bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porphyrin‐Based Design of Bioinspired Multitarget Quadruplex Ligands
Authors: Laguerre Aurélien , Desbois Nicolas , Stefan Loic , Richard Philippe , Gros Claude P. , Monchaud David 
Published: February 2014

AbstractSecondary nucleic acid structures, such as DNA and RNA quadruplexes, are potential targets for cancer therapies. Ligands that interact with these targets could thus find application as anticancer agents. Synthetic G‐quartets have recently found numerous applications, including use as bioinspired G‐quadruplex ligands. Herein, the design, synthesis and preliminary biophysical evaluation of a new prototype multitarget G‐quadruplex ligand, PNAPorphySQ, are reported, where peptidic nucleic acid guanine (PNAG) was incorporated in the porphyrin‐templated synthetic G‐quartet (PorphySQ). Using fluorescence resonance energy transfer (FRET)‐melting experiments, PorphySQ was shown to possess enhanced quadruplex‐interacting properties thanks to the presence of four positively charged PNAG residues that improve its electrostatic interactions with the binding site of both DNA and RNA quadruplexes (i.e., their negatively charged and accessible G‐quartets), thereby making PNAPorphySQ an interesting prototype of a multitarget ligand. Both the chemical stability and water solubility of PNAPorphySQ are improved over the non‐PNA derivative (PorphySQ), which are desirable properties for drug development, and while improvements remain to be made, this ligand is a promising lead for the further development of multitarget G‐quadruplex ligands.
Characteristics of individuals with breast cancer rearrangements in BRCA1 and BRCA2
Authors: Jackson Sarah A. , Davis Andrew A. , Li Jun , Yi Nengjun , McCormick Shelley R. , Grant Carly , Fallen Taya , Crawford Beth , Loranger Kate , Litton Jennifer , Arun Banu , Vande Wydeven Kimberly , Sidani Amer , Farmer Katie , Sanders Merideth , Hoskins Kent , Nussbaum Robert , Esserman Laura , Garber Judy E. , Kaklamani Virginia G. ,   the Northwestern Cancer Genetics Group
Published: February 2014

BACKGROUNDLarge rearrangements in BRCA1 and BRCA2 occur in a small percentage (< 1%) of patients tested for hereditary breast (BC) and ovarian cancer. It is unclear what factors predict BRACAnalysis Large Rearrangement Test (BART) positivity.METHODSData from 6 centers were included in this analysis. Individuals with negative Comprehensive BRACAnalysis tested for BART were included.RESULTSFrom 1300 individuals, 42 (3.2%) were BART positivity. Factors positively associated with BART positivity were Myriad score, first‐degree relatives with BC, infiltrating BC with ductal carcinoma in situ, younger age at BC diagnosis, estrogen receptor–negative BC for both the first and second BC, and Latin American/Caribbean ethnicity. Presence of unilateral BC was inversely associated with BART positivity. Several analyses were performed on the variables available to find the model that best predicts for BART positivity. The BART predictive model, including first BC, ovarian cancer, primary maternal ancestry being Latin America/Caribbean, number of first‐degree relatives with BC of 1 or more versus 0, and family history of prostate and pancreatic cancer, had good predictive ability with an area under the curve of 0.77.CONCLUSIONSSeveral factors are significantly associated with BART positivity. Among them we have found that Latin American/Caribbean ancestry, Myriad score, first degree relatives with BC, younger age at BC diagnosis, estrogen receptor–negative status of BC, and infiltrating ductal carcinoma with ductal carcinoma in situ features are significantly associated with BART positivity. A BART predictive model may help in a clinical setting. Cancer 2014;120:1557–1564. © 2014 American Cancer Society.
Use of hybrid discrete cellular models for identification of macroscopic nutrient loss in reaction–diffusion models of tissues
Authors: Aristotelous Andreas C. , Haider Mansoor A. 
Published: February 2014

