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PubMed2003

Theoretical and experimental study of binary perturbation peaks with focus on peculiar retention behaviour and vanishing peaks in chiral liquid chromatography.

The perturbation peak theory was recently developed for acquiring binary isotherm data using the perturbation method (PM) and it was applied for some chiral systems. However, the binary plateaus of these systems were only weakly to moderately nonlinear. In this article the perturbation theory for LC, is developed for both retention times and peak areas and is verified by systematic experiments over the whole range of non-linearity. Attention is focused on non-linear effects that complicate the proper use of the PM method under moderately to strongly non-linear conditions. A serious complication was that the second perturbation peak vanished already at moderate plateau concentrations. A solution to this problem based on a firm theoretical basis and verified experimentally is presented. We also investigated a peculiar retention dependence on the binary plateau concentration, as the retentions of the two perturbation peaks of the binary plateau was compared with the single plateau peak of the more retained enantiomer.

Analysis of Variance↗
PubMed2004

Tracking evolving communities in large linked networks.

We are interested in tracking changes in large-scale data by periodically creating an agglomerative clustering and examining the evolution of clusters (communities) over time. We examine a large real-world data set: the NEC CiteSeer database, a linked network of >250,000 papers. Tracking changes over time requires a clustering algorithm that produces clusters stable under small perturbations of the input data. However, small perturbations of the CiteSeer data lead to significant changes to most of the clusters. One reason for this is that the order in which papers within communities are combined is somewhat arbitrary. However, certain subsets of papers, called natural communities, correspond to real structure in the CiteSeer database and thus appear in any clustering. By identifying the subset of clusters that remain stable under multiple clustering runs, we get the set of natural communities that we can track over time. We demonstrate that such natural communities allow us to identify emerging communities and track temporal changes in the underlying structure of our network data.

Cluster Analysis↗
PubMed2006

Electropalatographic, acoustic, and perceptual data on adaptation to a palatal perturbation.

Exploring the compensatory responses of the speech production system to perturbation has provided valuable insights into speech motor control. The present experiment was conducted to examine compensation for one such perturbation-a palatal perturbation in the production of the fricative /s/. Subjects wore a specially designed electropalatographic (EPG) appliance with a buildup of acrylic over the alveolar ridge as well as a normal EPG palate. In this way, compensatory tongue positioning could be assessed during a period of target specific and intense practice and compared to nonperturbed conditions. Electropalatographic, acoustic, and perceptual analyses of productions of /asa/ elicited from nine speakers over the course of a one-hour practice period were conducted. Acoustic and perceptual results confirmed earlier findings, which showed improvement in production with a thick artificial palate in place over the practice period; the EPG data showed overall increased maximum contact as well as increased medial and posterior contact for speakers with the thick palate in place, but little change over time. Negative aftereffects were observed in the productions with the thin palate, indicating recalibration of sensorimotor processes in the face of the oral-articulatory perturbation. Findings are discussed with regard to the nature of adaptive articulatory skills.

Adult↗
PubMed2026

Predicting cellular responses to perturbation across diverse contexts with State.

While machine learning models offer potential for predicting transcriptomic effects of perturbation, they currently struggle to generalize across cellular contexts. Here, we introduce State, a machine learning model that predicts perturbation effects while accounting for cellular heterogeneity within and across experiments. State is trained using single-cell gene expression data to predict perturbation effects across sets of cells. State improved discrimination of effects on large datasets by more than 30% and identified differentially expressed genes across genetic, signaling, and chemical perturbations with significantly improved accuracy compared with baselines. Its cell embeddings trained on observational data from 167 million cells enable the identification of strong perturbations in cellular contexts where no perturbations were observed during training. We further introduce Cell-Eval, a comprehensive evaluation framework that can be used to evaluate future models. Overall, the performance and flexibility of State set the stage for scaling the development of AI models of cell state.

Machine Learning↗
PubMed1988

Conversion of CuA to a type II copper in cytochrome c oxidase.

