Citations

Abstract Background Dose‐driven continuous scanning (DDCS) is a type of beam delivery in Hitachi pencil beam scanning (PBS) particle therapy system. Particle beam is irradiated continuously between spots to achieve a higher effective dose rate and a shorter beam delivery time. The beam is only turned off at break spots, the end of a treatment layer and during spill change. The break spot is a unique feature of the DDCS introduced by the treatment planning system (TPS) to interrupt continuous scanning. DDCS separates the dose delivery of a spot into a move dose and stop dose components. The move dose is controlled by the scanning speed and beam current, while the stop dose delivers the remaining monitor units (MUs). Hence, rigorous quality assurance (QA) of the scanning speed and functionality of break spot are required to ensure safe and successful DDCS delivery. Purpose We aim to report for the first time the QA methodology and result for DDCS, focusing on the scanning speed and break spot validation. Methods A rectangular spiral irradiation pattern with different degree of break spots were irradiated on a 2D strip ionization chamber (CROSSmini) detector using 50 time resolution to validate the break spots. Four methods of measuring scanning speeds were proposed. Using a spiral irradiation pattern, methods one and two applied linear regression to the scanning time measured by the CROSSmini for different inter‐spot distances, with measurements taken at sampling rates of 5 and 20 kHz, respectively. Methods three and four measured the scanning time of single inter‐spot distances in the X and Y directions. Method three measured the scanning time with the CROSSmini while method four measured the rise and fall time of the scanning magnet (SCM) current. All measurements were performed with 70.2, 150.2 and 228.7 MeV proton beam energies and three different beam currents of 8, 14 and 20 MU/s. Lastly, the scanning speed tolerance limit was calculated analytically under the requirement of avoiding a beam abort when the stop dose was less than zero. Results The data recorded by the CROSSmini under the spiral irradiation patterns with break spots was reconstructed into a 2D dose, and the break spots’ operations were visually validated for all the energies and beam currents. There were no statistically significant difference in the measured X and Y scanning speeds across the four methods. However, the last method involving the SCM current yielded the largest type A uncertainty of up to 25% () due to the noisy signal. The first method with the linear regression and 5 kHz acquisition rate was preferred due to a smaller type A uncertainty of up to 2.0% and a lower false negative rate in detecting the rising and falling edges during scanning. The calculated tolerance limit based on our current DDCS setting was found to be 0.50 times of the expected scanning speed. Conclusion We have introduced QA protocols for DDCS, designed to ensure complete and safe beam delivery without interruptions caused by move doses exceeding planned spot doses.

Objective: We comparatively analyzed the longitudinal outcomes of conversion to open procedure, laparoscopic subtotal cholecystectomy (CCY), and laparoscopic cholecystostomy tube placement. Background: Severe cholecystitis often causes dense inflammation that distorts the hepatocystic anatomy and can make safe dissection during CCY challenging. However, controversy exists regarding the optimal bailout procedure in such situations. Methods: The New York and Florida State all-claims databases were queried for patients who underwent laparoscopic CCY for acute cholecystitis from 2012 to 2021. Hierarchical logistic regression models were used to obtain adjusted estimates, with fixed effects assigned to patient-level variables and random effects assigned to hospital identifiers to adjust for intraclass correlation. Results: Of 384,948 laparoscopic CCYs performed, 5448 (1.4%) were not completed laparoscopically; 1370 underwent conversion to open procedure, 2646 underwent laparoscopic subtotal CCY, and 1432 underwent laparoscopic cholecystostomy tube placement. The conversion to open rate decreased from 0.6% in 2012 to 0.3% in 2021, while the laparoscopic subtotal CCY rate increased from 0.2% in 2012 to 1.4% in 2021. The 1-year bile duct injury (BDI) rate was highest for the conversion to open group (4.4%), followed by the laparoscopic subtotal CCY (0.8%) and laparoscopic cholecystostomy tube groups (0.3%, P<0.001). On adjusted analyses with the conversion to open group as the control, laparoscopic subtotal CCY (OR: 0.17, P<0.001) and laparoscopic cholecystostomy tube were associated with lower BDI rates (OR: 0.08, P<0.001, Figure). The 1-year postoperative endoscopic biliary intervention rate was lowest for the conversion to open group (4.2%), followed by the laparoscopic subtotal CCY (8.4%) and the laparoscopic cholecystostomy tube groups (8.8%, P<0.001). The completion CCY rates for the laparoscopic subtotal CCY and laparoscopic cholecystostomy tube groups were 2.1% and 23.4%, respectively. Among completion CCYs, the open rates were 56.4% in the laparoscopic subtotal CCY group versus 24.5% in the laparoscopic cholecystostomy tube group (P<0.001). Conclusions: In patients with severe cholecystitis requiring a bailout procedure, the BDI rate was highest after conversion to open procedure. Laparoscopic subtotal CCY and laparoscopic cholecystostomy tube were associated with lower BDI rates at the cost of higher postoperative endoscopic biliary intervention rates. Completion CCYs were required in 2.1% and 23.4% of patients who underwent laparoscopic subtotal CCY and laparoscopic cholecystostomy tube placement, respectively, of which the former group’s CCY was more likely to require an open operation.

