Biology subjects

Jani, M.

Publications and source records attributed to Jani, M..

5 recordsLinked to original sources

bioRxiv2026

Deep Learning-Based Reconstruction: Model Comparison for Variable-Density GRAPPA 1H MRSI

Proton magnetic resonance spectroscopic imaging (1H MRSI) enables quantitative mapping of brain metabolites, but its clinical use remains limited by long acquisition time. The goal of this work to improve the applicability of high-resolution 1H FID-MRSI at 7T by enhancing GRAPPA-based acceleration through deep learning-driven k-space reconstruction. In particular, compared with conventional GRAPPA, MultiNet PyGRAPPA enables substantially higher in-plane acceleration while suppressing residual lipid aliasing and preserving metabolite map fidelity in non-lipid-suppressed MRSI. Building on the MultiNet PyGRAPPA framework, we introduce a comprehensive comparison of advanced machine-learning models for predicting missing k-space points. Multiple architectures--including multilayer perceptrons, convolutional neural networks, and several U-Net variants--were trained within a variable-density k-space undersampling scheme to support acceleration factors of R = 4, 6, and 7. The proposed U-Net model extends the MultiNet concept by leveraging nonlinear hierarchical feature extraction, thereby improving reconstruction fidelity while maintaining robustness to noise.The methods were evaluated in vivo using retrospectively undersampled 7T 1H FID-MRSI datasets from healthy volunteers and patients. Quantitative analyses demonstrate that the U-Net outperforms the original MultiNet approach, offering improved SNR retention rate, reduced lipid RMSE, and higher structural similarity of major metabolites. Metabolite maps reconstructed with the U-Net showed reduced lipid artifacts and improved anatomical consistency. In conclusion, integrating deep convolutional networks into GRAPPA-based k-space prediction provides a more reliable and higher-fidelity reconstruction pipeline. When combined with variable-density undersampling, this approach enables faster acquisition of high-resolution 1H MRSI without compromising spectral quality or metabolite quantification.

bioengineering↗

bioRxiv2025

OmniShim - a vendor-independent B0 Shimming software toolbox

PurposeTo introduce the OmniShim Toolbox, a software package designed to calibrate and perform B0 shimming in user-defined regions of interest across systems from different vendors, supporting various shim orders. MethodsIn this study, we systematically compared the performance of vendor-implemented B0 shim routines with our custom developed OmniShim toolbox, designed to improve static magnetic field homogeneity. Single-voxel magnetic resonance spectroscopy (MRS) data were acquired from the prefrontal cortex and occipital lobe, while magnetic resonance spectroscopic imaging (MRSI) data were collected from regions above and below the corpus callosum in healthy volunteers. Measurements were conducted on both 3T and 7T MR systems to evaluate the robustness and scalability of each B0 shimming strategy across different field strengths. Additionally, functional MRI (fMRI) data were acquired at 7T to assess the impact of improved shimming on EPI data quality and BOLD contrast. ResultsThe OmniShim Toolbox demonstrated superior B0 homogeneity across all applications and field strength, leading to reduced signal dropout in fMRI and MRSI data, significantly improved spectral linewidths in SV MRS and MRSI data as well improved detection of neural networks by resting state fMRI. ConclusionThe proposed OmniShim Toolbox offers a robust and flexible approach to control B0 inhomogeneity, resulting in substantial improvements in image quality and spectral resolution. These enhancements benefit a broad range of MR applications.

bioengineering↗

bioRxiv2025

Characterization of real B0 shim fields generated by higher order B0 shim systems of whole body human 3T and 7T MRI systems

PurposeEnsuring optimal homogeneity of the static magnetic field (B0) is critically important for significantly enhancing the image quality, spectral resolution, and overall diagnostic accuracy of magnetic resonance imaging (MRI) and magnetic resonance spectroscopy/spectroscopic imaging (MRS/MRSI), especially at high and ultra-high field strengths. Achieving this goal relies on the deployment of advanced, higher-order shim hardware, which is indispensable for effective and precise B0 shimming. MethodsIn this study, we acquired B0 field maps to characterize the performance of each shim channel of vendor-provided B0 shim hardware integrated into whole body human 7T MRI system. To rigorously evaluate and compare the B0 field homogeneity achievable using these devices, we utilized spherical harmonic expansions to fit the measured B0 distributions for each shim channel in each of the investigated built-in B0 shim systems. This methodology enabled a systematic assessment of shim field "purity" and the effectiveness of different B0 shim configurations. ResultsWhile our analysis confirmed that the linear-order shim terms provided by the gradient coils maintained high purity, certain second-order shim terms and all third-order B0 shim coils of all vendors 7T whole body human MRI systems exhibit a high level of impurity and more specifically introduce substantial linear field components. These unintended linear contributions interfere with the linear shim fields provided by the gradient coils negating their corrective influence. As a result, the 3rd order B0 shim coils and some 2nd order B0 shim coil elements compromised the overall effectiveness of the B0 shimming process rather than improving it. Although pure higher order B0 shim fields were previously shown to substantially improve B0 field inhomogeneity, the vendor implemented versions of higher order B0 shim systems in current 7T whole-body human MRI scanners cannot achieve the desired level of uniformity and partly perform worse than first order B0 shimming. Substantial deviations between 2nd order and especially 3rd order real shim fields versus ideal shim fields demonstrate the necessity of real shim field calibration and call for improvement of future 2nd and 3rd order B0 shim coil design for human whole-body MRI scanners. Our findings offer valuable guidance for optimizing B0 shimming strategies at high and ultra-high field strengths, ultimately enhancing image quality. ConclusionRecent evaluations have demonstrated that certain second- and third-order shim coils, as implemented in current commercial 7T human whole-body MRI systems, introduce unintended lower-order (linear) field components. These field "impurities" substantially deviate from the desired higher-order spatial harmonics, thereby diminishing the orthogonality of the higher order B0 shim system. This in turn largely compromises the effectiveness of higher-order B0 shimming at whole-body 7T MRI scanners. These findings emphasize the necessity of conducting accurate shim field calibration to best utilize the current 7T B0 shim system configurations on one hand. On the other hand, improving the purity of these commercial B0 shim systems in the design phase to ensure that the higher-order terms accurately match their intended spherical harmonic profiles, particularly for the third-order shim terms--would largely enhance the achievable B0 field homogeneity at 7T. This improvement has directly clinically significant outcomes.

