pinecone/core-2020-05-10-deduplication huggingface dataset:
A survey of the year 2007 literature on applications of isothermal titration calorimetry

Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method
Library screening by fragment-based docking

We review our computational tools for high-throughput screening by fragment-based docking of large collections of small molecules. Applications to six different enzymes, four proteases, and two protein kinases, are presented. Remarkably, several low-micromolar inhibitors were discovered in each of the high-throughput docking campaigns. Probable reasons for the lack of submicromolar inhibitors are the tiny fraction of chemical space covered by the libraries of available compounds, as well as the approximations in the methods employed for scoring, and the use of a rigid conformation of the target protein
Evaluation of a dedicated dual phased-array surface coil using a black-blood FSE sequence for high resolution MRI of the carotid vessel wall

Purpose: To investigate the ability of magnetic resonance imaging (MRI) to visualize the carotid vessel wall using a phased-array coil and a black-blood (BB) fast spin-echo (FSE) sequence. Materials and Methods: The phased-array coil was compared with a three-inch coil. Images from volunteers were evaluated for artifacts, wall layers, and wall signal intensity. Signal intensity and homogeneity of atherosclerosis were assessed. Lumen diameter and vessel area were measured. Results: Comparison between the phased-array coil and the three-inch coil showed a 100% increase in signal-to-noise ratio. BB-FSE imaging resulted in good delineation between blood and vessel wall. Most volunteers had a two-layered vessel wall with a hyperintense inner layer. MRI showed both homogeneous hyperintense and heterogeneous plaques, which consisted of a main hyperintense part with hypointense spots and/or intermediate regions. MRI lumen and area measurements were performed easily. Conclusion: High resolution MRI of carotid atherosclerosis is feasible with a phased-array coil and a BB-FSE sequence
Improvement in the Quantification of Myocardial Perfusion Using an Automatic Spline-Based Registration Algorithm

Purpose: To improve the quantification of myocardial perfusion by registering the time series of magnetic resonance (MR) images with injection of gadolinium. Materials and Methods: Eight patients underwent MR scans to perform myocardial perfusion exam. Two short axis views of the left ventricle (LV) were acquired in free breathing. Two masks for performing the spatial registration of the images were evaluated. The registration was based on pixel intensity in a multi-resolution scheme. The efficiency of this correction was evaluated by calculating geometric residual displacement of the LV and by fitting the data to a compartment model fit with two parameters: K1, the blood-to-myocardium transfer coefficient, and Vd, the distribution volume of the contrast media.   Results: The registration stage allowed a decrease in the observed motion of the LV from more than 1.98 ± 0.68 mm to less than 0.56 ± 0.18 mm (mean ± SD). Variability obtained in the perfusion analysis decreased from 46 ± 103% to 5 ± 4% for K1 parameter and from 18 ± 21% to 5 ± 5% for Vd parameter. Conclusion: As with manual correction, this automatic motion correction leads to accurate perfusion parameters in dynamic cardiac MR imaging after contrast agent injection. This automatic stage requires placing only one mask over one frame of the perfusion study instead of manually shifting each image to fit a reference image of the perfusion study
Vinflunine - an active chemotherapy for treatment of advanced non-small-cell lung cancer previously treated with a platinum-based regimen: results of a phase II study

