Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

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

ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling

Previous studies including ours have demonstrated a critical function of the transcription factor ETV2 (ets variant 2; also known as ER71) in determining the fate of cardiovascular lineage development. However, the underlying mechanisms of ETV2 function remain largely unknown. In this study, we demonstrated the novel function of the miR (micro RNA)-126-MAPK (mitogen-activated protein kinase) pathway in ETV2-mediated FLK1 (fetal liver kinase 1; also known as VEGFR2)+ cell generation from the mouse embryonic stem cells (mESCs). By performing a series of experiments including miRNA sequencing and ChIP (chromatin immunoprecipitation)-PCR, we found that miR-126 is directly induced by ETV2. Further, we identified that miR-126 can positively regulate the generation of FLK1+ cells by activating the MAPK pathway through targeting SPRED1 (sprouty-related EVH1 domain containing 1). Further, we showed evidence that JUN/FOS activate the enhancer region of FLK1 through AP1 (activator protein 1) binding sequences. Our findings provide insight into the novel molecular mechanisms of ETV2 function in regulating cardiovascular lineage development from mESCs

Teaching phonological awareness skill to students with hearing impairment: Current perspectives

2010This study deals with the current debate whether teaching phonological awareness skill to the hearing impaired students would be helpful for the reading comprehension. Purpose of this study is to present the theoretical grounds of teaching phonological awareness skill to the hearing impaired students. This study was done by a literature analysis based on a recent cognitive reading mechanism, the duel route cascade model of reading. This research explained why teaching phonological awareness skill to the hearing impaired students would be an effective method to building their reading comprehension.This work was originally supported by the National Research Foundation of Korea(NRF) grant funded by the Korea government(MEST)(2010-0027582)

Perceived Neighborhood Environment Associated with Sarcopenia in Urban-Dwelling Older Adults: The Korean Frailty and Aging Cohort Study (KFACS)

Sarcopenia is associated with adverse health outcomes among older individuals. However, little is known about its association with neighborhood environmental factors. We explored the relationship between sarcopenia and perceived neighborhood environmental factors among community-dwelling older adults aged 70–84 years. We analyzed 1778 participants (mean age of 75.9 ± 3.8 years; 54.0% women) who lived in urban areas and underwent dual-energy X-ray absorptiometry from the Korean Frailty and Aging Cohort Study. Sarcopenia was defined according to the Asian Working Group for Sarcopenia 2019 definition. Perceived neighborhood environmental factors were assessed using the Environmental Module of the International Physical Activity Questionnaire (IPAQ-E). In the multivariate analysis, compared to the fifth quintile of the IPAQ-E score, the odds ratios (ORs) and 95% confidence intervals (CIs) for sarcopenia in the first, second, third, and fourth quintiles were 2.13 (1.40–3.24), 1.72 (1.12–2.64), 1.75 (1.15–2.66), and 1.62 (1.06–2.47), respectively. These neighborhood environmental characteristics were linked with an increased likelihood of sarcopenia: no public transportation access (OR = 2.04; 95% CI = 1.19–3.48), poor recreational facilities access (OR = 1.39; 95% CI = 1.01–1.90), absence of destination (OR = 1.53; 95% CI = 1.06–2.20), many hill hazards (OR = 1.36; 95% CI = 1.03–1.78), and lack of traffic safety (OR = 1.35; 95% CI = 1.02–1.78). Thus, better neighborhood environmental strategies may help prevent sarcopenia among urban-dwelling older adults

Identifying Defect-Induced Trion in Monolayer WS2 via Carrier Screening Engineering

Unusually high exciton binding energies (BEs), as much as similar to 1 eV in monolayer transition-metal dichalcogenides, provide opportunities for exploring exotic and stable excitonic many-body effects. These include many-body neutral excitons, trions, biexcitons, and defect-induced excitons at room temperature, rarely realized in bulk materials. Nevertheless, the defect-induced trions correlated with charge screening have never been observed, and the corresponding BEs remain unknown. Here we report defect-induced A-trions and B-trions in monolayer tungsten disulfide (WS2) via carrier screening engineering with photogenerated carrier modulation, external doping, and substrate scattering. Defect-induced trions strongly couple with inherent SiO2 hole traps under high photocarrier densities and become more prominent in rhenium-doped WS2. The absence of defect-induced trion peaks was confirmed using a trap-free hexagonal boron nitride substrate, regardless of power density. Moreover, many-body excitonic charge states and their BEs were compared via carrier screening engineering at room temperature. The highest BE was observed in the defect-induced A-trion state (similar to 214 meV), comparably higher than the trion (209 meV) and neutral exciton (174 meV), and further tuned by external photoinduced carrier density control. This investigation allows us to demonstrate defect-induced trion BE localization via spatial BE mapping in the monolayer WS2 midflake regions distinctive from the flake edges.11Nsciescopu

Spectroscopic Evidence of Energy Transfer in BODIPY-Incorporated Nano-Porphyrinic Metal-Organic Frameworks

Metal–organic frameworks (MOFs) represent a class of solid-state hybrid compounds consisting of multitopic organic struts and metal-based nodes that are interconnected by coordination bonds, and they are ideal for light harvesting due to their highly ordered structure. These structures can be constructed with chromophore organic ligands structures for the purpose of efficient light harvesting. Here, we prepared porphyrin-based nano-scaled MOFs (nPCN-222) with BODIPY and I2BODIPY photosensitizers by incorporating BODIPY/I2BODIPY into nPCN-222 (nPCN-BDP/nPCN-I2BDP) and demonstrated resonance energy transfer from the donor (BODIPY/I2BODIPY) to the acceptor (nPCN-222) resulting in greatly enhanced fluorescence of nPCN-222, as visually manifested by time-resolved and space-resolved fluorescence imaging of the nano-scaled MOFs

