Standard Sequence Research Articles

IMG-06. RADIOMIC-BASED RISK STRATIFICATION OF PEDIATRIC LOW-GRADE GLIOMA REVEALS DIFFERENTIALLY EXPRESSED MOLECULAR PROCESSES CONTRIBUTING TO VARIABLE PATIENT PROGNOSIS

Abstract In pediatric low-grade gliomas (pLGG), prognosis and responses to treatments are heterogeneous. This heterogeneity may be explained by the differences in molecular composition of the tumors of the same histology and the likely upstream alterations following administered radiation or systemic therapy. Integration of radiomics and clinical variables could generate a non-invasive biomarker that provides upfront prediction about patient’s risk of progression. We show that our proposed radiomic-based risk-stratification signature for pLGGs is associated with alterations in transcriptomic pathways. Standard multiparametric MRI sequences of 134 pLGG patients from Children’s Brain Tumor Network (CBTN) were retrospectively collected and 881 quantitative radiomic features were extracted. A multivariate Cox proportional hazard’s (Cox-PH) regression model was fitted on clinical (age, sex, tumor location, and extent of tumor resection) along with radiomic variables using 5-fold cross-validation, to predict patient’s risk of progression. The Cox-PH model showed excellent performance in prediction of PFS and patient’s risk scores, supported by the concordance index of 0.78. Radiogenomic analysis was performed to determine the transcriptomic pathways (1594 pathways, c2 MsigDb Reactome v2022.1) that contribute to the pLGG risk, predicted by the radiomic signature. ElasticNet regression was applied on the scores obtained by gene set enrichment analysis (GSEA) (in 70/134 subjects) to predict radiomic-based risk scores. Increased risk, corresponded to upregulation of DNA repair pathways, dysregulation of lipophagy, fatty acid beta oxidation, and vitamin D pathways, which are tumor-promoting. BRAFfusion signaling inversely correlated with risk, consistent with known favorable prognosis of KIAA1549-BRAF fused pLGGs. Upregulation in immune related pathways and Toll-Like Receptor (TLR) signaling was associated with lower risk. This study elucidates the synergistic dynamics between the biological processes that promote the risk of progression and radiomic-based risk-stratification signature. The proposed biomarker may be used to encourage targeted therapies in patients with increased predicted risk.

IMG-05. A MULTI-INSTITUTIONAL AND MULTI-HISTOLOGY PEDIATRIC-SPECIFIC BRAIN TUMOR SUBREGION SEGMENTATION TOOL: FACILITATING RAPNO-BASED ASSESSMENT OF TREATMENT RESPONSE

Abstract Current response assessment in pediatric brain tumors (PBTs), as recommended by the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group, relies on 2D measurements of changes in tumor size. However, there is growing evidence of underestimation of tumor size in PBTs using 2D compared to volumetric (3D) measurement approach. Accordingly, automated methods that reduce manual burden and intra- and inter-rater variability in segmenting tumor subregions and volumetric evaluations are warranted to facilitate tumor response assessment of PBTs. We have developed a fully automatic deep learning (DL) model using the nnUNet architecture on a large cohort of multi-institutional and multi-histology PBTs. The model was trained on widely available standard multiparametric MRI sequences (T1-pre, T1-post, T2, T2-FLAIR) for segmentation of the whole tumor and RAPNO-recommended subregions, including enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). As a prerequisite step for accurate tumor segmentation, we also generated another DL model based on DeepMedic for brain extraction from mpMRIs. The models were trained on an institutional cohort of 151 subjects and independently tested on 64 subjects from the internal and 29 patients from external institutions. The trained models showed excellent performance with median Dice scores of 0.98±0.02/0.97±0.02 for brain tissue segmentation, 0.92±0.08/0.90±0.17 for whole tumor segmentation, 0.76±0.31/0.87±0.29 for ET subregion, and 0.82±0.15/0.80±0.28 for segmentation of non-enhancing components (combination of NET, CC, and ED) in internal/external test sets, respectively. The automated segmentation demonstrated strong agreement with expert segmentations in volumetric measurement of tumor components, with Pearson’s correlation coefficients of 0.97, 0.97, 0.99, and 0.79 (p<0.0001) for ET, NET, CC, and ED regions, respectively. Our proposed multi-institutional and multi-histology automated segmentation method has the potential to aid clinical neuro-oncology practice by providing reliable and reproducible volumetric measurements for treatment response assessment.

