Clin Physiol Funct Imaging
January 2025
Purpose: Brachial blood pressure (BP) is the current gold standard for BP assessment; however, measures of pulse wave velocity (PWV) and central blood pressure (CBP) may contribute uniquely to assessment of cardiovascular health status. As of yet, standards for assessment of CBP and PWV have not addressed the impact of hydration status on proper measurement. To understand the impact of hydration, PWV and CBP should be measured in a euhydrated and hypohydrated state.
View Article and Find Full Text PDFThe National Survey of Disinfection By-Products and Selected Emerging Contaminants investigated the formation of various disinfection by-products and contaminants in 65 water treatment systems (WTSs) across Canada. Results for six iodo-trihalomethanes (iodo-THMs) are reported in this paper. The participating water treatment systems included large, medium and small systems using water sources and treatment processes which were representative of Canadian drinking water.
View Article and Find Full Text PDFIntroduction: New York City Article 47 regulations, implemented in 2007, require licensed child care centers to improve the nutrition, physical activity, and television-viewing behaviors of enrolled children. To supplement an evaluation of the Article 47 regulations, we conducted an exploratory ecologic study to examine changes in childhood obesity prevalence among low-income preschool children enrolled in the Nutrition Program for Women, Infants, and Children (WIC) in New York City neighborhoods with or without a district public health office. We conducted the study 3 years before (from 2004 through 2006) and after (from 2008 through 2010) the implementation of the regulations in 2007.
View Article and Find Full Text PDFWith the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease.
View Article and Find Full Text PDFBackground: HR HPV genotypes when assayed collectively, achieve high sensitivity but low specificity for the prediction of CIN2+. Knowledge of the specific genotypes in an infection may facilitate the use of HR HPV detection in routine clinical practice.
Objectives: To compare the rate of HR HPV detection and the accuracy of CIN2+ prediction between PapType test (Genera Biosystems) and other commercially available HR HPV assays, and to examine the value of full HPV genotyping.
Int J Nurs Educ Scholarsh
March 2014
Interviewing standardized patients (SPs) trained to model psychiatric disorders can promote student nurses' interview skills and therapeutic communication, while at the same time increasing their confidence and decreasing anxiety. From a constructivist view of education and Kolb's (1984; Experiential learning: Experience as the source of learning and development. Edgewood Cliffs, NJ: Prentice-Hall) theory of experiential learning, this article describes the development and use of SPs as a learning strategy.
View Article and Find Full Text PDFEnviron Sci Pollut Res Int
October 2014
Nano-silver is increasingly used in consumer products from washing machines and refrigerators to devices marketed for the disinfection of drinking water or recreational water. The nano-silver in these products may be released, ending up in surface water bodies which may be used as drinking water sources. Little information is available about the stability of the nano-silver in sources of drinking water, its fate during drinking water disinfection processes, and its interaction with disinfection agents and disinfection by-products (DBPs).
View Article and Find Full Text PDFPeppy, the proteogenomic/proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial probabilities: the probability that a fragment ion will randomly align with a peptide ion, the probability that the aligning ions will be selected from subsets of the most intense peaks, and the probability that the intensities of fragment ions identified as y-ions are greater than those of their counterpart b-ions. The scores produced by the method act as global confidence scores, which facilitate the accurate comparison of results and the estimation of false discovery rates.
View Article and Find Full Text PDFThe alarming rise of ciprofloxacin-resistant Pseudomonas aeruginosa has been reported in several clinical studies. Though the mutation of resistance genes and their role in drug resistance has been researched, the process by which the bacterium acquires high-level resistance is still not well understood. How does the genomic evolution of P.
View Article and Find Full Text PDFProteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have been limited to small genomes, as large genomes can prove impractical due to the required amount of computer memory and computation time.
View Article and Find Full Text PDFTheor Biol Med Model
April 2013
Background: It is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10-20% of the population. Many aspects of the phenomenon are believed to be due to the variable expression of critical genes: a stochastic occurrence termed "noise" which has made the phenomenon difficult to examine directly by lab experimentation.
Methods: To capture and model noise in this system and further understand the emergence of competence both at the intracellular and culture levels in B.
Background: Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the ENcyclopedia of DNA Elements (ENCODE) project, we applied proteogenomic mapping to produce proteogenomic tracks for the UCSC Genome Browser, to explore which putative translational regions may be missing from the human genome.
