Relevant bibliographies by topics / Sequential and selective labeling

Academic literature on the topic 'Sequential and selective labeling'

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Published: 10 March 2023

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Journal articles on the topic "Sequential and selective labeling"

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Luchinat, Enrico, Erica Secci, Francesca Cencetti, and Paola Bruni. "Sequential protein expression and selective labeling for in-cell NMR in human cells." Biochimica et Biophysica Acta (BBA) - General Subjects 1860, no. 3 (March 2016): 527–33. http://dx.doi.org/10.1016/j.bbagen.2015.12.023.

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Matos, Maria J., Libby Brown, Barbara Bernardim, Ana Guerreiro, Gonzalo Jiménez-Osés, and Gonçalo J. L. Bernardes. "Sequential dual site-selective protein labelling enabled by lysine modification." Bioorganic & Medicinal Chemistry 28, no. 22 (November 2020): 115783. http://dx.doi.org/10.1016/j.bmc.2020.115783.

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Morató, Anna, Carlos A. Elena-Real, Matija Popovic, Aurélie Fournet, Karen Zhang, Frédéric Allemand, Nathalie Sibille, Annika Urbanek, and Pau Bernadó. "Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins." Biomolecules 10, no. 10 (October 19, 2020): 1458. http://dx.doi.org/10.3390/biom10101458.

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The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.
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Yoshida, Jun-ichi, Heejin Kim, Hyune-Jea Lee, Daiki Torii, and Yongju Jeon. "Integrated Synthesis Using Isothiocyanate-Substituted Aryllithiums by Flow Chemistry." Synlett 31, no. 19 (August 21, 2020): 1899–902. http://dx.doi.org/10.1055/s-0040-1707251.

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The isothiocyanate (NCS) group is an attractive functional group in the field of organic and pharmaceutical chemistry. It can be transformed into other heteroatomic functional groups. It usually acts as the inductive group of biological activity and has also been traditionally used as the fluorescent-labeling reagent. However, it is not compatible with strong bases. When the NCS group is at para position in halobenzenes, it generally undergoes nucleophilic additions upon reaction with strong bases. To the best of our knowledge, there is currently no general methodology for the formation and reactions of NCS-functionalized aryllithiums for meta and para substituents. Herein, we report the continuous-flow generation of NCS-substituted aryllithiums from the corresponding haloarenes via a selective halogen–lithium exchange reaction and its reaction with various electrophiles to yield NCS-containing products. We also achieved an integrated synthesis through sequential reactions of the NCS-containing compounds with additional nucleophiles using the continuous-flow reactors.
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Gruba, Natalia, Ewa Bielecka, Magdalena Wysocka, Anna Wojtysiak, Magdalena Brzezińska-Bodal, Kamila Sychowska, Magdalena Kalińska, et al. "Development of Chemical Tools to Monitor Human Kallikrein 13 (KLK13) Activity." International Journal of Molecular Sciences 20, no. 7 (March 28, 2019): 1557. http://dx.doi.org/10.3390/ijms20071557.

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Kallikrein 13 (KLK13) was first identified as an enzyme that is downregulated in a subset of breast tumors. This serine protease has since been implicated in a number of pathological processes including ovarian, lung and gastric cancers. Here we report the design, synthesis and deconvolution of libraries of internally quenched fluorogenic peptide substrates to determine the specificity of substrate binding subsites of KLK13 in prime and non-prime regions (according to the Schechter and Berger convention). The substrate with the consensus sequential motive ABZ-Val-Arg-Phe-Arg-ANB-NH2 demonstrated selectivity towards KLK13 and was successfully converted into an activity-based probe by the incorporation of a chloromethylketone warhead and biotin bait. The compounds described may serve as suitable tools to detect KLK13 activity in diverse biological samples, as exemplified by overexpression experiments and targeted labeling of KLK13 in cell lysates and saliva. In addition, we describe the development of selective activity-based probes targeting KLK13, to our knowledge the first tool to analyze the presence of the active enzyme in biological samples.
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Di Liberto, Maurizio, Xiangao Huang, Jamieson Bretz, Scott A. Ely, Rediet Zewdu, David Jayabalan, Suzhen Chen, et al. "Induction of Metabolic Impairment In Prolonged Early G1 Arrest Induced by CDK4/CDK6 Inhibition Sensitizes Myeloma Cells for Proteasome Inhibitor Killing During Subsequent S Phase Synchronization." Blood 116, no. 21 (November 19, 2010): 2989. http://dx.doi.org/10.1182/blood.v116.21.2989.2989.

