COMPREHENSIVE CALCULATION-BASED IMRT QA USING R&V DATA, TREATMENT RECORDS, AND A SECOND TREATMENT PLANNING SYSTEM

Purpose: Traditional patient-specific IMRT QA measurements are labor intensive and consume machine time. Calculation-based IMRT QA methods typically are not comprehensive. We have developed a comprehensive calculation-based IMRT QA method to detect uncertainties introduced by the initial dose calculation, the data transfer through the Record-and-Verify (R&V) system, and various aspects of the physical delivery. Methods: We recomputed the treatment plans in the patient geometry for 48 cases using data from the R&V, and from the delivery unit to calculate the “as-transferred” and “as-delivered” doses respectively. These data were sent to the original TPS to verify transfer and delivery or to a second TPS to verify the original calculation. For each dataset we examined the dose computed from the R&V record (RV) and from the delivery records (Tx), and the dose computed with a second verification TPS (vTPS). Each verification dose was compared to the clinical dose distribution using 3D gamma analysis and by comparison of mean dose and ROI-specific dose levels to target volumes. Plans were also compared to IMRT QA absolute and relative dose measurements. Results: The average 3D gamma passing percentages using 3%-3mm, 2%-2mm, and 1%-1mm criteria for the RV plan were 100.0 (σ=0.0), 100.0 (σ=0.0), and 100.0 (σ=0.1); for the Tx plan they were 100.0 (σ=0.0), 100.0 (σ=0.0), and 99.0 (σ=1.4); and for the vTPS plan they were 99.3 (σ=0.6), 97.2 (σ=1.5), and 79.0 (σ=8.6). When comparing target volume doses in the RV, Tx, and vTPS plans to the clinical plans, the average ratios of ROI mean doses were 0.999 (σ=0.001), 1.001 (σ=0.002), and 0.990 (σ=0.009) and ROI-specific dose levels were 0.999 (σ=0.001), 1.001 (σ=0.002), and 0.980 (σ=0.043), respectively. Comparing the clinical, RV, TR, and vTPS calculated doses to the IMRT QA measurements for all 48 patients, the average ratios for absolute doses were 0.999 (σ=0.013), 0.998 (σ=0.013), 0.999 σ=0.015), and 0.990 (σ=0.012), respectively, and the average 2D gamma(5%-3mm) passing percentages for relative doses for 9 patients was were 99.36 (σ=0.68), 99.50 (σ=0.49), 99.13 (σ=0.84), and 98.76 (σ=1.66), respectively. Conclusions: Together with mechanical and dosimetric QA, our calculation-based IMRT QA method promises to minimize the need for patient-specific QA measurements by identifying outliers in need of further review

Late toxicity and biochemical recurrence after external-beam radiotherapy combined with permanent-source prostate brachytherapy

BACKGROUND The combination of external-beam radiotherapy and brachytherapy is used commonly to treat men with prostate cancer. In this analysis, the authors examined the rate of biochemical recurrence (BR) and late grade ≥3 genitourinary (GU) and gastrointestinal (GI) toxicity after treatment with external-beam radiotherapy and brachytherapy in a multiinstitutional, cooperative group setting. METHODS All eligible patients received external-beam radiotherapy (45 Gray [Gy] in 25 fractions) followed 2 to 6 weeks later by an interstitial implant using iodine-125 to deliver an additional 108 Gy. BR was defined in 2 ways: according to the American Society for Therapeutic Radiology and Oncology (ASTRO) Consensus Definition (ACD) and according to the Phoenix definition (PD) (prostate-specific antigen nadir +2 ng/mL). The Radiation Therapy Oncology Group(RTOG)/European Organization for Research and Treatment of Cancer late radiation morbidity scoring system was used to grade all toxicity. RESULTS One hundred thirty-eight patients were enrolled, and 130 were eligible for the current analysis. The median follow-up for surviving patients was 49 months (range, 20–60 months). The 48-month estimate of late grade ≥3 GU/GI toxicity was 15% (95% confidence interval [95% CI], 8–21%), and the 48-month estimate of BR was 19% (95% CI, 12–26%) and 14% (95% CI, 8–20%) according to the ACD and PD, respectively. CONCLUSIONS The morbidity observed in this multiinstitutional, cooperative group study was slightly higher than that reported in recent RTOG studies using brachytherapy alone or high-dose external-beam radiotherapy. The BR rate observed in this report was similar to that observed with high-dose external-beam radiotherapy alone in similar patients. Cancer 2007. © 2007 American Cancer Society.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55987/1/22560_ftp.pd

Effect of anatomic motion on proton therapy dose distributions in prostate cancer treatment

