Incomplete Saturation Research Articles

Transferrin‐immune complex disease: A potentially overlooked gammopathy mediated by IgM and IgG

The combination of marked hypersideremia, hypertransferrinemia, and monoclonal gammopathy of underdetermined significance (MGUS) should alert clinicians to the possible presence of an anti-transferrin immunoglobulin, an uncommon acquired disorder also defined as transferrin-immune complex disease (TICD). The authors have previously described a case of TICD with 100% transferrin saturation and liver iron overload. However, the findings in the few cases so far reported are heterogeneous, and the presence of high transferrin saturation and liver iron overload is not universal. In this article, the authors have described the identification of two additional patients with anti-transferrin monoclonal gammopathy, hypersideremia, and hypertransferrinemia, but with incomplete transferrin saturation and no hepatic iron overload. The autoantibodies were purified by using transferrin as affinity bait and characterized. One subject showed a high-titer monoclonal anti-transferrin IgM with a κ-type light chain. This finding is the first observation of IgM autoantibodies against transferrin. The other patient developed the disease after pregnancy. In this study, monoclonal antibody was an IgG mounting a κ-type light chain with altered molecular weight. These results highlight that transferrin might induce the development of a monoclonal immune response of different classes and specificity. The identification, in a single hematologic center, of three different subjects with anti-transferrin monoclonal gammopathy suggests that the disease probably represents a still underdiagnosed condition. From a clinical standpoint, these patients must be followed up both as MGUS and as hemochromatosis.

Abstract 2676: Measuring extracellular pH within in vivo tumors using acidoCEST MRI.

Abstract INTRODUCTION. Extracelluar pH (pHe) is a hallmark for tumor microenvironment. We have developed a non-invasive MRI method that can accurately measure pHe to assess tumor acidosis, termed “acidoCEST MRI”. This method measures a ratio of the Chemical Exchange Saturation Transfer (CEST) effects of Iopromide, a FDA approved contrast agent for CT. Iopromide has two amides that generate different CEST effects, and a ratio of these CEST effects is correlated with pH over a range of 6.0-7.2 pH units, with a precision of 0.06 pH units, and in a manner that is independent of the agent's concentration and the sample's T1 relaxation time. We have applied acidoCEST MRI to monitor the effects of bicarbonate treatment on tumors. METHOD. A CEST-FISP pulse sequence (2.8 μT, 5 sec, 90 Hz), with 54 saturation frequencies (+10 to -10 ppm) was used to acquire an acidoCEST image in 4.7 min on 7T MRI scanner. Each CEST spectrum was fitted to a sum of three Lorentzian line shapes (Matlab R2012B). A mouse model of MDA-MB-231 mammary carcinoma subcutaneous flank tumor was treated with 200 mM of bicarbonate ad libitum. acidoCEST MRI was performed 1 day before and 1 day after introducing bicarbonate treatment. A bolus of 200 μL of 976 mM iopromide was injected i.v., followed by an infusion of 150 μL/hour of iopromide. Six series of acidoCEST spectroscopic images were acquired for 28 min. RESULTS: We were able to measure an increased in pH in tumor before and after bicarbonate therapy. As shown in the table, only half of the mice studied showed a significant increase in pH after bicarbonate treatment. This is because the limit of quantification of acidoCEST using Iopromide as contrast agent was pH 7.20. Discussion: acidoCEST MRI using Iopromide as contrast agent can measure pH of the tumor with good precision and can be applied to monitor pH-modulating therapy such as bicarbonate treatment. Our method has strong clinical translation potential because it uses low saturation powers, incomplete saturation, and a clinically approved contrast agent. Summary of acidoCEST measurements on mammary carcinoma tumors before and after bicarbonate treatment Mouse before bicarbonate treatment after bicarbonate treatment #1 pH 6.50 ± 0.09 pH 7.15 ± 0.14 (p < 0.01) #2 pH 6.49 ± 0.09 pH 7.20 ± 0.00 (p < 0.01) #3 pH 6.53 ± 0.10 pH 7.14 ± 0.14 (p < 0.01) #4 pH 6.91 ± 0.11 pH 7.10 ± 0.13 (p < 0.02) #5 pH 7.13 ± 0.12 pH 7.16 ± 0.12 #6 pH 7.02 ± 0.13 pH 7.13 ± 0.10 #7 (necrotic tumor) pH 7.20 ± 0.00 pH 7.19 ± 0.06 #8 (necrotic tumor) pH 7.17 ± 0.09 pH 7.17 ± 0.10 Citation Format: Liu Qi Chen, Christine Howison, Justin Jeffery, Ian Robey, Mark Pagel. Measuring extracellular pH within in vivo tumors using acidoCEST MRI. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2676. doi:10.1158/1538-7445.AM2013-2676