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Abstract Abstract 2989 Sequential drug combination is a rational approach to maximize tumor killing and minimize side effects in cancer therapy. However, this is rarely achieved because the mechanism of drug action is often incompletely understood and the cell cycle specificity of individual drugs unknown. Dysregulation of cyclin-dependent kinase (CDK)4 and CDK6 is common in human cancer and precedes unrestrained proliferation of tumor cells in multiple myeloma (MM) patients, especially during refractory relapse. This highlights the critical importance of targeting CDK4/CDK6 in MM. We have now developed, for the first time, a novel therapeutic strategy to selectively inhibit CDK4/CDK6 in sequential combination with clinically relevant cytotoxic drugs for maximal tumor killing at reduced doses in MM. CDK4 and CDK6 promote reentry and progression of the cell cycle through G1. PD 0332991, the only known CDK4/CDK6-specific inhibitor, is potent, reversible and bioavailable. We showed that inhibition of CDK4/CDK6 with PD 0332991 induces early G1 arrest and upon release from the G1 block, synchronous progression to S phase and G2/M with exceptional precision and efficiency in MM cells in vitro and in animal models. This provides a unique means to determine the cell cycle targeting specificity of individual compounds for optimal combination. Simultaneous analysis of BrdU pulse-labeling (30 minutes) and DNA content per cell reveals that bortezomib, a reversible proteasome inhibitor; carfilzomib (PR-171), an irreversible selective inhibitor of the proteasom; and its oral analog ONX-0912 (PR-047) all preferentially target MM cells synchronized into S phase over those arrested in G1, but not cells in G2/M. On this basis, killing of myeloma cells by proteasome inhibitors is markedly enhanced in prolonged G1 arrest induced by PD 0332991 and further augmented during synchronous entry into and progression through S phase upon release from the G1 block, in vitro and in vivo in the native bone marrow niches. Induction of early G1 arrest by PD 0332991 requires Rb, the substrate of CDK4 and CDK6, but not p53. Importantly, the increase in carfilzomib, ONX-0912 or bortezomib mediated killing after S phase synchronization significantly surpasses the enrichment of S phase cells. It is in fact proportional to the time of prior G1 arrest. Kinetics analyses of global gene expression patterns, specific RNA and protein levels and functional shRNA interference show that prolonging early G1 arrest leads to time-dependent uncoupling of gene expression from the cell cycle. PD 0332991 withdraw rapidly restores the CDK4 and CDK6 catalytic activity and scheduled expression of cell cycle genes, hence synchronous progression to S phase and mitosis. This includes upregulation of cyclin A synthesis and Skp2 mediated ubiquitin-proteasome degradation of p27 for S phase entry, mini chromosome maintenance(MCM)s and thymidine kinase for DNA replication, and genes critical for G2/M checkpoint control and mitosis. However, it fails to fully reverse the metabolic impairment (altered glucose, nucleotide and ATP metabolism) induced in prolonged early G1 arrest. This culminates in the loss of IRF-4 required for myeloma survival and selective gain of pro-apoptotic Bim function in G1 arrest and Noxa in S phase in synergy with carfilzomib and bortezomib, which lowers the threshold for activation of the intrinsic apoptosis pathway. Selective inhibition of CDK4/CDK6 in sequential combination therapy thus not only halts tumor cell proliferation but also potently induces synergistic tumor killing. This sequential combination therapy has been implemented in a multi-center phase 1/2 clinical trial targeting CDK4/6 with PD 0332991 in combination with bortezomib and dexamethasone in relapsed refractory MM. Phase 1 data indicate that PD 0332991 is well tolerated, and directly and completely inhibits CDK4/CDK6 and the cell cycle in tumor cells in MM patients with promising clinical efficacy. Evidence from phase 2 trials of carfilzomib indicates that it is also well tolerated. The peripheral neuropathy commonly observed with bortezomib appears to be less severe and less frequent. Selective combination with carfilzomib or the oral agent ONX-0912 thus represents a promising alternative to refine targeting CDK4/6 in sequential combination therapy for multiple myeloma and potentially other cancers. Disclosures: Off Label Use: PD 0332991 is a cell cycle CDK4/CDK6 inhibitor Carfilzomib is a proteasome inhibitor. Kirk:Onyx: Employment, Equity Ownership. Randolph:Pfizer: Employment, Equity Ownership. Niesvizky:Celgene: Consultancy, Research Funding, Speakers Bureau; Onyx: Consultancy, Research Funding, Speakers Bureau; Millennium: Consultancy, Research Funding, Speakers Bureau.
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Falk Delgado, Alberto, Francesca De Luca, Danielle van Westen, and Anna Falk Delgado. "Arterial spin labeling MR imaging for differentiation between high- and low-grade glioma—a meta-analysis." Neuro-Oncology 20, no. 11 (June 2, 2018): 1450–61. http://dx.doi.org/10.1093/neuonc/noy095.

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Abstract Background Arterial spin labeling is an MR imaging technique that measures cerebral blood flow (CBF) non-invasively. The aim of the study is to assess the diagnostic performance of arterial spin labeling (ASL) MR imaging for differentiation between high-grade glioma and low-grade glioma. Methods Cochrane Library, Embase, Medline, and Web of Science Core Collection were searched. Study selection ended November 2017. This study was prospectively registered in PROSPERO (CRD42017080885). Two authors screened all titles and abstracts for possible inclusion. Data were extracted independently by 2 authors. Bivariate random effects meta-analysis was used to describe summary receiver operating characteristics. Trial sequential analysis (TSA) was performed. Results In total, 15 studies with 505 patients were included. The diagnostic performance of ASL CBF for glioma grading was 0.90 with summary sensitivity 0.89 (0.79–0.90) and specificity 0.80 (0.72–0.89). The diagnostic performance was similar between pulsed ASL (AUC 0.90) with a sensitivity 0.85 (0.71–0.91) and specificity 0.83 (0.69–0.92) and pseudocontinuous ASL (AUC 0.88) with a sensitivity 0.86 (0.79–0.91) and specificity 0.80 (0.65–0.87). In astrocytomas, the diagnostic performance was 0.89 with sensitivity 0.86 (0.79 to 0.91) and specificity 0.79 (0.63 to 0.89). Sensitivity analysis confirmed the robustness of the findings. TSA revealed that the meta-analysis was adequately powered. Conclusion Arterial spin labeling MR imaging had an excellent diagnostic accuracy for differentiation between high-grade and low-grade glioma. Given its low cost, non-invasiveness, and efficacy, ASL MR imaging should be considered for implementation in the routine workup of patients with glioma.
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Adnan, Ahmed, Abdullah Muhammed, Abdul Azim Abd Ghani, Azizol Abdullah, and Fahrul Hakim. "Hyper-Heuristic Framework for Sequential Semi-Supervised Classification Based on Core Clustering." Symmetry 12, no. 8 (August 4, 2020): 1292. http://dx.doi.org/10.3390/sym12081292.

