Plasma EBV DNA in Nasopharyngeal Cancer (NPC) Treated with Definitive Radiotherapy (RT)

PURPOSE/OBJECTIVE(S)

EBV DNA has well-studied roles in NPC including early detection and surveillance. There are limited North American data on EBV DNA testing. Our center has used EBV DNA testing since 2010. We hypothesized: (1) higher first post-RT EBV DNA level is associated with worse prognosis, and (2) surveillance EBV DNA is specific for recurrence at a low detection threshold.

MATERIALS/METHODS

We retrospectively reviewed all patients with non-metastatic (TNM-7 stage I-IVB) NPC treated with definitive RT/chemoRT (CRT) ± adjuvant chemotherapy (AC) between 2010-2017. EBV DNA was assayed by quantitative PCR in a CAP/CLIA-certified laboratory and reported in copies/mL of plasma. Pre-RT is defined as 0-90 days before the first RT fraction and post-RT within one year after RT. We report log odds ratios (LOR) from a linear model of T- and N-category with log-adjusted EBV DNA as the response variable. Survival outcomes were analyzed with log-rank tests and Cox multivariate analyses (MVA) adjusted for age, stage, and treatment, reporting hazard ratios (HR). A total of 95% confidence intervals of LOR and HR are reported. The detection threshold that maximized the F1 accuracy score was considered optimal.

RESULTS

Of 271 patients in the study window, 179 had pre-RT +/- post-RT EBV DNA testing. Six received RT, 43 CRT, and 130 CRT+AC. With 7-yr median follow-up, 37 recurred and 37 died. Detectable pre-RT EBV DNA was found in 154 (86%) with a median of 928 copies/mL (range: 1-239214). EBV DNA level correlated with higher N category (LOR: 0.28, 0.15-0.42, p<0.001), but not T category (0.04, -0.06-0.13, p = 0.5). Above-median pre-RT EBV DNA was associated with worse recurrence-free survival (RFS) by log-rank test (p = 0.016) and Cox MVA (HR: 2.2, 1.1-4.8, p = 0.03) along with N category, age, and no AC. Post-RT EBV DNA was available in 99 patients at a median of 54 days. RFS, progression-free survival (PFS), and overall survival (OS) were worse in patients with detectable post-RT EBV DNA (Table). RFS and PFS drop further to 20% if EBV DNA was detectable after the full treatment (RT±AC, n = 71). In Cox MVA, post-RT EBV DNA remained independently prognostic (Table). EBV DNA was performed within 30 days of recurrence in 30 patients, and 24 were detectable (80% sensitivity). Conversely, of 152 patients without recurrence and at least 3-yr follow-up, 95 had post-RT EBV DNA testing and 84 were undetectable (88% specificity). An EBV DNA threshold of 31 copies maximized F1 accuracy metric, yielding 74% sensitivity and 97% specificity.

CONCLUSION

Pre-RT EBV DNA is prognostic and associated with higher N-category. Post-RT EBV DNA is a strong, independent predictor of RFS, PFS, and OS; 31 copies/mL may be a useful threshold to detect recurrence.

Outcomes after Contemporary Definitive Radiotherapy Alone in Patients with TNM-7 Stage III/IV Head and Neck Squamous Cell Carcinoma

PURPOSE/OBJECTIVE(S)

This study was undertaken to determine outcomes and prognostic factors of definitive intensity-modulated radiotherapy (IMRT) alone for patients with TNM-7 stage III/IV HNSCC who did not receive concurrent chemotherapy.

MATERIALS/METHODS

We evaluated TNM-7 stage III/IV HNSCC patients treated with definitive IMRT alone in our institution from 2004-2019. Patients were reclassified according to TNM-8 staging. Stage II HPV+ oropharyngeal cancers (OPC) were subdivided into T1-2N2 and T3N0-2 for analysis. The rationale for chemotherapy omission was obtained retrospectively from clinical documentation. Recurrence-free survival (RFS) and overall survival (OS) were estimated stratified by HPV status (determined by p16 staining, sometimes supplemented by HPV DNA testing). Multivariable analysis (MVA) identified prognostic factors for RFS and OS, taking into account stage and IMRT regimen. Age, performance status, and smoking were also examined for OS.

RESULTS

A total of 1083 patients were included (460 HPV+ and 623 HPV-). Reasons for omission of chemotherapy were: age >70 years or frailty (n = 551, 51%), cisplatin contraindication (n = 241, 22%), patient refusal (n = 106, 10%), and clinician's decision (n = 185, 17%). Median age was 67 years for HPV+ and 70 years for HPV- cohorts. IMRT mostly utilized altered fractionation regimens (n = 1016, 94%): moderately accelerated (Acc) (70 Gy/35 fractions [f]/6 weeks [w], 55%), hypofractionated (Hypo) (60 Gy/25f/5w, 14%), and hyperfractionated-accelerated (Hyper) (64 Gy/40f/4w, 25%). Median follow-up was 5 years. Five-year RFS and OS for HPV+ TNM-8 stage I/T1-2N2/T3N0-N2/III were 89%/86%/76%/52% and 83%/80%/64%/33% respectively (p<0.01). The same outcomes for HPV- TNM-8 stage III/IVA/IVB were 58%/52%/39% and 47%/27%/13%, respectively (p<0.01). MVA confirmed that HPV+ T3N0-2 subset within stage II and stage III (vs stage I) had lower RFS, and HPV- stage IVA and IVB (vs stage III) carried worse RFS and OS (Table).

CONCLUSION

Despite the retrospective nature and inherent selection bias, this large single institutional study shows that altered fractionated IMRT alone is an acceptable alternative for elderly, frail or cisplatin ineligible patients with HPV+ stage I/IIA (T1-2N2) OPC. Patients with HPV+ T3N0-2/stage III OPC and HPV- stage III/IV HNSCC have poor outcomes with IMRT alone and may benefit from alternative strategies.

Difference in Radiotherapeutic Plan of HyperArc-Based and CyberKnife-Based Stereotactic Radiotherapy (SRT) Techniques for Multiple Brain Metastases

PURPOSE/OBJECTIVE(S)

The purpose of this study is to compare the dosimetric quality and dose to surrounding normal tissue of HyperArc-based stereotactic radiotherapy (SRT) technique with a frameless robotic radiosurgery system for patients with multiple brain metastases.

MATERIALS/METHODS

Nineteen patients with multiple brain metastases (2-5 lesions) treated in our center were enrolled. The prescribed dose was 2100 cGy to 3250 cGy in three to five fractions. In order to determine the dosimetric quality, we compared the conformity index (CI), Gradient radius (GR), homogeneity index (HI), dose distribution in planning target volume, and dose to several organs at risk (OARs). All of the data were compared using pair-T test.

RESULTS

Both planning systems have prescribed dose coverage to GTV and PTV with no significant difference (P = 0.243; P = 0.312). The conformity index (CI), and homogeneity index (HI) were 1.27 ±0.022, and 1.08 ±0.006, respectively, for HyperArc plan and 1.76 ±0.065 and 1.22 ±0.009, respectively, for the CK plan (both, P< 0.001). The Gradient radius (GR) was 0.732 ±0.056 cm for HyperArc plan and 0.847 ±0.762 cm for CK plan (P = 0.002). These indicated that HyperArc plan had better CI, HI, and GR when compared to CK plan. Maximum dose to brainstem for HyperArc and CK plans were 485.1 ±128.65 and 723.6 ±126.93 cGy, respectively (P < 0.001). Moreover, HyperArc plan had less mean dose to optic chiasm, bilateral eyes, bilateral lens, and bilateral optic nerves (all, P < 0.05). Brain V5, V12, V24 were all much smaller in HyperArc plan (all, P < 0.05), indicating that HyperArc plan delivered less dose to normal brain tissue.

CONCLUSION

For patients with two to five brain metastases, HyperArc-based SRT provide excellent dosimetric quality and less dose to normal tissue.

Disparities in Inpatient Care Including Receipt of Radiotherapy and Mortality in Unhoused Adults with Cancer in the United States

PURPOSE/OBJECTIVE(S)

Cancer is the second leading cause of death among unhoused individuals in the United States. This study aims to assess inpatient care and outcomes of unhoused vs. housed adults with cancer. We hypothesize that unhoused patients receive less intensive care than housed patients during hospitalization.

MATERIALS/METHODS

All hospitalized adults age ≥18 with a principal cancer diagnosis were identified in the 2016-2020 National Inpatient Sample (NIS). Logistic regression models tested for associations between housing status and primary outcomes: care management (i.e., receipt of invasive procedures, systemic therapy, or radiation therapy [RT]) and inpatient death. Adjusted analyses accounted for patient demographics, socioeconomic status, comorbidities, and potential interactions between housing status and length of stay (LOS).