The magnetic structure of Co(NCNH)2 as determined by (spin-polarized) neutron diffraction

The magnetic structure of Co(NCNH) 2 has been studied by neutron diffraction data below 10 K using the SPODI and DNS instruments at FRM II, Munich. There is an intensity change in the (1 1 0) and (0 2 0) reflections around 4 K, to be attributed to the onset of a magnetic ordering of the Co 2+ spins. Four different spin orientations have been evaluated on the basis of Rietveld refinements, comprising antiferromagnetic as well as ferromagnetic ordering along all three crystallographic axes. Both residual values and supplementary susceptibility measurements evidence that only a ferromagnetic ordering with all Co 2+ spins parallel to the c axis is a suitable description of the low-temperature magnetic ground state of Co(NCNH) 2 . The deviation of the magnetic moment derived by the Rietveld refinement from the expectancy value may be explained either by an incomplete saturation of the moment at temperatures slightly below the Curie temperature or by a small Jahn–Teller distortion. The magnetic ground state of Co(NCNH) 2 has been clarified by (spin-polarized) neutron diffraction data at low temperatures. Intensity changes below 4 K arise due to the onset of ferromagnetic ordering of the Co 2+ spins parallel to the c axis, corroborated by various (magnetic) Rietveld refinements. • Powderous Co(NCNH) 2 has been subjected to (spin-polarized) neutron diffraction. • Magnetic susceptibility data of Co(NCNH) 2 have been collected. • Below 4 K, the magnetic moments align ferromagnetically with all Co 2+ spins parallel to the c axis. • The magnetic susceptibility data yield an effective magnetic moment of 4.68 and a Weiss constant of −13(2) K. • The ferromagnetic Rietveld refinement leads to a magnetic moment of 2.6 which is close to the expectancy value of 3.

Synthesis of Functionalized Microspheres with High Magnetic Concentration for Microscale Force Application

Magnetic microspheres are commercially available in a wide range of diameters and with a variety of chemical functionalities for applications such as cell sorting, protein isolation, or microscale force spectroscopy. The most commonly-used products are magnetic spheres one micron in diameter or larger. These spheres generally consist of a polymer core which is swollen in a solvent and saturated with a solution of iron oxide nanoparticles. This top-down process tends to result in incomplete saturation of the polymer spheres and therefore a diminishing magnetic concentration as spheres grow larger since the magnetic content does not scale with volume.We present here a bottom-up approach to microsphere fabrication which begins with a high-permeability magnetic fluid consisting of magnetite nanoparticles complexed with poly(dimethyl siloxane-co-aminopropylmethyl siloxane). The magnetic content of the fluid may be adjusted smoothly from 0 - 50% wt. without any nanoparticle aggregation, resulting in a highly-magnetic silicone fluid which is homogenous at scales well below 100 nm. Using this material, we demonstrate the production of solid, spherical microbeads in diameters ranging from 2 - 30 microns. Since magnetic nanoparticles are distributed uniformly throughout the material, magnetic content scales directly with volume, resulting in a significant advantage over competitors in terms of magnetic force application at larger sizes. Controlling for diameter, the high magnetic content of these spheres results in nearly four times the force-generating capabilities of the leading 2.8-micron competitor, with advantages increasing in larger spheres. In addition, we use a cell-targeting assay to demonstrate our ability to functionalize the microsphere surface with a variety of ligands.