bioengineering↗

bioRxiv2025

The Tricuspid Valve is Transcriptionally Active During Prolonged Pressure Overload, Right-Sided Heart Failure, and Valve Regurgitation

BackgroundRight-sided heart failure (RHF), in the presence of tricuspid valve regurgitation (TR), can result from left-sided heart failure (LHF), pulmonary hypertension (PH), or heart malformations. The occurrence of RHF and TR represents a critical indicator of hospitalization rates and all-cause mortality. However, RHF has remained understudied, specifically with respect to the tricuspid valve, with few animal models to investigate the transformative processes and identify novel interventions. MethodsUsing the outbred sheep (Ovis aries) model of pulmonary artery banding (PAB) that induces RHF and TR, we generated three batches of ribosomal reduced RNA sequencing for 354 samples (NCBI SRA PRJNA1182691) containing right ventricle, left ventricle, each tricuspid valve leaflet, each mitral valve leaflet, and the pulmonary artery that represents both male and female sheep. The reads were assembled into a de novo sheep heart transcriptome for differential analysis. ResultsThe de novo sheep heart transcriptome enhanced transcript mapping of reads by 43-45% in the heart valves relative to the known sheep reference transcriptome. The identified transcripts produce validated tissue-specific pathways in ventricles (2,756 isoforms), pulmonary arteries (535 isoforms), and valves (1,215 isoforms), with transcript differences between the mitral and tricuspid valve involved in extracellular and endocrine signaling. The transcriptome also produced robust sex differences encoded by sex chromosomes and autosomes, highlighting epigenetic and sex hormone differences in the heart. Echocardiography and differential expression suggest that 8 weeks after PAB, the right ventricle has extensive morphological changes and known stress-induced lipid processing dysregulation. At 16-weeks post-PAB, tricuspid valve leaflets show the most significant transcriptional changes, with alterations in endocrine and immune pathway genes involved in cellular and extracellular remodeling. Genes within the tricuspid valve with differential expression and known human or mouse heart phenotypes include FLNA, LTBP4, VDR, CR2, PIGQ, CENPF, ACKR3, CR1, KLF2, and HIF3A. ConclusionsThis project highlights the complexity of heart valve tissues and their transcriptional activity in a sheep model of RHF. It suggests potential therapeutic interventions in heart valve remodeling in PAH, RHF, and TR. This work highlights the need for further human and model organism research into the dynamic valve cells and genes. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABS- Improved cardiac and valve specific transcriptome mapping through de novo transcriptome for clinically relevant ovine model. - Tricuspid valves show a sex dependent and active transcriptional response to pulmonary artery banding induced pulmonary hypertension and right sided heart failure. - Transcriptional phenotypes in ovine model mirror known human heart disease phenotypes. - Several transcripts identified with therapeutic potential for treating pressure overload conditions such as pulmonary hypertension. What Are the Clinical Implications?- Tricuspid valve remodeling due to pulmonary hypertension is accompanied by transcriptional alterations, and mechanical alterations alone may not be sufficient to address valve insufficiency. - Valve and ventricle sex specific gene expression changes following pulmonary hypertension indicate a potential role for hormonal influences and a need for personalized treatment strategies. - Improved patient outcomes for right heart failure, including diagnosis, early detection, and improved treatment strategies can be elucidated through the ovine model and supported through expanded interrogation of human tissues.

genomics↗

bioRxiv2024

Dysconnectivity of the cerebellum and somatomotor network correlates with the severity of alogia in chronic schizophrenia

Recent fMRI resting-state findings show aberrant functional connectivity within somatomotor network (SMN) in schizophrenia. Moreover, functional connectivity aberrations of the motor system are often reported to be related to the severity of psychotic symptoms. Thus, it is important to validate those findings and confirm their relationship with psychopathology. Therefore, we decided to take an entirely data-driven approach in our fMRI resting-state study of 30 chronic schizophrenia outpatients and 30 matched control subjects. We used independent component analysis (ICA), dual regression, and seed-based connectivity analysis. We found reduced functional connectivity within SMN in schizophrenia patients compared to controls and SMN hypoconnectivity with the cerebellum in schizophrenia patients. The latter is strongly correlated with the intensity of alogia, i.e. poverty of speech and reduction in spontaneous speech, demonstrated by patients. Our results are consistent with the recent knowledge about the role of the cerebellum in cognitive functioning and its abnormalities in psychiatric disorders, e.g. schizophrenia. In conclusion, the presented results, for the first time clearly showed the involvement of the cerebellum hypoconnectivity with SMN in the persistence and severity of alogia symptoms in schizophrenia.

neuroscience↗