RESULTS

A total of 9,030 unhoused and 2,758,693 housed hospitalized adults with cancer were included in this study. At baseline, there were significant (p<0.05) differences in age <65 years (77% unhoused vs. 41% housed), male sex (75% vs. 53%), race (Black, 25% vs. 13%; White, 58% vs. 71%), and insurance type (Private, 6% vs. 27%; Medicaid, 53% vs. 11%) between groups. There were also differences in the prevalence of certain cancer histologies, including lung (17% vs. 14%) and liver (8% vs. 3%) cancer. Additionally, while comorbidities such as congestive heart failure (18% vs. 15%) and HIV (10% vs. 1%) were more common among unhoused patients, other conditions such as autoimmune disease (21% vs. 26%) and diabetes mellitus (38% vs. 43%) were more common among housed patients. Compared to housed patients, unhoused patients had longer LOS (median 6 vs. 4 days), with 62% hospitalized for ≥5 days (vs. 46%). On adjusted analysis, unhoused patients were less likely to undergo invasive procedures (48% vs. 58%; aOR [95% CI], 0.34 [0.27-0.42]) or receive systemic therapy (6% vs. 8%; 0.41 [0.20-0.85]) while inpatient. There were no significant differences in odds of receipt of RT (2% vs. 1%; 0.85 [0.21-3.41]) or odds of inpatient death (4% vs. 6%; 0.78 [0.52-1.15]) between groups.

CONCLUSION

In this first nationally representative analysis of housing status among hospitalized adults with cancer, unhoused adults were significantly less likely to receive invasive procedures or systemic therapy while inpatient, despite a higher prevalence of certain aggressive cancers and serious comorbidities compared to housed adults. Although there were no significant differences in the receipt of RT or death, disparities in inpatient management among unhoused patients highlight missed opportunities to promote equitable cancer care in this vulnerable population.

Palliative Care as a Component of High Value and Cost-Saving Care During Hospitalization for Metastatic Cancer

PURPOSE/OBJECTIVE(S)

Randomized controlled trials have demonstrated that palliative care can improve both quality of life and survival for outpatients with advanced cancer, but there is limited population-based data on the value of inpatient palliative care. We assessed palliative care as a component of high-value care among a nationally representative sample of inpatients with metastatic cancer. We further identified care, patient, and hospital characteristics significantly associated with high costs.

MATERIALS/METHODS

This study analyzed hospitalizations of patients ≥18 years with a primary diagnosis of metastatic cancer from the National Inpatient Sample (covering 97% of the U.S. population) from 2010-2019. We utilized multivariable mixed-effects logistic regression to assess medical services (receipt of palliative care, invasive medical ventilation [IMV], systemic therapy), patient demographics, and hospital characteristics that were associated with high charges billed to insurance and hospital costs. We utilized generalized linear mixed-effects models to determine cost savings associated with provision of palliative care.

RESULTS

Among 397,691 hospitalizations from 2010 to 2019, the median charge per admission increased by 24.9%, from $44,904 in 2010 to $56,098 in 2019, while the median cost remained stable at $14,300. Receipt of inpatient palliative care was associated with significantly lower charges (Odds Ratio [OR], 0.62; 95% CI, 0.61-0.64; P <.001) and costs (OR, 0.59; 95% CI, 0.58-0.61; P<.001). Factors associated with high charges were receipt of invasive medical ventilation (P<.001) or systemic therapy (P<.001), Hispanic patients (P<.001), and young age (18-49 years, P<.001). For-profit hospitals were more likely to bill high charges (OR, 5.05; 95% CI, 4.78-5.33, P<.001) but less likely to incur high hospital costs (OR, 0.51; 95% CI, 0.48-0.54, P<.001) than public hospitals. In adjusted generalized linear mixed effects regression, palliative care provision was associated with a $1,293 (-13.4%, P<.001) reduction in costs per hospitalization compared to no palliative care, independent of receipt of invasive care and age. Significant interactions were observed between receipt of palliative care and patient age group (-9.6% for 18-49 years; -14.7% for ≥70 years), receipt of IMV (-6.4% for IMV receipt; -14.0% for no IMV), hospital ownership (-19.6% for for-profit; -10.5% for public), and year of hospitalization (-15.4% for 2010; -8.9% for 2019).

CONCLUSION

Inpatient palliative care is associated with reduced hospital costs for patients with metastatic cancer, irrespective of age and receipt of aggressive interventions. Assuming inpatient palliative care receipt increases by 50%, we estimate $4,045,000 in annual national savings. Integration of inpatient palliative care may de-escalate costs incurred through low-value inpatient interventions.

The Titrated Mannitol Improved Central [99mTc] Tc TRODAT-1 Uptake in an Animal Model-A Clinically Feasible Application

[^99mTc]Tc TRODAT-1 is a widely used single photon emission tomography (SPECT) radiopharmaceutical in Asian practice for early detection of central dopaminergic disorders. However, its imaging quality remains sub-optimal. To overcome this problem, mannitol, an osmotic agent was used to observe its effect on improving striatal [^99mTc]Tc TRODAT-1 uptake in rat brain by titrated human dosages to investigate a clinically feasible way to improve human imaging quality. [^99mTc]Tc TRODAT-1 synthesis and quality control were performed as described. Sprague-Dawley rats were used for this study. The animal in vivo nanoSPECT/CT and ex vivo autoradiography were employed to observe and verify the striatal [^99mTc]Tc TRODAT-1 uptake in rat brains using clinically equivalent doses (i.e., 0, 1 and 2 mL groups, each n = 5) of mannitol (20% w/v, equivalent to 200 mg/mL) by an intravenous administration. Specific binding ratios (SBRs) were calculated to express the central striatal uptake in different experimental groups. In the NanoSPECT/CT imaging, the highest SBRs of striatal [^99mTc]Tc TRODAT-1 were reached at 75-90 min post-injection. The averaged striatal SBRs were 0.85 ± 0.13 (2 mL normal saline, the control group), 0.94 ± 0.26 (1 mL mannitol group) and 1.36 ± 0.12 (2 mL mannitol group, p < 0.01 which were significantly different than the control as well as 1 mL mannitol groups (p < 0.05). The SBRs from ex vivo autoradiography also showed a comparable trend of the striatal [^99mTc]Tc TRODAT-1 uptake in the 2 mL, 1 mL mannitol and the control groups (1.76 ± 0.52, 0.91 ± 0.29, and 0.21 ± 0.03, respectively, p < 0.05). No remarkable changes of vital signs were found in the mannitol groups and the controls. Pre-treated mannitol revealed a significant increase of the central striatal [^99mTc]Tc TRODAT-1 uptake in a rat model which not only enabled us to perform pre-clinical studies of dopaminergic related disorders but also provided a potential way to further optimize image quality in clinical practice.

3,4-Methylenedioxymethamphetamine (MDMA) Model: In Vivo 4-[18F]-ADAM PET Imaging

Numerous studies have confirmed that 3,4-Methylenedioxymethamphetamine (MDMA) produces long-lasting changes to the density of the serotonin reuptake transporter (SERT). Amitriptyline (AMI) has been shown to exert neuroprotective properties in neuropathologic injury. Here, we used a SERT-specific radionuclide, 4-[¹⁸F]-ADAM, to assess the longitudinal alterations in SERT binding and evaluate the synergistic neuroprotective effect of AMI in a rat MDMA model. In response to MDMA treatment regimens, SERT binding was significantly reduced in rat brains. Region-specific recovery rate (normalized to baseline) in the MDMA group at day 14 was 71.29% ± 3.21%, and progressively increased to 90.90% ± 7.63% at day 35. AMI dramatically increased SERT binding in all brain regions, enhancing average ~18% recovery rate at day 14 when compared with the MDMA group. The immunochemical staining revealed that AMI markedly increased the serotonergic fiber density in the cingulate and thalamus after MDMA-induction, and confirmed the PET findings. Using in vivo longitudinal PET imaging, we demonstrated that SERT recovery was positively correlated with the duration of MDMA abstinence, implying that lower SERT densities in MDMA-induced rats reflected neurotoxic effects and were (varied) region-specific and reversible. AMI globally accelerated the recovery rate of SERT binding and increased SERT fiber density with possible neuroprotective effects.

