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PubMed2005

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry interlaboratory comparison of mixtures of polystyrene with different end groups: statistical analysis of mass fractions and mass moments.

A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) interlaboratory comparison was conducted on mixtures of synthetic polymers having the same repeat unit and closely matching molecular mass distributions but with different end groups. The interlaboratory comparison was designed to see how well the results from a group of experienced laboratories would agree on the mass fraction, and molecular mass distribution, of each polymer in a series of binary mixtures. Polystyrenes of a molecular mass near 9000 u were used. Both polystyrenes were initiated with the same butyl initiator; however, one was terminated with -H (termed PSH) and the other was terminated with -CH2CH2OH (termed PSOH). End group composition of the individual polymers was checked by MALDI-TOF MS and by nuclear magnetic resonance (NMR). Five mixtures were created gravimetrically with mass ratios between 95:5 and 10:90 PSOH/PSH. Mixture compositions where measured by NMR and by Fourier transform infrared spectrometry (FT-IR). NMR and FT-IR were used to benchmark the performance of these methods in comparison to MALDI-TOF MS. Samples of these mixtures were sent to any institution requesting it. A total of 14 institutions participated. Analysis of variance was used to examine the influences of the independent parameters (participating laboratory, MALDI matrix, instrument manufacturer, TOF mass separation mode) on the measured mass fractions and molecular mass distributions for each polymer in each mixture. Two parameters, participating laboratory and instrument manufacturer, were determined to have a statistically significant influence. MALDI matrix and TOF mass separation mode (linear or reflectron) were found not to have a significant influence. Improper mass calibration, inadequate instrument optimization with respect to high signal-to-noise ratio across the entire mass range, and poor data analysis methods (e.g., baseline subtraction and peak integration) seemed to be the greatest obstacles in the correct application of MALDI-TOF MS to this problem. Each of these problems can be addressed with proper laboratory technique.

Journal Article↗

PubMed2001

Structural comparison of monomeric variants of the chemokine MIP-1beta having differing ability to bind the receptor CCR5.

MIP-1beta, a member of the chemokine family of proteins, tightly binds the receptor CCR5 as part of its natural function in the immune response, and in doing so also blocks the ability of many strains of HIV to enter the cell. The single most important MIP-1beta residue known to contribute to its interaction with the receptor is Phe13, which when mutated reduces the ability of MIP-1beta to bind to CCR5 by more than 1000-fold. To obtain a structural understanding of the dramatic effect of the absence of Phe13 in MIP-1beta, we used multidimensional heteronuclear NMR to determine the three-dimensional structure of the MIP-1beta F13A variant. We had previously shown that, unlike the wild-type protein which has been shown to be a tight dimer, the F13A mutant is monomeric even at high concentrations [Laurence, J. S., Blanpain, C., Burgner, J. W., Parmentier, M., and LiWang, P. J. (2000) Biochemistry 39, 3401-3409], leading to significant changes in the NMR spectra of F13A and the wild-type protein. We have obtained a total of 940 structural restraints for MIP-1beta F13A, and have calculated a family of structures having a backbone rmsd from the average of 0.55 A (residues 12-67). A structural comparison of the F13A mutant with a fully active monomeric variant, P8A, shows that despite some differences in the (1)H-(15)N HSQC spectra the two are nearly identical in NOE distance restraints and in backbone conformation. A comparison of F13A with the wild-type protein shows largely the same fold, although differences exist in the N-terminal and loop regions for which the loss of the dimer in F13A can mainly account. A dynamics comparison confirms greater flexibility in F13A than in the wild-type protein in regions of dimer contact in the wild-type protein. In an analysis to determine if the large functional effect resulting from the loss of Phe13 is due to the local side chain change or due to more global structural changes, we conclude that local effects predominate. This suggests that a strategy for designing tight binding anti-CCR5 therapeutics should include a Phe-like component.

Amino Acid Substitution↗

PubMed2006

Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution.