Pediatric posterior fossa tumors

Tumors of the posterior fossa account for about 50-55% of brain tumors in childhood. The most frequent tumor entities are medulloblastomas, pilocytic astrocytomas, ependymomas, diffuse midline gliomas and atypical teratoid-rhabdoid tumors. Neuroradiological differential diagnosis with magnetic resonance imaging (MRI) is of considerable importance for preoperative planning as well as planning of follow-up therapy. Most important findings for differential diagnosis of pediatric posterior fossa tumors are tumor location, patient age and the intratumoral apparent diffusion assessed by diffusion-weighted imaging. Advanced MR techniques like MRI perfusion and MR spectroscopy can be helpful both in the initial differential diagnosis and in tumor surveillance, but exceptional characteristics of certain tumor entities should be kept in mind. Standard clinical MRI sequences including diffusion-weighted imaging are the main diagnostic tool in evaluating posterior fossa tumors in children. Advanced imaging methods can be helpful, but should never be interpreted separately from conventional MRI sequences.

Resource-efficient digital characterization and control of classical non-Gaussian noise

We show the usefulness of frame-based characterization and control [PRX Quantum 2, 030315 (2021)] for non-Markovian open quantum systems subject to classical non-Gaussian dephasing. By focusing on the paradigmatic case of random telegraph noise and working in a digital window frame, we demonstrate how to achieve higher-order control-adapted spectral estimation for the noise-optimized dynamical decoupling design. We find that, depending on the operating parameter regime, control that is optimized based on non-Gaussian noise spectroscopy can substantially outperform standard Walsh decoupling sequences as well as sequences that are optimized based solely on Gaussian noise spectroscopy. This approach is also intrinsically more resource-efficient than frequency-domain comb-based methods.

Multisystemic Enterococcosis in Brown Anoles (Anolis sagrei) from Florida, USA.

Beginning in July 2019, numerous free-ranging brown anoles (Anolis sagrei), an invasive lizard species in Florida, USA, were reported with large, soft, subcutaneous masses and disfiguring facial swellings. Postmortem evaluations of six affected animals, including cytology, histology, and electron microscopy, identified the presence of myriad chain-forming coccoid bacteria surrounded by a prominent clear capsule and abundant lightly basophilic matrix material with minimal associated granulomatous inflammation and effacement of normal tissue. Standard PCR and sequencing of the lesions revealed 100% nucleotide identity to Enterococcus lacertideformus. This bacterium was first observed in 2014 as the cause of a severe, multisystemic infection in several species of lizards (geckos and skinks) on Christmas Island, an Australian external territory in the Indian Ocean. Previously, analysis of E. lacertideformus had been hindered by an inability to grow the bacterium in standard culture conditions. We successfully cultured the organism on primary anole kidney cells. Given the growing recognition of host species diversity and geographic distribution noted for this organism, there is potential concern for spread to native North American lizards, especially the green anole (Anolis carolinensis), whose population numbers have apparently decreased due to introduced brown anoles.

