Biology subjects

Alipour, A.

Publications and source records attributed to Alipour, A..

7 recordsLinked to original sources

bioRxiv2026

Frequency Shift Imaging Using an Adiabatic SLR Self-Refocused Pulse for Positive-Contrast SPION Imaging at 7T

Abstract: Purpose: Superparamagnetic iron oxide nanoparticles (SPION) are widely used as MRI contrast agents for cell tracking and molecular imaging. However, their detection using conventional T2/T2* weighted and susceptibility-weighted MRI relies on negative contrast (signal voids), which lacks specificity because similar hypointense signals can arise from other sources of magnetic susceptibility. This study introduces Frequency Shift Imaging (FSI), a positive-contrast technique based on an adiabatic Shinnar-Le Roux (SLR) self-refocused pulse that addresses the limited specificity of conventional SPION imaging. Methods: An adiabatic self-refocused RF pulse was designed using the SLR algorithm for frequency-selective positive-contrast imaging. The optimized pulse had a spectral bandwidth of 370 Hz, a peak RF amplitude of 14 T, and a duration of 15 ms. FSI data were acquired on a 7T MRI scanner. Phantom experiments used agarose-embedded 30 nm cell-labeled SPION at 0%, 25%, 75%, and 100% concentrations (pure). In vivo validation was performed following intramuscular SPION injection into the hind limb of a mouse. FSI images were compared with conventional acquisitions. Results: Quantitative phantom analysis showed normalized FSI signal intensities of 25.02% and 75.16% for samples containing 25% and 75% labeled cells, respectively, demonstrating an approximately proportional relationship between FSI signal and labeled-cell concentration. In vivo, FSI generated localized hyperintense positive contrast at the SPIO injection site, providing improved conspicuity and localization compared with the corresponding negative-contrast signal void. Discussion and Conclusion: FSI enables robust, B1-insensitive, positive-contrast SPION imaging at 7T with reduced echo time and SAR compared to paired adiabatic approaches, supporting its potential for quantitative cell tracking and molecular imaging applications.

bioengineering↗

bioRxiv2026

RNA-dependent chromatin organization during development

Embryonic development is characterized by controlled spatiotemporal remodeling of the nuclear landscape. To understand how this process is regulated, it is crucial to identify the factors controlling nano and mesoscale nuclear organization. Here, we developed an improved Chromatin Expansion Microscopy approach to visualize nuclear organization in developing zebrafish embryos at nanometer-scale resolution. We observe a stepwise emergence of chromatin compaction during early development, coincident with the onset of heterochromatin formation. Perturbation of the facultative heterochromatin mark H3K27me3 reveals that it is neither necessary nor sufficient for chromatin compaction in vivo. Instead, inhibiting transcription elongation disrupts chromatin compaction, while increasing nuclear RNA levels enhances compaction independently of transcriptional activity. Together, these results identify nuclear RNA as a major determinant of chromatin organization during development and support a model in which RNA promotes mesoscale chromatin compaction independently of canonical heterochromatin pathways. One-Sentence SummaryIn vivo nanoscale imaging reveals RNA-dependent chromatin compaction during development.

developmental biology↗

bioRxiv2026

Receive-Only Coupled Wireless Radiofrequency Probe for Endocavity MR Imaging Using a pTx System

PurposeTo enhance the SNR in MRI within a localized region of interest using a novel interventional wireless RF resonator probe combined with a dual-drive pTx system. MethodsA dual-drive body birdcage coil was operated in a linearly-polarized mode to decouple a passive RF resonator probe from the transmit field while maintaining the resonator in a receive-only coupled mode. The resonator was fabricated using standard microfabrication techniques and tuned to the Larmor frequency of a 3T MRI system. The 10-g specific absorption rate (SAR) distribution was simulated to identify potential hot spots around the resonator prior to heating experiments. To evaluate the interaction between the resonator probe and the linearly-polarized transmit field, SNR and flip-angle distributions were measured in a phantom. In vivo imaging studies were subsequently performed using the resonator probe in conjunction with the linearly-polarized dual-drive birdcage coil. ResultsTemperature measurements demonstrated a normalized temperature increase of less than 0.10{degrees}C, corresponding to a SAR value below 1.21 W/kg. Experimental flip-angle mapping confirmed effective magnetic decoupling of the resonator probe using linearly-polarized dual-drive transmission. An SNR enhancement factor of 1.6 was achieved within the region of interest in phantom experiments. In vivo imaging demonstrated a 2.0 {+/-} 0.2-fold SNR enhancement in the vicinity of the resonator probe. ConclusionA novel interventional approach for localized SNR enhancement in MRI was demonstrated using a wireless RF resonator probe and a dual-drive pTx system. The proposed technique enables local signal enhancement while minimizing transmit-field interactions, thereby facilitating safe interventional MRI and potentially improving image quality and diagnostic performance.

bioengineering↗

bioRxiv2025

Optimized Quantitative Susceptibility Mapping at 7T MRI for Assessing Iron Deposition in Alzheimers Disease