The rapid expansion of the amount of genomic and structural data has provided many examples of enzymes with evolutionarily related active sites that catalyze different reactions. Functional comparisons of these active sites can provide insight into the origins of the enormous catalytic proficiency of enzymes and the evolutionary changes that can lead to different enzyme activities. The alkaline phosphatase (AP) superfamily is an ideal system to use in making such comparisons given the extensive data available on both nonenzymatic and enzymatic phosphoryl transfer reactions. Some superfamily members, such as AP itself, preferentially hydrolyze phosphate monoesters, whereas others, such as nucleotide pyrophosphatase/phosphodiesterase (NPP), preferentially hydrolyze phosphate diesters. We have measured rate constants for NPP-catalyzed hydrolysis of phosphate diesters and monoesters. NPP preferentially catalyzes diester hydrolysis by factors of 10(2)-10(6), depending on the identity of the diester substrate. To identify features of the NPP active site that could lead to preferential phosphate diester hydrolysis, we have determined the structure of NPP in the absence of ligands and in complexes with vanadate and AMP. Comparisons to existing structures of AP reveal bimetallo cores that are structurally indistinguishable, but there are several distinct structural features outside of the conserved bimetallo site. The structural and functional data together suggest that some of these distinct functional groups provide specific substrate binding interactions, whereas others tune the properties of the bimetallo active site itself to discriminate between phosphate diester and monoester substrates.

Adenosine Monophosphate↗

PubMedDate not supplied

Lipase-catalyzed transformations for the synthesis of butyl lactate: a comparison between esterification and transesterification.

The alpha-hydroxy esters are increasingly employed in cosmetic, food, and pharmaceutical formulations as they determine reduced skin-irritant effects in comparison with the respective acids, offering similar hygroscopic, emulsifying, and exfoliating properties. The enzymatic synthesis of lactate esters in nonaqueous systems was studied as regards the influence of the critical process parameters, to enable a comparison between the most commonly used synthetic routes, namely, esterification and transesterification. The experimental results showed that the direct esterification of lactic acid with butanol may be limited by the reduced lipase stability in the presence of the acid (substrate) and of the water (product), in particular when solvent-free media are used. The stability of the enzyme is further reduced as polar solvents are required as a result of the polarity of the lactic acid. Therefore, the use of the lactic acid as substrate is of practical interest only when the acid is significantly cheaper in comparison with its short-chain esters. If this is not the case, the transesterification of the ethyl lactate with butanol is to be preferred for the higher flexibility in the choice of the experimental conditions, the operability of solvent-free systems, and the simplicity of the product removal assembly.

Catalysis↗

PubMedDate not supplied

DIVSEL and COMPLIB--strategies for the design and comparison of combinatorial libraries using pharmacophoric descriptors.

Screening synthetic combinatorial libraries may facilitate rapid drug lead discovery by substantially increasing the number of molecules tested. Drug discovery efficiency and productivity can be further improved by designing libraries to maximize their molecular diversity or by comparing them to existing collections of compounds and/or libraries to select those that complement the properties already well represented. In this paper we describe two strategies to aid in the design and comparison of combinatorial libraries. The methods employ multi-pharmacophore three-dimensional (3D) descriptors in combination with two recent proposals for dissimilarity-based compound selection and library comparison. This method allows the design to be performed in product space and library comparison to consider all pair-wise intermolecular contributions to the diversity.

Drug Design↗

PubMed2003

Interlaboratory comparison of extraction efficiency of pesticides from surface and laboratory water using solid-phase extraction disks.

