TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data.

Motivation: Prediction of T-cell receptor (TCR)-epitope interactions is important for many applications in biomedical research, such as cancer immunotherapy and vaccine design. The prediction of TCR-epitope interactions remains challenging especially for novel epitopes, due to the scarcity of available data.

Results: We propose TSpred, a new deep learning approach for the pan-specific prediction of TCR binding specificity based on paired chain TCR data.

The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex.

Neoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUS and VACINUS VACINUS incorporates physical binding between peptides and MHCs (pMHCs), and VACINUS integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs).

Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics.

Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities.

G-RANK: an equivariant graph neural network for the scoring of protein-protein docking models.

Motivation: Protein complex structure prediction is important for many applications in bioengineering. A widely used method for predicting the structure of protein complexes is computational docking. Although many tools for scoring protein-protein docking models have been developed, it is still a challenge to accurately identify near-native models for unknown protein complexes.

A Sensitive Immunodetection Assay Using Antibodies Specific to Staphylococcal Enterotoxin B Produced by Baculovirus Expression.

Staphylococcal enterotoxin B (SEB) is a potent bacterial toxin that causes inflammatory stimulation and toxic shock, thus it is necessary to detect SEB in food and environmental samples. Here, we developed a sensitive immunodetection system using monoclonal antibodies (mAbs). Our study is the first to employ a baculovirus expression vector system (BEVS) to produce recombinant wild-type SEB.

Phenotype-based single cell sequencing identifies diverse genetic subclones in CD133 positive cancer stem cells.

Tumor heterogeneity is one of the ongoing huddles in the field of colon cancer therapy. It is evident that there are countless clones which exhibit different phenotypes and therefore, single cell analysis is inevitable. Cancer stem cells (CSCs) are rare cell population within tumor which is known to function in cancer metastasis and recurrence.

Targeted sequencing aids in identifying clonality in chronic myelomonocytic leukemia.

Chronic myelomonocytic leukemia (CMML) typically shows monocytosis in the peripheral blood (PB), which must be differentiated from reactive monocytosis. To determine the clonality of CMML, we performed molecular and cytogenetic analysis in Korean patients. To investigate whether monocytes in the PB harbored clonal mutational changes, we performed single-cell sequencing after selecting monocytes, neutrophils, and lymphocytes by morphology-aided laser microdissection.

Characteristics of Waldenström Macroglobulinemia in Korean Patients According to Mutational Status of MYD88 and CXCR4: Analysis Using Ultra-Deep Sequencing.

Background: Little is known about the mutational frequency of myeloid differentiation factor 88 (MYD88) and C-X-C chemokine receptor type 4 (CXCR4) and the corresponding characteristics in Asian individuals afflicted with Waldenström macroglobulinemia (WM). We investigated the characteristics of WM according to mutational status of MYD88/CXCR4, and attempted to determine the lineage commitment among hematopoietic cells by MYD88 single-cell sequencing on bone marrow (BM) smear slides.

Materials And Methods: CXCR4 mutations (muts) were detected using ultra-deep sequencing using target capture.

Ginkgetin, a biflavone from Ginkgo biloba leaves, prevents adipogenesis through STAT5-mediated PPARγ and C/EBPα regulation.

Adipogenesis involved in hypertrophy and hyperplasia of adipocytes is responsible for expanding the mass of adipose tissues in obese individuals. Peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα) are two principal transcription factors induced by delicate signaling pathways, including signal transducer and activator of transcription 5 (STAT5), in adipogenesis. Here, we demonstrated a novel role of ginkgetin, a biflavone from Ginkgo biloba leaves, as a STAT5 inhibitor that blocks the differentiation of preadipocytes into adipocytes.

Author Correction: Evaluating Tumor Evolution via Genomic Profiling of Individual Tumor Spheroids in a Malignant Ascites.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing.

Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe PHLI-seq, a novel approach that enables high-throughput isolation and genome-wide sequence analysis of single cells or small numbers of cells to construct genomic maps within cancer tissue in relation to the images or phenotypes of the cells. By applying PHLI-seq, we reveal the heterogeneity of breast cancer tissues at a high resolution and map the genomic landscape of the cells to their corresponding spatial locations and phenotypes in the 3D tumor mass.

Evaluating Tumor Evolution via Genomic Profiling of Individual Tumor Spheroids in a Malignant Ascites.

Epithelial ovarian cancer (EOC) is a silent but mostly lethal gynecologic malignancy. Most patients present with malignant ascites and peritoneal seeding at diagnosis. In the present study, we used a laser-aided isolation technique to investigate the clonal relationship between the primary tumor and tumor spheroids found in the malignant ascites of an EOC patient.

Preferential Impairment of the Contralesional Posterior Semicircular Canal in Internuclear Ophthalmoplegia.

Background: The vertical vestibulo-ocular reflex (VOR) may be impaired in internuclear ophthalmoplegia (INO) as the medial longitudinal fasciculus (MLF) conveys VOR-signals from the vertical semicircular canals. It has been proposed that signals from the contralesional posterior semicircular canal (PSC) are exclusively transmitted through the MLF, while for the contralesional anterior canal other pathways exist.

