Pilot study of incidence of gastroesophageal reflux after lung resection.

Patients undergoing lung resection may be at risk of gastroesophageal reflux (GER) and silent aspiration following surgery. Defining high-risk patients may lead to prevention strategies for silent aspiration and subsequent exacerbation of underlying pulmonary disease. A pilot study of 50 patients was performed to investigate postoperative gastroesophageal reflux disease (GERD) symptoms and the pepsin concentration in saliva.

Isolation of porcine circovirus 3 using primary porcine bone marrow-derived cells.

Porcine circovirus 3 (PCV3) was first reported in the United States in 2016; this virus is considered to be involved in diverse pathologies, such as multisystem inflammation, porcine dermatitis and nephropathy syndrome, and reproductive disorders. However, successful isolation of PCV3 using cultured cells has been rare. In this study, we aimed to isolate PCV3 using primary porcine bone marrow-derived cells.

Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor.

Double-stranded RNA (dsRNA) is a molecular pattern uniquely produced in cells infected with various viruses as a product or byproduct of replication. Cells detect such molecules, which indicate non-self invasion, and induce diverse immune responses to eliminate them. The degradation of virus-derived molecules can also play a role in the removal of pathogens and suppression of their replication.

Experimental inoculation of a tissue homogenate containing porcine circovirus type 3 obtained after two in vivo passages in NIBS miniature pigs.

Porcine circovirus type 3 (PCV3) is a novel porcine circovirus that has been detected in pigs showing various clinical and pathological conditions, as well as in many asymptomatic pigs. The pathogenesis of PCV3 infection in pigs remains unclear. To evaluate the in vivo growth and pathogenicity of PCV3, we performed two experiments on PCV3 infection in laboratory-grade miniature pigs with strictly controlled genetic backgrounds and microbiological status.

Diffuse pleural thickening and thoracic contraction: An indistinguishable case from malignant pleural mesothelioma.

The differential diagnosis of reactive mesothelial hyperplasia and mesothelioma is difficult. We present a rare case of diffuse pleural thickening with thoracic contraction that was indistinguishable from mesothelioma. A 66-year-old woman with no history of asbestos exposure visited our hospital with a complaint of dyspnea.

Immunological features of a lung cancer patient achieving an objective response with anti-programmed death-1 blockade therapy.

The role of immune checkpoint inhibitors in metastatic lung cancer has been established in recent years and the pretherapeutic profiles of the tumor microenvironment in responders have been increasingly reported. The role of salvage surgery and the immune profiles of the posttherapeutic specimens in patients achieving an objective response have rarely been studied. We report a case of metastatic lung cancer treated by anti-programmed death-1 Ab followed by surgical resection.

Classification of lung adenocarcinoma transcriptome subtypes from pathological images using deep convolutional networks.

Purpose: Convolutional neural networks have become rapidly popular for image recognition and image analysis because of its powerful potential. In this paper, we developed a method for classifying subtypes of lung adenocarcinoma from pathological images using neural network whose that can evaluate phenotypic features from wider area to consider cellular distributions.

Methods: In order to recognize the types of tumors, we need not only to detail features of cells, but also to incorporate statistical distribution of the different types of cells.

First detection of porcine circovirus type 3 in Japan.

Porcine circovirus associated diseases (PCVAD) have multiple manifestations that have been attributed to porcine circovirus type 2 (PCV2). Recently, a novel porcine circovirus, PCV type 3 (PCV3), was identified in pigs with systemic inflammation of unknown etiology. In this study, we tried to detect the PCV3 genome in tissue samples collected from Japanese pig herds in 2016.

An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease.

Background: There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predict novel associations of genes and pathways with inflammatory bowel disease (IBD) by integrating information of differential gene expression, protein-protein interaction and known disease genes related to IBD.

Purification and characterization of immunogenic recombinant virus-like particles of porcine circovirus type 2 expressed in silkworm pupae.

Porcine circovirus type 2 (PCV2) is a primary causative agent of postweaningmultisystemic wasting syndrome (PMWS), which has a significant economic impact on the swine industry. The capsid protein (Cap) encoded by ORF2 of the viral genome has been used effectively as a vaccine against PCV2 infection. The Cap protein can spontaneously assemble into virus-like particles (VLPs) that are safe and highly immunogenic for vaccine applications.

Efficacy of genogroup 1 based porcine epidemic diarrhea live vaccine against genogroup 2 field strain in Japan.

Background: Porcine epidemic diarrhea (PED) is a lethal infectious disease in suckling piglets with symptoms including watery diarrhea caused by PED virus (PEDV). Since the late 1990's, live vaccines based on genogroup 1 virus have been used in Japan, and a significant amount of the vaccine has been used even after new genogroups invaded in 2013. In this study, we evaluated the effect of a conventional PED live vaccine on a newly prevalent genogroup 2 field strain in experimental and field situations.

