Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups.

BACKGROUND: Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics. RESULTS: Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency >0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype-phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories. CONCLUSIONS: Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome-phenome associations. The large-scale pathological whole genome-wide omics data will become a powerful set for genome-phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.

Automated classification of liver fibrosis stages using ultrasound imaging.

BACKGROUND: Ultrasound imaging is the most frequently performed for the patients with chronic hepatitis or liver cirrhosis. However, ultrasound imaging is highly operator dependent and interpretation of ultrasound images is subjective, thus well-trained radiologist is required for evaluation. Automated classification of liver fibrosis could alleviate the shortage of skilled radiologist especially in low-to-middle income countries. The purposed of this study is to evaluate deep convolutional neural networks (DCNNs) for classifying the degree of liver fibrosis according to the METAVIR score using US images. METHODS: We used ultrasound (US) images from two tertiary university hospitals. A total of 7920 US images from 933 patients were used for training/validation of DCNNs. All patient were underwent liver biopsy or hepatectomy, and liver fibrosis was categorized based on pathology results using the METAVIR score. Five well-established DCNNs (VGGNet, ResNet, DenseNet, EfficientNet and ViT) was implemented to predict the METAVIR score. The performance of DCNNs for five-level (F0/F1/F2/F3/F4) classification was evaluated through area under the receiver operating characteristic curve (AUC) with 95% confidential interval, accuracy, sensitivity, specificity, positive and negative likelihood ratio. RESULTS: Similar mean AUC values were achieved for five models; VGGNet (0.96), ResNet (0.96), DenseNet (0.95), EfficientNet (0.96), and ViT (0.95). The same mean accuracy (0.94) and specificity values (0.96) were yielded for all models. In terms of sensitivity, EffcientNet achieved highest mean value (0.85) while the other models produced slightly lower values range from 0.82 to 0.84. CONCLUSION: In this study, we demonstrated that DCNNs can classify the staging of liver fibrosis according to METAVIR score with high performance using conventional B-mode images. Among them, EfficientNET that have fewer parameters and computation cost produced highest performance. From the results, we believe that DCNNs based classification of liver fibrosis may allow fast and accurate diagnosis of liver fibrosis without needs of additional equipment for add-on test and may be powerful tool for supporting radiologists in clinical practice.

High-Frequency Ultrasound Imaging With Sub-Nyquist Sampling.

Implementation of a high-frequency ultrasound (HFUS) beamformer is computationally challenging because of its high sampling rate. This article introduces an efficient beamformer with sub-Nyquist sampling (or bandpass sampling) that is suitable for HFUS imaging. Our approach used channel radio frequency data sampled at bandpass sampling rate (i.e., 4/ 3fc ) and postfiltering-based interpolation to reduce the computational complexity. A polyphase structure for interpolation was used to further reduce the computational burden while maintaining an adequate delay resolution ( δ ). The performance of the proposed beamformer (i.e., 4/ 3fc sampling with sixfold interpolation, δ = 8fc ) was compared with that of the conventional method (i.e., 4fc sampling with fourfold interpolation, δ = 16fc ). Ultrafast coherent compounding imaging was used in simulation, in vitro and in vivo imaging experiments. Axial/lateral resolution and contrast-to-noise ratio (CNR) values were measured for quantitative evaluation. The number of transmit pulse cycles was varied from 1 to 3 using two transducers with different fractional bandwidths (67% and 98%). In the simulation, the proposed and conventional methods showed the similar -6-dB axial beam widths (63.5 and 61.5 µm , respectively) from the two-cycle transmit pulse using the transducer with a bandwidth of 67%. In vitro and in vivo imaging experiments were performed using a Verasonics ultrasound research platform equipped with a high-frequency array transducer (20-46 MHz). The in vitro imaging results using a wire target showed consistent results with the simulation study (i.e., disparity at -6-dB axial resolution). The in vivo feasibility study with a murine mouse model with breast cancer was also performed, and the proposed method yielded a similar image quality compared with the conventional method. From these studies, it was demonstrated that the proposed HFUS beamformer based on the bandpass sampling can substantially reduce the computational complexity while minimizing the loss of spatial resolution for HFUS imaging.