A continuation of an earlier interlaboratory comparison was conducted (1) to assess solid-phase extraction (SPE) using Empore disks to extract atrazine, bromacil, metolachlor, and chlorpyrifos from various water sources accompanied by different sample shipping and quantitative techniques and (2) to compare quantitative results of individual laboratories with results of one common laboratory. Three replicates of a composite surface water (SW) sample were fortified with the analytes along with three replicates of deionized water (DW). A nonfortified DW sample and a nonfortified SW sample were also extracted. All samples were extracted using Empore C(18) disks. After extraction, part of the samples were eluted and analyzed in-house. Duplicate samples were evaporated in a 2-mL vial, shipped dry to a central laboratory (SDC), redissolved, and analyzed. Overall, samples analyzed in-house had higher recoveries than SDC samples. Laboratory x analysis type and laboratory x water source interactions were significant for all four compounds. Seven laboratories participated in this interlaboratory comparison program. No differences in atrazine recoveries were observed from in-house samples analyzed by laboratories A, B, D, and G compared with the recovery of SDC samples. In-house atrazine recoveries from laboratories C and F were higher when compared with recovery from SDC samples. However, laboratory E had lower recoveries from in-house samples compared with SDC samples. For each laboratory, lower recoveries were observed for chlorpyrifos from the SDC samples compared with samples analyzed in-house. Bromacil recovery was <65% at two of the seven laboratories in the study. Bromacil recoveries for the remaining laboratories were >75%. Three laboratories showed no differences in metolachlor recovery; two laboratories had higher recoveries for samples analyzed in-house, and two other laboratories showed higher metolachlor recovery for SDC samples. Laboratory G had a higher recovery in SW for all four compounds compared with DW. Other laboratories that had significant differences in pesticide recovery between the two water sources showed higher recovery in DW than in the SW regardless of the compound. In comparison to earlier work, recovery of these compounds using SPE disks as a temporary storage matrix may be more effective than shipping dried samples in a vial. Problems with analytes such as chlorpyrifos are unavoidable, and it should not be assumed that an extraction procedure using SPE disks will be adequate for all compounds and transferrable across all chromatographic conditions.

Acetamides↗

PubMed1993

Molecular shape comparison of angiotensin II receptor antagonists.

A new and powerful analytical method for comparing molecular shapes by optimizing the overlap of molecular volumes has been developed. This shape comparison method provides both a quantitative measure of the shape similarity of molecules and a means to align molecules such that shape similarity if maximized. Our MSC method has been enhanced with an option to allow discrimination between groups with different chemical properties. Atoms or groups of atoms may be assigned to different classes based on specific properties such as electrostatic potential, hydrogen bonding ability, or hydrophobicity. This enables matches based on criteria such as alignment of hydrophobic groups or hydrogen bond acceptor groups. In this study, we report shape comparisons of angiotensin II (AII) receptor antagonists from two structural classes, 4-(biphenyl-4-ylmethoxy)-quinoline derivatives such as ICI D8731 and N-(biphenyl-4-ylmethyl)imidazole derivatives, such as DuP753. Starting with a list of low-energy conformations for the two molecules, each conformation of the first molecule is paired with each of the conformations of the second molecule. For each of these conformational pairs, an MSC comparison, which generates multiple MSC maxima, is initiated. Eight high scoring conformational pairings were found with shape matching based on the intersection of the total molecular volume, while nine high-scoring pairs were identified with matching by atom type. MSC identifies conformational pairs with high shape similarity, as measured by the intersection volume, and thus generates and prioritizes several alternative models for the AII antagonist pharmacophore.

Angiotensin Receptor Antagonists↗

PubMed1997

Comparison of protein surfaces using a genetic algorithm.

A genetic algorithm (GA) is described which is used to compare the solvent-accessible surfaces of two proteins or fragments of proteins, represented by a dot surface calculated using the Connolly algorithm. The GA is used to move one surface relative to the other to locate the most similar surface region between the two. The matching process is enhanced by the use of the surface normals and shape terms provided by the Connolly program and also by a simple hydrogen-bonding descriptor and an additional shape descriptor. The algorithm has been tested in applications ranging from the comparison of small surface patches to the comparison of whole protein surfaces, and it has performed correctly in all cases. Examples of the matches are given and a quantitative analysis of the quality of the matches is performed. A number of possible future enhancements to the program are described which would allow the GA to be used for more complex surface comparisons.