SUMMARYMacroscopic models accounting for cellular effects in natural or engineered tissues may involve unknown constitutive terms that are highly dependent on interactions at the scale of individual cells. Hybrid discrete models, which represent cells individually, were used to develop and apply techniques for modeling diffusive nutrient transport and cellular uptake to identify a nonlinear nutrient loss term in a macroscopic reaction–diffusion model of the system. Flexible and robust numerical methods were used, based on discontinuous Galerkin finite elements in space and a Crank–Nicolson temporal discretization. Scales were bridged via averaging operations over a complete set of subdomains yielding data for identification of a macroscopic nutrient loss term that was accurately captured via a fifth‐order polynomial. Accuracy of the identified macroscopic model was demonstrated by direct, quantitative comparisons of the tissue and cellular scale models in terms of three error norms computed on a mesoscale mesh. Copyright © 2014 John Wiley & Sons, Ltd.
A computational study on brain tissue under blast: primary and tertiary blast injuries
Authors: Rezaei A. , Salimi Jazi M. , Karami G. , Ziejewski M. 
Published: February 2014

SUMMARYIn this paper, a biomechanical study of a human head model exposed to blast shock waves followed by a blunt impact with the surface of the enclosing walls of a confined space is carried out. Under blast, the head may experience primary blast injury (PBI) due to exposure to the shockwaves and tertiary blast injury (TeBI) due to a possible blunt impact. We examine the brain response data in a deformable finite element head model in terms of the inflicted stress/pressure, velocity, and acceleration on the brain for several blast scenarios with different intensities. The data will be compared for open space and confined spaces. Following the initial impact of the shock front in the confined space, one can see the fluctuations in biomechanical data due to wave reflections. Although the severity of the PBI and TeBI is dependent on the situation, for the cases studied here, PBI is considerably more pronounced than TeBI in confined spaces. Copyright © 2014 John Wiley & Sons, Ltd.
ResAna: a resource analysis toolset for (real‐time) JAVA
Authors: Kersten Rody W. J. , van Gastel Bernard E. , Shkaravska Olha , Montenegro Manuel , van Eekelen Marko C. J. D. 
Published: February 2014

SUMMARYFor real‐time and embedded systems, limiting the consumption of time and memory resources is often an important part of the requirements. Being able to predict bounds on the consumption of such resources during the development process of the code can be of great value. In this paper, we focus mainly on memory‐related bounds. Recent research results have advanced the state of the art of resource consumption analysis. In this paper, we present a toolset that makes it possible to apply these research results in practice for (real‐time) systems enabling JAVA developers to analyse symbolic loop bounds, symbolic bounds on heap size and both symbolic and numeric bounds on stack size. We describe which theoretical additions were needed in order to achieve this. We give an overview of the capabilities of the RESANA (Radboud University Nijmegen, The Netherlands) toolset that is the result of this effort. The toolset can not only perform generally applicable analyses, but it also contains a part of the analysis that is dedicated to the developers' (real‐time) virtual machine, such that the results apply directly to the actual development environment that is used in practice. Copyright © 2013 John Wiley & Sons, Ltd.
Fast construction of nanosecond level snapshots of financial markets
Authors: Gai Jiading , Choi Dong Ju , O'Neal David , Ye Mao , Sinkovits Robert S. 
Published: February 2014

SUMMARYThe goal of this project is to rapidly construct an order‐by‐order level snapshot of financial markets with nanosecond resolution time stamps. We are particularly interested in understanding the impact of high‐frequency traders on the security, stability, and fairness of these markets. In this paper, we describe our computational approach, the optimizations that were applied to improve the performance of the software by a factor of more than 125×, and the new capabilities that can be enabled using a combination of fast algorithms and XSEDE resources. Copyright © 2014 John Wiley & Sons, Ltd.
Preparation of Pt Nanoclusters with Different Emission Wavelengths and Their Application in Co2+ Detection
Authors: Huang Xin , Aoki Koichi , Ishitobi Hidekazu , Inouye Yasushi 
Published: February 2014