Elevational Synthetic Aperture Focusing for Three-Dimensional Photoacoustic Imaging Using a Clinical One-Dimensional Array Transducer.

OBJECTIVE: Two-dimensional (2D) photoacoustic (PA) imaging based on array transducers provide high spatial resolution in the lateral direction by adopting receive dynamic focusing. However, the quality of PA image is often deteriorated by poor elevational resolution which is achieved by an acoustic lens. To overcome this limitation, we present a three-dimensional (3D) image reconstruction method using a commercial one-dimensional (1D) array transducer. METHODS: In the method, the elevational resolution is improved by applying synthetic aperture focusing (SAF) technique along the elevational direction. For this, a commercially available 1D array transducer with an acoustic lens is modeled and appropriate synthetic focusing delay that can minimize the effect of the acoustic lens is derived by mathematical analysis. RESULTS: From the simulation and experiment results, it was demonstrated that the proposed method can enhance the image quality of PA imaging, i.e., elevational resolution and signal-to-noise ratio (SNR). CONCLUSION: 3D PA images with improved elevational resolution were achieved using a clinical 1D array transducer. SIGNIFICANCE: The presented method may be useful for clinical application such as detecting microcalcification, imaging of tumor vasculature and guidance of biopsy in real time.

Precursor Heterogeneity Driven Mo-Te Nanoparticle Structural Diversification for Cancer Photo-Theranostics.

Chemical reactions between homogeneous precursors are typically used to synthesize monodisperse nanoparticles with well-controlled size and morphology. It is difficult to predict the evolved nanostructures when using two heterogeneous precursors. In this study, three types of Mo-Te nanoparticles shaped like leaves, spindles, and rice grains (denoted respectively as nanoleaf, nanospindle, and nanorice) were obtained from dextrose-mediated proton-coupled electron transfer reaction between the solid polyoxomolybdate (POM) and the ionic tellurite anion as precursors. All produced nanoparticles had excellent optical absorption in the ultraviolet(UV)-visible(Vis)-near-infrared(NIR) regions, with only slight deviations among them. After confirming nanoparticles' photothermal conversion and photocatalytic activity at multiple wavelengths, the Mo-Te nanorice was tested as a potential agent for cancer treatment due to its minimum toxicity, excellent colloidal stability, and intrinsic anticancer effect. Excellent treatment efficacy and clearance were confirmed in vitro and in vivo. Due to their photoacoustic imaging capability, the injection of pristine nanoparticles could also realize phototheranostics without using additional drugs, probes, or photosensitizers.

LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads.

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly, constructed using 57× nanopore long reads and polished using 47× short paired-end reads. We utilized 72 GB of Hi-C chromosomal mapping data for scaffolding, to maximize assembly contiguity and accuracy. The contig assembly of LT1 was 2.73 Gbp in length, comprising 4490 contigs with an NG50 value of 12.0 Mbp. After scaffolding with Hi-C data and manual curation, the final assembly has an NG50 value of 137 Mbp and 4699 scaffolds. Assessment of gene prediction quality using Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 89.3% of the single-copy orthologous genes included in the benchmark. Detailed characterization of LT1 suggests it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,616 short indels, and 12,079 large structural variants. These data may be used as a benchmark for further in-depth genomic analyses of Baltic populations.

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates.

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.

Combined Application of Prototype Ultrasound and BSA-Loaded PLGA Particles for Protein Delivery.