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Existing stream data learning models with limited labeling have many limitations, most importantly, algorithms that suffer from a limited capability to adapt to the evolving nature of data, which is called concept drift. Hence, the algorithm must overcome the problem of dynamic update in the internal parameters or countering the concept drift. However, using neural network-based semi-supervised stream data learning is not adequate due to the need for capturing quickly the changes in the distribution and characteristics of various classes of the data whilst avoiding the effect of the outdated stored knowledge in neural networks (NN). This article presents a prominent framework that integrates each of the NN, a meta-heuristic based on evolutionary genetic algorithm (GA) and a core online-offline clustering (Core). The framework trains the NN on previously labeled data and its knowledge is used to calculate the error of the core online-offline clustering block. The genetic optimization is responsible for selecting the best parameters of the core model to minimize the error. This integration aims to handle the concept drift. We designated this model as hyper-heuristic framework for semi-supervised classification or HH-F. Experimental results of the application of HH-F on real datasets prove the superiority of the proposed framework over the existing state-of-the art approaches used in the literature for sequential classification data with evolving nature.
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Martinez-Pena y Valenzuela, Isabel, and Mohammed Akaaboune. "Acetylcholinesterase Mobility and Stability at the Neuromuscular Junction of Living Mice." Molecular Biology of the Cell 18, no. 8 (August 2007): 2904–11. http://dx.doi.org/10.1091/mbc.e07-02-0093.

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Acetylcholinesterase (AChE) is an enzyme that terminates acetylcholine neurotransmitter function at the synaptic cleft of cholinergic synapses. However, the mechanism by which AChE number and density are maintained at the synaptic cleft is poorly understood. In this work, we used fluorescence recovery after photobleaching, photo-unbinding, and quantitative fluorescence imaging to investigate the surface mobility and stability of AChE at the adult innervated neuromuscular junction of living mice. In wild-type synapses, we found that nonsynaptic (perisynaptic and extrasynaptic) AChEs are mobile and gradually recruited into synaptic sites and that most of the trapped AChEs come from the perijunctional pool. Selective labeling of a subset of synaptic AChEs within the synapse by using sequential unbinding and relabeling with different colors of streptavidin followed by time-lapse imaging showed that synaptic AChEs are nearly immobile. At neuromuscular junctions of mice deficient in α-dystrobrevin, a component of the dystrophin glycoprotein complex, we found that the density and distribution of synaptic AChEs are profoundly altered and that the loss rate of AChE significantly increased. These results demonstrate that nonsynaptic AChEs are mobile, whereas synaptic AChEs are more stable, and that α-dystrobrevin is important for controlling the density and stability of AChEs at neuromuscular synapses.
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Todd, Melvi, Timothy Guetterman, Jako Volschenk, Martin Kidd, and Elizabeth Joubert. "Healthy or Not Healthy? A Mixed-Methods Approach to Evaluate Front-of-Pack Nutrition Labels as a Tool to Guide Consumers." Nutrients 14, no. 14 (July 8, 2022): 2801. http://dx.doi.org/10.3390/nu14142801.

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This study explored how South African food labels could be improved, with a focus on comparison of front-of-pack (FOP) nutrition labels as a quick assessment tool to enhance customer evaluation of the overall healthiness of packaged food. The exploratory sequential mixed-methods design used qualitative interviews (n = 49) to gain insight into labeling challenges and select FOP nutrition labels for consumer testing. Consumers (n = 1261) randomly assessed two of six possible FOP nutrition labels relative to a ‘no-label’ control applied to a fictitious cereal product in 12 online surveys. A mixed-model analysis of variance was used to compare the differences in health ratings for the different FOP nutrition labels. The interviews revealed three themes for label improvement, that are presented over three time horizons. In terms of helping consumers identify less healthy products, the effect sizes were most prominent for health warnings (p < 0.01) and low health star ratings (p < 0.01). The findings of this research not only clarify whether FOP nutrition labeling formats used in other regions such as Europe, South America and Australia could be useful in the South African context, but they can assist policymakers and decision-makers in selecting an effective FOP label.
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Dissertations / Theses on the topic "Sequential and selective labeling"

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Park, Joonsuk. "Using Sequential Sampling Models to Detect Selective Infuences: Pitfalls and Recommendations." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu157470864789277.

