Visualizing genomic data: The mixing perspective.

We report on a novel way to visualize genomic data. By considering genome coding sequences, cds, as sets of the N=61 non-stop codons, one obtains a partition of the total number of codons in each cds. Partitions exhibit a statistical property known as mixing character which characterizes how mixed the partition is. Mixing characters have been shown mathematically to exhibit a partial order known as majorization (Ruch, 1975). In previous work (Seitz and Kirwan, 2022) we developed an approach that combined mixing and entropy that is visualized as a scatter plot. If we consider all 1,121,505 partitions of 61 codons, this produces a plot we call the theoretical mixing space, TGMS. A normalization procedure is developed here and applied to real genomic data to produce the genome mixing signature, GMS. Example GMS's of 19 species, including Homo sapiens, are shown and discussed.

Pre-procedural high-pitch coronary CT angiography assessment of patients undergoing transcatheter aortic valve implantation (TAVI) without patient-specific adjustment: analysis of diagnostic performance.

AIM: To evaluate the ability to assess the coronary arteries using pre-procedural computed tomography (CT; high-pitch mode) in patients referred for transcatheter aortic valve implantation (TAVI). METHODS AND MATERIALS: CT and invasive coronary angiography (ICA) were performed pre-TAVI in 100 patients (46 women; 79 ± 5.9 years). CT was performed in prospectively ECG-triggered high-pitch mode after intravenous administration of 70 ml iodinated contrast medium. Image quality was assessed using a four-point scale (graded 0-3). Significant coronary artery stenosis (≥50% diameter) was graded as either present or absent by one observer and in one-third of patients by two observers independently. ICA was the standard of reference. Results were reported per segment and per patient. RESULTS: Twenty-two percent of patients had known coronary artery disease (CAD). In two cases, a coronary anomaly was detected. Diagnostic image quality (grade 1-3) was achieved in 30.3% of segments. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 75%, 80.5%, 16%, and 98.5%, respectively. Significant coronary stenosis could be ruled out completely in all segments in three patients. The interrater agreement per patient was excellent (kappa = 1). CONCLUSION: Relevant coronary findings can frequently be observed in high-pitch TAVI-planning CT. Despite the limitations of the technique and in patients referred to pre-TAVI evaluation (rapid heart rate, coronary calcifications, etc.), a valid evaluation of coronary arteries is possible in a considerable proportion of segments with a high NPV; however, few studies were completely free of motion artefacts to dependably exclude CAD using this technique in this challenging group of patients.

Interventions in primary care to improve cardiovascular risk factors and glycated haemoglobin (HbA1c) levels in patients with diabetes: a systematic review.

Most patients with diabetes are treated in primary care (PC). We performed a systematic review to assess the effect of single and combined interventions on cardiovascular risk factors (CVRFs) and glycated haemoglobin (HbA1c) levels in patients with diabetes in PC settings. We searched the MEDLINE database from January 1990 to October 2008. According to the Cochrane Effective Practice and Organization of Care Group (EPOC) criteria, (cluster-)randomized control studies and controlled before-and-after studies were selected and reviewed. Identified interventions were classified according to a modified EPOC intervention taxonomy. We included 68 studies. Forty-five studies evaluated the effect of any intervention on HbA1c. Seventeen studies presented a significant improvement in HbA1c. Nine out of 27 studies evaluating CVRFs [cholesterol, blood pressure (BP)] and HbA1c showed a significant improvement in at least two of these factors. Audit and feedback on performance, clinical decision support systems, multi-professional teams and patient education seemed to be successful strategies. The increasing evidence regarding the treatment of persons with chronic illnesses, summarized in the Chronic Care Model (CCM), is not reflected in most recent studies about diabetes treatment in PC. Most interventions still seem only partly adapted to the CCM. The methodological quality of many studies is still poor and often the pivotal outcomes, CVRFs and HbA1c, are not appropriately addressed. As a consequence, the potential of PC in the care of patients with diabetes may still be underestimated.

High-density electrode array for imaging in vitro electrophysiological activity.

