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Jia, Yan, Zhi Ling Yang, Xiao Tian Cheng, and Jin Rong Nie. "Research on Identification of Cement Laboratory Samples Management." Applied Mechanics and Materials 438-439 (October 2013): 416–20. http://dx.doi.org/10.4028/www.scientific.net/amm.438-439.416.
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In allusion to the management characteristics of the cement laboratory samples, this paper conducts introduction and comparative analysis on such four kinds of identification as inspection organization, traditional cement sample identification of corporate laboratory, paper-electronic tags and wireless monitoring devices. It shows that wireless monitoring devices are superior to the traditional sample identification and paper-electronic tags, and can achieve intelligent management of cement samples ensuring objective and fair inspection data.
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Neufeld, Josh D., and William W. Mohn. "Unexpectedly High Bacterial Diversity in Arctic Tundra Relative to Boreal Forest Soils, Revealed by Serial Analysis of Ribosomal Sequence Tags." Applied and Environmental Microbiology 71, no. 10 (2005): 5710–18. http://dx.doi.org/10.1128/aem.71.10.5710-5718.2005.
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ABSTRACT Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82oN). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.
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Alimohammadi, Dariush. "Measurement of the presence of keywords and description meta‐tags on a selected number of Iranian Web sites." Online Information Review 28, no. 3 (2004): 220–23. http://dx.doi.org/10.1108/14684520410543661.
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Digital information retrieval has been as a problem, and at the same time a research interest for information scientists in recent years. They have planned some solutions to solve problems manifested during the 1990s. Designing meta‐tags and applying them to HTML documents was a remedy in this direction. Meta‐tags can help authors, publishers and indexers of Web pages to analyze intended content more precisely and efficiently. The aim of the present survey is to measure meta‐tags of the Iranian Web sites in accordance with an international criterion. To carry out the research, 346 Iranian Web sites were selected among 3,342, which represented a sample of all Web sites existed in Iranhoo, an Iranian Web directory. The source codes of the sample home pages were reviewed in terms of the presence of keywords and description meta‐tags. The findings of the survey showed that 31.5 percent and 24.6 percent of the Iranian Web sites have keywords and description meta‐tags respectively. The paper concludes that the Iranian Web sites are lower than non‐Iranian Web sites in terms of the use of meta‐tags.
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Wilson, David W., Gustavo M. Sbatella, QiQi Wang, and Stephen D. Miller. "Suitability of Passive Integrated Transponder (PIT) Tags for Tracking Weed Seed Movement in Soils." Weed Technology 24, no. 3 (2010): 386–91. http://dx.doi.org/10.1614/wt-d-09-00028.1.
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Information linking seed movement, along with changes in seed viability, is critical for understanding weed seed dynamics. Studies were conducted to examine the use of passive integrated transponder (PIT) tags placed in nylon mesh packets in combination with GPS (Global Positioning System) technology to track weed seed movement after tillage. Cylindrical PIT tags 11.5, 12, 20, and 23 mm long by 2 mm wide were evaluated in water and soil. Detection improved as tag size increased because of greater signal strength. Tags with the main axis oriented vertically were recovered at greater depths than when placed horizontally. Average detection depths for 12-mm PIT tags were 29.5 cm in water, 18.2 cm in sand, 24 cm in artificial soil, and 21.2 cm in sandy loam soil. Tests also showed that PIT tags and nylon mesh packets were resilient to intense tillage with a rototiller. No significant differences in displacement because of tillage were observed between free PIT tags and PIT-tagged packets. PIT tag performance was further tested in a 2-yr field experiment conducted between September 2003 and October 2005 at six sites in Nebraska and Wyoming. Tilled and no-till blocks were established at each site. PIT-tagged packets in the tilled block and untagged packets in the no-till block were used. Sample burial depths were 0, 2.5, 7.5, and 15 cm. Sample recovery rate did not differ between tilled and no-till blocks. Time of recovery was the main factor affecting recovery of packets buried at 0 and 2.5 cm in both blocks. Seed predation by small rodents and movement of samples beyond the area of study by tillage implements were the main sources of packet loss. Nevertheless, 2 yr after initiation of the study, more than 85% of the samples were recovered. Future development of PIT tag technology will lead to an enhanced ability to monitor seed movement.
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Brennich, Martha E., Stephanie Hutin, Katharina Weinhäupl, et al. "From size exclusion to HIS-tags: increasing sample purity for BioSAXS." Acta Crystallographica Section A Foundations and Advances 72, a1 (2016): s13. http://dx.doi.org/10.1107/s2053273316099782.
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Hu, Qian, Xin Lin, Shuguang Han, and Lei Li. "An investigation of cross-cultural social tagging behaviours between Chinese and Americans." Electronic Library 36, no. 1 (2018): 103–18. http://dx.doi.org/10.1108/el-08-2016-0173.
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Purpose The purpose of this paper is to explore different tagging behaviours between Chinese and Americans by analysing the movie tags, and explore the feasibility of applying cultural differences to tag recommendations. Design/methodology/approach This paper introduced hypotheses based on several well-established psychological theories and tested them with social tags for the same movies generated by Chinese and Americans. And to prove the utility of the cultural factor consideration, this paper conducted a cross-cultural tag recommendation experiment. Findings The results show that compared with Americans, Chinese users tend to add more tags about movies’ background information (e.g. release year) and global contextual characteristics (e.g. genre); they also prefer to add tags about production countries and factual tags, and cultural factors can be applied for recommending more accurate tags. Research limitations/implications Other reasons for tagging differences beyond cultural factors have not be explored. Tags for some sample movies in MovieLens might be unstable, as they had been tagged by a small scale of users; as a result, the tags’ type distribution might be influenced. Practical implications The results and conclusion of this study will be beneficial for the cross-cultural applications of social tags and mining users’ interests based on tags. Originality/value This paper provided a deeper investigation of the cross-cultural effect in people’s social tagging behaviours from cognitive perspective, and an empirical analysis has been performed to explore proper approaches of incorporating cultural differences for tag recommendation.
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Chavez, Rosa A., Isabel M. Valdivia, and Marcelo E. Oliva. "Local variability in metazoan parasites of the pelagic fish species, Engraulis ringens: implications for fish stock assessment using parasites as biological tags." Journal of Helminthology 81, no. 2 (2007): 113–16. http://dx.doi.org/10.1017/s0022149x07726573.
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AbstractParasites have been used successfully as biological tags in population studies, mainly in marine fishes, but also in marine mammals, crustaceans and molluscs. Almost all published information dealing with parasites as biological tags evaluates differences between localities. However, local variability in the component community has not been assessed. In this work, we examined whether local variation of the metazoan parasite fauna of Engraulis ringens, extracted from five independent samples from two nearby localities in northern Chile, can be a factor causing bias in stock identification. Our results show that local variability, as estimated by a single sample, may suffice to represent component community variability with no need for replicated data.
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Meng, Hongu, Antony Warden, Lulu Zhang, et al. "A Mass-Ratiometry-Based CD45 Barcoding Method for Mass Cytometry Detection." SLAS TECHNOLOGY: Translating Life Sciences Innovation 24, no. 4 (2019): 408–19. http://dx.doi.org/10.1177/2472630319834057.
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Mass cytometry (CyTOF) is a critical cell profiling tool in acquiring multiparameter proteome data at the single-cell level. A major challenge in CyTOF analysis is sample-to-sample variance arising from the pipetting process, staining variation, and instrument sensitivity. To reduce such variations, cell barcoding strategies that enable the combination of individual samples prior to antibody staining and data acquisition on CyTOF are often utilized. The most prevalent barcoding strategy is based on a binary scheme that cross-examines the existence or nonexistence of certain mass signals; however, it is limited by low barcoding efficiency and high cost, especially for large sample size. Herein, we present a novel barcoding method for CyTOF application based on mass ratiometry. Different mass tags with specific fixed ratios are used to label CD45 antibody to achieve sample barcoding. The presented method exponentially increases the number of possible barcoded samples with the same amount of mass tags compared with conventional methods. It also reduces the overall time for the labeling process to 40 min and avoids the need for expensive commercial barcoding buffer reagents. Moreover, unlike the conventional barcoding process, this strategy does not pre-permeabilize cells before the barcoding procedure, which offers additional benefits in preserving surface biomarker signals.