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Tener, Greg. "ATTACKS ON DIFFICULT INSTANCES OF GRAPH ISOMORPHISM: SEQUENTIAL AND PARALLEL ALGORITHMS." Doctoral diss., University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2631.

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The graph isomorphism problem has received a great deal of attention on both theoretical and practical fronts. However, a polynomial algorithm for the problem has yet to be found. Even so, the best of the existing algorithms perform well in practice; so well that it is challenging to find hard instances for them. The most efficient algorithms, for determining if a pair of graphs are isomorphic, are based on the individualization-refinement paradigm, pioneered by Brendan McKay in 1981 with his algorithm nauty. Nauty and various improved descendants of nauty, such as bliss and saucy, solve the graph isomorphism problem by determining a canonical representative for each of the graphs. The graphs are isomorphic if and only if their canonical representatives are identical. These algorithms also detect the symmetries in a graph which are used to speed up the search for the canonical representative--an approach that performs well in practice. Yet, several families of graphs have been shown to exist which are hard for nauty-like algorithms. This dissertation investigates why these graph families pose difficulty for individualization-refinement algorithms and proposes several techniques for circumventing these limitations. The first technique we propose addresses a fundamental problem pointed out by Miyazaki in 1993. He constructed a family of colored graphs which require exponential time for nauty (and nauty's improved descendants). We analyze Miyazaki's construction to determine the source of difficulty and identify a solution. We modify the base individualization-refinement algorithm by exploiting the symmetries discovered in a graph to guide the search for its canonical representative. This is accomplished with the help of a novel data structure called a guide tree. As a consequence, colored Miyazaki graphs are processed in polynomial time--thus obviating the only known exponential upper-bound on individualization-refinement algorithms (which has stood for the last 16 years). The preceding technique can only help if a graph has enough symmetry to exploit. It cannot be used for another family of hard graphs that have a high degree of regularity, but possess few actual symmetries. To handle these instances, we introduce an adaptive refinement method which utilizes the guide-tree data structure of the preceding technique to use a stronger vertex-invariant, but only when needed. We show that adaptive refinement is very effective, and it can result in dramatic speedups. We then present a third technique ideally suited for large graphs with a preponderance of sparse symmetries. A method was devised by Darga et al. for dealing with these large and highly symmetric graphs, which can reduce runtime by an order of magnitude. We explain the method and show how to incorporate it into our algorithm. Finally, we develop and implement a parallel algorithm for detecting the symmetries in, and finding a canonical representative of a graph. Our novel parallel algorithm divides the search for the symmetries and canonical representative among each processor, allowing for a high degree of scalability. The parallel algorithm is benchmarked on the hardest problem instances, and shown to be effective in subdividing the search space.
Ph.D.
School of Electrical Engineering and Computer Science
Engineering and Computer Science
Computer Science PhD
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Tamura, Tomonori. "Endogenous protein imaging and analysis in living cells by selective chemical labeling methods." 京都大学 (Kyoto University), 2013. http://hdl.handle.net/2433/174965.

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Beller, Nicole C. "Selective Pulse Chase-SILAC Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1586292839111678.

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Meakin, James A. "Velocity selective preparations in Magnetic Resonance Imaging." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:a4247c64-d113-42e6-beee-5795e78a4cdc.

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Arterial Spin Labeling (ASL) is a Magnetic Resonance Imaging (MRI) technique that is able to non-invasively quantify the rate of delivery of arterial blood to tissue, known as perfusion. In this thesis a method that uses Velocity Selective (VS) preparations to generate contrast between blood and tissue spins is investigated. The systematic errors associated with performing a VSASL experiment on imperfect hardware is first investigated. It is shown through simulations and experiments that some VS preparations will underestimate perfusion due to static and transmit magnetic field errors, and that eddy currents caused by switching of magnetic gradients lead to an overestimation of perfusion with VSASL by up to a factor 2. A novel VS preparation, BIR-8, is presented which is shown to be the most robust to these imperfections. The BIR-8 VSASL technique is then applied in brain tumours where it is found that significant VSASL signal can be detected in less than 5 minutes. However, in a comparison with a spatially selective ASL technique it is found that VSASL overestimates perfusion in these tumours, despite agreeing in Grey Matter. The systematic errors due to physiology are then modelled, and it is shown that both diffusion and bulk motion will systematically bias the VSASL measurement. A diffusion insensitive VSASL technique, VS-TILT, is then developed and it is found that a significant proportion of the VSASL signal originates from diffusion effects. Theoretical models for the shape of the bolus in vascular networks are also derived, and it is shown that an isotropic network of laminar vessels produces the most efficient saturation, but saturation is also achieved with plug flow. The diffusion insensitive VS preparation is then applied in an attempt to isolate the venous compartment in order to measure Oxygen Extraction Fraction. A kinetic model is derived in order to optimise the acquisition. However, it is found that accurate measurements of OEF would not be produced by this sequence in a clinically realistic time.
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Flake, Darl D. II. "Separation of Points and Interval Estimation in Mixed Dose-Response Curves with Selective Component Labeling." DigitalCommons@USU, 2016. https://digitalcommons.usu.edu/etd/4697.