GR.2 A deep intronic FGF14 GAA repeat expansion causes late-onset cerebellar ataxia

Background: The late-onset cerebellar ataxias (LOCAs) have until recently resisted molecular diagnosis. Contributing to this diagnostic gap is that non-coding structural variations, such as repeat expansions, are not fully accessible to standard short-read sequencing analysis. Methods: We combined bioinformatics analysis of whole-genome sequencing and long-read sequencing to search for repeat expansions in patients with LOCA. We enrolled 66 French-Canadian, 228 German, 20 Australian and 31 Indian patients. Pathogenic mechanisms were studied in post-mortem cerebellum and induced pluripotent stem cell (iPSC)-derived motor neurons from 2 patients. Results: We identified 128 patients who carried an autosomal dominant GAA repeat expansion in the first intron of the FGF14 gene. The expansion was present in 61%, 18%, 15% and 10% of patients in the French-Canadian, German, Australian and Indian cohorts, respectively. The pathogenic threshold was determined to be (GAA)≥250, although incomplete penetrance was observed in the (GAA)250-300 range. Patients developed a slowly progressive cerebellar syndrome at an average age of 59 years. Patient-derived post-mortem cerebellum and induced motor neurons both showed reduction in FGF14 RNA and protein expression compared to controls. Conclusions: This intronic, dominantly inherited GAA repeat expansion in FGF14 represents one of the most common genetic causes of LOCA uncovered to date.

Prevalence of BRCA1 and BRCA2 mutations in an unselected cohort of Indian women with breast cancer.

e13004 Background: Familial breast cancer accounts for 10-15% of breast cancer cases. The prevalence of germline pathogenic mutations in breast cancer susceptibility genes 1 and 2 ( BRCA1/2) among female breast cancer patients remained variable across studies depending on the population/settings studied. The estimate varied between 8-10% of the unselected female breast cancer population. There is a lack of data regarding the prevalence of BRCA1/2 among female breast cancer patients in India. Methods: This prospective observational study included consecutive patients with breast cancer in females, registered at All India Institute of Medical Sciences (AIIMS), New Delhi, India between the period of 1st September 2022 to 25th January 2023(5 months duration). The staging description was done as per anatomic TNM staging according to AJCC 7th edition. Mutation testing was performed in all patients by a standard next-generation sequencing (NGS) assay covering the BRCA1/2 gene. The reflex multiplex ligation by probe amplification method was performed in all cases that were negative by NGS. For patients with detected germline mutations in BRCA1/2, post-test counseling was done, and family screening was also advised. Results: A total of 210 female patients with breast cancer were sequentially included in the study. Young breast cancer (less than 35 years of age) constituted 40 (19.04%) cases. Thirty-eight patients (18.09%) women had a positive significant family history. The median age of the cohort was 46 years (range 18-85 years). Synchronous breast cancer was present in 7 (3.3%) cases. The stage distribution was stage I, 11(5.23%); stage II, 73 (34.76%); stage III, 83 (39.52%); and stage IV, 43 (20.47) %. One hundred and ten patients (52.38%) were hormone-receptor-positive, whereas 66 (31.42%) patients were HER2/neu positive. Triple-negative breast cancer (TNBC) was found in 65 (30.95%) cases. Overall, the prevalence of germline BRCA1/2 mutations was 35/210 (16.6%), which included BRCA 1 and 2 mutations in 22 (10.47%) and 12 (5.71) cases respectively. One case had mutations in both BRCA 1 and BRCA2. Young ( < 35) TNBCs (22 cases/210, 10.47%) have a high propensity for detecting pathogenic BRCA1 mutation (8/22, 36.36%). Conclusions: The prevalence of pathogenic BRCA1/2 in 16.6% of our cohort of unselected consecutive breast cancer patients. It is higher than that reported in the Western population likely due to the younger population and more proportion of triple-negative breast cancer patients in our cohort.

