacular functional groups at the arene periphery were reported. A new C3v‐symmetrical hexakis(chloromethyl)‐substituted TBTQ derivative was used as the key intermediate, and other derivatives were synthesized with high efficiency by either sixfold nucleophilic substitution reactions with phenols or sixfold Friedel–Crafts alkylation reactions with various arenes.
Inverse‐Opal Conducting Polymer Monoliths in Microfluidic Channels
Authors: Gorey Brian , Galineau Jeremy , White Blanaid , Smyth Malcolm R. , Morrin Aoife 
Published: May 2012

AbstractInverse opal monolithic flow‐through structures of conducting polymer (CP) were achieved in microfluidic channels for lab‐on‐a‐chip (LOC) applications. In order to achieve the uniformly porous monolith, polystyrene (PS) colloidal crystal (CC) templates were fabricated in microfluidic channels. Consequently, an inverse opal polyaniline (PANI) structure was achieved on‐chip, through a two‐step process involving the electrochemical growth of PANI and subsequent removal of the template. In this work the effect of CP electropolymerisation time on these structures is discussed. It was found that growth time is critical in achieving an ordered structure with well‐defined flow‐through pores. This is significant as these optimised porous structures will allow for maximising the surface area of the monolith and will also result in well‐defined flow profiles through the microchannel.
Determination of Sb(V) Using Differential Pulse Anodic Stripping Voltammetry at an Unmodified Edge Plane Pyrolytic Graphite Electrode
Authors: Lu Min , Rees Neil V. , Compton Richard G. 
Published: May 2012

AbstractAntimony(V) determination at an unmodified edge plane pyrolytic graphite (EPPG) electrode using anodic stripping voltammetry (ASV) by depositing beyond the hydrogen wave is shown in this paper. By depositing beyond the hydrogen wave, we report a sensitive method to determine pentavalent antimony at a carbon electrode in 0.25 M HCl. Using differential pulse anodic stripping voltammetry (DPASV), a bare EPPG electrode gave a detection limit of 5.8±0.02 nM without the need for surface modification. This level is greatly within the EU limit for drinking water of 40 nM.
DIAPH3 governs the cellular transition to the amoeboid tumour phenotype
Authors: Hager Martin H. , Morley Samantha , Bielenberg Diane R. , Gao Sizhen , Morello Matteo , Holcomb Ilona N. , Liu Wennuan , Mouneimne Ghassan , Demichelis Francesca , Kim Jayoung , Solomon Keith R. , Adam Rosalyn M. , Isaacs William B. , Higgs Henry N. , Vessella Robert L. , Di Vizio Dolores , Freeman Michael R. 
Published: May 2012

AbstractTherapies for most malignancies are generally ineffective once metastasis occurs. While tumour cells migrate through tissues using diverse strategies, the signalling networks controlling such behaviours in human tumours are poorly understood. Here we define a role for the Diaphanous‐related formin‐3 (DIAPH3) as a non‐canonical regulator of metastasis that restrains conversion to amoeboid cell behaviour in multiple cancer types. The DIAPH3 locus is close to RB1, within a narrow consensus region of deletion on chromosome 13q in prostate, breast and hepatocellular carcinomas. DIAPH3 silencing in human carcinoma cells destabilized microtubules and induced defective endocytic trafficking, endosomal accumulation of EGFR, and hyperactivation of EGFR/MEK/ERK signalling. Silencing also evoked amoeboid properties, increased invasion and promoted metastasis in mice. In human tumours, DIAPH3 down‐regulation was associated with aggressive or metastatic disease. DIAPH3‐silenced cells were sensitive to MEK inhibition, but showed reduced sensitivity to EGFR inhibition. These findings have implications for understanding mechanisms of metastasis, and suggest that identifying patients with chromosomal deletions at DIAPH3 may have prognostic value.
On utility‐optimised router‐level bandwidth allocation
Authors: Tan Liansheng , Yang Peng , Zhang Wei , Ge Fei 
Published: May 2012

