An inventory of patient-image based risk/dose, image quality and body habitus/size metrics for adult abdomino-pelvic CT protocol optimisation.

PURPOSE: Patient-specific protocol optimisation in abdomino-pelvic Computed Tomography (CT) requires measurement of body habitus/size (BH), sensitivity-specificity (surrogates image quality (IQ) metrics) and risk (surrogates often dose quantities) (RD). This work provides an updated inventory of metrics available for each of these three categories of optimisation variables derivable directly from patient measurements or images. We consider objective IQ metrics mostly in the spatial domain (i.e., those related directly to sharpness, contrast, noise quantity/texture and perceived detectability as these are used by radiologists to assess the acceptability or otherwise of patient images in practice). MATERIALS AND METHODS: The search engine used was PubMed with the search period being 2010-2024. The key words used were: 'comput* tomography', 'CT', 'abdom*', 'dose', 'risk', 'SSDE', 'image quality', 'water equivalent diameter', 'size', 'body composition', 'habit*', 'BMI', 'obes*', 'overweight'. Since BH is critical for patient specific optimisation, articles correlating RD vs BH, and IQ vs BH were reviewed. RESULTS: The inventory includes 11 BH, 12 IQ and 6 RD metrics. 25 RD vs BH correlation studies and 9 IQ vs BH correlation studies were identified. 7 articles in the latter group correlated metrics from all three categories concurrently. CONCLUSIONS: Protocol optimisation should be fine-tuned to the level of the individual patient and particular clinical query. This would require a judicious choice of metrics from each of the three categories. It is suggested that, for increased utility in clinical practice, more future optimisation studies be clinical task based and involve the three categories of metrics concurrently.

Development and application of a novel extraction protocol for the monitoring of microplastic contamination in widely consumed ruminant feeds.

Plastics and, in particular, microplastics (MPs) (< 5 mm) are emerging environmental pollutants responsible for interconnected risks to environmental, human, and animal health. The livestock sector is highly affected by these contaminants, with 50-60 % of the foreign bodies found in slaughtered domestic cattle being recognized as plastic-based materials. Additionally, microplastics were recently detected inside ruminant bodies and in their feces. MPs presence in ruminants could be explained by the intensive usage of plastic materials on farms, in particular to store feeds (i.e. to cover horizontal silos and to wrap hay bales). Although feed could be one of the main sources of plastics, especially of microplastics, a specific protocol to detect them in ruminant feeds is not actually present. Hence, the aim of this study was to optimize a specific protocol for the extraction, quantification, and identification of five microplastic polymers (high-density polyethylene, low-density polyethylene, polyamide fibers/particles, polyethylene terephthalate and polystyrene) from feeds typically used in ruminant diets (corn silage, hay, high protein feedstuff and total mixed ration). Several combinations of Fenton reactions and KOH digestion were tested. The final extraction protocol involved a KOH digestion (60 °C for 24 h), followed by two/three cycles of Fenton reactions. The extraction recoveries were of 100 % for high-density, low-density polyethylene, polyamide particles, and polystyrene and higher than 85 % for polyethylene terephthalate and polyamide fibers. Finally, the optimized protocol was successfully applied in the extraction of microplastics from real feed samples. All the feeds contained microplastics, particularly polyethylene, thus confirming the exposure of ruminants to MPs.

Optimizing Clinical Trial Eligibility Design Using Natural Language Processing Models and Real-World Data: Algorithm Development and Validation.