Thermal inkjet bioprinting drastically alters cell phenotype

Since the first description of inkjet bioprinting of cells in 2003, quantifying the input and measuring the output of the printers has been the hallmark of the field of bioprinting, as it is virtually impossible to characterize cells that are inside the printing orifices or extrusion needles. We will describe here some recent discoveries of cell behavior due to inkjet bioprinting. Primary and immortalized adult dermal fibroblasts were expanded for 2–3 passages upon receiving. The cells were harvested, resuspended in PBS, and bioprinted into a 96-well plate with pluriSTEM media. Cells were then transferred either into precoated 96-well plates or 20 µl drops were pipetted for hanging drop culture. IPC differentiation protocols were applied and the induction was begun approximately 45 min after printing. When differentiating aggregates, the initiation happened 45 min after the aggregates were transferred into the 96 wells. Standard immunostaining and RNA sequencing (RNA-Seq) were used to analyze the cell phenotypes. Preliminary results indicate that all cells expressed the three pluripotency markers oct-4, nanog, and sox-2. After applying a cardiomyocyte differentiation protocol, the cells stained positively for troponin-3. The cells also elongated and became more cardiomyocyte-like in their morphology. We analyzed bulk RNA seq data and our preliminary results show upregulation of some genes that have been implicated as stem cell markers: EPCAM, LEFTY1, ZFP42, and TEX19. In addition, differential expression of genes associated with pluripotency-relevant pathways shows some pathways are off like the MAPK/p38, MAPK/JNK1-3 which is expected for a pluripotent state. We also have data supporting the activation of the hippo pathway with transcriptional co-activator with PDZ binding motif (TAZ) highly upregulated and yes-associated protein staining the cell body. In addition, GSK3B is off and TGFB1, LIF/PIK3, and AKT1 are on as expected for pluripotency. Examining the gene network of upregulated genes, one can clearly distinguish the pivotal role of FOS, FOXO1, and PIK3 all related to pluripotency. Bioprinted fibroblasts will at least temporarily adopt a more primitive or dedifferentiated state, reminiscent of pluripotency. While immunochemistry shows the classic transcription factors required for pluripotency, gene expression shows a more nuanced picture of the transformations that occur upon printing. Understanding these transformations, even if temporary will be crucial when trying to build tissues using bioprinting technologies.

A robust Freeman-Hill-inspired pulse protocol for ringdown-free T1 relaxation measurements

A new difference-spectroscopy method is introduced for measuring T1 relaxation times. It is inspired by the earlier work of Freeman and Hill and eliminates the need for recording signal intensities at thermodynamic equilibrium. The new method is termed SIP-R (Split-Inversion Pulse and Recovery) and reduces the number of refinable parameters in the curve fitting process of relaxation-delay-dependent signal intensities by using two instead of the three parameters typically used in the standard inversion-recovery sequence. The SIP-R method preserves the dynamic range of measurement of the standard inversion-recovery method but converts the rise-to-maximum mathematical functionality of the recorded data into a decay-to-zero functionality. The decay-to-zero functionality renders the SIP-R sequence advantageous for inverse Laplace transformation numerical optimizations. The new technique proves to be extremely robust with respect to pulse imperfections, pulse-power changes during the pulse sequence, pulse-width miscalibrations, resonance offsets, and radiofrequency field variations. It also compensates for acoustic ring-down effects and proves reliable for measurements with inhomogeneously broadened signals up to several kilohertz linewidth. 1H NMR experiments with methane gas at pressures up to 50 atm in toroid-cavity pressure vessel probes and in the presence of the methane-to-methanol conversion catalyst Cu-ZnO/Al2O3 are used to show the usefulness of the new method for relaxation time investigations under pressure, at strong radiofrequency field gradients, and in the presence of paramagnetic materials.

