BOLD signal compartmentalization based on the apparent diffusion coefficient.

Functional MRI (fMRI) can detect blood oxygenation level dependent (BOLD) hemodynamic responses secondary to neuronal activity. The most commonly used method for detecting fMRI signals is the gradient-echo echo-planar imaging (EPI) technique because of its sensitivity and speed. However, it is generally believed that a significant portion of these signals arises from large veins, with additional contribution from the capillaries and parenchyma. Early experiments using diffusion-weighted gradient-echo EPI have suggested that intra-voxel incoherent motion (IVIM) weighting inherent in the sequence can selectively attenuate contributions from different vessels based on the differences in the mobility of the blood within them. In the present study, we used similar approach to characterize the apparent diffusion coefficient (ADC) distribution within the activated areas of BOLD contrast. It is shown that the voxel values of the ADCs obtained from this technique can infer various vascular contributions to the BOLD signal.

Radiotherapy Assessment Using Diffusion Weighted MRI

Purpose: There are two goals of this study. The first goal of this study is to investigate the feasibility of using classic textural feature extraction in radiotherapy response assessment among a unique cohort of early stage breast cancer patients who received the single-dose preoperative radiotherapy. The second goal of this study is to investigate the clinical feasibility of using classic texture features as potential biomarkers which are supplementary to regional apparent diffusion coefficient in gynecological cancer radiotherapy response assessment.

Methods and Materials: For the breast cancer study, 15 patients with early stage breast cancer were enrolled in this retrospective study. Each patient received a single-fraction radiation treatment, and DWI and DCE-MRI scans were conducted before and after the radiotherapy. DWI scans were acquired using a spin-echo EPI sequence with diffusion weighting factors of b = 0 and b = 500 mm2/s, and the apparent diffusion coefficient (ADC) maps were calculated. DCE-MRI scans were acquired using a T1-weighted 3D SPGR sequence with a temporal resolution of about 1 minute. The contrast agent (CA) was intravenously injected with a 0.1 mmol/kg bodyweight dose at 2 ml/s. Two parameters, volume transfer constant (Ktrans) and kep were analyzed using the two-compartment Tofts pharmacokinetic model. For pharmacokinetic parametric maps and ADC maps, 33 textural features were generated from the clinical target volume (CTV) in a 3D fashion using the classic gray level co-occurrence matrix (GLCOM) and gray level run length matrix (GLRLM). Wilcoxon signed-rank test was used to determine the significance of each texture feature’s change after the radiotherapy. The significance was set to 0.05 with Bonferroni correction.

For the gynecological cancer study, 12 female patients with gynecologic cancer treated with fractionated external beam radiotherapy (EBRT) combined with high dose rate (HDR) intracavitary brachytherapy were studied. Each patient first received EBRT treatment followed by five fractions of HDR treatment. Before EBRT and before each fraction of brachytherapy, Diffusion Weighted MRI (DWI-MRI) and CT scans were acquired. DWI scans were acquired in sagittal plane utilizing a spin-echo echo-planar imaging sequence with weighting factors of b = 500 s/mm2 and b = 1000 s/mm2, one set of images of b = 0 s/mm2 were also acquired. ADC maps were calculated using linear least-square fitting method. Distributed diffusion coefficient (DDC) maps and stretching parameter α were calculated. For ADC and DDC maps, 33 classic texture features were generated utilizing the classic gray level run length matrix (GLRLM) and gray level co-occurrence matrix (GLCOM) from high-risk clinical target volume (HR-CTV). Wilcoxon signed-rank statistics test was applied to determine the significance of each feature’s numerical value change after radiotherapy. Significance level was set to 0.05 with multi-comparison correction if applicable.

Results: For the breast cancer study, regarding ADC maps calculated from DWI-MRI, 24 out of 33 CTV features changed significantly after the radiotherapy. For DCE-MRI pharmacokinetic parameters, all 33 CTV features of Ktrans and 33 features of kep changed significantly.

For the gynecological cancer study, regarding ADC maps, 28 out of 33 HR-CTV texture features showed significant changes after the EBRT treatment. 28 out of 33 HR-CTV texture features indicated significant changes after HDR treatments. The texture features that indicated significant changes after HDR treatments are the same as those after EBRT treatment. 28 out of 33 HR-CTV texture features showed significant changes after whole radiotherapy treatment process. The texture features that indicated significant changes for the whole treatment process are the same as those after HDR treatments.

Conclusion: Initial results indicate that certain classic texture features are sensitive to radiation-induced changes. Classic texture features with significant numerical changes can be used in monitoring radiotherapy effect. This might suggest that certain texture features might be used as biomarkers which are supplementary to ADC and DDC for assessment of radiotherapy response in breast cancer and gynecological cancer.