PURPOSE: To develop an in vitro culture system for tissue engineering to mimic the in vivo environment and evaluate the applicability of ultrasound and PLGA particle system. METHODS: For tissue engineering, large molecules such as growth factors for cell differentiation should be supplied in a controlled manner into the culture system, and the in vivo microenvironment need to be reproduced in the system for the regulation of cellular function. In this study, portable prototype ultrasound with low intensity was devised and tested for protein release from bovine serum albumin (BSA)-loaded poly(lactic-co-glycolic acid) (PLGA) particles. RESULTS: BSA-loaded PLGA particles were prepared using various types of PLGA reagents and their physicochemical properties were characterized including particle size, shape, or aqueous wetting profiles. The BSA-loaded formulation showed nano-ranged size distribution with optimal physical stability during storage period, and protein release behaviors in a controlled manner. Notably, the application of prototype ultrasound with low intensity influenced protein release patterns in the culture system containing the BSA-loaded PLGA formulation. The results revealed that the portable ultrasound set controlled by the computer could contribute for the protein delivery in the culture medium. CONCLUSIONS: This study suggests that combined application with ultrasound and protein-loaded PLGA encapsulation system could be utilized to improve culture system for tissue engineering or cell regeneration therapy.

Recent Advances in Imaging Sensors and Applications.

Recent advances in sensor technology have allowed us to develop many interesting applications and enhance the quality of human life [...].

Synergistic Effect of Growth Factor Releasing Polymeric Nanoparticles and Ultrasound Stimulation on Osteogenic Differentiation.

Mesenchymal stem cells (MSCs) have been extensively used in the tissue regeneration therapy. Ex vivo therapy with well-differentiated osteogenic cells is known as an efficient treatment for musculoskeletal diseases, including rheumatoid diseases. However, along with its high cost, the current therapy has limitations in terms of restoring bone regeneration procedures. An efficient process for the cell differentiation to obtain a large number of functionalized osteogenic cells is necessary. Therefore, it is strongly recommended to develop strategies to produce sufficient numbers of well-differentiated osteogenic cells from the MSCs. In general, differentiation media with growth factors have been used to facilitate cell differentiation. In the present study, the poly (lactic-co-glycolic acid) (PLGA) nanoparticles incorporating the growth factors were included in the media, resulting in releasing growth factors (dexamethasone and ß-glycerophosphate) in the media in the controlled manner. Stable growth and early differentiation of osteogenic cells were achieved by the PLGA-based growth factor releasing system. Moreover, low intensity pulsed ultrasound was applied to this system to induce cell differentiation process. The results revealed that, as a biomarker at early stage of osteogenic cell differentiation, Lamin A/C nuclear protein was efficiently expressed in the cells growing in the presence of PLGA-based growth factor reservoirs and ultrasound. In conclusion, our results showed that the ultrasound stimulation combined with polymeric nanoparticles releasing growth factors could potentially induce osteogenic cell differentiation.

Synthetic Aperture Imaging Using High-Frequency Convex Array for Ophthalmic Ultrasound Applications.

High-frequency ultrasound (HFUS) imaging has emerged as an essential tool for pre-clinical studies and clinical applications such as ophthalmic and dermatologic imaging. HFUS imaging systems based on array transducers capable of dynamic receive focusing have considerably improved the image quality in terms of spatial resolution and signal-to-noise ratio (SNR) compared to those by the single-element transducer-based one. However, the array system still suffers from low spatial resolution and SNR in out-of-focus regions, resulting in a blurred image and a limited penetration depth. In this paper, we present synthetic aperture imaging with a virtual source (SA-VS) for an ophthalmic application using a high-frequency convex array transducer. The performances of the SA-VS were evaluated with phantom and ex vivo experiments in comparison with the conventional dynamic receive focusing method. Pre-beamformed radio-frequency (RF) data from phantoms and excised bovine eye were acquired using a custom-built 64-channel imaging system. In the phantom experiments, the SA-VS method showed improved lateral resolution (>10%) and sidelobe level (>4.4 dB) compared to those by the conventional method. The SNR was also improved, resulting in an increased penetration depth: 16 mm and 23 mm for the conventional and SA-VS methods, respectively. Ex vivo images with the SA-VS showed improved image quality at the entire depth and visualized structures that were obscured by noise in conventional imaging.

