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Enhanced UV stability of perovskite solar cells with a SrO interlayer
Lee, Sang-Won,Kim, Seongtak,Bae, Soohyun,Cho, Kyungjin,Chung, Taewon,Hwang, Jae-Keun,Song, Inseol,Lee, Wonkyu,Park, Sungeun,Jung, Jaebong,Chun, Jihun,Lee, Yoon Jung,Moon, Yeon Ji,Lee, Hae-Seok,Kim, Do Elsevier 2018 Organic Electronics Vol.63 No.-
<P><B>Abstract</B></P> <P>We investigated strontium oxide (SrO) as an interlayer material to enhance the UV stability of a CH<SUB>3</SUB>NH<SUB>3</SUB>PbI<SUB>3</SUB> perovskite solar cell. Moisture and over 400 nm wavelength of light were excluded to investigate the effect of UV light only. Two different interlayer fabrication processes were examined to optimize the performance of this solar cell. Devices fabricated by dipping for 30 min in SrO solution exhibited photoconversion efficiencies of 15.5%, whereas those fabricated with 60-min dipping showed photoconversion efficiencies of 15% and exhibited local Sr agglomeration. Devices with SrO displayed lower initial efficiencies than those without any SrO layer (17.6%), However, a device without SrO retained only 34.4% of its initial efficiency after 100 h of UV exposure. In contrast, SrO-incorporated devices retained almost 60.0% of their initial efficiency. Severe μ-PL mapping intensity degradation was observed in devices that did not include the interlayer, but no degradation was observed in those with the SrO interlayer. This can be attributed to the passivation of the degradation sites by SrO.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Perovskite UV stability was tested under conditions except moisture, oxygen and wavelengths exceeding 400 nm. </LI> <LI> With high resolution μ-PL mapping technique, direct evidence is provided about the area perovskite UV degradation begins. </LI> <LI> UV degradation is initiated at the ETL/perovskite interface. </LI> <LI> Effect of the SrO interlayer on UV stability was examined in an inert atmosphere. </LI> <LI> UV stability is enhanced by SrO interface passivation. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
Lee, Soohyun,Seo, Chae Hwa,Lim, Byungho,Yang, Jin Ok,Oh, Jeongsu,Kim, Minjin,Lee, Sooncheol,Lee, Byungwook,Kang, Changwon,Lee, Sanghyuk Oxford University Press 2011 Nucleic acids research Vol.39 No.2
<P>We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. Quantitative RT–PCR based on 27 randomly selected genes in two human cell lines and computer simulation experiments demonstrated superior accuracy of NEUMA over other recently developed methods. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (‘consistency coefficient’) for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. We propose that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data.</P>
Fluorescence Enhancement from Nitro-Compound-Sensitive Bacteria within Spherical Hydrogel Scaffolds
Kim, Soohyun,Kim, Hyunji,Qiao, Tian,Cha, Chaenyung,Lee, Sung Kuk,Lee, Kangseok,Ro, Hyun Ji,Kim, Youngkyun,Lee, Wonmok,Lee, Hyunjung American Chemical Society 2019 ACS APPLIED MATERIALS & INTERFACES Vol.11 No.15
<P>For the safety of both production and life, it is a very significant issue to detect explosive nitro compounds in a remote way or over a long distance. Here, we report that nitro compounds were detected by the bacterial sensor based on hydrogel microbeads as a platform. Green fluorescent protein-producing <I>Escherichia coli</I>, which was genetically engineered to be sensitive to nitro compounds, was loaded within poly(2-hydroxyethyl methacrylate) [poly(HEMA)]-based hydrogel beads, in which fluorescent signals from bacteria were concentrated and strong enough to be easily detected. For efficient loading of negatively charged bacteria, the surface charge of poly(HEMA)-based beads was controlled by copolymerization with 2-(methacryloyloxy)ethyltrimethylammonium chloride (MAETC) as a cationic monomer. With the addition of MAETC, the cell affinity was nine times enhanced by the interaction between the positively charged poly(HEMA-<I>co</I>-MAETC) beads and negatively charged bacteria. The increased cell affinity resulted in an enhancement of a sensing signal. After exposure to 2,4,6-trinitrotoluene, a typical explosive nitro compound, the fluorescence intensity of bacterial sensors using poly(HEMA-<I>co</I>-MAETC) beads having 80 wt % MAETC was five times increased compared to those based on poly(HEMA) beads. This amplification of the fluorescent signal enables easier detection of explosives efficiently by a remote detection, even over a long distance.</P> [FIG OMISSION]</BR>
Jae-Geun Lee,Soohyun Lee,Juhee Jeon,Hyun Gi Kong,Hyun-Ju Cho,Jong-Hwan Kim,Seon-Young Kim,Myung Jin Oh,Daum Lee,Nari Seo,Ki Hun Park,Kweon Yu,Hyun Joo An,Choong-Min Ryu,Jeong-Soo Lee 한국당과학회 2022 한국당과학회 학술대회 Vol.2022 No.07
Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that contributes to the development of CAC, remains unknown. We found that zebrafish tp53 mutant larvae exhibited elevated intestinal inflammation, by monitoring the NFκB activity in the mid-distal intestines of zebrafish larvae using an NFκB:EGFP transgenic reporter line in vivo as well as neutrophil infiltration into the intestine. This inflammation was due to dysbiotic gut microbiota with reduced diversity, revealed using both 16S rRNA amplicon sequencing and a germfree larva model. In this dysbiosis, Aeromonas spp. were aberrantly enriched as major pathobionts and exhibited the capacity for aggressive colonization in tp53 mutants. Importantly, the ex-germfree experiments supported the causality of the host tp53 mutation for inducing the inflammation. Transcriptome and high performance liquid chromatography analyses of the host gastrointestinal tracts identified dysregulated sialic acid (SA) metabolism concomitant with increased host Neu5Gc levels as the key determinant of aberrant inflammation, which was reversed by the sialidase inhibitors oseltamivir and Philippin A. These results demonstrate a crucial role for host tp53 in maintaining symbiosis and immune homeostasis via SA metabolism. Disturbed SA metabolism via a tp53 mutation may be exploited by specific elements of the gut microbiome, eliciting both dysbiosis and inflammation. Manipulating sialometabolism may therefore provide an efficacious therapeutic strategy for tp53 mutation-induced dysbiosis, inflammation, and, ultimately, related cancers.
Lee, Soohyun,Seo, Chae Hwa,Alver, Burak Han,Lee, Sanghyuk,Park, Peter J. BioMed Central 2015 BMC bioinformatics Vol.16 No.-
<P><B>Background</B></P><P>RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost.</P><P><B>Results</B></P><P>We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods.</P><P><B>Conclusions</B></P><P>EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-015-0704-z) contains supplementary material, which is available to authorized users.</P>
Lee, Sejoon,Lee, Soohyun,Ouellette, Scott,Park, Woong-Yang,Lee, Eunjung A.,Park, Peter J. Oxford University Press 2017 Nucleic acids research Vol.45 No.11
<P><B>Abstract</B></P><P>In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies. Availability: https://github.com/parklab/NGSCheckMate</P>