bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational biospectroscopy coupled with multivariate analysis extracts potentially diagnostic features in blood plasma/serum of ovarian cancer patients
Authors: Owens Gemma L. , Gajjar Ketan , Trevisan Júlio , Fogarty Simon W. , Taylor Siân E. , Da Gama‐Rose Bianca , Martin‐Hirsch Pierre L. , Martin Francis L. 
Published: November 2013

AbstractDespite numerous advances in “omics” research, early detection of ovarian cancer still remains a challenge. The aim of this study was to determine whether attenuated total reflection Fourier‐transform infrared (ATR‐FTIR) or Raman spectroscopy could characterise alterations in the biomolecular signatures of human blood plasma/serum obtained from ovarian cancer patients compared to non‐cancer controls. Blood samples isolated from ovarian cancer patients (n = 30) and healthy controls (n = 30) were analysed using ATR‐FTIR spectroscopy. For comparison, a smaller cohort of samples (n = 8) were analysed using an InVia Renishaw Raman spectrometer. Resultant spectra were pre‐processed prior to being inputted into principal component analysis (PCA) and linear discriminant analysis (LDA). Statistically significant differences (P < 0.001) were observed between spectra of ovarian cancer versus control subjects for both biospectroscopy methods. Using a support vector machine classifier for Raman spectra of blood plasma, a diagnostic accuracy of 74% was achieved, while the same classifier showed 93.3% accuracy for IR spectra of blood plasma. These observations suggest that a biospectroscopy approach could be applied to identify spectral alterations associated with the presence of insidious ovarian cancer. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Closed‐loop optimization of chromatography column sizing strategies in biopharmaceutical manufacture
Authors: Allmendinger Richard , Simaria Ana S. , Turner Richard , Farid Suzanne S. 
Published: November 2013

AbstractBACKGROUNDThis paper considers a real‐world optimization problem involving the identification of cost‐effective equipment sizing strategies for the sequence of chromatography steps employed to purify biopharmaceuticals. Tackling this problem requires solving a combinatorial optimization problem subject to multiple constraints, uncertain parameters, and time‐consuming fitness evaluations.RESULTSAn industrially‐relevant case study is used to illustrate that evolutionary algorithms can identify chromatography sizing strategies with significant improvements in performance criteria related to process cost, time and product waste over the base case. The results demonstrate also that evolutionary algorithms perform best when infeasible solutions are repaired intelligently, the population size is set appropriately, and elitism is combined with a low number of Monte Carlo trials (needed to account for uncertainty). Adopting this setup turns out to be more important for scenarios where less time is available for the purification process. Finally, a data‐visualization tool is employed to illustrate how user preferences can be accounted for when it comes to selecting a sizing strategy to be implemented in a real industrial setting.CONCLUSIONThis work demonstrates that closed‐loop evolutionary optimization, when tuned properly and combined with a detailed manufacturing cost model, acts as a powerful decisional tool for the identification of cost‐effective purification strategies. © 2013 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
T2‐weighted prostate MRI at 7 tesla using a simplified external transmit‐receive coil array: Correlation with radical prostatectomy findings in two prostate cancer patients
Authors: Rosenkrantz Andrew B. , Zhang Bei , Ben‐Eliezer Noam , Le Nobin Julien , Melamed Jonathan , Deng Fang‐Ming , Taneja Samir S. , Wiggins Graham C. 
Published: November 2013

