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Creators/Authors contains: "Khan, Ali"

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  1. Free, publicly-accessible full text available May 19, 2026
  2. Free, publicly-accessible full text available January 1, 2026
  3. The social amoeba Dictyostelium discoideum is a commonly used eukaryotic model organism for the study of cell division, chemotaxis, differentiation, phagocytosis, and other cellular processes. Electroporation is an effective and efficient method for delivering plasmid DNA into D. discoideum, an invaluable tool for studying intracellular processes. The technology is readily available but often prohibitively expensive. Although several custom-built electroporation devices have been developed, none deliver the specific 8.5kV/cm exponentially decaying waveform required for D. discoideum transformation. The present study examined whether a simple, inexpensive device can be built to produce this waveform through a simple resistor-capacitor (RC) circuit. A pulse generator RC circuit was built incorporating inexpensive electronic components and a 3D printed cuvette chamber. All four possible combinations of custom-built and commercial pulse generators and custom-built and commercial cuvette chambers were used to transform D. discoideum cells with a plasmid encoding green fluorescent protein (GFP). There were no significant differences in the number of surviving cells immediately following or 24 hours post-transformation between the systems. All combinations of custom-built and commercial systems achieved comparably high transformation efficiency shown by percent of cells expressing GFP six days after the transformation. Since the waveform-specific electroporation system we present here can be built by non-experts with easily obtainable materials and 3D printing, we envision this device to benefit investigators in areas with low research budgets and educators in multiple STEM fields. 
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  4. Abstract Objective. Spontaneous fluctuations of cerebral hemodynamics measured by functional magnetic resonance imaging (fMRI) are widely used to study the network organization of the brain. The temporal correlations among the ultra-slow, <0.1 Hz fluctuations across the brain regions are interpreted as functional connectivity maps and used for diagnostics of neurological disorders. However, despite the interest narrowed in the ultra-slow fluctuations, hemodynamic activity that exists beyond the ultra-slow frequency range could contribute to the functional connectivity, which remains unclear.Approach. In the present study, we have measured the brain-wide hemodynamics in the human participants with functional near-infrared spectroscopy (fNIRS) in a whole-head, cap-based and high-density montage at a sampling rate of 6.25 Hz. In addition, we have acquired resting state fMRI scans in the same group of participants for cross-modal evaluation of the connectivity maps. Then fNIRS data were deliberately down-sampled to a typical fMRI sampling rate of ∼0.5 Hz and the resulted differential connectivity maps were subject to a k-means clustering.Main results. Our diffuse optical topographical analysis of fNIRS data have revealed a default mode network (DMN) in the spontaneous deoxygenated and oxygenated hemoglobin changes, which remarkably resemble the same fMRI network derived from participants. Moreover, we have shown that the aliased activities in the down-sampled optical signals have altered the connectivity patterns, resulting in a network organization of aliased functional connectivity in the cerebral hemodynamics.Significance.The results have for the first time demonstrated that fNIRS as a broadly accessible modality can image the resting-state functional connectivity in the posterior midline, prefrontal and parietal structures of the DMN in the human brain, in a consistent pattern with fMRI. Further empowered by the fast sampling rate of fNIRS, our findings suggest the presence of aliased connectivity in the current understanding of the human brain organization. 
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  5. The brain processes memories as we sleep, generating rhythms of electrical activity called ‘sleep spindles’. Sleep spindles were long thought to be a state where the entire brain was fully synchronized by this rhythm. This was based on EEG recordings, short for electroencephalogram, a technique that uses electrodes on the scalp to measure electrical activity in the outermost layer of the brain, the cortex. But more recent intracranial recordings of people undergoing brain surgery have challenged this idea and suggested that sleep spindles may not be a state of global brain synchronization, but rather localised to specific areas. Mofrad et al. sought to clarify the extent to which spindles co-occur at multiple sites in the brain, which could shed light on how networks of neurons coordinate memory storage during sleep. To analyse highly variable brain wave recordings, Mofrad et al. adapted deep learning algorithms initially developed for detecting earthquakes and gravitational waves. The resulting algorithm, designed to more sensitively detect spindles amongst other brain activity, was then applied to a range of sleep recordings from humans and macaque monkeys. The analyses revealed that widespread and complex patterns of spindle rhythms, spanning multiple areas in the cortex of the brain, actually appear much more frequently than previously thought. This finding was consistent across all the recordings analysed, even recordings under the skull, which provide the clearest window into brain circuits. Further analyses found that these multi-area spindles occurred more often in sleep after people had completed tasks that required holding many visual scenes in memory, as opposed to control conditions with fewer visual scenes. In summary, Mofrad et al. show that neuroscientists had previously not appreciated the complex and dynamic patterns in this sleep rhythm. These patterns in sleep spindles may be able to adapt based on the demands needed for memory storage, and this will be the subject of future work. Moreover, the findings support the idea that sleep spindles help coordinate the consolidation of memories in brain circuits that stretch across the cortex. Understanding this mechanism may provide insights into how memory falters in aging and sleep-related diseases, such as Alzheimer’s disease. Lastly, the algorithm developed by Mofrad et al. stands to be a useful tool for analysing other rhythmic waveforms in noisy recordings. 
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  6. Mobile soft robots offer compelling applications in fields ranging from urban search and rescue to planetary exploration. A critical challenge of soft robotic control is that the nonlinear dynamics imposed by soft materials often result in complex behaviors that are counter-intuitive and hard to model or predict. As a consequence, most behaviors for mobile soft robots are discovered through empirical trial and error and hand-tuning. A second challenge is that soft materials are difficult to simulate with high fidelity - leading to a significant reality gap when trying to discover or optimize new behaviors. In this work we employ a Quality Diversity Algorithm running model-free on a physical soft tensegrity robot that autonomously generates a behavioral repertoire with no a priori knowledge of the robot's dynamics, and minimal human intervention. The resulting behavior repertoire displays a diversity of unique locomotive gaits useful for a variety of tasks. These results help provide a road map for increasing the behavioral capabilities of mobile soft robots through real-world automation. 
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  7. Abstract The Jiangmen Underground Neutrino Observatory (JUNO) is a large-scale neutrino experiment with multiple physics goals including determining the neutrino mass hierarchy, the accurate measurement of neutrino oscillation parameters, the neutrino detection from supernovae, the Sun, and the Earth, etc. JUNO puts forward physically and technologically stringent requirements for its central detector (CD), including a large volume and target mass (20 kt liquid scintillator, LS), a high-energy resolution (3% at 1 MeV), a high light transmittance, the largest possible photomultiplier (PMT) coverage, the lowest possible radioactive background, etc. The CD design, using a spherical acrylic vessel with a diameter of 35.4 m to contain the LS and a stainless steel structure to support the acrylic vessel and PMTs, was chosen and optimized. The acrylic vessel and the stainless steel structure will be immersed in pure water to shield the radioactive background and bear great buoyancy. The challenging requirements of the acrylic sphere have been achieved, such as a low intrinsic radioactivity and high transmittance of the manufactured acrylic panels, the tensile and compressive acrylic node design with embedded stainless steel pad, and one-time polymerization for multiple bonding lines. Moreover, several technical challenges of the stainless steel structure have been solved: the production of low radioactivity stainless steel material, the deformation and precision control during production and assembly, and the usage of high-strength stainless steel rivet bolt and of high friction efficient linkage plate. Finally, the design of the ancillary equipment such as the LS filling, overflowing, and circulating system was done. 
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    Free, publicly-accessible full text available December 26, 2025