Differential Imaging of Liver Tumors before and after Microwave Ablation with Electrode Displacement Elastography.

Liver cancer is a leading cause of cancer-related deaths; however, primary treatment options such as surgical resection and liver transplant may not be viable for many patients. Minimally invasive image-guided microwave ablation (MWA) provides a locally effective treatment option for these patients with an impact comparable to that of surgery for both cancer-specific and overall survival. MWA efficacy is correlated with accurate image guidance; however, conventional modalities such as B-mode ultrasound and computed tomography have limitations. Alternatively, ultrasound elastography has been used to demarcate post-ablation zones, yet has limitations for pre-ablation visualization because of variability in strain contrast between cancer types. This study attempted to characterize both pre-ablation tumors and post-ablation zones using electrode displacement elastography (EDE) for 13 patients with hepatocellular carcinoma or liver metastasis. Typically, MWA ablation margins of 0.5-1.0 cm are desired, which are strongly correlated with treatment efficacy. Our results revealed an average estimated ablation margin inner quartile range of 0.54-1.21 cm with a median value of 0.84 cm. These treatment margins lie within or above the targeted ablative margin, indicating the potential to use EDE for differentiating index tumors and ablated zones during clinical ablations. We also obtained a high correlation between corresponding segmented cross-sectional areas from contrast-enhanced computed tomography, the current clinical gold standard, when compared with EDE strain images, with r2 values of 0.97 and 0.98 for pre- and post-ablation regions.

Comparing Outcomes for Patients with Clinical T1b Renal Cell Carcinoma Treated With Either Percutaneous Microwave Ablation or Surgery.

OBJECTIVE: To compare perioperative and oncologic outcomes for patients with clinical T1b renal cell carcinoma following treatment with microwave ablation (MW), partial nephrectomy (PN), or radical nephrectomy (RN). METHODS: Comprehensive clinical and pathologic data were collected for nonmetastatic renal cell carcinoma patients with cT1b tumors following MW, PN, or RN from 2000 to 2018. Local recurrence-free, metastasis-free, cancer-specific and overall survival were estimated using Kaplan-Meier method. Prognostic factors for complications and survival were determined using logistic regression and Cox hazard models, respectively. RESULTS: A total of 325 patients (40 MW, 74 PN, and 211 RN) were identified. Patients treated with MW were older with higher Charlson comorbidity indices compared to surgical patients. Median length of hospitalization was shorter for MW compared to surgical patients (1 day vs 4 days, P <.0001). Post-treatment estimated glomerular filtration rate decreased by median 4.5% for MW compared to 3.2% for PN (P = .58) and 29% for RN (P <.001). Median follow-up was 34, 35, and 49 months following MW, PN, and RN, respectively. Estimated 5-year local recurrence-free survival was 94.5% for MW vs 97.9% for PN (P = .34) and 99.2% for RN (P = .02). Two patients recurred after MW and underwent repeat ablation without subsequent recurrence. No difference in 5-year metastasis-free survival or cancer-specific survival was found among MW, PN, or RN. Four (10%) MW patients had high-grade complication. Only prior abdominal surgery predicted high-grade complication (OR 6.29, P = .017). CONCLUSION: Microwave ablation is a feasible alternative to surgery in select comorbid patients with clinical T1b renal cell carcinoma.

Comparison of Displacement Tracking Algorithms for in Vivo Electrode Displacement Elastography.

