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PubMed2005

Selective monomorphic and polymorphic HLA class I antigenic determinant loss in surgically removed melanoma lesions.

The analysis of human leukocyte antigen (HLA) class I allospecificity expression in malignant lesions has been hampered by the limited availability of HLA class I allospecificity-specific monoclonal antibodies (mAbs) which stain tissues in immunohistochemical (IHC) reactions. During the 12th International Histocompatibility Workshop, the HLA and cancer component made available a panel of mAbs capable of detecting monomorphic, locus- and allo-specific HLA class I antigenic determinants in surgically removed frozen tissue sections by IHC staining. In the present study, we have utilized this panel of mAbs to analyze the expression of HLA class I allospecificities in 33 primary and in 11 metastatic lesions surgically removed from HLA-typed patients with malignant melanoma, as this information contributes to determine the extent of HLA class I antigen abnormalities in melanoma lesions. HLA class I antigens were downregulated in six (18.2%) of the primary lesions and in six (54.5%) of the metastatic lesions. Selective loss of HLA-A and HLA-B antigens was detected in two (6.1%) and in one (3.0%), respectively, of the primary lesions, but in none of the metastases. HLA-A and HLA-B antigens were downregulated in three (9.1%) and four (36.4%) of the primary and metastatic lesions, respectively. Selective loss of one or more HLA class I allospecificities was found in 10 (33.0%) and two (18.0%) of the 33 primary and 11 metastatic melanoma lesions analyzed, respectively. HLA class I antigen abnormalities were present in 16 (48.5%) of the 33 primary lesions analyzed (i.e. six lesions demonstrating abnormal reactivity with HLA class I monomorphic-specific mAb, two lesions demonstrating selective abnormal reactivity with HLA-B locus-specific mAb, one lesion demonstrating selective abnormal reactivity with HLA-A and HLA-B locus-specific mAbs, and seven lesions demonstrating selective abnormal reactivity with HLA class I allele-specific mAb). Furthermore, HLA class I antigen abnormalities were present in nine (81.8%) of the 11 metastatic lesions analyzed (i.e. six lesions demonstrating abnormal reactivity with HLA class I monomorphic-specific mAb, one lesion demonstrating selective abnormal reactivity with HLA-A locus-specific mAb, and two lesions demonstrating selective abnormal reactivity with HLA class I allele-specific mAb). It cannot be ruled out that the frequency of HLA class I allospecificity abnormalities is higher, as the expression of several HLA class I allospecificities could not be investigated because of the lack of appropriate probes. The frequency of HLA class I antigen defects in primary lesions was significantly correlated with primary lesion thickness, an important prognostic marker in melanoma, arguing for a potential clinical significance of HLA class I antigen abnormalities in melanoma. In conclusion, the results of the present study (i) demonstrate that the frequency of HLA class I allospecificity abnormalities in primary melanoma lesions is markedly higher than that of total HLA class I antigen downregulation described in the literature; (ii) corroborate our previous findings that staining of melanoma lesions with mAb to monomorphic determinants of HLA class I antigens does not detect selective HLA class I allospecificity loss; and (iii) demonstrate for the first time selective loss of antigenic determinants expressed on HLA class I molecules in melanoma lesions. The latter finding indicates that at least two mAbs recognizing distinct antigenic determinants on the HLA molecule being investigated should be used for IHC staining of tissue sections in order to prove that lack of immunostaining reflects actual loss of the corresponding HLA molecule and not selective loss of antigenic determinants.

Adult↗
PubMed1996

Characterization of the endothelin receptor selective agonist, BQ3020 and antagonists BQ123, FR139317, BQ788, 50235, Ro462005 and bosentan in the heart.

