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Results for “data fragmentation”

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At least 127 records · Page 7Linked to original sources

PubMed1999

SPME-MS-MVA as an electronic nose for the study of off-flavors in milk.

A new technique using solid-phase microextraction, mass spectrometry, and multivariate analysis (SPME-MS-MVA) was developed for the study of off-flavors in milk. The analytical column of a GC/MS system was replaced with a 1-m deactivated fused-silica column, which served as a transfer line to deliver volatiles extracted from milk samples with a Carboxen-SPME fiber to the mass spectrometer. Mass fragmentation data resulting from the unresolved milk volatile components were subjected to MVA. Principal component analysis based on SPME-MS-MVA provided rapid differentiation of control reduced-fat milk (2% butterfat content) samples from reduced-fat milk samples abused by light, heat, copper, and microbial contamination. The three psychrotrophic bacteria studied included Pseudomonas fluorescens, Pseudomonas aureofaciens, and Pseudomonas putrefaciens. SPME-MS-MVA is rapid and offers significant advantages over commercial electronic nose instruments currently being used as quality assurance tools to differentiate normal-tasting food and beverage samples from those containing off-flavors and malodors.

Animals↗

PubMed1997

Mechanisms of oxygen taxis in bacteria.

Since 1881 when Englemann reported aerotaxis in bacteria, an understanding of the molecular nature of the signal transduction remains a daring goal for microbiologists. This short review discusses known facts and recent advances in the field including the discovery of the flavoprotein receptor which drives Escherichia coli towards oxygen. Possible mechanisms of oxygen sensing in various bacterial species are considered in connection with the existing, often fragmental, data on phototaxis, redox taxis and taxis repellent effect of the reactive oxygen species (ROS).

Bacteria↗

PubMed2005

Fragmentation of HCN in optically selected mass spectrometry: nonthermal ion cooling in helium nanodroplets.

A technique that combines infrared laser spectroscopy and helium nanodroplet mass spectrometry, which we refer to as optically selected mass spectrometry, is used to study the efficiency of ion cooling in helium. Electron-impact ionization is used to form He(+) ions within the droplets, which go on to transfer their charge to the HCN dopant molecules. Depending upon the droplet size, the newly formed ion either fragments or is cooled by the helium before fragmentation can occur. Comparisons with gas-phase fragmentation data suggest that the cooling provided by the helium is highly nonthermal. An "explosive" model is proposed for the cooling process, given that the initially hot ion is embedded in such a cold solvent.

Journal Article↗

PubMed2003

Structural analysis of the DNA-binding domain of the Erwinia amylovora RcsB protein and its interaction with the RcsAB box.

The transcriptional regulator RcsB interacts with other coactivators to control the expression of biosynthetic operons in enterobacteria. While in a heterodimer complex with the regulator RcsA the RcsAB box consensus is recognized, DNA binding sites for RcsB without RcsA have also been identified. The conformation of RcsB might therefore be modulated upon interaction with various coactivators, resulting in the recognition of different DNA targets. We report the solution structure of the C-terminal DNA-binding domain of the RcsB protein from Erwinia amylovora spanning amino acid residues 129-215 solved by heteronuclear magnetic resonance (NMR) spectroscopy. The C-terminal domain is composed of four alpha-helices where two central helices form a helix-turn-helix motif similar to the structures of the regulatory proteins GerE, NarL, and TraR. Amino acid residues involved in the RcsA independent DNA binding of RcsB were identified by titration studies with a RcsAB box consensus fragment. Data obtained from NMR spectroscopy together with surface plasmon resonance measurements demonstrate that the RcsAB box is specifically recognized by the RcsAB heterodimer as well as by RcsB alone. However, the binding constant of RcsB alone at target promoters from Escherichia coli, E. amylovora, and Pantoea stewartii was approximately 1 order of magnitude higher compared with that of the RcsAB heterodimer. We present evidence that the obvious role of RcsA is not to alter the DNA binding specificity of RcsB but to stabilize RcsB-DNA complexes.

Amino Acid Motifs↗

PubMed1972

Preparation of plasma membrane from isolated neurons.