When cytochrome c oxidase is incubated at 43 degrees C for approximately 75 min in a solution containing the zwitterionic detergent sulfobetaine 12, the CuA site is converted into a type II copper as judged by changes in the 830-nm absorption band and the EPR spectrum of the enzyme. SDS-PAGE and sucrose gradient ultracentrifugation indicate concomitant loss of subunit III and monomerization of the enzyme during the heat treatment. Comparison of the optical and resonance Raman spectra of the heat-treated and native protein shows that the heme chromophores are not significantly perturbed; the resonance Raman data indicate that the small heme perturbations observed are limited to the cytochrome a3 site. Proton pumping measurements, conducted on the modified enzyme reconstituted into phospholipid vesicles, indicate that these vesicles are unusually permeable toward protons during turnover, as previously reported for the p-(hydroxymercuri)benzoate-modified oxidase and the modified enzyme obtained by heat treatment in lauryl maltoside. The sulfobetaine 12 modified enzyme is no longer capable of undergoing the recently reported conformational transition in which the tryptophan fluorescence changes upon reduction of the low-potential metal centers. Control studies on the monomeric and subunit III dissociated enzymes suggest that the disruption of this conformational change in the heat-treated oxidase is most likely associated with perturbation of the CuA site. These results lend support to the suggestion that the fluorescence-monitored conformational change of the native enzyme is initiated by reduction of the CuA site [Copeland et al. (1987) Biochemistry 26, 7311].

Animals↗
PubMed2001

Inferring subnetworks from perturbed expression profiles.

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.

Bayes Theorem↗
PubMed2005

Adomian's decomposition method for electromagnetically induced transparency.

We developed the Adomian's decomposition method to work for the electromagnetically induced transparency (EIT) problem. The method is general and capable to solve the coupled nonlinear partial differential equations for a light pulse passing through a three-level -type coherent medium. This EIT system is described by the coupled Maxwell-Schrödinger equations and optical Bloch equations. In the weak probe field case, the results agree with perturbation solutions and experimental data. In the stronger probe field case while perturbation may fail, our results reproduce experimental data well. With the techniques of spatial and time partitions, we extend the decomposition method that will be versatile for the investigation of the light pulse propagating through a coherent atomic medium.

Journal Article↗
PubMed2004

HIV accessory proteins and surviving the host cell.

Human immunodeficiency virus generates the accessory proteins Nef, viral infectivity factor (Vif), viral protein R, and viral protein U or viral protein X during viral replication in host cells. Although the significance of these accessory proteins is often lost in vitro, they are essential for viral pathogenesis in vivo. Therefore, these proteins have much potential as antiviral targets. Recent data reveal Vif perturbs an ill-defined antiviral pathway in host cells allowing HIV replication. These data highlight a common feature among HIV accessory proteins in manipulating the host to aid viral pathogenesis. Therefore, these new insights into Vif and other HIV accessory proteins are reviewed, emphasizing host cell interactions and new targets for therapeutic intervention.

HIV Infections↗
PubMed2006

Measurements of the generalized electric and magnetic polarizabilities of the proton at low Q2 using the virtual-compton-scattering reaction.

The mean square polarizability radii of the proton have been measured for the first time in a virtual-Compton-scattering experiment performed at the MIT-Bates out-of-plane scattering facility. Response functions and polarizabilities obtained from a dispersion analysis of the data at Q2 = 0.057 GeV2/c2 are in agreement with O(p3) heavy baryon chiral perturbation theory. The data support the dominance of mesonic effects in the polarizabilities.

Journal Article↗
PubMed2005

Cardiac-specific loss of N-cadherin leads to alteration in connexins with conduction slowing and arrhythmogenesis.