BACKGROUND: Clinical trials are vital for developing new therapies but can also delay drug development. Efficient trial data management, optimized trial protocol, and accurate patient identification are critical for reducing trial timelines. Natural language processing (NLP) has the potential to achieve these objectives. OBJECTIVE: This study aims to assess the feasibility of using data-driven approaches to optimize clinical trial protocol design and identify eligible patients. This involves creating a comprehensive eligibility criteria knowledge base integrated within electronic health records using deep learning-based NLP techniques. METHODS: We obtained data of 3281 industry-sponsored phase 2 or 3 interventional clinical trials recruiting patients with non-small cell lung cancer, prostate cancer, breast cancer, multiple myeloma, ulcerative colitis, and Crohn disease from ClinicalTrials.gov, spanning the period between 2013 and 2020. A customized bidirectional long short-term memory- and conditional random field-based NLP pipeline was used to extract all eligibility criteria attributes and convert hypernym concepts into computable hyponyms along with their corresponding values. To illustrate the simulation of clinical trial design for optimization purposes, we selected a subset of patients with non-small cell lung cancer (n=2775), curated from the Mount Sinai Health System, as a pilot study. RESULTS: We manually annotated the clinical trial eligibility corpus (485/3281, 14.78% trials) and constructed an eligibility criteria-specific ontology. Our customized NLP pipeline, developed based on the eligibility criteria-specific ontology that we created through manual annotation, achieved high precision (0.91, range 0.67-1.00) and recall (0.79, range 0.50-1) scores, as well as a high F1-score (0.83, range 0.67-1), enabling the efficient extraction of granular criteria entities and relevant attributes from 3281 clinical trials. A standardized eligibility criteria knowledge base, compatible with electronic health records, was developed by transforming hypernym concepts into machine-interpretable hyponyms along with their corresponding values. In addition, an interface prototype demonstrated the practicality of leveraging real-world data for optimizing clinical trial protocols and identifying eligible patients. CONCLUSIONS: Our customized NLP pipeline successfully generated a standardized eligibility criteria knowledge base by transforming hypernym criteria into machine-readable hyponyms along with their corresponding values. A prototype interface integrating real-world patient information allows us to assess the impact of each eligibility criterion on the number of patients eligible for the trial. Leveraging NLP and real-world data in a data-driven approach holds promise for streamlining the overall clinical trial process, optimizing processes, and improving efficiency in patient identification.

Virtual Non-Contrast versus True Native in Photon-Counting CT: Stability of Density of Upper Abdominal Organs and Vessels.

The clinical use of photon-counting CT (PCCT) allows for the generation of virtual non-contrast (VNC) series from contrast-enhanced images. In routine clinical practice, specific issues such as ruling out acute bleeding require non-contrast images. The aim of this study is to evaluate the use of PCCT-derived VNC reconstructions in abdominal imaging. PCCT scans of 17 patients including early arterial, portal venous and native sequences were enrolled. VNC reconstructions have been calculated. In every sequence and VNC reconstruction, 10 ROIs were measured (portal vein, descending aorta, inferior vena cava, liver parenchyma, spleen parenchyma, erector spinae muscle, subcutaneous adipose tissue, first lumbar vertebral body, air, and psoas muscle) and density values were compared. The VNC reconstructions show significant changes in density compared to the contrast-enhanced images. However, there were no significant differences present between the true non-contrast (TNC) and any VNC reconstructions in the observed organs and vessels. Significant differences (p < 0.05) between the measured mean density values in the TNC versus VNC reconstructions were found in fat and bone tissue. The PCCT-derived VNC reconstructions seemed to be comparable to the TNC images, despite some deviations shown in the adipose tissue and bone structures. However, the further benefits in terms of specific clinical issues need to be evaluated.

Development and validation of a noise insertion algorithm for photon-counting-detector CT.