Purpose: To determine the dosimetric impact of interfraction anatomic movements in prostate cancer patients receiving proton therapy. Methods and Materials: For each of the 10 patients studied, 8 computed tomography (CT) scans were selected from sets of daily setup CT images that were acquired from a cohort of prostate cancer patients. The images were acquired in the treatment room using the CT-on-rails system. First, standard proton therapy and intensity-modulated radiation therapy (IMRT) plans were designed for each patient using standard modality-specific methods. The images, the proton plan, and the IMRT plan were then aligned to the eight CT images based on skin marks. The doses were recalculated on these eight CT images using beam from the standard plans. Second, the plans were redesigned and evaluated assuming a smaller clinical target volume to planning target volume margin (3 mm). The images and the corresponding plans were then realigned based on the center of volume of the prostate. Dose distributions were evaluated using isodose displays, dose-volume histograms, and target coverage. Results: For the skin-marker alignment method, 4 of the 10 IMRT plans were deficient, whereas 3 of 10 proton plans were compromised. For the alignment method based on the center of volume of the prostate, only the proton plan for 1 patient was deficient, whereas 3 of the 10 IMRT plans were suboptimal. Conclusion: A comparison of passively scattered proton therapy and highly conformal IMRT plans for prostate cancer revealed that the dosimetric impact of interfractional anatomic motions was similar for both modalities. © 2007 Elsevier Inc. All rights reserved

Open-book examination in analytical chemistry: A valuable approach that promotes inclusivity in education, as seen by students

An open-book examination is a valuable approach that promotes inclusivity in education by placing greater emphasis on critical thinking, analysis, and the practical application of knowledge, rather than mere rote memorization. It enables students to consult the course materials, textbooks, and additional resources during the exam, thus creating an equitable platform for all learners. This brief communication delves into the students’ perception of open-book examinations within the realm of analytical chemistry, a subject taught as part of the undergraduate chemistry programme. Both surveys and individual interviews conducted by the researchers were used in a complementary way as methods for data collection. Thematic and content analysis of surveys and interview outcomes were subsequently undertaken. By exploring the viewpoints, we gained valuable insights into the advantages and challenges associated with implementing open-book assessments in this specific field. This article was published open access under a CC BY licence: https://creativecommons.org/licences/by/4.0 . </jats:p

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein

© 2006 Davids et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The definitive version was published in PLoS ONE 1 (2006): e44, doi:10.1371/journal.pone.0000044.Since the Giardia lamblia cyst wall is necessary for survival in the environment and host infection, we tested the hypothesis that it contains proteins other than the three known cyst wall proteins. Serial analysis of gene expression during growth and encystation revealed a gene, “HCNCp” (High Cysteine Non-variant Cyst protein), that was upregulated late in encystation, and that resembled the classic Giardia variable surface proteins (VSPs) that cover the trophozoite plasmalemma. HCNCp is 13.9% cysteine, with many “CxxC” tetrapeptide motifs and a transmembrane sequence near the C-terminus. However, HCNCp has multiple “CxC” motifs rarely found in VSPs, and does not localize to the trophozoite plasmalemma. Moreover, the HCNCp C-terminus differed from the canonical VSP signature. Full-length epitope-tagged HCNCp expressed under its own promoter was upregulated during encystation with highest expression in cysts, including 42 and 21 kDa C-terminal fragments. Tagged HCNCp targeted to the nuclear envelope in trophozoites, and co-localized with cyst proteins to encystation-specific secretory vesicles during encystation. HCNCp defined a novel trafficking pathway as it localized to the wall and body of cysts, while the cyst proteins were exclusively in the wall. Unlike VSPs, HCNCp is expressed in at least five giardial strains and four WB subclones expressing different VSPs. Bioinformatics identified 60 additional large high cysteine membrane proteins (HCMp) containing ≥20 CxxC/CxC's lacking the VSP-specific C-terminal CRGKA. HCMp were absent or rare in other model or parasite genomes, except for Tetrahymena thermophila with 30. MEME analysis classified the 61 gHCMp genes into nine groups with similar internal motifs. Our data suggest that HCNCp is a novel invariant cyst protein belonging to a new HCMp family that is abundant in the Giardia genome. HCNCp and the other HCMp provide a rich source for developing parasite-specific diagnostic reagents, vaccine candidates, and subjects for further research into Giardia biology

Establishing the feasibility of the dosimetric compliance criteria of RTOG 1308: phase III randomized trial comparing overall survival after photon versus proton radiochemotherapy for inoperable stage II-IIIB NSCLC.