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Bernard, David R., Robert P. Marshall, and John E. Clark. "Planning programs to estimate salmon harvest with coded-wire tags." Canadian Journal of Fisheries and Aquatic Sciences 55, no. 8 (1998): 1983–95. http://dx.doi.org/10.1139/f98-069.
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Methods are presented for planning individual catch-sampling, tagging, and field-sampling programs to estimate salmon (Oncorhynchus spp.) harvest in recreational and commercial fisheries from several hatchery-produced and wild cohorts through recovery of coded-wire tags. We show how to determine sample sizes sufficiently large to detect harvest and link sample sizes to expenditures through linear and allometric cost functions to determine optimal tagging and catch-sampling rates. Sample sizes that will minimize bias and variance are charted for field-sampling programs designed to estimate the fraction of a cohort with tags. We describe sampling strategies that can be used to detect or to minimize bias in harvest estimates from tag loss, tag-induced mortality, tag-induced straying, and nonrandom sampling. Methods are demonstrated with data on cohorts of chinook (O. tshawytscha) and coho salmon (O. kisutch) from Alaska.
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Pedersen, Gitte. "Hypothesis-free biomarker discovery platform evolving into a companion diagnostic using bioinformatics." Journal of Clinical Oncology 30, no. 30_suppl (2012): 52. http://dx.doi.org/10.1200/jco.2012.30.30_suppl.52.
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52 Background: Cancer drug discovery is hypothesis driven focused on addressing specific mechanisms; however the patient’s individual tumor harbor much more diversity and therefore the biomarkers behind the hypothesis are often insufficient in explaining the differences in individual drug response. A Danish Private Public Partnership is developing biomarkers for cancer prognostics under a $30 million grant. The Danish National Biobank was established by another $20 million grant and hosts approximately 15 million biological samples associated with cradle-to-grave electronic medical records. Methods: Proposing a hypothesis-free biomarker-discovery platform using intelligent target-filtering technology integrated with sequencing short reads on a small chip addressing the sample prep and data analysis bottlenecks in current sequencing platforms. By using bioinformatics on existing sequence data it is possible to optimize the proposed strategy and develop novel diagnostic applications. The intelligent target-filtering process generates a single-stranded tag library. Because the tags are single stranded, it is possible to detect all possible tags using a universal high-throughput platform. The cost per sample is low, the content/test very high, and hypotheses free. This approach represents a paradigm shift in the biomarker-discovery process, saving significant time and money while increasing the probability of success. The diagnostic becomes a bioinformatics exercise that allows the drug discovery company to optimize the definition of responders. Results: The result of the digital gene expression experiment was compared to RNA-seq and Affymetrix whole genome array. Conclusions: The platform offers a more cost-effective way of providing an open and hypothesis free platform compared to sequencing. The platform also offers cost-effective open-ended solution for such diverse applications as expression profiling, genome wide methylation profiling, genome wide duplication/deletion analysis, environmental microbiome profiling, and single gene mutation detection with only relatively minor adjustments in how the single stranded tags are extracted from the sample.
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Kim, H. S., M. Babu, and S. J. Hong. "Microstructure And Thermoelectric Properties Of Tags-90 Compounds Fabricated By Mechanical Milling Process." Archives of Metallurgy and Materials 60, no. 2 (2015): 1231–34. http://dx.doi.org/10.1515/amm-2015-0104.
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Abstract TAGS-90 compound powder was directly prepared from the elements by high-energy ball milling (HEBM) and subsequently consolidated by a spark plasma sintering (SPS). Effect of milling time on the microstructure and thermoelectric properties of the samples were investigated. The particle size of fabricated powders were decreased with increasing milling time, finally fine particles with ~1μm size was obtained at 90 min. The SPS samples exhibited higher relative densities (>99%) with fine grain size. X-ray diffraction analysis (XRD) and energy dispersion analysis (EDS) results revealed that all the samples were single phase of GeTe with exact composition. The electrical conductivity of samples were decreased with milling time, whereas Seebeck coefficient increased over the temperature range of RT~450°C. The highest power factor was 1.12×10−3W/mK2 obtained for the sample with 90 min milling at 450°C.
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Blomberg, L., T. Sonstegard, C. Van Tassell, and K. Zuelke. "213 SAGE ANALYSIS OF TRANSITIONS IN THE PORCINE CONCEPTUS TRANSCRIPTOME DURING TROPHECTODERM ELONGATION." Reproduction, Fertility and Development 17, no. 2 (2005): 257. http://dx.doi.org/10.1071/rdv17n2ab213.
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Rapid elongation of the pre-implantation conceptus trophectoderm between gestational days 11 and 12 represents a critical developmental period in swine. Serial analysis of gene expression (SAGE) in ovoid (Ovd; 7 mm diameter) and filamentous (Fil; 150 mm length) conceptuses has identified unique transcriptomes associated with these transitional states. The initial utility of SAGE prompted an investigation of the intermediate tubular conceptus (Tub; 15–20 mm length) as well as the development of micro-SAGE methodologies, small-amplified RNA-SAGE (SAR-SAGE) and PCR-amplified SAGE (m-SAGE), for future use with early pre-implantation conceptus stages. Total RNA from in vivo-derived Tub conceptuses was used to construct an unamplified SAGE library (Tub SAGE) and two micro-SAGE libraries (160X less template RNA) by SAR-SAGE and m-SAGE. Comparative analyses of the amplification proportionality between the Tub SAGE and amplified libraries, consisting of 12,000 tags each, demonstrated that SAR-SAGE was a more reliable amplification method. Seventy-five percent of the SAR-SAGE tags, in contrast to 43% of m-SAGE tags, had less than a 2-fold frequency difference when compared to Tub SAGE tags occurring at least 10 times in a library. The Tub SAGE library size was extended to a total of 42,415 tags representing 12,779 unique putative transcripts. Comparing the Tub SAGE tags with previously generated Ovd and Fil SAGE libraries (NCBI GEO Acc. Nos. GSM24470 and GSM24471, respectively) yielded a total of 33,191 unique tags, of which 3,575 tags (10.8%) were common to all three libraries. Chi-square-based analyses (SAGE2000 software; 1997 Gen. Res. 7, 986–995) of the tag frequencies revealed the differential expression of 479 tags between Ovd:Tub libraries and 362 tags between Tub:Fil libraries at a P < 0.05 significance. The Tub SAGE tags were annotated following batch BLASTS against the TIGR porcine index database and then classified according to function. Real-time RT-PCR was used to confirm the differential expression patterns identified between Ovd:Tub, Ovd:Fil, and Fil:Tub. For example, the relative quantity of mRNA for steroidogenic acute regulatory protein, 1.0:6.4:11.1 (Ovd:Tub:Fil), and cytokeratin 8, 1.1:0.6:0.4 (Ovd:Tub:Fil), demonstrated an increase and decrease (ANOVA; P < 0.05), respectively, throughout these three developmental stages. Based on their putative functional annotations, the differentially expressed genes revealed by SAGE are potentially involved in regulating embryo growth, cellular differentiation, apoptosis, steroidogenesis, and energy metabolism during embryo elongation. The present SAGE analyses have elucidated the tubular conceptus transcriptome and enabled the identification of genes that are differentially regulated during the 24-h period that encompasses pig embryo elongation. Furthermore, the decreased template requirement of SAR-SAGE makes this technique a suitable option for SAGE analyses of early stage embryos where the sample is small and limited.
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Deng, Zhen-Shan, Xiao-Dong Liu, Bao-Cheng Zhang, et al. "The Root Endophytic Fungi Community Structure of Pennisetum sinese from Four Representative Provinces in China." Microorganisms 7, no. 9 (2019): 332. http://dx.doi.org/10.3390/microorganisms7090332.
