Weighted simultaneous iterative reconstruction technique for single-axis tomography

Tomographic techniques play a crucial role in imaging methods such as transmission electron microscopy (TEM) due to their unique capabilities to reconstruct three-dimensional object information. However, the accuracy of the two standard tomographic reconstruction techniques, the weighted back-projection (W-BP) and the simultaneous iterative reconstruction technique (SIRT) is reduced under common experimental restrictions, such as limited tilt range or noise. We demonstrate that the combination of W-BP and SIRT leads to an improved tomographic reconstruction technique: the weighted SIRT. Convergence, resolution and reconstruction error of the W-SIRT are analyzed by a detailed analytical, numerical, and experimental comparison with established methods. Our reconstruction technique is not restricted to TEM tomography but can be applied to all problems sharing single axis imaging geometry.

Numerical Analysis of Cooling Air Systems in Film Blowing

Air rings, used today in film blowing systems, have been developed down the years through trial and error experiments. They represent the limiting factor concerning the efficiency of film blowing lines with respect to throughput and take-off speed. Numerical simulation of the cooling process in film blowing provides a tool for the design and optimization of future cooling systems. Individual process and geometric parameters can be changed interactively with the effects on flow and heat transfer processes being analysed and applied to similar situations. The knowledge acquired regarding the physical interactions in the cooling of blown film makes a targeted optimization possible. The purpose of this paper is to present the foundamentals for calculating turbulent air flows in blown film extrusion and, additionally, a model for complete FE-simulation of the flow and heat transfer processes. Furthermore, the achieved simulation results will be discussed.

Ovarian cancer stem cells

Because of its semi-solid character in dissemination and growth, advanced ovarian cancer with its hundreds of peritoneal tumor nodules and plaques appears to be an excellent in vivo model for studying the cancer stem cell hypothesis. The most important obstacle, however, is to adequately define and isolate these tumor-initiating cells endowed with the properties of anoikis-resistance and unlimited self-renewal. Until now, no universal single marker or marker constellation has been found to faithfully isolate (ovarian) cancer stem cells. As these multipotent cells are known to possess highly elaborated efflux systems for cytotoxic agents, these pump systems have been exploited to outline putative stem cells as a side-population (SP) via dye exclusion analysis. Furthermore, the cells in question have been isolated via flow cytometry on the basis of cell surface markers thought to be characteristic for stem cells.In the Vienna variant of the ovarian cancer cell line A2780 a proof-of-principle model with both a stable SP and a stable ALDH1A1+ cell population was established. Double staining clearly revealed that both cell fractions were not identical. Of note, A2780V cells were negative for expression of surface markers CD44 and CD117 (c-kit). When cultured on monolayers of healthy human mesothelial cells, green-fluorescence-protein (GFP)-transfected SP of A2780V exhibited spheroid-formation, whereas non-side-population (NSP) developed a spare monolayer growing over the healthy mesothelium. Furthermore, A2780V SP was found to be partially resistant to platinum. However, this resistance could not be explained by over-expression of the "excision repair cross-complementation group 1" (ERCC1) gene, which is essentially involved in the repair of platinated DNA damage. ERCC1 was, nonetheless, over-expressed in A2780V cells grown as spheres under stem cell-selective conditions as compared to adherent monolayers cultured under differentiating conditions. The same was true for the primary ovarian cancer cells B-57.In summary our investigations indicate that even in multi-passaged cancer cell lines hierarchic government of growth and differentiation is conserved and that the key cancer stem cell population may be composed of small overlapping cell fractions defined by various arbitrary markers.

One-year maintenance outcomes among patients with moderately-to-severely active ulcerative colitis who responded to induction therapy with adalimumab: subgroup analyses from ULTRA 2

BACKGROUND

Patients with moderately-to-severely active ulcerative colitis (UC) are unlikely to continue anti-TNF therapy in the absence of early therapeutic response.

AIM

To assess week 52 efficacy, safety and benefit/risk balance of adalimumab treatment in patients with moderately-to-severely active UC failing conventional therapy who achieved clinical response at week 8 in the 52-week ULTRA 2 trial.

METHODS

Patients randomised to adalimumab (160/80 mg, week 0/2; 40 mg, every other week thereafter) in ULTRA 2 who achieved clinical response at week 8 per partial Mayo score (Mayo score without endoscopy subscore) were assessed for week 52 clinical remission, clinical response, mucosal healing, steroid-free remission and steroid discontinuation rates, overall and by prior anti-TNF use. Benefit/risk balance for the overall ITT population (regardless of week 8 responder status) was assessed using 'net efficacy adjusted for risk' (NEAR) odds ratios. Safety was assessed using adverse event rates.

