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PubMed2004

Fourier transform infrared-attenuated total reflection nitrate determination of soil pastes using principal component regression, partial least squares, and cross-correlation.

This paper investigates the use of Fourier transform infrared (FTIR) attenuated total reflectance (ATR) spectroscopy as a fast and simple way for direct determination of nitrate concentration in soil pastes, which would assist precision fertilizer placement and reduce nitrate pollution. Eight types of soils are investigated, with nitrate concentrations ranging from 0 to 1000 ppm-N. The spectral region around the nitrate band (1300-1550 cm(-1)) is analyzed by (1) principal component regression (PCR), (2) partial least squares (PLS), and (3) cross-correlation with reference libraries that include spectra of pure ions and/or soils. The main obstacle to accurate nitrate measurement appears to be an interfering band present in calcareous soils. This band, which may be due to carbonate, is located around 1450 cm(-1) and overlaps with the nitrate band centered around 1370 cm(-1). For non-calcareous soils, and in particular for light sandy agricultural soils, PLS and cross-correlation with a reference library containing only spectra of ions in water give similar results (about 8 ppm-N on dry soil basis), while PCR leads to slightly poorer results. When calcareous soils are included in the analysis, the prediction errors are about twice as large. In this case, the best results are obtained using PLS, followed by PCR, while cross-correlation with reference libraries leads to poorer results.

Algorithms↗

PubMed2005

An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings.

Nuclear Overhauser effect (NOE) distance restraints are the main experimental data from protein nuclear magnetic resonance (NMR) spectroscopy for computing a complete three dimensional solution structure including sidechain conformations. In general, NOE restraints must be assigned before they can be used in a structure determination program. NOE assignment is very time-consuming to do manually, challenging to fully automate, and has become a key bottleneck for high-throughput NMR structure determination. The difficulty in automated NOE assignment is ambiguity: there can be tens of possible different assignments for an NOE peak based solely on its chemical shifts. Previous automated NOE assignment approaches rely on an ensemble of structures, computed from a subset of all the NOEs, to iteratively filter ambiguous assignments. These algorithms are heuristic in nature, provide no guarantees on solution quality or running time, and are slow in practice. In this paper we present an accurate, efficient NOE assignment algorithm. The algorithm first invokes the algorithm in [30, 29] to compute an accurate backbone structure using only two backbone residual dipolar couplings (RDCs) per residue. The algorithm then filters ambiguous NOE assignments by merging an ensemble of intra-residue vectors from a protein rotamer database, together with internuclear vectors from the computed backbone structure. The protein rotamer database was built from ultra-high resolution structures (<1.0 A) in the Protein Data Bank (PDB). The algorithm has been successfully applied to assign more than 1,700 NOE distance restraints with better than 90% accuracy on the protein human ubiquitin using real experimentally-recorded NMR data. The algorithm assigns these NOE restraints in less than one second on a single-processor workstation.

Algorithms↗

PubMed1986

Primary structure and cDNA cloning of human fibroblast collagenase inhibitor.

We report the primary structure and cDNA cloning of human fibroblast collagenase inhibitor, a glycoprotein that appears to play a central role in modulating the activity of a number of metalloendoproteases of connective tissue origin including collagenase, gelatinase, and proteoglycanase. Secreted human fibroblast collagenase inhibitor was purified and subjected to automated Edman degradation. The secreted protein consists of 184 amino acid residues; it contains two sites of N-linked oligosaccharide linkage and six disulfide bonds. Synthetic oligonucleotide probes based on selected amino acid sequences of the inhibitor were used to screen a lambda gt10 cDNA library from a human fibroblast line. Two overlapping cDNA clones were characterized to determine the complete coding and noncoding sequences of the specific mRNA. The amino acid sequence deduced from the nucleotide sequence agrees with that determined by protein sequencing. One clone appears to contain the complete 5' end and, in addition, the cDNA sequence predicts a 23-amino acid leader peptide. The other clone represents the 3' end of the mature message and includes a short poly(A)+ tract. This 3' sequence is remarkably similar to a reported cDNA encoding part of the protein derived from mouse fibroblast poly(A)+ RNA. However, this inhibitor has no substantial homology with previously sequenced protease inhibitors.