Alcohol Dehydrogenase↗

PubMed1996

In-vitro dissolution profile comparison: statistics and analysis, model dependent approach.

PURPOSE: To develop and propose a "model dependent' approach for the in-vitro dissolution profiles comparison. METHODS: Diltiazem hydrochloride tablet dissolution profiles were compared using a statistical approach based on a mathematical model. A similarity region (SR) was defined based on the intra- and inter-lot parameter variances of the final production size standard lots. Statistical distances between the test and reference lot parameter means were computed and normalized. A 90% confidence region (CR) was developed around the statistical distance. The confidence region was compared with the similarity region to assess the similarity or dis-similarity of the test and reference (REF) lot dissolution profiles. Two test lots, one with a "minor' modification (mm) the other with a "major' modification (MM), were evaluated. RESULTS: "Weibull' was selected as the "model' function. A comparison of the confidence regions around the statistical distance of "mm-REF' and "MM-REF' with the similarity region, suggested that the dissolution profiles of the "minor' modification lot were similar and that of "major' modification lot were dis-similar to the reference lot. CONCLUSIONS: A "model dependent' approach was shown to be useful for the inter-lot in-vitro dissolution profiles comparison.

Cardiovascular Agents↗

PubMed2004

Color-encoded semiautomatic analysis of multi-slice first-pass magnetic resonance perfusion: comparison to tetrofosmin single photon emission computed tomography perfusion and X-ray angiography.

BACKGROUND AND PURPOSE: Cardiovascular magnetic resonance (CMR) perfusion can accurately detect coronary artery disease (CAD). However, the absence of efficient, easy-to-use and reliable image analysis software is an obstacle to its introduction into clinical practice. The aim of this study was to evaluate new color-encoded semiautomatic software for analysis of first-pass CMR perfusion in comparison to tetrofosmin myocardial single photon emission computed tomography (SPECT), using X-ray angiography as the standard of truth for the detection of CAD. METHODS: Thirty-two patients underwent both SPECT and CMR perfusion at rest and adenosine stress. Twenty of these patients also underwent X-ray angiography. Off-line CMR image analysis consisted of six steps to generate a color display of the myocardial perfusion reserve index (MPRI). The MPRI color-maps were analyzed visually and compared to SPECT. RESULTS: In comparison to X-ray angiography overall accuracy was 87% for CMR and 77% for SPECT perfusion to detect significant CAD (stenosis > or =70%). In comparison with SPECT sensitivity was 80%, specificity 91%, and the overall agreement 89% for CMR. CONCLUSIONS: Post-processing of CMR perfusion data using new semiautomatic software to generate and display the MPRI visually as color-encoded images is feasible and fast. In this study it yielded higher accuracy than SPECT to detect significant CAD on X-ray angiography. Correlation between SPECT and CMR accuracy for detection of perfusion defects was high. This method may accelerate the time-consuming analysis of CMR perfusion data, thus enabling a more widespread clinical utility.

Adenosine↗

PubMed2005

Two-digit comparison: decomposed, holistic, or hybrid?

We investigate whether two-digit numbers are decomposed for purposes of numerical comparison (e.g., choosing the larger one). Earlier theorists concluded that numbers are processed holistically (Brysbaert, 1995; Dehaene, Dupoux, & Mehler, 1990), or that holistic and decomposed processes operate in parallel (Nuerk, Weger, & Willmes, 2001). In the present experiment, we presented pairs of two-digit numbers with a decade distance of either zero (e.g., 54-57) or one (54-61). If a holistic process contributes to two-digit comparison, there should be an overall distance effect for number pairs with a decade distance of one. On the other hand, if numbers are decomposed and a holistic comparison does not contribute, this overall distance effect should be absent for these number pairs. Evidence is found that, at least in the present task settings, numbers are not compared holistically. The results are interpreted in terms of a recently proposed theory of numerical cognition (Verguts & Fias, 2004; Verguts, Fias, & Stevens, in press).