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Pennisetum sinese is a good forage grass with high biomass production and crude proteins. However, little is known about the endophytic fungi diversity of P. sinese, which might play an important role in the plant’s growth and biomass production. Here, we used high throughput sequencing of the Internal Transcribed Spacer (ITS) sequences based on primers ITS5-1737 and ITS2-2043R to investigate the endophytic fungi diversity of P. sinese roots at the maturity stage, as collected from four provinces (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China). The ITS sequences were processed using QIIME and R software. A total of 374,875 effective tags were obtained, and 708 operational taxonomic units (OTUs) were yielded with 97% identity in the five samples. Ascomycota and Basidiomycota were the two dominant phyla in the five samples, and the genera Khuskia and Heydenia were the most abundant in the FJ and XJ samples, respectively, while the most abundant tags in the other three samples could not be annotated at the genus level. In addition, our study revealed that the FJ sample possessed the highest OTU numbers (242) and the NS sample had the lowest (86). Moreover, only 22 OTUs were present in all samples simultaneously. The beta diversity analysis suggested a division of two endophytic fungi groups: the FJ sample from the south of China and the other four samples from north or northwest China. Correlation analysis between the environmental factors and endophytic fungi at the class level revealed that Sordariomycetes and Pucciniomycetes had extremely significant positive correlations with the total carbon, annual average precipitation, and annual average temperature, while Leotiomycetes showed an extremely significant negative correlation with quick acting potassium. The results revealed significant differences in the root endophytic fungi diversity of P. sinese in different provinces and might be useful for growth promotion and biomass production in the future.
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Lin, Y. F., C. T. Liao, H. M. Chen, and Z. D. Jiang. "Compact folded square‐loop antenna for reading near‐field RFID tags in blood sample tracking system." Electronics Letters 53, no. 25 (2017): 1627–28. http://dx.doi.org/10.1049/el.2017.1859.
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Marchiori, Patricia Zeni, Andre Luiz Appel, Eduardo Michellotti Bettoni, Denise Fukumi Tsunoda, and Frank Coelho de Alcântara. "Elements of social representation theory incollaborative tagging systems." Transinformação 26, no. 1 (2014): 27–37. http://dx.doi.org/10.1590/s0103-37862014000100004.
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This article discusses the information representation process based on the Moscovici's Social Representation Theory and domain analysis in Information Science. The aim was to identify mechanisms and constituent dimensions of social representation in collaborative tagging systems/social bookmarking systems. Scientific knowledge was defined as the object/phenomenon of representation in these systems; and the tag as the shareable structure of meaning that connects participants and resources. The empirical research involved descriptive statistical techniques applied to a corpora of tags available in CiteULike, which is a social tagging system developed for the academic community. The data analysis, performed in a sample of groups derived from the dataset, showed that the users' reuse of their own tags resembles the anchorage mechanism. The reuse of tags by other participants - in the same group - reveals some evidence of the objectification mechanism. Some speculation arose about the cognitive effort made by the individual, under group influence, with regard to the tagging activity, user's choice of resources, and sharing styles. Further studies on social bookmarking systems depend both on a "gain scale" of users and items tagged, requiring techniques and procedures redesigned by Information Science, Statistics, Network Analysis, Linguistics/Sociolinguistics and Social Psychology.
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Wilson, David, and Norelle L. Daly. "Nuclear Magnetic Resonance seq (NMRseq): A New Approach to Peptide Sequence Tags." Toxins 10, no. 11 (2018): 437. http://dx.doi.org/10.3390/toxins10110437.
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Structural analysis of peptides with nuclear magnetic resonance (NMR) spectroscopy generally relies on knowledge of the primary sequence to enable assignment of the resonances prior to determination of the three-dimensional structure. Resonance assignment without knowledge of the sequence is complicated by redundancy in amino acid type, making complete de novo sequencing using NMR spectroscopy unlikely to be feasible. Despite this redundancy, we show here that NMR spectroscopy can be used to identify short sequence tags that can be used to elucidate full-length peptide sequences via database searching. In the current study, we have used this approach to identify conotoxins from the venom of the cone snail Conus geographus and determined the three-dimensional structure of a member of the I3 superfamily. This approach is most likely to be useful for the characterization of disulfide-rich peptides, such as those that were chosen for this study, as they generally have well-defined structures, which enhances the quality of the NMR spectra. In contrast to other sequencing methods, the lack of sample manipulation, such as protease digestion, allows for subsequent bioassays to be carried out using the native sample used for sequence identification.
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Levytskyi, S. M. "Influence of laser radiation on optical transparent dielectrics." Physics and Chemistry of Solid State 21, no. 2 (2020): 279–83. http://dx.doi.org/10.15330/pcss.21.2.279-283.
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This paper deals with the main characteristics of the influence of pulsed laser radiation and its application for the labeling of transparent dielectrics. On the basis of the analysis of the literature data and the study of the possibilities of using laser radiation for marking different materials, it is proposed to investigate the effect of the radiation wavelength on the size of the received defect inside the material. Experimentally shown that the pulse laser processing of samples with laser irradiation energy below 3.4 mJ/cm2 visual tags in the sample are not formed. Thus, you can control the geometric dimensions of the mark.
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Shatz, Itamar. "Refining and modifying the EFCAMDAT." International Journal of Learner Corpus Research 6, no. 2 (2020): 220–36. http://dx.doi.org/10.1075/ijlcr.20009.sha.
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Abstract This report outlines the development of a new corpus, which was created by refining and modifying the largest open-access L2 English learner database – the EFCAMDAT. The extensive data-curation process, which can inform the development and use of other corpora, included procedures such as converting the database from XML to a tabular format, and removing problematic markup tags and non-English texts. The final dataset contains two corresponding samples, written by similar learners in response to different prompts, which represents a unique research opportunity when it comes to analyzing task effects and conducting replication studies. Overall, the resulting corpus contains ~406,000 texts in the first sample and ~317,000 texts in the second sample, written by learners representing diverse L1s and a large range of L2 proficiency levels.
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Figeys, D., and R. Aebersold. "Microfabricated Modules for Sample Handling, Sample Concentration and Flow Mixing: Application to Protein Analysis by Tandem Mass Spectrometry." Journal of Biomechanical Engineering 121, no. 1 (1999): 7–12. http://dx.doi.org/10.1115/1.2798048.
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The comprehensive analysis of biological systems requires a combination of genomic and proteomic efforts. The large-scale application of current genomic technologies provides complete genomic DNA sequences, sequence tags for expressed genes (EST’s), and quantitative profiles of expressed genes at the mRNA level. In contrast, protein analytical technology lacks the sensitivity and the sample throughput for the systematic analysis of all the proteins expressed by a tissue or cell. The sensitivity of protein analysis technology is primarily limited by the loss of analytes, due to adsorption to surfaces, and sample contamination during handling. Here we summarize our work on the development and use of microfabricated fluidic systems for the manipulation of minute amounts of peptides and delivery to an electrospray ionization tandem mass spectrometer. New data are also presented that further demonstrate the potential of these novel approaches. Specifically, we describe the use of microfabricated devices as modules to deliver femtomole amounts of protein digests to the mass spectrometer for protein identification. We also describe the use of a microfabricated module for the generation of solvent gradients at nl/min flow rates for gradient chromatography-tandem mass spectrometry. The use of microfabricated fluidic systems reduces the risk of sample contamination and sample loss due to adsorption to wetted surfaces. The ability to assemble dedicated modular systems and to operate them automatically makes the use of microfabricated systems attractive for the sensitive and large-scale analysis of proteins.
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Smith, Nicholas, and Cathleen Waters. "Variation and change in a specialized register." International Journal of Corpus Linguistics 24, no. 2 (2019): 169–201. http://dx.doi.org/10.1075/ijcl.17117.smi.
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Abstract Corpus-based studies of specialized registers typically sample texts using random methods as far as possible, but they disregard social characteristics of the speakers/writers. In contrast, in corpus-based studies of conversation and quantitative sociolinguistic studies, sampling is more typically designed to optimize social representation. To our knowledge, this study is the first to compare linguistic outcomes from random versus sociolinguistic sampling in a specialized register. Our data comes from the biographical radio chat show, Desert Island Discs (DID), at different points in time. We constructed two versions of a DID corpus: a sociolinguistic judgment sample based on guest demographics, and a random sample. We compare grammatical usage between them using an inductive (‘key POS-tags’) method and close manual analysis, uncovering some evidence of significant grammatical differences between the samples and differing patterns of diachronic change. We discuss the implications of our research for corpus design, representativeness and analysis in specialized registers.
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Yu, Qing, Haopeng Xiao, Mark P. Jedrychowski, et al. "Sample multiplexing for targeted pathway proteomics in aging mice." Proceedings of the National Academy of Sciences 117, no. 18 (2020): 9723–32. http://dx.doi.org/10.1073/pnas.1919410117.