Intake, digestibility, and passage of a commercially designed diet by two Propithecus species.

The digestibility and passage of an experimental diet was used to compare the digestive physiology of two Propithecus species: P. verreauxi and P. tattersalli. Though both animals have a similar feeding ecology, the captive status of P. verreauxi is considered more stable than that of P. tattersalli. The test diet included a local tree species, Rhus copallina, at 15% of dry matter intake (DMI) and Mazuri Leafeater Primate Diet at 85% of DMI. The chemical composition of the diet (dry matter basis) was 25% crude protein, 34% neutral detergent fiber (NDF), and 22% acid detergent fiber (ADF) with a gross energy of 4.52 kcal/g. After a 6 week acclimation to the experimental diet, animals were placed in research caging. After a 7 day adjustment period, animals were dosed with chromium mordant and Co-EDTA as markers for digesta passage and all feed refusals and feces were collected at timed intervals for 7 days. Digestibility values, similar for both species, were approximately 65% for dry matter, crude protein, and energy, and 40% and 35% respectively, for NDF and ADF. Transit times (17-18.5 hr) and mean retention times (31-34 hr) were not significantly different between species, and there was no difference between the chromium mordant and Co-EDTA. Serum values for glucose, urea, and non-esterified fatty acids (NEFA) were obtained during four different time periods to monitor nutritional status. While there was no change in serum glucose, serum urea increased over time. The NEFAs increased across all four time periods for P. verreauxi and increased for the first three periods then decreased in the last period for P. tattersalli. Results obtained indicate no difference in digestibility nor digesta passage between species, and that both Propithecus species were similar to other post-gastric folivores.

Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements.

The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded (U), intermediate (I), and sulfate-bound folded (F) states of RNase P protein, using an efficient and accurate nuclear magnetic resonance-monitored titration approach that utilizes internal reference compounds and a parametric fitting method. The three histidines in the sulfate-bound folded protein have pKa values depressed by 0.21 ± 0.01, 0.49 ± 0.01, and 1.00 ± 0.01 units, respectively, relative to that of the model compound N-acetyl-l-histidine methylamide. In the unliganded and unfolded protein, the pKa values are depressed relative to that of the model compound by 0.73 ± 0.02, 0.45 ± 0.02, and 0.68 ± 0.02 units, respectively. Above pH 5.5, H22 displays a separate resonance, which we have assigned to I, whose apparent pKa value is depressed by 1.03 ± 0.25 units, which is ∼0.5 units more than in either U or F. The depressed pKa values we observe are consistent with repulsive interactions between protonated histidine side chains and the net positive charge of the protein. However, the pKa differences between F and U are small for all three histidines, and they have little ionic strength dependence in F. Taken together, these observations suggest that unfavorable electrostatics alone do not account for the fact that RNase P protein is intrinsically unfolded in the absence of ligand. Multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.

Based on Pulay's direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan-Hall (ARH) energy function, proposed recently by Høst and co-workers [J. Chem. Phys. 129, 124106 (2008)], is used as the object of minimization for obtaining the linear coefficients of Fock matrices within DIIS. This differs from the traditional DIIS of Pulay, which uses an object function derived from the commutator of the density and Fock matrices. Our results show that the present algorithm, abbreviated ADIIS, is more robust and efficient than the energy-DIIS (EDIIS) approach. In particular, several examples demonstrate that the combination of ADIIS and DIIS ("ADIIS+DIIS") is highly reliable and efficient in accelerating SCF convergence.

Quality control autophagy: a joint effort of ubiquitin, protein deacetylase and actin cytoskeleton.

Autophagy has been predominantly studied as a nonselective self-digestion process that recycles macromolecules and produces energy in response to starvation. However, autophagy independent of nutrient status has long been known to exist. Recent evidence suggests that this form of autophagy enforces intracellular quality control by selectively disposing of aberrant protein aggregates and damaged organelles--common denominators in various forms of neurodegenerative diseases. By definition, this form of autophagy, termed quality-control (QC) autophagy, must be different from nutrient-regulated autophagy in substrate selectivity, regulation and function. We have recently identified the ubiquitin-binding deacetylase, HDAC6, as a key component that establishes QC. HDAC6 is not required for autophagy activation per se; rather, it is recruited to ubiquitinated autophagic substrates where it stimulates autophagosome-lysosome fusion by promoting F-actin remodeling in a cortactin-dependent manner. Remarkably, HDAC6 and cortactin are dispensable for starvation-induced autophagy. These findings reveal that autophagosomes associated with QC are molecularly and biochemically distinct from those associated with starvation autophagy, thereby providing a new molecular framework to understand the emerging complexity of autophagy and therapeutic potential of this unique machinery.