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This dissertation develops, applies, and investigates new methods to improve the analysis of logistic regression mixture models. An interesting dose-response experiment was previously carried out on a mixed population, in which the class membership of only a subset of subjects (survivors) were subsequently labeled. In early analyses of the dataset, challenges with separation of points and asymmetric confidence intervals were encountered. This dissertation extends the previous analyses by characterizing the model in terms of a mixture of penalized (Firth) logistic regressions and developing methods for constructing profile likelihood-based confidence and inverse intervals, and confidence bands in the context of such a model. The proposed methods are applied to the motivating dataset and another related dataset, resulting in improved inference on model parameters. Additionally, a simulation experiment is carried out to further illustrate the benefits of the proposed methods and to begin to explore better designs for future studies. The penalized model is shown to be less biased than the traditional model and profile likelihood-based intervals are shown to have better coverage probability than Wald-type intervals. Some limitations, extensions, and alternatives to the proposed methods are discussed.
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Mulakhudair, Ali R. "Microbubble mediated sequential saccharification, inactivation, and aerobic fermentation with in situ selective product removal." Thesis, University of Sheffield, 2017. http://etheses.whiterose.ac.uk/18942/.

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Microbubble mediated technologies are employed for pretreatment steps due to the characteristics of the gas-liquid interface. Traditionally, pretreatment processes are energy intensive operations and use hazardous chemicals such as sulfuric acid and hydrochloric acid, which need to be removed from the pretreatment slurry before feeding it to the fermentation process. Alternative approaches to microbubbles for pretreatment, however, have significant challenges. For example, conventional bubbles are several orders of magnitude larger than the bubble exit pore and therefore have less direct contact with the biomass or delivery the ozone efficiently to the pretreatment slurry. Consequently, these concerns have been addressed in this research, and microbubble-microbe synergy and Ozonolysis-microbe synergy for biomass pretreatment with the developing of microbubbles driven systems, were used to facilitate microbubble generation suitable for pretreatment processes. The first approach was achieved by exploiting the synergy between microbubble-microbe to pretreat lignocellulosic biomass and glucose was the target product. The effects of microbubbles, microbe and the synergy between them on morphology, functional groups and glucose yield were investigated. It was found that free radicals around the gas-liquid interface of the microbubble can readily attack and degrade lignocellulosic biomass, rendering it more amenable to digestion. The combination of microbubbles and Pseudomonas putida—a robust delignification and cellulolytic microbe, further improved biomass degradation and consequently, increased glucose production from wheat straw in comparison to solo pretreatment of the biomass with microbubbles and Pseudomonas putida respectively. In addition, it was found that the highest glucose achieved was 0.27 mg/ml. The second was conducted by exploiting ozonolysis-microbe synergy to pretreat lignocellulosic biomass and glucose was also the target product. The effects of ozonation at various pHs and ozone concentrations, biological pretreatment by Pseudomonas putida and the synergy between them on morphology, functional groups and glucose yield were explored. Ozone is a strong oxidative agent that reacts with lignin by attacking the carbon-carbon double bonds, while P. putida preferentially hydrolyses the exposed cellulolytic parts of the biomass to simple sugars. It was found that both lignin and cellulose contents were reduced under this pretreatment with relatively high glucose recovery. The highest glucose concentration reached was 1.1 mg/ml after 24 hr ozonation at 8.86 mg/L ozone and pH 3 with 50 % reduction in the biological pretreatment duration but crucially, increasing microbial biomass. Using the synergetic approach for the biomass pretreatment is promising approach but leaves the pretreatment slurry contaminated with the cellulolytic microbe, Pseudomonas putida, which needs to be inactivated or removed before feeding the pretreatment slurry into the fermenter. The ability of carbon dioxide enriched microbubbles to inactivate Pseudomonas putida was subsequently investigated. Many drawbacks of the traditional sterilization methods were avoided by using carbon dioxide enriched microbubbles, such as high energy consumption and using toxic and corrosive reagents. It was found that 2-Log reduction in the bacterial population after 90 min was achieved using carbon dioxide enriched microbubbles. Further reductions were achieved by adding additives such as ethanol and acetic acid and the highest reduction performed was 3.5 Log with 10 % ethanol, while a 2.5-Log reduction was achieved with 0.5 % acetic acid. These reductions in the bacterial population were concurrent with changing cells shape from rod cells to coccus shape with cell damage such as lesions and cells death. Subsequently, aerobic fermentation with glucose as a carbon source proceeded with Zymomonas mobilis ZM4 as the microbial fermentation agent. Acetaldehyde has drawn the attention in this research because it is an important chemical, and it can be used in many processes such as plastic manufacturing and fuels production such as ethanol and butanol. Several attempts to produce acetaldehyde from Zymomonas mobilis or genetically modified microbes contained some genes from Zymomonas are reported, but the inhibition of microbial growth by the accumulated acetaldehyde was the main challenge to keep its continuous production. This challenge has been addressed in this study and microbubbles generated by fluidic oscillation were used to remove both acetaldehyde and carbon dioxide from the fermentation broth. Additionally, the oxygenation concurrent with the stripping process by microbubbles efficiently maintained the oxygen concentration in the fermentation broth above the critical oxygen concentration, leading to stable aerobic conditions. The results show that 45 % yield of ethanol and 1 % yield of acetaldehyde with 110 % yield of microbial biomass in comparison with 70 %, 0.5 % and 90 % yield for ethanol, acetaldehyde, and biomass respectively in the initially sparged group were achieved. Also, acetaldehyde was removed from the fermentation broth with 99 % efficiency. Acetaldehyde production in the fermentation was enhanced by selecting the mutant cells with attenuated or modified alcohol dehydrogenase activity using increasing concentrations of allyl alcohol. The results show that 17-fold increase was achieved in the mutant strain in comparison with the wild strain. In addition, the mutant strain produced 90 % less ethanol than the wild VI strain. Also, the acetaldehyde removal efficiency was 88.5 % in comparison with 42 % efficiency achieved with the fine bubbles (bigger bubbles). Additionally, biomass yield produced by the mutant strain was less by a half than the yield produced by the wild strain. To enhance the biomass yield of the mutant strain, different techniques were used to grow this bacterium aerobically, but maintaining sufficient oxygen concentration was challenging in the bacterial propagation stage. Oxygen is the limiting factor in the aerobically grown bacterial cultures, but similarly, the impact of mixing can be critical. The results show that the oxygen uptake rate and mass transfer coefficient are substantial increased using microbubbles technology and there were 41-fold and 150-fold increase in the oxygen uptake rate and mass transfer coefficient respectively in the microbubbles-dosed culture in comparison with the shaking flask culture. This technology can also achieve a proper mixing. Regarding the biomass yield, the mutant strain of Zymomonas mobilis shows an increased yield using the shaking flask (around 100 % and 133 % increases) in comparison with other (microbubbles-dosed and stationary respectively) techniques, while the wild strain produces more biomass in the microbubble-based technique (around 50 % and 100 %) than other (shaking flask and stationary respectively) techniques. In addition, a propagation unit was designed and simulated to grow the mutant strain aerobically in the propagation stage before using this grown biomass as an inoculum to the fermentation process. Fundamentally, the results obtained in this study are achieved in a laminar flow with several orders of magnitude lower energy density than conventional benchmarks, which are a highly turbulent flow.
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Yasueda, Yuuki. "A method for chemical proteomics based on the selective localization of labeling molecules in living systems." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215578.