PurposeTo report design of a simplified external transmit‐receive coil array for 7 Tesla (T) prostate MRI, including demonstration of the array for tumor localization using T2‐weighted imaging (T2WI) at 7T before prostatectomy.Materials and MethodsFollowing simulations of transmitter designs not requiring parallel transmission or radiofrequency‐shimming, a coil array was constructed using loop elements, with anterior and posterior rows comprising one transmit‐receive element and three receive‐only elements. This coil structure was optimized using a whole‐body phantom. In vivo sequence optimization was performed to optimize achieved flip angle (FA) and signal to noise ratio (SNR) in prostate. The system was evaluated in a healthy volunteer at 3T and 7T. The 7T T2WI was performed in two prostate cancer patients before prostatectomy, and localization of dominant tumors was subjectively compared with histopathological findings. Image quality was compared between 3T and 7T in these patients.ResultsSimulations of the B1+ field in prostate using two‐loop design showed good magnitude (B1+ of 0.245 A/m/w1/2) and uniformity (nonuniformity [SD/mean] of 10.4%). In the volunteer, 90° FA was achieved in prostate using 225 v 1 ms hard‐pulse (indicating good efficiency), FA maps confirmed good uniformity (14.1% nonuniformity), and SNR maps showed SNR gain of 2.1 at 7T versus 3T. In patients, 7T T2WI showed excellent visual correspondence with prostatectomy findings. 7T images demonstrated higher estimated SNR (eSNR) in benign peripheral zone (PZ) and tumor compared with 3T, but lower eSNR in fat and slight decreases in tumor‐to‐PZ contrast and PZ‐homogeneity.ConclusionWe have demonstrated feasibility of a simplified external coil array for high‐resolution T2‐weighted prostate MRI at 7T. J. Magn. Reson. Imaging 2015;41:226–232. © 2013 Wiley Periodicals, Inc.
Fabrication of modeling platform for fused deposition modeling using vacuum casting
Authors: Kuo C.‐C. 
Published: November 2013

AbstractThis study presents a cost‐effective approach for rapid fabricating modeling platforms utilized in fused deposition modeling three‐dimensional printing system. A small‐batch production of modeling platforms about 20 pieces can be obtained economically through silicone rubber mold using vacuum casting without applying the plastic injection molding. The air venting systems is crucial for fabricating modeling platform using vacuum casting. Modeling platforms fabricated can be used for building rapid prototyping model after sandblasting. This study offers industrial value because it has both time‐effectiveness and cost‐effectiveness.
A cost‐effective method to fabricate micro‐featured mold for microstructures replication
Authors: Kuo C.‐C. , Hsu H.‐J. 
Published: November 2013

AbstractThis study demonstrated a method for manufacturing a micro‐featured mold insert of Fresnel lens. The transcription rate of this process is about 92.5%. A plastic Fresnel lens was fabricated using micro‐hot embossing process. The transcription rate of the embossed part is about 95.1%. The micro‐featured mold insert not only reduces the fabrication cost, but has higher form accuracy as well. In comparison with conventional method for fabricating a pair of mold insert, a cost reduction of 60.4% can be achieved using the hybrid method proposed in this study.
Selenite protects Caenorhabditis elegans from oxidative stress via DAF‐16 and TRXR‐1
Authors: Li Wen‐Hsuan , Shi Yeu‐Ching , Chang Chun‐Han , Huang Chi‐Wei , Hsiu‐Chuan Liao Vivian 
Published: November 2013

ScopeSelenium is an essential micronutrient. In the present study, trace amount of selenite (0.01 μM) was evaluated for oxidative stress resistance and potential associated factors in Caenorhabditis elegans.Methods and resultsSelenite‐treated C. elegans showed an increased survival under oxidative stress and thermal stress compared to untreated controls. Further studies demonstrated that the significant stress resistance of selenite on C. elegans could be attributed to its in vivo free radical‐scavenging ability. We also found that the oxidative and thermal stress resistance phenotypes by selenite were absent from the forkhead transcription factor daf‐16 mutant worms. Moreover, selenite influenced the subcellular distribution of DAF‐16 in C. elegans. Furthermore, selenite increased mRNA levels of stress‐resistance‐related proteins, including superoxide dismutase‐3 and heat shock protein‐16.2. Additionally, selenite (0.01 μM) upregulated expressions of transgenic C. elegans carrying sod‐3::green fluorescent protein (GFP) and hsp‐16.2::GFP, whereas this effect was abolished by feeding daf‐16 RNA interference in C. elegans. Finally, unlike the wild‐type N2 worms, the oxidative stress resistance phenotypes by selenite were both absent from the C. elegans selenoprotein trxr‐1 mutant worms and trxr‐1 mutants feeding with daf‐16 RNA interference.ConclusionThese findings suggest that the antioxidant effects of selenite in C. elegans are mediated via DAF‐16 and TRXR‐1.
Effect of diffusion time on liver DWI: An experimental study of normal and fibrotic livers
Authors: Zhou Iris Y. , Gao Darwin S. , Chow April M. , Fan Shujuan , Cheung Matthew M. , Ling Changchun , Liu Xiaobing , Cao Peng , Guo Hua , Man Kwan , Wu Ed X. 
Published: November 2013