1. In this study we used ligand binding techniques to determine the affinity and selectivity of endothelin receptor agonists and antagonists in human left ventricle which expresses both ETA and ETB receptors, and compared these results with cardiovascular tissues from rat and porcine hearts. 2. The linear tripeptide antagonist, FR139317 competed for [125I]-ET-1 binding to human left ventricle with over 200,000 fold selectivity for the ETA receptor (KD ETA = 1.20 +/- 0.28 nM, KDETB = 287 +/- 93 microM). The ETA-selective non-peptide antagonist, 50235, competed with lower affinity and selectivity (KDETA = 162 +/- 61 nM, KDETB = 171 +/- 42 microM) in this tissue. BQ123 and FR139317 also showed high selectivity (greater than 20,000 fold) and affinity in rat (BQ123: KDETA = 1.18 +/- 0.16 nM, KDETB = 1370 +/- 1150 microM; FR139317: KDETA = 2.28 +/- 0.30 nM, KDETB = 292 +/- 114 microM) and pig heart (BQ123: KDETA = 0.52 +/- 0.05 nM, KDETB = 70.4 +/- 4.0 microM; FR139317: KDETA = 2.17 +/- 0.51 nM, KDETB = 47.1 +/- 5.7 microM) (n > or = 3 individuals +/- s.e.mean). 3. Although BQ3020 competed with over 1000 fold selectivity for the ETB subtype in human heart (KDETB = 1.38 +/- 0.72 nM, KDETA = 2.04 +/- 0.21 microM) the peptide inhibited only the binding of [125I]-ET-1 at concentrations greater than 100 nM in rat and porcine heart. This is in contrast to the data from the ETA-selective antagonists which indicated the presence of ETB sites in these tissues from animal hearts. 4. The peptide antagonist, BQ788, had a low, micromolar affinity (KD = 1.98 +/- 0.13 microM) using human left ventricle and no significant selectivity for the human ETB-subtype in this tissue. 5. The non-peptide ET antagonists, Ro462005 (KD = 50.3 +/- 9.5 microM) and bosentan (Ro470203; KD = 77.9 +/- 7.9 nM) competed monophasically for [125I]-ET-1 binding sites in human left ventricle. 6. The results show that the ETA antagonists, BQ123 and FR139317, are highly selective for ETA receptors in all cardiac tissues tested, whereas BQ788 has a low affinity and no selectivity in this human tissue. Further we showed that there are species differences in the binding of BQ3020 to the ETB receptors in the hearts derived from human, rat and pig.

Adult↗
PubMed2000

Selecting target conditions for quality of care improvement in vulnerable older adults.

OBJECTIVE: To identify a set of geriatric conditions as optimal targets for quality improvement to be used in a quality measurement system for vulnerable older adults. DESIGN: Discussion and two rounds of ranking of conditions by a panel of geriatric clinical experts informed by literature reviews. METHODS: A list of 78 conditions common among vulnerable older people was reduced to 35 on the basis of their (1) prevalence, (2) impact on health and quality of life, (3) effectiveness of interventions in improving mortality and quality of life, (4) disparity in the quality of care across providers and geographic areas, and (5) feasibility of obtaining the data needed to test compliance with quality indicators. A panel of 12 experts in geriatric care discussed and then ranked the 35 conditions on the basis of the same five criteria. We then selected 21 conditions, based on panelists' iterative rankings. Using available national data, we compiled information about prevalence of the selected conditions for community-dwelling older people and older nursing home residents and estimated the proportion of inpatient and outpatient care attributable to the selected conditions. RESULTS: The 21 conditions selected as targets for quality improvement among vulnerable older adults include (in rank order): pharmacologic management; depression; dementia; heart failure; stroke (and atrial fibrillation); hospitalization and surgery; falls and mobility disorders; diabetes mellitus; end-of-life care; ischemic heart disease; hypertension; pressure ulcers; osteoporosis; urinary incontinence; pain management; preventive services; hearing impairment; pneumonia and influenza; vision impairment; malnutrition; and osteoarthritis. The selected conditions had mean rank scores from 1.2 to 3.8, and those excluded from 4.6 to 6.9, on a scale from 1 (highest ranking) to 7 (lowest ranking). Prevalence of the selected conditions ranges from 10 to 50% among community-dwelling older adults and from 25 to 80% in nursing home residents for the six most common selected conditions. The 21 target conditions account for at least 43% of all acute hospital discharges and 33% of physician office visits among persons 65 years of age and older. Actual figures must be higher because several of the selected conditions (e.g., end-of-life care) are not recorded as diagnoses. CONCLUSIONS: Twenty-one conditions were selected as targets for quality improvement in vulnerable older people for use in a quality measurement system. The 21 geriatric conditions selected are highly prevalent in this group and likely account for more than half of the care provided to this group in hospital and ambulatory settings.

