Carsten Bruckner - Academia.edu (original) (raw)
Papers by Carsten Bruckner
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
Clinical pharmacology and therapeutics, Jan 19, 2015
This manuscript provides nomenclature recommendations developed by an international workgroup to ... more This manuscript provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward. This article is protected by copyright. All rights reserved.
Tappi Journal, 2002
... 7. Liu, Y., Gustafson, R., Callis, J., and McKean, W., TAPPI J. 82(9): 109(1999). ... This pa... more ... 7. Liu, Y., Gustafson, R., Callis, J., and McKean, W., TAPPI J. 82(9): 109(1999). ... This paper is also published on TAPPI's web site <www.tappi.org> and summa-rized in the December Solutions! for People, Processes and Paper magazine (Vol. 85 No. 12) Page 6. ...
Journal of Microcolumn Separations, 1999
ABSTRACT
Talanta, 1996
A chemical sensor for gas phase measurements is reported which combines the principles of chemica... more A chemical sensor for gas phase measurements is reported which combines the principles of chemical separation and fiber optic detection. The analyzer incorporates an annular column chromatographic sensor. constructed by inserting a polymer-clad optical fiber into a silica capillary. Light from a helium-neon laser is launched down the fiber, producing a steady intensity distribution within the fiber. but a low background of scattered light. When sample vapor is introduced to the sensor. and an analyte-rich volume interacts with the polymer cladding, chromatographic retention is observed .+znultaneous/~~ with a change in the local refractive index of the cladding. An increase in cladding refractive index (RI) causes light to be coupled out of the fiber, with detection at a right-angle to the annular column length to provide optimum S:N ratio. This detection mechanism is called mode-filtered light detection. We report a gas chromatographic separation on a 3.1 m annular column (320 /lrn id. silica tube. 228 pm o.d. fiber with a 12 jlrn fluorinated silicone clad) of methane, benzene, butanone and chlorobenzene in 6 min. The annular column length was reduced to 22 cm to function as a sensor, with selected organic vapors exhibiting unique retention times and detection selectivity. The detection selectivity is determined by the analyte RI and the partition coefficient into the cladding. The calculated limit of detection (LOD) for benzene vapor is 0.03% by volume in nitrogen, and several chlorinated species had LOD values less than 1%. For binary mixtures of organic vapors, the detected response appears to be the linear combination of the two organic standards, suggesting that the annular column may be useful as a general approach for designing chemical sensors that incorporate separation and optical detection principles simultaneously.
Analytical Chemistry, 1998
... MIO-16XE-50, National Instruments, Austin, TX) to monitor the GC×GC FID signal at ... 5 shows... more ... MIO-16XE-50, National Instruments, Austin, TX) to monitor the GC×GC FID signal at ... 5 shows an overlay of four GC×GC analyses of a white gas sample, each ... developed a standardization technique for multidimensional liquid chromatography/UV−visible absorbance data, which ...
Analytical Chemistry, 1999
reported. An injected sample is first split between two GC columns that provide complementary sep... more reported. An injected sample is first split between two GC columns that provide complementary separations. The effluent from the two columns is recombined prior to detection with a single TOF-MS. Switching from single to parallel columns increases the chemical selectivity of a GC/TOF-MS data set without increasing analysis time, by doubling the number of peaks, or features, in the chromatographic dimension. The resulting analyzer can be used to reduce analysis times for partially resolved peaks. Simulations compare the quantitative precision of paralleland single-column instruments using the generalized rank annihilation method (GRAM). Results indicate that a parallel column GC/TOF-MS should substantially improve the chemical selectivity and quantitative precision of the analysis relative to a single-column instrument. For a column at half its peak capacity, for example, a singlecolumn instrument met the target precision less than 75% of the time, while a parallel-column instrument achieved 95% success. Parallel-column analyses of methyl tertbutyl ether (MTBE) and benzene in gasoline samples were also performed to support the simulation studies. An objective chromatographic standardization technique corrected for retention time shifts before GRAM was applied. Although MTBE and benzene were poorly resolved in the 40-s runs, chemometric techniques successfully quantitated them.