Very-Low-Dose Radiation and Clinical Molecular Nuclear Medicine

Emerging molecular and precision medicine makes nuclear medicine a de facto choice of imaging, especially in the era of target-oriented medical care. Nuclear medicine is minimally invasive, four-dimensional (space and time or dynamic space), and functional imaging using radioactive biochemical tracers in evaluating human diseases on an anatomically configured image. Many radiopharmaceuticals are also used in therapies. However, there have been concerns over the emission of radiation from the radionuclides, resulting in wrongly neglecting the potential benefits against little or any risks at all of imaging to the patients. The sound concepts of radiation and radiation protection are critical for promoting the optimal use of radiopharmaceuticals to patients, and alleviating concerns from caregivers, nuclear medicine staff, medical colleagues, and the public alike.

Preliminary Results on the Long-Term Effects of Dextromethorphan on MDMA-Mediated Serotonergic Deficiency and Volumetric Changes in Primates Based on 4-[18F]-ADAM PET/MRI

Alterations to the serotonergic system due to 3,4-methylenedioxymethamphetamine (MDMA) (ecstasy) consumption have been extensively documented. However, knowledge of the reversibility of these neurotoxic effects based on in vivo evaluations of serotonin transport (SERT) availability remains limited. This study aimed to evaluate the long-term neurotoxicity of MDMA after 66 months abstinence and explored whether Dextromethorphan, a non-competitive N-methyl-D-aspartate (NMDA) receptor, could attenuate MDMA-induced neurotoxicity using 4-[18F]-ADAM, an imaging ligand that selectively targets SERT, with positron emission tomography technology (PET). Nine monkeys (Macaca cyclopis) were used in this study: control, MDMA, and DM + MDMA. Static 4-[18F]-ADAM PET was performed at 60 and 66 months after drug treatment. Serotonin transport (SERT) availability was presented as the specific uptake ratios (SURs) of 4-[18F]-ADAM in brain regions. Voxel-based region-specific SERT availability was calculated to generate 3D PET/MR images. Structural Magnetic Resonance Imaging (MRI) volumetric analysis was also conducted at 60 months. Significantly decreased 4-[18F]-ADAM SURs were observed in the striatum and thalamus of the MDMA group at 60 and 66 months compared to controls; the midbrain and frontal cortex SURs were similar at 60 and 66 months in the MDMA and control groups. All eleven brain regions showed significantly lower (∼13%) self-recovery rates over time; the occipital cortex and cingulate recovered to baseline by 66 months. DM attenuated MDMA-induced SERT deficiency on average, by ∼8 and ∼1% at 60 and 66 months, respectively; whereas significant differences were observed between the thalamus and amygdala of the MDMA and DM + MDMA groups at 66 months. Compared to controls, the MDMA group exhibited significantly increased (∼6.6%) gray matter volumes in the frontal cortex, occipital cortex, caudate nucleus, hippocampus, midbrain, and amygdala. Moreover, the gray matter volumes of the occipital cortex, hippocampus and amygdala correlated negatively with the 4-[18F]-ADAM SURs of the same regions. DM (n = 2) did not appear to affect MDMA-induced volumetric changes. The 4-[18F]-ADAM SURs, lower self-recovery rate and increased volumetric values indicate the occipital cortex, hippocampus and amygdala still exhibit MDMA-induced neurotoxicity after 66 months’ abstinence. Moreover, DM may prevent MDMA-induced serotonergic deficiency, as indicated by increased 4-[18F]-ADAM SURs and SERT availability, but not volumetric changes.

99mTc-TRODAT-1 SPECT Revealed That Striatal Dopamine Transport Availability Significantly Decreases in Late Mid-Aged Healthy Taiwanese and Then Remains Stable

OBJECTIVES

Neuroimaging studies in the past 20 years have documented an age-related decline in striatal dopamine transporters (DATs), which is a marker of dopaminergic neurodegeneration; however, concerns about ethnic variations in the decline in DAT with age have not been addressed. The purpose of this study was to assess the rate of striatal DAT loss in healthy Taiwanese adults using kit-based 99mTc-TRODAT-1, a radioligand for DAT SPECT.

PATIENTS AND METHODS

Fifty healthy subjects (mean age ± SD, 63 ± 12 years; range, 30-80 years) were studied. 99mTc-TRODAT-1 was prepared from a lyophilized kit. Brain DAT SPECT imaging was acquired between 165 and 195 minutes postinjection (~740 MBq or 20 mCi) using a dual-head camera equipped with fan-beam collimators (Helix SPX; GE). Specific uptake in the striatum (ST), caudate nucleus (CA), and putamen (PU) were calculated from reconstructed transaxial slices at the level of maximal striatal activity. Occipital cortices were used as reference areas. Data were presented as specific binding ratios.

RESULTS

Age had a significant moderate to large negative effect on striatal DAT, which declined by -25.7% ± 6.10% between the ages of 30 and 80 years, equivalent to 6.4% loss per decade. The rates of decline in the CA and PU were 6.9% and 7.3% per decade, respectively.

CONCLUSIONS

This study suggests ethnic variations may not significantly affect the age-related decline in DAT. The data generated in this study could also be used as a reference to estimate DAT loss/occupancy in patients with DAT-related diseases.

Benign Parathyroid Hyperplasia With Incidental Pulmonary Seeding on 99mTc-MIBI Scintigraphy and FDG PET/CT

ABSTRACT

A 50-year-old woman with end-stage renal disease presented with recurrent hyperparathyroidism after parathyroidectomy. 99mTc-MIBI scintigraphy did not show MIBI-avid lesion in the neck or mediastinum but in bilateral lung fields instead. On suspicion of malignancy, 18F-FDG PET/CT was performed and depicted no significant FDG uptake throughout the whole body. After resection of the pulmonary nodules, the final histopathology revealed benign parathyroid hyperplasia with pulmonary seeding, which is exceptionally a rare entity.

Investigation of a Novel Decision Support Metric for Head and Neck Adaptive Radiation Therapy Using a Real-Time In Vivo Portal Dosimetry System

In adaptive radiation therapy of head and neck cancer, any significant anatomical changes observed are used to adapt the treatment plan to maintain target coverage without elevating the risk of xerostomia. However, the additional resources required for adaptive radiation therapy pose a challenge for broad-based implementation. It is hypothesized that a change in transit fluence is associated with volumetric change in the vicinity of the target and therefore can be used as a decision support metric for adaptive radiation therapy. This was evaluated by comparing the fluence with volumetric changes in 12 patients. Transit fluence was measured by an in vivo portal dosimetry system. Weekly cone beam computed tomography was used to determine volume change in the rectangular region of interest from condyloid process to C6. The integrated transit fluence through the region of interest on the day of the cone beam computed tomography scan was calculated with the first treatment as the baseline. The correlation between fluence change and volume change was determined. A logistic regression model was also used to associate the 5% region of interest volume reduction replanning trigger point and the fluence change. The model was assessed by a chi-square test. The area under the receiver-operating characteristic curve was also determined. A total of 46 pairs of measurements were obtained. The correlation between fluence and volumetric changes was found to be -0.776 (P value <.001). The negative correlation is attributed to the increase in the photon fluence transport resulting from the volume reduction. The chi-square of the logistic regression was found to be 17.4 (P value <.001). The area under the receiver-operating characteristic curve was found to be 0.88. Results indicate the change in transit fluence, which can be measured without consuming clinical resources or requiring additional time in the treatment room, can be used as a decision support metric for adaptive therapy.

Abstract P6-08-04: National trends in mastectomy for operable breast cancers treated with neoadjuvant chemotherapy

Objective: Although neoadjuvant chemotherapy (NAC) has not been shown to improve survival compared with adjuvant therapy for patients with operable invasive breast cancer (IBC), it is often used to allow more limited surgery in the breast and axilla without compromising local control. We sought to evaluate national trends in mastectomy among patients with operable breast cancer treated with NAC and to characterize the contribution of demographic and tumor characteristics to changing trends.

Methods: We queried the National Cancer Database (NCDB) 2014 Participant User File for adult women who underwent surgery and received chemotherapy for unilateral T1-3N0-3M0 IBC diagnosed between 2010 and 2014. Surgery was classified as lumpectomy (BCS), unilateral mastectomy (UM) or bilateral mastectomy (BM). Molecular subtype was categorized according to ER, PR, and HER2 status. We used logistic regression to model surgery use (BM or UM vs BCS), adjusting for the following clinical covariates that were selected a priori: age, race/ethnicity, year of diagnosis, comorbidity score, metropolitan vs urban/rural residence, patient distance from treating facility, % with less than high school education (zip code based), insurance type, clinical stage, histology, and molecular subtype. As those who achieved pathologic complete response (pCR) after NAC should be ideal candidates for BCS, we also looked at this group separately. We then performed sensitivity analyses further controlling for region of the country and facility type, and for facility.

