NGS for Sequence Variants.

Recent technological advances in next-generation sequencing (NGS) provide unprecedented power to sequence personal genomes, characterize genomic landscapes, and detect a large number of sequence variants. The discovery of disease-causing variants in patients' genomes has dramatically changed our perspective on precision medicine. This chapter provides an overview of sequence variant detection and analysis in NGS study.

Intracellular TRPA1 mediates Ca2+ release from lysosomes in dorsal root ganglion neurons.

Transient receptor potential A1 (TRPA1) is a nonselective cation channel implicated in thermosensation and inflammatory pain. In this study, we show that TRPA1 (activated by allyl isothiocyanate, acrolein, and 4-hydroxynonenal) elevates the intracellular Ca concentration ([Ca]) in dorsal root ganglion (DRG) neurons in the presence and absence of extracellular Ca Pharmacological and immunocytochemical analyses revealed the presence of TRPA1 channels both on the plasma membrane and in endolysosomes. Confocal line-scan imaging demonstrated Ca signals elicited from individual endolysosomes ("lysosome Ca sparks") by TRPA1 activation.

Oxidation of KCNB1 Potassium Channels Causes Neurotoxicity and Cognitive Impairment in a Mouse Model of Traumatic Brain Injury.

Unlabelled: The delayed rectifier potassium (K) channel KCNB1 (Kv2.1), which conducts a major somatodendritic current in cortex and hippocampus, is known to undergo oxidation in the brain, but whether this can cause neurodegeneration and cognitive impairment is not known. Here, we used transgenic mice harboring human KCNB1 wild-type (Tg-WT) or a nonoxidable C73A mutant (Tg-C73A) in cortex and hippocampus to determine whether oxidized KCNB1 channels affect brain function.

Applicability of an in-House Saponin-Based Extraction Method in Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Bacterial and Fungal Species in Positively Flagged Blood Cultures.

We used an in-house saponin-based extraction method to evaluate the performance of the Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) system for the identification of bacteria and fungi in 405 positively flagged blood culture bottles. Results obtained from MALDI-TOF/MS were compared with those obtained using conventional phenotypic identification methods. Of the 405 positively flagged blood culture bottles, 365 showed monomicrobal growth and were correctly identified to the species (72.

Epidemiology and outcomes of acute kidney injury in elderly chinese patients: a subgroup analysis from the EACH study.

Background: Information on acute kidney injury (AKI) in elderly hospitalized patients is limited. This study aims to assess the incidence, risk factors and outcomes of AKI in elderly Chinese patients.

Method: The Epidemiology of AKI in Chinese Hospitalized adults (EACH) study is a multicenter, retrospective cohort study conducted in nine regional central hospitals across China.

Facile preparation of nickel/carbonized wood nanocomposite for environmentally friendly supercapacitor electrodes.

We are reporting a facile way to prepare nickel/carbon nanocomposites from wood as a novel electrode material for supercapacitors. The surface morphology and the structure of the as-prepared electrodes were studied by using X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). The results indicate that after high-temperature carbonization process, the wood is converted into graphitic carbon with nickel nanoparticles uniformly distributed within the three dimensional structure of the wood.

SMYD3-Mediated H2A.Z.1 Methylation Promotes Cell Cycle and Cancer Proliferation.

SMYD3 methyltransferase is nearly undetectable in normal human tissues but highly expressed in several cancers, including breast cancer, although its contributions to pathogenesis in this setting are unclear. Here we report that histone H2A.Z.

Women with endometriosis have higher comorbidities: Analysis of domestic data in Taiwan.

Endometriosis, defined by the presence of viable extrauterine endometrial glands and stroma, can grow or bleed cyclically, and possesses characteristics including a destructive, invasive, and metastatic nature. Since endometriosis may result in pelvic inflammation, adhesion, chronic pain, and infertility, and can progress to biologically malignant tumors, it is a long-term major health issue in women of reproductive age. In this review, we analyze the Taiwan domestic research addressing associations between endometriosis and other diseases.

Use of negative pressure wound therapy in burn patients.

According to previous research, adjunctive negative pressure wound therapy (NPWT) can help manage infected wounds when applied along with appropriate debridement and antibiotic therapy as deemed clinically relevant. NPWT not only removes fluid, and reduces oedema, but also promotes perfusion around the wounds. In addition, NPWT may lead to improved graft fixation when used as a bolster, especially in patients who are less compliant or have poor graft fixation that result from using traditional methods.

Temperature-sensitive albino gene TCD5, encoding a monooxygenase, affects chloroplast development at low temperatures.

Chloroplasts are essential for photosynthesis and play critical roles in plant development. In this study, we characterized the temperature-sensitive chlorophyll-deficient rice mutant tcd5, which develops albino leaves at low temperatures (20 °C) and normal green leaves at high temperatures (32 °C). The development of chloroplasts and etioplasts is impaired in tcd5 plants at 20 °C, and the temperature-sensitive period for the albino phenotype is the P4 stage of leaf development.

Estimating functional brain networks by incorporating a modularity prior.

Functional brain network analysis has become one principled way of revealing informative organization architectures in healthy brains, and providing sensitive biomarkers for diagnosis of neurological disorders. Prior to any post hoc analysis, however, a natural issue is how to construct "ideal" brain networks given, for example, a set of functional magnetic resonance imaging (fMRI) time series associated with different brain regions. Although many methods have been developed, it is currently still an open field to estimate biologically meaningful and statistically robust brain networks due to our limited understanding of the human brain as well as complex noises in the observed data.

