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Showing papers by "Agilent Technologies published in 2013"


Journal ArticleDOI
07 Feb 2013-Nature
TL;DR: Theoretical analysis indicates that the DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving.
Abstract: Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.

900 citations


Journal ArticleDOI
TL;DR: It is shown that planar graphene/h-BN heterostructures can be formed by growing graphene in lithographically patterned h-BN atomic layers and that the technique can be used to fabricate two-dimensional devices, such as a split closed-loop resonator that works as a bandpass filter.
Abstract: By growing graphene in patterned hexagonal boron nitride layers, planar heterostructures can be fabricated and used to create two-dimensional devices.

819 citations


Journal ArticleDOI
TL;DR: These hexagonal boron nitride atomic layer coatings, which can be synthesized via scalable chemical vapour deposition method down to only two layers, could be the thinnest coating ever shown to withstand such extreme environments and find applications as chemically stable high-temperature coatings.
Abstract: Hexagonal boron nitride is a two-dimensional layered material that can be stable at 1,500 °C in air and will not react with most chemicals. Here we demonstrate large-scale, ultrathin, oxidation-resistant coatings of high-quality hexagonal boron nitride layers with controlled thicknesses from double layers to bulk. We show that such ultrathin hexagonal boron nitride films are impervious to oxygen diffusion even at high temperatures and can serve as high-performance oxidation-resistant coatings for nickel up to 1,100 °C in oxidizing atmospheres. Furthermore, graphene layers coated with a few hexagonal boron nitride layers are also protected at similarly high temperatures. These hexagonal boron nitride atomic layer coatings, which can be synthesized via scalable chemical vapour deposition method down to only two layers, could be the thinnest coating ever shown to withstand such extreme environments and find applications as chemically stable high-temperature coatings.

547 citations


Journal ArticleDOI
14 Feb 2013-Cell
TL;DR: The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.

347 citations


Journal ArticleDOI
13 Dec 2013-Science
TL;DR: It is found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites, and TF-imposed constraint appears to be a major driver of codon usage bias.
Abstract: Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.

274 citations


Journal ArticleDOI
Huige Wei1, Jiahua Zhu1, Shijie Wu2, Suying Wei1, Zhanhu Guo1 
22 Mar 2013-Polymer
TL;DR: In this paper, a polyaniline (PANI)/graphite oxide (GO) nanocomposite films were fabricated by electropolymerization of aniline monomers onto GO coated indium tin oxide (ITO) glass slides, which were prepared by spin coating technique.

273 citations


Journal ArticleDOI
TL;DR: A temperature controlled dual water/oil on-off switch is achieved by using a PMMA-b-PNIPAAm block-copolymer coated mesh, determined by the conformational change of the PNIP AAm chain around the lower critical solution temperature (LCST).
Abstract: A temperature controlled dual water/oil on-off switch is achieved by using a PMMA-b-PNIPAAm block-copolymer coated mesh, determined by the conformational change of the PNIPAAm chain around the lower critical solution temperature (LCST) and also the cooperation between PNIPAAm and PMMA. Water can permeate through the BCP-coated mesh, and oil cannot below the LCST, whereas oil can and water cannot above the LCST.

190 citations


Journal ArticleDOI
TL;DR: This paper presents a power- and area-efficient 24-way time-interleaved successive-approximation-register (SAR) analog-to-digital converter (ADC) that achieves 2.8 GS/s and 8.1 ENOB in 65 nm CMOS.
Abstract: This paper presents a power- and area-efficient 24-way time-interleaved successive-approximation-register (SAR) analog-to-digital converter (ADC) that achieves 2.8 GS/s and 8.1 ENOB in 65 nm CMOS. To minimize the power and the area, the capacitors in the capacitive DAC are sized to meet the thermal noise requirements rather than the matching requirements, leading to the LSB capacitance of 50 aF. An on-chip digital background calibration is used to calibrate the capacitor mismatches in individual ADC channels, as well as the inter-channel offset, gain and timing mismatches. Measurement results at the 2.8 GS/s sampling rate show that the ADC chip prototype consumes 44.6 mW of power from a 1.2 V supply while achieving peak SNDR of 50.9 dB and retaining SNDR higher than 48.2 dB across the entire first Nyquist zone with a 1.8Vpp-diff input signal. The prototype chip occupies an area of 1.03 × 1.66 mm2, including the pads and the testing circuits. The figure of merit (FoM) of this ADC, calculated with the minimum SNDR in the first Nyquist zone, is 76 fJ/conversion-step.