Polygenic risk score validation using Korean genomes of 265 early-onset acute myocardial infarction patients and 636 healthy controls.

BACKGROUND: The polygenic risk score (PRS) developed for coronary artery disease (CAD) is known to be effective for classifying patients with CAD and predicting subsequent events. However, the PRS was developed mainly based on the analysis of Caucasian genomes and has not been validated for East Asians. We aimed to evaluate the PRS in the genomes of Korean early-onset AMI patients (n = 265, age ≤50 years) following PCI and controls (n = 636) to examine whether the PRS improves risk prediction beyond conventional risk factors. RESULTS: The odds ratio of the PRS was 1.83 (95% confidence interval [CI]: 1.69-1.99) for early-onset AMI patients compared with the controls. For the classification of patients, the area under the curve (AUC) for the combined model with the six conventional risk factors (diabetes mellitus, family history of CAD, hypertension, body mass index, hypercholesterolemia, and current smoking) and PRS was 0.92 (95% CI: 0.90-0.94) while that for the six conventional risk factors was 0.91 (95% CI: 0.85-0.93). Although the AUC for PRS alone was 0.65 (95% CI: 0.61-0.69), adding the PRS to the six conventional risk factors significantly improved the accuracy of the prediction model (P = 0.015). Patients with the upper 50% of PRS showed a higher frequency of repeat revascularization (hazard ratio = 2.19, 95% CI: 1.47-3.26) than the others. CONCLUSIONS: The PRS using 265 early-onset AMI genomes showed improvement in the identification of patients in the Korean population and showed potential for genomic screening in early life to complement conventional risk prediction.

Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling.

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20-96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public's understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.

Investigation of Ultrasound-Mediated Intracellular Ca2+ Oscillations in HIT-T15 Pancreatic ß-Cell Line.

In glucose-stimulated insulin secretion (GSIS) of pancreatic ß-cells, the rise of free cytosolic Ca2+ concentration through voltage-gated calcium channels (VGCCs) triggers the exocytosis of insulin-containing granules. Recently, mechanically induced insulin secretion pathways were also reported, which utilize free cytosolic Ca2+ ions as a direct regulator of exocytosis. In this study, we aimed to investigate intracellular Ca2+ responses on the HIT-T15 pancreatic ß-cell line upon low-intensity pulsed ultrasound (LIPUS) stimulation and found that ultrasound induces two distinct types of intracellular Ca2+ oscillation, fast-irregular and slow-periodic, from otherwise resting cells. Both Ca2+ patterns depend on the purinergic signaling activated by the rise of extracellular ATP or ADP concentration upon ultrasound stimulation, which facilitates the release through mechanosensitive hemichannels on the plasma membrane. Further study demonstrated that two subtypes of purinergic receptors, P2X and P2Y, are working in a competitive manner depending on the level of glucose in the cell media. The findings can serve as an essential groundwork providing an underlying mechanism for the development of a new therapeutic approach for diabetic conditions with further validation.

Decoding a highly mixed Kazakh genome.

We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.

Investigation of cell mechanics using single-beam acoustic tweezers as a versatile tool for the diagnosis and treatment of highly invasive breast cancer cell lines: an in vitro study.

Advancements in diagnostic systems for metastatic cancer over the last few decades have played a significant role in providing patients with effective treatment by evaluating the characteristics of cancer cells. Despite the progress made in cancer prognosis, we still rely on the visual analysis of tissues or cells from histopathologists, where the subjectivity of traditional manual interpretation persists. This paper presents the development of a dual diagnosis and treatment tool using an in vitro acoustic tweezers platform with a 50 MHz ultrasonic transducer for label-free trapping and bursting of human breast cancer cells. For cancer cell detection and classification, the mechanical properties of a single cancer cell were quantified by single-beam acoustic tweezers (SBAT), a noncontact assessment tool using a focused acoustic beam. Cell-mimicking phantoms and agarose hydrogel spheres (AHSs) served to standardize the biomechanical characteristics of the cells. Based on the analytical comparison of deformability levels between the cells and the AHSs, the mechanical properties of the cells could be indirectly measured by interpolating the Young's moduli of the AHSs. As a result, the calculated Young's moduli, i.e., 1.527 kPa for MDA-MB-231 (highly invasive breast cancer cells), 2.650 kPa for MCF-7 (weakly invasive breast cancer cells), and 2.772 kPa for SKBR-3 (weakly invasive breast cancer cells), indicate that highly invasive cancer cells exhibited a lower Young's moduli than weakly invasive cells, which indicates a higher deformability of highly invasive cancer cells, leading to a higher metastasis rate. Single-cell treatment may also be carried out by bursting a highly invasive cell with high-intensity, focused ultrasound.

