bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrogation of MS/MS search data with an pI Filter algorithm to increase protein identification success
Authors: Uwaje Nkemdilim C. , Mueller Nikola S. , Maccarrone Giuseppina , Turck Christoph W. 
Published: May 2007

AbstractIn high‐throughput proteomics, the bottom‐up approach has become a widely used method for the identification of proteins that is based on tryptic peptide MS/MS analysis. Separation methodologies that use IEF of tryptic peptides have recently been introduced and provide an extra dimension of peptide separation. In addition to its great fractionation capability, tryptic peptide prefractionation by IEF can also increase the protein identification success. The pI information of the peptide gained can be successfully used in a post‐database search filtering step. We introduce a filtering algorithm that is based on the comparison of the experimental and theoretical pI's to validate peptide identifications by MS/MS data search engines.
Incidence of non-Hodgkin's lymphoma among individuals with chronic hepatitis B virus infection
Authors: Ulcickas Yood Marianne , Quesenberry Charles P. , Guo Dianlin , Caldwell Cary , Wells Karen , Shan Jun , Sanders Lynn , Skovron Mary Lou , Iloeje Uchenna , Manos Michele M. 
Published: May 2007

Abstract

Although hepatitis C virus (HCV) infection has been shown to be associated with development of non-Hodgkin's lymphoma (NHL), few studies have investigated the association between chronic HBV infection and NHL. The purpose of this study was to compare the incidence of NHL between patients with and without chronic hepatitis B virus (HBV) infection. Using automated laboratory result and clinical data from two United States health systems, we identified individuals with chronic HBV infection from January 1, 1995 through December 31, 2001. Using each health system's population-based tumor registry, we identified all cases of NHL diagnosed through December 31, 2002. We excluded any individual with a history of NHL or human immunodeficiency virus (HIV). We fit Cox proportional hazards models to calculate hazard ratios comparing the incidence of NHL between chronic HBV-infected patients (N = 3,888) and patients without HBV (N = 205,203) drawn from the source populations. We identified 8 NHL cases in the chronic HBV infection cohort and 111 cases in the comparison cohort. Patients with chronic HBV infection were 2.8 times more likely to develop NHL than matched comparison patients (adjusted hazard ratio = 2.80, 95% confidence interval = 1.16-6.75), after controlling for age, race, sex, income, Charlson comorbidity index, study site, and HCV infection.

Conclusion:

chronic HBV-infected patients were nearly 3 times more likely to develop NHL than comparison patients. (HEPATOLOGY 2007.)
Redox-dependent and ligand-independent trans -activation of insulin receptor by globular adiponectin
Authors: Fiaschi Tania , Buricchi Francesca , Cozzi Giacomo , Matthias Stephanie , Parri Matteo , Raugei Giovanni , Ramponi Giampietro , Chiarugi Paola 
Published: May 2007

Abstract

Adiponectin/ACRP30 is an adipose tissue–derived hormone with antiatherogenic, antidiabetic, and insulin-sensitizing properties. Although the metabolic effects of adiponectin on glucose and lipid metabolism are well known, the signaling pathways triggered by adiponectin receptors remain to be elucidated. We report evidence that in hepatic cells, adiponectin stimulation produces a transient burst of reactive oxygen species (ROS) through activation of the small GTPase Rac1 and 5-lypoxigenase. Furthermore, adiponectin-induced oxidants cause the oxidation/inhibition of protein-tyrosine phosphatase (PTP) 1B, one of the major phosphotyrosine phosphatases involved in the control of insulin receptor phosphorylation. Adiponectin causes increased association of PTP1B to insulin receptor and the oxidation/inhibition of the phosphatase, ultimately provoking the ligand-independent

trans

-phosphorylation of insulin receptor. We also report evidence that redox signaling plays a key role in both mitogen-activated protein kinase activation and hepatic glucose consumption induced by adiponectin.

Conclusion:

These results point to ROS as critical regulators of the cross-talk between adiponectin and insulin pathways and provide a redox-based molecular mechanism for the insulin-sensitizing function of adiponectin. (HEPATOLOGY 2007.)
On the structure of the inverse kinematics map of a fragment of protein backbone
Authors: Milgram R. J. , Liu Guanfeng , Latombe J. C. 
Published: May 2007