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Ochtrop, Philipp. "Selective protein functionalisation via enzymatic phosphocholination." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-140349.

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Proteins are the most abundant biomolecules within a cell and are involved in all biochemical cellular processes ultimately determining cellular function. Therefore, to develop a complete understanding of cellular processes, obtaining knowledge about protein function and interaction at a molecular level is critical. Consequently, the investigation of proteins in their native environment or in partially purified mixtures is a major endeavour in modern life sciences. Due to their high chemical similarity, the inherent problem of studying proteins in complex mixtures is to specifically differentiate one protein of interest from the bulk of other proteins. Site-specific protein functionalisation strategies have become an indispensable tool in biochemical- and cell biology studies. This thesis presents the development of a new enzymatic site-specific protein functionalisation strategy that is based on the reversible covalent phosphocholination of short amino acid sequences in intact proteins. A synthetic strategy has been established that allows access to functionalised CDP-choline derivatives carrying fluorescent reporter groups, affinity tags or bioorthogonal handles. These CDP-choline derivatives serve as co-substrates for the bacterial phosphocholinating enzyme AnkX from Legionella pneumophila, which transfers a phosphocholine moiety to the switch II region of its native target protein Rab1b during infection. We identified the octapeptide sequence TITSSYYR as the minimum recognition sequence required to direct the AnkX catalysed phosphocholination and demonstrated the functionalisation of proteins of interest carrying this recognition tag at the N- or C-terminus as well as in internal loop regions. Moreover, this covalent modification can be hydrolytically reversed by the action of the Legionella enzyme Lem3, which makes the labeling strategy the first example of a covalent and reversible approach that is fully orthogonal to current existing methodologies. Thus, the here presented protein functionalisation approach holds the potential to increase the scope of possible labeling strategies in complex biological systems. In addition to the labeling of tagged target proteins, a CDP-choline derivative equipped with a biotin affinity-tag was synthesised and used in pull-down experiments to investigate the substrate scope of AnkX and to elucidate the role of protein phosphocholination during Legionella pneumophila infection.
Proteiner utgör huvudbeståndsdelen av alla biomolekyler i en cell. Dessa är involverade i alla cellulära processer som bestämmer cellens egenskaper. För att förstå de cellulära processerna är det nödvändigt att förstå proteinernas funktion på molekylär nivå. Att studera proteiner i deras naturliga omgivning, det vill säga inuti en cell eller i ett cellextrakt, är en stor utmaning i dagens livsvetenskaper. Eftersom proteiner är kemiskt lika varandra så är det svårt att skilja ett från tusentals andra. Att specifikt märka proteiner för att skilja ut dem från bakgrunden har blivit ett viktigt arbetssätt i modern biokemi och cellbiologi. Avhandlingen beskriver utvecklandet av en ny metod för reversibel och kovalent enzymatisk märkning baserat på fosfokolinering/defosfokolinering av en kort aminosyrasekvens i intakta proteiner. En syntesmetod för att framställa onaturliga CDP-kolinderivat har etablerats vilket tillåter oss att framställa CDP-kolin som bär en funktionalitet, vilket kan vara ett färgämne eller en affinitetstagg. Dessa onaturliga CDP-kolinderivat accepteras som co-substrat av enzymet AnkX från Legionella pneumophila vilket transfererar den funktionaliserade delen av CDP-kolinderivatet till en kort aminosyrasekvens baserad på AnkX’s naturliga substrat vid infektion, det lilla GTPaset Rab1. Under avhandlingsarbetets gång identifierades den kortaste aminosyrasekvensen som känns igen av AnkX, endast de åtta aminosyrorna TITSSYYR är nödvändiga för igenkänning av AnkX. Dessa åtta aminosyror kan genetiskt infogas i början, slutet eller mitt i ett protein för igenkänning och funktionalisering via AnkX och våra syntetiska CDP-kolinderivat. Vid Legionellainfektion i eukaryota celler klyvs fosfokolineringen efter en viss tid, eftersom Legionella pneumophila producerar ett fosfodiesteras, Lem3, som tar bort de fosfokolineringar som AnkX har installerat när de inte längre behövs. Vi har använt Lem3 för att ta bort märkning i sekvensen TITSS(PC)YYR, vilket gör vår strategi helt reversibel. Vi har kunnat demonstrera att AnkX-Lem3 systemet accepterar ett brett spektrum av CDP-kolinderivat, vilket gör metoden till den första av sitt slag, eftersom den är fullt reversibel. Vi har vidare undersökt vilka proteiner AnkX reagerar med inuti celler, vi använde oss av ett CDP-kolinderivat funktionaliserat med biotin, vilket har tillåtit oss att fiska ut alla de proteiner som fosfokolineras av AnkX. Förutom de små GTPaserna i Rab-familjen så identifierade vi även IMPDH2, ett enzym som reglerar det hastighetsbestämmande steget i syntesen av guanosin-nukleotider. Detta är mycket intressant, eftersom det leder till frågan ifall Legionella pneumophila manipulerar sin värdcell genom att förändra mängden GTP i förhållande till ATP.
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Bock, Paul B. "The sequential self-selection auction mechanism for selective reenlistment bonuses potential cost savings to the U.S. Marine Corps." Thesis, Monterey, Calif. : Naval Postgraduate School, 2007. http://bosun.nps.edu/uhtbin/hyperion-image.exe/07Jun%5FBock.pdf.