The remodeling of ventricular gap junctions, as defined by changes in size, distribution, or function, is a prominent feature of diseased myocardium. However, the regulation of assembly and maintenance of gap junctions remains poorly understood. To investigate N-cadherin function in the adult myocardium, we used a floxed N-cadherin gene in conjunction with a cardiac-specific tamoxifen-inducible Cre transgene. The mutant animals appeared active and healthy until their sudden death approximately 2 months after deleting N-cadherin from the heart. Electrophysiologic analysis revealed abnormal conduction in the ventricles of mutant animals, including diminished QRS complex amplitude consistent with loss of electrical coupling in the myocardium. A significant decrease in the gap junction proteins, connexin-43 and connexin-40, was observed in N-cadherin-depleted myocytes. Perturbation of connexin function resulted in decreased ventricular conduction velocity, as determined by optical mapping. Our data suggest that perturbation of the N-cadherin/catenin complex in heart disease may be an underlying cause, leading to the establishment of the arrythmogenic substrate by destabilizing gap junctions at the cell surface.

Animals↗
PubMed1999

Nonactive antenna compensation for fixed-array microwave imaging: Part II--Imaging results.

Model-based imaging techniques utilizing microwave signal illumination rely heavily on the ability to accurately represent the wave propagation with a suitable numerical model. To date, the highest quality images from our prototype system have been achieved utilizing a single transmitter/single receiver measurement system where both antennas are manually repositioned to facilitate multiple illuminations of the imaging region, thus requiring long data acquisition times. In an effort to develop a system that can acquire data in a real time manner, a 32-channel network has been fabricated with all ports capable of being electronically selected for either transmit or receive mode. The presence of a complete array of antenna elements at data collection time perturbs the field distributions being measured, which can subsequently degrade the image reconstruction due to increased data-model mismatch. Incorporating the nonactive antenna-compensation model from Part I of this paper into our hybrid element near field image reconstruction algorithm is shown to restore image quality when fixed antenna-array data acquisition is used. Improvements are most dramatic for inclusions located in near proximity to the antenna array itself, although cases of improvement in the recovery of centered heterogeneities are also illustrated. Increases in the frequency of illumination are found to warrant an increased need for nonactive antenna compensation. Quantitative measures of recovered inclusion shape and position reveal a systematic improvement in image reconstruction quality when the nonactive antenna-compensation model is employed. Improvements in electrical property value recovery of localized heterogeneities are also observed. Image reconstructions in freshly excised breast tissue illustrate the applicability of the approach when used with our two-dimensional microwave imaging system.

Algorithms↗
PubMed1975

Effects of double and multiple doses of hydroxyurea on mouse duodenum and mammary tumors.

Previous data on the effects of a single dose of hydroxyurea on C3H mouse duodenum and mammary tumors from a fast growing line (S102F) were used to predict times that may be optimal (i.e., minimize killing of the duodenal S-phase cells while enhancing the killing of tumor S-phase cells) for the administration of subsequent doses of hydroxyurea. These predicted protocols were tested by giving tumor-bearing mice injections of 2 doses at 24 hr intervals. A preliminary in vivo tumor treatment experiment was also done wherein multiple doses (up to 10) were given either at 12, 20, or 24 hr intervals with the mouse survival, body weights, and tumor volumes being recorded daily. The data show that partial cell synchronization was achieved in both tissues and the initial knetics of the surviving cells was essentially the same after a single dose, 2 doses, or 4 doses of hydoxyurea. Also, the different intervals between the 2 doses did not affect the timing of the initital peaks of DNA synthesis in partially synchronized cells; however, the height of the peaks was affected The results demonstrate that kinetic data can be useful for predicting optimal intervals for 2-dose regimes and probably multiple-dose regimes involving a single cell-cycle phase-speeific drug when applied to a mouse tumor model. However, the recovery phenomena in the respective tissues are extremely complicated and more animal tumor data need to be collected before one can make adquate use of cell-synchronizing agents and perturbed cellular kinetic data for routine clinical chemotherapy or combined modality therapy.

Animals↗
PubMed1998

Is follicular atresia biphasic?

