bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotemplates in the green synthesis of silver nanoparticles
Authors: Vijayaraghavan Krishnan , Nalini S. P. Kamala 
Published: July 2010

AbstractThis article recapitulates the scientific advancement towards the greener synthesis of silver nanoparticles. Applications of noble metals have increased throughout human civilization, and the uses for nano‐sized particles are even more remarkable. “Green” nanoparticle synthesis has been achieved using environmentally acceptable solvent systems and eco‐friendly reducing and capping agents. Numerous microorganisms and plant extracts have been applied to synthesize inorganic nanostructures either intracellularly or extracellularly. The use of nanoparticles derived from noble metals has spread to many areas including jewelery, medical fields, electronics, water treatment and sport utilities, thus improving the longevity and comfort in human life. The application of nanoparticles as delivery vehicles for bactericidal agents represents a new paradigm in the design of antibacterial therapeutics. Orientation, size and physical properties of nanoparticles influences the performance and reproducibility of a potential device, thus making the synthesis and assembly of shape‐ and size‐controlled nanocrystals an essential component for any practical application. This need has motivated researchers to explore different synthesis protocols.
Continued chemotherapy after complete response to primary therapy among women with advanced ovarian cancer
Authors: Hess Lisa M. , Rong Nan , Monahan Patrick O. , Gupta Paridha , Thomaskutty Champ , Matei Daniela 
Published: July 2010

AbstractBACKGROUND.Ovarian cancer (OC) is associated with a >75% risk of recurrence after completion of primary therapy. Several clinical trials have explored the role of continued therapy after complete response to primary adjuvant therapy to reduce the risk of recurrence; however, these trials have largely been underpowered, leading to inconclusive results.METHODS.A systematic search strategy was initiated to identify all clinical trials involving consolidation or maintenance therapy regimens for OC in first complete remission. A meta‐analysis was conducted to evaluate toxicity and progression‐free (PFS) and overall survival (OS).RESULTS.There were 37 publications meeting all eligibility criteria, representing 20 consolidation and 9 maintenance therapy trials. Consolidation and maintenance therapies were associated with improved PFS (hazard ratio [HR], 0.79 [P = .003] and HR, 0.82 [P = .02], respectively) and OS (HR, 0.68 [P = .0008] and HR, 0.68 [P = .007], respectively). This relationship remained statistically significant when the analysis was limited to randomized trials and across other sensitivity analyses.CONCLUSIONS.Although individual studies have not yet convincingly shown a survival advantage with maintenance chemotherapy in OC, this meta‐analysis demonstrates that continued chemotherapy after completion of primary therapy for OC improves PFS and OS. Benefits are greatest in patients with advanced stage OC who reach complete clinical or pathologic response after primary therapy. Cancer 2010. © 2010 American Cancer Society.
Pre‐LNA smart soft antenna selection for MIMO spatial multiplexing/diversity system when amplifier/sky noise dominates
Authors: Ahmadi‐Shokouh J. , Jamali S. H. , Safavi‐Naeini S. 
Published: July 2010

AbstractDue to a beamforming capability, Soft Antenna Selection (SAS) techniques have shown great performance improvements over the traditional antenna sub‐set selection schemes for Multi‐Input and Multi‐Output (MIMO) communication systems. A SAS method is basically defined by a pre‐processing matrix which is located in RF domain, either before or after the Low Noise Amplifier (LNA). In this paper, we propose a pre‐LNA SAS module which is adaptively tuned to maximise the mutual information or the Signal to Noise Ratio (SNR) gain for spatial multiplexing or diversity transmissions, respectively. The SAS optimality is discussed for the two practical cases where either the sky noise or the amplifier noise dominates. We analytically show that the pre‐LNA SAS method even outperforms the full‐complexity MIMO system for when the number of receive Radio Frequency (RF) chains is greater than or equal to the number of the transmit RF chains. The simulation results verify this claim and also superiority of the proposed scheme to the post‐LNA SAS. Copyright © 2010 John Wiley & Sons, Ltd.
A genetic variant in a PP2A regulatory subunit encoded by the PPP2R2B gene associates with altered breast cancer risk and recurrence
Authors: Vazquez Alexei , Kulkarni Diptee , Grochola Lukasz F. , Bond Gareth L. , Barnard Nicola , Toppmeyer Deborah , Levine Arnold J. , Hirshfield Kim M. 
Published: July 2010