AbstractLoop closure in proteins requires computing the values of the inverse kinematics (IK) map for a backbone fragment with 2n ≥ 6 torsional degrees of freedom (dofs). It occurs in a variety of contexts, e.g., structure determination from electron‐density maps, loop insertion in homology‐based structure prediction, backbone tweaking for protein energy minimization, and the study of protein mobility in folded states. The first part of this paper analyzes the global structure of the IK map for a fragment of protein backbone with 6 torsional dofs for a slightly idealized kinematic model, called the canonical model. This model, which assumes that every two consecutive torsional bonds CαC and NCα are exactly parallel, makes it possible to separately compute the inverse orientation map and the inverse position map. The singularities of both maps and their images, the critical sets, respectively, decompose SO(3) × ℝ3 into open regions where the number of IK solutions is constant. This decomposition leads to a constructive proof of the existence of a region in ℝ3 × SO(3) where the IK of the 6‐dof fragment attains its theoretical maximum of 16 solutions. The second part of this paper extends this analysis to study fragments with more than 6 torsional dofs. It describes an efficient recursive algorithm to sample IK solutions for such fragments, by identifying the feasible range of each successive torsional dof. A numerical homotopy algorithm is then used to deform the IK solutions for a canonical fragment into solutions for a noncanonical fragment. Computational results for fragments ranging from 8 to 30 dofs are presented. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Rapid dark‐blood carotid vessel‐wall imaging with random bipolar gradients in a radial SSFP acquisition
Authors: Lin Hung‐Yu , Flask Chris A. , Dale Brian M. , Duerk Jeffrey L. 
Published: May 2007

AbstractPurposeTo investigate and evaluate a new rapid dark‐blood vessel‐wall imaging method using random bipolar gradients with a radial steady‐state free precession (SSFP) acquisition in carotid applications.Materials and MethodsThe carotid artery bifurcations of four asymptomatic volunteers (28–37 years old, mean age = 31 years) were included in this study. Dark‐blood contrast was achieved through the use of random bipolar gradients applied prior to the signal acquisition of each radial projection in a balanced SSFP acquisition. The resulting phase variation for moving spins established significant destructive interference in the low‐frequency region of k‐space. This phase variation resulted in a net nulling of the signal from flowing spins, while the bipolar gradients had a minimal effect on the static spins. The net effect was that the regular SSFP signal amplitude (SA) in stationary tissues was preserved while dark‐blood contrast was achieved for moving spins. In this implementation, application of the random bipolar gradient pulses along all three spatial directions nulled the signal from both in‐plane and through‐plane flow in phantom and in vivo studies.ResultsIn vivo imaging trials confirmed that dark‐blood contrast can be achieved with the radial random bipolar SSFP method, thereby substantially reversing the vessel‐to‐lumen contrast‐to‐noise ratio (CNR) of a conventional rectilinear SSFP “bright‐blood” acquisition from bright blood to dark blood with only a modest increase in TR (∼4 msec) to accommodate the additional bipolar gradients.ConclusionOverall, this sequence offers a simple and effective dark‐blood contrast mechanism for high‐SNR SSFP acquisitions in vessel wall imaging within a short acquisition time. J. Magn. Reson. Imaging 2007;25:1299–1304. © 2007 Wiley‐Liss, Inc.
Magnetic resonance imaging to assess acute changes in atrial and ventricular parameters after transcatheter closure of atrial septal defects
Authors: Burgstahler Christof , Wöhrle Jochen , Kochs Matthias , Nusser Thorsten , Löffler Christine , Kunze Markus , Höher Martin , Gawaz Meinrad P. , Hombach Vinzenz , Merkle Nico 
Published: May 2007