BACKGROUND: To establish the feasibility of the dosimetric compliance criteria of the RTOG 1308 trial through testing against Intensity Modulation Radiation Therapy (IMRT) and Passive Scattering Proton Therapy (PSPT) plans. METHODS: Twenty-six lung IMRT and 26 proton PSPT plans were included in the study. Dose Volume Histograms (DVHs) for targets and normal structures were analyzed. The quality of IMRT plans was assessed using a knowledge-based engineering tool. RESULTS: Most of the RTOG 1308 dosimetric criteria were achieved. The deviation unacceptable rates were less than 10 % for most criteria; however, a deviation unacceptable rate of more than 20 % was computed for the planning target volume minimum dose compliance criterion. Dose parameters for the target volume were very close for the IMRT and PSPT plans. However, the PSPT plans led to lower dose values for normal structures. The dose parameters in which PSPT plans resulted in lower values than IMRT plans were: lung V5Gy (%) (34.4 in PSPT and 47.2 in IMRT); maximum spinal cord dose (31.7 Gy in PSPT and 43.5 Gy in IMRT); heart V5Gy (%) (19 in PSPT and 47 in IMRT); heart V30Gy (%) (11 in PSPT and 19 in IMRT); heart V45Gy (%) (7.8 in PSPT and 12.1 in IMRT); heart V50% (Gy) (7.1 in PSPT and 9.8 in IMRT) and mean heart dose (7.7 Gy in PSPT and 14.9 Gy in IMRT). CONCLUSIONS: The revised RTOG 1308 dosimetric compliance criteria are feasible and achievable

Transcriptome analyses of the Giardia lamblia life cycle

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Molecular and Biochemical Parasitology 174 (2010): 62-65, doi:10.1016/j.molbiopara.2010.05.010.We quantified mRNA abundance from 10 stages in the Giardia lamblia life cycle in vitro using Serial Analysis of Gene Expression (SAGE). 163 abundant transcripts were expressed constitutively. 71 transcripts were upregulated specifically during excystation and 42 during encystation. Nonetheless, the transcriptomes of cysts and trophozoites showed major differences. SAGE detected co-expressed clusters of 284 transcripts differentially expressed in cysts and excyzoites and 287 transcripts in vegetative trophozoites and encysting cells. All clusters included known genes and pathways as well as proteins unique to Giardia or diplomonads. SAGE analysis of the Giardia life cycle identified a number of kinases, phosphatases, and DNA replication proteins involved in excystation and encystation, which could be important for examining the roles of cell signaling in giardial differentiation. Overall, these data pave the way for directed gene discovery and a better understanding of the biology of Giardia lamblia.BJD, DSR, and FDG were supported by NIH grants AI42488, GM61896, DK35108, and AI051687. DP and SGS were supported by grants from the Swedish Natural Science Research Council, the Swedish Medical Research Council, and the Karolinska Institutet. AGM, SRB, SPP, and MJC were supported by NIH grant AI51089 and by the Marine Biological Laboratory’s Program in Global Infectious Diseases, funded by the Ellison Medical Foundation

Protein phosphatase 2A plays a crucial role in Giardia lamblia differentiation

Author Posting. © The Authors, 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Molecular and Biochemical Parasitology 152 (2007): 80-89, doi:10.1016/j.molbiopara.2006.12.001.The ability of Giardia lamblia to undergo two distinct differentiations in response to physiologic stimuli is central to its pathogenesis. The giardial cytoskeleton changes drastically during encystation and excystation. However, the signal transduction pathways mediating these transformations are poorly understood. We tested the hypothesis that PP2A, a highly conserved serine/threonine protein phosphatase, might be important in giardial differentiation. We found that in vegetatively growing trophozoites, gPP2A-C protein localizes to basal bodies/centrosomes, and to cytoskeletal structures unique to Giardia: the ventral disk, and the dense rods of the anterior, posterior-lateral, and caudal flagella. During encystation, gPP2A-C protein disappears from only the anterior flagellar dense rods. During excystation, gPP2A-C localizes to the cyst wall in excysting cysts but is not found in the wall of cysts with emerging excyzoites. Transcriptome and immunoblot analyses indicated that gPP2A-C mRNA and protein are upregulated in mature cysts and during the early stage of excystation that models passage through the host stomach. Stable expression of gPP2A-C antisense RNA did not affect vegetative growth, but strongly inhibited the formation of encystation secretory vesicles (ESV) and water-resistant cysts. Moreover, the few cysts that formed were highly defective in excystation. Thus, gPP2A-C localizes to universal cytoskeletal structures and to structures unique to Giardia. It is also important for encystation and excystation, crucial giardial transformations that entail entry into and exit from dormancy.This work was funded by NIH grants GM61896, AI51687, AI42488, and DK35108. Dr. A.G. McArthur was supported by NIH grant AI51089 and the Marine Biological Laboratory’s Program in Global Infectious Diseases, funded by the Ellison Medical Foundation