Various histone purification and in vitro chromatin reconstitution for the study of biophysical properties with magnetic tweezers assay

Department of Biological SciencesEukaryotic DNA has a compacted high-ordered structure, known as chromatin. The fundamental units of chromatin are nucleosomes, which consist of DNA and histone proteins. Chromatin structure has many biological functions. For instance, chromatin protects DNA from damaging factors. DNA metabolism such as transcription and DNA repair is also regulated by chromatin structure. In addition, histone tail regions are targets for post-translational modification, which is associated with epigenetic control of DNA metabolism. In this paper, I purified all canonical Xenopus laevis core histone proteins in E. coli system with a milligram scale. Histone octamer was well assembled with dialysis and purified as size exclusion in vitro condition. Then, a single nucleosome was successfully reconstituted in vitro. Nucleosome reconstitution was confirmed with electrophoretic shift assay and micrococcal nuclease assay. Multiple nucleosomes were also reconstituted with multiple Widom 601 sequences, which have high binding affinity to histone octamer, in vitro. To investigate the tail effect on nucleosome stability, histones, in which tail region is deleted, were generated using mutagenesis. The tailless histone was overexpressed in E. coli system and purified using size exclusion and ion-exchange chromatographic techniques, successively. Purified tailless histones can be still reconstituted into nucleosomes. Magnetic tweezers technique is one of the single molecule techniques to characterize the physical properties of DNA molecules. The multiple-nucleosome formation was confirmed using magnetic tweezers. With the method of this paper, in vitro multiple tailless nucleosomes will be able to reconstitute. In this case, it will be the key to histone tail effects research in vitro with magnetic tweezers. The undisclosed mechanism of some histone chaperones can be revealed with in vitro chromatin reconstitution and single molecule techniques.ope

Machine Learning Based PCB/Package Stack-up Optimization For Signal Integrity

PCB/package stack-up design optimization is time-consuming and requiring a great deal of experience. Although some iterative optimization algorithms are applied to implement automatic stack-up design, evaluating the results of each iteration is still time-intensive. This paper proposes a combined Bayesian optimization-artificial neural network (BO-ANN) algorithm, utilizing a trained ANN-based surrogate model to replace a 2D cross-section analysis tool for fast PCB/package stack-up design optimization. With the acceleration of ANN, the proposed BO-ANN algorithm can finish 100 iterations in 40 seconds while achieving the target characteristic impedance. To better generalize the BO-ANN algorithm, a strategy of effective dielectric calculation is applied to multiple-dielectric stack-up optimization. the BO-ANN algorithm will be able to output optimized stack-up designs with dielectric layers chosen from the pre-defined library and the obtained designs are verified by 2D solver

Smaller pineal gland is associated with rapid eye movement sleep behavior disorder in Alzheimers disease

Background To investigate the association between pineal gland volume and symptoms of rapid eye movement (REM) sleep behavior disorder (RBD) in Alzheimers disease (AD) patients without any feature of dementia with Lewy bodies. Methods We enrolled 296 community-dwelling probable AD patients who did not meet the diagnostic criteria for possible or probable dementia with Lewy bodies. Among them, 93 were amyloid beta (Aβ) positive on 18F-florbetaben amyloid brain positron emission tomography. We measured RBD symptoms using the REM Sleep Behavior Disorder Screening Questionnaire (RBDSQ) and defined probable RBD (pRBD) as the RBDSQ of 5 or higher. We manually segmented pineal gland on 3T structural T1-weighted brain magnetic resonance imaging. Results The participants with pRBD had smaller pineal parenchyma volume (VPP) than those without pRBD (p <  0.001). The smaller the VPP, the more severe the RBD symptoms (p <  0.001). VPP was inversely associated with risk of prevalent pRBD (odds ratio = 0.909, 95% confidence interval [CI] = 0.878–0.942, p <  0.001). Area under the receiver operator characteristic curve for pRBD of VPP was 0.80 (95% CI = 0.750–0.844, p <  0.0001). These results were not changed when we analyzed the 93 participants with Aβ-positive AD separately. Conclusions In AD patients, reduced pineal gland volume may be associated with RBD.This study was supported by the grants from the Korean Health Technology R&D Project, Ministry of Health and Welfare, Republic of Korea (grant no.HI09C1379 [A092077]) and the Institute for Information & Communications Technology Promotion (IITP) grant funded by the Korea government (MSIT) (2018-2-00861, Intelligent SW Technology Development for Medical Data Analysis)

DenSE SwinHDR: SDRTV to HDRTV Conversion Using Densely Connected Swin Transformer With Squeeze and Excitation Module

Modern displays have the capability of rendering video contents encoded with high dynamic range (HDR) standards. HDR contents deliver more realistic visual experiences by wider color gamut and luminance compared to standard dynamic range (SDR) contents. However, most of the available contents are encoded with SDR standards. To provide HDR contents, the technology converts existing SDR contents to HDR contents, what we call SDRTV-to-HDRTV, is highly demanded by providers such as IPTV or broadcasting services. In this paper, we divide SDRTV-to-HDRTV conversion problem into global and local mapping problems. Transformers recently achieve significant performance and are known for conducting global mapping effectively. Convolution Neural Networks (CNN) are specialized for extracting and converting local features. In this regard, we introduce a combined model with a transformer for global mapping and CNN for local mapping, which solves the SDRTD-to-HDRTV problem in a complementary manner. We intensively explore the best combination strategy for transformers and CNNs. Through comprehensive objective/subjective experiments, we verified that the proposed method achieves the highest performance compared to the existing models in both fidelity and visual quality perspectives. To the best of our knowledge, we are the first to utilize Vision Transformer for the SDRTV-to-HDRTV conversion problem. To boost the performance, we combined Vision Transformer with architectural strategies which are previously applied on convolutional neural networks such as residual connection, dense connection, and squeeze-and-excitation module. We introduce a new Vision Transformer architecture denoted as DenSE-SwinHDR. Our method outperforms in terms of objective scores and visual quality compared to the state-of-the-art methods. Specifically, DenSE-SwinHDR achieved 0.79 dB PSNR, 0.93 dB PU-PSNR gain over HDRTVNet. Also, our proposed method achieve best performance on subjective quality assessment

Fast Saccadic Eye Movements Contribute to the Worsened Postural Sway in Older Adults Who Have Experienced Falls

The purpose of this study was to examine changes and between-group differences in postural sway during saccadic eye movement in older adults (n = 152). The participants were stratified into older adults who have experienced a fall (n = 58) (faller group) and those who have not (n = 94) (non-faller group). We measured postural sway during saccadic eye movement. Saccadic eye movement speed was such that the target was displayed at 0.5 Hz, 2 Hz, and 3 Hz. Postural sway was measured based on path length, velocity, and length between the maximal and minimal position of center of pressure in mediolateral and anteroposterior direction. In the faller group, path length, velocity, and mediolateral displacement of the center of pressure increased significantly during 3 Hz saccadic eye movement stimulation. However, in the non-faller group, there was no significant change in the center of pressure parameters during saccadic eye movement stimulation. Mediolateral displacement of the center of pressure increased significantly in both groups during saccadic eye movement, especially at 3 Hz. Therefore, rapid saccadic eye movement stimulation can contribute to the worsened postural sway in older adults who have experienced falls, and rapid external environmental stimuli may contribute to the deterioration of the upright standing stability in older adults