Characterization of the Reader Width Using the Micro-Track Test in Perpendicular Recording

Micro-track test is a valuable tool used to characterize the electrical reader width in perpendicular recording. The test is based on trimming both sides of a track written with a single tone and followed by a cross-track scan of the remaining track. The reader cross-track profile or read sensitivity function is characterized by a narrow band measurement of the read-back signal as a function of cross-track position. With increasing track density, the signal amplitude decreases due to incomplete media saturation and to an increase in the off-track noise due to percolation and opposite polarity media saturation. These effects cause a lump at the edge of the micro-track profile that changes the width of the profile (MT10 and MT50). Micro-magnetic analysis indicates that the off-track demagnetization field creates a track-edge section in the media with opposite polarity relative to the originally written track. This section is coherent with the main track and decreases the read-back signal during the scan of the micro-track. Consequently, the shape of the cross-track read sensitivity function becomes distorted, causing a reduction in MT10 and a side lump. The solution to this problem is to increase the amplitude of the micro-track read-back signal by reduced trimming and by the use of a higher density (KFCI) in the main track that minimizes the off-track demagnetization field. These test improvements are shown to preserve the integrity of the micro-track profile and to enable an accurate measurement of MT10 and MT50. Optimizing reader and writer widths in perpendicular recording requires an accurate measurement of these parameters.

Basiliximab Does Not Increase Efficacy of Corticosteroids in Patients With Steroid-Refractory Ulcerative Colitis

Basiliximab is a chimeric monoclonal antibody that binds CD25 and thereby inhibits interleukin (IL)-2-mediated proliferation of lymphocytes. IL-2 might contribute to the resistance of T cells to corticosteroids. We investigated the efficacy and safety of basiliximab as a corticosteroid-sensitizing agent in patients with corticosteroid-refractory ulcerative colitis (UC). We studied 149 patients with moderate to severe UC (Mayo score ≥6 and endoscopic subscore ≥2) despite treatment for at least 14 days with oral prednisone (40-50 mg/day). Subjects were randomly assigned to groups that were given 20 mg (n = 46) or 40 mg (n = 52) basiliximab or placebo (n = 51) at weeks 0, 2, and 4. All subjects received 30 mg/day prednisone through week 2; the dose was reduced by 5 mg each week to 20 mg/day, which was maintained until week 8. At week 8, we compared the rates of clinical remission (Mayo score ≤2, no subscore >1) for patients given basiliximab with the rate for patients given placebo. Twenty-eight percent of patients given placebo, 29% of those given the 40-mg dose of basiliximab, and 26% of those given the 20-mg dose of basiliximab achieved clinical remission (P = 1.00 vs placebo for each dose). Basiliximab was generally well tolerated. Six subjects who received basiliximab had serious adverse events (6.1%) compared with 2 who received placebo (3.9%; P = .72). In subjects given basiliximab, incomplete saturation of CD25 (<50%) on peripheral T cells was associated with the presence of anti-basiliximab antibodies (odds ratio, 21; 95% confidence interval, 2.4-184). Basiliximab does not increase the effect of corticosteroids in the induction of remission in outpatients with corticosteroid-resistant moderate to severe UC.