The development of a high-density active microelectrode array for in vitro electrophysiology is reported. Based on the Active Pixel Sensor (APS) concept, the array integrates 4096 gold microelectrodes (electrode separation 20 microm) on a surface of 2.5 mmx2.5 mm as well as a high-speed random addressing logic allowing the sequential selection of the measuring pixels. Following the electrical characterization in a phosphate solution, the functional evaluation has been carried out by recording the spontaneous electrical activity of neonatal rat cardiomyocytes. Signals with amplitudes from 130 microVp-p to 300 microVp-p could be recorded from different pixels. The results demonstrate the suitability of the APS concept for developing a new generation of high-resolution extracellular recording devices for in vitro electrophysiology.

Parathyroid hormone-related protein overexpression in the human colon cancer cell line HT-29 enhances adhesion of the cells to collagen type I.

The present experiments examined the potential ability of parathyroid hormone-related protein (PTHrP) to influence growth of the human colon cancer cell HT-29 and the ability of the cell to adhere to several extracellular matrix (ECM) proteins found in normal tissues. Addition of PTHrP analogs, PTHrP (1-34), PTHrP (67-86), or PTHrP (107-139), to HT-29 cells in culture did not influence cell growth or the adhesion of the cells to wells coated with fibronectin, laminin, or collagen type I. Likewise, in HT-29 cells induced to overexpress PTHrP by stable transfection with PTHrP cDNA, compared to vector-transfected control HT-29 cells, no effect on cell growth occurred. However, in the transfected cells, the increased production of PTHrP significantly enhanced cell adhesion to type I collagen but not to fibronectin or laminin. The results raise the possibility that PTHrP might play a role in colon tumor invasion and metastasis by influencing cell adhesion to specific extracellular matrix proteins.

Overexpression of parathyroid hormone-related protein promotes cell growth in the rat intestinal cell line IEC-6.

The rat intestinal cell line, IEC-6, was used as a model to study effects of parathyroid hormone-related protein (PTHrP) on crypt cell growth. Studies showed that addition of PTHrP analogs (1-34), (67-86), or (107-139) to growth medium did not affect proliferation of cells grown in either high (10% Nu-Serum) or low serum (1% Nu-Serum). However, studies on clonal lines of IEC-6 cells stably transfected with PTHrP cDNA and overexpressing PTHrP showed that increased PTHrP production enhanced cell growth and 3H-thymidine incorporation in high, but not low, serum. Additional studies examined the role of the nuclear localization sequence (NLS) of PTHrP in mediating the growth effect. In three clonal IEC-6 lines transfected with PTHrP cDNA bearing a mutated NLS, the ability of PTHrP to stimulate 3H-thymidine incorporation and cell growth was lost. The results suggest that endogenously produced PTHrP can promote proliferation of IEC-6 cells and that the integrity of the NLS of PTHrP is required for its growth effects.

Overexpression of parathyroid hormone-related protein enhances apoptosis in the rat intestinal cell line, IEC-6.

We used the rat intestinal cell line, IEC-6, to study potential effects of overexpression of PTH-related protein (PTHrP) on apoptosis. A clonal line of PTHrP-overexpressing cells was established by stably transfecting parental cells with PTHrP complementary DNA in a sense orientation (sense). A similarly transfected line stably, transfected with empty vector, served as control (vector). Immunoreactive PTHrP, measured in culture medium, showed that sense cells secreted approximately 30 times as much PTHrP as did vector control cells. Apoptosis induced by serum withdrawal was evaluated by several methods. DNA laddering was demonstrable in sense-transfected cells as early as 12 h after serum withdrawal but not until later time points in vector-transfected control cells. Flow cytometric analysis of propidium iodide-stained cells showed a greater increase in the sub-G1 (apoptotic) population in sense cells, compared with vector. Fluorescent microscopy with Hoechst 33258 dye showed increased nuclear fragmentation and condensation in sense cells. Studies of apoptotic gene expression by ribonuclease protection assay, and protein by Western blot analysis, showed an enhanced ratio of Bax to Bcl-x(L) in sense cells. Mutation of the PTHrP nuclear localization amino acid sequence negated the ability of PTHrP to enhance apoptosis.