AbstractDifferently colored fluorescent Pt nanoclusters (NCs) are easily prepared using polyethyleneimine as the stabilizing ligand and environmentally friendly L‐ascorbic acid as the reducing agent. The quantum yields of the blue‐ (1:5), green‐ (1:20), and yellow‐emitting (1:25) NCs are 4 %, 11 %, and 7 %, respectively. The fluorescent Pt NCs show excellent photostability and are sensitive to Co2+ ions (with a detection limit of 500 nM).
High Mobility in Solution‐Processed 2,7‐Dialkyl‐[1]benzothieno[3,2‐b][1]benzothiophene‐Based Field‐Effect Transistors Prepared with a Simplified Deposition Method
Authors: Colella Silvia , Ruzié Christian , Schweicher Guillaume , Arlin Jean‐Baptiste , Karpinska Jolanta , Geerts Yves , Samorì Paolo 
Published: February 2014

AbstractA high performing solution‐processed field‐effect transistors based on 2,7‐didodecyl[1]benzothieno[3,2‐b][1]benzothiophene (C12‐BTBT) has been fabricated by using a simple and straightforward two‐step process. We have demonstrated that UV/ozone treatment of the Si/SiO2 substrates makes it possible to notably enhance the field‐effect mobility in spin‐coated C12‐BTBT based OFETs reaching values as high as 2.7 cm2 V−1 s−1. The influence of this treatment relies essentially on the coverage of the dielectric surface, while the crystalline order remains unaffected. Importantly, the employed method is simple, cheap and easily up‐scalable and provides outstanding OFET performances that are comparable to those obtained using expensive and complicated treatments.
Ultrasounds in Melted Poly(ethylene glycol) Promote Copper‐Catalyzed Cyanation of Aryl Halides with K4[Fe(CN)6]
Authors: Giachi Guido , Frediani Marco , Oberhauser Werner , Lamaty Frederic , Martinez Jean , Colacino Evelina 
Published: February 2014

AbstractMelted poly(ethylene glycols) (PEGs) were used for the first time as solvent for the sonochemically promoted cyanation of aryl halides employing inexpensive and safe K4[Fe(CN)6] and a relatively low amount of Cu‐based catalyst. The Mw (weight‐average polymer molecular weight) of PEG proved to notably influence the substrate conversion, which is indicative of a strong dependence of the sonication efficacy on solvent properties. Gel permeation chromatography (GPC), X‐ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) contributed to the characterization of the polymer and the elucidation of the catalytic system.
Enhanced Heterogeneous Catalytic Conversion of Furfuryl Alcohol into Butyl Levulinate
Authors: Demma Carà Piera , Ciriminna Rosaria , Shiju N. R. , Rothenberg Gadi , Pagliaro Mario 
Published: February 2014

AbstractWe study the catalytic condensation of furfuryl alcohol with 1‐butanol to butyl levulinate. A screening of several commercial and as‐synthesized solid acid catalysts shows that propylsulfonic acid‐functionalized mesoporous silica outperforms the state‐of‐the‐art phosphotungstate acid catalysts. The catalyst is prepared via template‐assisted sol‐gel polycondensation of TEOS and MPTMS. It gives 96 % yield (and 100 % selectivity) of butyl levulinate in 4 h at 110 °C. Reaction profiles before and after a hot filtration test confirm that the active catalytic species do not leach into the solution. The catalyst synthesis, characterization, and mode of operation are presented and discussed.
Green‐Engineered All‐Substrate Mesoporous TiO2 Photoanodes with Superior Light‐Harvesting Structure and Performance
Authors: Benehkohal Nima Parsi , Demopoulos George P. 
Published: February 2014

