Media 3: Generation of microswimmers from passive Brownian particles in a spherically aberrated optical trap

Originally published in Optics Express on 23 March 2015 (oe-23-6-8021

Media 4: Generation of microswimmers from passive Brownian particles in a spherically aberrated optical trap

Originally published in Optics Express on 23 March 2015 (oe-23-6-8021

Media 2: Generation of microswimmers from passive Brownian particles in a spherically aberrated optical trap

Originally published in Optics Express on 23 March 2015 (oe-23-6-8021

Observation of Larmor-like precession of a single birefringent particle due to spin-dependent forces in tilted optical tweezers

We observe clear precessional motion of highly birefringent liquid crystal (LC) particles trapped in a spherically aberrated optical trap which is built around a tilted refractive index stratified medium. For input circularly polarized light, the breaking of azimuthal symmetry induced by the tilt leads to an asymmetric intensity distribution in the radial direction near the trap focal plane, which - in combination with the spin-orbit conversion effects for input circularly polarized light - results in non-uniform canonical and spin momentum densities in those regions. In addition, while the canonical momentum remains always oriented towards the axial direction, the spin momentum reverses direction along spatial loops in the radial direction. As a consequence, the total momentum precesses around the canonical momentum vector along elliptical spatial loops - akin to a Larmor-like precession of magnetic moment (total momentum in our case) around a magnetic field (canonical momentum). We probe this precession experimentally using the single trapped LC particles - with the direction of precession determined by the helicity of the input light and the precession frequency varying linearly with the laser power. Our experimental results are validated by numerical simulations of the system where we employ the Debye-Wolf theory for tight focusing in the presence of a tilted stratified media

Data_Sheet_1_The expert's knowledge combined with AI outperforms AI alone in seizure onset zone localization using resting state fMRI.docx

We evaluated whether integration of expert guidance on seizure onset zone (SOZ) identification from resting state functional MRI (rs-fMRI) connectomics combined with deep learning (DL) techniques enhances the SOZ delineation in patients with refractory epilepsy (RE), compared to utilizing DL alone. Rs-fMRI was collected from 52 children with RE who had subsequently undergone ic-EEG and then, if indicated, surgery for seizure control (n = 25). The resting state functional connectomics data were previously independently classified by two expert epileptologists, as indicative of measurement noise, typical resting state network connectivity, or SOZ. An expert knowledge integrated deep network was trained on functional connectomics data to identify SOZ. Expert knowledge integrated with DL showed a SOZ localization accuracy of 84.8 ± 4.5% and F1 score, harmonic mean of positive predictive value and sensitivity, of 91.7 ± 2.6%. Conversely, a DL only model yielded an accuracy of <50% (F1 score 63%). Activations that initiate in gray matter, extend through white matter, and end in vascular regions are seen as the most discriminative expert-identified SOZ characteristics. Integration of expert knowledge of functional connectomics can not only enhance the performance of DL in localizing SOZ in RE but also lead toward potentially useful explanations of prevalent co-activation patterns in SOZ. RE with surgical outcomes and preoperative rs-fMRI studies can yield expert knowledge most salient for SOZ identification.</p

Runner sequence offers modest release from transcription termination.

<p><i>A</i>, The inclusion of 2.6 kilobases of dsred tetrameric sequence downstream (3′) to the ACT and HBB sequences provides modest release from transcription termination. Transcription was induced with doxycycline and cells harvested after 24 hours. The y-axis values are hRLUC/FLUC expression ratios normalized to a positive cell lysate run in each plate and expressed as a percentage of the dsred control cell line. All of the changes are significant (p<0.05) when compared to the dsred control. The error bars indicate the S.E.M. for a sample number of three. <i>B</i>, Real-time RT-PCR analysis. FLUC and hRLUC mRNA was measured by real-time RT-PCR and expressed as the relative ratio of hRLUC/FLUC mRNA. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006193#s2" target="_blank">Results</a> are shown as a percentage of the dsred control cell line. The ratio decreased as larger tracts of polyadenylation sequence are included in the tandem construct. Error bars indicate the S.E.M. for a sample number of three.</p

Xrn2 and Senataxin knockdowns provide limited release from transcription termination.

<p><i>A</i>, Western blot analysis of Xrn2 knockdown in whole cell extracts. TAN dsred control cell line was grown as indicated in the methods and transfected with a plasmid expressing an shRNA targeting Xrn2. Samples were run on duplicate gels in parallel, blotted and then probed for Xrn2 expression. Anti-Xrn2 antibody (Bethyl Laboratories) produces a doublet, shown here. The lower band disappears with shRNA targeting Xrn2, and the upper band shows reduced density. Anti-human β-actin antibody serves as a control. The analysis was performed three times, with a representative blot shown. <i>B</i>, Xrn2 and senataxin knockdowns each provide little release from transcription termination. Cell lines were grown as detailed in the methods. The y-axis values are hRLUC/FLUC expression ratios normalized to a positive cell lysate run in each plate. Error bars indicate the S.E.M. for a sample number of three. Significant differences (p<0.05) from the corresponding vector (pLKO) treated samples are indicated by asterisks.</p

The use of tandem reporters to measure transcription elongation.

