Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and Redecoding

Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error correcting codes (ECCs). Previous works on recovering the data from the sequenced DNA pool with errors have utilized hard decoding algorithms based on a majority decision rule. To improve the correction capability of ECCs and robustness of the DNA storage system, we propose a new iterative soft decoding algorithm, where soft information is obtained from FASTQ files and channel statistics. In particular, we propose a new formula for log-likelihood ratio (LLR) calculation using quality scores (Q-scores) and a redecoding method which may be suitable for the error correction and detection in the DNA sequencing area. Based on the widely adopted encoding scheme of the fountain code structure proposed by Erlich et al., we use three different sets of sequenced data to show consistency for the performance evaluation. The proposed soft decoding algorithm gives 2.3% ~ 7.0% improvement of the reading number reduction compared to the state-of-the-art decoding method and it is shown that it can deal with erroneous sequenced oligo reads with insertion and deletion errors

The First Korean Case of Cutaneous Lung Tissue Heterotopia

Cutaneous lung tissue heterotopia is a very rare disorder where mature lung tissues develop in the skin. This is only the second known report of cutaneous lung tissue heterotopia, with the first by Singer et al. in 1998. A newborn infant had a hemangioma-like, freely movable mass connected to the anterior aspect of the sternal manubrium. Pathologic findings showed mature lung tissues with bronchi, bronchioles, and alveoli through the dermis and subcutis, and it was diagnosed as cutaneous lung tissue heterotopia. Cutaneous lung tissue heterotopia is hypervascular, so grossly it looks like a hemangioma. It can be differentiated from pulmonary sequestration, teratoma, bronchogenic cyst, and branchial cleft cyst by histology and the location of the mass. We describe the clinical, radiologic, and pathologic findings of a cutaneous lung tissue heterotopia, the first reported in Korea

Snake fang-inspired stamping patch for transdermal delivery of liquid formulations

A flexible microneedle patch that can transdermally deliver liquid-phase therapeutics would enable direct use of existing, approved drugs and vaccines, which are mostly in liquid form, without the need for additional drug solidification, efficacy verification, and subsequent approval. Specialized dissolving or coated microneedle patches that deliver reformulated, solidified therapeutics have made considerable advances; however, microneedles that can deliver liquid drugs and vaccines still remain elusive because of technical limitations. Here, we present a snake fang-inspired microneedle patch that can administer existing liquid formulations to patients in an ultrafast manner (< 15 s). Rear-fanged snakes have an intriguing molar with a groove on the surface, which enables rapid and efficient infusion of venom or saliva into prey. Liquid delivery is based on surface tension and capillary action. The microneedle patch uses multiple open groove architectures that emulate the grooved fangs of rear-fanged snakes: Similar to snake fangs, the microneedles can rapidly and efficiently deliver diverse liquid-phase drugs and vaccines in seconds under capillary action with only gentle thumb pressure, without requiring a complex pumping system. Hydrodynamic simulations show that the snake fang-inspired open groove architectures enable rapid capillary force-driven delivery of liquid formulations with varied surface tensions and viscosities. We demonstrate that administration of ovalbumin and influenza virus with the snake fang-inspired microneedle patch induces robust antibody production and protective immune response in guinea pigs and mice

Caloric restriction of db/db mice reverts hepatic steatosis and body weight with divergent hepatic metabolism