Results: We generated ~1 million high-resolution tandem mass (MS/MS) spectra for Tier 1 ENCODE cell lines K562 and GM12878 and mapped them against the UCSC hg19 human genome, and the GENCODE V7 annotated protein and transcript sets.
Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and resistance to proteolysis, both of which could lead to low recovery and low identification rates of membrane proteins. Here, we introduce a novel integrated approach, GELFrEE Optimized FASP Technology (GOFAST) for large-scale and comprehensive membrane proteins analysis. Using an array of sample preparation techniques including gel-eluted liquid fraction entrapment electrophoresis (GELFrEE), filter-aided sample preparation (FASP), and microwave-assisted on-filter enzymatic digestion, we identified 2 090 proteins from the membrane fraction of a leukemia cell line (K562).
View Article and Find Full Text PDFData from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA- fractions in the cell lines K562 and GM12878. We used the machine-learning algorithm RuleFit3 to regress the peptide data against RNA expression data.
View Article and Find Full Text PDFEukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function.
View Article and Find Full Text PDFMotivation: Post-translational modifications are vital to the function of proteins, but are hard to study, especially since several modified isoforms of a protein may be present simultaneously. Mass spectrometers are a great tool for investigating modified proteins, but the data they provide is often incomplete, ambiguous and difficult to interpret. Combining data from multiple experimental techniques-especially bottom-up and top-down mass spectrometry-provides complementary information.
View Article and Find Full Text PDFThis chapter describes using the Protein Inference Engine (PIE) to integrate various types of data--especially top down and bottom up mass spectrometer (MS) data--to describe a protein's posttranslational modifications (PTMs). PTMs include cleavage events such as the n-terminal loss of methionine and residue modifications like phosphorylation. Modifications are key elements in many biological processes, but are difficult to study as no single, general method adequately characterizes a protein's PTMs; manually integrating data from several MS experiments is usually required.
View Article and Find Full Text PDFMicrobes have developed resistance to nearly every antibiotic, yet the steps leading to drug resistance remain unclear. Here we report a multistage process by which Pseudomonas aeruginosa acquires drug resistance following exposure to ciprofloxacin at levels ranging from 0.5× to 8× the initial MIC.
View Article and Find Full Text PDFWe report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimuli. Agent-based modeling is a stochastic and bottom-up approach, where individual components of the modeled system are explicitly represented, and bulk properties emerge from their movement and interactions. We present the Chemoscape model: a collection of agents representing both fixed membrane-embedded and mobile cytoplasmic proteins, each governed by a set of rules representing knowledge or hypotheses about their function.
View Article and Find Full Text PDFBackground: Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve.
View Article and Find Full Text PDFHydroxyl-selective electrophiles, including N-methylisatoic anhydride (NMIA) and 1-methyl-7-nitroisatoic anhydride (1M7), are broadly useful for RNA structure analysis because they react preferentially with the ribose 2'-OH group at conformationally unconstrained or flexible nucleotides. Each nucleotide in an RNA has the potential to form an adduct with these reagents to yield a comprehensive, nucleotide-resolution, view of RNA structure. However, it is possible that factors other than local structure modulate reactivity.
View Article and Find Full Text PDFAnalysis of the long-range architecture of RNA is a challenging experimental and computational problem. Local nucleotide flexibility, which directly reports underlying base pairing and tertiary interactions in an RNA, can be comprehensively assessed at single nucleotide resolution using high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE). hSHAPE resolves structure-sensitive chemical modification information by high-resolution capillary electrophoresis and typically yields quantitative nucleotide flexibility information for 300-650 nucleotides (nt) per experiment.
View Article and Find Full Text PDFReplication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles.
View Article and Find Full Text PDFCurr Protoc Bioinformatics
March 2008
Genome-based peptide fingerprint scanning (GFS) directly maps several types of protein mass spectral (MS) data to the loci in the genome that may have encoded for the protein. This process can be used either for protein identification or for proteogenomic mapping, which is gene-finding and annotation based on proteomic data. Inputs to the program are one or more mass spectrometry files from peptide mass fingerprinting and/or tandem MS (MS/MS) along with one or more sequences to search them against, and the output is the coordinates of any matches found.
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