RESULTS

Of 248 adalimumab-treated patients, 123 (49.6%) achieved clinical response at week 8. Of these, 30.9%, 49.6%, and 43.1% achieved clinical remission, clinical response, and mucosal healing, respectively, at week 52. Of the week 8 responders using corticosteroids at baseline (N = 90), 21.1% achieved steroid-free remission and 37.8% were steroid-free at week 52. NEAR odds ratios indicated a positive benefit/risk balance for achievement of week 8 and week 52 response or remission without serious adverse events or serious infections. No safety concerns were identified.

CONCLUSIONS

Adalimumab treatment was associated with a positive benefit/risk balance in the overall population of patients with moderately-to-severely active ulcerative colitis in ULTRA 2; early response was predictive of a positive outcome at 1 year (NCT00408629).

Abstract P3-04-01: Protein pathway activation mapping of the I-SPY 1 biopsy specimens identifies new network focused drug targets for patients with triple negative tumors

Background: Identification of new therapies and predictive biomarkers is needed for patients with triple negative (TN) breast cancer. Elucidating pathway activation in cancer is critical as these proteins represent targets for many of the new molecular therapeutics and companion diagnostic markers. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane-based chemotherapy that provides longitudinal biopsy specimens and molecular and clinical/pathological characterization.

Methods: Tumor epithelium was procured by Laser Capture Microdissection from 149 pretreatment frozen biopsy specimens (T1) and 102 frozen biopsy specimens collected 1–4 days after first chemotherapy treatment (T2). Reverse Phase Protein Microarray was used to measure the activation of 39 and 100 signaling proteins in the T1 and T2 biopsies, respectively, including drug targets for Phase I-III and FDA cleared therapeutics. Associations between pathway activation and response to chemotherapy (RCB 0/1 vs. 2/3) and relapse-free survival (RFS) were evaluated for the triple-negative (TN) patient population at each time point and for changes between T1 and T2. Significance thresholds for response and RFS were as follows: Wilcoxon rank sum test p < 0.05; Cox proportional hazard model, likelihood ratio p < 0.05.

Results: We focused our analysis on protein changes in patients who had poor clinical outcomes (Table 1)

Abstract P3-04-02: Protein pathway activation mapping of I-SPY 1 biopsy specimens identifies new network focused drug targets for patients with HR+/HER2− tumors

Background: Profiling protein signaling activation in cancer is critical as these proteins represent targets for new molecular therapeutics. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane- based chemotherapy that longitudinally collected biopsy specimens and molecular and clinical/pathological characterization.

Methods: Tumor epithelium was procured by Laser Capture Microdissection from 149 pretreatment frozen biopsy specimens (T1) and 102 frozen biopsy specimens (T2, 1–4 days post-chemotherapy). Reverse Phase Protein Microarray technology was used to quantitatively measure the activation of 39 and 100 key signaling proteins in the T1 and T2 biopsies, respectively, including numerous drug targets for Phase I-III and FDA-cleared therapeutics. Associations between protein activation and response to chemotherapy (RCB 0/1 vs 2/3) and relapse-free survival (RFS) were evaluated for the HR+/HER2− patient population at each time point and for changes between T1 and T2. Significance thresholds for response and RFS were as follows: Wilcoxon rank sum test p < 0.05; Cox proportional hazard model, likelihood ratio p < 0.05.

Results: We focused our analysis on protein changes in patients who had poor clinical outcomes (Table 1)

Dosimetric consequences of breath-hold respiration in conformal radiotherapy of esophageal cancer

The objective of this paper is to study the dosimetric impact of respiratory gated radiotherapy in locally advanced esophageal carcinomaand to define the optimal respiratory phase for this treatment. The study included 8 consecutive patients with squamous-cell carcinoma (SCC) or histologically proved adenocarcinoma, for both at least T3-T4 NX or TX N1 M0 stage. Informed consent was obtained before beginning the study. Three spiral scans were performed in breath-hold respiration: one acquisition in end expiration (EBH), one in end inspiration (IBH) and one in deep inspiration breathhold (DIBH); and one acquisition was performed in Free Breathing (FB). A 3 mm-margin was defined as Internal Target Volume (ITV) on FB CT-scan. No ITV was applied on EBH, IBH and DIBH CT-scan. Target volumes were analyzed and we performed dosimetric comparisons on DVH data of each CT-scan for PTV and Organs at Risk (OAR) (Conformity Index, V(dose), D(mean), Equivalent Uniform Dose). DIBH and IBH correlated with a 32% (p=0.77) and 20% (p=0.52) decrease in lung V(20) respectively as compared to FB (13.5%and 15.6% respectively versus 19.9%). DIBH and IBH correlated with a 25% (p=0.25) and 17% (p=0.39) decrease in cardiac V(40) respectively, as compared with FB (16.9% and 18.9% respectively versus 22.7%). For spinal cord irradiation, the minimum dose was obtained in IBH (36.5 Gy). Conformal radiotherapy with respiratory gating for esophageal cancer decreases the irradiated dose to OAR. We suggest that DIBH technique should be used when irradiation is performed using the spirometric system. In the Tidal Volume, the inspiration phase is the most favourable and should be chosen for irradiation with a free breathing gating system.

