A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens

Because off-target effects hamper interpretation and validation of RNAi screens, we developed a bioinformatics method, Genome-wide Enrichment of Seed Sequence matches (GESS), to identify candidate off-targeted transcripts from direct analysis of primary screening data. GESS identified a prominent off-targeted transcript in several screens, including MAD2 in a screen for components of the spindle assembly checkpoint. We demonstrate how incorporation of the results of GESS analysis can enhance the validation rate in RNAi screens

Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks

A balance between Six2-dependent self-renewal and canonical Wnt signaling-directed commitment regulates mammalian nephrogenesis. Intersectional studies using chromatin immunoprecipitation and transcriptional profiling identified direct target genes shared by each pathway within nephron progenitors. Wnt4 and Fgf8 are essential for progenitor commitment; cis-regulatory modules flanking each gene are co-bound by Six2 and β-catenin, and dependent on conserved Lef/Tcf binding sites for activity. In vitro and in vivo analyses suggest that Six2 and Lef/Tcf factors form a regulatory complex that promotes progenitor maintenance while entry of β-catenin into this complex promotes nephrogenesis. Alternative transcriptional responses associated with Six2 and β-catenin co-binding events occur through non-Lef/Tcf DNA binding mechanisms highlighting the regulatory complexity downstream of Wnt signaling in the developing mammalian kidney

Modified cardiovascular SOFA score in sepsis: development and internal and external validation

Background : The Sepsis-3 criteria introduced the system that uses the Sequential Organ-Failure Assessment (SOFA) score to define sepsis. The cardiovascular SOFA (CV SOFA) scoring system needs modification due to the change in guideline-recommended vasopressors. In this study, we aimed to develop and to validate the modified CV SOFA score. Methods : We developed, internally validated, and externally validated the modified CV SOFA score using the suspected infection cohort, sepsis cohort, and septic shock cohort. The primary outcome was 28-day mortality. The modified CV SOFA score system was constructed with consideration of the recently recommended use of the vasopressor norepinephrine with or without lactate level. The predictive validity of the modified SOFA score was evaluated by the discrimination for the primary outcome. Discrimination was assessed using the area under the receiver operating characteristics curve (AUC). Calibration was assessed using the calibration curve. We compared the prognostic performance of the original CV/total SOFA score and the modified CV/total SOFA score to detect mortality in patients with suspected infection, sepsis, or septic shock. Results : We identified 7,393 patients in the suspected cohort, 4038 patients in the sepsis cohort, and 3,107 patients in the septic shock cohort in seven Korean emergency departments (EDs). The 28-day mortality rates were 7.9%, 21.4%, and 20.5%, respectively, in the suspected infection, sepsis, and septic shock cohorts. The model performance is higher when vasopressor and lactate were used in combination than the vasopressor only used model. The modified CV/total SOFA score was well-developed and internally and externally validated in terms of discrimination and calibration. Predictive validity of the modified CV SOFA was significantly higher than that of the original CV SOFA in the development set (0.682 vs 0.624, p < 0.001), test set (0.716 vs 0.638), and all other cohorts (0.648 vs 0.557, 0.674 vs 0.589). Calibration was modest. In the suspected infection cohort, the modified model classified more patients to sepsis (66.0 vs 62.5%) and identified more patients at risk of septic mortality than the SOFA score (92.6 vs 89.5%). Conclusions : Among ED patients with suspected infection, sepsis, and septic shock, the newly-developed modified CV/total SOFA score had higher predictive validity and identified more patients at risk of septic mortality.National Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (NRF2020R1A2C3004508) to Kyuseok Kim. National Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (NRF2020R1F1A1052908) to Tae Gun Shin

Comparison of measured and Monte Carlo-calculated peak scatter factors for 10X10 cm2 field size in 6 MV and 18 MV photon beams

The purpose of this thesis is to measure the peak scatter factors (PSFs) for a 10X10 cm2 field size in 6 MV and 18 MV photon beams using a Solid WaterTM phantom and build-up caps made of LuciteTM, aluminum, brass, and copper. The PSF for the 10X10 cm2 field size was first determined by extrapolating the measured normalized peak scatter factor (NPSF) to 0X0 cm2 field size. The extrapolated NPSF was the reciprocal of the PSF(10, hv). The measured PSF(10, hv) was then compared to the PSF determined with Monte Carlo methods. We used Monte Carlo methods to investigate the dependence of the measured signal on the build-up cap material. This was carried out by calculating the primary and scatter dose contributions to the measured signal in the air cavity of the ionization chamber. Based on Monte Carlo studies, a factor was calculated to obtain the PSF from the measurements.L'objectif de cette thèse est d'obtenir le peak scatter factor (PSF) de faisceaux de photons de 6 et 18 MV. Les champs utilisés étaient de 10x10 cm^2 et les mesures furent effectuées à l'aide d'un fantôme de Solid Water tm couplé à des capuchons d'accumulation fait de Lucite tm, d'aluminium, de laiton et de cuivre. Le PSF du champ de 10x10cm2 a été déterminé en extrapolant le peak scatter factor normalisé (NPSF) d'un champ de 0x0cm2. Le NPSF extrapolé correspond à la réciproque du PSF(10,hv). Le PSF(10, hv) fut ensuite comparé à celui déterminé à l'aide de méthodes Monte Carlo. Les méthodes Monte Carlo furent utilisées pour étudier la dépendance entre le signal mesuré et le matériel du capuchon d'accumulation. Ceci fut accompli en décomposant le signal provenant de la cavité de la chambre d'ionisation en dose primaire et diffusée. Un facteur liant le PSF et les mesures fut calculé à l'aide d'études Monte Carlo