A One-Sided Acoustic Trap for Cell Immobilization Using 30-MHz Array Transducer.

Biological studies often involve the investigation of immobilized (or trapped) particles and cells. Various trapping methods without touching, such as optical, magnetic, and acoustic tweezers, have been developed to trap small particles. Here, we present the manipulation of a single cell or multiple cells using ultrasound-array-based single-beam acoustic tweezers (UA-SBATs). In SBATs, only a one-sided tightly focused acoustic beam produces a high acoustic gradient force-a mechanism that mirrors that of optical tweezers. As a result, targeted cells can be attracted to the beam center and immobilized within its trapping zone. Since an array transducer allows acoustic beam steering and scanning electronically instead of mechanical translation, it can manipulate cells more simply and quickly compared with single-element transducers, especially in biocompatible setup. In this experiment, a customized 30-MHz array transducer with an interdigitally bonded (IB) 2-2 piezocomposite was employed to immobilize MCF-12F cells. Cells were attracted to the center of the beam and laterally displaced with the array transducer without any damages to the cells. These findings suggest that UA-SBAT can be a promising tool for cell manipulation and may pave the way for exploring new biological applications.

Monitoring of Adult Zebrafish Heart Regeneration Using High-Frequency Ultrasound Spectral Doppler and Nakagami Imaging.

This paper reports the feasibility of Nakagami imaging in monitoring the regeneration process of zebrafish hearts in a noninvasive manner. In addition, spectral Doppler waveforms that are typically used to access the diastolic function were measured to validate the performance of Nakagami imaging. A 30-MHz high-frequency ultrasound array transducer was used to acquire backscattered echo signal for spectral Doppler and Nakagami imaging. The performances of both methods were validated with flow and tissue-mimicking phantom experiments. For in vivo experiments, both spectral Doppler and Nakagami imaging were simultaneously obtained from adult zebrafish with amputated hearts. Longitudinal measurements were performed for five zebrafish. From the experiments, the E/A ratio measured using spectral Doppler imaging increased at 3 days post-amputation (3 dpa) and then decreased to the value before amputation, which were consistent with previous studies. Similar results were obtained from the Nakagami imaging where the Nakagami parameter value increased at 3 dpa and decreased to its original value. These results suggested that the Nakagami and spectral Doppler imaging would be useful techniques in monitoring the regeneration of heart or tissues.

Real-Time Lossless Compression Algorithm for Ultrasound Data Using BL Universal Code.

Software-based ultrasound imaging systems provide high flexibility that allows easy and fast adoption of newly developed algorithms. However, the extremely high data rate required for data transfer from sensors (e.g., transducers) to the ultrasound imaging systems is a major bottleneck in the software-based architecture, especially in the context of real-time imaging. To overcome this limitation, in this paper, we present a Binary cLuster (BL) code, which yields an improved compression ratio compared to the exponential Golomb code. Owing to the real-time encoding/decoding features without overheads, the universal code is a good solution to reduce the data transfer rate for software-based ultrasound imaging. The performance of the proposed method was evaluated using in vitro and in vivo data sets. It was demonstrated that the BL-beta code has a good stable lossless compression performance of 20%~30% while requiring no auxiliary memory or storage.