Results: We identified 235,339 patients who fulfilled our inclusion criteria. Of these patients, 25.3% were treated with NAC. Rates of pCR increased from 33.3% in 2010 to 46.3% in 2014 (p&lt;0.001). Rates of BCS increased from 37.0% in 2010 to 40.8% in 2014 (p&lt;0.001). While rates of UM decreased from 43.3% in 2010 to 34.7% in 2014 (p&lt;0.001), rates of BM with or without reconstruction increased from 19.7% in 2010 to 24.6% in 2014 (p&lt;0.001). Rates of BM without immediate reconstruction remained stable over time, from 11.8% in 2010 to 11.5% in 2014.

Among patients who received NAC, factors that were independently associated with both UM and BM (versus BCS) for both the entire cohort and those who achieved pCR included younger age, greater patient distance from facility, and higher clinical stage. Factors that were inversely associated with both UM and BM included black race and ductal histology. More recent year of diagnosis was inversely associated with UM and directly associated with BM. Asian race was associated with UM while non-Hispanic white race was associated with BM. Private or managed care insurance and higher area education were also associated with BM. These results were materially unchanged in sensitivity analyses.

Conclusion: Rates of pCR have increased over time among patients with operable IBC treated with NAC. While the rate of UM has declined over time, the rate of BM has increased. Significant sociodemographic differences exist between women who undergo BCS, and women who undergo UM and BM. Further study of factors that influence surgical decision-making in the NAC setting is warranted.

Citation Format: Pollom E, Qian Y, Dirbas F, Horst K, Tsai CJ. National trends in mastectomy for operable breast cancers treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-08-04.

Influences of pH and hydraulic retention time on anaerobes converting beer processing wastes into hydrogen

To convert high-solids organic wastes (3% w./w.) to high-value hydrogen, a full factorial experimental design was employed in planning the experiments for learning the effects of pH and hydraulic retention time (HRT) on the hydrogen production in a chemostat reactor using waste yeast obtained from beer processing wastes. For determining which experimental variable settings affect hydrogen production, predictive polynomial quadratic equation and response surface methodology were employed to determine and explain the conditions required for high-value hydrogen production. Experimental results indicate that a maximum hydrogen production rate of 460 mL/gVSS/d was obtained at pH = 5.8 and HRT = 32 hours. Moreover, hydrogenase targeted RT-PCR results indicate that Clostridium thermocellum and Klebsiella pneumoniae predominated.

Transient, highly populated, building blocks folding model

Protein folding is a hierarchical event, in which transiently formed local structural elements assemble to yield the native conformation. In principle, multiple paths glide down the energy landscape, but, in practice, only a few of the paths are highly traveled. Here, the literature is reviewed in this light, and, particularly, a hierarchical, building block protein-folding model is presented, putting it in the context of a broad range of experimental and theoretical results published over the past few years. The model is based on two premises: First, although the local building block elements may be unstable, they nevertheless have higher population times than all alternate conformations; and, second, protein folding progresses through a combinatorial assembly of these elements. Through the binding of the most favorable building block conformers, there is a redistribution of the conformers in solution, propagating the protein-folding reaction. We describe the algorithm, and illustrate its usefulness, then we focus on its utility in assigning simple vs complex folding pathways, on chaperonin-assisted folding, on its relevance to domain-swapping processes, and on its relevance and relationship to disconnectivity graphs and tree diagrams. Considering protein folding as initiating from local transient structural elements is consistent with available experimental and theoretical results. Here, we have shown that, early in the folding process, sequential interactions are likely to take place, even if the final native fold is a complex, nonsequential one. Such a route is favorable kinetically and entropically. Through the construction of anatomy trees, the model enables derivation of the major folding pathways and their bumps, and qualitatively explains the kinetics of protein folding.

Transmission electron microscopy investigation of the formation of C54-TiSi(2) phase on stressed (001)Si

The effects of stress on the formation of C54-TiSi2 phase in Ti/(001)Si samples have been investigated by high-resolution transmission electron microscopy in conjunction with auto-correlation function (ACF) analysis. The C54-TiSi2 phase transformation temperature in tensily stressed samples was found to be lowered by about 100 degrees C than that in compressively stressed samples. The thickness of amorphous interlayers (a-interlayers) between Ti metal thin films and Si substrates was found to be thicker and thinner in the tensily and compressively stressed Si samples, respectively. Furthermore, the thicker a-interlayer was found to consist of a higher density of crystallites from the ACF analysis. With a higher density of crystallites in the a-interlayer, the grain size of C49-TiSi2 was reduced since more nucleation sites are available for the formation of C49-TiSi2. The small grain size of C49-TiSi2 in turn enhances the formation of C54-TiSi2. As a result, the phase transformation of C49- to C54-TiSi2 is enhanced by the tensile stress present in silicon substrates.

Thermodynamic differences among homologous thermophilic and mesophilic proteins

Here, we analyze the thermodynamic parameters and their correlations in families containing homologous thermophilic and mesophilic proteins which show reversible two-state folding <--> unfolding transitions between the native and the denatured states. For the proteins in these families, the melting temperatures correlate with the maximal protein stability change (between the native and the denatured states) as well as with the enthalpic and entropic changes at the melting temperature. In contrast, the heat capacity change is uncorrelated with the melting temperature. These and additional results illustrate that higher melting temperatures are largely obtained via an upshift and broadening of the protein stability curves. Both thermophilic and mesophilic proteins are maximally stable around room temperature. However, the maximal stabilities of thermophilic proteins are considerably greater than those of their mesophilic homologues. At the living temperatures of their respective source organisms, homologous thermophilic and mesophilic proteins have similar stabilities. The protein stability at the living temperature of the source organism does not correlate with the living temperature of the protein. We tie thermodynamic observations to microscopics via the hydrophobic effect and a two-state model of the water structure. We conclude that, to achieve higher stability and greater resistance to high and low temperatures, specific interactions, particularly electrostatic, should be engineered into the protein. The effect of these specific interactions is largely reflected in an increased enthalpy change at the melting temperature.

The building block folding model and the kinetics of protein folding

Here we show that qualitatively, the building blocks folding model accounts for three-state versus the two-state protein folding. Additionally, it is consistent with the faster versus slower folding rates of the two-state proteins. Specifically, we illustrate that the building blocks size, their mode of associations in the native structure, the number of ways they can combinatorially assemble, their population times and the way they are split in the iterative, step-by-step structural dissection which yields the anatomy trees, explain a broad range of folding rates. We further show that proteins with similar general topologies may have different folding pathways, and hence different folding rates. On the other hand, the effect of mutations resembles that of changes in conditions, shifting the population times and hence the energy landscapes. Hence, together with the secondary structure type and the extent of local versus non-local interactions, a coherent, consistent rationale for folding kinetics can be outlined, in agreement with experimental results. Given the native structure of a protein, these guidelines enable a qualitative prediction of the folding kinetics. We further describe these in the context of the protein folding energy landscape. Quantitatively, in principle, the diffusion-collision model for the building block association can be used. However, the folding rates of the building blocks and traps in their formation and association, need to be considered.

Structured disorder and conformational selection

Traditionally, molecular disorder has been viewed as local or global instability. Molecules or regions displaying disorder have been considered inherently unstructured. The term has been routinely applied to cases for which no atomic coordinates can be derived from crystallized molecules. Yet, even when it appears that the molecules are disordered, prevailing conformations exist, with population times higher than those of all alternate conformations. Disordered molecules are the outcome of rugged energy landscapes away from the native state around the bottom of the funnel. Ruggedness has a biological function, creating a distribution of structured conformers that bind via conformational selection, driving association and multimolecular complex formation, whether chain-linked in folding or unlinked in binding. We classify disordered molecules into two types. The first type possesses a hydrophobic core. Here, even if the native conformation is unstable, it still has a large enough population time, enabling its experimental detection. In the second type, no such hydrophobic core exists. Hence, the native conformations of molecules belonging to this category have shorter population times, hindering their experimental detection. Although there is a continuum of distribution of hydrophobic cores in proteins, an empirical, statistically based hydrophobicity function may be used as a guideline for distinguishing the two disordered molecule types. Furthermore, the two types relate to steps in the protein folding reaction. With respect to protein design, this leads us to propose that engineering-optimized specific electrostatic interactions to avoid electrostatic repulsion would reduce the type I disordered state, driving the molten globule (MG) --> native (N) state. In contrast, for overcoming the type II disordered state, in addition to specific interactions, a stronger hydrophobic core is also indicated, leading to the denatured --> MG --> N state.