Amino Acid Sequence↗

PubMed2004

Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR.

A commercially available repetitive-sequence-based PCR (rep-PCR) DNA fingerprinting assay adapted to an automated format, the DiversiLab system, enables rapid microbial identification and strain typing. We explored the performance of the DiversiLab system as a molecular typing tool for 69 Aspergillus isolates (38 A. fumigatus, 15 A. flavus, and 16 A. terreus isolates) had been previously characterized by morphological analysis. Initially, 27 Aspergillus isolates (10 A. fumigatus, 9 A. flavus, and 8 A. terreus isolates) were used as controls to create a rep-PCR-based DNA fingerprint library with the DiversiLab software. Then, 42 blinded Aspergillus isolates were typed using the system. The rep-PCR-based profile revealed 98% concordance with morphology-based identification. rep-PCR-based DNA fingerprints were reproducible and were consistent for DNA from both hyphae and conidia. DiversiLab dendrogram reports correctly identified all A. fumigatus (n = 28), A. terreus (n = 8), and A. flavus (n = 6) isolates in the 42 blinded Aspergillus isolates. rep-PCR-based identification of all isolates was 100% in agreement with the contiguous internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) sequence-based identification of the respective isolates. Additionally, the DiversiLab system could demonstrate strain-level differentiation of A. flavus and A. terreus. Automated rep-PCR may be a time-efficient, effective, easy-to-use, novel genotyping tool for identifying and determining the strain relatedness of fungi. This system may be useful for epidemiological studies, molecular typing, and surveillance of Aspergillus species.

Aspergillus↗

PubMed1998

Constructing multigenome views of whole microbial genomes.

We have designed and implemented a system to carry out cross-genome comparisons of open reading frames (ORFs) from multiple genomes. This implementation includes a genome profiling system that allows us to explore pairwise comparisons at different levels of match similarity and ask biologically motivated queries involving number and identity of ORFs, their function, functional category, distribution in genomes or in biological domains, and statistics on their matches and match families. This analysis required precise definition of new classification terms and concepts. We define the terms genomic signature, summary signature, biologic domain signature, domain class, match level, match family, and extended match family, then use these terms to define concepts, including genomically universal proteins and proteins characteristics of sets of genomes. We initiate an analysis based on automated FASTA (Pearson, 1996) comparison of 22,419 conceptually translated protein sequences from nine microbial genomes.

Amino Acid Sequence↗

PubMed2005

Image registration using log-polar mappings for recovery of large-scale similarity and projective transformations.

This paper describes a novel technique to recover large similarity transformations (rotation/scale/translation) and moderate perspective deformations among image pairs. We introduce a hybrid algorithm that features log-polar mappings and nonlinear least squares optimization. The use of log-polar techniques in the spatial domain is introduced as a preprocessing module to recover large scale changes (e.g., at least four-fold) and arbitrary rotations. Although log-polar techniques are used in the Fourier-Mellin transform to accommodate rotation and scale in the frequency domain, its use in registering images subjected to very large scale changes has not yet been exploited in the spatial domain. In this paper, we demonstrate the superior performance of the log-polar transform in featureless image registration in the spatial domain. We achieve subpixel accuracy through the use of nonlinear least squares optimization. The registration process yields the eight parameters of the perspective transformation that best aligns the two input images. Extensive testing was performed on uncalibrated real images and an array of 10,000 image pairs with known transformations derived from the Corel Stock Photo Library of royalty-free photographic images.

Algorithms↗

PubMed2004

Solid-phase synthesis and screening of macrocyclic nucleotide-hybrid compounds targeted to hepatitis C NS5B.