AbstractElectrophoretic deposition (EPD) is employed successfully in a suspension of multicomponent TiO2 nanoparticulates of different sizes and morphologies to engineer a very robust bifunctional electrode structure for dye‐sensitized solar cell (DSSC) applications that shows excellent light‐harvesting and photoelectrochemical performance. Aqueous‐synthesized anatase nanocrystallites and sub‐micrometer‐sized “sea urchin”‐like rutile aggregates are formulated in a stable isopropanol suspension without resorting to binders or charging agents. Interestingly, extremely robust films are obtained because of the high surface reactivity, electrophoretic mobility, and unique morphology of the rutile aggregates. DSSCs built with the newly configured bifunctional electrode yielded a record efficiency (8.59 %) for EPD‐fabricated devices without resorting to mechanical compression. Such green‐engineered mesoporous electrode structures can be built on both metallic and plastic substrates and can find applications in various energy and environmental fields.
Towards a Sustainable Manufacture of Hierarchical Zeolites
Authors: Verboekend Danny , Pérez‐Ramírez Javier 
Published: February 2014

AbstractHierarchical zeolites have been established as a superior type of aluminosilicate catalysts compared to their conventional (purely microporous) counterparts. An impressive array of bottom‐up and top‐down approaches has been developed during the last decade to design and subsequently exploit these exciting materials catalytically. However, the sustainability of the developed synthetic methods has rarely been addressed. This paper highlights important criteria to ensure the ecological and economic viability of the manufacture of hierarchical zeolites. Moreover, by using base leaching as a promising case study, we verify a variety of approaches to increase reactor productivity, recycle waste streams, prevent the combustion of organic compounds, and minimize separation efforts. By reducing their synthetic footprint, hierarchical zeolites are positioned as an integral part of sustainable chemistry.
Analyses of copy number variation reveal putative susceptibility loci in MTX‐induced mouse neural tube defects
Authors: Wang Jianhua , Wang Xiuwei , Guan Tao , Xiang Qian , Wang Mingsheng , Zhang Zhi , Guan Zhen , Wang Guoliang , Zhu Zhiqiang , Xie Qiu , Li Guannan , Guo Jin , Wang Fang , Zhang Zhengguo , Niu Bo , Zhang Ting 
Published: February 2014

ABSTRACTCopy number variations (CNVs) are thought to act as an important genetic mechanism underlying phenotypic heterogeneity. Impaired folate metabolism can result in neural tube defects (NTDs). However, the precise nature of the relationship between low folate status and NTDs remains unclear. Using an array‐comparative genomic hybridization (aCGH) assay, we investigated whether CNVs could be detected in the NTD embryonic neural tissues of methotrexate (MTX)‐induced folate dysmetabolism pregnant C57BL/6 mice and confirmed the findings with quantitative real‐time PCR (qPCR). The CNVs were then comprehensively investigated using bioinformatics methods to prioritize candidate genes. We measured dihydrofolate reductase (DHFR) activity and concentrations of folate and relevant metabolites in maternal serum using enzymologic method and liquid chromatography/tandem mass spectrometry (LC/MS/MS). Three high confidence CNVs on XqA1.1, XqA1.1‐qA2, and XqE3 were found in the NTD embryonic neural tissues. Twelve putative genes and three microRNAs were identified as potential susceptibility candidates in MTX‐induced NTDs and possible roles in NTD pathogenesis. DHFR activity and 5‐methyltetrahydrofolate (5‐MeTHF), 5‐formyltetrahydrofolate (5‐FoTHF), and S‐adenosylmethionine (SAM) concentrations of maternal serum decreased significantly after MTX injection. These findings suggest that CNVs caused by defects in folate metabolism lead to NTD, and further support the hypothesis that folate dysmetabolism is a direct cause for CNVs in MTX‐induced NTDs. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 74: 877–893, 2014
Prospective evaluation of potential toxicity of repeated doses of Thymus vulgaris L. extracts in rats by means of clinical chemistry, histopathology and NMR‐based metabonomic approach
Authors: Benourad Fouzia , Kahvecioglu Zehra , Youcef‐Benkada Mokhtar , Colet Jean‐Marie 
Published: February 2014