Collection efficiency and capacity of three samplers for acidic and basic gases

This paper compares the collection efficiency and capacity of a coated porous metal disk with those of a silica gel tube and an impinger at the acid or basic aerosol concentration of two times the permissible exposure limitation (Taiwan IOSH, Institute of Occupational Safety and Health), relative humidity of 80 +/- 5%, and temperature of 30 +/- 3 degrees C in the laboratory. Using 5% sodium carbonate/glycerin coating, the collection efficiencies of the porous metal disk for nitric acid, hydrogen chloride, and hydrogen fluoride are found to be higher than those of the silica gel tube and the impinger when the sampling time is less than 3.0 h. The gas collection capacity of the porous metal disk coated with 5% sodium carbonate is calculated to be 3.9, 5.8, and >2.5 mg for nitric acid, hydrogen chloride, and hydrogen fluoride, respectively. For ammonia, the porous metal disk coated using 4% citric acid performs slightly better than the impinger, and the corresponding capacity is slightly greater than 33.6 mg.

Protein folding and function: the N-terminal fragment in adenylate kinase

Three-dimensional protein folds range from simple to highly complex architectures. In complex folds, some building block fragments are more important for correct protein folding than others. Such fragments are typically buried in the protein core and mediate interactions between other fragments. Here we present an automated, surface area-based algorithm that is able to indicate which, among all local elements of the structure, is critical for the formation of the native fold, and apply it to structurally well-characterized proteins. In particular, we focus on adenylate kinase. The fragment containing the phosphate binding, P-loop (the "giant anion hole") flanked by a beta-strand and an alpha-helix near the N-terminus, is identified as a critical building block. This building block shows a high degree of sequence and structural conservation in all adenylate kinases. The results of our molecular dynamics simulations are consistent with this identification. In its absence, the protein flips to a stable, non-native state. In this misfolded conformation, the other local elements of the structure are in their native-like conformations; however, their association is non-native. Furthermore, this element is critically important for the function of the enzyme, coupling folding, and function.

Fluconazole disk diffusion test with methylene blue- and glucose-enriched Mueller-Hinton agar for determining susceptibility of Candida species

A 25-microg fluconazole disk diffusion test using a Mueller-Hinton agar plate containing 2% glucose and 5 microg of methylene blue/ml (GM-MH) was compared to the macrodilution reference method for 210 Candida species. The GM-MH agar plate was read at 24 h. The predictive values of disks with susceptible, intermediate, and resistant results on the GM-MH agar plate at 24 h were 97.1, 56.3, and 76.5%, respectively.

A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer

We propose a model illustrating how proteins, which differ in their overall sequences and structures, can form the propagating, twisted beta-sheet conformations, characteristic of amyloids. Some cases of amyloid formation can be explained through a "domain swapping" event, where the swapped segment is either a beta-hairpin or an unstable conformation which can partially unfold and assume a beta-hairpin structure. As in domain swapping, here the swapped beta-hairpin is at the edge of the structure, has few (if any) salt bridges and hydrogen bonds connecting it to the remainder of the structure and variable extents of buried non-polar surface areas. Additionally, in both cases the swapped piece constitutes a transient "building block" of the structure, with a high population time. Whereas in domain swapping the swapped fragment has been shown to be an alpha-helix, loop, strand or an entire domain, but so far not a beta-hairpin, despite the large number of cases in which it was already detected, here swapping may involve such a structural motif. We show how the swapping of beta-hairpins would form an interdigitated, twisted beta-sheet conformation, explaining the remarkable high stability of the protofibril in vitro. Such a swapping mechanism is attractive as it involves a universal mechanism in proteins, critical for their function, namely hinge-bending motions. Our proposal is consistent with structural superpositioning of mutational variants. While the overall r.m.s.d.s of the wild-type and mutants are small, the proposed hinge-bending region consistently shows larger deviations. These larger deviations illustrate that this region is more prone to respond to the mutational changes, regardless of their location in the sequence or in the structure. Nevertheless, above all, we stress that this proposition is hypothetical, since it is based on assumptions lacking definitive experimental support.

Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations

We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations have shown fragments 1--36, 37--88, and 89--159 to be unstable, with a C(alpha)RMSD (C(alpha) root mean squared deviation) >5 A after 3.0 nsec of simulation. The unfolding of fragment 1--36 was immediate, whereas fragments 37--88 and 89--159 gradually unfolded because of the presence of the beta-sheet core structure. In the absence of residues 1--36, the two distinct domains comprising fragment 39--159 associated with each other, resulting in a stable conformation. This conformation retained most of its native structural elements. We have further simulated fragments derived from computational protein cutting. These were also found to be unstable, with the exception of fragment 104--159. In the absence of alpha(4), the loose loop region of residues 120--127 exhibited a beta-strand-like behavior, associating itself with the beta-sheet core of the protein fragment. The current study suggests that the folding of dihydrofolate reductase involves cooperative folding of distinct domains which otherwise would have been unstable as independent folded units in solution. Finally, the critical role of residues 1--36 in allowing the two distinct domains of fragment 104--159 to fold into the final native conformation is discussed.

Use of two different acidic aerosol samplers to measure acidic aerosols in Hsinchu, Taiwan

Acidic aerosol concentrations measured by an annular denuder system (ADS) and a honeycomb denuder system (HDS) in Hsinchu, Taiwan, were compared. Aerosols were also sampled by a MOUDI (micro-orifice uniform deposit impactor) and analyzed by an ion chromatograph to determine the size distributions of different species. Using the measured aerosol size distribution, theoretical analysis showed that positive HNO3 artifact due to volatilization of NH4NO3 is generally negligible for both samplers. Comparing two different denuder samplers, the average concentration of HNO3 measured by the ADS was found to be lower than that measured by the HDS, while the difference between the two samplers for the average concentration of other species was found to be within +/- 15%. A possible cause of the difference in HNO3 concentrations is due to a greater loss of HNO3 in the cyclone used by the ADS than in the impactor used by the HDS. The study also showed incomplete absorption of the evaporated HCl and HNO3 from the particles on the Teflon filter by the first nylon filter in the filter pack of the ADS. Collection efficiency and capacity of HCl and HNO3 by the nylon filters need further investigation.

A systematic study of the vibrational free energies of polypeptides in folded and random states

Molecular vibrations, especially low frequency motions, may be used as an indication of the rigidity or the flatness of the protein folding energy landscape. We have studied the vibrational properties of native folded as well as random coil structures of more than 60 polypeptides. The picture we obtain allows us to perceive how and why the energy landscape progressively rigidifies while still allowing potential flexibility. Compared with random coil structures, both alpha-helices and beta-hairpins are vibrationally more flexible. The vibrational properties of loop structures are similar to those of the corresponding random coil structures. Inclusion of an alpha-helix tends to rigidify peptides and so-called building blocks of the structure, whereas the addition of a beta-structure has less effect. When small building blocks coalesce to form larger domains, the protein rigidifies. However, some folded native conformations are still found to be vibrationally more flexible than random coil structures, for example, beta(2)-microglobulin and the SH3 domain. Vibrational free energy contributes significantly to the thermodynamics of protein folding and affects the distribution of the conformational substates. We found a weak correlation between the vibrational folding energy and the protein size, consistent with both previous experimental estimates and theoretical partition of the heat capacity change in protein folding.

Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape

Here, we depict the anatomy of protein structures in terms of the protein folding process. Via an iterative, top-down dissecting procedure, tertiary structures are spliced down to reveal their anatomy: first, to produce domains (defined by visual three-dimensional inspection criteria); then, hydrophobic folding units (HFU); and, at the end of a multilevel process, a set of building blocks. The resulting anatomy tree organization not only clearly depicts the organization of a one-dimensional polypeptide chain in three-dimensional space but also straightforwardly describes the most likely folding pathway(s). Comparison of the tree with the formation of the hydrophobic folding units through combinatorial assembly of the building blocks illustrates how the chain folds in a sequential or a complex folding pathway. Further, the tree points to the kinetics of the folding, whether the chain is a fast or a slow folder, and the probability of misfolding. Our ability to successfully dissect the protein into an anatomy tree illustrates that protein folding is a hierarchical process and further validates a building blocks protein folding model.

Clinical correlates of antifungal macrodilution susceptibility test results for non-AIDS patients with severe Candida infections treated with fluconazole

Although the clinical correlates of the reference antifungal susceptibility test results in hematogenous and deep-seated Candida infection are still controversial, we evaluated the clinical correlates of this test in deep-seated Candida infections in non-AIDS patients. Thirty-two non-AIDS patients with hematogenous or deep-seated Candida infections were treated with intravenous fluconazole (400 mg a day), and the clinical outcomes were evaluated. Coexisting bacterial infections were treated with appropriate antibiotics, superinfection or reinfection was excluded, inadequate fluconazole therapy was avoided, and essential surgical intervention was performed. The MICs of fluconazole for these 32 Candida isolates were determined according to the M27-A procedure approved by the National Committee on Clinical Laboratory Standards. MICs were interpreted as susceptible (< or =8 microg/ml), dose-dependent susceptible (16 to 32 microg/ml), and resistant (> or =64 microg/ml) according to the criteria of the M27-A standard. The success rates were 79% (19 of 24; 95% confidence interval [CI], 59 to 93%) in the susceptible category, 66% (4 of 6; 95% CI, 19 to 95%) in the dose-dependent susceptible category, and 0% (0 of 2; 95% CI, 0 to 84%) in the resistant category. We conclude that the clinical correlation of the reference antifungal susceptibility test results is high in hematogenous and deep-seated Candida infections.