A Quantitative 3D Physical Simulation Method of Waterflooding in Fractured Reservoirs

Quantitative 3D physical simulation is very important to researches on waterflooding mechanism of fractured reservoirs. Considering reservoir, well network, wellbore, and fluid medium, the quantitative 3D physical reservoir simulation method is established based on the similarity criteria. The similarities of permeability anisotropy, matrix-fracture imbibition, power system, and resistance system are achieved by using accurate manufacture of fractured porous media, incomplete vacuum saturation technique, equivalent process of well radius, and selection of laboratory fluids, respectively. Based on this method, a typical oil reservoir is physically simulated. The lab model can quantitatively forecast reservoir performance and production indexes. A new physical research means of fractured reservoir is provided.

High Permeability Silicone-Based Magnetic Microspheres for Microscale Force Spectroscopy

A wide variety of magnetic microspheres are currently available for applications such as cell sorting, chemical separations, or microscale force spectroscopy. The smallest spheres (10 nm - 500 nm) generally consist of solid iron-oxide nanoparticles synthesized via the coprecipitation of iron salts, while many larger products (2 μm - 100 μm) consist of polymer microspheres which are subsequently saturated with magnetic nanoparticles. However, the latter process may result in incomplete saturation and therefore diminishing magnetic concentration as sphere diameter increases. In addition, a lack of confluence between these two methods of production has resulted in a dearth of products in the 0.5 - 2 μm range. We present here a bottom-up approach to magnetic microsphere fabrication which allows us to scale the diameter of our microspheres between 0.2 - 100 microns while maintaining a constant magnetic content throughout. In this approach, we use a novel magnetic silicone consisting of magnetite nanoparticles complexed with a monolayer of poly(dimethyl siloxane-co-aminopropylmethyl siloxane). The magnetic content of the composite may be tuned from 0 - 50% wt. without nanoparticle aggregation, resulting in a highly magnetic silicone fluid which is homogenous at scales below 100 nm. We demonstrate the production of microspheres of this material by an emulsion process in which microsphere diameter may be tuned by careful selection of surfactant type and concentration. Finally, we show that the resulting spheres compare favorably with leading commercial competitors in terms of magnetic force application.

Improved pH measurements with a single PARACEST MRI contrast agent.

The measurement of extracellular pH has potential utility for assessing the therapeutic effects of pH-dependent and pH-altering therapies. A PARAmagnetic chemical exchange saturation transfer (PARACEST) MRI contrast agent, Yb-DO3A-oAA, has two CEST effects that are dependent on pH. A ratio derived from these CEST effects was linearly correlated with pH throughout the physiological pH range. The pH can be measured with a precision of 0.21 pH units and an accuracy of 0.09 pH units. The pH measurement is independent of concentration and T₁ relaxation times, but is dependent on temperature. Although MR coalescence affects the CEST measurements, especially at high pH, the ratiometric analysis of the CEST effects can account for incomplete saturation of the agent's amide and amine that results from MR coalescence. Provided that an empirical calibration is determined with saturation conditions, magnetic field strength and temperature that can be used for subsequent studies, these results demonstrate that this single PARACEST MRI contrast agent can accurately measure pH.

Fast Detection of Biomolecules in Diffusion-Limited Regime Using Micromechanical Pillars

We have developed a micromechanical sensor based on vertically oriented oscillating beams, in which contrary to what is normally done (for example with oscillating cantilevers) the sensitive area is located at the free end of the oscillator. In the micropillar geometry used here, analyte adsorption is confined only to the tip of the micropillar, thus reducing the volume from which the analyte molecules must diffuse to saturate the surface to a sphere of radius more than 2 orders of magnitude smaller than the corresponding linear distance valid for adsorption on a macroscopic surface. Hence the absorption rate is 3 orders of magnitude faster than on a typical 200 × 20 square micrometer cantilever. Pillar oscillations are detected by means of an optical lever method, but the geometry is suitable for multiplexing with compact integrated detection. We demonstrate our technology by investigating the formation of a single-strand DNA self-assembled monolayer (SAM) consisting of less than 10(6) DNA molecules and by measuring their hybridization efficiency. We show that the binding rate is 1000 times faster than on a "macroscopic" surface. We also show that the hybridization of a SAM of maximum density DNA is 40% or 4 times the value reported in the literature. These results suggest that the lower values previously reported in the literature can be attributed to incomplete saturation of the surface due to the slower adsorption rate on the "macroscopic" surfaces used.