Association Learning↗

PubMed2001

Comparisons of cutaneous blood flow reactivity to norepinephrine and sodium nitroprusside between patients with heart transplantation and healthy subjects.

Heart transplant patients are reported to have impaired regulation of the microvasculature. The purpose of this study was to investigate the cutaneous blood flow and its reactivity to sodium nitroprusside (vasodilator, Nipride 0.1%) and norepinephrine (vasoconstrictor, Levophed 0.1%) in patients after heart transplantation in comparison to normal healthy individuals. Eighteen patients after heart transplantation and 16 healthy, nonsmoking individuals served as subjects of the study. Sodium nitroprusside and norepinephrine were introduced by iontophoresis to the skin of the right and left forearms, respectively. After measuring cutaneous blood flow reactivity in the pre-exercise state by laser Doppler flowmetry, subjects were then asked to close and open their fists for 2 min. The same measurements were repeated after exercise. Comparisons between the groups were carried out by the Wilcoxan signed rank test. The Mann Whitney U-test was used for comparison between pre-exercise and post-exercise states. The results demonstrated that sodium nitroprusside significantly increased forearm cutaneous perfusion at rest but produced only a mild increase after exercise. This reactivity was significantly lower after exercise with no significant differences between groups. Norepinephrine decreased cutaneous blood flow at rest. The transplant patients were significantly less sensitive to norepinephrine before but not after exercise. The changes in norepinephrine reactivity with exercise were significantly different between groups (p < 0.05).

Exercise↗

PubMed2002

Ultraviolet protection factor of fabrics: comparison of laboratory and field-based measurements.

BACKGROUND/PURPOSE: Spectrophotometry has become an accepted laboratory-based method for the determination of the ultraviolet protection factor (UPF) of fabrics. However, the validity of the UPF determined in the laboratory has been a controversial issue with regard to its significance in the field. To compare UPF values obtained by spectrophotometry, determination of the minimal erythema dose (MED), and biological dosimetry, we conducted laboratory and field-based measurements on various fabric materials. METHODS: One cotton, two viscose, and two polyester fabrics were enrolled into the study. Spectrophotometric (SP) testing was performed in accordance with the European standard. In vivo "on skin" (IV) testing on human subjects was performed with and without fabric protection. For determination of MED, a solar-simulator was used. In another part of the study, biological dosimetry (BD) testing was employed for laboratory testing with solar-simulated radiation (laboratory BD testing) as well as field-based measurements with natural sunlight in stationary (stationary BD testing) and "real life" exposure situations (mobile subject BD testing). For field-based measurements one light-weight polyester fabric was selected. RESULTS: The differences of the mean UPF values obtained by the laboratory-based methods were significant (MANOVA; P = 0.05), except for fabric no. 2 (MANOVA; P = 0.097). In 4 of the 5 fabrics tested, UPF values obtained by IV testing were significantly lower than those obtained by SP testing (t-test; P = 0.05). In 3 fabrics, SP testing revealed significantly higher UPF values in comparison to laboratory BD testing (t-test; P = 0.05). The differences of UPF values obtained by the laboratory and field-based measurements employed for the light-weight polyester fabric were significant (ANOVA; P = 0.05). In comparison to SP testing (UPF 3.8), stationary BD testing resulted in significantly lower (UPF 3.5) and mobile subject BD testing in a significantly higher UPF of 4.4 (t-test; P = 0.05). The UPF obtained by mobile subject BD testing differed significantly from the UPF obtained by stationary BD testing (t-test; P = 0.05). CONCLUSIONS: Comparison of the presented methods indicates that IV testing generally results in lower UPF values. By contrast BD testing in "real life" exposure situations reveals relatively high UPF values. Although an overestimation of the spectrophotometrically measured UPF has been observed in comparative laboratory testing, UPF values obtained by field-based measurements are in relatively good agreement, or even surpass UPF values obtained by spectrophotometry. It is, therefore, suggested that SP testing provides "safe" UPF values which may be also valid in extreme real exposure situations. Biological UV dosimetry is, however, a promising alternative method for UPF testing: the test is easily performed in realistic exposure situations, the test is relatively inexpensive, and the measurements are valid.