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Pathway proteomics strategies measure protein expression changes in specific cellular processes that carry out related functions. Using targeted tandem mass tags-based sample multiplexing, hundreds of proteins can be quantified across 10 or more samples simultaneously. To facilitate these highly complex experiments, we introduce a strategy that provides complete control over targeted sample multiplexing experiments, termed Tomahto, and present its implementation on the Orbitrap Tribrid mass spectrometer platform. Importantly, this software monitors via the external desktop computer to the data stream and inserts optimized MS2 and MS3 scans in real time based on an application programming interface with the mass spectrometer. Hundreds of proteins of interest from diverse biological samples can be targeted and accurately quantified in a sensitive and high-throughput fashion. It achieves sensitivity comparable to, if not better than, deep fractionation and requires minimal total sample input (∼10 µg). As a proof-of-principle experiment, we selected four pathways important in metabolism- and inflammation-related processes (260 proteins/520 peptides) and measured their abundance across 90 samples (nine tissues from five old and five young mice) to explore effects of aging. Tissue-specific aging is presented here and we highlight the role of inflammation- and metabolism-related processes in white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community.
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Fiers, Floor. "Hiding Traces of Status Seeking: Contradictory Tagging Strategies on Instagram." Social Media + Society 6, no. 2 (2020): 205630512093731. http://dx.doi.org/10.1177/2056305120937318.
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The prevailing presence of social media in the twenty-first century has changed processes of self-presentation. This study questions how Instagram users employ the platform’s tagging features to claim and seek status. Content analysis on a random sample of 787 posts carrying the hashtag “instagood” revealed that they utilize the tagging affordances to make their audience aware of their capital. In addition to displaying their capital through tags, however, users employ hashtags and account tags to increase their visibility on the platform. Interestingly, analysis shows the prevalence of attempts to conceal these obvious paratextual status-seeking strategies. Over half of the Instagram posts in the sample showed traces of the creators taking active steps to hide their use of like-hunter hashtags, through which users explicitly ask other Instagrammers for likes and follows. This finding builds upon Marwick’s concept of aspirational production: The perfecting of one’s online presentation does not only happen by producing a high-status image, but also by concealing the “inauthentic” nature of this production. Furthermore, the fact that traces of obvious status seeking can be found online implies that the lines between Goffman’s front- and backstage are blurred in the digital age.
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Eastwood, L. C., C. A. Boykin, M. K. Harris, et al. "National Beef Quality Audit-2016: Transportation, mobility, and harvest-floor assessments of targeted characteristics that affect quality and value of cattle, carcasses, and by-products1." Translational Animal Science 1, no. 2 (2017): 229–38. http://dx.doi.org/10.2527/tas2017.0029.
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Abstract The National Beef Quality Audit-2016 (NBQA-2016) was conducted to assess current transportation, mobility, and quality characteristics of U.S. fed steers and heifers. Data were collected at 17 beef processing facilities between March and November 2016. About 8,000 live cattle were evaluated for transportation and mobility, and about 25,000 carcasses were evaluated on the slaughter floor. Cattle were in transit to the slaughter facility for a mean duration of 2.7 h from a mean distance of 218.5 km using trailers with dimensions ranging from 17.84 m2 to 59.09 m2. Area allotted per animal averaged 1.13 m2 and ranged from 0.85 m2 to 2.28 m2. A total of 96.8% of cattle received a mobility score of 1 (walks easily, no apparent lameness). Identification types (35.1% had multiple) were lot visual tags (61.5%), individual tags (55.0%), electronic tags (16.9%), metal-clip tags (9.2%), bar-coded tags (0.05%), wattles (0.01%), and other (2.6%). Cattle were black-hided (57.8%), Holstein (20.4%), red-hided (10.5%), yellow-hided (4.8%), gray-hided (2.9%), brown-hided (1.3%), and white-hided (1.1%). Unbranded hides were observed on 74.3% of cattle; 18.6% had brands located on the butt, 6.3% on the side, and 1.3% on the shoulder (values exceed 100% due to multiple brands). For hide-on carcasses, 37.7% displayed no mud or manure; specific locations for mud or manure were legs (40.8%), belly (33.0%), tail region (15.5%), side (6.8%), and top-line (3.9%). Cattle without horns represented 83.3% of the sample, and cattle that did have horns measured: &lt; 2.54 cm (5.5%), 2.54 to 12.7 cm (8.3%), and &gt; 12.7 cm (2.9%). Carcasses without bruises represented 61.1% of those sampled, whereas 28.2% had 1, 8.2% had 2, 2.1% had 3, and 0.3% had 4 bruises. Of those carcasses with a bruise, the bruise was located on the loin (29.7%), round (27.8%), chuck (16.4%), rib (14.4%), and brisket/plate/flank (11.6%). Frequencies of offal condemnations were livers (30.8%), lungs (18.2%), viscera (16.3%), hearts (11.1%), heads (2.7%), and tongues (2.0%). Compared to NBQA-2011, fewer cattle were identified for traceability, fewer were black-hided, a greater number were Holstein cattle, more with no brand and no horns, fewer without bruises, more liver, lung, and viscera condemnations, and fewer heads and tongues were condemned. The NBQA remains an influential survey for the U.S. beef industry to provide benchmarks and strategic plans for continued improvement of beef quality and consistency.
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Hafrén, Anders, and Kristiina Mäkinen. "Purification of viral genome-linked protein VPg from potato virus A-infected plants reveals several post-translationally modified forms of the protein." Journal of General Virology 89, no. 6 (2008): 1509–18. http://dx.doi.org/10.1099/vir.0.83649-0.
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In order to be able to analyse post-translational modifications and protein interactions of viral genome-linked protein VPg taking place during potato virus A (PVA) infection, an affinity tag-based purification system was developed by inserting a sequence encoding a six-histidine and haemagglutinin (HisHA) tag to the 3′ end of the VPg coding sequence within the infectious cDNA clone of PVA. The engineered virus was fully functional and the HisHA tag-encoding sequence remained stable in the PVA genome throughout the infection process. Purification under denaturing conditions resulted in a protein sample that contained multiple VPg and NIa forms carrying post-translational modifications that altered their isoelectric points. Non-modified tagged VPg (pI 8) was a minor product in the protein sample derived from total leaf proteins, but when the replication-associated membranes were used as starting material, its relative amount increased. Further characterization demonstrated that some of the PVA VPg isoforms were modified by multiple phosphorylation events. Purity of the proteins derived from the native purifications with either of the tags was evaluated. A clearly purer VPg sample was obtained by performing tandem affinity purification utilizing both tags sequentially. NIb, CI and HC-Pro co-purified in an affinity-tagged VPg-dependent manner, indicating that the system was able to isolate protein complexes operating during PVA infection.
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Musselman, W. Chris, Thomas A. Worthington, Joshua Mouser, Desiree M. Williams, and Shannon K. Brewer. "Passive Integrated Transponder Tags: Review of Studies on Warmwater Fishes With Notes on Additional Species." Journal of Fish and Wildlife Management 8, no. 2 (2017): 353–64. http://dx.doi.org/10.3996/122016-jfwm-091.
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Abstract Although numerous studies have assessed retention and survival of passive integrated transponder (PIT) tags, data are scattered and information gaps remain for many diminutive fishes. Our study objectives were to 1) systematically review PIT tag studies and summarize retention, growth, and survival data for warmwater fishes; and 2) conduct a laboratory study to evaluate the retention, survival, and growth effects of intracoelomic-placed, half duplex PIT tags on six small-bodied species common to warmwater streams. Our systematic review suggested small sample sizes were common within PIT tag retention and survival studies (39% with n ≤ 20) and that many experiments (15%, 14 of 97) failed to use control fish as part of their evaluations. Studies focused primarily on short-term changes (15 d to 2 y) in tag retention and survival. Tag retention was equal to or greater than 90% in 85% of the experiments reviewed and median survival was 92%. Growth was reported by fishes in the majority of reviewed studies. We found similar results after PIT tagging (peritoneum tagging using 12- or 23-mm half duplex tags) adult Cardinal Shiner Luxilus cardinalis, Central Stoneroller Campostoma annomalum, Greenside Darter Etheostoma blennioides, Orangethroat Darter Etheostoma spectabile, Slender Madtom Noturus exilis, and juvenile Smallmouth Bass Micropterus dolomieu. Tag retention for all species was high, with only one tag loss recorded after 60 d. Survival was also high (≥88%) for all of our species with the exception of Orangethroat Darter (56% survival). No significant difference in mean growth between treatment and control groups was found. Both our results and the findings of the literature review suggested generally high tag retention and low mortality in tagged fishes (across 31 species reviewed). However, within our study (e.g., Orangethroat Darter) and from the literature, examples of negative effects of PIT tagging on fishes were apparent, suggesting methodological testing is prudent before using PIT tags in field studies. We suggest future studies would benefit from addressing the behavioral implications that may be associated with tagging and examination of longer-term tag retention. Furthermore, standard reporting (i.e., sample sizes) in PIT tag studies would be beneficial, and use of control subjects or groups for statistical comparisons is needed.
