In Vitro Model of Vascular Remodeling Under Microfluidic Perfusion.

We developed a portable microfluidic system that combines spontaneous lumen formation from human umbilical endothelial cells (HUVECs) in fibrin-collagen hydrogels with active perfusion controlled by a braille actuator. Adaptive interstitial flow and feedthrough perfusion switching enabled the successful culture of spontaneously formed naturally branched lumens for more than one month. We obtained many large-area (2 mm × 3 mm) long-term (more than 30 days per run) time-lapse image datasets of the in vitro luminal network using this microfluidic system.

Satisfaction, effectiveness, and usability of telerehabilitation for Parkinson's disease patients.

Objective: To evaluate the satisfaction, effectiveness, and usability of a telerehabilitation programme for Parkinson's disease (PD) patients.

Design: Prospective cohort study.

Subjects/patients: PD patients based on the diagnostic criteria for clinically established or probable PD published by the International Parkinson and Movement Disorder Society.

Acute Calcific Tendinitis of the Flexor Hallucis Brevis Associated With Muay Thai.

Calcific tendinitis manifesting in the foot and toes is a rare condition that often goes unnoticed, even by podiatric specialists and healthcare practitioners. Characterized by an acute onset, this condition presents with pronounced local inflammatory indicators accompanied by pain, often complicating its differentiation from other conditions. We document our experience with a 27-year-old female patient presenting with calcific tendinitis in the flexor hallucis brevis (FHB), along with a review of the relevant literature.

An Integrated Pulsation-Free, Backflow-Free Micropump Using the Analog Waveform-Driven Braille Actuator.

The widespread adoption of long-term organs-on-a-chip culture necessitates both active perfusions that mimic physiological flow conditions and minimization of the complexity of microfluidic system and fluid handling. In particular, flow in microtissue such as microvascular is free of pulsation and backflow. The refreshable Braille actuator-based integrated microfluidic system can be employed with simple microchannels and setups.

Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ.

Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and the molecular target of thiazolidinedione-class antidiabetic drugs. It has been reported that the loss of function R288H mutation in the human PPARγ ligand-binding domain (LBD) may be associated with the onset of colon cancer. A previous in vitro study showed that this mutation dampens 15-deoxy-Δ-prostaglandin J2 (15d-PGJ2, a natural PPARγ agonist)-dependent transcriptional activation; however, it is poorly understood why the function of the R288H mutant is impaired and what role this arginine (Arg) residue plays.

Cathodoluminescence Spectroscopic Stress Analysis for Silicon Oxide Film and Its Damage Evaluation.

We describe the stress analysis of silicon oxide (SiO) thin film using cathodoluminescence (CL) spectroscopy and discuss its availability in this paper. To directly measure the CL spectra of the film under uniaxial tensile stresses, specially developed uniaxial tensile test equipment is used in a scanning electron microscope (SEM) equipped with a CL system. As tensile stress increases, the peak position and intensity proportionally increase.

Insights into PPARγ Phosphorylation and Its Inhibition Mechanism.

PPARγ represents a key target for the treatment of type 2 diabetes and metabolic syndrome. Synthetic antidiabetic drugs activating PPARγ are accompanied by serious undesirable side effects related to their agonism. In the search for new PPARγ regulators, inhibitors of PPARγ phosphorylation on S245 mediated by CDK5 represent an opportunity for the development of an improved generation of antidiabetic drugs acting through this nuclear receptor.

DNA hypermethyation and silencing of correlated with advanced stage and poor postoperative prognosis of esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed.

Gateways to the FANTOM5 promoter level mammalian expression atlas.

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.

Database construction for PromoterCAD: synthetic promoter design for mammals and plants.

Synthetic promoters can control a gene's timing, location, and expression level. The PromoterCAD web server ( http://promotercad.org ) allows the design of synthetic promoters to control plant gene expression, by novel arrangement of cis-regulatory elements.

PromoterCAD: Data-driven design of plant regulatory DNA.

Synthetic promoters can control the timing, location and amount of gene expression for any organism. PromoterCAD is a web application for designing synthetic promoters with altered transcriptional regulation. We use a data-first approach, using published high-throughput expression and motif data from for Arabidopsis thaliana to guide DNA design.

PosMed: Ranking genes and bioresources based on Semantic Web Association Study.