Clinical characteristic of parenteral iron supplementation in hemodialysis patients receiving erythropoietin therapy

BACKGROUND

Iron deficiency constitutes the major cause of erythropoietin hyporesponse in uremic patients receiving erythropoietin therapy; therefore, iron supplementation is necessary for these patients. Recent data suggested that intravenous iron supply is a preferable route for iron supplementation. However, it remains unclear whether a single large dose or multiple small doses are a better way of administering an intravenous iron supply.

METHODS

To determine the effect of different dosing schedules of intravenous iron therapy on the hematocrit level, we randomly assigned 18 patients to 3 groups. The first group of patients (n = 6) received a single dose of 800 mg intravenous fesin (ferric saccharate). The second group of patients (n = 6) received 400 mg intravenous fesin once weekly for 2 successive weeks. The third group of patients (n = 6) received 120 mg of intravenous fesin for 7 successive hemodialysis sessions. EPO was given at a fixed dose for all individuals in the study period.

RESULTS

The results showed that all 3 groups of patients had a progressive increase in hematocrit (Hct) level following intravenous iron therapy. Serum ferritin levels increased rapidly following iron therapy and then declined gradually in all 3 groups. But no statistical significance could be found among the 3 groups because of the small patient number. Also, no differences were observed in Hct or serum ferritin levels among these 3 groups of patients at all stages.

CONCLUSION

In this study, we found that a large single dose as well as small multiple doses of parenteral iron therapy had similar effects in correcting the iron deficiency in hemodialysis patients treated with erythropoietin. To save manpower and costs, we recommend the large single dosing schedule.

Binding and folding: in search of intramolecular chaperone-like building block fragments

We propose an intramolecular chaperone which catalyzes folding and neither dissociates nor is cleaved. This uncleaved foldase is an intramolecular chain-linked chaperone, which constitutes a critical building block of the structure. Macroscopically, all molecular chaperones facilitate folding reactions and manifest similar energy landscapes. However, microscopically they differ. While intermolecular chaperones catalyze folding by unfolding misfolded conformations or prevent misfolding, the chain-linked cleaved (proregion) and uncleaved intramolecular chaperone-like building blocks suggested here, catalyze folding by binding to, stabilizing and increasing the populations of native conformations of adjacent building block fragments. In both, the more stable the intramolecular chaperone fragment region, the faster is the folding rate. Hence, mechanistically, intramolecular chaperones and chaperone-like segments are similar. Both play a dual role, in folding and in protein function. However, while the functional role of the proregions is inhibitory, necessitating their cleavage, the function of the uncleaved intramolecular chaperone-like building blocks does not require their subsequent removal. On the contrary, it requires that they remain in the structure. This may lead to the difference in the type of control they are under: proteins folding with the assistance of the proregion have been shown to be under kinetic control. It has been suggested that kinetically controlled folding reactions, with the proregion catalyst removed, lend longevity under harsh conditions. On the other hand, proteins with uncleaved intramolecular chaperone-like building blocks, with their 'foldases' still attached, are largely under thermodynamic control, consistent with the control observed in most protein folding reactions. We propose that an uncleaved intramolecular chaperone-like fragment occurs frequently in proteins. We further propose that such proteins would be prone to changing conditions and in particular, to mutations in this critical building block region. We describe the features qualifying it for its proposed chaperone-like role, compare it with inter- and intramolecular chaperones and review current literature in this light. We further propose a mechanism showing how it lowers the barrier heights, leading to faster folding reaction rates. Since these fragments constitute an intergal part of the protein structure, we call these critical building blocks intramolecular, chaperone-like fragments, to clarify, distinguish and adhere to the definition of the transiently associating chaperones. The new mechanism presented here differs from the concept of 'folding nuclei'. While the concept of folding nuclei focuses on a non-sequential distribution of the folding information along the entire protein chain, the chaperone-like building block fragments proposition focuses on a segmental distribution of the folding information. This segmental distribution controls the distributions of the populations throughout the hierarchical folding processes.

Identification of the spinocerebellar ataxia type 7 mutation in Taiwan: application of PCR-based Southern blot

Spinocerebellar ataxia (SCA) type 7 is an autosomal dominant disorder characterized by neural loss, mainly in the cerebellum and regions of the brainstem and particularly the inferior olivary complex. This neurodegeneration disease is associated with expansion of unstable CAG repeats within the 5'-translated region of the SCA7 gene, located on chromosome 3p. We conducted a local survey of the normal population and candidate patients for the analysis of the CAG repeats in the SCA7 gene. The distributions of the CAG repeat units of SCA7 gene in the normal population in Taiwan were established in this study by using the radioactive genomic polymerase chain reaction (PCR). The normal range of CAG repeats is from 6 to 17 repeats, with the more common being around 8-13 repeats. The range is narrower than that reported for other ethnic groups (7-35 CAGs). Meanwhile, by the use of a combination of PCR and Southern blot analysis, one SCA7 family was identified and is reported here. A marked instability of the CAG repeat number during transmission from father to son (41 vs. 100) was observed in the SCA7 family. Clinical anticipation is significant in this family including an infantile case, who was found to have nystagmus from the age of 1 month. To date, the SCA7 mutation has been detected in one of 73 families with autosomal dominant cerebellar ataxia phenotypes, which is about 1.4% of the ataxia families referred to us, compared to 1.4% SCA1, 9.6% SCA2, and 27.3% SCA3/Machado-Joseph disease in our collection. In addition, we demonstrate that the PCR-based Southern blot analysis, with the advantages of sensitivity of PCR and specificity of Southern blot, is a reliable diagnostic method for SCA7 mutation screening. The molecular analysis technique makes possible the quick and accurate diagnosis of SCA7 patients and in the future will hopefully be applied to prenatal screening for SCA7 families.

Relation of Helicobacter pylori infection and angiographically demonstrated coronary artery disease

Conventional coronary risk factors explain only part of the variation in the incidence of cases of coronary heart disease. Recently H. pylori genomic material has been demonstrated in the coronary arteries of myocardial infarct. In searching for additional coronary risk factors, the potential role of H. pylori infection deserves to be investigated. To clarify if H. pylori infection is associated with an increased risk of coronary heart disease, a series of patients admitted to the Cardiac Catheterization Laboratory for coronary angiography were recruited prospectively. Cases (N = 165) were defined as those who had at least one coronary artery lesion occupying at least 50% of the luminal diameter on coronary angiography. Patients who had normal coronary angiography were selected as controls (N = 127). Demographic data, cardiovascular risk factors, and socioeconomic status were measured in both of the patients and controls. Stored serum specimens from both groups were tested for the presence of serum IgG antibody to H. pylori using enzyme-linked immunosorbent assay; 69.1% of the cases and 77.2% of the controls were seropositive for H. pylori (odds ratio 0.66, 95% CI 0.38-1.16, P = 0.12). After adjustment for age, gender, cardiovascular risk factors, and socioeconomic class, this remained nonsignificant (odds ratio 0.59, 95% CI 0.32-1.09, P = 0.09). H. pylori seropositivity was not associated with several coronary risk factors in either cases or controls. The proportion of H. pylori-positive patients was higher among the cases with triple vessel disease (77.5%) than those with double vessel disease (67.3%) and single vessel disease (65.7%); however, the differences were not statistically significant (odds ratio 0.57, 95% CI 0.23-1.4, P = 0.19). In this study no increase was found in H. pylori seropositivity in subjects with coronary artery disease. This minor association suggests that previous H. pylori infection, reflecting the early childhood environment, may not be important in determining the risk of coronary heart disease.