BACKGROUND: Inserting noise into existing patient projection data to simulate lower-radiation-dose exams has been frequently used in traditional energy-integrating-detector (EID)-CT to optimize radiation dose in clinical protocols and to generate paired images for training deep-learning-based reconstruction and noise reduction methods. Recent introduction of photon counting detector CT (PCD-CT) also requires such a method to accomplish these tasks. However, clinical PCD-CT scanners often restrict the users access to the raw count data, exporting only the preprocessed, log-normalized sinogram. Therefore, it remains a challenge to employ projection domain noise insertion algorithms on PCD-CT. PURPOSE: To develop and validate a projection domain noise insertion algorithm for PCD-CT that does not require access to the raw count data. MATERIALS AND METHODS: A projection-domain noise model developed originally for EID-CT was adapted for PCD-CT. This model requires, as input, a map of the incident number of photons at each detector pixel when no object is in the beam. To obtain the map of incident number of photons, air scans were acquired on a PCD-CT scanner, then the noise equivalent photon number (NEPN) was calculated from the variance in the log normalized projection data of each scan. Additional air scans were acquired at various mA settings to investigate the impact of pulse pileup on the linearity of NEPN measurement. To validate the noise insertion algorithm, Noise Power Spectra (NPS) were generated from a 30 cm water tank scan and used to compare the noise texture and noise level of measured and simulated half dose and quarter dose images. An anthropomorphic thorax phantom was scanned with automatic exposure control, and noise levels at different slice locations were compared between simulated and measured half dose and quarter dose images. Spectral correlation between energy thresholds T1 and T2, and energy bins, B1 and B2, was compared between simulated and measured data across a wide range of tube current. Additionally, noise insertion was performed on a clinical patient case for qualitative assessment. RESULTS: The NPS generated from simulated low dose water tank images showed similar shape and amplitude to that generated from the measured low dose images, differing by a maximum of 5.0% for half dose (HD) T1 images, 6.3% for HD T2 images, 4.1% for quarter dose (QD) T1 images, and 6.1% for QD T2 images. Noise versus slice measurements of the lung phantom showed comparable results between measured and simulated low dose images, with root mean square percent errors of 5.9%, 5.4%, 5.0%, and 4.6% for QD T1, HD T1, QD T2, and HD T2, respectively. NEPN measurements in air were linear up until 112 mA, after which pulse pileup effects significantly distort the air scan NEPN profile. Spectral correlation between T1 and T2 in simulation agreed well with that in the measured data in typical dose ranges. CONCLUSIONS: A projection-domain noise insertion algorithm was developed and validated for PCD-CT to synthesize low-dose images from existing scans. It can be used for optimizing scanning protocols and generating paired images for training deep-learning-based methods.

Automated Web-based Software for CT Quality Control Testing of Low-contrast Detectability using Model Observers.

The Channelized Hotelling observer (CHO) is well correlated with human observer performance in many CT detection/classification tasks but has not been widely adopted in routine CT quality control and performance evaluation, mainly because of the lack of an easily available, efficient, and validated software tool. We developed a highly automated solution - CT image quality evaluation and Protocol Optimization (CTPro), a web-based software platform that includes CHO and other traditional image quality assessment tools such as modulation transfer function and noise power spectrum. This tool can allow easy access to the CHO for both the research and clinical community and enable efficient, accurate image quality evaluation without the need of installing additional software. Its application was demonstrated by comparing the low-contrast detectability on a clinical photon-counting-detector (PCD)-CT with a traditional energy-integrating-detector (EID)-CT, which showed UHR-T3D had 6.2% higher d' than EID-CT with IR (p = 0.047) and 4.1% lower d' without IR (p = 0.122).

Optimizing scan time and bayesian penalized likelihood reconstruction algorithm in copper-64 PET/CT imaging: a phantom study.

Objectives: The aim of this study was to evaluate Cu-64 PET phantom image quality using Bayesian Penalized Likelihood (BPL) and Ordered Subset Expectation Maximum with point-spread function modeling (OSEM-PSF) reconstruction algorithms. In the BPL, the regularization parameterßwas varied to identify the optimum value for image quality. In the OSEM-PSF, the effect of acquisition time was evaluated to assess the feasibility of shortened scan duration.Methods: A NEMA IEC PET body phantom was filled with known activities of water soluble Cu-64. The phantom was imaged on a PET/CT scanner and was reconstructed using BPL and OSEM-PSF algorithms. For the BPL reconstruction, variousßvalues (150, 250, 350, 450, and 550) were evaluated. For the OSEM-PSF algorithm, reconstructions were performed using list-mode data intervals ranging from 7.5 to 240 s. Image quality was assessed by evaluating the signal to noise ratio (SNR), contrast to noise ratio (CNR), and background variability (BV).Results: The SNR and CNR were higher in images reconstructed with BPL compared to OSEM-PSF. Both the SNR and CNR increased with increasingß, peaking atß= 550. The CNR for allß, sphere sizes and tumor-to-background ratios (TBRs) satisfied the Rose criterion for image detectability (CNR > 5). BPL reconstructed images withß= 550 demonstrated the highest improvement in image quality. For OSEM-PSF reconstructed images with list-mode data duration ≥ 120 s, the noise level and CNR were not significantly different from the baseline 240 s list-mode data duration.Conclusions: BPL reconstruction improved Cu-64 PET phantom image quality by increasing SNR and CNR relative to OSEM-PSF reconstruction. Additionally, this study demonstrated scan time can be reduced from 240 to 120 s when using OSEM-PSF reconstruction while maintaining similar image quality. This study provides baseline data that may guide future studies aimed to improve clinical Cu-64 imaging.