Optical coherence topography based on a two-dimensional smart detector array.

A low-coherence reflectometer based on a conventional Michelson interferometer and a novel silicon detector chip with a two-dimensional array of pixels that allows parallel heterodyne detection is presented. We demonstrate acquisition of three-dimensional images with more than 100,000 voxels per scan at a sensitivity of -58 dB and a rate of 6 Hz.

The use of visible speech cues for improving auditory detection of spoken sentences.

Classic accounts of the benefits of speechreading to speech recognition treat auditory and visual channels as independent sources of information that are integrated fairly early in the speech perception process. The primary question addressed in this study was whether visible movements of the speech articulators could be used to improve the detection of speech in noise, thus demonstrating an influence of speechreading on the ability to detect, rather than recognize, speech. In the first experiment, ten normal-hearing subjects detected the presence of three known spoken sentences in noise under three conditions: auditory-only (A), auditory plus speechreading with a visually matched sentence (AV(M)) and auditory plus speechreading with a visually unmatched sentence (AV(UM). When the speechread sentence matched the target sentence, average detection thresholds improved by about 1.6 dB relative to the auditory condition. However, the amount of threshold reduction varied significantly for the three target sentences (from 0.8 to 2.2 dB). There was no difference in detection thresholds between the AV(UM) condition and the A condition. In a second experiment, the effects of visually matched orthographic stimuli on detection thresholds was examined for the same three target sentences in six subjects who participated in the earlier experiment. When the orthographic stimuli were presented just prior to each trial, average detection thresholds improved by about 0.5 dB relative to the A condition. However, unlike the AV(M) condition, the detection improvement due to orthography was not dependent on the target sentence. Analyses of correlations between area of mouth opening and acoustic envelopes derived from selected spectral regions of each sentence (corresponding to the wide-band speech, and first, second, and third formant regions) suggested that AV(M) threshold reduction may be determined by the degree of auditory-visual temporal coherence, especially between the area of lip opening and the envelope derived from mid- to high-frequency acoustic energy. Taken together, the data (for these sentences at least) suggest that visual cues derived from the dynamic movements of the fact during speech production interact with time-aligned auditory cues to enhance sensitivity in auditory detection. The amount of visual influence depends in part on the degree of correlation between acoustic envelopes and visible movement of the articulators.

Regulation of PTH/PTH-related protein receptor expression by endogenous PTH-related protein in the rat osteosarcoma cell line ROS 17/2.8.

We have utilized clonal lines of the rat osteoblastic cell line ROS 17/2.8 stably transfected with full-length parathyroid hormone-related protein (PTHrP) cDNA in a sense or an antisense orientation to examine the effects of alteration in the production of endogenous PTHrP on expression of the PTH/PTHrP receptor. In the stably transfected clonal cell lines, changes in PTH/PTHrP receptor expression were evaluated by Northern blot analysis, whole-cell ligand binding of 125I-[Tyr36] PTHrP (1-36), and exogenous PTHrP (1-34)-stimulated cyclic adenosine monophosphate (cAMP) accumulation. Compared to control (vector-transfected) cells, PTHP-overproducing (sense-transfected) cells exhibited a marked decrease in the expression of PTH/PTHrP receptor mRNA and PTHrP ligand binding, as well as a corresponding decrease in the PTHrP (1-34)-stimulated cAMP response. By contrast, the antisense-transfected cells showed a marked increase in expression of PTH/PTHrP receptor mRNA and PTHrP (1-34) ligand binding, but a significant increase in the PTHrP (1-34)-stimulated cAMP response was not detected. Using antisense-transfected ROS cells, PTH/PTHrP receptor mRNA expression and 125I-[Tyr36] PTHrP (1-36) binding were downregulated by treatment for 24 h with exogenous PTHrP (1-36), forskolin, or dibutyryl cAMP. The findings extend those of earlier studies showing receptor downregulation by exogenous PTH by indicating that endogenous PTHrP, as well as circulating PTH, may help regulate receptor production; and suggesting that even very low concentrations of the peptide may influence receptor production.