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Bailey, R. E., L. Margolis, and C. Groot. "Estimating Stock Composition of Migrating Juvenile Fraser River (British Columbia) Sockeye Salmon, Oncorhynchus nerka, Using Parasites as Natural Tags." Canadian Journal of Fisheries and Aquatic Sciences 45, no. 4 (1988): 586–91. http://dx.doi.org/10.1139/f88-071.
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Simulated mixtures of juvenile sockeye salmon (Oncorhynchus nerka) were constructed using parasite data to represent proportionally the major component stocks of Fraser River and Lake Washington sockeye migrating within the Strait of Georgia, British Columbia, in 1982–84. Samples of migrating juveniles were also collected from Bedwell Harbour, South Pender Island, British Columbia, each year and analyzed for parasites and stock composition. The compositions of simulated and sample mixtures were estimated using a maximum likelihood stock composition model. Simulated mixture compositions were accurately estimated for most stocks for all year-classes. When significant misassignment occurred between stocks, the stocks were analyzed as a complex using the allocate-sum procedure. Sample mixture estimates correctly identified the dominant stock for each year-class, although for 1984 the dominant group was determined as a complex of three stocks because the individual stocks were not distinguishable. The results indicate that it is feasible to use parasites as natural tags to estimate stock compositions of migrating juvenile sockeye salmon in the Strait of Georgia.
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Bąchor, Remigiusz, Mateusz Waliczek, Piotr Stefanowicz, and Zbigniew Szewczuk. "Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics." Molecules 24, no. 4 (2019): 701. http://dx.doi.org/10.3390/molecules24040701.
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Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application.
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Daud, Ali, Jamal Ahmad Khan, Jamal Abdul Nasir, Rabeeh Ayaz Abbasi, Naif Radi Aljohani, and Jalal S. Alowibdi. "Latent Dirichlet Allocation and POS Tags Based Method for External Plagiarism Detection." International Journal on Semantic Web and Information Systems 14, no. 3 (2018): 53–69. http://dx.doi.org/10.4018/ijswis.2018070103.
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In this article we present a new semantic and syntactic-based method for external plagiarism detection. In the proposed approach, latent dirichlet allocation (LDA) and parts of speech (POS) tags are used together to detect plagiarism between the sample and a number of source documents. The basic hypothesis is that considering semantic and syntactic information between two text documents may improve the performance of the plagiarism detection task. Our method is based on two steps, naming, which is a pre-processing where we detect the topics from the sentences in documents using the LDA and convert each sentence in POS tags array; then a post processing step where the suspicious cases are verified purely on the basis of semantic rules. For two types of external plagiarism (copy and random obfuscation), we empirically compare our approach to the state-of-the-art N-gram based and stop-word N-gram based methods and observe significant improvements.
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Chen, Yi-Jhen, Yuan-Yu Chen, Kai-Hao Wang, et al. "Integration of a Thermoelectric Heating Unit with Ionic Wind-Induced Droplet Centrifugation Chip to Develop Miniaturized Concentration Device for Rapid Determination of Salmonella on Food Samples Using Antibody-Functionalized SERS Tags." Sensors 20, no. 24 (2020): 7177. http://dx.doi.org/10.3390/s20247177.
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When a centrifugation-enriched sample of 100 μL containing the surface-enhanced Raman scattering (SERS) tag-bound bacteria (Salmonella in this study) is siphoned onto a glass slide next to an embedded thermoelectric heating chip, such a sessile droplet is quickly evaporated. As the size of the sample droplet is significantly reduced during the heating process, ionic wind streams from a corona discharge needle, stationed above the sample, sweep across the liquid surface to produce centrifugal vortex flow. Tag-bound Salmonella in the sample are then dragged and trapped at the center of droplet bottom. Finally, when the sample is dried, unlike the “coffee ring” effect, the SERS tag-bound Salmonella is concentrated in one small spot to allow sensitive detection of a Raman signal. Compared with our previous electrohydrodynamic concentration device containing only a corona discharge needle, this thermoelectric evaporation-assisted device is more time-effective, with the time of concentrating and drying about 100 μL sample reduced from 2 h to 30 min. Hence, sample throughput can be accelerated with this device for practical use. It is also more sensitive, with SERS detection of a few cells of Salmonella in neat samples achievable. We also evaluated the feasibility of using this device to detect Salmonella in food samples without performing the culturing procedures. Having spiked a few Salmonella cells into ice cubes and lettuce leaves, we use filtration and ultracentrifugation steps to obtain enriched tag-bound Salmonella samples of 200 μL. After loading an aliquot of 100 μL of sample onto this concentration device, the SERS tag signals from samples of 100 g ice cubes containing two Salmonella cells and 20 g lettuce leaf containing 5 Salmonella cells can be successfully detected.
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Brickle, Paul, and Ken MacKenzie. "Parasites as biological tags for Eleginops maclovinus (Teleostei: Eleginopidae) around the Falkland Islands." Journal of Helminthology 81, no. 2 (2007): 147–53. http://dx.doi.org/10.1017/s0022149x07750514.
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AbstractThis is the first study of the parasite fauna of Eleginops maclovinus in the Falkland Islands. It was undertaken to catalogue the parasite fauna of E. maclovinus in order to provide a baseline for future studies and to determine whether parasites might be used as biological tags. Between 21 January and 17 March 2002 samples were taken from three stations, Teal Creek (30 fish), Port Louis (30 fish) and Camilla Creek (10 fish), all in East Falkland, and examined for protozoan and metazoan parasites. Twenty-four parasite taxa were recorded, of which three were possible new species, two new host records and five new geographical records. Because of the small number of fish in the Camilla Creek sample it was excluded from further analyses. E. maclovinus is a protandrous hermaphrodite and all fish greater than 53 cm total length were found to be female, so these too were excluded from further analyses. The parasite data from the remaining fish were analysed by an agglomerative hierarchical cluster analysis using an average linkage and a Jaccard measure of similarity, followed by a linear discriminant function analysis (LDA). Both analyses misclassified only one fish from Port Louis as being from Teal Creek, with the LDA giving an overall correct classification of 97.5% (39/40). The results support mechanical tagging data in suggesting that smaller male E. maclovinus are resident in the creeks in which they are caught, and that at this stage of their lives they tend not to migrate over long distances.
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Chen, Jianjun, Miao Sun, Roger T. Luo, et al. "Genes Similarly Abnormally Expressed in Both Human and Murine MLL-Associated Leukemia." Blood 106, no. 11 (2005): 3000. http://dx.doi.org/10.1182/blood.v106.11.3000.3000.