<p><i>A</i>, A tetracycline-regulated promoter drives transcription through the tandem reporters. Self-cleaving hammerhead ribozymes cut the RNA transcript, separating both FLUC and hRLUC expressing RNA fragments from the test sequence. An internal ribosome entry sequence (IRES) enhances translation of the uncapped hRLUC expression fragment by replacing functions of the 5′ cap and untranslated region (5′ UTR). The relative ratio between the reporters measures the transcriptional impediment presented by an insert. The 5′ reporter (FLUC) is firefly luciferase and the 3′ reporter (hRLUC) is a humanized sea pansy luciferase. If the RNA polymerase terminates transcription in the inserted test sequence, the 3′ reporter will not be transcribed. <i>B</i>, Robust, reproducible induction of FLUC and hRLUC activities in clonal cell lines. Graphs display the mean luciferase activity per cell in Relative Light Units (RLU) for FLUC and hRLUC from clonal cell lines containing a single integrated copy of a control tandem reporter construct. Cells were cultured without (−) or with (+) the addition of doxycycline for 24 hours to induce transcription from the promoter. Extracts representing 15,000 cells were assayed for luciferase activity. The mean induction for FLUC expression was 237±29 fold, and 56±3 for hRLUC. Error bars indicate the S.E.M. for a sample number of three. <i>C</i>, Ribozymes self-cleave in a human cell line. Gel shows yield of RT-PCR products Transcription was induced with doxycycline and RNA was harvested after 24 hours. RT-PCR was conducted using primers designed for FLUC and hRLUC coding regions, and primers designed to span the ribozymes and the 275 bp of linker sequence between the two ribozymes. TAN-NR does not contain self-cleaving ribozymes, and all three sets of primers successfully amplify the target. β-actin primers were included as an amplification control. RT-PCR products were separated on a 1% agarose gel.</p

Inhomogeneous spin momentum induced orbital motion of birefringent particles in tight focusing of vector beams in optical tweezers

Spin orbit interaction (SOI) due to tight focusing of light in optical tweezers has led to exciting and exotic avenues towards inducing rotation in microscopic particles. However, instances where the back action of the particles influences and modifies SOI effects so as to induce rotational motion are rarely known. Here, we tightly focus a vector beam having radial/azimuthal polarization carrying no intrinsic angular momentum, into a refractive index stratified medium, and observe orbital rotation of birefringent particles around the beam propagation axis. In order to validate our experimental findings, we perform numerical simulations of the underlying equations. Our simulations reveal that the interaction of light with a birefringent particle gives rise to inhomogeneous spin currents near the focus, resulting in a finite spin momentum. This spin momentum combines with the canonical momentum to finally generate an origin-dependent orbital angular momentum which is manifested in the rotation of the birefringent particles around the beam axis. Our study describes a unique modulation of the SOI of light due to interaction with anisotropic particles that can be used to identify new avenues for exotic and complex particle manipulation in optical tweezers

Table_4_Automated seizure onset zone locator from resting-state functional MRI in drug-resistant epilepsy.docx

ObjectiveAccurate localization of a seizure onset zone (SOZ) from independent components (IC) of resting-state functional magnetic resonance imaging (rs-fMRI) improves surgical outcomes in children with drug-resistant epilepsy (DRE). Automated IC sorting has limited success in identifying SOZ localizing ICs in adult normal rs-fMRI or uncategorized epilepsy. Children face unique challenges due to the developing brain and its associated surgical risks. This study proposes a novel SOZ localization algorithm (EPIK) for children with DRE.MethodsEPIK is developed in a phased approach, where fMRI noise-related biomarkers are used through high-fidelity image processing techniques to eliminate noise ICs. Then, the SOZ markers are used through a maximum likelihood-based classifier to determine SOZ localizing ICs. The performance of EPIK was evaluated on a unique pediatric DRE dataset (n = 52). A total of 24 children underwent surgical resection or ablation of an rs-fMRI identified SOZ, concurrently evaluated with an EEG and anatomical MRI. Two state-of-art techniques were used for comparison: (a) least squares support-vector machine and (b) convolutional neural networks. The performance was benchmarked against expert IC sorting and Engel outcomes for surgical SOZ resection or ablation. The analysis was stratified across age and sex.ResultsEPIK outperformed state-of-art techniques for SOZ localizing IC identification with a mean accuracy of 84.7% (4% higher), a precision of 74.1% (22% higher), a specificity of 81.9% (3.2% higher), and a sensitivity of 88.6% (16.5% higher). EPIK showed consistent performance across age and sex with the best performance in those SignificanceAutomated SOZ localization from rs-fMRI, validated against surgical outcomes, indicates the potential for clinical feasibility. It eliminates the need for expert sorting, outperforms prior automated methods, and is consistent across age and sex.</p