Enhanced exchange and reduced magnetization of Gd in an Fe/Gd/Fe trilayer

The exchange interaction of Gd adjacent to Fe has been characterized by transport measurements on a double spin valve with a Fe/Gd/Fe trilayer as the middle layer. Our measurements show that the ferromagnetism of the Gd is enhanced by the presence of the Fe, and it remains ferromagnetic over its Curie temperature up to a thickness no smaller than 1 nm adjacent to the Fe. This thickness is more than double what has been reported before. Additionally, the saturation magnetization of the thin Gd layer sandwiched in Fe was found to be half of its bulk value. This reduced magnetization does not seem to be related to the proximity of Fe but rather to the incomplete saturation of Gd even for very high fields.

Regulation of integrin affinity on cell surfaces

Lymphocyte activation triggers adhesiveness of lymphocyte function-associated antigen-1 (LFA-1; integrin α(L)β(2)) for intercellular adhesion molecules (ICAMs) on endothelia or antigen-presenting cells. Whether the activation signal, after transmission through multiple domains to the ligand-binding αI domain, results in affinity changes for ligand has been hotly debated. Here, we present the first comprehensive measurements of LFA-1 affinities on T lymphocytes for ICAM-1 under a broad array of activating conditions. Only a modest increase in affinity for soluble ligand was detected after activation by chemokine or T-cell receptor ligation, conditions that primed LFA-1 and robustly induced lymphocyte adhesion to ICAM-1 substrates. By stabilizing well-defined LFA-1 conformations by Fab, we demonstrate the absolute requirement of the open LFA-1 headpiece for adhesiveness and high affinity. Interaction of primed LFA-1 with immobilized but not soluble ICAM-1 triggers energy-dependent affinity maturation of LFA-1 to an adhesive, high affinity state. Our results lend support to the traction or translational motion dependence of integrin activation.

Protein adsorption and transport in dextran-modified ion-exchange media. II. Intraparticle uptake and column breakthrough

Abstract Protein transport behavior was compared for the traditional SP Sepharose Fast Flow and the dextran-modified SP Sepharose XL and Capto S resins. Examination of the dynamic binding capacities (DBCs) revealed a fundamental difference in the balance between transport and equilibrium capacity limitations when comparing the two resin classes, as reflected by differences in the locations of the maximum DBCs as a function of salt. In order to quantitatively compare transport behavior, confocal microscopy and batch uptake experiments were used to obtain estimates of intraparticle protein diffusivities. For the traditional particle, such diffusivity estimates could be used to predict column breakthrough behavior accurately. However, for the dextran-modified media, neither the pore- nor the homogeneous-diffusion model was adequate, as experimental dynamic binding capacities were consistently lower than predicted. In examining the shapes of breakthrough curves, it was apparent that the model predictions failed to capture two features observed for the dextran-modified media, but never seen for the traditional resin. Comparison of estimated effective pore diffusivities from confocal microscopy and batch uptake experiments revealed a discrepancy that led to the hypothesis that protein uptake in the dextran-modified resins could occur with a shrinking-core-like sharp uptake front, but with incomplete saturation. The reason for the incomplete saturation is speculated to be that protein initially fills the dextran layer with inefficient packing, but can rearrange over time to accommodate more protein. A conceptual model was developed to account for the partial shrinking-core uptake to test whether the physical intuition led to predictions consistent with experimental behavior. The model could correctly reproduce the two unique features of the breakthrough curves and, in sample applications, parameters found from the fit of one breakthrough curve could be used to adequately match breakthrough at a different flow rate or batch uptake behavior.