Endogenous parathyroid hormone-related peptide enhances proliferation and inhibits differentiation in the osteoblast-like cell line ROS 17/2.8.

To investigate potential effects of endogenous parathyroid hormone-related peptide (PTHrP) on osteoblast function, ROS 17/2.8 cells were transfected with full-length PTHrP cDNA in a sense or antisense orientation to alter PTHrP production. Compared with vector-transfected control cells, PTHrP-overproducing (sense-transfected) cells showed increased DNA synthesis ([(3)H]-thymidine incorporation) and increased growth (cell number). The extent of apoptosis was compared for the different clones using the terminal deoxynucleotide-mediated dUTP nick-end-labeling assay (TUNEL) and Hoechst staining. No differences in percentages of apoptotic cells were found under basal culture conditions or after 3 days of serum deprivation, which, itself, markedly increased numbers of apoptotic cells. The effect of PTHrP on osteoblast differentiation was assessed by examining two protein markers of differentiation, alkaline phosphatase, and bone morphogenetic protein (BMP)-2. Alkaline phosphatase activity was decreased in sense-transfected cells and increased in antisense-transfected cells, compared with cells transfected with empty vector. PTHrP-overproducing cells also showed decreased numbers of BMP-2-positive cells, whereas antisense-transfected cells showed no difference compared with vector control. The results indicate that: (a) endogenously produced PTHrP can increase growth of these osteoblastic cells by stimulating proliferation while not affecting apoptosis; and (b) the increased cell proliferation produced by PTHrP was accompanied by a reduction in activity or amount of two proteins normally expressed by differentiated osteoblasts.

The recognition of isolated words and words in sentences: individual variability in the use of sentence context.

Estimates of the ability to make use of sentence context in 34 postlingually hearing-impaired (HI) individuals were obtained using formulas developed by Boothroyd and Nittrouer [Boothroyd and Nittrouer, J. Acoust. Sco. Am. 84, 101-114 (1988)] which relate scores for isolated words to words in meaningful sentences. Sentence materials were constructed by concatenating digitized productions of isolated words to ensure physical equivalence among the test items in the two conditions. Isolated words and words in sentences were tested at three levels of intelligibility (targeting 29%, 50%, and 79% correct). Thus, for each subject, three estimates of context ability, or k factors, were obtained. In addition, auditory, visual, and auditory-visual sentence recognition was evaluated using natural productions of sentence materials. Two main questions were addressed: (1) Is context ability constant for speech materials produced with different degrees of clarity? and (2) What are the relations between individual estimates of k and sentence recognition as a function of presentation modality? Results showed that estimates of k were not constant across different levels of intelligibility: k was greater for the more degraded condition relative to conditions of higher word intelligibility. Estimates of k also were influenced strongly by the test order of isolated words and words in sentences. That is, prior exposure to words in sentences improved later recognition of the same words when presented in isolation (and vice versa), even though the 1500 key words comprising the test materials were presented under degraded (filtered) conditions without feedback. The impact of this order effect was to reduce individual estimates of k for subjects exposed to sentence materials first and to increase estimates of k for subjects exposed to isolated words first. Finally, significant relationships were found between individual k scores and sentence recognition scores in all three presentation modalities, suggesting that k is a useful measure of individual differences in the ability to use sentence context.

Single-column purification and bio-characterization of recombinant human parathyroid hormone-related protein (1-139).

