Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

Comparison of novel peptides identified from real proteogenomic databases. (DOCX 68 kb

The Early Light Curve of a Type Ia Supernova 2021hpr in NGC 3147: Progenitor Constraints with the Companion Interaction Model

The progenitor system of Type Ia supernovae (SNe Ia) is expected to be a close binary system of a carbon/oxygen white dwarf (WD) and a non-degenerate star or another WD. Here, we present results from a high-cadence monitoring observation of SN 2021hpr in a spiral galaxy, NGC 3147, and constraints on the progenitor system based on its early multi-color light curve data. First, we classify SN 2021hpr as a normal SN Ia from its long-term photometric and spectroscopic data. More interestingly, we found a significant "early excess" in the light curve over a simple power-law $\sim t^{2}$ evolution. The early light curve evolves from blue to red and blue during the first week. To explain this, we fitted the early part of $BVRI$-band light curves with a two-component model of the ejecta-companion interaction and a simple power-law model. The early excess and its color can be explained by shock cooling emission due to a companion star having a radius of $8.84\pm0.58$$R_{\odot}$. We also examined HST pre-explosion images with no detection of a progenitor candidate, consistent with the above result. However, we could not detect signs of a significant amount of the stripped mass from a non-degenerate companion star ($\lesssim0.003\,M_{\odot}$ for H$\alpha$ emission). The early excess light in the multi-band light curve supports a non-degenerate companion in the progenitor system of SN 2021hpr. At the same time, the non-detection of emission lines opens a door for other methods to explain this event.Comment: 26 pages, 13 figures + appendix, Accepted for publication in Ap

Very virulent infectious bursal disease virus isolated from wild birds in Korea: Epidemiological implications

To explore the epidemiological link between infectious bursal disease virus (IBDV) in wild birds and domestic chickens in Korea, we examined 107 free-living wild birds, representing 7 species, that were found dead of apparent natural causes in Korea over the past two years for the presence of IBDV. Five birds were tested positive for IBDV by RT-PCR assay: black-billed magpie (n = 1), mallard duck (n = 2), bean goose (n = 1) and white-fronted goose (n = 1). IBDV was isolated from RT-PCR-positive tissues following chicken embryo inoculation. Sequence analysis of the VP2 gene indicated that all of the isolates from the wild birds encode amino acids A222, I242, I256, I294 and S299 of VP2, which are conserved among strains of very virulent IBDV (vvIBDV). Phylogenetic analysis revealed that the wild bird IBDV isolates are closely related to strains of vvIBDV. An IBDV isolate from a magpie showed 60% mortality in SPF chickens and severe bursal atrophy. The epidemiological implications of IBDV in free-living wild birds are discussed. To our knowledge, this is the first report of vvIBDV in free-living wild birds.This study was supported by the National Veterinary Research and Quarantine Service of the Ministry of Agriculture and Fishery, Korea

Optical Property and Alighment of KAO Wide Field Telescope (NEOPAT-3)

We have investigated the optical property of the KAO(Korea Astronomy Observatory) wide field telescope (named NEOPAT-3; Near Earth Object and Satellite Patrol-3) and aligned optical system. The NEOPAT-3 is restricted to V,R,I-filters because of the refractive property of the correcting lens system. Because of the fast focal ratio, the optical performance of the NEOPAT-3 is very sensitive to its alignment factors of the optical system. To make the spot radius smaller than 8μm in rms over 2degree×2degree field, the optical system must satisfy the following conditions: 1) The tilt error between detector plane and focal plane should be less than 0.05degree. 2) The decenter error between the primary mirror and the correcting lens system should be less than 1mm. 3) The distance error between the primary mirror and the correcting lens system should be less than 2.3mm. In order to align the optical system accurately, we measured the aberrations of the telescope quantitatively by means of curvature sensing technique. NEOPAT-3 is installed temporary on the roof of the TRAO(Taeduk Radio Astronomy Observatory) main building to normalize system performance and to develop automatic observation