A multicentre, single-arm, phase II trial designed to determine the efficacy of single-agent vinflunine in patients with advanced non-small-cell lung cancer (NSCLC) previously treated with a platinum-based regimen. The objectives were to assess efficacy in terms of tumour response rate (primary end point), duration of response, progression-free survival (PFS) and overall survival (OS), and to evaluate the toxicity associated with this treatment. Patients with advanced NSCLC with progressive disease having failed prior platinum-based first-line treatment for advanced disease. Five responses out of the 63 treated patients were documented by WHO criteria and validated by an independent panel review (IRP), yielding a response rate of 7.9% (95% CI: 2.6-17.6) in the intent-to-treat analysis and 8.3% (95% CI: 2.8-18.4) in the evaluable population. Disease control was achieved in 35 out of 60 evaluable patients (58.3%). The median duration of response (complete response+partial response), according to modified WHO criteria was 7.8 months (95% CI: 4.6-NR). Median PFS was 2.6 months (95% CI: 1.4-3.8), and the median survival was 7.0 months (95% CI: 5.8-9.2). Grades 3-4 neutropenia was reported in 50% of patients; febrile neutropenia was observed in two patients (3.2%); grades 3-4 myalgia and grade 3 constipation were experienced by 10 (15.9%) and six (9.5%) of patients, respectively. Constipation was manageable, non-cumulative and could be prevented with laxative prophylaxis. The encouraging results from this phase II study with vinflunine warrant further investigations in phase III trials as second- or first-line treatment of advanced non-small-cell lung carcinoma, as a single agent or in combination with other active drugs
MR study of postnatal development of myocardial structure and left ventricular function

Purpose: To investigate postnatal development of left ventricular (LV) cardiac function and myocardium structure. Materials and Methods: In vivo cardiac MR and ex vivo diffusion tensor imaging (DTI) were performed in normal Sprague-Dawley rats at postnatal day 2, 4, 7, 14, 21, 28, and 56 (N = 6 per group). Results: Morphologically, LV size increased with age. Functionally, stroke volume and cardiac output increased. Heart rate increased gradually and became stable after day 14. On average, ejection fraction increased within the first 4 days, decreased at day 7, gradually increased until day 21, and became stable afterward. Structurally, double-helical myocardial structure was found as early as day 2. Myocardial fiber parameters, described by fractional anisotropy, mean apparent diffusion coefficient, and axial diffusivity, increased within the first 4 days. Then radial diffusivity increased until day 7 while other parameters decreased up to day 56. Conclusion: Postnatal heart development was documented by MRI. DTI findings are in agreement with the two known stages of early postnatal growth: hyperplasia and hypertrophy. These results can serve as the baselines for study of postnatal heart developmental abnormalities. They also demonstrate the ability of DTI to reveal microstructural alterations in myocardium. © 2009 Wiley-Liss, Inc.link_to_subscribed_fulltex
Right coronary artery flow velocity and volume assessment with spiral K-space sampled breathhold velocity-encoded MRI at 3 tesla: accuracy and reproducibility.

PURPOSE: To evaluate accuracy and reproducibility of flow velocity and volume measurements in a phantom and in human coronary arteries using breathhold velocity-encoded (VE) MRI with spiral k-space sampling at 3 Tesla. MATERIALS AND METHODS: Flow velocity assessment was performed using VE MRI with spiral k-space sampling. Accuracy of VE MRI was tested in vitro at five constant flow rates. Reproducibility was investigated in 19 healthy subjects (mean age 25.4 +/- 1.2 years, 11 men) by repeated acquisition in the right coronary artery (RCA). RESULTS: MRI-measured flow rates correlated strongly with volumetric collection (Pearson correlation r = 0.99; P &lt; 0.01). Due to limited sample resolution, VE MRI overestimated the flow rate by 47% on average when nonconstricted region-of-interest segmentation was used. Using constricted region-of-interest segmentation with lumen size equal to ground-truth luminal size, less than 13% error in flow rate was found. In vivo RCA flow velocity assessment was successful in 82% of the applied studies. High interscan, intra- and inter-observer agreement was found for almost all indices describing coronary flow velocity. Reproducibility for repeated acquisitions varied by less than 16% for peak velocity values and by less than 24% for flow volumes. CONCLUSION: 3T breathhold VE MRI with spiral k-space sampling enables accurate and reproducible assessment of RCA flow velocity
Magnetic resonance histologic correlation in rotator cuff tendons