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
Proceedings of SPIE - The International Society for Optical Engineering
A novel chemical analyzer is described in which an optical fiber is inserted into a transparent c... more A novel chemical analyzer is described in which an optical fiber is inserted into a transparent capillary tube, such that the inner diameter of the tube is only a few microns larger than the outer diameter of the fiber cladding. This configuration is referred to as a torus column. When a sample volume is introduced to the torus column at a low flow rate, propagated light is mode-filtered due to a change in the critical angle at the core/clad interface, as a result of in-situ extracted chemical species. Conventionally, chemical species extracted into the cladding are sensed as a change in the transmitted light at the end of the fiber. An alternative approach, measuring this mode-filtered light directly along the side of the fiber, is reported. The new approach has a signal-to-noise advantage over the conventional approach. The result is a low volume sensor that temporally separates, as well as detects, chemical species that partition into the fiber cladding. The temporal information enhances sensor performance, providing first order information for subsequent data analysis. We have examined the modulation of the critical angle by chemical species of interest at steady-state concentrations, and as transient concentration profiles that were shifted in time. In summary, the analyzer has chemical selectivity provided by differences in the refractive index, distribution coefficient, and transient time of the concentration profile of each chemical species in a sample. The chemical analyzer should be a promising tool for process and environmental monitoring.
Advances in chromatography
Genome Research
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. ... more Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of approximately 90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high...
Chemical, Biochemical, and Environmental Fiber Sensors VI, 1994
ABSTRACT
Advances in Chromatography, 2003
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
A novel chemical analyzer is described in which an optical fiber is inserted into a transparent c... more A novel chemical analyzer is described in which an optical fiber is inserted into a transparent capillary tube, such that the inner diameter of the tube is only a few microns larger than the outer diameter of the fiber cladding. This configuration is referred to as a torus column. When a sample volume is introduced to the torus column at a low flow rate, propagated light is mode-filtered due to a change in the critical angle at the core/clad interface, as a result of in-situ extracted chemical species. Conventionally, chemical species extracted into the cladding are sensed as a change in the transmitted light at the end of the fiber. An alternative approach, measuring this mode-filtered light directly along the side of the fiber, is reported. The new approach has a signal-to-noise advantage over the conventional approach. The result is a low volume sensor that temporally separates, as well as detects, chemical species that partition into the fiber cladding. The temporal information ...
Proceedings of the National Academy of Sciences, 2005
Identification of the genetic basis of common disease may require comprehensive sequence analysis... more Identification of the genetic basis of common disease may require comprehensive sequence analysis of coding regions and regulatory elements in patients and controls to find genetic effects caused by rare or heterogeneous mutations. In this study, we demonstrate how mismatch repair detection on tag arrays can be applied in a case-control study. Mismatch repair detection allows >1,000 amplicons to be screened for variations in a single laboratory reaction. Variation scanning in 939 amplicons, mostly in coding regions within a linkage peak, was done for 372 patients and 404 controls. In total, >180 Mb of DNA was scanned. Several variants more prevalent in patients than in controls were identified. This study demonstrates an approach to the discovery of susceptibility genes for common disease: large-scale direct sequence comparison between patients and controls. We believe this approach can be scaled up to allow sequence comparison in the whole-genome coding regions among large sets of cases and controls at a reasonable cost in the near future.
Pharmacogenomics, 2007
The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporte... more The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporter genes can contribute to considerable interindividual variation in drug disposition and response. Therefore, it has been of increasing interest to generate scalable, flexible and cost-effective technologies for large-scale genotyping of the drug-metabolizing enzyme and transporter genes. However, the number of drug-metabolizing enzyme and transporter gene variants exceeds the capacity of current technologies to comprehensively assess multiple polymorphisms in a single, multiplexed assay. The Targeted Genotyping System (Affymetrix, CA, USA) provides a solution to this challenge, by combining molecular inversion probe technology with universal microarrays to provide a method that is capable of analyzing thousands of variants in a single reaction, while remaining relatively insensitive to cross-reactivity between reaction components. This review will focus on the Targeted Genotyping System and how this technology was adapted to enable comprehensive analysis of drug-metabolizing enzyme and transporter gene polymorphisms.
Genome Research, 2005
fax (650) 228-7405. Article and publication date are at
European Journal of Human Genetics, 2006
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
Clinical pharmacology and therapeutics, Jan 19, 2015
This manuscript provides nomenclature recommendations developed by an international workgroup to ... more This manuscript provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward. This article is protected by copyright. All rights reserved.