Hepatocellular carcinoma and liver metastases are common hepatic malignancies presenting with high mortality rates. Minimally invasive microwave ablation (MWA) yields high success rates similar to surgical resection. However, MWA procedures require accurate image guidance during the procedure and for post-procedure assessments. Ultrasound electrode displacement elastography (EDE) has demonstrated utility for non-ionizing imaging of regions of thermal necrosis created with MWA in the ablation suite. Three strategies for displacement vector tracking and strain tensor estimation, namely coupled subsample displacement estimation (CSDE), a multilevel 2-D normalized cross-correlation method, and quality-guided displacement tracking (QGDT) have previously shown accurate estimations for EDE. This paper reports on a qualitative and quantitative comparison of these three algorithms over 79 patients after an MWA procedure. Qualitatively, CSDE presents sharply delineated, clean ablated regions with low noise except for the distal boundary of the ablated region. Multilevel and QGDT contain more visible noise artifacts, but delineation is seen over the entire ablated region. Quantitative comparison indicates CSDE with more consistent mean and standard deviations of region of interest within the mass of strain tensor magnitudes and higher contrast, while Multilevel and QGDT provide higher CNR. This fact along with highest success rates of 89% and 79% on axial and lateral strain tensor images for visualization of thermal necrosis using the Multilevel approach leads to it being the best choice in a clinical setting. All methods, however, provide consistent and reproducible delineation for EDE in the ablation suite.

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.

Delineation of Post-Procedure Ablation Regions with Electrode Displacement Elastography with a Comparison to Acoustic Radiation Force Impulse Imaging.

We compared a quasi-static ultrasound elastography technique, referred to as electrode displacement elastography (EDE), with acoustic radiation force impulse imaging (ARFI) for monitoring microwave ablation (MWA) procedures on patients diagnosed with liver neoplasms. Forty-nine patients recruited to this study underwent EDE and ARFI with a Siemens Acuson S2000 system after an MWA procedure. On the basis of visualization results from two observers, the ablated region in ARFI images was recognizable on 20 patients on average in conjunction with B-mode imaging, whereas delineable ablation boundaries could be generated on 4 patients on average. With EDE, the ablated region was delineable on 40 patients on average, with less imaging depth dependence. Study of tissue-mimicking phantoms revealed that the ablation region dimensions measured on EDE and ARFI images were within 8%, whereas the image contrast and contrast-to-noise ratio with EDE was two to three times higher than that obtained with ARFI. This study indicated that EDE provided improved monitoring results for minimally invasive MWA in clinical procedures for liver cancer and metastases.

Post-Procedure Evaluation of Microwave Ablations of Hepatocellular Carcinomas Using Electrode Displacement Elastography.

Microwave ablation has been used clinically as an alternative to surgical resection. However, lack of real-time imaging to assess treated regions may compromise treatment outcomes. We previously introduced electrode displacement elastography (EDE) for strain imaging and verified its feasibility in vivo on porcine animal models. In this study, we evaluated EDE on 44 patients diagnosed with hepatocellular carcinoma, treated using microwave ablation. The ablated region was identified on EDE images for 40 of the 44 patients. Ablation areas averaged 13.38 ± 4.99 cm2 on EDE, compared with 7.61 ± 3.21 cm2 on B-mode imaging. Contrast and contrast-to-noise ratios obtained with EDE were 232% and 98%, respectively, significantly higher than values measured on B-mode images (p < 0.001). This study indicates that EDE is feasible in patients and provides improved visualization of the ablation zone compared with B-mode ultrasound.

Introduction of a polar core into the de novo designed protein Top7.

Design of polar interactions is a current challenge for protein design. The de novo designed protein Top7, like almost all designed proteins, has an entirely nonpolar core. Here we describe the replacing of a sizable fraction (5 residues) of this core with a designed polar hydrogen bond network. The polar core design is expressed at high levels in E. coli, has a folding free energy of 10 kcal/mol, and retains the multiphasic folding kinetics of the original Top7. The NMR structure of the design shows that conformations of three of the five residues, and the designed hydrogen bonds between them, are very close to those in the design model. The remaining two residues, which are more solvent exposed, sample a wide range of conformations in the NMR ensemble. These results show that hydrogen bond networks can be designed in protein cores, but also highlight challenges that need to be overcome when there is competition with solvent.

Thrombocytosis is Predictive of Postoperative Pulmonary Embolism in Patients With Gynecologic Cancer.