Heterogeneous modulation of exciton emission in triangular WS2 monolayers by chemical treatment

Chemical treatments were recently shown to be very effective in enhancing the exciton emission of monolayer transition metal dichalcogenides (1L-TMDs) by suppressing the exciton quenching caused by structural defects. However, the effects of these chemical treatments varied greatly depending on the synthesis method and the type of 1L-TMD; therefore, the exact origin of the emission enhancement is still elusive. Here we report the spatially heterogeneous effects of bis(trifluoromethane) sulfonimide (TFSI) and benzyl viologen (BV) treatment on the optical properties of triangular 1L-WS2 grown by chemical vapor deposition (CVD). Nanoscale photoluminescence (PL) and Raman spectral maps showed that TFSI had a minimal effect on the inner region of the triangular WS2 grain, whereas the PL of the edge region was enhanced up to 25 times; further, BV reduced the PL, also more strikingly in the edge region. Systematic variation of the spectral weights among neutral excitons, trions, and bi-excitons indicated that p-doping and n-doping with TFSI and BV, respectively, occurred in both the inner and edge regions; however, the PL enhancement was attributed mainly to the reduction of structural defects caused by TFSI treatment. Our observation of the spatially heterogeneous effects of chemical treatment suggests that the inner and edge regions of CVD-grown 1L-WS2 are populated with different types of structural defects and helps in clarifying the mechanism by which chemical treatment enhances the optical properties of 1L-TMDs. This journal is ©The Royal Society of Chemistry 20176

Electrical modulation of excitonic transition in monolayer tungsten disulfide on periodically poled ferroelectric substrates

© 2022 Korean Physical Society. Although the spectral investigation of monolayer two-dimensional transition metal dichalcogenide (1L-TMD) has been extensively performed for identifying modulation of excitonic transition, study of excitonic transition in ferroelectric/TMD hybrid structure is essential to understand and design high speed and low loss devices based on in-plane junctions. Here, we demonstrate electrical modulation of excitonic transition by transferring 1L-tungsten disulfide (WS2) onto a ferroelectric domain surface, a periodically poled lithium niobate (PPLN). We observe that exciton (A0) and trion (A−) emissions of 1L-WS2 are spatially modulated depending on the sign of the phase domain, such that A0 and A− emission is stronger at the positive (D+) and negative (D−) domain, respectively. In addition, different trends of excitonic transition of 1L-WS2 between D+ and D− domain are demonstrated by applying a back-gate bias voltage. The spatial modulation of electrical and optical characteristics of 1L-TMDs will help to design the homo- or hetero p-n junctions based on TMDs.11Nsciescopuskc

Diverse Genetic Landscape of Suspected Retinitis Pigmentosa in a Large Korean Cohort

We conducted targeted next-generation sequencing (TGS) and/or whole exome sequencing (WES) to assess the genetic profiles of clinically suspected retinitis pigmentosa (RP) in the Korean population. A cohort of 279 unrelated Korean patients with clinically diagnosed RP and available family members underwent molecular analyses using TGS consisting of 88 RP-causing genes and/or WES with clinical variant interpretation. The combined genetic tests (TGS and/or WES) found a mutation in the 44 RP-causing genes and seven inherited retinal disease (IRD)-causing genes, and the total mutation detection rate was 57%. The mutation detection rate was higher in patients who experienced visual deterioration at a younger age (75.4%, age of symptom onset under 10 years) and who had a family history of RP (70.7%). The most common causative genes were EYS (8.2%), USH2A (6.8%), and PDE6B (4.7%), but mutations were dispersed among the 51 RP/IRD genes generally. Meanwhile, the PDE6B mutation was the most common in patients experiencing initial symptoms in their first decade, EYS in their second to third decades, and USH2A in their fifth decades and older. Of note, WES revealed some unexpected genotypes: ABCC6, CHM, CYP4V2, RS1, TGFBI, VPS13B, and WDR19, which were verified by ophthalmological re-phenotyping

Efficient and Stable Solar Hydrogen Generation of Hydrophilic Rhenium-Disulfide-Based Photocatalysts via Chemically Controlled Charge Transfer Paths

© 2020 American Chemical Society.Effective charge separation and rapid transport of photogenerated charge carriers without self-oxidation in transition metal dichalcogenide photocatalysts are required for highly efficient and stable hydrogen generation. Here, we report that a molecular junction as an electron transfer path toward two-dimensional rhenium disulfide (2D ReS2) nanosheets from zero-dimensional titanium dioxide (0D TiO2) nanoparticles induces high efficiency and stability of solar hydrogen generation by balanced charge transport of photogenerated charge carriers. The molecular junctions are created through the chemical bonds between the functionalized ReS2 nanosheets (e.g., -COOH groups) and -OH groups of two-phase TiO2 (i.e., ReS2-C6H5C(≠O)-O-TiO2 denoted by ReS2-BzO-TiO2). This enhances the chemical energy at the conduction band minimum of ReS2 in ReS2-BzO-TiO2, leading to efficiently improved hydrogen reduction. Through the molecular junction (a Z-scheme charge transfer path) in ReS2-BzO-TiO2, recombination of photogenerated charges and self-oxidation of the photocatalyst are restrained, resulting in a high photocatalytic activity (9.5 mmol h-1 per gram of ReS2 nanosheets, a 4750-fold enhancement compared to bulk ReS2) toward solar hydrogen generation with high cycling stability of more than 20 h. Our results provide an effective charge transfer path of photocatalytic TMDs by preventing self-oxidation, leading to increases in photocatalytic durability and a transport rate of the photogenerated charge carrier