Aged↗
PubMed2006

Combined use of selective inhibitors and fluorogenic substrates to study the specificity of somatic wild-type angiotensin-converting enzyme.

Somatic angiotensin-converting enzyme (ACE) contains two homologous domains, each bearing a functional active site. Studies on the selectivity of these ACE domains towards either substrates or inhibitors have mostly relied on the use of mutants or isolated domains of ACE. To determine directly the selectivity properties of each ACE domain, working with wild-type enzyme, we developed an approach based on the combined use of N-domain-selective and C-domain-selective ACE inhibitors and fluorogenic substrates. With this approach, marked differences in substrate selectivity were revealed between rat, mouse and human somatic ACE. In particular, the fluorogenic substrate Mca-Ala-Ser-Asp-Lys-DpaOH was shown to be a strict N-domain-selective substrate of mouse ACE, whereas with rat ACE it displayed marked C-domain selectivity. Similar differences in selectivity between these ACE species were also observed with a new fluorogenic substrate of ACE, Mca-Arg-Pro-Pro-Gly-Phe-Ser-Pro-DpaOH. In support of these results, changes in amino-acid composition in the binding site of these three ACE species were pinpointed. Together these data demonstrate that the substrate selectivity of the N-domain and C-domain depends on the ACE species. These results raise concerns about the interpretation of functional studies performed in animals using N-domain and C-domain substrate selectivity data derived only from human ACE.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2006

Identification of bombesin receptor subtype-specific ligands: effect of N-methyl scanning, truncation, substitution, and evaluation of putative reported selective ligands.

Mammalian bombesin (Bn) receptors include the gastrin-releasing peptide receptor, neuromedin B receptor, and bombesin receptor subtype 3 (BRS-3). These receptors are involved in a variety of physiological/pathologic processes, including thermoregulation, secretion, motility, chemotaxis, and mitogenic effects on both normal and malignant cells. Tumors frequently overexpress these receptors, and their presence is now used for imaging and receptor-mediated cytotoxicity. For these reasons, there is an increased need to develop synthetic, selective receptor subtype-specific ligands, especially agonists for these receptors. In this study, we used a number of strategies to identify useful receptor subtype-selective ligands, including synthesizing new analogs (N-methyl-substituted constrained analogs, truncations, and substitutions) in [d-Tyr(6),betaAla(11),Phe(13),Nle(14)]Bn(6-14), which has high affinity for all Bn receptors and is metabolically stable, as well as completely pharmacologically characterized analogs recently reported to be selective for these receptors in [Ca(2+)](i) assays. Affinities and potencies of each analog were determined for each human Bn receptor subtype. N-Methyl substitutions in positions 14, 12, 11, 10, 9, and 8 did not result in selective analogs, with the exception of position 11, which markedly decreased affinity/potency. N-Terminal truncations or position 12 substitutions did not increase selectivity as previously reported by others. Of the four shortened analogs of [d-Phe(6),betaAla(11),Phe(13),Nle(14)]Bn(6-14) reported to be potent selective BRS-3 ligands on [Ca(2+)](i) assays, only AcPhe,Trp,Ala,His(tauBzl),Nip,Gly,Arg-NH(2) had moderate selectivity for hBRS-3; however, it was less selective than previously reported Apa(11) analogs, demonstrating these are still the most selective BRS-3 analogs available. However, both of these analogs should be useful templates to develop more selective BRS-3 ligands.

Animals↗
PubMed2004

Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain.