AbstractA recent candidate gene association study identified a single nucleotide polymorphism (SNP) in the PPP2R2B gene (rs319217, A/G) that manifests allelic differences in the cellular responses to treatment with chemotherapeutic agents (Vazquez et al., Nat Rev Drug Discov 2008;7:979‐87). This gene encodes a regulatory subunit of protein phosphatase 2A (PP2A), one of the major Ser/Thr phosphatases implicated in the negative control of cell growth and division. Given the tumor suppressor activities of PP2A, here we evaluate whether this genetic variant associates with the age of diagnosis and recurrence of breast cancer in women. To investigate the linkage disequilibrium in the vicinity of this SNP, PPP2R2B haplotypes were analyzed using HapMap data for 90 Caucasians. It is found that the A variant of rs319217 tags a haplotype that appears to be under positive selection in the Caucasian population, implying that this SNP is functional. Subsequently, associations with cellular responses were investigated using data reported by the NCI anticancer drug screen and associations with breast cancer clinical variables were analyzed in a cohort of 819 Caucasian women. The A allele associates with a better response of tumor derived cell lines, lower risk of breast cancer recurrence, later time to recurrence, and later age of diagnosis of breast cancer in Caucasian women. Taken together these results indicate that the A variant of the rs319217 SNP is a marker of better prognosis in breast cancer.
Genome‐wide DNA methylation analysis of neuroblastic tumors reveals clinically relevant epigenetic events and large‐scale epigenomic alterations localized to telomeric regions
Authors: Buckley Patrick G. , Das Sudipto , Bryan Kenneth , Watters Karen M. , Alcock Leah , Koster Jan , Versteeg Rogier , Stallings Raymond L. 
Published: July 2010

AbstractThe downregulation of specific genes through DNA hypermethylation is a major hallmark of cancer, although the extent and genomic distribution of hypermethylation occurring within cancer genomes is poorly understood. We report on the first genome‐wide analysis of DNA methylation alterations in different neuroblastic tumor subtypes and cell lines, revealing higher order organization and clinically relevant alterations of the epigenome. The methylation status of 33,485 discrete loci representing all annotated CpG islands and RefSeq gene promoters was assessed in primary neuroblastic tumors and cell lines. A comparison of genes that were hypermethylated exclusively in the clinically favorable ganglioneuroma/ganglioneuroblastoma tumors revealed that nine genes were associated with poor clinical outcome when overexpressed in the unfavorable neuroblastoma (NB) tumors. Moreover, an integrated DNA methylation and copy number analysis identified 80 genes that were recurrently concomitantly deleted and hypermethylated in NB, with 37 reactivated by 5‐aza‐deoxycytidine. Lower expression of four of these genes was correlated with poor clinical outcome, further implicating their inactivation in aggressive disease pathogenesis. Analysis of genome‐wide hypermethylation patterns revealed 70 recurrent large‐scale blocks of contiguously hypermethylated promoters/CpG islands, up to 590 kb in length, with a distribution bias toward telomeric regions. Genome‐wide hypermethylation events in neuroblastic tumors are extensive and frequently occur in large‐scale blocks with a significant bias toward telomeric regions, indicating that some methylation alterations have occurred in a coordinated manner. Our results indicate that methylation contributes toward the clinicopathological features of neuroblastic tumors, revealing numerous genes associated with poor patient survival in NB.
Research priorities in land use and land‐cover change for the Earth system and integrated assessment modelling
Authors: Hibbard Kathy , Janetos Anthony , van Vuuren Detlef P. , Pongratz Julia , Rose Steven K. , Betts Richard , Herold Martin , Feddema Johannes J. 
Published: July 2010