184 citations


Journal ArticleDOI
TL;DR: Three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolites in a regulatory context are addressed.
Abstract: Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological status of a biological system, and about the changes caused by chemicals. Metabolomics analysis is used in many fields, ranging from the analysis of the physiological status of genetically modified organisms in safety science to the evaluation of human health conditions. In toxicology, metabolomics is the -omics discipline that is most closely related to classical knowledge of disturbed biochemical pathways. It allows rapid identification of the potential targets of a hazardous compound. It can give information on target organs and often can help to improve our understanding regarding the mode-of-action of a given compound. Such insights aid the discovery of biomarkers that either indicate pathophysiological conditions or help the monitoring of the efficacy of drug therapies. The first toxicological applications of metabolomics were for mechanistic research, but different ways to use the technology in a regulatory context are being explored. Ideally, further progress in that direction will position the metabolomics approach to address the challenges of toxicology of the 21st century. To address these issues, scientists from academia, industry, and regulatory bodies came together in a workshop to discuss the current status of applied metabolomics and its potential in the safety assessment of compounds. We report here on the conclusions of three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolomics in a regulatory context.

174 citations


Journal ArticleDOI
TL;DR: In this paper, the effect of multiwalled carbon nanotubes (MWCNTs) on the mechanical and electrical properties of fly ash (FA) geopolymeric composites was investigated.

172 citations


Journal ArticleDOI
TL;DR: Adding periodic BIRD J-refocusing (BIRD=bilinear rotation decoupling) to data acquisition in an HSQC experiment causes broadband homonuclear decoupled, giving a single signal for each proton chemical shift.
Abstract: BIRD's eye view: Adding periodic BIRD J-refocusing (BIRD=bilinear rotation decoupling) to data acquisition in an HSQC experiment causes broadband homonuclear decoupling, giving a single signal for each proton chemical shift. This pure shift method improves both resolution and signal-to-noise ratio, without the need for special data processing.

Journal ArticleDOI
TL;DR: New software, Morpheus, designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products, gives more spectrum, peptide, and protein identifications than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest.
Abstract: The acquisition of high-resolution tandem mass spectra (MS/MS) is becoming more prevalent in proteomics, but most researchers employ peptide identification algorithms that were designed prior to this development. Here, we demonstrate new software, Morpheus, designed specifically for high–mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a variety of organisms (E. coli, yeast, human) acquired on a variety of instruments (quadrupole–time-of-flight, ion trap–orbitrap, and quadrupole–orbitrap) in different laboratories, Morpheus gives more spectrum, peptide, and protein identifications at a 1% false discovery rate (FDR) than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest. Additionally, Morpheus is 1.5 to 4.6 times faster, depending on the data set, than the next fastest algorithm, OMSSA. Morpheus was developed in C# .NET and is available free and open source under a permissive license.

Journal ArticleDOI
TL;DR: It is demonstrated that topotecan treatment stabilizes the formation of RNA:DNA hybrids (R loops) at G-skewed repeat elements within paternal Snord116, corresponding to increased chromatin decondensation and inhibition of Ube3a-ATS expression.
Abstract: Prader–Willi syndrome (PWS) and Angelman syndrome (AS) are oppositely imprinted autism-spectrum disorders with known genetic bases, but complex epigenetic mechanisms underlie their pathogenesis. The PWS/AS locus on 15q11–q13 is regulated by an imprinting control region that is maternally methylated and silenced. The PWS imprinting control region is the promoter for a one megabase paternal transcript encoding the ubiquitous protein-coding Snrpn gene and multiple neuron-specific noncoding RNAs, including the PWS-related Snord116 repetitive locus of small nucleolar RNAs and host genes, and the antisense transcript to AS-causing ubiquitin ligase encoding Ube3a (Ube3a-ATS). Neuron-specific transcriptional progression through Ube3a-ATS correlates with paternal Ube3a silencing and chromatin decondensation. Interestingly, topoisomerase inhibitors, including topotecan, were recently identified in an unbiased drug screen for compounds that could reverse the silent paternal allele of Ube3a in neurons, but the mechanism of topotecan action on the PWS/AS locus is unknown. Here, we demonstrate that topotecan treatment stabilizes the formation of RNA:DNA hybrids (R loops) at G-skewed repeat elements within paternal Snord116, corresponding to increased chromatin decondensation and inhibition of Ube3a-ATS expression. Neural precursor cells from paternal Snord116 deletion mice exhibit increased Ube3a-ATS levels in differentiated neurons and show a reduced effect of topotecan compared with wild-type neurons. These results demonstrate that the AS candidate drug topotecan acts predominantly through stabilizing R loops and chromatin decondensation at the paternally expressed PWS Snord116 locus. Our study holds promise for targeted therapies to the Snord116 locus for both AS and PWS.