Prognostic Factors for Pulmonary Fibrosis Following Pneumonia in Patients with COVID-19: A Prospective Study

The frequency and clinical manifestation of lung fibrosis accompanied by coronavirus disease (COVID-19) are not well-established. We aimed to identify the factors attributed to post-COVID-19 fibrosis. This single-center prospective study included patients diagnosed with COVID-19 pneumonia from 12 April to 22 October 2021 in the Republic of Korea. The primary outcome was the presence of pulmonary fibrosis on a CT scan 3 months after discharge; the fibrosis risk was estimated by a multiple logistic regression. The mean patient age was 55.03 ± 12.32 (range 27–85) years; 65 (66.3%) were men and 33 (33.7%) were women. The age, Charlson Comorbidity Index, lactate dehydrogenase level, aspartate aminotransferase level, and Krebs von den Lungen-6 level were significantly higher and the albumin level and the saturation of the peripheral oxygen/fraction of inspired oxygen (SpO2/FiO2) ratio were significantly lower in the fibrosis group than in the non-fibrosis group; the need for initial oxygen support was also greater in the fibrosis group. An older age (adjusted odds ratio (AOR) 1.12; 95% confidence interval (CI) 1.03–1.21) and a lower initial SpO2/FiO2 ratio (AOR 7.17; 95% CI 1.72–29.91) were significant independent risk factors for pulmonary fibrosis after COVID-19 pneumonia. An older age and a low initial SpO2/FiO2 ratio were crucial in predicting pulmonary fibrosis after COVID-19 pneumonia

CDK4 amplification predicts recurrence of well-differentiated liposarcoma of the abdomen.

The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD) and dedifferentiated (DD) liposarcomas.From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR).There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05). Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7%) and MDM2 amplification in 46 cases (95.8%). WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041). High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54) was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012) and multivariate analyses (P = 0.020).Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection

Comparative evaluation of QuantiFERON-TB Gold Plus for diagnosis of latent tuberculosis infection during solid organ transplantation

Background : The diagnosis of latent tuberculosis infection (LTBI) in solid organ transplantation (SOT) patients under lifelong immunosuppression has profound effects on preoperative and postoperative management. Interferon-gamma release assay (IGRA) is widely used to screen LTBI before or after transplantation. Methods : We evaluated the effect of posttransplantation immunosuppression on IGRA and influencing factors by measuring interval change of QuantiFERON-TB Gold Plus (QFT-Plus) between pretransplantation (pre-QFT-Plus) and posttransplantation (post-QFT-Plus) state in 20 patients who previously had reactive IGRA but not taken LTBI treatment. Results : Eleven (55%) out of 20 pre-QFT-Plus reactive patients became nonreactive state in repeated QFT-Plus (post-QFT-Plus) at 194-413 days (median, 257 days) after transplantation (discordant group). Even in persistently reactive group (concordant group), interferon-gamma (IFN-γ) levels after transplantation were decreased about 34% and 36% of their pretransplantation levels for TB1 and TB2, respectively. The only significant factors that affect interval change of QFT-Plus between pre- and post-SOT status were the concentrations of IFN-γ in pre-QFT-Plus (6.93 vs. 0.44 IU/mL in TB1 and 7.33 vs. 0.71 IU/mL in TB2). Conclusions: The reactivity of QFT-Plus is significantly compromised by immunosuppressive therapy, which increase the risk of false negative, particularly in patients with low level of IGRA reactivity. Therefore, interpretation of IGRA under immunosuppressive treatment require a caution and eventually, more sensitive tuberculosis-specific cytokine markers might be needed

Quantitative real-time PCR results of <i>CDK4</i> amplification by a) well-differentiated (WD) and dedifferentiated (DD) liposarcomas: amplification levels were not different between the two histologic subtypes.

<p>Quantitative real-time PCR results of <i>CDK4</i> amplification in <b>b)</b> WD and <b>c)</b> DD liposarcomas according to tumor recurrence: amplification was higher in WD liposarcomas with recurrence after surgical resection, but not different in DD liposarcomas regardless of tumor recurrence.</p