A Prediction Method for In-Plane Permeability and Manufacturing Applications in the VARTM Process

VARTM (Vacuum Assisted Resin Transfer Molding) is a popular method for manufacturing large-scaled, single-sided mold composite structures, such as wind turbine blades and yachts. Simulation to find the proper infusion scenario before manufacturing is essential to avoid dry spots as well as incomplete saturation and various fiber weaves with different permeability affect numerical simulation tremendously. This study focused on deriving the in-plane permeability prediction method for FRP (Fiber Reinforced Plastics) laminates in the VARTM process by experimental measurements and numerical analysis. The method provided an efficient way to determine the permeability of laminates without conducting lots of experiments in the future. In-plane permeability imported into the software, RTM-Worx, to simulate resin flowing pattern before the infusion experiments of a 3D ship hull with two different infusion scenarios. The close agreement between experiments and simulations proved the correctness and applicability of the prediction method for the in-plane permeability.

Impact of in vivo alemtuzumab dose before reduced intensity conditioning and HLA-identical sibling stem cell transplantation: pharmacokinetics, GVHD, and immune reconstitution

AbstractIn vivo alemtuzumab reduces the risk of graft-versus-host disease (GVHD) and nonrelapse mortality after reduced intensity allogeneic transplantation. However, it also delays immune reconstitution, leading to frequent infections and potential loss of graft-versus-tumor responses. Here, we tested the feasibility of alemtuzumab dose deescalation in the context of fludarabine-melphalan conditioning and human leukocyte antigen (HLA)–identical sibling transplantation. Alemtuzumab was given 1-2 days before graft infusion, and dose reduced from 60 mg to 20 mg in 4 sequential cohorts (total n = 106). Pharmacokinetic studies were fitted to a linear, 2-compartment model in which dose reduction led to incomplete saturation of CD52 binding sites and greater antibody clearance. Increased elimination was particularly evident in the 20-mg group in patients who had CD52-expressing tumors at time of transplantation. The 20-mg dose was also associated with greater risk of severe GVHD (acute grade III-IV or chronic extensive) compared with > 20 mg (hazard ratio, 6.7; 95% CI, 2.5-18.3). In contrast, dose reduction to 30 mg on day −1 was associated with equivalent clinical outcomes to higher doses but better lymphocyte recovery at 12 months. In conclusion, alemtuzumab dose reduction to 30 mg is safe in the context of reduced intensity conditioning and HLA-identical sibling transplantation. This trial was registered at http://www.ncrn.org.uk as UKCRN study 1415.

Saturation criteria for heavy overconsolidated cohesive soils

Saturation criteria for heavy over- consolidated cohesive soils. The paper concerns signifi cance of properly carried out saturation procedure and its role in evaluation of undrained response of heavy preconsolidated cohesive soils. In particular the saturation criteria are addressed which should be fulfi lled during saturation of preconsolidated clay specimens of various plas- ticity. Infl uence of incomplete saturation on shear strength parameters is briefl y characterized. On the basis of experimental data the back pressure method is shown to be the most effi cient method in obtaining full saturation in overconsolidated clay of various plasticity. Analysis of the test results made possible to propose full saturation criteria for low, medium and high plasticity clays which are based on reduced value of Skempton's B parameter.

Water 1H relaxation dispersion analysis on a nitroxide radical provides information on the maximal signal enhancement in Overhauser dynamic nuclear polarization experiments

Water (1)H relaxation rate measurements of (15)N-(2)H-TEMPONE solutions at temperatures ranging from 298 to 328 K have been performed as a function of magnetic field from 0.00023 to 9.4 T, corresponding to (1)H Larmor frequencies of 0.01 to 400 MHz. The relaxation profiles were analyzed according to the full theory for dipolar and contact relaxation, and used to estimate the coupling factor responsible for observed solution DNP effects. The experimental DNP enhancement at (1)H Larmor frequency of 15 MHz obtained by saturating one of the lines of the (15)N doublet is only ca. 20% lower than the limiting value predicted from the relaxation data, indicating that the experimental DNP setup is nearly optimal, the residual discrepancy arising from incomplete saturation of the other line.