AbstractThis special issue has highlighted recent and innovative methods and results that integrate observations and modelling analyses of regional to global aspect of biophysical and biogeochemical interactions of land‐cover change with the climate system. Both the Earth System and the Integrated Assessment modeling communities recognize the importance of an accurate representation of land use and land‐cover change to understand and quantify the interactions and feedbacks with the climate and socio‐economic systems, respectively. To date, cooperation between these communities has been limited. Based on common interests, this work discusses research priorities in representing land use and land‐cover change for improved collaboration across modelling, observing and measurement communities. Major research topics in land use and land‐cover change are those that help us better understand (1) the interaction of land use and land cover with the climate system (e.g. carbon cycle feedbacks), (2) the provision of goods and ecosystem services by terrestrial (natural and anthropogenic) land‐cover types (e.g. food production), (3) land use and management decisions and (4) opportunities and limitations for managing climate change (for both mitigation and adaptation strategies). Copyright © 2010 Royal Meteorological Society and Crown Copyright.
Climate change impact on the hydrological balance of the Itaipu Basin
Authors: Rivarola Sosa J. M. , Brandani Giada , Dibari Camilla , Moriondo Marco , Ferrise Roberto , Trombi Giacomo , Bindi Marco 
Published: July 2010

AbstractThis study aimed at carrying out an assessment of the impact of climate change on water availability for the Itaipu hydrological basin, located on the frontier between Brazil and Paraguay, with particular reference to river runoff and hydropower. Climate data for the SRES future scenario A2 were generated for the Paraná hydrological basin (which includes the Itaipu hydrological basin) and hydrological impacts were studied. Present and future rainfall data were downscaled from the Canadian General Circulation Model (CGCM) for the A2 SRES scenario (periods 2010–2040 and 2070–2100) on a local meteorological network covering the Itaipu hydrologic basin and used as driving parameters for the Sacramento hydrological model to estimate the river runoff. The results of this analysis for the first period have shown an unchanged average annual runoff as the effect of an asymmetric impact on a seasonal scale. Climate change resulted in a higher runoff in summer–spring, whilst runoff in winter–autumn was lower with respect to the baseline. The second period resulted in a general decrease in runoff on both seasonal and annual scales. Possible impacts on hydropower production are discussed. Copyright © 2010 Royal Meteorological Society
A graph‐based approach for automatic cardiac tractography
Authors: Frindel Carole , Robini Marc , Schaerer Joël , Croisille Pierre , Zhu Yue‐Min 
Published: July 2010

AbstractA new automatic algorithm for assessing fiber‐bundle organization in the human heart using diffusion‐tensor magnetic resonance imaging is presented. The proposed approach distinguishes from the locally “greedy” paradigm, which uses voxel‐wise seed initialization intrinsic to conventional tracking algorithms. It formulates the fiber tracking problem as the global problem of computing paths in a boolean‐weighted undirected graph, where each voxel is a vertex and each pair of neighboring voxels is connected with an edge. This leads to a global optimization task that can be solved by iterated conditional modes‐like algorithms or Metropolis‐type annealing. A new deterministic optimization strategy, namely iterated conditional modes with α‐relaxation using (t2)‐ and (t4)‐moves, is also proposed; it has similar performance to annealing but offers a substantial computational gain. This approach offers some important benefits. The global nature of our tractography method reduces sensitivity to noise and modeling errors. The discrete framework allows an optimal balance between the density of fiber bundles and the amount of available data. Besides, seed points are no longer needed; fibers are predicted in one shot for the whole diffusion‐tensor magnetic resonance imaging volume, in a completely automatic way. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Robust EPI Nyquist ghost elimination via spatial and temporal encoding
Authors: Hoge W. Scott , Tan Huan , Kraft Robert A. 
Published: July 2010