A convergent strategy for the synthesis of cyclic nucleotide-hybrid molecules on controlled pore glass is reported. A major advantage of the approach is the lack of restrictions on the sequence and structural variation, allowing the incorporation of modified ribonucleosides (such as 2'-OMe-ribonucleotides), as well as threoninol derivatives. This methodology allows a fully automated assembly by means of standard phosphoramidite chemistry and is based on a recently published procedure for the preparation of cyclic oligodinucleotides in the DNA series (M. Smietana, E. T. Kool, Angew. Chem. 2002, 114, 3856-3859; Angew. Chem. Int. Ed. Engl. 2002, 41, 3704-3707). A library of potential cyclic hybrid inhibitor compounds targeting hepatitis C virus NS5B enzyme (the replicating polymerase of HCV) was generated by means of the parallel-pool strategy. Screening of the library revealed that cyclic hybrid c(C(OME)EthenodA) was a significant inhibitor of NS5B, with an IC(50) of 40 microM. Preliminary structure-activity studies of this lead compound are described.

Animals↗

PubMed1989

Spectrometric and chromatographic methods for the analysis of polymeric explant materials.

Several analytical pyrolysis methods, namely pyrolysis mass spectrometry (Py-MS), time-resolved pyrolysis mass spectrometry (TRPy-MS), and pyrolysis short column gas chromatography mass spectrometry (Py-GC/MS) were used to analyze polymers of clinical interest both before and after implantation. A sample of Biomer, a poly(ether urethane urea) used in the Utah artificial heart, was analyzed using these methods. Two poly(ether urethanes) (Tecoflex and Pellethane) and a poly(dimethylsilicone) (Silastic) sample were analyzed using Py-GC/MS. The direct Py-MS of Biomer identified the components used in the manufacture of Biomer. Py-GC/MS of Biomer, Tecoflex, Pellethane, and Silastic also identified the components used in their manufacture. The analysis of explanted Biomer detected the presence of adsorbed cholestadiene, the reaction of chloride ions with a stabilizer, and the presence of a siloxane contaminant. The cholestadiene was detected on the outside housing of an artificial heart which had been implanted for 297 days. The cholestadiene was detected at low levels and was identified by library search on the MS data system. The siloxane contaminant was also identified by the MS data system. All of the methods demonstrated required only short instrumental analysis times (10 min or less). Data analysis required much more time, but much of the data analysis can be automated.

Biocompatible Materials↗

PubMedDate not supplied

Discovery of biomarker candidates within disease by protein profiling: principles and concepts.

Proteins and peptides present within clinical samples represent a valuable library of information regarding the ongoing processes within cells and tissues in health and disease. We have developed and validated novel technology applications that can be used to characterize the patterns of global protein expression in tissue and biofluids in either gel-based systems or by automated multidimensional nanocapillary liquid chromatography. Mass spectrophotometry platforms using MALDI MS and MS/MS or LTQ ion trap MS were capable of delivering sensitive and accurate identifications of hundreds of proteins contained in individual samples including individual forms of processing intermediates such as phospho peptides. The Systems Biology approach of integrating protein expression data with clinical data such as histopathology, clinical functional measurements, medical imaging scores, patient demographics, and clinical outcome provides a powerful tool for linking biomarker expression with biological processes that can be segmented and linked to disease presentation.

Animals↗

PubMed2006

MathDAMP: a package for differential analysis of metabolite profiles.