PurposeTo investigate whether diffusion time (Δ) affects the diffusion measurements in liver and their sensitivity in detecting fibrosis.MethodsLiver fibrosis was induced in Sprague‐Dawley rats (n = 12) by carbon tetrachloride (CCl4) injections. Diffusion‐weighted MRI was performed longitudinally during 8‐week CCl4 administration at 7 Tesla (T) using single‐shot stimulated‐echo EPI with five b‐values (0 to 1000 s/mm2) and three Δs. Apparent diffusion coefficient (ADC) and true diffusion coefficient (Dtrue) were calculated by using all five b‐values and large b‐values, respectively.ResultsADC and Dtrue decreased with Δ for both normal and fibrotic liver at each time point. ADC and Dtrue also generally decreased with the time after CCl4 insult. The reductions in Dtrue between 2‐week and 4‐week CCl4 insult were larger than the ADC reductions at all Δs. At each time point, Dtrue measured with long Δ (200 ms) detected the largest changes among the 3 Δs examined. Histology revealed gradual collagen deposition and presence of intracellular fat vacuoles after CCl4 insult.ConclusionOur results demonstrated the Δ dependent diffusion measurements, indicating restricted diffusion in both normal and fibrotic liver. Dtrue measured with long Δ acted as a more sensitive index of the pathological alterations in liver microstructure during fibrogenesis. Magn Reson Med 72:1389–1396, 2014. © 2013 Wiley Periodicals, Inc.
In vivo three‐dimensional high resolution cardiac diffusion‐weighted MRI: A motion compensated diffusion‐prepared balanced steady‐state free precession approach
Authors: Nguyen Christopher , Fan Zhaoyang , Sharif Behzad , He Yi , Dharmakumar Rohan , Berman Daniel S. , Li Debiao 
Published: November 2013

PurposeThe aim of this study was to implement and optimize a novel application of diffusion‐prepared balanced steady‐state free precession (bSSFP) to perform in vivo cardiac diffusion‐weighted MRI.Theory and MethodsDiffusion‐prepared sequences have the flexibility to diffusion encode with a multi‐shot image readout. The diffusion preparation was optimized to reduce sensitivity to cardiac bulk motion with second order motion compensation (M1M2). The image readout consisted of a three‐dimensional (3D) centric‐encoded segmented bSSFP acquisition that incorporated a prospective navigator. Ten healthy subjects were scanned twice using the proposed technique diffusion preparation with and without M1M2 using three orthogonal directions under varying off‐resonance conditions. Trace apparent diffusion coefficient (trADC) maps and the left ventricular (LV) trADC were calculated.ResultsM1M2 diffusion‐prepared scans resulted in LV trADC values of 1.5 ± 0.4 × 10−3 mm2/s that were reproducible yielding no statistical differences (P = 0.54). M1M2 diffusion‐prepared images showed no ghosting artifacts and/or signal fallout. The non–motion‐compensated diffusion‐prepared scans yielded LV trADC values of 6.6 ± 0.9 × 10−3 mm2/s and diffusion‐prepared images with severe bulk motion‐induced artifacts.ConclusionWe developed a novel free‐breathing bulk motion compensated diffusion‐prepared 3D segmented bSSFP technique able to perform in vivo cardiac diffusion‐weighted MRI on a conventional clinical MR scanner. Magn Reson Med 72:1257–1267, 2014. © 2013 Wiley Periodicals, Inc.
Reduced chaos expansions with random coefficientsin reduced‐dimensional stochastic modeling of coupled problems
Authors: Arnst M. , Ghanem R. , Phipps E. , Red‐Horse J. 
Published: November 2013