Journal ArticleDOI
TL;DR: It is shown that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in post-natal neurons and during sleep.
Abstract: Prader-Willi syndrome (PWS), a genetic disorder of obesity, intellectual disability and sleep abnormalities, is caused by loss of non-coding RNAs on paternal chromosome 15q11-q13. The imprinted minimal PWS locus encompasses a long non-coding RNA (lncRNA) transcript processed into multiple SNORD116 small nucleolar RNAs and the spliced exons of the host gene, 116HG. However, both the molecular function and the disease relevance of the spliced lncRNA 116HG are unknown. Here, we show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in post-natal neurons and during sleep. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to the dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1 and Per2. These combined genomic and metabolic analyses demonstrate that 116HG regulates the diurnal energy expenditure of the brain. These novel molecular insights into the energy imbalance in PWS should lead to improved therapies and understanding of lncRNA roles in complex neurodevelopmental and metabolic disorders.

Journal ArticleDOI
TL;DR: In this article, an external magnetic field was applied to both graphene and MGNC electrodes to enhance the capacitance of the electrodes, and the results showed that the magnetic field played a critical role in restricting the interfacial relaxation process and thus enhanced the electrode capacitance.
Abstract: Magnetic graphene nanocomposites (MGNCs) synthesized by a facile thermal decomposition method have been introduced. TEM observations reveal a uniform distribution of the Fe2O3 nanoparticle size and preferential nuclei growth along the edge defects. Both graphene and its Fe2O3 nanocomposites are prepared as electrochemical electrodes to evaluate their capacitor performances. Under normal conditions (without a magnetic field), the MGNCs show lower capacitance than graphene due to the large particle loading (52.5 wt%), which brings larger internal resistance and thus prevents efficient electron transportation within the electrodes. However, in the presence of an external magnetic field, both graphene and MGNC electrodes exhibit significantly enhanced capacitance as compared to the results obtained under normal conditions. Specifically, the capacitance of graphene is increased by 67.1 and 26.8% at the sweeping rates of 2 and 10 mV s−1, respectively. Even larger enhancements of 154.6 and 98.2% were observed in MGNCs at the same sweeping rates of 2 and 10 mV s−1, respectively. The energy density and power density of the electroactive materials are also dramatically enhanced in the presence of a magnetic field. Equivalent circuit modeling of impedance spectra revealed that the magnetic field played a critical role in restricting the interfacial relaxation process and thus enhanced the electrode capacitance. These findings present a potential revolution of traditional electrochemical capacitors by simply applying an external magnetic field to enhance the capacitance dramatically (even doubling it depending on the electroactive materials) without material replacement and structural modification.

Journal ArticleDOI
TL;DR: A multi-target method for the determination of 191 fungal metabolites in almonds, hazelnuts, peanuts and pistachios was developed, and the applicability of the developed method was demonstrated through the analysis of 53 naturally contaminated nut samples from Austria and Turkey.
Abstract: A multi-target method for the determination of 191 fungal metabolites in almonds, hazelnuts, peanuts and pistachios was developed. The method includes all mycotoxins regulated in the European Union and mycotoxins regularly found in food. After extraction with an acidified acetonitrile water mixture, the raw extract was diluted and injected directly into the UHPLC-MS/MS system. In two chromatographic runs, analysis was performed in positive and in negative ionisation mode. The method was in-house validated for the most important 65 analytes in these four commodities. Apparent recoveries between 80 and 120 % were obtained for about half of the analyte–matrix combinations. Good repeatabilities (standard deviations < 10 %) were achieved for the vast majority (83 %) of all cases. Only in 6 % of all combinations did the standard deviations exceed 15 %. Matrix effects, arising during electrospray ionisation, significantly influenced the determination. For instance, signal suppression was observed for several early-eluting analytes and also signal enhancement up to 295 % for physcion in peanuts was determined. Concerning extraction recovery, 94 % of the analyte–matrix combinations showed values higher than 50 %. Lower limits of quantification ranged between 0.04 μg kg−1 for enniatin B3 in peanuts and 500 μg kg−1 for HC toxin in hazelnuts. Additionally, the applicability of the developed method was demonstrated through the analysis of 53 naturally contaminated nut samples from Austria and Turkey. Overall, 40 toxins were quantified; the most frequently found mycotoxins were beauvericin (79 %), enniatin B (62 %) and macrosporin (57 %). In the most contaminated hazelnut sample, 26 different fungal metabolites were detected.