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Abstract Although more than 50 different loci translocate to the MLL gene at chromosome band 11q23, resulting in either acute myeloid leukemia (AML) or acute lymphoblastic leukemia (ALL), no unifying property is shared by all partner genes. The translocations result in a functional fusion of the N-terminal part of MLL gene and the C-terminal part of each partner gene, presumably leading to changes in the expression of the normal target genes, most of which have not been identified. Although genetically engineered mouse leukemia models have been widely used, few systematic studies have evaluated whether such models are valid equivalents of human leukemia. We used serial analysis of gene expression (SAGE) to obtain genome-wide gene expression profiles in normal myeloid progenitor cells from human CD15+ and mouse Gr-1+ cells. We also analyzed four patient samples (two with each fusion) and two retrovirally-induced mouse leukemias containing either MLL-ELL [t(11;19)(q23;p13.1)] or MLL-ENL [t(11;19)(q23;p13.3)] fusions, and a cell line from a leukemia mouse transduced with an MLL-ELL fusion. MLL-ELL and MLL-ENL fusions are frequently involved in human AML, while MLL-ENL is also seen in human ALL. 484,303 SAGE tags were identified from the nine samples (40,000 to 100,000 tags per sample), yielding 103,899 unique SAGE tags in the human and 60,993 in the mouse samples. Analysis of the SAGE data identified 43 candidate genes that appear to be abnormally expressed in both human and mouse myeloid leukemia progenitor cells with either MLL-ELL or MLL-ENL fusions (9 up-regulated and 34 down-regulated; Table 1). Increasing evidence suggests that endogenous antisense RNAs may play critical roles in gene regulation and cancer. Natural antisense RNAs include cis-encoded antisense RNAs transcribed from the opposite strand of the same genomic locus as the sense target genes, and trans-encoded antisense RNAs such as microRNAs (miRNAs) transcribed from a genomic locus different from the sense target genes. 26 of the 43 candidate genes have antisense partners (with a total of 7 cis-encoded antisense RNAs and 36 trans-encoded miRNAs) and thereby might be regulated by endogenous antisense RNAs. We are currently validating the expression pattern of the 43 candidate genes in at least 30 different human and mouse leukemia and normal control samples with quantitative RT-PCR, and measuring the level of expression of all known miRNAs via microarray in these samples. Our studies on the abnormally expressed genes and their potential antisense partners will provide important insights into the complex functional pathways related to MLL rearrangements in the development of acute leukemia, which may lead to more effective therapy for these leukemias. Table 1. Genes deregulated in both human and mouse leukemiasa Total number Up-regulated genes Down-regulated genes Genes with antisense partner(s) aThe genes have at least 3 fold difference in expression with a significance P &lt; 0.05 between each leukemia sample and the normal control sample. In MLL-ELL fusions 21 1 20 12 In MLL-ENL fusions 33 8 25 21 In both types of fusions 11 0 11 7 Total unique genes 43 9 34 26
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Pepping, Michelle Y., Sean M. O’Rourke, Connie Huang, Jacob V. E. Katz, Carson Jeffres, and Michael R. Miller. "Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids." PLOS ONE 15, no. 11 (2020): e0239221. http://dx.doi.org/10.1371/journal.pone.0239221.
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Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.
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Higuchi, Rumi, Taichiro Goto, Yosuke Hirotsu, et al. "Streptococcus australis and Ralstonia pickettii as Major Microbiota in Mesotheliomas." Journal of Personalized Medicine 11, no. 4 (2021): 297. http://dx.doi.org/10.3390/jpm11040297.
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The microbiota has been reported to be correlated with carcinogenesis and cancer progression. However, its involvement in the pathology of mesothelioma remains unknown. In this study, we aimed to identify mesothelioma-specific microbiota using resected or biopsied mesothelioma samples. Eight mesothelioma tissue samples were analyzed via polymerase chain reaction (PCR) amplification and 16S rRNA gene sequencing. The operational taxonomic units (OTUs) of the effective tags were analyzed in order to determine the taxon composition of each sample. For the three patients who underwent extra pleural pneumonectomy, normal peripheral lung tissues adjacent to the tumor were also included, and the same analysis was performed. In total, 61 OTUs were identified in the tumor and lung tissues, which were classified into 36 species. Streptococcus australis and Ralstonia pickettii were identified as abundant species in almost all tumor and lung samples. Streptococcus australis and Ralstonia pickettii were found to comprise mesothelioma-specific microbiota involved in tumor progression; thus, they could serve as targets for the prevention of mesothelioma.
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Gu, Guorong, Weizhong Cheng, Chenling Yao, et al. "Quantitative Proteomics Analysis by Isobaric Tags for Relative and Absolute Quantitation Identified Lumican as a Potential Marker for Acute Aortic Dissection." Journal of Biomedicine and Biotechnology 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/920763.
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Acute aortic dissection (AAD) is a serious vascular disease. Currently the diagnosis relies on clinical and radiological means whereas serum biomarkers are lacking. The purpose of this study was to identify potential serum biomarkers for AAD using isobaric tags for relative and absolute quantitation (iTRAQ) approach. A total of 120 serum samples were collected from three groups: AAD patients (n=60), patients with acute myocardial infarction (AMI,n=30), and healthy volunteers (n=30), whereas the first 10 samples from each group were used for iTRAQ analysis. Using iTRAQ approach, a total of 174 proteins were identified as significantly different between AAD patients and healthy subjects. Among them, forty-six proteins increased more than twofold, full-scale analysis using serum sample for the entire 120 subjects demonstrated that Lumican level was significantly increased relative to control and AMI samples. Further, Lumican level correlated with time from onset to admission in AAD but not AMI samples. Using iTRAQ approach, our study showed that Lumican may be a potential AAD-related serum marker that may assist the diagnosis of AAD.
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Aguilar, Alberto, Adeline Boyreau, and Pierre Bon. "Label-free super-resolution imaging below 90-nm using photon-reassignment." Open Research Europe 1 (March 24, 2021): 3. http://dx.doi.org/10.12688/openreseurope.13066.1.
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Background: Achieving resolutions below 100 nm is key for many fields, including biology and nanomaterial characterization. Although nearfield and electron microscopy are the gold standards for studying the nanoscale, optical microscopy has seen its resolution drastically improve in the last decades. So-called super-resolution microscopy is generally based on fluorescence photophysics and requires modification of the sample at least by adding fluorescent tags, an inevitably invasive step. Therefore, it remains very challenging and rewarding to achieve optical resolutions beyond the diffraction limit in label-free samples. Methods: Here, we present a breakthrough to unlock label-free 3D super-resolution imaging of any object including living biological samples. It is based on optical photon-reassignment in confocal reflectance imaging mode. Results: We demonstrate that we surpass the resolution of all fluorescence-based confocal systems by a factor ~1.5. We have obtained images with a 3D (x,y,z) optical resolution of (86x86x248) nm3 using a visible wavelength (445 nm) and a regular microscope objective (NA=1.3). The results are presented on nanoparticles as well as on (living) biological samples. Conclusions: This cost-effective approach double the resolution of reflectance confocal microscope with minimal modifications. It is therefore compatible with any microscope and sample, works in real-time, and does not require any signal processing.
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Kwon, Jaimyoung, and Pravin Varaiya. "Real-Time Estimation of Origin–Destination Matrices with Partial Trajectories from Electronic Toll Collection Tag Data." Transportation Research Record: Journal of the Transportation Research Board 1923, no. 1 (2005): 119–26. http://dx.doi.org/10.1177/0361198105192300113.
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The origin–destination (O-D) matrix of a traffic network is usually estimated from link traffic counts combined with a sample survey. Partially observed vehicle trajectories obtained with vehicle reidentification or automatic vehicle identification techniques such as electronic tags provide a new data source for real-time O-D matrix estimation. However, because of incomplete sampling, accurate estimation of O-D matrices from these data is not trivial. A statistical model was developed for such data, and an unbiased estimator of the O-D matrix was derived based on the method of moments. With further exploitation of the sound statistical model, the bootstrap standard error estimate of the O-D matrix estimator was also developed. The algorithm can be computed quickly and performs well under simulation compared with simpler estimators. Applied to data from vehicles with electronic toll collection tags in the San Francisco Bay Area, the algorithm produces a realistic time series of the hourly O-D matrix. The relationship of the proposed estimator with similar methods in the literature was also studied and extension of the methods to general, more complex networks is discussed.
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Binan, Loïc, Elliot A. Drobetsky, and Santiago Costantino. "Exploiting Molecular Barcodes in High-Throughput Cellular Assays." SLAS TECHNOLOGY: Translating Life Sciences Innovation 24, no. 3 (2019): 298–307. http://dx.doi.org/10.1177/2472630318824337.
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Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.
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Dunkley, T. P. J., P. Dupree, R. B. Watson, and K. S. Lilley. "The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana." Biochemical Society Transactions 32, no. 3 (2004): 520–23. http://dx.doi.org/10.1042/bst0320520.