AbstractPurposeTo evaluate acute changes in atrial and ventricular parameters by the use of cardiac magnetic resonance imaging (MRI) in patients with percutaneous transcatheter atrial septal defects (ASD) closure.Materials and MethodsThe study included 14 patients (six males and eight females, 45 ± 18 years) with congenital ASD. Cardiac MRI (1.5T Philips Intera CV) was performed before and within 24 hours after transcatheter ASD closure. Right atrial (RA) and left atrial (LA) dimensions, as well as right (RV) and left (LV) ventricular end‐diastolic (ED) volumes were determined. Atrial size was assessed by planimetry of the maximum RA and LA areas in a standard four‐chamber view, and ventricular volumes were calculated according to a modified Simpson's rule in short‐axis views.ResultsThe mean RA decreased significantly from 27.6 ± 6.4 cm2 before closure to 24.4 ± 5.6 cm2 after the procedure (P = 0.0018), whereas the LA area did not change (24.1 ± 4.7 cm2 vs. 23.8 ± 5.2 cm2, P = 0.76). The RV volumes, volume index, and ejection fraction (EF) decreased significantly from 229 ± 64 mL to 181 ± 43 mL (P < 0.001, average reduction = 19% ± 15%), from 126.0 ± 37.2 mL/m2 to 96.6 ± 28.6 mL/m2 (P < 0.0001) and from 64 ± 5% to 58% ± 7% (P = 0.01), respectively. The LV volumes and volume index remained unchanged (114 ± 25 mL vs. 118 ± 22 mL, P = 0.18, 63.5 ± 13.5 mL/m2 vs. 63.0 ± 17.4 mL/m2, P = 0.83). Left–right shunting decreased from 40% ± 15% to 9% ± 15% (P < 0.001).ConclusionCardiac MRI can reveal detailed information on acute changes in shunt fraction and ventricular dimensions after ASD closure. ASD closure by percutaneous transcatheter device implantation results within 24 hours in a significant reduction of shunt fraction, RA and RV sizes, and RV function, whereas LA and LV dimensions remain unchanged. J. Magn. Reson. Imaging 2007;25:1136–1140. © 2007 Wiley‐Liss, Inc.
Normalized left ventricular volumes and function in thalassemia major patients with normal myocardial iron
Authors: Westwood Mark A. , Anderson Lisa J. , Maceira Alicia M. , Shah Farrukh T. , Prescott Emma , Porter John B. , Wonke Beatrix , Walker J. Malcolm , Pennell Dudley J. 
Published: May 2007

AbstractPurposeTo determine the reference range in thalassemia major (TM) for left ventricular (LV) function.Materials and MethodsWe used cardiovascular magnetic resonance (CMR) to measure heart volumes and function in 81 TM patients with normal myocardial T2* measurements (T2* > 20 msec) and by inference without excess myocardial iron. Forty age‐ and gender‐matched healthy controls were also studied.ResultsResting LV volumes and function normalized to body surface area differed significantly between TM patients and controls. The lower limit and the mean for ejection fraction (EF) were higher in TM patients (males 59 vs. 55%, mean 71% vs. 65%; females 63 vs. 59%, mean 71% vs. 67%; both P < 0.001). The upper limit and mean for end‐diastolic volume index were higher in TM patients (males 152 vs. 105 mL/m2, mean 97 vs. 84 mL/m2; females 121 vs. 99 mL/m2, mean 87 vs. 79 mL/m2; both P < 0.05). In TM patients the cardiac index (P < 0.001) was increased.ConclusionAt rest, TM patients with a normal myocardial T2* have different “normal” values for LV volume and function parameters compared to controls, and this has the potential to lead to a misdiagnosis of cardiomyopathy. We present new reference “normal” ranges in TM to alleviate this problem. J. Magn. Reson. Imaging 2007;25:1147–1151. © 2007 Wiley‐Liss, Inc.
High‐speed 3T MR spectroscopic imaging of prostate with flyback echo‐planar encoding
Authors: Chen Albert P. , Cunningham Charles H. , Ozturk‐Isik Esin , Xu Duan , Hurd Ralph E. , Kelley Douglas A.C. , Pauly John M. , Kurhanewicz John , Nelson Sarah J. , Vigneron Daniel B. 
Published: May 2007

AbstractProstate MR spectroscopic imaging (MRSI) at 3T may provide two‐fold higher spatial resolution over 1.5T, but this can result in longer acquisition times to cover the entire gland using conventional phase‐encoding. In this study, flyback echo‐planar readout trajectories were incorporated into a Malcolm Levitt's composite‐pulse decoupling sequence (MLEV)–point‐resolved spectroscopy sequence (PRESS) to accelerate the acquisition of large array (16 × 16 × 8), high spatial (0.154 cm3) resolution MRSI data by eight‐fold to just 8.5 minutes. Artifact free, high‐quality MRSI data was obtained in nine prostate cancer patients. Easy data reconstruction and the robustness of the flyback echo‐planar encoding make this technique particularly suitable for the clinical setting. The short acquisition time provided by this method reduces the 3T prostate MRI/MRSI exam time, allows longer repetition times, and/or allows the acquisition of additional MR acquisitions within the same exam. J. Magn. Reson. Imaging 2007;25:1288–1292. © 2007 Wiley‐Liss, Inc.
Cardiac amyloidosis: MR imaging findings and T1 quantification, comparison with control subjects
Authors: Krombach Gabriele A. , Hahn Christa , Tomars Maren , Buecker Arno , Grawe Armin , Günther Rolf W. , Kühl Harald P. 
Published: May 2007