SUMMARYWe address the curse of dimensionality in methods for solving stochastic coupled problems with an emphasis on stochastic expansion methods such as those involving polynomial chaos expansions. The proposed method entails a partitioned iterative solution algorithm that relies on a reduced‐dimensional representation of information exchanged between subproblems to allow each subproblem to be solved within its own stochastic dimension while interacting with a reduced projection of the other subproblems. The proposed method extends previous work by the authors by introducing a reduced chaos expansion with random coefficients. The representation of the exchanged information by using this reduced chaos expansion with random coefficients enables an expeditious construction of doubly stochastic polynomial chaos expansions that separate the effect of uncertainty local to a subproblem from the effect of statistically independent uncertainty coming from other subproblems through the coupling. After laying out the theoretical framework, we apply the proposed method to a multiphysics problem from nuclear engineering. Copyright © 2013 John Wiley & Sons, Ltd.
An effective Coarse‐grained model for biological simulations: Recent refinements and validations
Authors: Vicatos Spyridon , Rychkova Anna , Mukherjee Shayantani , Warshel Arieh 
Published: November 2013

ABSTRACTExploring the free energy landscape of proteins and modeling the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect, our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinements, extensions, and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes, electrolytes and electrodes, as well as studies of voltage‐activated proteins, protein insertion through the translocon, the action of molecular motors, and even the coupling of the stalled ribosome and the translocon. The examples discussed here illustrate the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes. Proteins 2014; 82:1168–1185. © 2013 Wiley Periodicals, Inc.
Effect of the orthorhombic/rhombohedral volume ratio on the piezoelectric properties of BaCaxTiO3–0.04LiF ceramics
Authors: Zhao Lei , Zhang Bo‐Ping , Zhou Peng‐Fei , Zhao Xiao‐Kun , Zhu Li‐Feng 
Published: November 2013

AbstractBaCaxTiO3–0.04LiF (0.010 ≤ x ≤ 0.045) ceramics were prepared by normal sintering at 1100 °C in air. A two‐phase coexisted region across orthorhombic and rhombohedral symmetry was designed by refining the components. The detailed phase structure was analyzed quantitatively by the Rietveld refinement. BaCa0.035TiO3–0.04LiF ceramic showed better properties with d33 = 354 pC N−1, kp = 39%, Qm = 314, and TC = 65 °C, in which the relative proportion of rhombohedral symmetry was 74.86%, the grain size was 6.0 µm and the relative density was 91%, indicating that the synergistic effect of the phase structure, fine grain, and relatively high density contributed to the outstanding piezoelectric properties.
A new proxy for ground motion selection in seismic collapse assessment of tall buildings
Authors: Yakhchalian Masood , Ghodrati Amiri Gholamreza , Nicknam Ahmad 
Published: November 2013

SUMMARYTall buildings are long‐period structures that are sensitive to the long‐period content of ground motions. Selection of appropriate ground motions is an important step in seismic collapse assessment of tall buildings using nonlinear dynamic analyses. Epsilon (εSa) and eta (η) are two spectral shape indicators, which have been recently proposed for ground motion selection in the technical literature. In this study, a new parameter gamma (γ) is proposed, which has considerable correlation with the collapse capacity of long‐period structures having a fundamental period greater than 1 s. This parameter is a linear combination of εSa and the displacement spectrum intensity epsilon (εDSI). The parameter γ is obtained and optimized by applying the particle swarm optimization algorithm. Since γ has significant correlation with the collapse capacity of long‐period structures, it can be used as an efficient proxy for ground motion selection in seismic collapse assessment of tall buildings. The results of this study show that ground motion selection considering the new proxy γ causes reduction in the dispersion of structural response and also decrease in the mean annual frequency of collapse, when compared with ground motion selection based on εSa and η. Copyright © 2013 John Wiley & Sons, Ltd.
The origin, function, and diagnostic potential of extracellular microRNAs in human body fluids
Authors: Liang Hongwei , Gong Fei , Zhang Suyang , Zhang Chen‐Yu , Zen Ke , Chen Xi 
Published: November 2013