Objective: Here, we aimed to characterize dysfunction in individual canals in INO-patients using the video-head-impulse test (vHIT) and to test the hypothesis of dissociated vertical canal impairment in INO.

Gene Expression Profiling of Hepatocellular Carcinoma Derived Cancer Stem Like Cell under Hypoxia.

Purpose: Cancer stem like cells (CSCs), with unlimited self-renewal potential and other stem cell characteristics, occur in several cancers including hepatocellular carcinoma (HCC). Although CSCs can initiate tumors, malignant proliferation, relapse and multi-drug resistance, the ways how to activate them still remain unknown. This study aims to evaluate whether CSC acquire tumorigenic characters under tumor hypoxia, analyzed by microarray analysis.

Central positional nystagmus associated with cerebellar tumors: Clinical and topographical analysis.

Purpose: Positional nystagmus is usually caused by peripheral vestibular disorder, mostly benign paroxysmal positional vertigo (BPPV). However, positional nystagmus is also encountered in central lesions. We aimed to determine clinical characteristics of the structures responsible for central positional nystagmus (CPN) associated with brain tumors.

Programmable gradational micropatterning of functional materials using maskless lithography controlling absorption.

The demand for patterning functional materials precisely on surfaces of stimuli-responsive devices has increased in many research fields. In situ polymerization technology is one of the most convenient ways to place the functional materials on a desired location with micron-scale accuracy. To fabricate stimuli-responsive surfaces, controlling concentration of the functional material is much as important as micropatterning them.

A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform.

Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms.

Maxillary yaw as the primary predictor of maxillary dental midline deviation: 3D analysis using cone-beam computed tomography.

Purpose: The purpose of this study was to investigate which factors affect upper dental midline deviation in dentofacial deformity patients using cone-beam computed tomography analysis.

Patients And Methods: Twenty-eight patients were selected for this study. Subjects were divided into 2 groups according to the amount of upper incisor (U1) midline deviation from the clinical facial midline: group 1 (U1 deviation <2 mm) and group 2 (U1 deviation >2 mm).

Evaluation of Cardiac Function by Transthoracic Echocardiography in Subjects with ST-Segment Elevation Myocardial Infarction Following Primary Percutaneous Coronary Intervention according to Valsartan Dose: The Valsartan One Center Trial.

Background: The aim of this study was to evaluate the mid-term changes in cardiac function by transthoracic echocardiogram (TTE) in patients with ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PCI) according to valsartan dose.

Methods: Between April 2006 and February 2009, 78 subjects (mean age: 57 ± 12 years, M : F = 74 : 4) with STEMI who underwent primary PCI were enrolled. Fifty three patients received low dose valsartan (40 or 80 mg) and 25 patients received high dose valsartan (160 or 320 mg).

Pentraxin 3 as a novel marker predicting congestive heart failure in subjects with acute coronary syndrome.

Background And Objectives: Pentraxin 3 (PTX3) was shown to be elevated in the acute phase of acute myocardial infarction (AMI) and to have prognostic significance in AMI patients. The aim of this study was to estimate whether the value of PTX3 could be used as a prognostic biomarker, with the global registry of acute coronary events (GRACE) risk assessment tool, in patients with acute coronary syndrome (ACS).

Subjects And Methods: Between July 2007 and June 2008, 137 patient subjects (mean age : 61±12 years, M : F=108 : 29) with ACS who underwent coronary intervention, but did not have a prior percutaneous coronary intervention (PCI) and/or follow-up coronary angiogram, were enrolled.

The Relationship Between Serum Pentraxin 3 and Central Obesity in ST-Segment Elevation Myocardial Infarction Patients.

Background And Objectives: As shown in previous studies, pentraxin 3 (PTX3) can be a useful inflammatory marker for metabolic syndrome and central obesity. Serum PTX3 levels are also an independent factor associated with visceral fat area. The aim of this study was to assess the role of PTX3 as an inflammatory maker in patients with central obesity undergoing primary percutaneous coronary intervention (PCI) following an ST-segment elevation myocardial infarction (STEMI).

Effect of low-level laser treatment after installation of dental titanium implant-immunohistochemical study of RANKL, RANK, OPG: an experimental study in rats.

Background And Objectives: This experiment using an animal experimental model was conducted in order to investigate the effect of low-level laser therapy (LLLT) on the healing of the dental titanium implant.

Study Design/materials And Methods: The experimental group received LLLT for a week and the control group did not. Each group consisted of 10 rats.

Analysis of color distortions in a transmission-type holographic screen.

Full-color transmission-type holographic screens for displaying stereoscopic and multiview images suffer color distortions, especially at their edges. These distortions arise because the reconstructed image of the diffuser appears not at a specified location at different locations for different parts of the screen. Analysis shows that the diffuser strip, which is an object that records the screen, should be extended further in the photoplate direction than in the conventional position to remove the distortions and that use of a short-wavelength laser in the blue spectral region, along with extending the diffuser, is recommended for recording large-sized screens.