Journal ArticleDOI
TL;DR: Herein is a facile method for the post-synthetic modification of the intrinsic voids in the cage compound, which allows the pore structure of the resulting material to be “fine-tuned” in the solid state.
Abstract: Cage compounds are fascinating molecules for several reasons. They are defined molecular reaction vessels for “uncommon” products, or used to stabilize highly reactive species in their interior. Recently, materials made from purely organic cage compounds showed remarkable permanent porosities, with very high surface areas and good gassorption properties, both, in crystalline as well as amorphous phases. A feature that distinguishes the porous materials derived from cage compounds from those derived from extended network structures (such as metal organic frameworks (MOFs) and covalent organic frameworks (COFs)) is, that the intrinsically porous building units (the cage molecules) are soluble. This creates several possibilities, which cannot be easily achieved for extended network structures or are even impossible. For instance, Cooper et al. reported on the co-crystallization of organic cage compounds in a binary or even ternary fashion to create porous organic alloys. 11] Very recently, this property was exploited to grow microporous cage crystals in mesoporous silica. Another example of “processable” porosity has been demonstrated by our group: various cage compounds, which are highly porous in the bulk, can be deposited as thin films on quartz crystal microbalances (QMBs) by spray-coating. The modified QMBs showed very good affinities for several aromatic analytes. In 2008, we introduced the one-pot synthesis of the endofunctionalized [4+6] cage compound 3 by reacting four molecules of triamine 1 and six molecules of salicyldialdehyde 2 (Scheme1). What distinguishes this type of cage compounds from others, is that it bears six hydroxy groups pointing to the center of the cage cavity. This structural motif is very rare for organic cage compounds, and the functionalization of the cages interiors through reaction at the hydroxy groups was to date unsuccessful. Herein we present a facile method for the post-synthetic modification of the intrinsic voids in the cage compound, which allows the pore structure of the resulting material to be “fine-tuned” in the solid state. Initially, we attempted to directly synthesize 5 a by the reaction of O-methylated salicyldialdehyde 4a with triamine 1 (Method A in Scheme 1). Unfortunately, only a small amount of cage 5a was detected in the crude product by the MALDI-TOF mass spectroscopy. However, cage 5a could not be isolated by chromatographic methods. Further optimization of the reaction conditions did not offer a decent route to synthesize 5 a in reasonable yield (never exceeding 17 %). H NMR analysis of the crude product (Figure 1b) exemplifies the high complexity of the resulting mixture. Similarly, reactions of triamine 1 with other salicyldialdehyde ethers 4b–4d failed too. These unsuccessful experiments forced us to switch to an indirect approach (see Scheme 1. Synthesis of cavity-modified cage compounds 5a–5e by two different approaches. Method A: direct route by 12-fold imine condensation. Method B: Post-synthetically modification by sixfold Williamson ether formation. For reaction conditions, results, and yields, see Table 1 and Supporting Information.

Journal ArticleDOI
TL;DR: The overall diagnostic rate was 42%, but this varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for Persons with bilateral autosomal recessive NSHL, which highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations.
Abstract: Background Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we tested 100 persons with presumed genetic NSHL and in so doing established sequencing requirements for maximum sensitivity and defined MPS quality score metrics that obviate Sanger validation of variants. Methods We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance computing cluster for bioinformatics analysis. Results To obtain maximum variant sensitivity with this platform 3.2–6.3 million total mapped sequencing reads per sample were required. Quality score analysis showed that Sanger validation was not required for 95% of variants. Our overall diagnostic rate was 42%, but this varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL. Conclusions These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas.