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Thesis (M.S. in Management)--Naval Postgraduate School, June 2007.
Thesis Advisor(s): William R. Gates, Peter J. Coughlan. "June 2007." Includes bibliographical references (p. 67-68). Also available in print.
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Books on the topic "Sequential and selective labeling"

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Donkin, Chris, Babette Rae, Andrew Heathcote, and Scott D. Brown. Why Is Accurately Labeling Simple Magnitudes So Hard? A Past, Present, and Future Look at Simple Perceptual Judgment. Edited by Jerome R. Busemeyer, Zheng Wang, James T. Townsend, and Ami Eidels. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199957996.013.6.

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Absolute identification is a deceptively simple task that has been the focus of empirical investigation and theoretical speculation for more than half a century. Since Miller’s (1956) seminal paper the puzzle of why people are severely limited in their capacity to accurately perform absolute identification has endured. Despite the apparent simplicity of absolute identification, many complicated and robust effects are observed in both response latency and accuracy, including capacity limitations, strong sequential effects and effects of the position of a stimulus within the set. Constructing a comprehensive theoretical account of these benchmark effects has proven difficult, and existing accounts all have shortcomings. We review classical empirical findings, as well as some newer findings that challenge existing theories. We then discuss a variety of theories, with a focus on the most recent proposals, make some broad conclusions about general classes of models, and discuss the challenges ahead for each class.
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Cheng, Jerry, and David Madigan. Bayesian approaches to aspects of the Vioxx trials: Non-ignorable dropout and sequential meta-analysis. Edited by Anthony O'Hagan and Mike West. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780198703174.013.3.

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This article discusses Bayesian approaches to aspects of the Vioxx trials study, with a focus on non-ignorable dropout and sequential meta-analysis. It first provides a background on Vioxx, a COX-2 selective, non-steroidal anti-inflammatory drug (NSAID) approved by the FDA in May 1999 for the relief of the signs and symptoms of osteoarthritis, the management of acute pain in adults, and for the treatment of menstrual symptoms. However, Vioxx was found to cause an array of cardiovascular side-effects such as myocardial infarction, stroke, and unstable angina. As a result, Vioxx was withdrawn from the market. The article describes an approach to sequential meta-analysis in the context of Vioxx before considering dropouts in the key APPROVe study. It also presents a Bayesian approach to handling dropout and showcases the utility of Bayesian analysis in addressing multiple, challenging statistical issues and questions arising from clinical trials.
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Book chapters on the topic "Sequential and selective labeling"

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McKinney, Michael L., and Julie L. Lockwood. "Biotic Homogenization: A Sequential and Selective Process." In Biotic Homogenization, 1–17. Boston, MA: Springer US, 2001. http://dx.doi.org/10.1007/978-1-4615-1261-5_1.