AbstractNyquist ghosts are an inherent artifact in echo planar imaging acquisitions. An approach to robustly eliminate Nyquist ghosts is presented that integrates two previous Nyquist ghost correction techniques: temporal domain encoding (phase labeling for additional coordinate encoding: PLACE and spatial domain encoding (phased array ghost elimination: PAGE). Temporal encoding modulates the echo planar imaging acquisition trajectory from frame to frame, enabling one to interleave data to remove inconsistencies that occur between sampling on positive and negative gradient readouts. With PLACE, one can coherently combine the interleaved data to cancel residual Nyquist ghosts. If the level of ghosting varies significantly from image to image, however, the signal cancellation that occurs with PLACE can adversely affect SNR‐sensitive applications such as perfusion imaging with arterial spin labeling. This work proposes integrating PLACE into a PAGE‐based reconstruction process to yield significantly better Nyquist ghost correction that is more robust than PLACE or PAGE alone. The robustness of this method is demonstrated in the presence of magnetic field drift with an in‐vivo arterial spin labeling perfusion experiment. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
31P Magnetic resonance spectroscopic imaging with polarisation transfer of phosphomono‐ and diesters at 3 T in the human brain: relation with age and spatial differences
Authors: Wijnen J. P. , Scheenen T. W. J. , Klomp D. W. J. , Heerschap A. 
Published: July 2010

AbstractTissue levels of the compounds phosphocholine (PC), phosphoethanolamine (PE), glycerophosphocholine (GPC) and glycerophosphoethanolamine (GPE) can be studied by in vivo 31P MRS. However, the detection of the signals of these compounds suffers from low sensitivity and contamination by underlying broad resonances of other phosphorylated compounds. Improved sensitivity without this contamination can be achieved with a method for optimal polarisation transfer of 1H to 31P spins in these molecules, called selective refocused insensitive nuclei‐enhanced polarisation transfer (sRINEPT). The aim of this study was to implement a three‐dimensional magnetic resonance spectroscopic imaging (MRSI) version of sRINEPT on a clinical 3 T magnetic resonance system to obtain spatially resolved relative levels of PC, PE, GPC and GPE in the human brain as a function of age, which could be used as a reference dataset for clinical applications. Good signal‐to‐noise ratios were obtained from voxels of 17 cm3 of the parietal and occipital lobes of the brain within a clinically acceptable measurement time of 17 min. Eighteen healthy subjects of different ages (16–70 years) were examined with this method. A strong inverse relation of the PE/GPE and PC/GPC ratios with age was found. Spatial resolution was sufficient to detect differences in metabolite ratios between white and grey matter. Moreover, we showed the feasibility of this method for clinical use in a pilot study of patients with brain tumours. The sRINEPT MRSI technique enables the exploration of phospholipid metabolism in brain diseases with a better sensitivity than was possible with earlier 31P MRS methods. Copyright © 2010 John Wiley & Sons, Ltd.
High‐sensitivity cerebral perfusion mapping in mice by kbGRASE‐FAIR at 9.4 T
Authors: Zheng Bingwen , Lee Philip Teck Hock , Golay Xavier 
Published: July 2010

AbstractThe combination of flow‐sensitive alternating inversion recovery (FAIR) and single‐shot k‐space‐banded gradient‐ and spin‐echo (kbGRASE) is proposed here to measure perfusion in the mouse brain with high sensitivity and stability. Signal‐to‐noise ratio (SNR) analysis showed that kbGRASE‐FAIR boosts image and temporal SNRs by 2.01 ± 0.08 and 2.50 ± 0.07 times, respectively, when compared with standard single‐shot echo planar imaging (EPI)‐FAIR implemented in our experimental systems, although the practically achievable spatial resolution was slightly reduced. The effects of varying physiological parameters on the precision and reproducibility of cerebral blood flow (CBF) measurements were studied following changes in anesthesia regime, capnia and body temperature. The functional MRI time courses with kbGRASE‐FAIR showed a more stable response to 5% CO2 than did those with EPI‐FAIR. The results establish kbGRASE‐FAIR as a practical and robust protocol for quantitative CBF measurements in mice at 9.4 T. Copyright © 2010 John Wiley & Sons, Ltd.
A method for rapid in vivo measurement of blood T1
Authors: Varela Marta , Hajnal Joseph V. , Petersen Esben T. , Golay Xavier , Merchant Nazakat , Larkman David J. 
Published: July 2010