Analysis of Variance↗

PubMed2000

Social comparisons of income in one's community: evidence from national surveys of income and happiness.

Two studies provide evidence for social comparison effects of income on subjective well-being (SWB). The 1st study of 7,023 persons from nationally representative samples in the United States shows that the range and skew of the income distribution in a community affects a person's happiness, as predicted by range-frequency theory. The 2nd study of 8 nations over a period of 25 years shows that decreasing the skew (inequality) of the income distribution in a country increases average national SWB. Both studies strongly support social comparison effects of income within a community, and both results are predicted by range-frequency theory. These studies are the first to successfully extend earlier results of R. H. Smith, E. Diener, and D. H. Wedell (1989) from the laboratory into naturalistic situations. The magnitude of the social comparison effects is smaller than the main effect of income, which implies that nations can avoid creating a "hedonic treadmill."

Data Collection↗

PubMed1992

Semantic congruity effects and theories of the comparison process.

Two experiments requiring comparisons of point locations on the line demonstrate that the magnitude of the response-time-based congruity effect parallels the form of the macro and the micro speed-accuracy trade-off function. This is predicted from the evidence accrual class of theories but is contrary to either the propositionally based semantic coding theory or the expectancy view. Very large accuracy-based congruity effects with comparisons of point locations in the plane are evident. Congruity effects arise because the duration of each evidence accrual is increased and the quality of the information is reduced as the distance of the stimulus representations from the instruction-activated reference point increases. This evidence accrual view is extended to account for the properties of perceptual and symbolic comparisons.

Adult↗

PubMed1995

Role of the syllable in the processing of spoken English: evidence from a nonword comparison task.

Previous research using monitoring tasks suggests that syllables do not play a role in the initial processing of speech by English listeners. The role of syllables in a different task, one involving the speeded comparison of 2 nonwords, was investigated. In 2 experiments, responses to nonword pairs that shared a complete syllable were significantly faster than responses to pairs that shared part of a syllable when the shared unit was at the beginning or in the middle of the nonwords. Results were mixed when the shared unit was at the end of the nonwords, possibly reflecting a confounding effect of rhyme. Findings suggest that syllabified representations of the nonwords may be used in a comparison task, even in English. Results are interpreted relative to different demands of the nonword comparison and monitoring tasks.

Adult↗

PubMed1980

Symbolic comparisons of objects on color attributes.

Symbolic comparisons of object brightness and color were investigated in two experiments using words and outline drawings as stimuli. Both experiments yielded orderly symbolic distance effects. Contrary to prediction, no reliable picture advantages emerged. For color comparison, individual differences in word fluency and color memory predicted decision time with word stimuli. These results contrast sharply with those of previous comparison studies involving concrete dimensions. The results are discussed in terms of dual-coding theory and the role of verbal mechanisms in memory for object color.

Color Perception↗

PubMed1983

The role of subtractions and comparisons in comparative judgments involving numerical reference points.

Experiments in which subjects are asked to decide which of two digits is closer in magnitude to a third raise problems for many theories of linear orders. Holyoak (1978), for example, performed a number of these reference point experiments and concluded that they posed serious difficulties for a number of leading models. In their place, he offered the distance ratio model in which the ease of the decision in a reference point task is a function of the ratio of the distances between each stimulus and the reference point. In the present article, three experiments are presented that bear on the adequacy of Holyoak's position. In the first two studies, we present evidence that an important assumption of the distance ratio model is incorrect. In the third experiment, we compare the empirical adequacy of the distance ratio model with our own subtraction model. This model treats the reference point task as a concatenation of two subtractions and a simple digit comparison. This comparison operation is equivalent to the magnitude comparison required in standard linear order experiments. Overall, the subtraction model gives a somewhat better account than the distance ratio.

Adolescent↗