Recombinant human parathyroid hormone-related protein (hPTHrP) (1-139) was expressed using the IMPACT T7 (intein-mediated purification with an affinity chitin-binding tag) system, allowing purification of free recombinant peptide in a single chromatographic step. This system utilizes an intein, which is a protein splicing element from the Saccharomyces cerevisiae VMA1 gene. The intein has been modified so that it undergoes a self-cleavage reaction at its N-terminus at low temperatures in the presence of 1,4-dithiothreitol (DTT). The cDNA encoding hPTHrP (1-139) was cloned into the pTYB1 vector to create an in-frame fusion at the N-terminus of the intein gene. The cDNA for the chitin-binding domain from Bacillus circulans is present at the C-terminus of intein for affinity purification of the three-part fusion protein on a chitin column. The recombinant plasmid was transfected into E. coli ER2566 cells and synthesis of the PTHrP fusion protein was induced with isopropyl-beta-D-thiogalactopyranoside (IPTG). This system produced pure hPTHrP (1-139) and an N-terminally truncated analogue, hPTHrP (27-139), as judged by sodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blot analysis, N-terminal sequence analysis and mass spectroscopy. hPTHrP (1-139) stimulated cAMP accumulation in ROS 17/2.8 osteoblastic bone cells, whereas hPTHrP (27-139) failed to elicit a response. hPTHrP (1-139) also inhibited the growth of the breast cancer cell line MDA-MB-231; the magnitude of the response was comparable with that of synthetic hPTHrP (1-34) and (1-86). Neutralization of endogenous PTHrP and added hPTHrP (1-139) and N-terminal species with an anti-PTHrP antiserum completely abolished the growth inhibitory effects. These results indicate that the added peptides modulate cell growth by acting at the cell surface. Availability of recombinant hPTHrP (1-139) will allow further study of its biological function, as well as its structure.

Video-rate optical low-coherence reflectometry based on a linear smart detector array.

A low-coherence reflectometer based on a conventional Michelson interferometer and a novel silicon detector chip that allows parallel heterodyne detection is presented. Cross-sectional images of 64x256 pixels covering an area of 1.92 mm x 1.3 mm are acquired at video rate and with a sensitivity close to the shot-noise limit. Applications in surface profiling and thickness measurement are demonstrated.

Economic outcomes of a targeted intervention program: the costs of treating allergic rhinitis patients.

OBJECTIVES: To determine the annual costs of treating allergic rhinitis patients in a managed care environment and to assess the effect of a treatment intervention program on direct and indirect costs. DESIGN: Two arms of an economics study were designed to calculate annual costs of treating allergic rhinitis in Lovelace Health Systems. Direct and indirect costs were also reviewed for patients participating in an intervention program designed to improve patient outcomes during the 1996 fall allergy season. PATIENTS AND METHODS: Annual medical costs of treating allergic rhinitis within the Lovelace system were reviewed using a patient database. A total of 7936 patients with allergic rhinitis symptoms were identified in the database using a case-finding algorithm. An equal number of patients without allergy conditions were selected for the comparison group. In addition to calculating annual costs of treating allergic rhinitis, direct and indirect costs were reviewed for patients participating in a rhinitis intervention program to determine differences in cost between the treatment and control groups. An intervention group of 247 patients was selected to receive care at clinics randomized to use practice guidelines to improve treatment, while 255 patients were treated in the control group clinics, which did not alter treatment practices. RESULTS: Annual expenditures were nearly $2 million more for the allergic rhinitis group than for the control group. In the intervention study, treatment and control groups expended the same in direct costs, but the intervention group showed a trend toward decreased indirect costs. CONCLUSION: Costs of allergic rhinitis are not trivial to a managed care organization; a specifically designed intervention program shows potential for minimizing the costs associated with the ailment.

Stimulatory effect of insulin on calcitonin secretion.

Infusion of insulin directly into thyroid arterial blood perfusing the surgically isolated in situ pig thyroid gland produced an increase in the secretion rate of calcitonin (CT) measured by immunoassay in thyroid venous effluent blood. Insulin in concentrations ranging from approximately 1 to 400 ng/ml produced a maximal stimulation of 4-5 fold. The stimulatory effect of insulin on CT could not be duplicated by infusion of either IGF-I or amylin. Specific binding of radiolabeled insulin was demonstrated using isolated pig thyroid plasma membranes and both rat (6-23) and human (TT) medullary thyroid carcinoma C-cells. Increased CT release was observed from C-cells exposed to a high concentration of insulin. The administration of glucose iv to pigs in order to stimulate secretion of endogenous insulin produced an increase in circulating insulin, which was accompanied by an increase in the secretion of CT. The results show that insulin, delivered directly to the pig thyroid gland, can stimulate CT release. The in vitro binding and secretion studies indicate that C-cells can bind insulin and respond with an increase in CT secretion, and the iv glucose experiments suggest that endogenous insulin is capable of stimulating CT secretion. The findings imply that insulin is capable of acting as a CT secretagogue and suggest that changes in CT secretion may accompany altered states of insulin production such as diabetes or insulin-secreting tumors.

