A nomogram model to predict non-retrieval of short-term retrievable inferior vena cava filters.

Objective: To develop and validate a nomogram for predicting non-retrieval of the short-term retrievable inferior vena cava (IVC) filters.

Methods: In this study, univariate and multivariate logistic regression analyses were performed to identify predictive factors of short-term retrievable filter (Aegisy or OptEase) non-retrieval, and a nomogram was then established based on these factors. The nomogram was created based on data from a training cohort and validated based on data from a validation cohort.

Characteristics of Option and Denali Inferior Vena Cava Filters.

Background: To assess the characteristics of Option and Denali filters and to identify associations between these characteristics in each filter type.

Methods: Consecutive patients who underwent Option or Denali filter placement between August 2019 and August 2022 were included in this retrospective study.

Results: A total of 119 patients (Option, n = 60; Denali, n = 59) were included.

Formation and composition of crust in the nephrostomy tube of patients undergoing percutaneous nephrostomy.

To investigate the formation and composition of crust in the nephrostomy tube (NT) of patients undergoing percutaneous nephrostomy (PCN). Consecutive patients undergoing PCN for the treatment of obstructive nephropathy who then underwent NT exchange between January 2020 and May 2022 were included in the study. The composition of crust in NTs was analyzed using infrared spectrum automatic analysis system.

NLRX1/FUNDC1/NIPSNAP1-2 axis regulates mitophagy and alleviates intestinal ischaemia/reperfusion injury.

Objectives: Mitophagy is considered to be a key mechanism in the pathogenesis of intestinal ischaemic reperfusion (IR) injury. NOD-like receptor X1 (NLRX1) is located in the mitochondria and is highly expressed in the intestine, and is known to modulate ROS production, mitochondrial damage, autophagy and apoptosis. However, the function of NLRX1 in intestinal IR injury is unclear.

Forceps-assisted Removal of Difficult-to-Retrieve Filters: Preliminary Results.

Background: The aim of this study is to retrospectively evaluate the safety and effectiveness of forceps-assisted removal of difficult-to-retrieve filters.

Methods: Patients who underwent forceps-assisted removal of difficult-to-retrieve filters (filters that could not be successfully removed with the standard loop-snare technique) between February 2008 and February 2019 were included in this study. Patients underwent forceps-assisted filter removal either immediately after failed loop-snare removal (same procedure) or at a later time (separate procedure).

ABrowse--a customizable next-generation genome browser framework.

Background: With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects.

Results: Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support.

Rice-Map: a new-generation rice genome browser.

Background: The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L.

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database.

We updated the plant transcription factor (TF) database to version 2.0 (PlantTFDB 2.0, http://planttfdb.

Computational identification of plant transcription factors and the construction of the PlantTFDB database.

Transcription factors (TFs) play an important role in gene regulation. Computational identification and annotation of TFs at genome scale are the first step toward understanding the mechanism of gene expression and regulation. We started to construct the database of Arabidopsis TFs in 2005 and developed a pipeline for systematic identification of plant TFs from genomic and transcript sequences.

BOAT: Basic Oligonucleotide Alignment Tool.

Background: Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks.

Expression pattern divergence of duplicated genes in rice.

Background: Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution, the divergence of expression patterns following duplication events has drawn great attention in recent years. Using large-scale whole-genome microarray data, we systematically analyzed expression divergence patterns of rice genes from block, tandem and dispersed duplications.

WebLab: a data-centric, knowledge-sharing bioinformatic platform.

With the rapid progress of biological research, great demands are proposed for integrative knowledge-sharing systems to efficiently support collaboration of biological researchers from various fields. To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface. Dedicated space is provided for users to store their input data and analysis results.

Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.

We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain).

PlantTFDB: a comprehensive plant transcription factor database.

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.

Identification of the critical regions in hepatitis B virus preS required for its stability.

As a hepatitis B virus (HBV) envelope domain, preS plays significant roles in receptor recognition and viral infection. However, the regions critical for maintaining a stable and functional conformation of preS are still unclear and require further investigation. In order to unravel these regions, serially truncated fragments of preS were constructed and expressed in Escherichia coli.

Serum levels of preS antigen (HBpreSAg) in chronic hepatitis B virus infected patients.

Background: Hepatitis B virus (HBV) infection is a serious health problem worldwide. Treatment recommendation and response are mainly indicated by viral load, e antigen (HBeAg) seroconversion, and ALT levels. The S antigen (HBsAg) seroconversion is much less frequent.

Crystal structure of Thermoanaerobacter tengcongensis hypoxanthine-guanine phosphoribosyl transferase L160I mutant--insights into inhibitor design.

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a potential target for structure-based inhibitor design for the treatment of parasitic diseases. We created point mutants of Thermoanaerobacter tengcongensis HGPRT and tested their activities to identify side chains that were important for function. Mutating residues Leu160 and Lys133 substantially diminished the activity of HGPRT, confirming their importance in catalysis.

Restructuring of the dinucleotide-binding fold in an NADP(H) sensor protein.

NAD(P) has long been known as an essential energy-carrying molecule in cells. Recent data, however, indicate that NAD(P) also plays critical signaling roles in regulating cellular functions. The crystal structure of a human protein, HSCARG, with functions previously unknown, has been determined to 2.

A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir.

The use of oseltamivir, widely stockpiled as one of the drugs for use in a possible avian influenza pandemic, has been reported to be associated with neuropsychiatric disorders and severe skin reactions, primarily in Japan. Here we identified a nonsynonymous SNP (single nucleotide polymorphism) in dbSNP database, R41Q, near the enzymatic active site of human cytosolic sialidase, a homologue of virus neuraminidase that is the target of oseltamivir. This SNP occurred in 9.

Protein expression, crystallization and preliminary X-ray crystallographic studies on HSCARG from Homo sapiens.

Human HSCARG has been annotated as a possible cancer related protein. Amino acid homology, although at a low percentage, suggested that HSCARG contains NmrA domain and might be a member of short chain dehydrogenase reductase superfamily. In order to investigate its structure and function, HSCARG gene has been successfully expressed and purified in E.