Journal ArticleDOI
TL;DR: A "dilute and shoot" method for the liquid chromatography-tandem mass spectrometric (LC-MS/MS) determination of multiple mycotoxins in wines and beers has been developed and validated and extended to include other mycot oxins.
Abstract: A “dilute and shoot” method for the liquid chromatography–tandem mass spectrometric (LC-MS/MS) determination of multiple mycotoxins (aflatoxins B1, B2, G1, G2, ochratoxin A (OTA), fumonisins (F) B1...

Journal ArticleDOI
TL;DR: An interlaboratory study is performed to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods, and the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteinomics, and glycomics methods.

Proceedings ArticleDOI
01 Oct 2013
TL;DR: The results show that the fingerprint definition is as important as the choice of location estimation algorithm and there is no single combination of these two that works across all environments or even all floors of a given environment.
Abstract: WiFi fingerprinting has received much attention for indoor mobile phone localization. In this study, we examine the impact of various aspects underlying a WiFi fingerprinting system. Specifically, we investigate different definitions for fingerprinting and location estimation algorithms across different indoor environments ranging from a multi-storey office building to shopping centers of different sizes. Our results show that the fingerprint definition is as important as the choice of location estimation algorithm and there is no single combination of these two that works across all environments or even all floors of a given environment. We then consider the effect of WiFi frequency bands (e.g., 2.4GHz and 5GHz) and the presence of virtual access points (VAPs) on location accuracy with WiFi fingerprinting. Our results demonstrate that 5GHz signals are less prone to variation and thus yield more accurate location estimation. We also find that the presence of VAPs improves location estimation accuracy.

Journal ArticleDOI
TL;DR: A novel resource allocation framework is proposed based on the bandwidth-power product minimization, which is an effective metric in evaluating the spectral resource consumption in a cognitive radio environment.
Abstract: In this paper, the problem of resource allocation optimization is studied for a single-cell multiuser cognitive radio network in the presence of primary user networks. The spectral access of the cognitive radio network is based on Orthogonal Frequency Division Multiple Access (OFDMA). A joint bandwidth and power allocation is performed so that users' rate requirements are satisfied, and the integrity of primary user communication is preserved. In this work, two unique challenges are addressed. The first is the incorporation of primary user activity in the design of resource allocation technique, and the second is the limited hardware capabilities of cognitive terminals compared to those available at the cognitive base station. To address these problems, a novel resource allocation framework is proposed based on the bandwidth-power product minimization, which is an effective metric in evaluating the spectral resource consumption in a cognitive radio environment. The framework takes into consideration the challenges aforementioned. The results show significant enhancement in spectral efficiency by using our framework compared to classical power adaptive optimization using iterative waterfilling scheme.

Book
26 Sep 2013
TL;DR: This is the definitive guide to X-parameters, written by the original inventors and developers of this powerful new paradigm for nonlinear RF and microwave components and systems, providing useful approximations that will greatly reduce the complexity of measuring, modeling and designing for non linear regimes of operation.
Abstract: This is the definitive guide to X-parameters, written by the original inventors and developers of this powerful new paradigm for nonlinear RF and microwave components and systems Learn how to use X-parameters to overcome intricate problems in nonlinear RF and microwave engineering The general theory behind X-parameters is carefully and intuitively introduced, and then simplified down to specific, practical cases, providing you with useful approximations that will greatly reduce the complexity of measuring, modeling and designing for nonlinear regimes of operation Containing real-world case studies, definitions of standard symbols and notation, detailed derivations within the appendices, and exercises with solutions, this is the definitive stand-alone reference for researchers, engineers, scientists and students looking to remain on the cutting-edge of RF and microwave engineering

Journal ArticleDOI
15 Aug 2013-Talanta
TL;DR: The new MP-AES platform can offer comparable or better performance compared to AA and/or ICP-OES with respect to routine analysis for a regulatory program.

Journal ArticleDOI
TL;DR: Three techniques to speedup fundamental problems in data mining algorithms on the CUDA platform are proposed: scalable thread scheduling scheme for irregular pattern, parallel distributed top-k scheme, and parallel high dimension reduction scheme.
Abstract: Recent development in Graphics Processing Units (GPUs) has enabled inexpensive high performance computing for general-purpose applications. Compute Unified Device Architecture (CUDA) programming model provides the programmers adequate C language like APIs to better exploit the parallel power of the GPU. Data mining is widely used and has significant applications in various domains. However, current data mining toolkits cannot meet the requirement of applications with large-scale databases in terms of speed. In this paper, we propose three techniques to speedup fundamental problems in data mining algorithms on the CUDA platform: scalable thread scheduling scheme for irregular pattern, parallel distributed top-k scheme, and parallel high dimension reduction scheme. They play a key role in our CUDA-based implementation of three representative data mining algorithms, CU-Apriori, CU-KNN, and CU-K-means. These parallel implementations outperform the other state-of-the-art implementations significantly on a HP xw8600 workstation with a Tesla C1060 GPU and a Core-quad Intel Xeon CPU. Our results have shown that GPU + CUDA parallel architecture is feasible and promising for data mining applications.