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Zhao, Zhongtang, Li Liu, Lingling Li, and Qian Ma. "SLOSELM: Self Labeling Online Sequential Extreme Learning Machine." In Internet and Distributed Computing Systems, 179–89. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-45940-0_16.

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Wang, Fei, Youdong Ding, Huan Liang, and Jing Wen. "Discriminative and Selective Pseudo-Labeling for Domain Adaptation." In MultiMedia Modeling, 365–77. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-67832-6_30.

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Chen, Gang, Ran Xu, and Sargur N. Srihari. "Sequential Labeling with Online Deep Learning: Exploring Model Initialization." In Machine Learning and Knowledge Discovery in Databases, 772–88. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-46227-1_48.

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Tsukiji, Shinya, and Itaru Hamachi. "Ligand-Directed Tosyl Chemistry for Selective Native Protein Labeling In Vitro, In Cells, and In Vivo." In Site-Specific Protein Labeling, 243–63. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2272-7_17.

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Kurishita, Yasutaka, and Itaru Hamachi. "Selective Labeling and Imaging of Protein Using Metal Complex." In Coordination Chemistry in Protein Cages, 221–39. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118571811.ch9.

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Luengo, Imanol, Mark Basham, and Andrew P. French. "Selective Labeling: Identifying Representative Sub-volumes for Interactive Segmentation." In Patch-Based Techniques in Medical Imaging, 17–24. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-47118-1_3.

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Betton, Jean-Michel, Nicolae Palibroda, Abdelkader Namane, Thomas Metzler, and Octavian Bârzu. "Selective Labeling of Proteins in the RTS 500 System." In Cell-Free Translation Systems, 219–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-59379-6_21.

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Wang, Xudong, Long Lian, and Stella X. Yu. "Unsupervised Selective Labeling for More Effective Semi-supervised Learning." In Lecture Notes in Computer Science, 427–45. Cham: Springer Nature Switzerland, 2022. http://dx.doi.org/10.1007/978-3-031-20056-4_25.

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Tong, Kit I., Masayuki Yamamoto, and Toshiyuki Tanaka. "Selective Isotope Labeling of Recombinant Proteins in Escherichia coli." In Intrinsically Disordered Protein Analysis, 439–48. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-3704-8_30.

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Conference papers on the topic "Sequential and selective labeling"

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Wang, Yiran, Hiroyuki Shindo, Yuji Matsumoto, and Taro Watanabe. "Structured Refinement for Sequential Labeling." In Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021. Stroudsburg, PA, USA: Association for Computational Linguistics, 2021. http://dx.doi.org/10.18653/v1/2021.findings-acl.164.

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Sun, Xu, and Jun'ichi Tsujii. "Sequential labeling with latent variables." In the 12th Conference of the European Chapter of the Association for Computational Linguistics. Morristown, NJ, USA: Association for Computational Linguistics, 2009. http://dx.doi.org/10.3115/1609067.1609153.

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Kang, Qiyu, and Wee Peng Tay. "Sequential multi-class labeling in crowdsourcing." In WI '17: International Conference on Web Intelligence 2017. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3106426.3106446.

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Màrquez, Lluís, Pere Comas, Jesús Giménez, and Neus Català. "Semantic role labeling as sequential tagging." In the Ninth Conference. Morristown, NJ, USA: Association for Computational Linguistics, 2005. http://dx.doi.org/10.3115/1706543.1706579.

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Chen, Sheng, Alan Fern, and Sinisa Todorovic. "Multi-object Tracking via Constrained Sequential Labeling." In 2014 IEEE Conference on Computer Vision and Pattern Recognition (CVPR). IEEE, 2014. http://dx.doi.org/10.1109/cvpr.2014.148.

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Qiao, Maoying, Wei Bian, Richard Yi Da Xu, and Dacheng Tao. "Diversified hidden Markov models for sequential labeling." In 2016 IEEE 32nd International Conference on Data Engineering (ICDE). IEEE, 2016. http://dx.doi.org/10.1109/icde.2016.7498400.

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Kim, Seokhwan, and Rafael E. Banchs. "Sequential Labeling for Tracking Dynamic Dialog States." In Proceedings of the 15th Annual Meeting of the Special Interest Group on Discourse and Dialogue (SIGDIAL). Stroudsburg, PA, USA: Association for Computational Linguistics, 2014. http://dx.doi.org/10.3115/v1/w14-4345.

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Truong, Anh, S. Rasoul Etesami, and Negar Kiyavash. "Selective Labeling in Learning with Expert Advice." In 2021 American Control Conference (ACC). IEEE, 2021. http://dx.doi.org/10.23919/acc50511.2021.9482705.

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Wu, W., and E. Wong. "Intravascular effect in velocity-selective arterial spin labeling." In 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1615804.

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Ono, Satoshi, Haruki Matsuyama, Ken-ichi Fukui, and Shigeki Hosoda. "Error detection of oceanic observation data using sequential labeling." In 2015 IEEE International Conference on Data Science and Advanced Analytics (DSAA). IEEE, 2015. http://dx.doi.org/10.1109/dsaa.2015.7344896.

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Reports on the topic "Sequential and selective labeling"

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Kaszychi, C. A., and G. E. M. Hall. Application of phase selective and sequential extraction methodologies in surficial geochemistry. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 1996. http://dx.doi.org/10.4095/207585.

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