We previously demonstrated that, in the D4 dopamine receptor, the aromatic microdomain that spans the interface of the second and third transmembrane segments influences the high-affinity interactions with the D4-selective ligand L750,667 [3-[[4-(4-iodophenyl) piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine] and the D2-selective ligands methylspiperone, aripiprazole, and its congener OPC4392 [7-[3-(4-(2,3-dimethylphenyl) piperazinyl) propoxy] 2-(1H)-quinolinone] (Schetz et al., 2000). Here we tested a variety of 1,4-disubstituted aromatic piperidines/piperazines (1,4-DAPs) with different subtype selectivities and functional properties against a panel of D4 receptor mutations in the aromatic microdomain to ascertain whether these ligands recognize this common site. Mutant D4 receptors were constructed by substituting the nonconserved amino acid(s) from the corresponding locations in the D2 receptor. The D4-L2.60W, D4-F2.61V, and D4-LM3.28-3.29FV substitutions result in alterations of the relative position of members of the aromatic microdomain. From these results and molecular models of the ligand-receptor complexes, we conclude that 9 of the 11 D4-selective 1,4-DAPs, including L750,667, have a common pattern of ligand-receptor recognition that depends upon favorable interactions with the phenylalanine at position 2.61 (D4-F2.61V, 20-96-fold decrease). Like methylspiperone, aripiprazole, and OPC4392, the two D4-selective 1,4-DAPs that are insensitive to the D4-F2.61V mutation are sensitive to aromatics at position 2.60 (D4-L2.60W, 7-20-fold increase), and they all have longer spacer arms that permit their tethered aromatics to adopt alternative orientations in the binding-site crevice. All 11 of the D4-selective 1,4-DAPs were sensitive to the D4-LM3.28-3.29FV mutation (13-494-fold decrease) but not the moderately D2-selective methylspiperone. The inferences suggest that subtype selectivity involves two different modes of interaction with the microdomain for the D4-selective 1,4-DAPs and a third mode for D2-selective 1,4-DAPs.

Animals↗
PubMed1995

Structure-activity and structure-selectivity studies on diaminoquinazolines and other inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase.

Twenty-eight 2,4-diaminopteridines with alkyl and aralkyl groups at the 6- and 7-positions, five 1,3-diamino-7,8,9,10-tetrahydropyrimido [4,5-c]isoquinolines with an alkyl, alkylthio, or aryl group at the 6-position, and nine 4,6-diamino-1,2-dihydro-s-triazines with one or two alkyl groups at the 2-position and a substituted phenyl or naphthyl group at the 1-position were evaluated as inhibitors of dihydrofolate reductase enzymes from Pneumocystis carinii, Toxoplasma gondii, and rat liver. Halogen substitution at the 5- or 6-position of 2,4-diaminoquinazoline favored selective binding to the P. carinii enzyme but not the T. gondii enzyme. For example, the 50% inhibitory concentrations of 2,4-diamino-6-chloroquinazoline as an inhibitor of P. carinii, T. gondii, and rat liver dihydrofolate reductase were 3.6, 14 and 29 microM, respectively, corresponding to 12-fold selectivity for the P. carinii enzyme but only marginal selectivity for the T. gondii enzyme. Greater than fivefold selectivity for P. carinii but not T. gondii dihydrofolate reductase was also observed for the 2,4-diaminoquinazolines with 5-methyl, 5-fluoro, 5- and 6-bromo, 6-chloro, and 5-chloro-6-bromo substitution. In contrast, alkyl and aralkyl substitution at the 6- and 7-positions of 2,4-diaminopteridines was found to be a favorable feature for selective inhibition of the T. gondii enzyme and, in two cases, for both enzymes. Nine of the fifty-one compounds tested against P. carinii dihydrofolate reductase and four of the thirty compounds tested against T. gondii dihydrofolate reductase displayed fivefold or greater selectivity for the microbial enzyme versus the rat liver enzyme. The most selective against both enzymes was 2,4-diamino-6,7-bis(cyclohexylmethyl) pteridine, with a selectivity ratio 2 orders of magnitude greater than the value reported for trimetrexate and piritrexim. Since substitution at the 7-position is generally considered to be detrimental to the binding of 2,4-diaminop-teridines and related compounds to mammalian dihydrofolate reductase, the selectivity observed in this study with the 6,7-bis(cyclohexylmethyl) analog may represent a useful approach to enhancing selective inhibition of the enzyme from nonmammalian species.