Synthesis, Characterization, and Biological Evaluation of Integrin αvβ3-Targeted PAMAM Dendrimers

Ligand size and valency strongly influence the receptor uptake and clearance of tumor angiogenesis imaging agents. The structures of successful imaging agents exhibit a high degree of variability, encompassing small monovalent arginine-glycine-aspartic acid (RGD)-containing peptides, multivalent RGD-oligomers, and a monoclonal antibody against integrin alpha-v-beta-3 (alpha-v-beta-3). We have pursued a nanoscale approach to imaging of angiogenesis using rationally designed polyamidoamine (PAMAM) dendrimers covalently adorned with RGD-cyclopeptides. An orthogonal oxime-ligation strategy was applied to chemoselectively effect conjugation of the PAMAM dendrimers with RGD-cyclopeptides for targeting alpha vbeta 3. Fluorescent dyes for optical imaging and chelates for gadolinium-based magnetic resonance (MR) imaging were subsequently appended to create robust multimodal macromolecular imaging agents. Fluorescence microscopy revealed selective binding of the resulting RGD peptide-bearing dendrimer with empty chelates to alpha-v-beta-3-expressing cells, but somewhat reduced selectivity was observed following Gd(III) complexation. The expected incomplete saturation of chelates with Gd(III) ions permitted radiometal complexation, and an in vivo tissue distribution of the resulting agent in M21 melanoma tumor-bearing mice showed mostly renal and reticuloendothelial accumulation, with the tumor:blood ratio peaking (3.30+/-0.03) at 2 h postinjection.

ChipcheckII—Predicting Binding Curves for Multiple Analyte Strands on Small DNA Microarrays

Incomplete binding, saturation, and cross-hybridization between partially complementary strands complicate the parallel detection of nucleic acids via DNA microarrays. Treating the competing equilibria governing binding to microarrays requires computational tools. We have developed the web-based program ChipCheckII that calculates total hybridization matrices for target strands interacting with probes on small DNA microarrays. The program can be used to compute the extent of cross-hybridization and other phenomena affecting fidelity of detection based on sequences, quantities of strands, and hybridization conditions as inputs. Enthalpy and entropy of duplex formation are generated locally with UNAfold, including those for complexes that are partially matched. Simulated binding versus temperature curves for portions of a commercial genome chip demonstrate the extent to which cross-hybridization can complicate DNA detection. ChipCheckII is expected to aid nucleic acid chemists in developing high fidelity DNA microarrays.

Correcting reaction rates measured by saturation-transfer magnetic resonance spectroscopy

Off-resonance or spillover irradiation and incomplete saturation can introduce significant errors in the estimates of chemical rate constants measured by saturation-transfer magnetic resonance spectroscopy (MRS). Existing methods of correction are effective only over a limited parameter range. Here, a general approach of numerically solving the Bloch–McConnell equations to calculate exchange rates, relaxation times and concentrations for the saturation-transfer experiment is investigated, but found to require more measurements and higher signal-to-noise ratios than in vivo studies can practically afford. As an alternative, correction formulae for the reaction rate are provided which account for the expected parameter ranges and limited measurements available in vivo. The correction term is a quadratic function of experimental measurements. In computer simulations, the new formulae showed negligible bias and reduced the maximum error in the rate constants by about 3-fold compared to traditional formulae, and the error scatter by about 4-fold, over a wide range of parameters for conventional saturation transfer employing progressive saturation, and for the four-angle saturation-transfer method applied to the creatine kinase (CK) reaction in the human heart at 1.5T. In normal in vivo spectra affected by spillover, the correction increases the mean calculated forward CK reaction rate by 6–16% over traditional and prior correction formulae.