Correction of a migrated Tenckhoff peritoneal dialysis catheter using a Lunderquist guidewire: report of two cases

Two chronic ambulatory peritoneal dialysis (CAPD) patients who experienced from ultrafiltration failure resulting from malposition of a Tenckhoff catheter were treated. Conservative management such as changing body position, saline infusion, and enemas had been tried, but had failed. To avoid surgical intervention, we attempted to correct the malposition using a 120-cm-long Lunderquist guidewire (Nycomed, NY) with a 15-cm-long soft and flexible tip at its distal end. Under fluoroscopy, we successfully repositioned these two migrated Tenckhoff catheters using a Lunderquist guidewire. To the best of our knowledge, this is the first report of using a Lunderquist guidewire to correct a malfunctioning Tenckhoff catheter in CAPD patients. The Lunderquist guide wire has the advantages of being relatively non-invasive and easily used and it provides a reduced morbidity rate. Moreover, using this guidewire allows the Tenckhoff catheter to produce torque and whiplash, buckling, sweeping and rotating maneuvers that can help to correct malposition of the catheter and redirect the catheter to its ideal position. We therefore suggest that patients who receive surgical revision for a malfunctioning Tenckhoff catheter have at least one attempt at correction using this safe and easy procedure before surgery.

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

Proteins are not rigid structures; they are dynamic entities, with numerous conformational isomers (substates). The dynamic nature of protein structures amplifies the structural variation of the transition state for chemical reactions performed by proteins. This suggests that utilizing a transition state ensemble to describe chemical reactions involving proteins may be a useful representation. Here we re-examine the nature of the transition state of protein chemical reactions (enzyme catalysis), considering both recent developments in chemical reaction theory (Marcus theory for SN2 reactions), and protein dynamics effects. The classical theory of chemical reactions relies on the assumption that a reaction must pass through an obligatory transition-state structure. The widely accepted view of enzymatic catalysis holds that there is tight binding of the substrate to the transition-state structure, lowering the activation energy. This picture, may, however, be oversimplified. The real meaning of a transition state is a surface, not a single saddle point on the potential energy surface. In a reaction with a "loose" transition-state structure, the entire transition-state region, rather than a single saddle point, contributes to reaction kinetics. Consequently, here we explore the validity of such a model, namely, the enzymatic modulation of the transition-state surface. We examine its utility in explaining enzyme catalysis. We analyse the possibility that instead of optimizing binding to a well-defined transition-state structure, enzymes are optimized by evolution to bind efficiently with a transition-state ensemble, with a broad range of activated conformations. For enzyme catalysis, the key issue is still transition state (ensemble) stabilization. The source of the catalytic power is the modulation of the transition state. However, our definition of the transition state is the entire transition-state surface rather just than a single well-defined structure. This view of the transition-state ensemble is consistent with the nature of the protein molecule, as embodied and depicted in the protein energy landscape of folding, and binding, funnels.

Factors enhancing protein thermostability

Several sequence and structural factors have been proposed to contribute toward greater stability of thermophilic proteins. Here we present a statistical examination of structural and sequence parameters in representatives of 18 non-redundant families of thermophilic and mesophilic proteins. Our aim was to look for systematic differences among thermophilic and mesophilic proteins across the families. We observe that both thermophilic and mesophilic proteins have similar hydrophobicities, compactness, oligomeric states, polar and non-polar contribution to surface areas, main-chain and side-chain hydrogen bonds. Insertions/deletions and proline substitutions do not show consistent trends between the thermophilic and mesophilic members of the families. On the other hand, salt bridges and side chain-side chain hydrogen bonds increase in the majority of the thermophilic proteins. Additionally, comparisons of the sequences of the thermophile-mesophile homologous protein pairs indicate that Arg and Tyr are significantly more frequent, while Cys and Ser are less frequent in thermophilic proteins. Thermophiles both have a larger fraction of their residues in the alpha-helical conformation, and they avoid Pro in their alpha-helices to a greater extent than the mesophiles. These results indicate that thermostable proteins adapt dual strategies to withstand high temperatures. Our intention has been to explore factors contributing to the stability of proteins from thermophiles with respect to the melting temperatures (T(m)), the best descriptor of thermal stability. Unfortunately, T(m) values are available only for a few proteins in our high resolution dataset. Currently, this limits our ability to examine correlations in a meaningful way.

Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers

Here we seek to understand the higher frequency of occurrence of salt bridges in proteins from thermophiles as compared to their mesophile homologs. We focus on glutamate dehydrogenase, owing to the availability of high resolution thermophilic (from Pyrococcus furiosus) and mesophilic (from Clostridium symbiosum) protein structures, the large protein size and the large difference in melting temperatures. We investigate the location, statistics and electrostatic strengths of salt bridges and of their networks within corresponding monomers of the thermophilic and mesophilic enzymes. We find that many of the extra salt bridges which are present in the thermophilic glutamate dehydrogenase monomer but absent in the mesophilic enzyme, form around the active site of the protein. Furthermore, salt bridges in the thermostable glutamate dehydrogenase cluster within the hydrophobic folding units of the monomer, rather than between them. Computation of the electrostatic contribution of salt bridge energies by solving the Poisson equation in a continuum solvent medium, shows that the salt bridges in Pyrococcus furiosus glutamate dehydrogenase are highly stabilizing. In contrast, the salt bridges in the mesophilic Clostridium symbiosum glutamate dehydrogenase are only marginally stabilizing. This is largely the outcome of the difference in the protein environment around the salt bridges in the two proteins. The presence of a larger number of charges, and hence, of salt bridges contributes to an electrostatically more favorable protein energy term. Our results indicate that salt bridges and their networks may have an important role in resisting deformation/unfolding of the protein structure at high temperatures, particularly in critical regions such as around the active site.

GSTT1 and GSTM1 null genotypes and the risk of gastric cancer: a case-control study in a Chinese population

Glutathione S-transferase (GST) enzymes are involved in detoxification of many potentially carcinogenic compounds. The homozygous deletions or null genotypes of GSTT1 (theta class) and GSTM1 (mu class) genes may be associated with an increased risk of cancer. Few studies have evaluated the relationship between GSTT1, GSTM1 and the risk of gastric cancer, as well as the potential interactions between these genetic markers and other risk factors of gastric cancer in the Chinese population. We conducted a case-control study with 143 cases with gastric cancer, 166 chronic gastritis (CG) cases and 433 cancer-free population controls from Yangzhong County, China. The epidemiological data were collected by a standard questionnaire for all of the subjects, and blood samples were obtained from 91 gastric cancer cases, 146 CG cases, and 429 controls. GSTT1 and GSTM1 genotypes were assayed by the PCR method, and Helicobacter pylori infection was measured by the ELISA method. Using logistic regression model in SAS, we assessed the independent effects of GSTT1 and GSTM1 null genotypes on the risk of gastric cancer and their potential interactions with other factors. The prevalence of GSTM1 null genotype was 48% in gastric cancer cases, 60% in CG patients, and 51% in controls. The prevalence of GSTT1 null genotype was 54% in gastric cancer cases, 48% in CG patients, and 46% in controls. After controlling for age, gender, education, pack-years of smoking, alcohol drinking, body mass index, H. pylori infection, and fruit and salt intake, the adjusted odds ratio (OR) for GSTT1 and gastric cancer was 2.50 (95% confidence interval (CI), 1.01-6.22). When gastric cancer cases were compared with CG patients, the adjusted OR for GSTT1 was 2.33 (95% CI, 0.75-7.25). However, GSTT1 null genotype was not associated with the risk of CG when using population controls. No obvious association was found between GSTM1 and the risk of both gastric cancer and CG. Our results suggest that GSTT1 null genotype may be associated with an increased risk of gastric cancer in a Chinese population.

The value of gallium-67 and thallium-201 whole-body and single-photon emission tomography images in dialysis-related beta 2-microglobulin amyloid

The aim of this study was to investigate the value of gallium-67 and thallium-201 whole-body and single-photon emission tomography (SPET) images in long-term dialysis patients in whom dialysis-related beta 2-microglobulin amyloid (beta 2-MA) was clinically suspected. Twenty-three patients who had received dialysis for at least 10 years were included in the study. A technetium-99m methylene diphosphonate (MDP) whole-body scan was performed in all of the patients. If there was any MDP accumulation in the articular and/or peri-articular region, 67Ga and 201Tl whole-body and SPET images were then acquired. If any 67Ga and/or 201Tl uptake was observed, a CT-guided biopsy was done. In those patients who had articular and/or peri-articular uptake of 99mTc MDP, 67Ga and/or 201Tl and who were pathologically proven to have beta 2-MA, 99mTc MDP, 67Ga and 201Tl whole-body scans and SPET were carried out again, both 3 months and 1 year after initiation of treatment. This served to evaluate the therapeutic effect and allowed comparison with the clinical findings. Of the 23 patients, eight had abnormal 99mTc MDP uptake. Among these eight, six had intense 99mTc MDP, 67Ga and 201Tl uptake in the articular and peri-articular regions before medication. Three months after the start of treatment, there were very marked decreases in uptake on both the 67Ga and 201Tl scans but less obvious changes in uptake of 99mTc-MDP. In comparison with the other clinical manifestations such as limitation in range of motion, the more the painful disability improved, the less was the uptake on both 67Ga and 201Tl scans. There were virtually no differences in uptake pattern between the three scans of each radiopharmaceutical obtained for each patient in both 3 months and 1 year after initial of treatment. It is concluded that 99mTc-MDP whole-body bone scan can both detect active and pre-existing inactive deposits of beta 2-MA. 67Ga and 201Tl scans are helpful to differentiate active from inactive deposits of beta 2-MA and to evaluate the therapeutic effect on these patients. SPET images are usually needed to distinguish articular and periarticular lesions from bone lesions.