AbstractIn cardiac amyloidosis an interstitial deposition of amyloid fibrils causes concentric thickening of the atrial and ventricular walls. We describe the results of tissue characterization of the myocardium by T1 quantification and MRI findings in a patient with cardiac amyloidosis. The T1 time of the myocardium was elevated compared to that in individuals without amyloidosis. The T1 time of the myocardium was 1387 ± 63 msec (mean value obtained from four measurements ± standard deviation [SD]) in the patient with cardiac amyloidosis, while the reference value obtained from the myocardium of 10 individuals without known myocardial disease was 1083 ± 33 msec (mean value ± SD). In combination with other MR findings suggestive of amyloidosis, such as homogeneous thickening of the ventricular and atrial walls, thickening of the valve leaflets, restrictive filling pattern, and reduction of systolic function, T1 quantification may increase diagnostic confidence. J. Magn. Reson. Imaging 2007;25:1283–1287. © 2007 Wiley‐Liss, Inc.
High cerebral blood volume in human gliomas predicts deletion of chromosome 1p: Preliminary results of molecular studies in gliomas with elevated perfusion
Authors: Law Meng , Brodsky Jennie E. , Babb James , Rosenblum Marc , Miller Douglas C. , Zagzag David , Gruber Michael L. , Johnson Glyn 
Published: May 2007

AbstractPurposeTo determine if increased perfusion using dynamic susceptibility contrast perfusion MRI (DSC MRI) in gliomas may be predictive of 1p19q deletions. Loss of heterozygosity of chromosomes 1p and 19q confers responsiveness to chemotherapy improving survival in gliomas.Materials and MethodsWe retrospectively reviewed 16 patients who had DSC MRI and molecular studies of their excised gliomas for 1p19q deletions. Allelic status was assessed by loss of heterozygosity using polymerase chain reaction (PCR). DNA was extracted from paraffin curls of brain tumor sections and nail clippings. Relative cerebral blood volume (rCBV) measurements were then statistically compared with the presence of 1p and 19q deletions.ResultsPatients with 1p19q deletions (N = 7) demonstrated rCBV values of 10.54 ± 2.93. Patients without 1p deletions (N = 9) had rCBV values of 4.84 ± 2.4 (P = 0.012). Logistic regression demonstrated that rCBV was able to predict the presence of a 1p deletion to significance levels of 0.038 and 0.044, adjusted and not adjusted for age and sex, respectively. The kappa coefficient for the agreement between predicted deletion status using rCBV and the truedeletion status was 0.746 (P = 0.0028). Deletions of 19q alone, or together with 1p deletions, were not associated with high rCBV.ConclusionHistopathologic, molecular, and imaging evidence supports increased neovascularity in gliomas with 1p deletions in this preliminary study. We propose a diagnostic algorithm to obtain molecular studies in gliomas demonstrating high rCBV. J. Magn. Reson. Imaging 2007;25:1113–1119. © 2007 Wiley‐Liss, Inc.
Comparison of biphasic and reordered fat suppression for dynamic breast MRI
Authors: Desmond Kimberly L. , Ramsay Elizabeth A. , Plewes Donald B. 
Published: May 2007

AbstractPurposeTo optimize a reordered k‐space acquisition that applies intermittent fat saturation (FS) pulses to allow for a time‐efficient reduction of fat signal in breast MR images, and compare it with an elliptic‐centric biphasic FS method in terms of the degree of fat suppression and speed.Materials and MethodsThe behavior of the fat and water signals under the influence of the reordered sequence was characterized. This allowed us to optimize the flip angle and visualize the expected artifacts by deriving the point spread function (PSF) of the fat signal. We compared the two sequences by acquiring images with a varying number of FS pulses, with a corresponding difference in scan time. The quality of the images was assessed by comparison with images obtained with full fat suppression as measured by a root‐mean‐square (RMS) error metric.ResultsThe reordered sequence allowed for an approximately twofold reduction in error compared to the biphasic sequence for the same scan time. With the reordered sequence and optimized scan parameters, we were able to reduce the time spent on fat suppression by as much as 99% with no discernible reduction in image quality.ConclusionThis method will allow robust fat suppression with virtually no extension in imaging time for dynamic contrast‐enhanced (DCE)‐MRI. J. Magn. Reson. Imaging 2007;25:1293–1298. © 2007 Wiley‐Liss, Inc.
High temporal resolution breathheld 3D FIESTA CINE imaging: Validation of ventricular function in patients with chronic myocardial infarction
Authors: Rettmann Dan W. , Saranathan Manojkumar , Wu Katherine C. , Azevedo Clerio F. , Bluemke David A. , Foo Thomas K.F. 
Published: May 2007