OBJECTIVES: The prompt diagnosis of postoperative pulmonary embolism (PE) in gynecologic oncology patients is imperative, but the clinical presentation is nonspecific in this high-risk group. We sought to determine risk factors and clinical findings that may assist clinicians in diagnosing PE in the inpatient setting. METHODS: Radiology data were queried to identify patients with gynecologic cancer who had a postoperative PE evaluation with computed tomography pulmonary angiography (CT-PA). Patient clinical findings at the time of the PE evaluation were abstracted, and univariate and multivariate regression analyses were performed to identify predictors of PE. RESULTS: For 6 years, there were 2498 major gynecologic oncology surgical procedures performed at our institution. Within 14 days of surgery, 107 CT-PA studies were obtained with a positive study rate of 24.3%. In patients with and without PE, there was no significant difference noted for age, oxygen saturations, body mass index and heart rate. After controlling for stage, history of venous thromboembolism (VTE), heart rate, and oxygen saturation, platelet count (odds ratio, 1.26 per 50 counts increase; 95% confidence interval, 1.07-1.48; P = 0.006) and history of VTE (odds ratio, 17.1; 95% confidence interval, 1.77-Inf, P = 0.014) were identified as independent predictors of PE in the multivariate model. CONCLUSIONS: Although clinicians often use tachycardia and low oxygen saturation as triggers to order PE imaging studies, these signs have a very low specificity. Given the findings of our study, accounting for high platelet count and history of VTE increases the pretest probability of CT-PA study.

Benchmarking all-atom simulations using hydrogen exchange.

Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.

Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2.

The paralogous iron-responsive transcription factors Aft1 and Aft2 (activators of ferrous transport) regulate iron homeostasis in Saccharomyces cerevisiae by activating expression of iron-uptake and -transport genes when intracellular iron is low. We present the previously unidentified crystal structure of Aft2 bound to DNA that reveals the mechanism of DNA recognition via specific interactions of the iron-responsive element with a Zn(2+)-containing WRKY-GCM1 domain in Aft2. We also show that two Aft2 monomers bind a [2Fe-2S] cluster (or Fe(2+)) through a Cys-Asp-Cys motif, leading to dimerization of Aft2 and decreased DNA-binding affinity. Furthermore, we demonstrate that the [2Fe-2S]-bridged heterodimer formed between glutaredoxin-3 and the BolA-like protein Fe repressor of activation-2 transfers a [2Fe-2S] cluster to Aft2 that facilitates Aft2 dimerization. Previous in vivo findings strongly support the [2Fe-2S] cluster-induced dimerization model; however, given the available evidence, Fe(2+)-induced Aft2 dimerization cannot be completely ruled out as an alternative Aft2 inhibition mechanism. Taken together, these data provide insight into the molecular mechanism for iron-dependent transcriptional regulation of Aft2 and highlight the key role of Fe-S clusters as cellular iron signals.

Folding of a large protein at high structural resolution.

Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (~100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways.

A new diagnostic test for endometrial cancer?: Cytology analysis of sonohysterography distention media.

OBJECTIVE: During saline-infused sonohysterography (SIS), the distension fluid is typically discarded. If cytology analysis could identify those patients with endometrial cancer, many women would be spared from further procedures. METHODS: Thirty consecutive patients with clinical stage I or II endometrial adenocarcinoma were prospectively recruited preoperatively. Saline-infused sonohysterography was performed by instilling 5 mL of saline, withdrawing and sending for analysis. Saline was reinfused until complete SIS images were obtained and sent separately for cytology. RESULTS: Of the 30 women enrolled, SIS was technically successful in 29. Demographics included mean age (60.5 ± 6.99 years), body mass index (35.55 ± 8.18 kg/m), endometrioid histology (76%), and grade (grade 1, 67%). Prestudy diagnostic method included biopsy (70%), dilatation and curettage (17%), and hysteroscopy (10%). Adequate cytology specimens were obtained in 66% of the 5 mL flushes and 72% of the complete SIS collections. Of adequate specimens, the sensitivities to detect endometrial cancer for the 5-mL, complete, and combined fluid samples were 26% (95% confidence interval, 9%-51%), 36% (17%-59%), and 42% (22%-63%). Sensitivity based on the whole study sample (N = 30) was 33% (17%-53%). Statistical significance was not found in the association between a positive test and age, body mass index, grade, diagnostic method, or volume instilled or aspirated. CONCLUSIONS: Most patients with early endometrial cancer can undergo SIS procedures with adequate cytology specimens obtained from distention media. However, the sensitivity is low, and refinements are necessary before utilizing as a diagnostic test. In cases with positive results, the patient may be able to avoid other costly and painful procedures.

Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state.

The results of more than a dozen single-molecule Förster resonance energy transfer (smFRET) experiments suggest that chemically unfolded polypeptides invariably collapse from an expanded random coil to more compact dimensions as the denaturant concentration is reduced. In sharp contrast, small-angle X-ray scattering (SAXS) studies suggest that, at least for single-domain proteins at non-zero denaturant concentrations, such compaction may be rare. Here, we explore this discrepancy by studying protein L, a protein previously studied by SAXS (at 5 °C), which suggested fixed unfolded-state dimensions from 1.4 to 5 M guanidine hydrochloride (GuHCl), and by smFRET (at 25 °C), which suggested that, in contrast, the chain contracts by 15-30% over this same denaturant range. Repeating the earlier SAXS study under the same conditions employed in the smFRET studies, we observe little, if any, evidence that the unfolded state of protein L contracts as the concentration of GuHCl is reduced. For example, scattering profiles (and thus the shape and dimensions) collected within ∼4 ms after dilution to as low as 0.67 M GuHCl are effectively indistinguishable from those observed at equilibrium at higher denaturant. Our results thus argue that the disagreement between SAXS and smFRET is statistically significant and that the experimental evidence in favor of obligate polypeptide collapse at low denaturant cannot be considered conclusive yet.

Automated real-space refinement of protein structures using a realistic backbone move set.

Crystals of many important biological macromolecules diffract to limited resolution, rendering accurate model building and refinement difficult and time-consuming. We present a torsional optimization protocol that is applicable to many such situations and combines Protein Data Bank-based torsional optimization with real-space refinement against the electron density derived from crystallography or cryo-electron microscopy. Our method converts moderate- to low-resolution structures at initial (e.g., backbone trace only) or late stages of refinement to structures with increased numbers of hydrogen bonds, improved crystallographic R-factors, and superior backbone geometry. This automated method is applicable to DNA-binding and membrane proteins of any size and will aid studies of structural biology by improving model quality and saving considerable effort. The method can be extended to improve NMR and other structures. Our backbone score and its sequence profile provide an additional standard tool for evaluating structural quality.

Diagnostic radiology resident compliance with recommended health guidelines: effect of resident work environment.

RATIONALE AND OBJECTIVES: To determine diagnostic radiology resident compliance with recommended health guidelines for physical activity, body weight, diet, related health indicators, and the effects of the resident work environment on compliance. MATERIALS AND METHODS: A request was electronically mailed to members of the Association of Program Directors in Radiology and the Association of Program Coordinators in Radiology in May 2007 and again in June 2007, asking members to forward to their radiology residents an invitation to complete an online health survey. Frequency counts and Fisher's exact test, respectively, were used to summarize results and to determine statistically significant relationships between survey variables. RESULTS: A total of 811 radiology residents completed the survey, representing 18% of 4,412 diagnostic radiology residents. Five hundred forty-five (67.2%) of 811 were male and 264 (32.6%) female. Two hundred ten (25.9%) were first-year, 239 (29.5%) second-year, 201 (24.8%) third-year, and 161 (19.9%) fourth-year residents. Three hundred two (37.2%) engaged in recommended guidelines for physical activity and < or =465 (57.3%) complied with each of multiple federal dietary guidelines (excluding alcohol intake). Up to 329 (40.6%) residents did not know whether they were in compliance with various dietary guidelines. A total of 426 (52.5%) residents reported working > or =60 hours/week, which significantly correlated with less physical activity (P = .013). CONCLUSION: A substantial number of residents are out of compliance with federal guidelines for physical activity and diet and are not knowledgeable about their personal dietary intake. Long work hours are related to a lack of physical activity. Radiology programs may be able to influence resident health practices by modifying work hours and the working environment, encouraging healthy dietary intake and physical activity, and instituting campaigns to inform residents and faculty about health guidelines and available wellness programs.