Potential of photon counting computed tomography derived spectral reconstructions to reduce beam-hardening artifacts in chest CT.

PURPOSE: Aim of the recent study is to point out a method to optimize quality of CT scans in oncological patients with port systems. This study investigates the potential of photon counting computed tomography (PCCT) for reduction of beam hardening artifacts caused by port-implants in chest imaging by means of spectral reconstructions. METHOD: In this retrospective single-center study, 8 ROIs for 19 spectral reconstructions (polyenergetic imaging, monoenergetic reconstructions from 40 to 190 keV as well as iodine maps and virtual non contrast (VNC)) of 49 patients with pectoral port systems undergoing PCCT of the chest for staging of oncologic disease were measured. Mean values and standard deviation (SD) Hounsfield unit measurements of port-chamber associated hypo- and hyperdense artifacts, bilateral muscles and vessels has been carried out. Also, a structured assessment of artifacts and imaging findings was performed by two radiologists. RESULTS: A significant association of keV with iodine contrast as well as artifact intensity was noted (all p < 0.001). In qualitative assessment, utilization of 120 keV monoenergetic reconstructions could reduce severe and pronounced artifacts completely, as compared to lower keV reconstructions (p < 0.001). Regarding imaging findings, no significant difference between monoenergetic reconstructions was noted (all p > 0.05). In cases with very high iodine concentrations in the subclavian vein, image distortions were noted at 40 keV images (p < 0.01). CONCLUSIONS: The present study demonstrates that PCCT derived spectral reconstructions can be used in oncological imaging of the thorax to reduce port-derived beam-hardening artefacts. When evaluating image data sets within a staging, it can be particularly helpful to consider the 120 keV VMIs, in which the artefacts are comparatively low.

Assessment of Precision and Accuracy of Brain White Matter Microstructure using Combined Diffusion MRI and Relaxometry.

Joint modeling of diffusion and relaxation has seen growing interest due to its potential to provide complementary information about tissue microstructure. For brain white matter, we designed an optimal diffusion-relaxometry MRI protocol that samples multiple b-values, B-tensor shapes, and echo times (TE). This variable-TE protocol (27 min) has as subsets a fixed-TE protocol (15 min) and a 2-shell dMRI protocol (7 min), both characterizing diffusion only. We assessed the sensitivity, specificity and reproducibility of these protocols with synthetic experiments and in six healthy volunteers. Compared with the fixed-TE protocol, the variable-TE protocol enables estimation of free water fractions while also capturing compartmental T2 relaxation times. Jointly measuring diffusion and relaxation offers increased sensitivity and specificity to microstructure parameters in brain white matter with voxelwise coefficients of variation below 10%.

New Benchmarks on Protocol Amendment Practices, Trends and their Impact on Clinical Trial Performance.