A bulk fraction enriched with respect to neuronal cell bodies was used as starting material for the isolation of neuronal plasma membrane The cells were gently homogenized in isotonic sucrose and a crude membrane containing fraction sedimented at 3000 g. Subsequently, the membrane fraction was purified on a discontinuous sucrose density gradient between 35% and 25 5% sucrose (w/w). Enzymatic analyses showed a 4-5-fold enrichment in plasma membrane markers, and a 10-15% contamination of mitochondrial and microsomal material. Electron micrographs of the membrane fraction confirmed the enzymatic data Fragmented membranes were found, mainly in vesicular form No ribosomes, but a few mitochondria and some multilamellar membranes were seen

Adenosine Triphosphatases↗

PubMed1999

Bifocal reflector for electrohydraulic lithotripters.

OBJECTIVE: To describe the design and construction of a bifocal reflector that could be used in electrohydraulic extracorporeal shockwave lithotripters in order to increase their efficiency. METHODS: The new reflector is obtained by joining two sectors of two rotationally symmetric ellipsoidal reflectors having different distances between their foci, which results in a bifocal composite reflector with the F1 foci in coincidence and the two F2 foci separated by a certain distance. As in conventional reflectors, shockwaves are generated by the electrical breakdown of water between two electrodes, located at the focus (F1) closest to the reflector. A prototype was constructed and tested in an experimental shockwave generator of our own make, using two different types of kidney-stone models, one to test the stone fragmentation abilities, and the other to test the stone pitting abilities. Fragmentation data for the new reflector were compared with those of a conventional ellipsoidal reflector tested on the same device. RESULTS: The new design appeared to be more efficient in breaking up both types of kidney-stone models than the conventional reflector. Pressure measurements were obtained with both reflectors using needle hydrophones. The physical background of shockwave reflection on both reflectors is also explained. CONCLUSION: With this new reflector, it could be possible, in principle, to reduce the treatment time of extracorporeal shockwave lithotripsy.

Equipment Design↗

PubMed1994

Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision, and tests of disequilibrium with a maternally inherited mitochondrial polymorphism.

We have surveyed a chloroplast DNA restriction fragment length polymorphism in 745 individuals, distributed rangewide in eight allopatric natural populations of jack pine (Pinus banksiana Lamb.) and eight allopatric natural populations of lodgepole pine (Pinus contorta Dougl.). The polymorphic region of the chloroplast genome is located near duplicated psbA genes. Fourteen length variants were found in the survey, and these variants distinguished the two species qualitatively. Variant diversities were high in both species (hes = 0.43 in jack pine; hes = 0.44 in lodgepole pine). Population subdivision was weak within and among lodgepole pine subspecies and in jack pine (i.e., theta values were less than 0.05). This weak subdivision is compatible with theoretical predictions for paternally inherited markers in wind-pollinated outcrossers, as well as for polymorphisms with high length mutation rates. If these populations are at a drift-migration equilibrium, the chloroplast DNA restriction fragment data and previous mitochondrial frequency data from the same individuals are consistent with gene flow that is differential through seeds and pollen. The new data have permitted the first empirical tests of disequilibrium between maternally and paternally inherited factors. As expected, these tests failed to detect convincing evidence of nonrandom association between chloroplast and mitochondrial variants.

Chloroplasts↗

PubMedDate not supplied

Genetic divergence in South African Wildebeest: comparative cytogenetics and analysis of mitochondrial DNA.

The blue and the black wildebeest, Connochaetes taurinus and C. gnou, are currently classified as congeneric, but previous reports have placed C. taurinus in its own genus, Gorgon. To further clarify the evolutionary relationship between these two species, we examined and compared their mitotic chromosomes and mitochondrial DNA (mtDNA). No species-specific G-banded or C-banded chromosomal markers were found, and we conclude that the karyotypes are invariant at the level of resolution obtained. An evolutionary divergence time of approximately 1 million years was calculated from mtDNA restriction fragment data, indicating a close phylogenetic relationship for the two wildebeest species. The low nucleotide diversity detected within the black wildebeest (0.09%) is thought to reflect the recent population bottleneck to which the species has been subjected. In contrast, the limited heterogeneity (0.02%) within the South African blue wildebeest herds sampled in this study was surprising, and we argue that for many populations, especially those on smaller reserves, this may reflect common descent from a small number of animals through management-controlled translocations.