Purpose:\ud
To relate histologic changes in rotator cuff tendons to the appearance on T1-weighted as well as fat-suppressed T2-weighted and proton density-weighted magnetic resonance imaging (MRI) sequences.\ud
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Materials and Methods:\ud
T1-weighted, fat-suppressed T2-weighted and fat-suppressed proton density-weighted sequences of 18 cadaveric shoulders were acquired. The supraspinatus, infraspinatus, and subscapularis tendons were evaluated histologically. Twenty-six abnormalities were found in 23 of 37 tendons. In addition, histologically normal tendon parts (n = 32), including three segments with normal histology but abnormal MR signal, considered to represent magic angle effects, were defined. All regions of interest (ROIs) were evaluated by two musculoskeletal radiologists independently and blinded to histology.\ud
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Results:\ud
In the 26 areas with anatomically intact tendons but abnormal histological findings mucoid degeneration (n = 13), chondroid metaplasia (n = 11), fatty infiltration (n = 1), and foreign-body granuloma (n = 1) after tendon suture were found. Compared to normal tendon, mucoid degeneration was hyperintense on T2-weighted fat-suppressed (P = 0.007) and on proton density-weighted fat-suppressed images (P = 0.006). Chondroid metaplasia was hyperintense compared to normal tendon in all sequences (P < 0.05). Mucoid degeneration was hypointense compared to chondroid metaplasia on T2-weighted fat-suppressed images (P = 0.038) and hypointense compared to magic angle artifacts on T1-weighted images (P = 0.046).\ud
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Conclusion:\ud
Chondroid metaplasia of rotator cuff tendons appears to be more common than expected. Both mucoid degeneration and chondroid metaplasia may explain increased tendon signal on MR images of the rotator cuff
Practical signal-to-noise ratio quantification for sensitivity encoding: Application to coronary MR angiography.

Purpose: To develop and evaluate a practical method for the quantification of signal-to-noise ratio (SNR) on coronary MR angiograms (MRA) acquired with parallel imaging.Materials and Methods: To quantify the spatially varying noise due to parallel imaging reconstruction, a new method has been implemented incorporating image data acquisition followed by a fast noise scan during which radio-frequency pulses, cardiac triggering and navigator gating are disabled. The performance of this method was evaluated in a phantom study where SNR measurements were compared with those of a reference standard (multiple repetitions). Subsequently, SNR of myocardium and posterior skeletal muscle was determined on in vivo human coronary MRA.Results: In a phantom, the SNR measured using the proposed method deviated less than 10.1% from the reference method for small geometry factors (&lt;= 2). In vivo, the noise scan for a 10 min coronary MRA acquisition was acquired in 30 s. Higher signal and lower SNR, due to spatially varying noise, were found in myocardium compared with posterior skeletal muscle.Conclusion: SNR quantification based on a fast noise scan is a validated and easy-to-use method when applied to three-dimensional coronary MRA obtained with parallel imaging as long as the geometry factor remains low
Performance of a fully automatic lesion detection system for breast DCE-MRI

PURPOSE: To describe and test a new fully automatic lesion detection system for breast DCE-MRI. MATERIALS AND METHODS: Studies were collected from two institutions adopting different DCE-MRI sequences, one with and the other one without fat-saturation. The detection pipeline consists of (i) breast segmentation, to identify breast size and location; (ii) registration, to correct for patient movements; (iii) lesion detection, to extract contrast-enhanced regions using a new normalization technique based on the contrast-uptake of mammary vessels; (iv) false positive (FP) reduction, to exclude contrast-enhanced regions other than lesions. Detection rate (number of system-detected malignant and benign lesions over the total number of lesions) and sensitivity (system-detected malignant lesions over the total number of malignant lesions) were assessed. The number of FPs was also assessed. RESULTS: Forty-eight studies with 12 benign and 53 malignant lesions were evaluated. Median lesion diameter was 6 mm (range, 5-15 mm) for benign and 26 mm (range, 5-75 mm) for malignant lesions. Detection rate was 58/65 (89%; 95% confidence interval [CI] 79%-95%) and sensitivity was 52/53 (98%; 95% CI 90%-99%). Mammary median FPs per breast was 4 (1st-3rd quartiles 3-7.25). CONCLUSION: The system showed promising results on MR datasets obtained from different scanners producing fat-sat or non-fat-sat images with variable temporal and spatial resolution and could potentially be used for early diagnosis and staging of breast cancer to reduce reading time and to improve lesion detection. Further evaluation is needed before it may be used in clinical practice
Effects of MRI scan acceleration on brain volume measurement consistency.