Tappi Journal, 2002
... 7. Liu, Y., Gustafson, R., Callis, J., and McKean, W., TAPPI J. 82(9): 109(1999). ... This pa... more ... 7. Liu, Y., Gustafson, R., Callis, J., and McKean, W., TAPPI J. 82(9): 109(1999). ... This paper is also published on TAPPI's web site <www.tappi.org> and summa-rized in the December Solutions! for People, Processes and Paper magazine (Vol. 85 No. 12) Page 6. ...
Journal of Microcolumn Separations, 1999
ABSTRACT
Talanta, 1996
A chemical sensor for gas phase measurements is reported which combines the principles of chemica... more A chemical sensor for gas phase measurements is reported which combines the principles of chemical separation and fiber optic detection. The analyzer incorporates an annular column chromatographic sensor. constructed by inserting a polymer-clad optical fiber into a silica capillary. Light from a helium-neon laser is launched down the fiber, producing a steady intensity distribution within the fiber. but a low background of scattered light. When sample vapor is introduced to the sensor. and an analyte-rich volume interacts with the polymer cladding, chromatographic retention is observed .+znultaneous/~~ with a change in the local refractive index of the cladding. An increase in cladding refractive index (RI) causes light to be coupled out of the fiber, with detection at a right-angle to the annular column length to provide optimum S:N ratio. This detection mechanism is called mode-filtered light detection. We report a gas chromatographic separation on a 3.1 m annular column (320 /lrn id. silica tube. 228 pm o.d. fiber with a 12 jlrn fluorinated silicone clad) of methane, benzene, butanone and chlorobenzene in 6 min. The annular column length was reduced to 22 cm to function as a sensor, with selected organic vapors exhibiting unique retention times and detection selectivity. The detection selectivity is determined by the analyte RI and the partition coefficient into the cladding. The calculated limit of detection (LOD) for benzene vapor is 0.03% by volume in nitrogen, and several chlorinated species had LOD values less than 1%. For binary mixtures of organic vapors, the detected response appears to be the linear combination of the two organic standards, suggesting that the annular column may be useful as a general approach for designing chemical sensors that incorporate separation and optical detection principles simultaneously.
Analytical Chemistry, 1998
... MIO-16XE-50, National Instruments, Austin, TX) to monitor the GC×GC FID signal at ... 5 shows... more ... MIO-16XE-50, National Instruments, Austin, TX) to monitor the GC×GC FID signal at ... 5 shows an overlay of four GC×GC analyses of a white gas sample, each ... developed a standardization technique for multidimensional liquid chromatography/UV−visible absorbance data, which ...
Analytical Chemistry, 1999
reported. An injected sample is first split between two GC columns that provide complementary sep... more reported. An injected sample is first split between two GC columns that provide complementary separations. The effluent from the two columns is recombined prior to detection with a single TOF-MS. Switching from single to parallel columns increases the chemical selectivity of a GC/TOF-MS data set without increasing analysis time, by doubling the number of peaks, or features, in the chromatographic dimension. The resulting analyzer can be used to reduce analysis times for partially resolved peaks. Simulations compare the quantitative precision of paralleland single-column instruments using the generalized rank annihilation method (GRAM). Results indicate that a parallel column GC/TOF-MS should substantially improve the chemical selectivity and quantitative precision of the analysis relative to a single-column instrument. For a column at half its peak capacity, for example, a singlecolumn instrument met the target precision less than 75% of the time, while a parallel-column instrument achieved 95% success. Parallel-column analyses of methyl tertbutyl ether (MTBE) and benzene in gasoline samples were also performed to support the simulation studies. An objective chromatographic standardization technique corrected for retention time shifts before GRAM was applied. Although MTBE and benzene were poorly resolved in the 40-s runs, chemometric techniques successfully quantitated them.