Non-alcoholic fatty liver disease (NAFLD) is one of the most frequent causes of liver disease and its prevalence is a serious and growing clinical problem. Caloric restriction (CR) is commonly recommended for improvement of obesity-related diseases such as NAFLD. However, the effects of CR on hepatic metabolism remain unknown. We investigated the effects of CR on metabolic dysfunction in the liver of obese diabetic db/db mice. We found that CR of db/db mice reverted insulin resistance, hepatic steatosis, body weight and adiposity to those of db/m mice. H-NMR- and UPLC-QTOF-MS-based metabolite profiling data showed significant metabolic alterations related to lipogenesis, ketogenesis, and inflammation in db/db mice. Moreover, western blot analysis showed that lipogenesis pathway enzymes in the liver of db/db mice were reduced by CR. In addition, CR reversed ketogenesis pathway enzymes and the enhanced autophagy, mitochondrial biogenesis, collagen deposition and endoplasmic reticulum stress in db/db mice. In particular, hepatic inflammation-related proteins including lipocalin-2 in db/db mice were attenuated by CR. Hepatic metabolomic studies yielded multiple pathological mechanisms of NAFLD. Also, these findings showed that CR has a therapeutic effect by attenuating the deleterious effects of obesity and diabetes-induced multiple complications

Search for a dark vector gauge boson decaying to π+π−\pi^+ \pi^- using η→π+π−γ\eta \rightarrow \pi^+\pi^- \gamma decays

We report a search for a dark vector gauge boson $U^\prime$ that couples to quarks in the decay chain $D^{*+} \to D^0 \pi^+, D^0 \to K^0_S \eta, \eta \to U^\prime \gamma$, $U^\prime \to \pi^+ \pi^-$. No signal is found and we set a mass-dependent limit on the baryonic fine structure constant of $10^{-3} - 10^{-2}$ in the $U^\prime$ mass range of 290 to 520 MeV/$c^2$. This analysis is based on a data sample of 976 fb$^{-1}$ collected by the Belle experiment at the KEKB asymmetric-energy $e^+e^-$ collider.Comment: 6 pages, 4 figure

Measurement of the Decays B→ηℓνℓ\boldsymbol{B\to\eta\ell\nu_\ell} and B→η′ℓνℓ\boldsymbol{B\to\eta^\prime\ell\nu_\ell} in Fully Reconstructed Events at Belle

We report branching fraction measurements of the decays $B^+\to\eta\ell^+\nu_\ell$ and $B^+\to\eta^\prime\ell^+\nu_\ell$ based on 711~fb$^{-1}$ of data collected near the $\Upsilon(4S)$ resonance with the Belle experiment at the KEKB asymmetric-energy $e^+e^-$ collider. This data sample contains 772 million $B\bar B$~events. One of the two $B$~mesons is fully reconstructed in a hadronic decay mode. Among the remaining ("signal-$B$") daughters, we search for the $\eta$~meson in two decay channels, $\eta\to\gamma\gamma$ and $\eta\to\pi^+\pi^-\pi^0$, and reconstruct the $\eta^{\prime}$~meson in $\eta^\prime\to\eta\pi^+\pi^-$ with subsequent decay of the $\eta$ into $\gamma\gamma$. Combining the two $\eta$ modes and using an extended maximum likelihood, the $B^+\to\eta\ell^+\nu_\ell$ branching fraction is measured to be $(4.2\pm 1.1 (\rm stat.)\pm 0.3 (\rm syst.))\times 10^{-5}$. For $B^+\to\eta^\prime\ell^+\nu_\ell$, we observe no significant signal and set an upper limit of $0.72\times 10^{-4}$ at 90\% confidence level.Comment: 8 pages, 4 figure

Study of Excited Ξc\Xi_c States Decaying into Ξc0\Xi_c^0 and Ξc+\Xi_c^+ Baryons

Using a data sample of 980 ${\rm fb}^{-1}$ of $e^+e^-$ annihilation data taken with the Belle detector operating at the KEKB asymmetric-energy $e^+e^-$ collider, we report the results of a study of excited $\Xi_c$ states that decay, via the emission of photons and/or charged pions, into $\Xi_c^0$ or $\Xi_c^+$ ground state charmed-strange baryons. We present new measurements of the masses of all members of the $\Xi_c^{\prime}$, $\Xi_c(2645)$, $\Xi_c(2790)$, $\Xi_c(2815)$, and $\Xi_c(2980)$ isodoublets, measurements of the intrinsic widths of those that decay strongly, and evidence of previously unknown transitions.Comment: Submitted to PR