A Mathematical Model to Optimize the Neoadjuvant Chemotherapy Treatment Sequence for Triple-Negative Locally Advanced Breast Cancer

Background: Triple-negative locally advanced breast cancer is an aggressive tumor type. Currently, the standard sequence treatment is applied, administering anthracyclines first and then a taxane plus platinum. Clinical studies for all possible treatment combinations are not practical or affordable, but mathematical modeling of the active mitotic cell population is possible. Our study aims to show the regions with the tumor’s most substantial cellular population variation by utilizing all possible values of the parameters αsi that define the annihilatory drug capacity according to the proposed treatment. Method: A piecewise linear mathematical model was used to analyze the cell population growth by applying four treatments: standard sequences of 21 days (SS21) and 14 days (SS14), administering anthracyclines first, followed by a taxane plus platinum, and inverted sequences of 21 days (IS21) and 14 days (IS14), administering a taxane plus platinum first then anthracyclines. Results: The simulation showed a higher effect of IS14 over SS14 when the rate of drug resistance was larger in the cell population during DNA synthesis (G1 and S) compared to cells in mitosis (G2 and M). However, if the proportion of resistant cells in both populations was equivalent, then treatments did not differ. Conclusions: When resistance is considerable, IS14 is more efficient than SS14, reducing the tumor population to a minimum.

Clinical validation of MR imaging time reduction for substitute/synthetic CT generation for prostate MRI-only treatment planning.

Radiotherapy treatment planning based only on magnetic resonance imaging (MRI) has become clinically achievable. Though computed tomography (CT) is the gold standard for radiotherapy imaging, directly providing the electron density values needed for planning calculations, MRI has superior soft tissue visualisation to guide treatment planning decisions and optimisation. MRI-only planning removes the need for the CT scan, but requires generation of a substitute/synthetic/pseudo CT (sCT) for electron density information. Shortening the MRI imaging time would improve patient comfort and reduce the likelihood of motion artefacts. A volunteer study was previously carried out to investigate and optimise faster MRI sequences for a hybrid atlas-voxel conversion to sCT for prostate treatment planning. The aim of this follow-on study was to clinically validate the performance of the new optimised sequence for sCT generation in a treated MRI-only prostate patient cohort. 10 patients undergoing MRI-only treatment were scanned on a Siemens Skyra 3T MRI as part of the MRI-only sub-study of the NINJA clinical trial (ACTRN12618001806257). Two sequences were used, the standard 3D T2-weighted SPACE sequence used for sCT conversion which has been previously validated against CT, and a modified fast SPACE sequence, selected based on the volunteer study. Both were used to generate sCT scans. These were then compared to evaluate the fast sequence conversion for anatomical and dosimetric accuracy against the clinically approved treatment plans. The average Mean Absolute Error (MAE) for the body was 14.98 ± 2.35 HU, and for bone was 40.77 ± 5.51 HU. The external volume contour comparison produced a Dice Similarity Coefficient (DSC) of at least 0.976, and an average of 0.985 ± 0.004, and the bony anatomy contour comparison a DSC of at least 0.907, and an average of 0.950 ± 0.018. The fast SPACE sCT agreed with the gold standard sCT within an isocentre dose of -0.28% ± 0.16% and an average gamma pass rate of 99.66% ± 0.41% for a 1%/1 mm gamma tolerance. In this clinical validation study, the fast sequence, which reduced the required imaging time by approximately a factor of 4, produced an sCT with similar clinical dosimetric results compared to the standard sCT, demonstrating its potential for clinical use for treatment planning.

Magnetresonanz-Enterographie/Enteroklysma

Magnetic resonance enterography/enteroclysma (MRE) is an examination technique without ionizing radiation that allows assessment of bowel wall changes and extraluminal pathologies/complications such as in chronic inflammatory bowel diseases, among others. To discuss requirements for optimal MR imaging of the small bowel, technical basis of MRE and principles for the development and optimization of aMRE protocol, and clinical indications for this specific imaging technique. Guidelines, basic and review papers will be analyzed. MRE enables the diagnosis of inflammatory bowel diseases and neoplasms and their evaluation during therapy. In addition to intra- and transmural changes, extramural pathologies and complications can also be detected. Standard sequences include steady-state free precession sequences, T2-weighted single-shot fast spin echo sequences, and three-dimensional (3D) T1-weighted gradient echo (GRE) sequences with fat saturation after contrast administration. Prior to image acquisition, optimal patient preparation and distension of the bowel using intraluminal contrast agents is necessary. Careful patient preparation for MRE, understanding of optimal imaging technique, and appropriate clinical indications are essential to achieve high-quality images of the bowel for accurate assessment and diagnosis as well as therapy monitoring of small bowel disease.