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
Proceedings of SPIE - The International Society for Optical Engineering
A novel chemical analyzer is described in which an optical fiber is inserted into a transparent c... more A novel chemical analyzer is described in which an optical fiber is inserted into a transparent capillary tube, such that the inner diameter of the tube is only a few microns larger than the outer diameter of the fiber cladding. This configuration is referred to as a torus column. When a sample volume is introduced to the torus column at a low flow rate, propagated light is mode-filtered due to a change in the critical angle at the core/clad interface, as a result of in-situ extracted chemical species. Conventionally, chemical species extracted into the cladding are sensed as a change in the transmitted light at the end of the fiber. An alternative approach, measuring this mode-filtered light directly along the side of the fiber, is reported. The new approach has a signal-to-noise advantage over the conventional approach. The result is a low volume sensor that temporally separates, as well as detects, chemical species that partition into the fiber cladding. The temporal information enhances sensor performance, providing first order information for subsequent data analysis. We have examined the modulation of the critical angle by chemical species of interest at steady-state concentrations, and as transient concentration profiles that were shifted in time. In summary, the analyzer has chemical selectivity provided by differences in the refractive index, distribution coefficient, and transient time of the concentration profile of each chemical species in a sample. The chemical analyzer should be a promising tool for process and environmental monitoring.
Advances in chromatography
Genome Research
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. ... more Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of approximately 90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high...
Chemical, Biochemical, and Environmental Fiber Sensors VI, 1994
ABSTRACT
Advances in Chromatography, 2003
Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a s... more Paper pulp is added to a stain solution. The stain solution and pulp fibers are mixed to form a slurry. Samples are removed from the slurry and are admixed with dilution water and a bleach. Then, the fibers are moved into a flow cell where they are subjected to a light source adapted to stimulate fluorescence from the stained pulp fiber. Before the fiber slurry enters the flow cell it is mixed with a dilution water of bleach to reduce background fluorescence. The fluorescent light is collimated and directed through a dichroic filter onto a fluorescence splitting dichroic filter.
A novel chemical analyzer is described in which an optical fiber is inserted into a transparent c... more A novel chemical analyzer is described in which an optical fiber is inserted into a transparent capillary tube, such that the inner diameter of the tube is only a few microns larger than the outer diameter of the fiber cladding. This configuration is referred to as a torus column. When a sample volume is introduced to the torus column at a low flow rate, propagated light is mode-filtered due to a change in the critical angle at the core/clad interface, as a result of in-situ extracted chemical species. Conventionally, chemical species extracted into the cladding are sensed as a change in the transmitted light at the end of the fiber. An alternative approach, measuring this mode-filtered light directly along the side of the fiber, is reported. The new approach has a signal-to-noise advantage over the conventional approach. The result is a low volume sensor that temporally separates, as well as detects, chemical species that partition into the fiber cladding. The temporal information ...
Proceedings of the National Academy of Sciences, 2005
Identification of the genetic basis of common disease may require comprehensive sequence analysis... more Identification of the genetic basis of common disease may require comprehensive sequence analysis of coding regions and regulatory elements in patients and controls to find genetic effects caused by rare or heterogeneous mutations. In this study, we demonstrate how mismatch repair detection on tag arrays can be applied in a case-control study. Mismatch repair detection allows >1,000 amplicons to be screened for variations in a single laboratory reaction. Variation scanning in 939 amplicons, mostly in coding regions within a linkage peak, was done for 372 patients and 404 controls. In total, >180 Mb of DNA was scanned. Several variants more prevalent in patients than in controls were identified. This study demonstrates an approach to the discovery of susceptibility genes for common disease: large-scale direct sequence comparison between patients and controls. We believe this approach can be scaled up to allow sequence comparison in the whole-genome coding regions among large sets of cases and controls at a reasonable cost in the near future.
Pharmacogenomics, 2007
The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporte... more The combined effects of multiple polymorphisms in several drug-metabolizing enzyme and transporter genes can contribute to considerable interindividual variation in drug disposition and response. Therefore, it has been of increasing interest to generate scalable, flexible and cost-effective technologies for large-scale genotyping of the drug-metabolizing enzyme and transporter genes. However, the number of drug-metabolizing enzyme and transporter gene variants exceeds the capacity of current technologies to comprehensively assess multiple polymorphisms in a single, multiplexed assay. The Targeted Genotyping System (Affymetrix, CA, USA) provides a solution to this challenge, by combining molecular inversion probe technology with universal microarrays to provide a method that is capable of analyzing thousands of variants in a single reaction, while remaining relatively insensitive to cross-reactivity between reaction components. This review will focus on the Targeted Genotyping System and how this technology was adapted to enable comprehensive analysis of drug-metabolizing enzyme and transporter gene polymorphisms.
Genome Research, 2005
fax (650) 228-7405. Article and publication date are at
European Journal of Human Genetics, 2006