Animals↗
PubMed2006

Neural mechanisms underlying selectivity for the rate and direction of frequency-modulated sweeps in the auditory cortex of the pallid bat.

Frequency-modulated (FM) sweeps are common in vocalizations, including human speech. Selectivity for FM sweep rate and direction is present in the auditory cortex of many species. The present study sought to determine the mechanisms underlying FM sweep selectivity in the auditory cortex of pallid bats. In the pallid bat inferior colliculus (IC), two mechanisms underlie selectivity for FM sweep rate. The first mechanism depends on duration tuning for tones that arises as a consequence of early inhibition generated by an excitatory tone. The second mechanism depends on a narrow band of delayed high-frequency inhibition. Direction selectivity depends on a broad band of early low-frequency inhibition. Here, the contributions of these mechanisms to cortical FM sweep selectivity were determined in pentobarbital-anesthetized pallid bats. We show that the majority of cortical neurons tuned to echolocation frequencies are selective for the downward direction and rate of FM sweeps. Unlike in IC neurons tuned in the echolocation range, duration tuning is rare in cortical neurons with similar tuning. As in the IC, consistent spectrotemporal differences exist between low- and high-frequency sidebands. A narrow band of delayed high-frequency inhibition is necessary for FM rate selectivity. Low-frequency inhibition has a broad bandwidth, early arrival time, and creates direction selectivity. Cortical neurons respond better to slower FM rates and exhibit broader rate tuning than IC neurons. Relative arrival time of high-frequency inhibition is slower in the cortex than in the IC. Thus whereas similar mechanisms shape direction selectivity of neurons tuned in the echolocation range in the IC and the cortex, only one of the two mechanisms underlying rate selectivity in the IC is present in the cortex.

Acoustic Stimulation↗
PubMed1993

Speed and direction selectivity of macaque middle temporal neurons.

1. We tested quantitatively the responses of 147 middle temporal (MT) cells to light and dark bars moving at different speeds ranging over a 1,000-fold range (0.5-512 deg/s). 2. We derived the following quantities from the speed-response (SR) curves obtained for opposite directions of motion. Speed selectivity was characterized by the maximum response, optimum speed, upper cutoff speed, response to slow movement, and tuning width. Direction selectivity was characterized by the direction index (DI) averaged over speeds yielding significant responses (MDI) and by the direction index at optimal speed (PDI). 3. There was an excellent correlation between speed characteristics for light and dark bars. These correlations were stronger than the correlations between direction indexes. The strongest correlations were obtained for maximum response and upper cutoff. 4. SR curves were classified into three groups: low pass (25%), tuned (43%), and broadband (28%), leaving 4% unclassified. 5. In the majority (75%) of MT cells, there was an agreement between the typology of speed selectivity for light and dark bars. Cells were classified as tuned (33%), low pass (22%), broadband (19%), and mixed (22%), leaving 4% unclassified. In addition to differences in speed characteristics, these groups also differed in response level, direction selectivity, and distribution of preferred directions. 6. For tuned cells, there was a very tight correlation of most speed characteristics for light and dark bars. 7. Direction selectivity depended on stimulus speed in most neurons, yielding a tuned average speed-DI curve. 8. Speed characteristics, proportions of speed selectivity types, and direction selectivity indexes showed little dependence on laminar position. 9. Speed characteristics and direction selectivity indexes were not dependent on eccentricity. Proportion of speed selectivity types however, changed dramatically with eccentricity: low-pass cells dominated foveally, tuned cells parafoveally, and broadband cells peripherally. 10. There were also small eccentricity effects on the range of optimal speeds shown by tuned cells and on the speed at which direction selectivity decreases in the slow speed range.

Acceleration↗
PubMedDate not supplied

Genetic similarity and relationships of DNA fingerprints with performance and with heterosis in Japanese quail lines from two origins and under reciprocal recurrent or within-line selection for early egg production.