Bit depth enhancement method for low-contrast images based on sequence image fusion

To improve the visual effect of low-contrast images, a low-contrast image bit depth enhancement method based on sequence image fusion is proposed. The low-contrast image neighbourhood pixels are randomly discarded through Bernoulli trials. The corresponding weights of the local variance and deviation of the reserved pixels are obtained. The signal is used to build a denoising model, and the model is solved by the steepest descent method to complete the low-contrast image denoising process. Taking the denoised image as input, the useful information and features of the image are calculated, and the weight value is obtained. At the same time, the image is standardized, and different fusion rules are used to perform low-contrast image bit depth enhancement processing on the standardized sequence images. The experimental results show that the proposed method can effectively remove image noise, improve the image enhancement effect, and reduce the running time.

The Next Generation of Population-Based DFNB16 Carrier Screening and Diagnosis: STRC Copy-Number Variant Analysis from Genome Sequencing Data.

Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing. We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number. The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%-100%) and specificity (98.8%; 95% CI, 97.7%-99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%-2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number. We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.

3D magnetic resonance fingerprinting on a low-field 50 mT point-of-care system prototype: evaluation of muscle and lipid relaxation time mapping and comparison with standard techniques

ObjectiveTo implement magnetic resonance fingerprinting (MRF) on a permanent magnet 50 mT low-field system deployable as a future point-of-care (POC) unit and explore the quality of the parameter maps.Materials and methods3D MRF was implemented on a custom-built Halbach array using a slab-selective spoiled steady-state free precession sequence with 3D Cartesian readout. Undersampled scans were acquired with different MRF flip angle patterns and reconstructed using matrix completion and matched to the simulated dictionary, taking excitation profile and coil ringing into account. MRF relaxation times were compared to that of inversion recovery (IR) and multi-echo spin echo (MESE) experiments in phantom and in vivo. Furthermore, B0 inhomogeneities were encoded in the MRF sequence using an alternating TE pattern, and the estimated map was used to correct for image distortions in the MRF images using a model-based reconstruction.ResultsPhantom relaxation times measured with an optimized MRF sequence for low field were in better agreement with reference techniques than for a standard MRF sequence. In vivo muscle relaxation times measured with MRF were longer than those obtained with an IR sequence (T1: 182 ± 21.5 vs 168 ± 9.89 ms) and with an MESE sequence (T2: 69.8 ± 19.7 vs 46.1 ± 9.65 ms). In vivo lipid MRF relaxation times were also longer compared with IR (T1: 165 ± 15.1 ms vs 127 ± 8.28 ms) and with MESE (T2: 160 ± 15.0 ms vs 124 ± 4.27 ms). Integrated ΔB0 estimation and correction resulted in parameter maps with reduced distortions.DiscussionIt is possible to measure volumetric relaxation times with MRF at 2.5 × 2.5 × 3.0 mm3 resolution in a 13 min scan time on a 50 mT permanent magnet system. The measured MRF relaxation times are longer compared to those measured with reference techniques, especially for T2. This discrepancy can potentially be addressed by hardware, reconstruction and sequence design, but long-term reproducibility needs to be further improved.

Deep learning HASTE sequence compared with T2-weighted BLADE sequence for liver MRI at 3 Tesla: a qualitative and quantitative prospective study.