PURPOSE: To evaluate the effects of recent advances in magnetic resonance imaging (MRI) radiofrequency (RF) coil and parallel imaging technology on brain volume measurement consistency.
MATERIALS AND METHODS: In all, 103 whole-brain MRI volumes were acquired at a clinical 3T MRI, equipped with a 12- and 32-channel head coil, using the T1-weighted protocol as employed in the Alzheimer's Disease Neuroimaging Initiative study with parallel imaging accelerations ranging from 1 to 5. An experienced reader performed qualitative ratings of the images. For quantitative analysis, differences in composite width (CW, a measure of image similarity) and boundary shift integral (BSI, a measure of whole-brain atrophy) were calculated.
RESULTS: Intra- and intersession comparisons of CW and BSI measures from scans with equal acceleration demonstrated excellent scan-rescan accuracy, even at the highest acceleration applied. Pairs-of-scans acquired with different accelerations exhibited poor scan-rescan consistency only when differences in the acceleration factor were maximized. A change in the coil hardware between compared scans was found to bias the BSI measure.
CONCLUSION: The most important findings are that the accelerated acquisitions appear to be compatible with the assessment of high-quality quantitative information and that for highest scan-rescan accuracy in serial scans the acquisition protocol should be kept as consistent as possible over time. J. Magn. Reson. Imaging 2012;36:1234-1240. ©2012 Wiley Periodicals, Inc
Multi‐system repeatability and reproducibility of apparent diffusion coefficient measurement using an ice‐water phantom

Purpose:  To determine quantitative quality control procedures to evaluate technical variability in multi‐center measurements of the diffusion coefficient of water as a prerequisite to use of the biomarker apparent diffusion coefficient (ADC) in multi‐center clinical trials.    Materials and Methods:  A uniform data acquisition protocol was developed and shared with 18 participating test sites along with a temperature‐controlled diffusion phantom delivered to each site. Usable diffusion weighted imaging data of ice water at five b‐values were collected on 35 clinical MRI systems from three vendors at two field strengths (1.5 and 3 Tesla [T]) and analyzed at a central processing site.    Results:  Standard deviation of bore‐center ADCs measured across 35 scanners was <2%; error range: −2% to +5% from literature value. Day‐to‐day repeatability of the measurements was within 4.5%. Intra‐exam repeatability at the phantom center was within 1%. Excluding one outlier, inter‐site reproducibility of ADC at magnet isocenter was within 3%, although variability increased for off‐center measurements. Significant (>10%) vendor‐specific and system‐specific spatial nonuniformity ADC bias was detected for the off‐center measurement that was consistent with gradient nonlinearity.    Conclusion:  Standardization of DWI protocol has improved reproducibility of ADC measurements and allowed identifying spatial ADC nonuniformity as a source of error in multi‐site clinical studies. J. Magn. Reson. Imaging 2013;37:1238–1246. © 2012 Wiley Periodicals, Inc
Direct in vitro comparison of six three-dimensional positive contrast methods for susceptibility marker imaging.