Summary of Background Data: Intraductal papillary mucinous neoplasm (IPMN)-derived pancreatic cancer is typically managed like pancreatic intraepithelial neoplasia (PanIN)-derived pancreatic cancer. However, in IPMN-derived pancreatic cancer, the role of chemotherapy remains controversial, particularly in the neoadjuvant setting (NAT). Objective: To evaluate the role of neoadjuvant chemotherapy in IPMN-derived pancreatic cancer. Methods: Patients with IPMN-derived pancreatic cancer treated with either upfront surgery (US) or NAT were identified from eight international centers (2000-2023). Clinicopathologic data were compared. Date of first treatment was used for Kaplan-Meier and log-rank tests to compare overall (OS) and recurrence free survival (RFS). Multivariable Cox-regression was performed in patients that underwent NAT. Results: In 1,019 patients, 76 (7%) underwent NAT. Patients who received NAT had higher baseline CA19-9 levels (P<0.001). Of these 76 patients, 27 (36%), 20 (26%), and 29 (38%) had resectable, borderline resectable, or locally advanced pancreatic cancer at diagnosis, respectively. Advanced resectability stage was significantly more common in the NAT patients as compared to those who underwent US (P<0.001). OS for US patients was 38.0 months (95%CI: 33.7.1-44.3), which was not statistically different than those that received NAT [27.5 mo (95%CI: 23.1-46.7), P=0.121]. This was also valid for patients with resectable disease [US: 38.1 mo vs. NAT: 35.6 mo, P=0.920)]. Complete or marked pathological treatment response (P=0.046) and serological CA19-9 normalization after NAT (P=0.017) were associated with improved survival. On Cox-regression for OS, N2 disease [HR: 4.15 (95%CI: 1.71-10.10)], elevated CA19-9 [HR: 2.02 (95%CI:1.06-3.85)] and R1 margin [HR: 2.36 (95%CI:1.20-4.61)] was independently associated with OS after NAT, while resectability status was not. Conclusion: After NAT and resection, advanced resectability stage was not associated with worse OS indicating the value of this approach for borderline resectable and locally advanced IPMN-derived pancreatic cancer. The benefit of NAT in resectable disease is unclear and may require an individualized approach. Biological treatment effect can be assessed with CA19-9 and confirmed by pathologic response.