DNA fingerprints of Japanese quail male and female pure line breeders were obtained with probes 33.6, 33.15, and R18.1 and they yielded a total of 59 scoreable bands. Bandsharing (0<BS<1) was calculated within and between six quail lines of two origins, and under reciprocal recurrent (AA and BB), within-line (DD and EE) or no (PP and FF) selection. Twenty one pair types were compared. BS was 0.30 higher within line than between lines. BS with the control line was smaller for reciprocal recurrent selection lines than for lines under individual selection. Bandsharing between the two reciprocal recurrent selection lines was 0.19 lower than between lines under individual selection. These results indicate that the two selection methods had different effects on the genetic constitution of the lines, in agreement with previous observations made from the analysis of biochemical polymorphisms with the same set of birds. Egg production and weight traits of pure and crossbred progeny from fingerprinted quail were obtained and compared, and a linear relationship with the measure of bandsharing was estimated. No significant regression coefficient of performance on BS was found over all progeny genetic types. Heterosis from individual matings could also be estimated under the two selection methods since the same birds were parents of both pure and crossbred performance-tested quail. The association of heterosis with the difference between BS of parents of the purebreds and BS of parents of their half-sib crossbreds was favourable and significant for early production traits in lines DD and EE, but no relationship was found in lines AA and BB. These results indicate that the high level of heterosis obtained through reciprocal recurrent selection, and the heterosis observed under within-line selection may have, partly at least, a different genetic determinism. Therefore, the relationship of heterosis with BS may also depend on the past history of selection in the lines.

Journal Article↗
PubMed2005

Feature selection and nearest centroid classification for protein mass spectrometry.

BACKGROUND: The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry. RESULTS: This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets. CONCLUSION: This study tested a number of popular feature selection methods using the nearest centroid classifier and found that several reportedly state-of-the-art algorithms in fact perform rather poorly when tested via stratified cross-validation. The revealed inconsistencies provide clear evidence that algorithm evaluation should be performed on several data sets using a consistent (i.e., non-randomized, stratified) cross-validation procedure in order for the conclusions to be statistically sound.

Algorithms↗
PubMed2006

Feature selection using Haar wavelet power spectrum.

BACKGROUND: Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum. RESULTS: Haar wavelet power spectra of genes were analysed and it was observed to be different in different diagnostic categories. This difference in trend and magnitude of the spectrum may be utilized in gene selection. Most of the genes selected by earlier complex methods were selected by the very simple present method. Each earlier works proved only few genes are quite enough to approach the classification problem 1. Hence the present method may be tried in conjunction with other classification methods. The technique was applied without removing the noise in data to validate the robustness of the method against the noise or outliers in the data. No special software or complex implementation is needed. The qualities of the genes selected by the present method were analysed through their gene expression data. Most of them were observed to be related to solve the classification issue since they were dominant in the diagnostic category of the dataset for which they were selected as features. CONCLUSION: In the present paper, the problem of feature selection of microarray gene expression data was considered. We analyzed the wavelet power spectrum of genes and proposed a clustering and feature selection method useful for classification based on Haar wavelet power spectrum. Application of this technique in this area is novel, simple, and faster than other methods, fit for a wide range of data types. The results are encouraging and throw light into the possibility of using this technique for problem domains like disease classification, gene network identification and personalized drug design.

Artificial Intelligence↗
PubMed2005

Size, constant sequences, and optimal selection.

Because the abundance of functional molecules in RNA sequence space has many unexplored aspects, we compared the outcome of 11 independent selections, performed using the same affinity selection protocol and contiguous randomized regions of 16, 22, 26, 50, 70, and 90 nucleotides. All affinity selections targeted the simplest isoleucine aptamer, an asymmetric internal loop. This loop should be abundant in all selections, so that it can be compared across all experiments. In some cases, two primer sets intended to favor selection of different structures have also been compared. The simplest isoleucine aptamer dominates all selections except with the shortest tract, 16 contiguous randomized nucleotides. Here the isoleucine aptamer cannot be accommodated and no other motif can be selected. Our results suggest an optimum length for selection; surprisingly, both the shortest and the longest randomized tracts make it more difficult to recover the motif. Estimated apparent initial abundances suggest that the simplest isoleucine motif was 20- to 40-fold more frequent in selection with 50- or 70-nucleotide randomized regions than with any other length. Considering primer sets, a pre-formed stable stem within fixed flanking sequences had a five-to 10-fold negative effect on apparent motif abundance at all lengths. Differing random tract lengths also determined the probable motif permutation and the most abundant helix lengths. These data support a significant but lesser role for primer sequences in the outcome of selections.