INTRODUCTIONElevated brain iron levels are common in Alzheimers disease (AD). Quantitative Susceptibility Mapping (QSM) is an advanced MRI technique for assessing iron accumulation. The optimized QSM at 7 Tesla (7T) MRI may further improve the sensitivity to detect subtle susceptibility changes in AD. METHODSWe optimized a QSM processing pipeline for 7T MRI by systematically comparing multiple reconstruction algorithms. Evaluation criteria included image quality, artifact suppression, and anatomical clarity. The finalized pipeline was applied to individuals with AD and healthy controls (HCs). RESULTSThe results revealed significantly elevated magnetic susceptibility values in the globus pallidus and dentate nucleus of the AD group compared to HCs. These findings were confirmed through both visual inspection and quantitative analysis of high-resolution QSM maps. DISCUSSIONOur results highlight the importance of optimizing QSM pipelines at 7T for accurate susceptibility quantification. We identified an optimal pipeline suitable for future applications in patients with AD and other neurological conditions.

neuroscience↗

bioRxiv2020

A computational examination of the two-streams hypothesis: which pathway needs a longer memory?

The two visual streams hypothesis is a robust example of neural functional specialization that has inspired countless studies over the past four decades. According to one prominent version of the theory, the fundamental goal of the dorsal visual pathway is the transformation of retinal information for visually-guided motor behavior. To that end, the dorsal stream processes input using absolute (or veridical) metrics only when the movement is initiated, necessitating very little, or no, memory. Conversely, because the ventral visual pathway does not involve motor behavior (its output does not influence the real world), the ventral stream processes input using relative (or illusory) metrics and can accumulate or integrate sensory evidence over long time constants, which provides a substantial capacity for memory. In this study, we tested these relations between functional specialization, processing metrics, and memory by training identical recurrent neural networks to perform either a viewpoint-invariant object classification task or an orientation/size determination task. The former task relies on relative metrics, benefits from accumulating sensory evidence, and is usually attributed to the ventral stream. The latter task relies on absolute metrics, can be computed accurately in the moment, and is usually attributed to the dorsal stream. To quantify the amount of memory required for each task, we chose two types of neural network models. Using a long-short-term memory (LSTM) recurrent network, we found that viewpoint-invariant object categorization (object task) required a longer memory than orientation/size determination (orientation task). Additionally, to dissect this memory effect, we considered factors that contributed to longer memory in object tasks. First, we used two different sets of objects, one with self-occlusion of features and one without. Second, we defined object classes either strictly by visual feature similarity or (more liberally) by semantic label. The models required greater memory when features were self-occluded and when object classes were defined by visual feature similarity, showing that self-occlusion and visual similarity among object task samples are contributing to having a long memory. The same set of tasks modeled using modified leaky-integrator echo state recurrent networks (LiESN), however, did not replicate the results, except under some conditions. This may be because LiESNs cannot perform fine-grained memory adjustments due to their network-wide memory coefficient and fixed recurrent weights. In sum, the LSTM simulations suggest that longer memory is advantageous for performing viewpoint-invariant object classification (a putative ventral stream function) because it allows for interpolation of features across viewpoints. The results further suggest that orientation/size determination (a putative dorsal stream function) does not benefit from longer memory. These findings are consistent with the two visual streams theory of functional specialization.

neuroscience↗

bioRxiv2019

Microtubule Disruption does not Impair Learning in the Unicellular Organism Paramecium: Implications for Information Processing in Microtubules

Information processing in microtubules is an open question that has not been properly addressed yet. It was suggested that microtubules could store and process information in the nervous system or even support consciousness. The unicellular organism, Paramecium caudatum, that has a microtubular structure but does not have a neuron or neural network, shows intelligent behaviors such as associative learning. This may suggest that the microtubules are involved in intelligent behavior, information storage or information processing in paramecium. To test this hypothesis, we have utilized a paramecium learning task in which the organism associates brightness in its swimming medium with attractive cathodal shocks to study the role of microtubules in paramecium learning. We used an antimicrotubular agent (parbendazole) and disrupted microtubular dynamics in paramecium to see if microtubules are an integral part of information storage and processing in parameciums learning process. We observed that a partial allosteric modulator of GABA (midazolam) could disrupt the learning process in paramecium, but the antimicrotubular agent could not. Therefore, our results suggest that microtubules are probably not vital for the learning behavior in P. caudatum. Consequently, our results call for a further revisitation of the microtubular information processing hypothesis.

neuroscience↗

bioRxiv2017

Paramecium Learning: New Insights and Modifications

Learning is a fundamental process in neural systems. However, microorganisms without a nervous system have been shown to possess learning abilities. Specifically, Paramecium caudatum has been previously reported to be able to form associations between lighting conditions and cathodal shocks in its swimming medium. We have replicated previous reports on this phenomenon and tested the predictions of a molecular pathway hypothesis on paramecium learning. Our results indicated that in contrast to the previous reports, paramecium can only associate higher light intensities with cathodal stimulation and it cannot associate lower light intensities with cathodal stimulation. These results found to be in line with the predictions of the previously proposed model for the molecular mechanisms of learning in paramecium which depends on the effects of cathodal shocks on the interplay between Cyclic adenosine monophosphate concentration and phototactic behavior of paramecium.

animal behavior and cognition↗