BACKGROUND: With the advent of metabolomics as a powerful tool for both functional and biomarker discovery, the identification of specific differences between complex metabolite profiles is becoming a major challenge in the data analysis pipeline. The task remains difficult, given the datasets' size, complexity, and common shifts in migration (elution/retention) times between samples analyzed by hyphenated mass spectrometry methods. RESULTS: We present a Mathematica (Wolfram Research, Inc.) package MathDAMP (Mathematica package for Differential Analysis of Metabolite Profiles), which highlights differences between raw datasets acquired by hyphenated mass spectrometry methods by applying arithmetic operations to all corresponding signal intensities on a datapoint-by-datapoint basis. Peak identification and integration is thus bypassed and the results are displayed graphically. To facilitate direct comparisons, the raw datasets are automatically preprocessed and normalized in terms of both migration times and signal intensities. A combination of dynamic programming and global optimization is used for the alignment of the datasets along the migration time dimension. The processed datasets and the results of direct comparisons between them are visualized using density plots (axes represent migration time and m/z values while peaks appear as color-coded spots) providing an intuitive overall view. Various forms of comparisons and statistical tests can be applied to highlight subtle differences. Overlaid electropherograms (chromatograms) corresponding to the vicinities of the candidate differences from any result may be generated in a descending order of significance for visual confirmation. Additionally, a standard library table (a list of m/z values and migration times for known compounds) may be aligned and overlaid on the plots to allow easier identification of metabolites. CONCLUSION: Our tool facilitates the visualization and identification of differences between complex metabolite profiles according to various criteria in an automated fashion and is useful for data-driven discovery of biomarkers and functional genomics.

Biomarkers↗

PubMed2006

A community resource benchmarking predictions of peptide binding to MHC-I molecules.

Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here we make public a large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles. We use this data to establish a set of benchmark predictions with one neural network method and two matrix-based prediction methods extensively utilized in our groups. In general, the neural network outperforms the matrix-based predictions mainly due to its ability to generalize even on a small amount of data. We also retrieved predictions from tools publicly available on the internet. While differences in the data used to generate these predictions hamper direct comparisons, we do conclude that tools based on combinatorial peptide libraries perform remarkably well. The transparent prediction evaluation on this dataset provides tool developers with a benchmark for comparison of newly developed prediction methods. In addition, to generate and evaluate our own prediction methods, we have established an easily extensible web-based prediction framework that allows automated side-by-side comparisons of prediction methods implemented by experts. This is an advance over the current practice of tool developers having to generate reference predictions themselves, which can lead to underestimating the performance of prediction methods they are not as familiar with as their own. The overall goal of this effort is to provide a transparent prediction evaluation allowing bioinformaticians to identify promising features of prediction methods and providing guidance to immunologists regarding the reliability of prediction tools.

Animals↗

PubMed2003

Automated graphic image generation system for effective representation of infectious disease surveillance data.

Infectious disease surveillance schemes have been established to detect infectious disease outbreak in the early stages, to identify the causative viral strains, and to rapidly assess related morbidity and mortality. To make a scheme function well, two things are required. Firstly, it must have sufficient sensitivity and be timely to guarantee as short a delay as possible from collection to redistribution of information. Secondly, it must provide a good representation of the results of the surveillance. To do this, we have developed a database system that can redistribute the information via the Internet. The feature of this system is to automatically generate the graphic images based on the numerical data stored in the database by using Hypertext Preprocessor (PHP) script and Graphics Drawing (GD) library. It dynamically displays the information as a map or bar chart as well as a numerical impression according to the real time demand of the users. This system will be a useful tool for medical personnel and researchers working on infectious disease problems and will save significant time in the redistribution of information.

Automation↗

PubMed1997

Feasibility analysis of a case-based reasoning system for automated detection of coronary heart disease from myocardial scintigrams.

Myocardial perfusion scintigraphy is a noninvasive diagnostic method for the evaluation of patients with suspected or proven coronary artery disease (CAD). We utilized case-based reasoning (CBR) methods to develop the computer-based image interpretation system SCINA which automatically derives from a scintigraphic image data set an assessment concerning the presence of CAD. We compiled a case library of 100 patients who underwent both perfusion scintigraphy and coronary angiography to document or exclude the presence of CAD. The angiographic diagnosis of the retrieved nearest neighbor match of a scintigraphic input case was selected as the CBR diagnosis. We examined the effects of input data granularity, case indexing, similarity metric, and adaptation on the diagnostic accuracy of the CBR application SCINA. For the final prototype, sensitivity and specificity for detection of coronary heart disease were 98% and 70% suggesting that CBR systems may achieve a diagnostic accuracy that appears feasible for clinical use.