OBJECTIVE: To examine the rate of human follicular depletion and the interpretation of curved scatters on log-linear plots. DESIGN: Four mathematical models were tested with use of data drawn from published autopsy studies and histologic analyses of ovaries. SETTING: None. PATIENT(S): None. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): None. RESULT(S): Human oocyte depletion data do not support the inference of a biphasic follicular atresia. On original measurement scales there is no perturbation in the data between ages 37 and 40, and the instantaneous rate of follicle loss is lower after age 40 than ever before. CONCLUSION(S): There is no abrupt increase in the "rate" of follicular atresia that corresponds with a drop in fecundability or an increase in risk of chromosomal abnormalities at approximately age 38. The apparent abrupt increase in rate of follicular depletion is an artifact of log-linear transformation.

Adolescent↗
PubMed2003

Bounds on isocurvature perturbations from cosmic microwave background and large scale structure data.

We obtain very stringent bounds on the possible cold dark matter, baryon, and neutrino isocurvature contributions to the primordial fluctuations in the Universe, using recent cosmic microwave background and large scale structure data. Neglecting the possible effects of spatial curvature, tensor perturbations, and reionization, we perform a Bayesian likelihood analysis with nine free parameters, and find that the amplitude of the isocurvature component cannot be larger than about 31% for the cold dark matter mode, 91% for the baryon mode, 76% for the neutrino density mode, and 60% for the neutrino velocity mode, at 2sigma, for uncorrelated models. For correlated adiabatic and isocurvature components, the fraction could be slightly larger. However, the cross-correlation coefficient is strongly constrained, and maximally correlated/anticorrelated models are disfavored. This puts strong bounds on the curvaton model.

Journal Article↗
PubMed1988

Estimation of missing cone data in three-dimensional electron microscopy.

The range of tilt angles for which projected images of two-dimensionally periodic specimens can be obtained in electron microscopy is limited both by technical aspects, such as goniometer design, and by the more fundamental limitation of object thickness. The lack of a full set of projections causes a missing cone in the reciprocal space data for the object, which will give an anisotropic resolution in a three-dimensional reconstruction and may cause the quality to be impaired by spurious features. The problem is governed by a linear operator which maps the three-dimensional object onto the set of projections. The eigenvalue spectrum of this operator is determined by the range of tilt angles and the spatial extent of the object. If the object is spatially restricted, the eigenvalues are all positive, and it is in principle possible to retrieve experimentally unavailable structure data from those that are measured. However, with restricted angle data, some of the eigenvalues are extremely small, so the problem is 'ill-conditioned' or sensitive to small perturbations in the data, such as noise, and it is necessary to regularize the solution. We applied two methods of band-limited extrapolation and inference on electron microscope data. Alternating projections onto convex sets regularized by a regularization parameter and a least squares estimation regularized by the Shannon entropy functional yield similar results if a close object extent constraint is available. The criterion of maximum entropy, however, allows a relaxation of this constraint.

Bacteria↗
PubMed1988

A chemical kinetic model for ligand binding to identical and independent binding sites in vivo.

In living systems, hormones bind to receptor proteins that are continuously synthesized and degraded. Since these systems cannot be described by equilibrium binding equations, we present a chemical kinetic model for the binding of a hormone to a receptor with identical and independent binding sites in which synthesis and degradation occur. We have derived, from the model, equations that can be used to calculate the bound ligand concentration and the total protein concentration as a function of the free ligand concentration and time. These results show that the methods for experimental measurements, parameter estimation, interpretation of the parameters, and error analysis that are commonly used for equilibrium binding to identical and independent binding sites can be adapted for the analysis of steady-state binding data. The equations we derived for the steady-state ligand binding permit determination of the total receptor protein concentration and the binding affinity from experimental data. In contrast, if an equilibrium model were used, the values of these parameters would not necessarily approximate the true values. A useful approximation to the total receptor concentration as a function of time was found that requires only three of the five rate constants required for exact description by the model. This approximation is shown to be accurate in the biologically relevant range by using previously published parameters estimated from steroid binding data, and adding perturbations to include experimental error and variations among biological systems. When complexities exist, such that the model does not describe the data, these analyses aid in assessing the types of additional components and interactions that may exist.

Binding Sites↗