The Tufts Center for the Study of Drug Development (Tufts CSDD) conducted a follow-up study in 2022 to assess trends in protocol amendment experiences and the impact amendments have had on clinical trial performance, particularly during the COVID-19 pandemic. Sixteen pharmaceutical companies and contract research organizations provided data on 950 protocols and 2188 amendments. The results show that, since 2015, the prevalence of protocols with at least one amendment in phases I-IV has increased substantially (from 57 to 76%) and the mean number of amendments per protocol has increased 60% to 3.3, up from 2.1. Phase I and III protocols saw the highest increases in the mean number of amendments implemented per protocol. A much higher percentage of amendments-77%-were deemed unavoidable with regulatory agency requests and changes to the study strategy as the top reasons cited for amending a protocol. The total average duration to implement an amendment has nearly tripled during the past decade. The time from identifying the need-to-amend to last oversight approval now takes an average of 260 days and the mean duration during which investigative sites operate with different versions of the clinical trial protocol spans 215 days. Protocols that implemented at least one amendment were more effective at increasing patient screening volume and reducing the actual number of patients enrolled relative to plan. Lastly, the prevalence of protocols with at least one amendment and mean number of amendments was significantly higher for protocols conducted during the pandemic.

Protocol optimization for abdominal imaging using photon-counting CT: a consensus of two academic institutions.

PURPOSE: Photon-counting detector CT (PCD CT) is a promising technology for abdominal imaging due to its ability to provide high spatial and contrast resolution images with reduced patient radiation exposure. However, there is currently no consensus regarding the optimal imaging protocols for PCD CT. This article aims to present the PCD CT abdominal imaging protocols used by two tertiary care academic centers in the United States. METHODS: A review of PCD CT abdominal imaging protocols was conducted by two abdominal radiologists at different academic institutions. Protocols were compared in terms of acquisition parameters and reconstruction settings. Both imaging centers independently selected similar protocols for PCD CT abdominal imaging, using QuantumPlus mode. RESULTS: There were some differences in the use of reconstruction kernels and iterative reconstruction levels, however the individual combination at each site resulted in similar image impressions. Overall, the imaging protocols used by both centers provide high-quality images with low radiation exposure. CONCLUSION: These findings provide valuable insights into the development of standardized protocols for PCD CT abdominal imaging, which can help to ensure consistent as well as high-quality imaging across different institutions and allow for future multicenter research collaborations.

A Case Study Assessment on the Rationale for, and Relevance of, Non-Core Protocol Data.

To better understand the nature of Non-Core procedures and derive new insight into protocol simplification and optimization, Tufts CSDD collaborated with the FDA and sponsor companies to assess alignment on the rationale for collecting, and relevance of, Non-Core protocol data. Twelve sponsor companies classified and rated 700 distinct procedures from 19 pivotal trials supporting new drug and biologics approvals. FDA reviewers classified and rated 80 distinct procedures for three of the 19 pivotal trials. The results of this assessment indicate areas of alignment and misalignment. Sponsors and FDA reviewers agreed on the classification for more than half of endpoints. However, FDA reviewers classified a much higher percentage of procedures as Non-Core (26% vs. 18%) with the largest proportion (50%) of these procedures perceived as Core by sponsor companies. Sponsors indicated that one-out-of-six Non-Core procedures were administered due to perceived regulatory requirement and expectation. The results of this study characterize the challenge in aligning the different-and potentially conflicting-imperatives of sponsors and regulators and speak to the importance of more effective FDA-sponsor communication to help simplify protocol designs.

Survey on fan-beam computed tomography for radiotherapy: Imaging for dose calculation and delineation.

Background and purpose: To obtain an understanding of current practice, professional needs and future directions in the field of fan-beam CT in RT, a survey was conducted. This work presents the collected information regarding the use of CT imaging for dose calculation and structure delineation. Materials and methods: An online institutional survey was distributed to medical physics experts employed at Belgian and Dutch radiotherapy institutions to assess the status, challenges, and future directions of QA practices for fan-beam CT. A maximum of 143 questions covered topics such as CT scanner availability, CT scanner specifications, QA protocols, treatment simulation workflow, and radiotherapy dose calculation. Answer forms were collected between 1-Sep-2022 and 10-Oct-2022. Results: A 66 % response rate was achieved, yielding data on a total of 58 CT scanners. For MV photon therapy, all single-energy CT scans are reconstructed in Hounsfield Units for delineation or dose calculation, and a direct- or stoichiometric method was used to convert CT numbers for dose calculation. Limited use of dual-energy CT is reported for photon (N = 3) and proton dose calculations (N = 1). For brachytherapy, most institutions adopt water-based dose calculation, while approximately 26 % of the institutions take tissue heterogeneity into account. Commissioning and regular QA include eleven tasks, which are performed by two or more professions (29/31) with varying frequencies. Conclusions: Dual usage of a planning CT limits protocol optimization for both tissue characterization and delineation. DECT has been implemented only gradually. A variation of QA testing frequencies and tests are reported.