Adaptation, Physiological↗

PubMed2026

Closed-loop vasopressor systems for hemodynamic control in perioperative and critical care settings: a systematic review and meta-analysis.

Maintaining mean arterial pressure (MAP) within a predefined target is central to haemodynamic management in surgical and critically ill adults receiving vasopressors. Closed-loop vasopressor (CLV) systems automate titration to optimise blood pressure control, but their clinical effectiveness remains uncertain. We performed a systematic review and meta-analysis comparing CLV with manual titration. This PRISMA 2020-compliant review was prospectively registered in PROSPERO (CRD420250655697). MEDLINE, Embase, Scopus, Web of Science, CENTRAL, and the Cochrane Library were searched (January 2000-June 2025). Randomised controlled trials enrolling adults receiving vasopressors in perioperative or intensive care settings were included. Primary outcomes were time within the MAP target range and time spent in hypotension or hypertension. Risk of bias was assessed using RoB 2.0 and certainty of evidence using GRADE. Random- or fixed-effects models were selected according to heterogeneity. Six randomized controlled trials (215 patients) were included in the systematic review, whereas five perioperative trials contributed to the meta-analysis of haemodynamic control outcomes, and one ICU-based study was summarized narratively because it did not report comparable MAP control endpoints. CLV increased time within the MAP target range (mean difference [MD] 33.94%, 95% CI 20.41-47.46; I2 = 77%) and reduced time in hypotension (MD - 18.24%, 95% CI - 28.95 to - 7.53; I2 = 73%). There was no significant difference in time in hypertension, cumulative norepinephrine dose, or major/minor adverse events. ICU length of stay was not pooled because of clinical and methodological heterogeneity. Certainty of evidence ranged from low to high (moderate for haemodynamic control outcomes). CLV systems improved haemodynamic control, primarily in perioperative settings, but heterogeneity and small samples limit confidence in effect size and generalisability. Evidence in critically ill populations remains limited, and larger trials are needed to determine whether improvements in these physiological surrogate endpoints translate into meaningful patient-centred outcomes.

Humans↗

PubMed1994

Oligonucleotide arrays: new concepts and possibilities.

Advances in solid-phase oligonucleotide synthesis and hybridization techniques have led to an incipient technology based on the use of oligonucleotide arrays. The inclusion of a large number of oligonucleotide probes within a single array greatly reduces the cost of their synthesis and allows thousands of hybridizations to be carried out simultaneously. The range of potential applications of oligonucleotide arrays was expanded by the realization that nucleic acids can be sequenced by hybridizing them to all possible oligonucleotides of a given length. Additional possibilities are offered by novel types of oligonucleotide arrays that are capable of parallel sorting, isolating, and manipulating thousands, and even millions, of nucleic acid species. Fields, such as site-directed mutagenesis, protein engineering, and recombinant DNA technology, would benefit from using these arrays. Further, these approaches could enable the analysis of entire genomes by preparing ordered fragment libraries, and by sequencing complex pools of nucleic acids, in a novel approach that provides long-range sequence information by generating nested nucleic acids and then surveying the oligonucleotides contained in the nested strands. This would allow large diploid genomes to be sequenced directly in a completely automated procedure that does not require fragment cloning or chromosome mapping.

Alleles↗

PubMed1989

The librarian as consultant and educator for personal file management software.

Librarians are encouraged to extend their information managing skills to include familiarity with personal file management software. Knowledge of automated solutions to overgrown manual reprint files can be valuable to the institution that a librarian serves. The capabilities of REFERENCE MANAGER, PRO-CITE, ASKSAM, and SCI-MATE are compared in a series of classes given for faculty and staff by the Medical College of Wisconsin Libraries reference staff.

Consultants↗

PubMed1976

[Practice of computer use in radiotherapy planning].