Recently, numerous studies have documented the importance of microRNAs (miRNAs) as an essential cornerstone of the genetic system. Although RNA is usually considered an unstable molecule because of the ubiquitous ribonuclease, miRNAs are now known to circulate in the bloodstream and other body fluids in a stable, cell‐free form. Importantly, extracellular miRNAs are aberrantly present in plasma, serum, and other body fluids during the pathogenesis of many diseases and, thus, are promising noninvasive or minimally invasive biomarkers to assess the pathological status of the body. However, the origin and biological function of extracellular miRNAs remains incompletely understood. In this review, we summarize the recent literature on the biogenesis and working models of extracellular miRNAs, and we highlight the impact of extending these ongoing extracellular miRNA studies to clinical applications. WIREs RNA 2014, 5:285–300. doi: 10.1002/wrna.1208This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Phenotypic noise: effects of post‐transcriptional regulatory processes affecting mRNA
Authors: Arbel‐Goren Rinat , Tal Asaf , Stavans Joel 
Published: November 2013

The inherently stochastic nature of biomolecular processes is one of the main sources giving rise to cell‐to‐cell variations in protein and mRNA abundance, termed noise. Noise in isogenic populations can enhance survival under adverse conditions and stress, and has therefore played a fundamental role in evolution. On the other hand, noise may have detrimental effects and therefore cells must also display robustness to fluctuations and possess mechanisms of control in order to function properly. Noise can be introduced at every step in the cascade of intermediate events resulting in the production of functional proteins. While initial studies of noise focused on stochasticity introduced at the transcriptional level, recent years have witnessed a gradual shift of emphasis into the effects that post‐transcriptional processes have on phenotypic noise. Here, we survey the insights that have been gained on the effects of processes that modify RNA transcript populations on phenotypic noise, including regulation by noncoding RNAs in prokaryotes and eukaryotes, alternative splicing and transcriptional interference. WIREs RNA 2014, 5:197–207. doi: 10.1002/wrna.1209This article is categorized under:

RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
RNA Processing > RNA Editing and Modification
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
RNA in Disease and Development > RNA in Development
ASR FORUM: ENGAGING WITH AFRICAN INFORMAL ECONOMIES
Authors: Dolan Catherine , Roll Kate 
Published: November 2013

Abstract:Over the last decade, the bottom-of-the-pyramid (BoP) approach has gained prominence as a tool of “inclusive” capitalism in sub-Saharan Africa. This approach reframes development as a seamless outcome of core business activities, one that can ameliorate poverty by bringing much-needed products and services to the poor and generating employment opportunities for informal and subsistence workers as “micro-entrepreneurs.” Yet while transnational capital has set its sights on Africa’s “underserved” yet potentially buoyant markets, BoP initiatives do more than seize upon the entrepreneurial talent and aspirations of Africa’s informal economies. This article argues, rather, that these initiativescreateBoP economies through a set of market technologies, practices, and discourses that render the spaces and actors at the bottom of the pyramid knowable, calculable, and predictable to global business. The article describes how these technologies extend new forms of market governance over the informal poor, reconfiguring their habits, social practices, and economic strategies under the banner of poverty reduction.
ASR FORUM: ENGAGING WITH AFRICAN INFORMAL ECONOMIES
Authors: Cleaver Frances , Franks Tom , Maganga Faustin , Hall Kurt 
Published: November 2013

Abstract:This article furthers our understanding of how state and citizens interact to produce local institutions and examines the effects of these processes. It brings critical institutional theory into engagement with ideas about everyday governance to analyze how hybrid arrangements are formed through bricolage. Such a perspective helps us to understand governance arrangements as both negotiated and structured, benefiting some and disadvantaging others. To explore these points the article tracks the evolution of the Sungusungu, a hybrid pastoralist security institution in the Usangu Plains, Tanzania. It also considers the wider implications of such hybrid arrangements for livelihoods, social inclusion, distributive justice, and citizenship.