Animals↗

PubMed1998

Evaluation of aminoglycoside pharmacokinetics in postpartum patients using Bayesian forecasting.

Many postpartum women have suboptimal serum concentrations after standard doses of aminoglycosides. The purpose of this study was to characterize the pharmacokinetics of aminoglycosides in postpartum patients through the use of Bayesian forecasting and to test the ability of these subpopulation parameters to predict actual aminoglycoside serum concentrations. In phase I, 28 postpartum patients who received empiric gentamicin therapy were identified and Bayesian subpopulation parameters generated. In phase II, additional gentamicin concentrations (peaks and troughs) were evaluated to test bias and precision of Bayesian subpopulation versus traditional estimates in predicting actual aminoglycoside serum concentrations. In phase I, 56 gentamicin serum concentrations in 28 patients, (age, 26 +/- 7 years; actual body weight [ABW], 84.3 +/- 18.4 kg; ideal body weight [IBW], 54.6 +/- 5.1 kg; dosing weight [DW], 66.3 +/- 9.4 kg; creatinine clearance [Clcr], 140.4 +/- 34.0 ml/min / 1.73 m2), were evaluated to calculate subpopulation pharmacokinetic parameters of volume of distribution (Vd) 0.29 +/- 0.07 l/kg (DW); elimination rate constant (ke) 0.29 +/- 0.05 h-1 and half-life (t1/2) 2.5 +/- 0.5 hours. In phase II, 50 gentamicin serum concentrations in 25 patients (age, 23 +/- 4 years; ABW 79.4 +/- 17.5 kg; IBW 55.0 +/- 7.3 kg; DW 64.8 +/- 9.6 kg; Clcr 139.7 +/- 29.3 ml/min/1.73 m2) were evaluated to calculate subpopulation pharmacokinetic parameters of Vd 0.30 +/- 0.04 l/kg (DW); ke 0.27 +/- 0.06 h-1; and t1/2 2.9 +/- 0.8 hours. Predictive performance tests (95% confidence intervals) demonstrate that subpopulation postpartum Bayesian parameters show greater precision for peak concentrations and less bias for trough concentrations than do traditional population estimates (p < 0.05). Definition of the Bayesian subpopulation parameters will allow us to dose aminoglycosides optimally in postpartum patients who have fragmented data.

Adult↗

PubMed2001

Comparing vertebrate whole-genome shotgun reads to the human genome.

Multi-species sequence comparisons are a very efficient way to reveal conserved genes. Because sequence finishing is expensive and time consuming, many genome sequences are likely to stay incomplete. A challenge is to use these fragmented data for understanding the human genome. Methods for using cross-species whole-genome shotgun sequence (WGS) for genome annotation are described in this paper. About one-half million high-quality rat WGS reads (covering 7.5% of the rat genome) generated at the Baylor College of Medicine Human Genome Sequencing Center were compared with the human genome. Using computer-generated random reads as a negative control, a set of parameters was determined for reliable interpretation of BLAST search results. About 10% of the rat reads contain regions that are conserved in the human genomic sequence and about one-third of these include known gene-coding regions. Mapping the conserved regions to human chromosomes showed a 23-fold enrichment for coding regions compared with noncoding regions. This approach can also be applied to other mammalian genomes for gene finding. These data predicted approximately 42,500 genes in the human, slightly more than reported previously.

Animals↗

PubMed1984

Regeneration of insertionally inactivated streptococcal DNA fragments after excision of transposon Tn916 in Escherichia coli: strategy for targeting and cloning of genes from gram-positive bacteria.