The main problems of radiotherapy planning are discussed with respect to use of computers now being available for a greater number of centers. One of the most essential premises is apart from clear ideas on a modern target volume concept - a sufficiently high speed in producing realistic summarized isodose contours for any radiation therapy arrangement in any individual patient's cross section outline. This problem being solved, those individual summarized isodose figures have to be critically evaluated and therefore the importance of applicable meaningful optimization criteria come into account. The properties of such criteria, which must be quantifiable, generally applicable and really relevant for judgement on quality of a plan, had to be accepted, before automatic optimization procedures could be developed; principles involved are presented. By means of a short series of examples, namely 60Co fixed field combinations with and without use of wedges, combinations of arc therapy for a number of clinical tasks. It has been pointed out, that most experienced estimate by the eye would have been by far insufficient when compared to the automized computer optimization when using such simple criteria as 1. homogeneity of absorbed dose within target volume, 2. numerically limited absorbed dose within areas of risk, 3. as low as possible radiation effects to all "outside areas". It seems to be a real danger, that so called isodose libraries, how high their merits might be estimated, may change into an "isodose bcemetery", unless we'll be successful for each individual clinical case by use of computers, which are now prepared to supply the best possible variant of the standard plan or the primary radiotherapy idea. Regular use of computers in such a way will furthermore give an incomparable documentation material.

Breast Neoplasms↗

PubMed2001

The mouse lens fiber-cell intrinsic membrane protein MP19 gene (Lim2) and granule membrane protein GMP-17 gene (Nkg7): Isolation and sequence analysis of two neighboring genes.

PURPOSE: The lens fiber cell intrinsic membrane protein MP19 appears to play a key role in lens fiber cell structure or communication, and thus cataractogenesis. The goal of this study was to isolate and characterize the entire gene structure of the MP19 gene, termed Lim2, and to investigate gene sequences surrounding this lens-specific gene. METHODS: A 129/SvJ mouse genomic DNA library was screened using radioisotope labeled bovine MP19 cDNA. From this screening, an 11 kb genomic fragment was isolated which contained the entire Lim2 gene, and a neighboring gene, Nkg7, which codes for a 17 kDa granulocyte membrane protein termed GMP-17. The nucleotide sequence of this entire fragment was obtained using double strand automated sequencing techniques. Using CAT and green fluorescent protein reporter constructs, Lim2 5'-upstream promoter sequences were analyzed. RESULTS: An 11,182 base pair genomic clone containing the entire murine Lim2 gene and another downstream gene, Nkg7, was obtained and completely sequenced. These two genes are only 1,182 base pairs apart, from the poly(A) signal of the Lim2 gene to the published transcriptional start site of Nkg7. Interestingly, the protein coded for by Nkg7, GMP-17, is very similar to the product of the lens Lim2 gene, MP19, in many respects. Both proteins are transmembrane proteins, with each having 4 transmembrane loops. The amino acid sequence of the two proteins is 34% identical, and 49% with respect to similar amino acids. The size of mouse Lim2 is 5,896 base pairs from the transcriptional start site to the poly(A) signal, and contains five exons and four introns. Exons 2-5 of the Lim2 gene encode a polypeptide of 173 amino acids, having over 92% identity to human MP19. Using chloramphenicol acetyltransferase (CAT) and green fluorescent protein (GFP) reporter constructs, it was determined that about 160 bp of sequence upstream from the start of transcription is both necessary and sufficient for efficient expression levels as well as tissue specificity of expression. CONCLUSIONS: The mouse Lim2 gene is very similar to the human LIM2 gene, both having the same number of exons and introns. The coding nucleotide sequences from both species are 88% identical, and 92% identical at the amino acid level. In the immediate 5'-upstream region of these two genes, several highly conserved regions are observed. Due to the similarity of the MP19 and GMP-17 proteins, it is interesting to speculate that the lens MP19 and the lymphocyte-associated GMP-17 may have originated from one primordial gene which, through genetic drift, resulted in two separate proteins having similar functions in two widely separated tissue types.

Amino Acid Sequence↗