ABSTRACTKelly's network utility maximisation (NUM) problems and solutions are aimed to maximise the aggregate utility subject to link capacity constraints. They are formulated and solved by using the individual flow rate vector. Because of the architecture of the current networks such as the Internet, the individual flow rates are generally not measurable directly at the routers for the network service provider. However, the aggregate flow rates are more convenient to obtain and to adjust. In this paper, we still study the NUM problems for communication networks but from a router‐level bandwidth allocation standpoint. With the use of the generalised matrix inverse, we propose a general model of utility‐optimised router‐level bandwidth allocation and its solution, where the objective function and the constraints are formulated in terms of the aggregate flow rate vector rather than from the individual flow rate vector as in the usual NUM problem. We find that the new proposed models are equivalent to Kelly's NUM model in the sense that they lead to the same optimum and their solutions satisfy the given routing scheme. We also discuss the special cases where the routing matrix is of full row rank and where there is one single‐hop flow in every link in the network. We suggest a direct application to Internet Protocol‐based virtual private network of the latter case. We present the mathematical models and solution procedures that lead to the utility‐optimised aggregate flow rate vector and further illustrate them by numerical examples. We believe our approach is promising for deployment in communication networks. Copyright © 2012 John Wiley & Sons, Ltd.
Natural gas and electric distribution: Prior preparation, good communication key to recovering costs after storms
Authors: Stewart Calvin E. , Deric Miki 
Published: May 2012

AbstractEvery utility executive's worst fear is the type of punishing wind, snow, or ice storm that wreaks havoc on power systems, results in significant and often lengthy outages, and causes severe public outcry. But extreme weather can and does happen everywhere—no matter where in the country you operate. And one of the most common challenges utilities face is how to recoup the costs of restoring power after a significant weather event.
Natural gas matters: Changing estimates and today's low prices could cause bad policies
Authors: Smead Richard G. 
Published: May 2012

AbstractGasoline prices are at something like an all‐time high, and natural gas prices are at a ten‐year low. What a tumultuous, but promising, time for US natural gas. An obvious implication of this massive price disparity is that anywhere natural gas can compete with oil or with oil‐based energy pricing, many parties are eager to do so.
Electric regulation: The fracking buzz
Authors: Bowden Nicholas S. 
Published: May 2012

AbstractA news media buzz has solidified around the economic and environmental impacts resulting from hydraulic fracturing in natural gas wells. The strictest opponents of hydraulic fracturing assert environmental degradation threatens ecological and human health to a degree that is high enough to require the government to prohibit use of the technique. Proponents assert the need to develop this newly accessed source of safe domestic energy as a key component to the “nation's clean energy future.”
The CpG island shore of the GLT‐1 gene acts as a methylation‐sensitive enhancer
Authors: Perisic Tatjana , Holsboer Florian , Rein Theo , Zschocke Jürgen 
Published: May 2012

AbstractAstrocytic lineage commitment and brain region‐dependent specialization of glia are partly ascribed to epigenetic processes. Clearance of glutamate is an essential task, which astrocytes assume in a temporal‐spatial fashion by distinct glutamate transporter expression. Glutamate transporter subtype 1 (GLT‐1) is predominant in cortex (CTX), while it plays an inferior role in cerebellum (CER). Here, we set out to identify regulatory elements that could account for the differences in brain region‐specific activity as well as response to dexamethasone (DEX) or epigenetic factors. We found a distal promoter element at the shore of the CpG island exhibiting enhancer function in response to DEX in reporter gene assays. This shore region showed slight enrichment in repressive trimethyl‐histone H3 (Lys27) and under‐representation of acetyl‐histone H4 (H4ac) marks in DEX nonresponsive CER astrocytes as determined by chromatin immunoprecipitation. In addition, CpG sites of the shore region displayed higher methylation in CER than in CTX cells. Targeted in vitro methylation of CpG sites within the shore abrogated the stimulatory effects of DEX. Interestingly, the shore was characterized by a pronounced epigenetic plasticity in CTX cells since DEX exposure elicited an increase of H4ac in CTX in comparison to DEX nonresponsive CER. The transcriptional activity of this region was also affected by histone deacetylase inhibitors in a methylation‐ and brain region‐dependent manner. Together, our study highlights the impact of an epigenetically adaptive DNA element of the GLT‐1 promoter being decisive for brain region‐specific activity and reactivity. © 2012 Wiley Periodicals, Inc.