Development of radiation dosimetry techniques for non-standard beam radiotherapy

Use of composite non-uniform radiation fields, which consist of a multitude of small fields, is very common in modern radiotherapy techniques. The conventional reference dosimetry protocols, however, use a 10 × 10 cm2 field as the reference machine calibration condition. The purpose of this work is to develop new, direct absorbed dose calibration methods for modern radiotherapy techniques that use static and composite nonstandard fields. An IAEA-AAPM international working group [Med. Phys. 35:5179–5186 (2008)] proposed a new formalism and introduced two intermediate fields, machine specific reference (msr) field fmsr and plan-class specific reference (pcsr) field fpcsr, for reference dosimetry of static and composite nonstandard fields, respectively. In the new formalism, correction factors which account for the difference in chamber calibration conditions between the reference field and msr field k^fmsr,fref_Qmsr,Q , pcsr field k^fpcsr,fref_Qpcsr,Q or clinical field k^fclin,fref_Qclin,Q were defined. This thesis focuses on the characterization of these correction factors. The dosimetry techniques to accurately measure the absorbed dose to water in nonstandard fields were established using four different radiation detectors, for which collecting volumes are radiologically water-equivalent. The characteristics of each radiation detector response were thoroughly investigated. Dose measurementin a nonstandard field normalized to that in the reference 10 × 10 cm2 field can be performed with an uncertainty of 0.2–0.3% when the dose distribution in the reference measurement region is homogeneous. Correction factors k^fmsr,fref_Qmsr,Q and k^fpcsr,fref_Qpcsr,Q were measured for one static nonstandard field and two different composite nonstandard fields, respectively, using different types of air-filled ionization chambers. Using the established dosimetry techniques, the k^fpcsr,fref_Qpcsr,Q were measured for different composite nonstandard fields which deliver various dose distributions in the reference measurement region. This work proved that the values of k^fpcsr,fref_Qpcsr,Q depend on the dose heterogeneity over the chamber collecting volume. Based on the measurement results, guidelines were suggested to select a new intermediate field for reference dosimetry of composite nonstandard fields. Finally, the IAEA-AAPM new formalism with values of k^fclin,fref_Qclin,Q obtained by experiments and MC methods was applied to reference dose measurement of clinical composite nonstandard fields using a calibrated air-filled ionization chamber. The corrected measured dose for each clinical field was compared with dose calculated using clinical treatment planning software or Monte Carlo methods. It was found that the accurate positioning of the reference detector and air-filled ionization chamber becomes more important when the dose heterogeneity in the reference measurement region increases. In conclusion, this thesis provides a method for accurate dose measurements in static and composite nonstandard fields. This work will help pave the way to improve the dosimetric consistency in these dynamic modern radiotherapy techniques.L'utilisation de champs de rayonnement composes non uniformes, qui consistent en une multitude de petits champs, est tres commune dans les techniques modernes de radiotherapie. Cependant, les protocoles de dosimetrie de reference conventionnels utilisent un champ standard de 10×10 cm2 pour calibrer les appareils. Le but de ce travail est de developper de nouvelles methodes de calibration de la dose absorbee pour des techniques modernes de radiotherapie, ce en utilisant autant des champs statiques que des champs composes non standards. Le groupe de travail AIEA-AAPM a propose un nouveau formalisme qui introduit deux champs intermediaires, soient le champ specifique a l'appareil (fmsr) et le champ specifique au plan de traitement (fpcsr), ce pour la dosimetrie de reference des champs statiques et des champs composes non standards, respectivement. Dans ce nouveau formalisme, des facteurs de corrections ontete definis afin de tenir compte des conditions de calibration de la chambre qui different entre le champ de reference et les champs fmsr, fpcsr ainsi que les champs cliniques (fclin). Ces facteurs sont respectivement d´efinis ainsi: k^fmsr,fref_Qmsr,Q , k^fpcsr,fref_Qpcsr,Q et k^fclin,fref_Qclin,Q . Cette these comporte sur la caracterisation exprimentale de ces facteurs de correction. Les techniques de dosimetrie visant a mesurer precisement la dose absorbe dans l'eau pour des champs non standards ont ete etablies en utilisant quatre differents detecteurs de radiation, chacun ayant un volume sensible radiologiquement equivalent a l'eau. Les caracteristiques de chaque detecteur ont ete approfondies. Les mesures de dose dans un champ non standard normalise a un champ de reference de 10×10 cm2 peuvent etre obtenues avec une incertitude de 0.2-0.3% lorsque la distribution de dose dans la region de mesure de reference est homogene. Les facteurs de correction k^fmsr,fref_Qmsr,Q et k^fpcsr,fref_Qpcsr,Q ont ete mesures pour un champ statique non standard et pour deux differents champs composes non standards, respectivement, en utilisant differents types de chambres d'ionisation a air. En utilisant les techniques de dosimetries etablies, les k^fpcsr,fref_Qpcsr,Q ont ete mesures pour plusieurs champs composes non standards qui produisent diff´erentes distributions de dose dans la region de mesure de reference. Ce travail demontre que les valeurs de k^fpcsr,fref_Qpcsr,Q d´ependent de l'heterogeneite de la dose dans le volume sensible de la chambre. Base sur les resultats des mesures, des lignes de conduite sont suggereespour determiner un champ intermediaire necessaire a la dosimetrie de reference des champs composes non standards. Finalement, le nouveau formalisme de l'AIEA-AAPM a ete applique a des mesures de dose de reference de champs composes non standards cliniques avec les valeurs k^fclin,fref_Qclin,Q obtenues experimentalement et avec des methodes Monte Carlo pour une chambre d'ionisation a air etalonnee. La dose mesuree et corrigee pourchacun des champs a ete comparee avec la dose calculee en utilisant un logiciel de planification de traitement ou des methodes Monte Carlo. Il a ete determine que la precision du positionnement du detecteur de reference ainsi que celui de la chambre d'ionisation a air devient plus important lorsque l'heterogeneite de dose dans la regionde mesure augmente. En conclusion, cette these fournit une methode precise de mesure de la dose absorbee pour des champs statiques et des champs compose non standards. Ce travail aidera a ameliorer la coherence des methodes dosimetrique appliquables aux techniques modernes de radiotherapie