Positional MEDLINE (PosMed; http://biolod.org/PosMed) is a powerful Semantic Web Association Study engine that ranks biomedical resources such as genes, metabolites, diseases and drugs, based on the statistical significance of associations between user-specified phenotypic keywords and resources connected directly or inferentially through a Semantic Web of biological databases such as MEDLINE, OMIM, pathways, co-expressions, molecular interactions and ontology terms. Since 2005, PosMed has long been used for in silico positional cloning studies to infer candidate disease-responsible genes existing within chromosomal intervals.

Integrated database of information from structural genomics experiments.

Information from structural genomics experiments at the RIKEN SPring-8 Center, Japan has been compiled and published as an integrated database. The contents of the database are (i) experimental data from nine species of bacteria that cover a large variety of protein molecules in terms of both evolution and properties (http://database.riken.

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.

Background: Proteins interact with other proteins or biomolecules in complexes to perform cellular functions. Existing protein-protein interaction (PPI) databases and protein complex databases for human proteins are not organized to provide protein complex information or facilitate the discovery of novel subunits. Data integration of PPIs focused specifically on protein complexes, subunits, and their functions.

Comparative simulations of the ground state and the M-intermediate state of the sensory rhodopsin II-transducer complex with a HAMP domain model.

The complex of sensory rhodopsin II (SRII) and its cognate transducer HtrII (2:2 SRII-HtrII complex) consists of a photoreceptor and its signal transducer, respectively, associated with negative phototaxis in extreme halophiles. In this study to investigate how photoexcitation in SRII affects the structures of the complex, we conducted two series of molecular dynamics simulations of the complex of SRII and truncated HtrII (residues 1-136) of Natronomonas pharaonis linked with a modeled HAMP domain in the lipid bilayer using the two crystal structures of the ground state and the M-intermediate state as the starting structures. The simulation results showed significant enhancements of the structural differences observed between the two crystal structures.

In-situ cathodoluminescence spectroscopy of silicon oxide thin film under uniaxial tensile loading.

In this paper, in-situ cathodoluminescence (CL) stress analysis of a silicon oxide (SiO(x)) thin film prepared by wet thermal oxidation is described. The specially-developed uniaxial tensile loading jig was used to apply tensile displacement to the SiO(x) film specimen. CL spectra of the specimen during tensile loading were obtained, and the peak position of around 1.

The RIKEN integrated database of mammals.

The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies.

Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from .

The halobacterial transducer of sensory rhodopsin II (HtrII) is a photosignal transducer associated with phototaxis in extreme halophiles. The HAMP domain, a linker domain in HtrII, is considered to play an important role in transferring the signal from the membrane to the cytoplasmic region, although its structure in the complex remains undetermined. To establish the structural basis for understanding the mechanism of signal transduction, we present an atomic model of the structure of the N-terminal HAMP domain from (HtrII: 84-136), based on molecular dynamics (MD) simulations.

Contrary effects of octopamine receptor ligands on behavioral and neuronal changes in locomotion of lymnaea.

The pond snail Lymnaea stagnalis moves along the sides and bottom of an aquarium, but it can also glide upside down on its back below the water's surface. We have termed these two forms of locomotion "standard locomotion" and "upside-down gliding," respectively. Previous studies showed that standard locomotion is produced by both cilia activity on the foot and peristaltic contraction of the foot muscles, whereas upside-down gliding is mainly caused by cilia activity.

SERRS fiber probe: fabrication of silver nanoparticles at the aperture of an optical fiber used for SNOM.

At the aperture of an optical fiber coupled with a SNOM SERRS-active Ag nanoparticles were selectively fabricated in a mixture of AgNO(3) and sodium citrate aqueous solution by photo-reduction due to an evanescent field.

Upside-down gliding of Lymnaea.

The pond snail Lymnaea stagnalis can often be observed moving upside down on its back just below the surface of the water. We have termed this form of movement "upside-down gliding." To elucidate the mechanism of this locomotion, we performed a series of experiments involving behavioral analyses and microscopic observations.

Speed of back-swimming of Lymnaea.

The pond snail, Lymnaea stagnalis, can locomote on its back utilizing the surface tension of the water. We have called this form of movement 'back-swimming'. In order to perform this behavior, the snail must flip itself over on its back so that its foot is visible from above.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts.

Large-scale identification of protein-protein interaction of Escherichia coli K-12.

Protein-protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular activities, targeted-drug design, and whole cell engineering. A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library.