ABSTRACT Symmetry refers to properties that remain invariant upon mathematical transformations. The principles of symmetry have guided numerous important discoveries in physics and chemistry but not in biology and medicine. Here, we aim to explore the presence of symmetry relationships at the gene expression level as a mean to distinguish between healthy and disease states. We deployed Learning-Based Invariant Feature Engineering - LIFE, a hybrid machine learning approach implemented with two symmetric invariant feature functions (IFFs) to identify Invariant Feature Genes (IFGs), which are gene pairs whose IFF single-value outputs remain invariant across individual samples in a given biological phenotype. Our multiclass classification results across the transcriptomes of 25 normal organs, 25 cancer types, and blood samples obtained from 4 different types of neurodegenerative diseases revealed the presence of unique phenotype-specific IFGs. We constructed networks using these IFGs (IF-Nets) and intriguingly, we demonstrated that the hubs could serve as information encoders, capable of reconstructing sample-wise expression values in relation to their counterpart genes. More importantly, we found that hubs of cancer IF-Nets were enriched with both approved and clinical trial drugs, highlighting “symmetry breaking” as a novel approach for treating diseases.

Abstract Introduction . Dispersion in an accelerator quantifies the deviation of the proton trajectory when there is a momentum deviation. We present for the first time a safe method of measuring dispersion in the clinic, using a scintillator detector and the momentum deviations within a spill. This is an important accelerator quantity as we found that this is the reason behind the large dose fluctuation in our absolute dosimetry measurement. Methods . Dispersions are measured for nine energies in a Hitachi ProBeat system at three locations (isocenter and at two profile monitors) and at two gantry angles (0 and 90 degrees) by first measuring the spot position and momentum drift within a spill. The spot position drift is measured by the XRV-4000 at the isocenter, and by the two profile monitors located at 0.57 and 2.27 m from the isocenter. The momentum drift is calculated from the intra-spill range drift which is measured using the Ranger accessory. The dispersion at isocenter and its gradient are calculated using the weighted least square regression on the measured dispersions at the three locations. A constraint is formulated on the dispersion and its gradient to ensure minimal intra-spill spot position deviation around the isocenter. Results . The measured intra-spill range and spot positional drift at isocenter are less than 0.25 mm and 0.7 mm respectively. The momentum spread calculated from the range drift are less than 0.08%. The dispersion at the isocenter ranged from 0.50 to 4.30 m and the zero-crossing happens upstream of isocenter for all energies. 2 of the 9 energies (168.0 and 187.5 MeV) violated the constraint and has an intra-spill spot positional deviation greater than 1.0 within 5 cm from the isocenter. Conclusion . This measurement is recommended as part of commissioning and annual quality assurance for accelerator monitoring and to ensure intra-spill spot deviations remain low.

AbstractBackgroundAbsolute dosimetry measurement is an integral part of Treatment Planning System (TPS) commissioning and it involves measuring the integrated absorbed dose to water for all energies in a pencil beam scanning delivery system. During the commissioning of Singapore's first proton therapy center, a uniform scanned field with an Advanced Markus chamber method was employed for this measurement, and a large dose fluctuation of at least 5% was observed for 10% of the energy layers during repeated measurements.PurposeThis study aims to understand the root cause of this fluctuation by relating the actual delivered spot information in the log file with the charge measurement by the ion chambers.MethodsA dedicated pencil beam dose algorithm was developed, taking into account the log file parameters, to calculate the dose for a single energy layer in a homogeneous water phantom. Three energies, 70.2, 182.7, and 228.7 MeV were used in this study, with the 182.7 MeV energy exhibiting large dose fluctuation. The dose fluctuation was investigated as a function of detector's sizes (pinpoint 3D, Advanced Markus, PTW 34070, and PTW 34089) and water depth (2 , 6, and 20 cm). Twelve ion chambers measurements were performed for each chamber and depth. The comparison of the theoretically predicted integrated dose and the charge measurement served as a validation of the algorithm.ResultsAbout 5.9% and 9.6% dose fluctuation were observed in Advanced Markus and pinpoint 3D measurements at 2 cm depth for 182.7 MeV, while fluctuation of 1.6% and 1.1% were observed in Advanced Markus with 228.7 and 70.2 MeV at similar depth. Fluctuation of less than 0.1% was observed for PTW34070 and PTW 34089 for all energies. The fluctuation was found to diminish with larger spot size at 20 cm depth to 1.3% for 182.7 MeV. The theoretical and measured charge comparison showed a high linear correlation of for all datasets, indicating the fluctuation originated from the delivered spot characteristics. The cause of fluctuation was identified to be due to the spill change occurring close to the detector, and since the spot positional deviation profiles were different between two spills, this resulted in local hot spots between columns of spots. The actual position of spill change varies randomly during measurement, which led to a random occurrence of hot spot within the detector's sensitive volume and a fluctuating dose measurement.ConclusionThis is the first report of a dose fluctuation greater than 5% in absolute dosimetry measurement with a uniform scanned field and the cause of the fluctuation has been conclusively determined. It is important to choose the MU and scanning pattern carefully to avoid spill change happening when the spot delivery is near the detector.