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Organelle proteomics is the analysis of the protein contents of a subcellular compartment. Proteins identified in subcellular proteomic studies can only be assigned to an organelle if there are no contaminants present in the sample preparation. As a result, the majority of plant organelle proteomic studies have focused on the chloroplast and mitochondria, which can be isolated relatively easily. However, the isolation of components of the endomembrane system is far more difficult due to their similar sizes and densities. For this reason, quantitative proteomics methods are being developed to enable the assignment of proteins to a specific component of the endomembrane system without the need to obtain pure organelles.
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Papp, Gergely, Christopher Rossi, Robert Janocha, et al. "Towards a compact and precise sample holder for macromolecular crystallography." Acta Crystallographica Section D Structural Biology 73, no. 10 (2017): 829–40. http://dx.doi.org/10.1107/s2059798317013742.
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Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of miniSPINE was tested at different institutes using evaluation kits, and pilot beamlines are being equipped with compatible robotics for large-scale evaluation. A companion paper describes a new sample changer FlexED8 (Pappet al., 2017,Acta Cryst., D73, 841–851).
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Bradford, Russell W., Peta Hill, Campbell Davies, and Peter Grewe. "A new tool in the toolbox for large-scale, high-throughput fisheries mark-recapture studies using genetic identification." Marine and Freshwater Research 67, no. 8 (2016): 1081. http://dx.doi.org/10.1071/mf14423.
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The lack of independently verifiable estimates of catches and fisheries independent estimates of abundance and fishing mortality are major sources of uncertainty in the management of many fisheries. DNA profiling provides the potential to substantially improve the quality of data for assessments and act as an additional deterrent to illegal, unreported, and unregulated (IUU) fishing. Barriers to the implementation of this technology include cost of sample collection and processing, forensic grade quality control, and the ability to apply undetectable tags. We present the results of a comparison of two current and one new (gene tag tool, GTT) sampling techniques, using the highly valued southern bluefin tuna as an example. We demonstrate that fish sampled with two techniques are highly unlikely to be recognised as ‘tagged’, whereas one technique was easily recognisable after 73 days. The GTT reduced handling before DNA extraction, whereas both other techniques require additional labour, adding to cost and potential contamination of the evidentiary chain. Evidence of cross-contamination in the Whatman FTA Elute samples suggests they may not be as suitable for at-sea field applications. Two of the three sampling techniques are capable of obtaining high quality tissue samples for stock assessment and chain of custody purposes in a cost-effective and unidentifiable manner.
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Xu, Hongpan, Tingting Sun, Yuanfu Huang, Lian Song, Zhiyang Li, and Wei Wang. "Outstanding Performance of Novel Magnetic Beads for Efficient Purification of His-Tagged Proteins." Nanoscience and Nanotechnology Letters 10, no. 3 (2018): 435–39. http://dx.doi.org/10.1166/nnl.2018.2669.
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Placing of affinity tags at desired position of the proteins has been widely used to facilitate protein separation. One of the most commonly method for protein separation is nickel ion (Ni2+) affinity chromatography. Complex steps and time consuming in nickel ion affinity chromatography have caused high demand for alternative purification methods that allow direct and rapid separation of His-tagged proteins. In the present study, magnetic core–shell beads enriched with Ni2+-nitrilotriacetate (Ni-NTA) on their surface were prepared in this study by precipitation polymerization, with a uniform size of about 10 μm. The presented Ni2+ amount was 2.23%, which endowed the spheres with excellent magnetic responsivity and dispersity. We compared the magnetic beads enrichment method and nickel ion affinity chromatography method for extraction of His-tagged protein sample with different concentrations. The results revealed that, when compared with nickel ion affinity chromatography, extraction efficiency, purity of the extracted protein, and regeneration effort were much higher with the magnetic beads enrichment method. By using magnetic beads enrichment method, samples could be separated within 20 s, and purified within 1 h, with unlimited flow velocity and sample capacity. In addition, the magnetic beads enrichment method was particularly promising for the separation of His-tagged proteins in less samples.
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Relyea, Robert, Darshan Bhanushali, Karan Manghi, et al. "Improving Multimodal Localization Through Self-Supervision." Electronic Imaging 2020, no. 6 (2020): 14–1. http://dx.doi.org/10.2352/issn.2470-1173.2020.6.iriacv-014.
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Modern warehouses utilize fleets of robots for inventory management. To ensure efficient and safe operation, real-time localization of each agent is essential. Most robots follow metal tracks buried in the floor and use a grid of precisely mounted RFID tags for localization. As robotic agents in warehouses and manufacturing plants become ubiquitous, it would be advantageous to eliminate the need for these metal wires and RFID tags. Not only do they suffer from significant installation costs, the removal of wires would allow agents to travel to any area inside the building. Sensors including cameras and LiDAR have provided meaningful localization information for many different positioning system implementations. Fusing localization features from multiple sensor sources is a challenging task especially when the target localization task’s dataset is small. We propose a deep-learning based localization system which fuses features from an omnidirectional camera image and a 3D LiDAR point cloud to create a robust robot positioning model. Although the usage of vision and LiDAR eliminate the need for the precisely installed RFID tags, they do require the collection and annotation of ground truth training data. Deep neural networks thrive on lots of supervised data, and the collection of this data can be time consuming. Using a dataset collected in a warehouse environment, we evaluate the performance of two individual sensor models for localization accuracy. To minimize the need for extensive ground truth data collection, we introduce a self-supervised pretraining regimen to populate the image feature extraction network with meaningful weights before training on the target localization task with limited data. In this research, we demonstrate how our self-supervision improves accuracy and convergence of localization models without the need for additional sample annotation.
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Martínez, Ana Laura, Freda Anderson, Facundo Quiroz, et al. "Methodologies for Plasmopara halstedii Research." Helia 42, no. 71 (2019): 173–86. http://dx.doi.org/10.1515/helia-2019-0013.
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Abstract The objective of this work was to find practical procedures to overcome methodological drawbacks encountered during studies on sunflower downy mildew. Techniques for recovering living isolates of Plasmopara halstedii from the field and for the preservation of infected leaf samples for further molecular analysis were developed. A Polymerase Chain Reaction (PCR)-based test for the detection of P. halstedii in sunflower leaves and a method to remove azoxystrobin from fungicide-treated seeds are proposed. In situ-inoculations of pre-germinated seeds allowed the recovery of living isolates from the field. Three sample-preservation methods were evaluated (silica, heating and lyophilization) resulting in high yield and quality of the DNA extract. It was detected the presence of the pathogen in symptomless leaves through PCR using molecular markers based on expressed sequence tags. A treatment using sodium hypochlorite is recommended for the removal of azoxystrobin from fungicide treated seeds.
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Yeo, Sean, Ming Yang, Martin Nyachoti, Rolf Rauh, Johnny D. Callahan, and Charles Nfon. "Detection of Foot-and-Mouth Disease Virus in Swine Meat Juice." Pathogens 9, no. 6 (2020): 424. http://dx.doi.org/10.3390/pathogens9060424.
Full textAbstract:
Foot-and-mouth disease virus (FMDV) is a highly contagious agent that impacts livestock industries worldwide, leading to significant financial loss. Its impact can be avoided or minimized if the virus is detected early. FMDV detection relies on vesicular fluid, epithelial tags, swabs, serum, and other sample types from live animals. These samples might not always be available, necessitating the use of alternative sample types. Meat juice (MJ), collected after freeze-thaw cycles of skeletal muscle, is a potential sample type for FMDV detection, especially when meat is illegally imported. We have performed experiments to evaluate the suitability of MJ for FMDV detection. MJ was collected from pigs that were experimentally infected with FMDV. Ribonucleic acid (RNA) was extracted from MJ, sera, oral swabs, and lymph nodes from the same animals and tested for FMDV by real-time reverse transcription polymerase chain reaction (rRT-PCR). MJ was also tested for FMDV antigen by Lateral Flow Immunoassay (LFI). FMDV RNA was detected in MJ by rRT-PCR starting at one day post infection (DPI) and as late as 21 DPI. In contrast, FMDV RNA was detected in sera at 1–7 DPI. Antigen was also detected in MJ at 1–9 DPI by LFI. Live virus was not isolated directly from MJ, but was recovered from the viral genome by transfection into susceptible cells. The data show that MJ is a good sample type for FMDV detection.