PURPOSE: To compare different techniques for positive contrast imaging of susceptibility markers with MRI for three-dimensional visualization. As several different techniques have been reported, the choice of the suitable method depends on its properties with regard to the amount of positive contrast and the desired background suppression, as well as other imaging constraints needed for a specific application.
MATERIALS AND METHODS: Six different positive contrast techniques are investigated for their ability to image at 3 Tesla a single susceptibility marker in vitro. The white marker method (WM), susceptibility gradient mapping (SGM), inversion recovery with on-resonant water suppression (IRON), frequency selective excitation (FSX), fast low flip-angle positive contrast SSFP (FLAPS), and iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) were implemented and investigated.
RESULTS: The different methods were compared with respect to the volume of positive contrast, the product of volume and signal intensity, imaging time, and the level of background suppression. Quantitative results are provided, and strengths and weaknesses of the different approaches are discussed.
CONCLUSION: The appropriate choice of positive contrast imaging technique depends on the desired level of background suppression, acquisition speed, and robustness against artifacts, for which in vitro comparative data are now available
Steady-state equilibrium phase inversion recovery ON-resonant water suppression (IRON) MR angiography in conjunction with superparamagnetic nanoparticles. A robust technique for imaging within a wide range of contrast agent dosages.

PURPOSE: To investigate the ability of inversion recovery ON-resonant water suppression (IRON) in conjunction with P904 (superparamagnetic nanoparticles which consisting of a maghemite core coated with a low-molecular-weight amino-alcohol derivative of glucose) to perform steady-state equilibrium phase MR angiography (MRA) over a wide dose range.
MATERIALS AND METHODS: Experiments were approved by the institutional animal care committee. Rabbits (n = 12) were imaged at baseline and serially after the administration of 10 incremental dosages of 0.57-5.7 mgFe/Kg P904. Conventional T1-weighted and IRON MRA were obtained on a clinical 1.5 Tesla (T) scanner to image the thoracic and abdominal aorta, and peripheral vessels. Contrast-to-noise ratios (CNR) and vessel sharpness were quantified.
RESULTS: Using IRON MRA, CNR and vessel sharpness progressively increased with incremental dosages of the contrast agent P904, exhibiting constantly higher contrast values than T1 -weighted MRA over a very wide range of contrast agent doses (CNR of 18.8 ± 5.6 for IRON versus 11.1 ± 2.8 for T1 -weighted MRA at 1.71 mgFe/kg, P = 0.02 and 19.8 ± 5.9 for IRON versus -0.8 ± 1.4 for T1-weighted MRA at 3.99 mgFe/kg, P = 0.0002). Similar results were obtained for vessel sharpness in peripheral vessels, (Vessel sharpness of 46.76 ± 6.48% for IRON versus 33.20 ± 3.53% for T1-weighted MRA at 1.71 mgFe/Kg, P = 0.002, and of 48.66 ± 5.50% for IRON versus 19.00 ± 7.41% for T1-weighted MRA at 3.99 mgFe/Kg, P = 0.003).
CONCLUSION: Our study suggests that quantitative CNR and vessel sharpness after the injection of P904 are consistently higher for IRON MRA when compared with conventional T1-weighted MRA. These findings apply for a wide range of contrast agent dosages
T1 mapping in the rat myocardium at 7 Tesla using a modified CINE inversion recovery sequence

Purpose To evaluate the reproducibility and sensitivity of the modified CINE inversion recovery (mCINE-IR) acquisition on rats for measuring the myocardial T1 at 7 Tesla. Materials and Methods The recently published mCINE-IR acquisition on humans was applied on rats for the first time, enabling the possibility of translational studies with an identical sequence. Simulations were used to study signal evolution and heart rate dependency. Gadolinium phantoms, a heart specimen and a healthy rat were used to study reproducibility. Two cryo-infarcted rats were scanned to measure late gadolinium enhancement (LGE). Results In the phantom reproducibility studies the T1 measurements had a maximum coefficient of variation (COV) of 1.3%. For the in vivo reproducibility the COV was below 5% in the anterior cardiac segments. In simulations with phantoms and specimens, a heart rate dependency of approximately 0.5 ms/bpm was present. The T1 maps of the cryo-infarcted rats showed a clear lowering of T1 in de LGE region. Conclusion The results show that mCINE-IR is highly reproducible and that the sensitivity allows detecting T1 changes in the rat myocardium