Characterization and evaluation of an integrated quality monitoring system for online quality assurance of external beam radiation therapy

Abstract Purpose The aim of this work was to comprehensively evaluate a new large field ion chamber transmission detector, Integral Quality Monitor (IQM), for online external photon beam verification and quality assurance. The device is designed to be mounted on the linac accessory tray to measure and verify photon energy, field shape, gantry position, and fluence before and during patient treatment. Methods: Our institution evaluated the newly developed ion chamber's effect on photon beam fluence, response to dose, detection of photon fluence modification, and the accuracy of the integrated barometer, thermometer, and inclinometer. The detection of photon fluence modifications was performed by measuring 6 MV with fields of 10 cm × 10 cm and 1 cm × 1 cm “correct” beam, and then altering the beam modifiers to simulate minor and major delivery deviations. The type and magnitude of the deviations selected for evaluation were based on the specifications for photon output and MLC position reported in AAPM Task Group Report 142. Additionally, the change in ion chamber signal caused by a simulated IMRT delivery error is evaluated. Results: The device attenuated 6 MV, 10 MV, and 15 MV photon beams by 5.43 ± 0.02%, 4.60 ± 0.02%, and 4.21 ± 0.03%, respectively. Photon beam profiles were altered with the IQM by < 1.5% in the nonpenumbra regions of the beams. The photon beam profile for a 1 cm × 1 cm2 fields were unchanged by the presence of the device. The large area ion chamber measurements were reproducible on the same day with a 0.14% standard deviation and stable over 4 weeks with a 0.47% SD. The ion chamber's dose–response was linear (R2 = 0.99999). The integrated thermometer agreed to a calibrated thermometer to within 1.0 ± 0.7°C. The integrated barometer agreed to a mercury barometer to within 2.3 ± 0.4 mmHg. The integrated inclinometer gantry angle measurement agreed with the spirit level at 0 and 180 degrees within 0.03 ± 0.01 degrees and 0.27 ± 0.03 at 90 and 270 degrees. For the collimator angle measurement, the IQM inclinometer agreed with a plum‐bob within 0.3 ± 0.2 degrees. The simulated IMRT error increased the ion chamber signal by a factor of 11–238 times the baseline measurement for each segment. Conclusions: The device signal was dependent on variations in MU delivered, field position, single MLC leaf position, and nominal photon energy for both the 1 cm × 1 cm and 10 cm × 10 cm fields. This detector has demonstrated utility repeated photon beam measurement, including in IMRT and small field applications