The conjugative transposon Tn916 (15 kilobases), originally identified in Streptococcus faecalis DS16, has been cloned as an intact element on the pBR322-derived vector pGL101 in Escherichia coli. The EcoRI F' (EcoRI F::Tn916) fragment of pAM211 (pAD1::Tn916) was cloned into the single EcoRI site of pGL101 to form the chimera, pAM120, by selecting for the expression of Tn916-encoded tetracycline resistance (Tcr). Interestingly, in the absence of continued selection for Tcr, Tn916 excised from pAM120 at high frequency. This excision event resulted in a plasmid species consisting of the pGL101 vector and a 2.7-kilobase restriction fragment comigrating with the EcoRI F fragment of pAD1 during agarose gel electrophoresis. Filter blot hybridization experiments showed the 2.7-kilobase fragment generated as a result of Tn916 excision to be homologous with the EcoRI F fragment of pAD1. Analogous results were obtained with another chimera, pAM170, generated by ligating the EcoRI D' (EcoRI D::Tn916) fragment of pAM210 (pAD1::Tn916) to EcoRI-digested pGL101. Comparison of the AluI and RsaI cleavage patterns of the EcoRI F fragment isolated after Tn916 excision with those from an EcoRI F fragment derived from pAD1 failed to detect any difference in the two fragments: data in support of a precise Tn916 excision event in E. coli. Subcloning experiments showed that an intact transposon was required for Tn916 excision and located the Tcr determinant near the single HindIII site on Tn916. Although excision occurred with high frequency in E. coli, Tn916 insertion into the E. coli chromosome was a much rarer event. Tcr transformants were not obtained when pAM120 DNA was used to transform a polA1 strain, E. coli C2368.

Chromosomes, Bacterial↗

PubMed2006

Light stimulus frequency dependence of activity in the rat visual system as studied with high-resolution BOLD fMRI.

The neurophysiology of the rodent visual system has mainly been investigated by invasive and ex-vivo techniques providing fragmented data. This area of research has been deprived of functional MRI studies based on blood oxygenation level dependent (BOLD) contrast, which allows a whole brain approach with a high spatial and temporal resolution. In the present study, we looked at the neurovascular response properties of the visual system of the pigmented rat, focusing on the visual cortex (VC), the superior colliculus (SC) and the flocculus-paraflocculus of the cerebellum (FL-PFL), using BOLD fMRI under domitor anesthesia. Visual stimulation was performed monocularly or binocularly while flashing light from a strobe unit was presented. For each structure, we assessed the flashing frequency that evoked the optimal BOLD response: Neither the VC nor the FL-PFL displayed frequency dependence during monocular visual stimulation, but were most sensitive to low frequencies (1-5 Hz) when flashing light was provided binocularly. The SC responded optimally to high flashing rates (8-12 Hz) during both monocular and binocular stimulation. The signal intensity changes in the VC and FL-PFL were locked to the stimulation period, whereas the BOLD response in the SC showed a similar onset but a very slow recovery at offset. The VC and FL-PFL, but not the SC, showed signs of binocular competition. The observed correlation between frequency-dependent responses of different visual areas during binocular visual presentation suggests a functional relationship between the VC and FL-PFL rather than between the SC and FL-PFL.

Animals↗

PubMedDate not supplied

Characterization of plasma membrane proteins from ovarian cancer cells using mass spectrometry.

To determine how the repertoire of plasma membrane proteins change with disease state, specifically related to cancer, several methods for preparation of plasma membrane proteins were evaluated. Cultured cells derived from stage IV ovarian tumors were grown to 90% confluence and harvested in buffer containing CHAPS detergent. This preparation was centrifuged at low speed to remove insoluble cellular debris resulting in a crude homogenate. Glycosylated proteins in the crude homogenate were selectively enriched using lectin affinity chromatography. The crude homogenate and the lectin purified sample were prepared for mass spectrometric evaluation. The general procedure for protein identification began with trypsin digestion of protein fractions followed by separation by reversed phase liquid chromatography that was coupled directly to a conventional tandem mass spectrometer (i.e. LCQ ion trap). Mass and fragmentation data for the peptides were searched against a human proteome data base using the informatics program SEQUEST. Using this procedure 398 proteins were identified with high confidence, including receptors, membrane-associated ligands, proteases, phosphatases, as well as structural and adhesion proteins. Results indicate that lectin chromatography provides a select subset of proteins and that the number and quality of the identifications improve as does the confidence of the protein identifications for this subset. These results represent the first step in development of methods to separate and successfully identify plasma membrane proteins from advanced ovarian cancer cells. Further characterization of plasma membrane proteins will contribute to our understanding of the mechanisms underlying progression of this deadly disease and may lead to new targeted interventions as well as new biomarkers for diagnosis.