AbstractPurposeTo develop a gated single‐breathhold, high temporal resolution three‐dimensional (3D) CINE imaging technique and to evaluate its accuracy in volumetric and functional quantification in patients with chronic myocardial infarction.Materials and MethodsA 3D CINE steady‐state free precession (SSFP) pulse sequence was developed incorporating variable temporal sampling of the low and high spatial frequency k‐space data to reduce breathhold time and parallel imaging to increase temporal resolution. Reconstruction with retrospective interpolation enabled complete R‐R interval coverage. Feasibility was assessed in eight patients with chronic myocardial infarction and ventricular functional values were compared to those of a 2D CINE acquisition.ResultsThere was no significant difference between the 3D CINE and 2D CINE for end‐diastolic volume (168 ± 73 vs. 177 ± 59 mL, respectively; P < 0.27), end‐systolic volume (81 ± 62 vs. 79 ± 53 mL; P < 0.81), and ejection fraction (EF) measurements (55 ± 14% vs. 58 ± 14%; P < 0.14). The mean difference in EF was less than 2.5%. A wall motion assessment indicated a good agreement, with a weighted kappa value of 0.62.ConclusionHigh temporal resolution 3D CINE SSFP imaging of the whole heart can be obtained in a single breathhold and yield ventricular function measurements similar to 2D CINE methods. J. Magn. Reson. Imaging 2007;25:1141–1146. © 2007 Wiley‐Liss, Inc.
Misregistration artifacts in image‐derived arterial input function in non‐echo‐planar imaging‐based dynamic contrast‐enhanced MRI
Authors: Kuribayashi Hideto , Worthington Philip L. , Bradley Daniel P. , Checkley David R. , Tessier Jean J. , Waterton John C. 
Published: May 2007

AbstractPurposeTo characterize misregistration artifact in arterial input function (AIF) pixels in dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) using a two‐dimensional non‐echo‐planar imaging (EPI)‐based gradient‐recalled echo (GRE) sequence.Materials and MethodsDynamic gadopentetate‐enhanced MRI was acquired in the rat using a semikeyhole acquisition scheme. The AIF was obtained from abdominal aorta pixels. Different sliding‐window reconstruction techniques were applied to determine which lines in a series of the semikeyhole acquisition were associated with the misregistration artifacts.ResultsThe misregistration along the phase‐encoding direction arose when k‐space lines were acquired during the rise‐time of the aortic gadolinium concentration. The maximum blood concentration of gadolinium estimated from the phase shift calculation agreed with that estimated from dosage.ConclusionAIF misregistration results from a phase shift due to increasing gadolinium concentration in the aorta, and may need to be considered in small animal DCE‐MRI studies with a high rate of rise in the AIF in high‐field MR applications. J. Magn. Reson. Imaging 2007;25:1248–1255. © 2007 Wiley‐Liss, Inc.
Correction of temporal misregistration artifacts in jet flow by conventional phase‐contrast MRI
Authors: Doyle Mark , Kortright Eduardo , Anayiotos Andreas S. , Rayarao Geetha , Rathi Vikas K. , Caruppannan Kethes , Li Longchuan , Biederman Robert W.W. 
Published: May 2007

AbstractPurposeTo show that accuracy of jet flow representation by magnetic resonance (MR) phase‐contrast (PC) velocity‐encoded (VE) cine imaging is dominated by error terms resulting from the temporal distribution of data, and to present a generally applicable data interpolation‐based approach to correct for this phenomenon.Materials and MethodsPhase‐contrast data were acquired in a stenotic orifice flow phantom using a physiologic pulsatile flow waveform. A temporally registered scan, acquired without data segmentation or interleaving was obtained (17 minutes) and taken as the reference (REF). Conventional PC data sets were acquired using segmentation and data interleaving. An enhanced temporal registration (ETR) algorithm was applied to the acquired data to temporally interpolate component sets and output data at matching time points, thereby reducing temporal dispersion.ResultsCompared to the REF data, conventionally processed PC data consistently overestimated peak velocities in laminar jet flow regions (127% ± 28%) and exhibited relatively weak correlations (r = 0.67 ± 0.23). The ETR‐processed data better represented peak velocities (101% ± 13%, P < 0.001) and correlated more closely with the REF data (r = 0.94 ± 0.05, P < 0.001).ConclusionThe temporal distribution of PC data impacts the accuracy of velocity representation in pulsatile jet flow. A temporal registration postprocessing algorithm can minimize loss of accuracy. J. Magn. Reson. Imaging 2007;25:1256–1262. © 2007 Wiley‐Liss, Inc.