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk.

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Reject Analysis in Digital Radiography and Computed Tomography: A Belgian Imaging Department Case Study.

Objective: Reject analysis is usually performed in digital radiography (DR) for quality assurance. Data for computed tomography (CT) rejects remains sparse. The aim of this study is to help provide a straightforward benchmark for reject analysis of both DR and CT. Materials and methods: This retrospective observational study included 107,277 DR and 20,659 CT during 18 months in a tertiary care center. Rejected acquisitions were retrieved by Dose Archiving and Communication System (DACS). The DR and CT reject analysis included reject rates, reasons for rejection and supplementary radiation dose associated with these rejects. Results: 8,904 rejected DR and 514 rejected CT were retrieved. The DR reject rate was 8.3% whereas the CT reject rate was 2.5%. The cumulative effective dose (ED) of DR rejects was 377.3 mSv while the cumulative ED of CT rejects was 1267.4 mSv. The major reason for rejects was positioning for both DR (61%) and CT (44%). Conclusion: This study helps constitute a simple reproducible method to analyze both DR and CT rejects simultaneously. Although CT rejects are less often monitored than DR rejects, the radiation dose associated with CT rejects is much higher, which emphasizes the need to systematically monitor both DR and CT rejects. Investigating the reasons and the most frequently rejected examinations gives an opportunity for improvement of imaging techniques in cooperation with technologists.

Current and Future Use of Long Axial Field-of-View Positron Emission Tomography/Computed Tomography Scanners in Clinical Oncology.

The latest technical development in the field of positron emission tomography/computed tomography (PET/CT) imaging has been the extension of the PET axial field-of-view. As a result of the increased number of detectors, the long axial field-of-view (LAFOV) PET systems are not only characterized by a larger anatomical coverage but also by a substantially improved sensitivity, compared with conventional short axial field-of-view PET systems. In clinical practice, this innovation has led to the following optimization: (1) improved overall image quality, (2) decreased duration of PET examinations, (3) decreased amount of radioactivity administered to the patient, or (4) a combination of any of the above. In this review, novel applications of LAFOV PET in oncology are highlighted and future directions are discussed.

Optimising a landscape visual quality protocol. A Method for reducing respondent fatigue and obtaining site-specific indicators.

Evaluation of landscape visual quality is crucial for policymaking and planning but is still challenging. A wide range of visual assessment protocols is available, but there is still no consensus on appropriate indicators or approaches. Also, evaluation protocols can encompass many indicators, being exhaustive and complex and making the evaluation lengthy. Furthermore, protocols tend to be catered to a particular type of landscape or site-specific, and it can be tricky to ensure the protocol developed is adequate for the landscape under study. This paper proposes a methodology to optimise the selection of indicators for landscape visual assessments. There are two main goals: i) reduce the evaluation time to avoid respondent fatigue, and ii) make the protocol site-specific, choosing indicators that perform better and avoiding redundant indicators. •The presented method optimises the selection of indicators in expert visual assessments;•Indicators are rated in situ on a 5-point scale and go through a performance and redundancy test;•It helps to adapt complex evaluation protocols to the study landscape and to choose robust indicators in a supported and scientific way.

Dynamics of Organic Acids during the Droplet-Vitrification Cryopreservation Procedure Can Be a Signature of Oxidative Stress in Pogostemon yatabeanus.