Blood Proteins↗

PubMedDate not supplied

The use of power and influence: managing without authority.

All behaviors are the result of a person's perceptions of the best action to take, based on their analysis of the possible choices and likely outcomes. Fear of failure or embarrassment prevents many people from effectively communicating with others. Every communication comprises several data fragments, each of which is important in determining how influential the communication will be. Communicating a positive outcome is a powerful way to influence a person's desire to change.

Communication↗

PubMedDate not supplied

Implementation of a patient-centred and physician-oriented healthcare information system.

Integration of information has enabled expeditious operation in air transfer, banking, shopping, and stock brokerage, but not in healthcare. Existing health information systems (HIS) are concerned too much with departmental performance and charge billing, and neglect the end users--the patients and the physicians. The resultant HIS then has divergent operation to antagonize the physicians, and has fragmented data to the disadvantage of patients. Recognizing the problems and the trend of HIS, this study proposed and implemented a patient-centred and physician-oriented HIS in a Urology clinic. The proposed HIS had patient care as its core, and accurately coded the patient's diagnoses and therapy information. It also offered a friendly environment and complete function for the physician to administrate medical records and to provide healthcare services. The HIS had client/server structure and an open system to protect the hardware investment and the software implementation. It will be the key to success in complete hospital environments.

Hospital Information Systems↗

PubMed2003

Failed anterior cervical foraminotomy.

OBJECT: Anterior cervical foraminotomy has been advocated as a procedure that preserves the motion segment while treating radiculopathy due to degenerative cervical disc disease. Because the medical literature contains no long-term follow up or randomized studies related to this procedure, the authors reviewed their results, specifically examining cases of failure to determine the efficacy of the approach. METHODS: The authors identified 23 patients in whom unilateral cervical radiculopathy due to degenerative cervical disc disease was refractory to conservative therapy and in whom anterior cervical foraminotomy was performed between 1998 and 2000. The procedure involves ipsilateral exposure, microsurgical removal of the uncovertebral joint to identify the nerve root, and partial removal of the lateral anulus and or disc fragments. Data in those patients who underwent reoperation(s) were reviewed specifically for the procedure type, interval between index procedure and reoperation, and whether multiple procedures were performed. Of the 23 patients, 30% required at least one additional procedure. A good or excellent outcome at last follow-up examination was achieved in only 12 patients. CONCLUSIONS: In the current study the authors found a reoperation rate that is considerably higher than that in most series of anterior cervical surgery for radiculopathy. The presumed benefit of anterior cervical foraminotomy is preservation of the disc interspace; however, in this study, a significant number of patients failed to experience a satisfying outcome. Currently the authors do not recommend anterior cervical foraminotomy as a stand-alone procedure.

Adult↗

PubMed2026

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses.

Electronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkit's SAIGE family of pipelines - supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing - together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted.

Journal Article↗

PubMed2006

Landscape of current toxicity databases and database standards.

Having readily available historical information for modeling toxicity has become important throughout the various stages of research and development. The high cost of late-phase attrition and recent international regulatory legislations have made even more acute the need to be able to mine the fragmented data and information available across diverse databases. In addition, the general trend to accelerate regulatory processes globally makes the effective use of existing data an imperative. To achieve efficient screening, develop profiles and gain the ability to cross reference, databases must be interoperated to allow data exchange and integration. Several database standards and controlled vocabulary initiatives have been used in the development of toxicity data models to transform the current landscape. This review describes the major databases of toxicological information now available, and provides a simple example of standardization that demonstrates the benefits of a toxicity database containing such qualified data.

Animals↗