AbstractWe present a technique to measure the longitudinal relaxation time constant of venous blood (T1b) in vivo in a few seconds. The MRI sequence consists of a thick‐slab adiabatic inversion, followed by a series of slice‐selective excitations and single‐shot echo planar imaging readouts. The time intervals between excitations were chosen so that blood in macroscopic vessels is fully refreshed between excitations, making the blood signal follow an unperturbed inversion recovery curve. Static tissue, which experiences the inversion and all excitation pulses, quickly reaches a steady state at a low signal as a result of partial saturation. This allows blood‐filled voxels to be discriminated from those containing static tissue, and to be fitted voxel‐by‐voxel to a simple inversion recovery model. The sequence was tested on a flow phantom with the proposed method, yielding T1 values consistent to within 3% of those obtained using a conventional inversion recovery sequence with a spin‐echo readout. The method was applied to seven adult volunteers and 18 neonates. The blood T1 of the neonates (1799 ± 206 ms; range, 1393–2035 ms) was found to be more variable than that of adults (1717 ± 39 ms; range, 1662–1779 ms). A linear correlation between the inverse of T1b and the haematocrit was established in 12 neonates (R2 = 0.90). Copyright © 2010 John Wiley & Sons, Ltd.
Rank aggregation methods
Authors: Lin Shili 
Published: July 2010

AbstractThis article provides an overview of rank aggregation methods and algorithms, with an emphasis on modern biological applications. Rank aggregation methods have traditionally been used extensively in marketing and advertisement research, and in applied psychology in general. In recent years, rank aggregation methods have emerged as an important tool for combining information from different Internet search engines or from different omics‐scale biological studies. We discuss three classes of methods, namely distributional based, heuristic, and stochastic search. The original Thurstone's scaling and its extensions represent the first class of methods that are most appropriate for aggregating many short ranked lists. Aggregating results from consumer rankings of products falls into this category of problems. Its application to biological problems is also being explored. On the other hand, heuristic algorithms and stochastic search methods are applicable to the situation of aggregating a small number of long lists, the so‐called ‘high‐level’ meta‐analysis scenario. Combining results from different search engines/criteria and a number of omics‐scale biological applications fall into this category. Heuristic algorithms are deterministic in nature, ranging from simple arithmetic averages of ranks to Markov chains and stationary distributions. Stochastic search algorithms, on the other hand, aim at maximizing a particular criterion such as that following the Kemeny guideline. Several examples will be provided to illustrate, compare, and contrast the methods and algorithms. The examples range from simple and contrive to representing realistic scenarios. In particular, an application to aggregating results from gene expression microarray studies is provided to demonstrate applications of the methods to modern biological problems. Copyright © 2010 John Wiley & Sons, Inc.This article is categorized under:Statistical and Graphical Methods of Data Analysis > Robust Methods
Metabolic manipulators: a well founded strategy to combat mitochondrial dysfunction
Authors: Koene Saskia , Smeitink Jan 
Published: July 2010

AbstractWhilst the pathophysiology and genetics of mitochondrial disease are slowly being unraveled, currently no effective remedy for mitochondrial disorders is available. One particular strategy in mitochondrial medicine presently under study is metabolic manipulation. This approach is aimed at counteracting the deranged cell biological homeostasis caused by mitochondrial dysfunction, using dietary modifications or small molecule therapy. Cell biological alterations caused by mitochondrial dysfunction include increased reactive oxygen species production, enhanced lipid peroxidation and altered cellular calcium homeostasis. This review covers the five principles of metabolic manipulation: (1) prevention of oxidative damage by reactive oxygen species, (2) amelioration of lipid peroxidation, (3) correction of altered membrane potential, (4) restoration of calcium homeostasis, and (5) transcription regulation interference. We hypothesize that a combination of compounds targeting different metabolic pathways will abolish cellular disturbance arising as a consequences of mitochondrial dysfunction, and thereby improve or stabilize clinical features. However, only a handful of compounds have reached efficacy testing in mammals, and it remains unknown to what extent metabolic manipulation will affect the whole organism. Until a potent remedy is found, patients will remain dependent on supportive, not curative, interventions.