A Robust Gradient Based Method for Building Extraction from LiDAR and Photogrammetric Imagery.

Existing automatic building extraction methods are not effective in extracting buildings which are small in size and have transparent roofs. The application of large area threshold prohibits detection of small buildings and the use of ground points in generating the building mask prevents detection of transparent buildings. In addition, the existing methods use numerous parameters to extract buildings in complex environments, e.

Preparation and Characterization of Mesoporous Magnesium Silicate Gels and Application for Cobalt(II) Removal.

Two new mesoporous magnesium silicate gel adsorbents, MgO x 2SiO2 and MgO x 6SiO2, have been successfully prepared by hydrothermal method. The synthetic factors including reaction pH, temperature, time and calcination temperature were studied. The aiming products were characterized by N2 adsorption/desorption isotherms, FT-IR spectroscopy and Scanning Electron Microscopy (SEM).

High diversity of Pseudo-nitzschia along the northern coast of Sarawak (Malaysian Borneo), with descriptions of P. bipertita sp. nov. and P. limii sp. nov. (Bacillariophyceae).

Forty-eight isolates of Pseudo-nitzschia species were established from the Miri coast of Sarawak (Malaysian Borneo) and underwent TEM observation and molecular characterization. Ten species were found: P. abrensis, P.

Species diversity of fiddler crabs, genus Uca Leach, 1814 (Crustacea: Ocypodidae), from Taiwan and adjacent islands, with notes on the Japanese species.

The fiddler crabs, genus Uca Leach, 1814 (Decapoda, Ocypodidae) of Taiwan, including the offshore islands of Penghu (Pescadores), Kinmen (Quemoy), Matsu (Matzu), and Dongsha (Pratas), are revised, with the recognition of five subgenera and 15 species, viz. Uca (Austruca) Bott, 1973: U. lactea (De Haan, 1835), U.

Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models.

Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro - in vivo extrapolation need to be developed.

Capsid-CPSF6 Interaction Is Dispensable for HIV-1 Replication in Primary Cells but Is Selected during Virus Passage In Vivo.

Unlabelled: Cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a host factor that interacts with the HIV-1 capsid (CA) protein, is implicated in diverse functions during the early part of the HIV-1 life cycle, including uncoating, nuclear entry, and integration targeting. Preservation of CA binding to CPSF6 in vivo suggests that this interaction is fine-tuned for efficient HIV-1 replication in physiologically relevant settings. Nevertheless, this possibility has not been formally examined.

Development of an in vivo model of laryngeal burn injury.

Objectives/hypothesis: Inhalation injury significantly increases morbidity and mortality in burn patients. Approximately one in five burn patients have acute injury to the larynx, trachea, and/or lungs-and as many as 70% have long-term laryngeal abnormalities. Although inhalation injury to the lung has been studied extensively, no models exist to study these insults to the larynx.

Influence of biomechanical and biochemical stimulation on the proliferation and differentiation of bone marrow stromal cells seeded on polyurethane scaffolds.

The aim of the present investigation was to compare the effects of cyclic compression, perfusion, dexamethasone (DEX) and bone morphogenetic protein-7 (BMP-7) on the proliferation and differentiation of human bone marrow stromal cells (hBMSCs) in polyurethane scaffolds in a perfusion bioreactor. Polyurethane scaffolds seeded with hBMSCs were cultured under six different conditions, as follows: 10% Cyclic compression at 0.5 and 5 Hz; 10 ml/min perfusion; 100 nM DEX; 100 ng/ml BMP-7; and 1 ml/min perfusion without mechanical and biochemical stimulation (control).

Multiscale modelling approaches for assessing cosmetic ingredients safety.

The European Union's ban on animal testing for cosmetic ingredients and products has generated a strong momentum for the development of in silico and in vitro alternative methods. One of the focus of the COSMOS project was ab initio prediction of kinetics and toxic effects through multiscale pharmacokinetic modeling and in vitro data integration. In our experience, mathematical or computer modeling and in vitro experiments are complementary.

miR-1236 regulates hypoxia-induced epithelial-mesenchymal transition and cell migration/invasion through repressing SENP1 and HDAC3.

Intratumoral hypoxia induces epithelial-mesenchymal transition and promotes cancer metastasis. MicroRNAs (miRNAs) are endogenous, single-strand RNA molecules that regulate gene expression. MiRNAs control cell growth, proliferation, differentiation and cell death and may function as oncogenes or tumor suppressors.

HIF-1α activates hypoxia-induced BCL-9 expression in human colorectal cancer cells.

B-cell CLL/lymphoma 9 protein (BCL-9), a multi-functional co-factor in Wnt signaling, induced carcinogenesis as well as promoting tumor progression, metastasis and chemo-resistance in colorectal cancer (CRC). However, the mechanisms for increased BCL-9 expression in CRC were not well understood. Here, we report that hypoxia, a hallmark of solid tumors, induced BCL-9 mRNA expression in human CRC cells.

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Clinical and Environmental Isolates of Burkholderia pseudomallei.

Burkholderia pseudomallei is not represented in the current version of Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system. A total of 66 isolates of B. pseudomallei, including 30 clinical isolates collected from National Taiwan University Hospital (NTUH, n = 27) and Peking Union Medical College Hospital (PUMCH, n = 3), and 36 isolates of genetically confirmed strains, including 13 from clinical samples and 23 from environmental samples, collected from southern Taiwan were included in this study.