Cryopreservation in liquid nitrogen (LN, -196 °C) is a unique option for the long-term conservation of threatened plant species with non-orthodox or limitedly available seeds. In previous studies, a systematic approach was used to develop a droplet-vitrification (DV) cryopreservation protocol for Postemon yatabeanus shoot tips that includes preculture with 10% sucrose, osmoprotection with C4-35%, cryoprotection with A3-80% vitrification solution, and a three-step regrowth starting with the ammonium-free medium. The tricarboxylic acid (TCA) cycle is a crucial component of plant cell metabolism as it is involved in redox state regulation and energy provision. We hypothesized that organic acids (OAs) associated with the TCA and its side reactions indirectly indicate metabolism intensity and oxidative stress development in shoot tips under the cryopreservation procedure. In this study, the contents of 14 OAs were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS) in P. yatabeanus shoot tips in a series of treatments including individual steps of the DV procedure, additional stress imposed by non-optimum protocol conditions (no preculture, no osmoprotection, various vitrification solution composition, using vials instead of aluminum foils, etc.) and regrowth on different media with or without ammonium or growth regulators. The possible relation of OA content with the total cryoprotectant (CPA) concentration and shoot tips regeneration percentage was also explored. Regeneration of cryopreserved shoot tips reduced in descending order as follows: standard protocol condition (91%) > non-optimum vitrification solution (ca. 68%) > non-optimum preculture (60-62%) > regrowth medium (40-64%) > no osmoprotection, cryopreservation in vials (28-30%). Five OAs (glycolic, malic, citric, malonic, and lactic) were the most abundant in the fresh (control) shoot tips. The dynamic pattern of OAs during the DV procedure highly correlated (r = 0.951) with the total CPA concentration employed: it gradually increased through the preculture, osmoprotection, and cryoprotection, peaked at cooling/rewarming (6.38-fold above control level), and returned to the fresh control level after 5 days of regrowth (0.89-fold). The contents of four OAs (2-hydroxybutyric, 3-hydroxypropionic, lactic, and glycolic) showed the most significant (10-209-fold) increase at the cooling/rewarming step. Lactic and glycolic acids were the major OAs at cooling/rewarming, accounting for 81% of the total OAs content. The OAs were categorized into three groups based on their dynamics during the cryopreservation protocol, and these groups were differently affected by protocol step modifications. However, there was no straightforward relationship between the dynamics of OAs and shoot tip regeneration. The results suggest that active modulation of OAs metabolism may help shoot tips to cope with osmotic stress and the chemical cytotoxicity\ of CPAs. Further intensive studies are needed to investigate the effect of cryopreservation on cell primarily metabolism and identify oxidative stress-related biomarkers in plant materials.

Framing protocol optimization in oncological Patlak parametric imaging with uKinetics.

PURPOSE: Total-body PET imaging with ultra-high sensitivity makes high-temporal-resolution framing protocols possible for the first time, which allows to capture rapid tracer dynamic changes. However, whether protocols with higher number of temporal frames can justify the efficacy with substantially added computation burden for clinical application remains unclear. We have developed a kinetic modeling software package (uKinetics) with the advantage of practical, fast, and automatic workflow for dynamic total-body studies. The aim of this work is to verify the uKinetics with PMOD and to perform framing protocol optimization for the oncological Patlak parametric imaging. METHODS: Six different protocols with 100, 61, 48, 29, 19 and 12 temporal frames were applied to analyze 60-min dynamic 18F-FDG PET scans of 10 patients, respectively. Voxel-based Patlak analysis coupled with automatically extracted image-derived input function was applied to generate parametric images. Normal tissues and lesions were segmented manually or automatically to perform correlation analysis and Bland-Altman plots. Different protocols were compared with the protocol of 100 frames as reference. RESULTS: Minor differences were found between uKinetics and PMOD in the Patlak parametric imaging. Compared with the protocol with 100 frames, the relative difference of the input function and quantitative kinetic parameters remained low for protocols with at least 29 frames, but increased for the protocols with 19 and 12 frames. Significant difference of lesion Ki values was found between the protocols with 100 frames and 12 frames. CONCLUSION: uKinetics was proved providing equivalent oncological Patlak parametric imaging comparing to PMOD. Minor differences were found between protocols with 100 and 29 frames, which indicated that 29-frame protocol is sufficient and efficient for the oncological 18F-FDG Patlak applications, and the protocols with more frames are not needed. The protocol with 19 frames yielded acceptable results, while that with 12 frames is not recommended.