Base Sequence↗
PubMed2005

Coursework selection: a frame of reference approach using structural equation modelling.

BACKGROUND: Choice behaviour has far-reaching consequences on students' educational careers. Previous models on course selection for example, the model of achievement-related choices (Wigfield & Eccles, 2000) and of self-efficacy theory (Bandura, 1997), stress the importance of ability perceptions (self-concept of ability) as major determinants of choice. AIM: This article suggests a model of course selection, which assumes that comparisons within an internal frame of reference (as proposed by Marsh, 1986, for the association between achievement and self-concepts) can also be applied to the association between self-concepts and course selection. It is therefore hypothesized that course selection is not only positively influenced by the self-concept with respect to the corresponding subject, but also negatively with respect to alternative subjects. Moreover, it should be tested whether the effects of previous achievement on course selection are completely mediated by the self-concepts. SAMPLE: These assumptions were empirically tested using a sample of 296 students from secondary school classes, who were specializing in, for example, chemistry or biology in the following school term. METHOD: Self-concepts and course selection were assessed via questionnaire. The postulated models were tested using a structural equation modelling approach for ordinal variables. RESULTS: The core assumption, that course selection is determined by dimensional comparisons, was supported by significant negative paths from self-concepts on the selection of non-corresponding subjects. Furthermore, the effects of previous achievement on selection were completely mediated by self-concepts. CONCLUSION: Previous models of choice behaviour should be extended, by considering not only the selected alternatives, but also the unselected ones. The finding that the influence of achievement on choice is completely mediated by self-concepts, demonstrates that subjective interpretations of previous achievement determine subsequent behaviour.

Adolescent↗
PubMed2003

Effect on the partial least-squares prediction of yarn properties combining raman and infrared measurements and applying wavelength selection.

The combination of Raman and infrared spectroscopy on the one hand and wavelength selection on the other hand is used to improve the partial least-squares (PLS) prediction of seven selected yarn properties. These properties are important for on-line quality control during production. From 71 yarn samples, the Raman and infrared spectra are measured and reference methods are used to determine the selected properties. Making separate PLS models for all yarn properties using the Raman and infrared spectra, prior to wavelength selection, reveals that Raman spectroscopy outperforms infrared spectroscopy. If wavelength selection is applied, the PLS prediction error decreases and the correlation coefficient increases for all properties. However, a substantial wavelength selection effect is present for the infrared spectra compared to the Raman spectra. For the infrared spectra, wavelength selection results in PLS prediction errors comparable with the prediction performance of the Raman spectra prior to wavelength selection. Concatenating the Raman and infrared spectra does not enhance the PLS prediction performance, not even after wavelength selection. It is concluded that an infrared spectrometer, combined with a wavelength selection procedure, can be used if no (suitable) Raman instrument is available.

Algorithms↗
PubMed2003

The use of selective bronchography in predicting reversal of neoplastic obstructive atelectasis.