Journal ArticleDOI
TL;DR: In this article, an accurate, sensitive and fast analytical method for the determination of S in organic matrices by means of a recently developed triple quadrupole ICP-MS instrument, operated in MS/MS mode is described.
Abstract: Accurate determination of low levels of S in organic matrices by means of isotope dilution ICP-single quadrupole MS (eg, for quantification of S components in reverse phase HPLC-ICP-MS experiments) is often not feasible This work describes an accurate, sensitive and fast analytical method for the determination of S in organic matrices by means of a recently developed ‘triple quadrupole’ ICP-MS instrument, operated in MS/MS mode The added value of the MS/MS approach for this application has been clearly visualised by varying the width of the bandpass of the first quadrupole analyzer from “fully open” (standard mode) down to single mass width (MS/MS mode) As a proof-of-concept, a biodiesel reference material has been analysed for its S content with the proposed method, using isotope dilution for calibration, and the results obtained were in excellent agreement with the certified value (within experimental uncertainty)

Journal ArticleDOI
TL;DR: A high efficiency of the photo-Fenton process was observed in caffeine degradation by solar photocatalysis using a CPC reactor, as well as intermediates of low toxicity, demonstrating that photo- Fenton process can be a viable alternative for caffeine removal in wastewater.

Journal ArticleDOI
TL;DR: A newly developed concept of solid-phase microextraction (SPME) sorbent, which allows for direct immersion extraction in complex food matrices, has been applied in the analysis of 10 triazole fungicides in grapes and strawberries pulps, and was successfully applied inThe new SPME method was compared to a modified version of t QuEChERS AOAC method: the limits of quantitation reached by S PME were at least one order of magnitude lower than those achieved

Journal ArticleDOI
TL;DR: Technology for isolating RNA–protein partners efficiently and accurately using an engineered clustered regularly interspaced short palindromic repeats (CRISPR) endoribonuclease is presented and it is shown that this technology is suitable for analyzing diverse size transcripts, and that it is suitable to adaptation to a high-throughput discovery format.
Abstract: RNA-binding proteins control the fate and function of the transcriptome in all cells. Here we present technology for isolating RNA–protein partners efficiently and accurately using an engineered clustered regularly interspaced short palindromic repeats (CRISPR) endoribonuclease. An inactive version of the Csy4 nuclease binds irreversibly to transcripts engineered with a 16-nt hairpin sequence at their 5′ ends. Once immobilized by Csy4 on a solid support, contaminating proteins and other molecules can be removed by extensive washing. Upon addition of imidazole, Csy4 is activated to cleave the RNA, removing the hairpin tag and releasing the native transcript along with its specifically bound protein partners. This conditional Csy4 enzyme enables recovery of specific RNA-binding partners with minimal false-positive contamination. We use this method, coupled with quantitative MS, to identify cell type-specific human pre-microRNA-binding proteins. We also show that this technology is suitable for analyzing diverse size transcripts, and that it is suitable for adaptation to a high-throughput discovery format.

Journal ArticleDOI
25 Feb 2013-Small
TL;DR: Carbon dots (surface-passivated small carbon nanoparticles) are crosslinked to result in fluorescence probes containing one or multiple dots, which demonstrate that the fluorescence properties are additive, with more dots for higher emission intensities in a proportional fashion, thus enabling the preparation of ultra-bright fluorescent probes.
Abstract: Carbon dots (surface-passivated small carbon nanoparticles) are crosslinked to result in fluorescence probes containing one or multiple dots. For the single-dot probes, the crosslinking further stabilizes the dot structure, while for those packed with multiple dots, the individual probe imaging results demonstrate that the fluorescence properties are additive, with more dots for higher emission intensities in a proportional fashion, thus enabling the preparation of ultra-bright fluorescence probes.