In the field of natural extracts, research generally focuses on the study of their biological activities for food, cosmetic, or pharmacological purposes. The evaluation of their adverse effects is often overlooked. In this study, the extracts of Thymus vulgaris L. were obtained by two different extraction methods. Intraperitoneal injections of both extracts were given daily for four days to male Wistar Han rats, at two different doses for each extract. The evaluation of the potential toxic effects included histopathological examination of liver, kidney, and lung tissues, as well as serum biochemistry of liver and kidney parameters, and 1H‐NMR‐based metabonomic profiles of urine.The results showed that no histopathological changes were observed in the liver and kidney in rats treated with both extracts of thyme. Serum biochemical investigations revealed significant increases in blood urea nitrogen, creatinine, and uric acid in animals treated with polyphenolic extract at both doses. In these latter groups, metabonomic analysis revealed alterations in a number of urine metabolites involved in the energy metabolism in liver mitochondria. Indeed, the results showed alterations of glycolysis, Krebs cycle, and β‐oxidative pathways as evidenced by increases in lactate and ketone bodies, and decreases in citrate, α‐ketoglutarate, creatinine, hippurate, dimethylglycine, and dimethyalanine. In conclusion, this work showed that i.p. injection of repeated doses of thyme extracts causes some disturbances of intermediary metabolism in rats. The metabonomic study revealed interesting data which could be further used to determine the cellular pathways affected by such treatments. Copyright © 2014 John Wiley & Sons, Ltd.
Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia
Authors: Todd Erica V. , Blair David , Jerry Dean R. 
Published: February 2014

AbstractThe influence of Pleistocene climatic cycles on Southern Hemisphere biotas is not yet well understood. Australia's eastern coastal margin provides an ideal setting for examining the relative influence of landscape development, sea level fluctuation, and cyclic climatic aridity on the evolution of freshwater biodiversity. We examined the impact of climatic oscillations and physical biogeographic barriers on the evolutionary history of the wide‐ranging Krefft's river turtle (Emydura macquarii krefftii), using range‐wide sampling (649 individuals representing 18 locations across 11 drainages) and analysis of mitochondrial sequences (~1.3‐kb control region and ND4) and nuclear microsatellites (12 polymorphic loci). A range of phylogeographic (haplotype networks, molecular dating), demographic (neutrality tests, mismatch distributions), and population genetic analyses (pairwise FST, analysis of molecular variance, Bayesian clustering analysis) were implemented to differentiate between competing demographic (local persistence vs. range expansion) and biogeographic (arid corridor vs. drainage divide) scenarios. Genetic data reveal population genetic structure in Krefft's river turtles primarily reflects isolation across drainage divides. Striking north‐south regional divergence (2.2% ND4 p‐distance; c. 4.73 Ma, 95% higher posterior density (HPD) 2.08–8.16 Ma) was consistent with long‐term isolation across a major drainage divide, not an adjacent arid corridor. Ancient divergence among regional lineages implies persistence of northern Krefft's populations despite the recurrent phases of severe local aridity, but with very low contemporary genetic diversity. Stable demography and high levels of genetic diversity are inferred for southern populations, where aridity was less extreme. Range‐wide genetic structure in Krefft's river turtles reflects contemporary and historical drainage architecture, although regional differences in the extent of Plio–Pleistocene climatic aridity may be reflected in current levels of genetic diversity.
Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover
Authors: You Yeming , Wang Juan , Huang Xueman , Tang Zuoxin , Liu Shirong , Sun Osbert J. 
Published: February 2014

AbstractForest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β‐1,4‐glucosidase and cellobiohydrolase), chitin (i.e., β‐1,4‐N‐acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram‐negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.