Successful removal of porcine circovirus-1 from immunoglobulin G formulated in glycine solution using nanofiltration.

Porcine circovirus (PCV) is a potentially harmful virus that has been shown to contaminate biological products. The virus is resistant to many inactivation and/or removal procedures performed during manufacturing. Anion exchange chromatography has been shown to be useful for PCV type 1 (PCV1) removal; however, reduction of PCV1 using methods such as heat inactivation, low pH, nanofiltration, UV-C, and gamma irradiation has not been successful.

Comparison of Airway Measurements for Tracheobronchial Stenosis Between Stereoscopic Bronchoscope and MD-CT.

Background: Stereoscopic bronchoscopy is a new diagnostic tool to measure the diameter and cross-sectional area of the airway. The stereoscopic bronchoscope, which operates the same as a standard bronchoscope, utilizes 2 lenses to measure the airway using the principles of triangulation. Furthermore, the stereoscopic bronchoscope has the capability to measure the size of the airway during intervention in real-time, including variable stenosis.

Real-time prediction of cell division timing in developing zebrafish embryo.

Combination of live-imaging and live-manipulation of developing embryos in vivo provides a useful tool to study developmental processes. Identification and selection of target cells for an in vivo live-manipulation are generally performed by experience- and knowledge-based decision-making of the observer. Computer-assisted live-prediction method would be an additional approach to facilitate the identification and selection of the appropriate target cells.

Extracellular Release of Annexin A2 is Enhanced upon Oxidative Stress Response via the p38 MAPK Pathway after Low-Dose X-Ray Irradiation.

The extracellular microenvironment affects cellular responses to various stressors including radiation. Annexin A2, which was initially identified as an intracellular molecule, is also released into the extracellular environment and is known to regulate diverse cell surface events, however, the molecular mechanisms underlying its release are not well known. In this study, we found that in cultured human cancer and non-cancerous cells an extracellular release of annexin A2 was greatly enhanced 1-4 h after a single 20 cGy X-ray dose, but not after exposure to ultraviolet C (UVC) radiation.

Memory of cell shape biases stochastic fate decision-making despite mitotic rounding.

Cell shape influences function, and the current model suggests that such shape effect is transient. However, cells dynamically change their shapes, thus, the critical question is whether shape information remains influential on future cell function even after the original shape is lost. We address this question by integrating experimental and computational approaches.

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation.

Evaluation of a noninvasive deep body thermometer in measurement of specific positions.

This study tried to address the theoretical issue of a noninvasive deep body thermometer based on dual-heat-flux method about what depth does the thermometer measure and to what extent can it reflect the change of the real core body temperature (CBT). Authors built up two elaborate 3D models incorporated with the statistics of clinical studies and minute description of blood perfusion to mimic the situations when the thermometer was applied to forehead and thorax, respectively. The results based on finite element analysis show that the thermometer can approximate to the frontal bone and reach to the sternum.

Development and mining of a volatile organic compound database.

Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases.

A Glimpse to Background and Characteristics of Major Molecular Biological Networks.

Recently, biology has become a data intensive science because of huge data sets produced by high throughput molecular biological experiments in diverse areas including the fields of genomics, transcriptomics, proteomics, and metabolomics. These huge datasets have paved the way for system-level analysis of the processes and subprocesses of the cell. For system-level understanding, initially the elements of a system are connected based on their mutual relations and a network is formed.

Hochu‑ekki‑to (Bu‑zhong‑yi‑qi‑tang), a herbal medicine, enhances cisplatin‑induced apoptosis in HeLa cells.

Hochu‑ekki‑to (HET), a Kampō herbal medicine composed of ten medicinal plants, is traditionally used to improve the general state of patients with malignant diseases such as cancer. Recent studies showed that HET had an anti‑cancer effect against several cancer cell lines in vitro by inducing apoptosis. However, high doses of HET may have cytotoxic effects attributed to saponins or detergent‑like compounds.

Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species.

Curcuminoids, namely curcumin and its analogs, are secondary metabolites that act as the primary active constituents of turmeric (Curcuma longa). The contents of these curcuminoids vary among species in the genus Curcuma. For this reason, we compared two wild strains and two cultivars to understand the differences in the synthesis of curcuminoids.

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4).

Visualizing in vivo brain neural structures using volume rendered feature spaces.

Background: Dendrites of cortical neurons are widely spread across several layers of the cortex. Recently developed two-photon microscopy systems are capable of visualizing the morphology of neurons within deeper layers of the brain and generate large amounts of volumetric imaging data from living tissue.

Method: For visual exploration of the three-dimensional (3D) structure of dendrites and the connectivity among neurons in the brain, we propose a visualization software and interface for 3D images based on a new transfer function design using volume rendered feature spaces.