P4-09-19: PCNA+ Tumor Associated Macrophages Are Associated with M1 and M2 Gene Expression, and Confer Poor Prognosis in the Absence of Anti-Tumor Immune Environment

Background

Tumor associated macrophages (TAMs) promote breast tumor progression through the production of angiogenic factors, stromal breakdown factors, and the suppression of adaptive immunity. TAMs are recruited from the circulation to the tumor site, and can undergo a spectrum of phenotypic changes, with two contrasting activation states described in the literature: the M1 anti-tumoral and M2 pro-tumoral phenotypes. We previously identified a population of PCNA+ TAMs associated with high grade, hormone receptor (HR) negative tumors with poor outcomes. We hypothesized that high PCNA+ TAMs would be associated with expression of M2 related genes.

Methods

We used immunohistochemistry to measure PCNA+ TAM levels (double positive for PCNA and CD68) in 135 invasive breast cancer cases from the I-SPY 1 Trial, a prospective neoadjuvant trial with serial core biopsies and gene array data. We developed gene-sets representing M1 related, M2 related, and anti-tumoral immune response (represented by cytotoxic T cells and MHC Class II) genes based on literature review. We compared PCNA+ TAM levels, expression of these gene-sets, and outcomes.

Results

Higher than mean PCNA+ TAM counts were associated with increasing grade (p < 0.001), HR negativity (p < 0.001), and decreased recurrence free survival (RFS, p = 0.05). Among subjects who had a pathologic complete response (pCR), there was no difference in RFS between those with high versus low PCNA+ TAMs. Among subjects without pCR, those with high PCNA+ TAMs had significantly worse RFS than those with low PCNA+ TAMs (p = 0.0028). In the 95 subjects with both PCNA+ TAM results and gene expression arrays available, high PCNA+ TAM levels were associated with more M1 than M2 related genes. The gene-set representing anti-tumoral immune environment was not by itself associated with RFS. However, those subjects with both high PCNA+ TAMs and the absence of anti-tumoral immune response gene expression had significantly worse RFS than those with high PCNA+ TAMs but the presence of anti-tumoral immune related genes (p = 0.01).

Evolutionary genetics of an S-like polymorphism in Papaveraceae with putative function in self-incompatibility

BACKGROUND

Papaver rhoeas possesses a gametophytic self-incompatibility (SI) system not homologous to any other SI mechanism characterized at the molecular level. Four previously published full length stigmatic S-alleles from the genus Papaver exhibited remarkable sequence divergence, but these studies failed to amplify additional S-alleles despite crossing evidence for more than 60 S-alleles in Papaver rhoeas alone.

METHODOLOGY/PRINCIPAL FINDINGS

Using RT-PCR we identified 87 unique putative stigmatic S-allele sequences from the Papaveraceae Argemone munita, Papaver mcconnellii, P. nudicuale, Platystemon californicus and Romneya coulteri. Hand pollinations among two full-sib families of both A. munita and P. californicus indicate a strong correlation between the putative S-genotype and observed incompatibility phenotype. However, we also found more than two S-like sequences in some individuals of A. munita and P. californicus, with two products co-segregating in both full-sib families of P. californicus. Pairwise sequence divergence estimates within and among taxa show Papaver stigmatic S-alleles to be the most variable with lower divergence among putative S-alleles from other Papaveraceae. Genealogical analysis indicates little shared ancestral polymorphism among S-like sequences from different genera. Lack of shared ancestral polymorphism could be due to long divergence times among genera studied, reduced levels of balancing selection if some or all S-like sequences do not function in incompatibility, population bottlenecks, or different levels of recombination among taxa. Preliminary estimates of positive selection find many sites under selective constraint with a few undergoing positive selection, suggesting that self-recognition may depend on amino acid substitutions at only a few sites.

CONCLUSIONS/SIGNIFICANCE

Because of the strong correlation between genotype and SI phenotype, sequences reported here represent either functional stylar S-alleles, tightly linked paralogs of the S-locus or a combination of both. The considerable complexity revealed in this study shows we have much to learn about the evolutionary dynamics of self-incompatibility systems.