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Ferrer-Castelló, E., J. A. Raga, and F. J. Aznar. "Parasites as fish population tags and pseudoreplication problems: the case of striped red mullet Mullus surmuletus in the Spanish Mediterranean." Journal of Helminthology 81, no. 2 (2007): 169–78. http://dx.doi.org/10.1017/s0022149x07729553.
Full textAbstract:
AbstractStudies of parasites as fish population tags often apply a single round of sampling to identify potential stocks or predict harvest localities. However, the lack of replication generates pseudoreplication, implicitly assuming that infection levels are more similar between samples from the same locality than between samples from different localities. We evaluated this assumption in the case of the striped red mullet Mullus surmuletus in three localities of the Spanish Mediterranean separated by c. 300 km. Samples of 25 fish of similar size were collected in each locality in the summer and autumn of two consecutive years. Prevalence and abundance of three long-lived parasite taxa differed significantly among localities, indicating their potential as stock indicators. However, a cluster analysis (for prevalence) and a MANOVA (for abundance) indicated strong inter-sample variability, even within the same locality, with poor spatial segregation among samples. A linear discriminant analysis (LDA) based on the abundance of 17 parasite taxa correctly assigned over 80% of fish to their locality, and 95% bootstrap confidence intervals of percent classified fish per locality were narrow, indicating good and stable predictive power. However, when a LDA based on data from the first year was used to predict the locality of fish from the second year, predictive power dropped drastically (46% of correct allocation). Overall, we interpret that parasite communities of mullets change at a much lower spatial scale than that adopted in this study. This finding strongly suggests the need for proper replication to make reliable inferences about stock structure in fish populations based on parasitological data.
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Malecki, Marek, Lea Tiongco, Annie Hsu, and Nina Takeuchi. "SCFV-6HIS Bioengineered for High Fidelity Labeling." Microscopy and Microanalysis 6, S2 (2000): 338–39. http://dx.doi.org/10.1017/s1431927600034188.
Full textAbstract:
In life sciences, the essential part of the functional molecular analysis is the unambiguous identification of biochemical composition of the observed structures. This analysis is expected to create a bridge between functional data pouring from biochemistry and molecular biology laboratories with the molecular architecture data available from ultrastructural images. This goal can be attained by application of various ultrastructural tags (See: Albrecht et al. 1992).A new promising approach for high fidelity labeling is offered by molecular cloning and expression of molecules containing metal binding sites making them suitable for electron spectroscopic imaging (ESI) (Malecki 1995). A truly enormous potential of ESI relies in its ability for mapping of various elements within the same sample. Interactions of electrons with an atom result in the electrons specific energy loss. Based upon these energy losses distribution of the elements within the sample can be mapped.
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Hafez, Marwa Abdel, Mona Elkateb, Sonia El Shabrawy, Amel Mahmoud, and Omar El Meligy. "Microleakage Evaluation of Composite Restorations Following Papain-Based Chemo-Mechanical Caries Removal in Primary Teeth." Journal of Clinical Pediatric Dentistry 41, no. 1 (2017): 53–61. http://dx.doi.org/10.17796/1053-4628-41.1.53.
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Aim: To evaluate the microleakage of composite restorations following Papain-based chemo-mechanical caries removal compared to the conventional drilling method. The characteristic of the hybrid layer was also studied using scanning electron microscopy. Study design: The sample included thirty freshly extracted and exfoliated primary molars with open proximal carious dentin lesions. Teeth were divided into two equal groups, according to method of caries removal. Following caries removal, cavity preparations were restored with composite resin. After thermocycling, teeth were sealed apically and coated with nail polish except the surface of restorations and the surrounding 1mm. Teeth were immersed in basic fuschin dye solution, then they were sectioned mesiodistally. The extent of dye penetration was detected using a light stereomicroscope. After microleakage test, the resin/dentin interface was examined using scanning electron microscopy. Results: There was no significant difference in the degree of leakage between both groups. In the Papacarie group, longer and numerous resin tags were observed with statistically significant thicker hybrid layer than those following the drilling method. However, there was no significant difference between the diameters of resin tags of both groups. Conclusions: Papacarie does not adversely affect the microleakage of composite restorations and provides a suitable surface for bonding.
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LaFramboise, Thomas L., D. Neil Hayes, and Torstein Tengs. "Statistical Analysis of Genomic Tag Data." Statistical Applications in Genetics and Molecular Biology 3, no. 1 (2004): 1–22. http://dx.doi.org/10.2202/1544-6115.1099.
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We present a series of statistical solutions to challenges that commonly arise in the production and analysis of genomic tag libraries. Tag libraries are collections of fragments of DNA or RNA, with each unique fragment often present in millions or billions of copies. Inferences can be made from data obtained by sequencing a subset of the library. The statistical approaches outlined in this paper are divided into three parts. First, we demonstrate the application of classical capture-recapture theory to the question of library complexity, i.e. the number of unique fragments in the library. Simulation studies verify the accuracy, for sample sizes of magnitudes typical in genomic studies, of the formulas we use to make our estimates. Second, we present a straightforward statistical cost analysis of tag experiments designed to uncover either disease-causing pathogens or new genes. Third, we develop a hidden Markov model approach to karyotyping a sample using a tag library derived from the sample's genomic DNA. While the resolution of the approach depends upon the number of tags sequenced from the library, we show via simulation that copy number alterations can be reliably detected for lengths as small as 1 Mb, even when a moderate number of tags are sequenced. Simulations predict very good specificity as well. Finally, all three of our approaches are applied to data from real tag library experiments. The hidden Markov model results are in line with what was expected from simulation, and genomic alterations found by applying the method to a cancer cell line library are confirmed using PCR.The methods and data described in this paper are contained in an R package, tagAnalysis, freely available at http://meyerson.dfci.harvard.edu/~tl974/tagAnalysis.
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Hao, Ling, Samuel Thomas, Tyler Greer, et al. "Quantitative proteomic analysis of a genetically induced prostate inflammation mouse model via custom 4-plex DiLeu isobaric labeling." American Journal of Physiology-Renal Physiology 316, no. 6 (2019): F1236—F1243. http://dx.doi.org/10.1152/ajprenal.00387.2018.
Full textAbstract:
Inflammation is involved in many prostate pathologies including infection, benign prostatic hyperplasia, and prostate cancer. Preclinical models are critical to our understanding of disease mechanisms, yet few models are genetically tractable. Here, we present a comparative quantitative proteomic analysis of urine from mice with and without prostate-specific inflammation induced by conditional prostate epithelial IL-1β expression. Relative quantification and sample multiplexing was achieved using custom 4-plex N, N-dimethyl leucine (DiLeu) isobaric tags and nanoflow ultrahigh-performance liquid chromatography coupled to high-resolution tandem mass spectrometry. Each set of 4-plex DiLeu reagents allows four urine samples to be analyzed simultaneously, providing high-throughput and accurate quantification of urinary proteins. Proteins involved in the acute phase response, including haptoglobin, inter-α-trypsin inhibitor, and α1-antitrypsin 1-1, were differentially represented in the urine of mice with prostate inflammation. Mass spectrometry-based quantitative urinary proteomics represents a promising bioanalytical strategy for biomarker discovery and the elucidation of molecular mechanisms in urological research.
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Bhartia, Rohit, Everett C. Salas, William F. Hug, et al. "Label-Free Bacterial Imaging with Deep-UV-Laser-Induced Native Fluorescence." Applied and Environmental Microbiology 76, no. 21 (2010): 7231–37. http://dx.doi.org/10.1128/aem.00943-10.
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ABSTRACT We introduce a near-real-time optical imaging method that works via the detection of the intrinsic fluorescence of life forms upon excitation by deep-UV (DUV) illumination. A DUV (<250-nm) source enables the detection of microbes in their native state on natural materials, avoiding background autofluorescence and without the need for fluorescent dyes or tags. We demonstrate that DUV-laser-induced native fluorescence can detect bacteria on opaque surfaces at spatial scales ranging from tens of centimeters to micrometers and from communities to single cells. Given exposure times of 100 μs and low excitation intensities, this technique enables rapid imaging of bacterial communities and cells without irreversible sample alteration or destruction. We also demonstrate the first noninvasive detection of bacteria on in situ-incubated environmental experimental samples from the deep ocean (Lo'ihi Seamount), showing the use of DUV native fluorescence for in situ detection in the deep biosphere and other nutrient-limited environments.