OBJECTIVES: To assess the ability of selective bronchography to predict which patients with neoplastic postobstructive atelectasis will respond to interventional therapies directed at the reexpansion of the affected lung. Furthermore, to compare the utility of selective bronchography with the current predictive standard that reversal of postobstructive atelectasis is unlikely when it is > or = 4 weeks in duration (ie, the 4-week rule). DESIGN: A prospective observational study. SETTING: A tertiary care referral center/medical school. PATIENTS: Twenty-seven consecutive patients with advanced lung cancer or other malignancy, with documented neoplastic postobstructive atelectasis involving a total of 44 lobes. INTERVENTIONS: Lobar collapse was documented radiographically. The duration of atelectasis was investigated and quantified as accurately as possible. Prior to the use of interventional therapies, selective bronchography was performed on each collapsed lobe, and the results were documented. Bronchography results did not influence the decision to proceed with interventional therapies. Patients had each of their collapsed lobes manipulated by interventional techniques that were directed at reexpansion of the lung. One week after the patient underwent the intervention, the degree of reexpansion was assessed radiographically. RESULTS: Interventional therapies leading to significant reversal of airway narrowing were completed in all 44 lobes. These were successful in reexpanding 28 of 44 collapsed lobes (64%). Selective bronchography demonstrated the following two distinct patterns: an intact bronchial tree (ie, tree pattern); or the absence of a distinguishable, distal bronchial tree (ie, blush pattern). The sensitivity of selective bronchography to predict reexpansion is 1.00 (95% confidence interval [CI], 0.90 to 1.00), and its specificity is 0.56 (95% CI, 0.30 to 0.80). There were no complications attributable to selective bronchography. The sensitivity of the 4-week rule to predict reexpansion is 0.61 (95% CI, 0.41 to 0.78), and its specificity is 0.75 (95% CI, 0.48 to 0.93). The results of selective bronchography and use of the 4-week rule were significantly different in predicting which lobes would reexpand and which would not (p = 0.0026). Using selective bronchography to predict the reversal of lobar atelectasis, the positive predictive value of the tree pattern was 0.80 and the negative predictive value of the blush pattern was 1.00. The values for the 4-week rule are 0.81 and 0.52, respectively. CONCLUSIONS: Selective bronchography is a useful tool for predicting whether patients with neoplastic postobstructive atelectasis would benefit from interventional techniques that are directed at lobar reexpansion. Selective bronchography appears to be superior to the 4-week rule in this regard.

Aged↗
PubMed2004

Selective phenotyping for increased efficiency in genetic mapping studies.

The power of a genetic mapping study depends on the heritability of the trait, the number of individuals included in the analysis, and the genetic dissimilarity among them. In experiments that involve microarrays or other complex physiological assays, phenotyping can be expensive and time-consuming and may impose limits on the sample size. A random selection of individuals may not provide sufficient power to detect linkage until a large sample size is reached. We present an algorithm for selecting a subset of individuals solely on the basis of genotype data that can achieve substantial improvements in sensitivity compared to a random sample of the same size. The selective phenotyping method involves preferentially selecting individuals to maximize their genotypic dissimilarity. Selective phenotyping is most effective when prior knowledge of genetic architecture allows us to focus on specific genetic regions. However, it can also provide modest improvements in efficiency when applied on a whole-genome basis. Importantly, selective phenotyping does not reduce the efficiency of mapping as compared to a random sample in regions that are not considered in the selection process. In contrast to selective genotyping, inferences based solely on a selectively phenotyped population of individuals are representative of the whole population. The substantial improvement introduced by selective phenotyping is particularly useful when phenotyping is difficult or costly and thus limits the sample size in a genetic mapping study.

Animals↗
PubMed2006

Eigenanalysis of selection ratios from animal radio-tracking data.

The development of methods to analyze habitat selection when resources are defined by several categories (e.g., vegetation types) is a topical issue in radio-tracking studies. The White and Garrott statistic, an extension of the widely used test of Neu et al., can be used to determine whether habitat selection is significant. As well, Manly's selection ratio, a particularly useful measure of resource selectivity by resource users, allows detection of the most strongly selected habitat types. However, when both the number of animals and types of habitat are large, the biologist often has to deal with an excessively large number of measures. In this paper we present a new method, the eigenanalysis of selection ratios, that generalizes these two common methods within the framework of eigenanalyses. This method undertakes an additive linear partitioning of the White and Garrott statistic, so that the difference between habitat use and availability is maximized on the first factorial axes. The eigenanalysis of selection ratios is therefore optimal in habitat selection studies. Although we primarily consider the case where the habitat availability is the same for all animals (design II), we also extend this analysis to the case where the habitat availability varies from one animal to another (design III). An application of this method is provided using radio-tracking data collected on 17 squirrels in five habitat types. The results indicate variability in habitat selection, with two groups of animals displaying two patterns of preference. This difference between the two groups is explained by the patch structure of the study area. Because this method is mainly exploratory, and therefore does not rely on any distributional assumption, we recommend its use in studies of habitat selection.

Animals↗