Folding and binding cascades: dynamic landscapes and population shifts

Whereas previously we have successfully utilized the folding funnels concept to rationalize binding mechanisms (Ma B, Kumar S, Tsai CJ, Nussinov R, 1999, Protein Eng 12:713-720) and to describe binding (Tsai CJ, Kumar S, Ma B, Nussinov R, 1999, Protein Sci 8:1181-1190), here we further extend the concept of folding funnels, illustrating its utility in explaining enzyme pathways, multimolecular associations, and allostery. This extension is based on the recognition that funnels are not stationary; rather, they are dynamic, depending on the physical or binding conditions (Tsai CJ, Ma B, Nussinov R, 1999, Proc Natl Acad Sci USA 96:9970-9972). Different binding states change the surrounding environment of proteins. The changed environment is in turn expressed in shifted energy landscapes, with different shapes and distributions of populations of conformers. Hence, the function of a protein and its properties are not only decided by the static folded three-dimensional structure; they are determined by the distribution of its conformational substates, and in particular, by the redistributions of the populations under different environments. That is, protein function derives from its dynamic energy landscape, caused by changes in its surroundings.

Folding funnels and conformational transitions via hinge-bending motions

In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of "induced fit" binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels, a priori contain both the "open" and the "closed" conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes. This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield "domain swapping;" the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac repressor. Nonallosteric subunit transitions are also addressed, with some examples (aspartate receptor and BamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations.

Screening of protective antigens of Japanese encephalitis virus by DNA immunization: a comparative study with conventional viral vaccines

In this study, we evaluated the relative role of the structural and nonstructural proteins of the Japanese encephalitis virus (JEV) in inducing protective immunities and compared the results with those induced by the inactivated JEV vaccine. Several inbred and outbred mouse strains immunized with a plasmid (pE) encoding the JEV envelope protein elicited a high level of protection against a lethal JEV challenge similar to that achieved by the inactivated vaccine, whereas all the other genes tested, including those encoding the capsid protein and the nonstructural proteins NS1-2A, NS3, and NS5, were ineffective. Moreover, plasmid pE delivered by intramuscular or gene gun injections produced much stronger and longer-lasting JEV envelope-specific antibody responses than immunization of mice with the inactivated JEV vaccine did. Interestingly, intramuscular immunization of plasmid pE generated high-avidity antienvelope antibodies predominated by the immunoglobulin G2a (IgG2a) isotype similar to a sublethal live virus immunization, while gene gun DNA immunization and inactivated JEV vaccination produced antienvelope antibodies of significantly lower avidity accompanied by a higher IgG1-to-IgG2a ratio. Taken together, these results demonstrate that the JEV envelope protein represents the most critical antigen in providing protective immunity.

A non-radioactive polymerase chain reaction method for diagnosis of Machado-Joseph disease

Machado-Joseph disease (MJD)/spinocerebellar ataxia type 3 (SCA3) is caused by unstable CAG trinucleotide repeat expansion in the coding region of the MJD gene. In this study, we describe a non-radioactive polymerase chain reaction (PCR) method to detect the CAG repeat range of the MJD gene. This technique allows direct visualization of the PCR products on ethidium bromide-stained agarose gels within hours. In this study, genomic DNA samples isolated from peripheral lymphocytes, amniotic fluid cells, and chorionic villi were tested with two sets of commonly used MJD primers. PCR conditions were optimized, which resulted in clear visualization of both the primer sets on 3% agarose gels. Ten out of 25 candidate MJD patients have been identified with this method to date, with no false-positive or false-negative diagnoses. This simple, reliable, and cost-effective method can be used for patient diagnosis, pre-symptomatic diagnosis, and prenatal diagnosis.

Identification of five spinocerebellar ataxia type 2 pedigrees in patients with autosomal dominant cerebellar ataxia in Taiwan

OBJECTIVES

The autosomal dominant cerebellar ataxias (ADCAs) are a group of genetically diverse neurological conditions linked by progressive deterioration in balance and coordination. Spinocerebellar Ataxia Type 2 (SCA2) is one of the ADCAs and also belongs to a special group caused by the expansion of an unstable CAG repeat encoding a polyglutamine tract. We aimed to investigate the frequency of SCA2 mutation in the ataxia patients referred to the clinic.

MATERIALS AND METHODS

We screened 58 families with inherent cerebellar ataxia and 57 normal individuals by the use of radioactive genomic polymerase chain reaction (PCR) method. A simple non-radioactive PCR for rapid detection of the expanded SCA2 alleles via agarose gel electrophoresis was also employed.

RESULTS

Eight SCA2 affected patients and 1 at-risk individual in 5 unrelated SCA2 families were identified. The CAG repeats of normal alleles in the sample studied range in size from 16 to 30 repeat units, while those of SCA2 chromosomes are expanded to 34 to 49 repeat units. Our results also showed that unlike SCA 1 and SCA3/MJD, the size distribution of the normal alleles showed few polymorphisms, with the 22 repeat allele accounting for 90.1%. Homozygosity in normal individuals was 80.2%. No overlap in ataxin-2 allele size between normal and expanded chromosomes was observed.

CONCLUSION

This is the first report of the SCA2 gene distributions in the population of Taiwan. The SCA2 mutation accounts for 8.6% of ADCA type I families referred to us, intermediate between SCA1(1.7%) and SCA3/MJD (24%) of the ADCA type I families in our collection.

Does quantitative serologic testing for Helicobacter pylori predict peptic ulcer disease in cirrhosis?

BACKGROUND

Helicobacter Pylori is strongly associated with peptic ulcer disease. A correlation between high IgG serum antibody concentrations and a clinical diagnosis has been reported. It has been recognized that peptic ulcer disease occurs with increased frequency in cirrhosis. In this study, we attempted to establish a relation between the magnitude of serum IgG antibody to H pylori and the endoscopic diagnoses in H pylori-infected cirrhotic patients.

METHODS

All cirrhotic patients who had undergone esophagogastroduodenoscopy with a positive H pylori IgG serology and who did not receive anti-H pylori treatment or take medications noxious to the gastroduodenal mucosa were included in the study. H pylori IgG serology was determined by an enzyme-linked immunosorbent assay with values of greater than 50 units/mL being seropositive. The functional reserve of cirrhosis was classified by modified Pugh-Child criteria.

RESULTS

One hundred four seropositive cirrhotic patients were recruited. The serum IgG titers ranged from 51 to 1200 units/mL with a peak frequency at 50 to 99 units/mL (35. 6%). Statistical analysis did not reveal any relation between the quantitative H pylori IgG values and the endoscopic diagnoses, which included gastric ulcers, duodenal ulcers, gastroduodenal erosions, and normal findings.

CONCLUSIONS

In cirrhosis, the magnitude of H pylori IgG serology cannot be used to predict the presence or absence of peptic ulcer disease.

Porphyromonas gingivalis bacteremia and subhepatic abscess after renal transplantation: a case report

A uremic patient developed subhepatic abscess, Porphyromonas gingivalis bacteremia and cytomegalovirus viremia after a renal transplantation in mainland China. P. gingivalis infection has been reported to cause gingivitis and periodontitis. Bacteremia due to P. gingivalis, however, has not been reported in the literature. We report herein a case of subhepatic abscess and bacteremia due to P. gingivalis in a renal transplant recepient who was treated successfully with the well functioning renal graft.

Folding funnels and binding mechanisms

The long-held views on lock-and-key versus induced fit in binding arose from the notion that a protein exists in a single, most stable conformation, dictated by its sequence. However, in solution proteins exist in a range of conformations, which may be described by statistical mechanical laws and their populations follow statistical distributions. Upon binding, the equilibrium will shift in favor of the bound conformation from the ensemble of conformations around the bottom of the folding funnel. Hence here we extend the implications and the usefulness of the folding funnel concept to explain fundamental binding mechanisms.

Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding

We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers. A simple sequentially folded protein should, therefore, be less error prone and fold faster than a protein with a complex folding pattern.