Spatially resolved sequencing technologies help us dissect how cells are organized in space. Several available computational approaches focus on the identification of spatially variable genes (SVGs), genes whose expression patterns vary in space. The detection of SVGs is analogous to the identification of differentially expressed genes and permits us to understand how genes and associated molecular processes are spatially distributed within cellular niches. However, the expression activities of SVGs fail to encode all information inherent in the spatial distribution of cells. Here, we devised a deep learning model, Spatially Informed Artificial Intelligence (SPIN-AI), to identify spatially predictive genes (SPGs), whose expression can predict how cells are organized in space. We used SPIN-AI on spatial transcriptomic data from squamous cell carcinoma (SCC) as a proof of concept. Our results demonstrate that SPGs not only recapitulate the biology of SCC but also identify genes distinct from SVGs. Moreover, we found a substantial number of ribosomal genes that were SPGs but not SVGs. Since SPGs possess the capability to predict spatial cellular organization, we reason that SPGs capture more biologically relevant information for a given cellular niche than SVGs. Thus, SPIN-AI has broad applications for detecting SPGs and uncovering which biological processes play important roles in governing cellular organization.

AbstractBackgroundResection of colorectal liver metastasis (CLM) is beneficial when feasible. However, the benefit of second hepatectomy for hepatic recurrence in CLM remains unclear.MethodsThe Colorectal Liver Operative Metastasis International Collaborative retrospectively examined 1004 CLM cases from 2000 to 2018 from a total of 953 patients. Hepatic recurrence after initial hepatectomy was identified in 218 patients. Kaplan–Meier analysis was performed for overall survival (OS) and recurrence‐free survival (RFS). Propensity score matching (PSM) was performed to offset selection bias. Cox proportional‐hazards regression was performed to identify risk factors associated with OS.ResultsA total of 51 patients underwent second hepatectomy. Unadjusted median OS was 60.1 months in repeat‐hepatectomy versus 38.3 months in the single‐hepatectomy group (p = 0.015). In the PSM population, median OS remained significantly better in the repeat‐hepatectomy group (60.1 vs. 33.1 months; p = 0.0023); median RFS was 12.4 months for the repeat‐hepatectomy group, versus 9.8 months in the single‐hepatectomy group (p = 0.0050). Repeat hepatectomy was associated with lower risk of death (hazard ratio: 0.283; p = 0.000012). Obesity, tobacco use, and high intraoperative blood loss were associated with significant risk of death (p < 0.05).ConclusionIn CLM with hepatic recurrence, second hepatectomy was beneficial for OS. With PSM, the OS benefit of performing a second hepatectomy remained significant.

Abstract Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients can be a good model for studying human diseases and for future therapeutic regenerative medicine. Current initiatives to establish human iPSC (hiPSC) banking face challenges in recruiting large numbers of donors with diverse diseased, genetic, and phenotypic representations. In this study, we describe the efficient derivation of transgene-free hiPSCs from human finger-prick blood. Finger-prick sample collection can be performed on a “do-it-yourself” basis by donors and sent to the hiPSC facility for reprogramming. We show that single-drop volumes of finger-prick samples are sufficient for performing cellular reprogramming, DNA sequencing, and blood serotyping in parallel. Our novel strategy has the potential to facilitate the development of large-scale hiPSC banking worldwide.