Auditory-visual speech recognition by hearing-impaired subjects: consonant recognition, sentence recognition, and auditory-visual integration.

Factors leading to variability in auditory-visual (AV) speech recognition include the subject's ability to extract auditory (A) and visual (V) signal-related cues, the integration of A and V cues, and the use of phonological, syntactic, and semantic context. In this study, measures of A, V, and AV recognition of medial consonants in isolated nonsense syllables and of words in sentences were obtained in a group of 29 hearing-impaired subjects. The test materials were presented in a background of speech-shaped noise at 0-dB signal-to-noise ratio. Most subjects achieved substantial AV benefit for both sets of materials relative to A-alone recognition performance. However, there was considerable variability in AV speech recognition both in terms of the overall recognition score achieved and in the amount of audiovisual gain. To account for this variability, consonant confusions were analyzed in terms of phonetic features to determine the degree of redundancy between A and V sources of information. In addition, a measure of integration ability was derived for each subject using recently developed models of AV integration. The results indicated that (1) AV feature reception was determined primarily by visual place cues and auditory voicing + manner cues, (2) the ability to integrate A and V consonant cues varied significantly across subjects, with better integrators achieving more AV benefit, and (3) significant intra-modality correlations were found between consonant measures and sentence measures, with AV consonant scores accounting for approximately 54% of the variability observed for AV sentence recognition. Integration modeling results suggested that speechreading and AV integration training could be useful for some individuals, potentially providing as much as 26% improvement in AV consonant recognition.

Measures of auditory-visual integration in nonsense syllables and sentences.

For all but the most profoundly hearing-impaired (HI) individuals, auditory-visual (AV) speech has been shown consistently to afford more accurate recognition than auditory (A) or visual (V) speech. However, the amount of AV benefit achieved (i.e., the superiority of AV performance in relation to unimodal performance) can differ widely across HI individuals. To begin to explain these individual differences, several factors need to be considered. The most obvious of these are deficient A and V speech recognition skills. However, large differences in individuals' AV recognition scores persist even when unimodal skill levels are taken into account. These remaining differences might be attributable to differing efficiency in the operation of a perceptual process that integrates A and V speech information. There is at present no accepted measure of the putative integration process. In this study, several possible integration measures are compared using both congruent and discrepant AV nonsense syllable and sentence recognition tasks. Correlations were tested among the integration measures, and between each integration measure and independent measures of AV benefit for nonsense syllables and sentences in noise. Integration measures derived from tests using nonsense syllables were significantly correlated with each other; on these measures, HI subjects show generally high levels of integration ability. Integration measures derived from sentence recognition tests were also significantly correlated with each other, but were not significantly correlated with the measures derived from nonsense syllable tests. Similarly, the measures of AV benefit based on nonsense syllable recognition tests were found not to be significantly correlated with the benefit measures based on tests involving sentence materials. Finally, there were significant correlations between AV integration and benefit measures derived from the same class of speech materials, but nonsignificant correlations between integration and benefit measures derived from different classes of materials. These results suggest that the perceptual processes underlying AV benefit and the integration of A and V speech information might not operate in the same way on nonsense syllable and sentence input.

High-resolution optical position encoder with large mounting tolerances.

A high-resolution optical position encoder is described that consists of a scale as encountered in a standard moiré-based system, a simple imaging system with stabilized magnification and a novel segmented phase detector integrated circuit. Compared with encoder systems of comparable resolution and accuracy, the encoder presented offers large mechanical tolerances in the alignment of the reading head to the scale, while an interpolation accuracy of better than 0.1 mum is preserved. The system is especially well suited for high-resolution linear encoders as well as for the cost-effective fabrication of compact high-resolution rotary encoders.