To qualitatively and quantitatively compare a single breath-hold fast half-Fourier single-shot turbo spin echo sequence with deep learning reconstruction (DL HASTE) with T2-weighted BLADE sequence for liver MRI at 3T. From December 2020 to January 2021, patients with liver MRI were prospectively included. For qualitative analysis, sequence quality, presence of artifacts, conspicuity, and presumed nature of the smallest lesion were assessed using the chi-squared and McNemar tests. For quantitative analysis, number of liver lesions, size of the smallest lesion, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) in both sequences were assessed using the paired Wilcoxon signed-rank test. Intraclass correlation coefficients (ICCs) and kappa coefficients were used to assess agreement between the two readers. One hundred and twelve patients were evaluated. Overall image quality (p = .006), artifacts (p < .001), and conspicuity of the smallest lesion (p = .001) were significantly better for the DL HASTE sequence than for the T2-weighted BLADE sequence. Significantly more liver lesions were detected with the DL HASTE sequence (356 lesions) than with the T2-weighted BLADE sequence (320 lesions; p < .001). CNR was significantly higher for the DL HASTE sequence (p < .001). SNR was higher for the T2-weighted BLADE sequence (p < .001). Interreader agreement was moderate to excellent depending on the sequence. Of the 41 supernumerary lesions visible only on the DL HASTE sequence, 38 (93%) were true-positives. The DL HASTE sequence can be used to improve image quality and contrast and reduces artifacts, allowing the detection of more liver lesions than with the T2-weighted BLADE sequence. The DL HASTE sequence is superior to the T2-weighted BLADE sequence for the detection of focal liver lesions and can be used in daily practice as a standard sequence. • The half-Fourier acquisition single-shot turbo spin echo sequence with deep learning reconstruction (DL HASTE sequence) has better overall image quality, reduced artifacts (particularly motion artifacts), and improved contrast, allowing the detection of more liver lesions than with the T2-weighted BLADE sequence. • The acquisition time of the DL HASTE sequence is at least eight times faster (21s) than that of the T2-weighted BLADE sequence (3-5min). • The DL HASTE sequence could replace the conventional T2-weighted BLADE sequence to meet the growing indication for hepatic MRI in clinical practice, given its diagnostic and time-saving performance.

Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells.

RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to an RBP. When the RBP binds to an mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high-confidence targets. In Drosophila cells, RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.

Dosimetric comparison of VMAT standard optimization (SO) and multi-criteria optimization (MCO) treatment plans with standard mode delivery (STD) or sliding window (SW) for head and neck cancer.

A new development on the RayStation treatment planning system (TPS) allows a plan to be planned by imposing a constraint on the leaf sequencing: all leaves move in the same direction before moving again in the opposite direction to create a succession of sliding windows (SWs). The study aims to investigate this new leaf sequencing, coupled with standard optimization (SO) and multi-criteria optimization (MCO) and to compare it with the standard sequencing (STD). Sixty plans were replanned for 10 head and neck cancer patients (two dose levels simultaneously SIB, 56 and 70Gy in 35 fractions). All plans were compared, and a Wilcoxon signed-rank test was performed. Pre-processing QA and metrics of multileaf collimator (MLC) complexity were studied. All methodologies met the dose requirements for the planning target volumes (PTVs) and organs at risk (OARs). SO demonstrates significantly best results for homogeneity index (HI), conformity index (CI), and target coverage (TC). SO-SW gives best results for PTVs (D98% and D2% ) but the differences between techniques are less than 1%. Only the D2%,PTV-56Gy is higher with both MCO methods. MCO-STD offer the best sparing OARs (parotids, spinal cord, larynx, oral cavity). The gamma passing rates (GPRs) with 3%/3mm criteria between the measured and calculated dose distributions are higher than 95%, slightly lowest with SW. The number of monitor units (MUs) and MLC metrics are higher in SW show a higher modulation. All plans are feasible for the treatment. A clear advantage of SO-SW is that the treatment plan is more straightforward to planning by the user due to the more advanced modulation. MCO stands out for its ease of use and will allow a less experienced user to offer a better plan than in SO. In addition, MCO-STD will reduce the dose to the OARs while maintaining good TC.

Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.

Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.

Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity.

Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a diverse panel of Xtt.