Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

BACKGROUND: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term "patholog" to mean a homolog of a human disease-related gene encoding a product (transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. RESULTS: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity (70–85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool (FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic (53%), hereditary (24%), immunological (5%), cardio-vascular (4%), or other (14%), disorders. CONCLUSIONS: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets

A Toy Model of Flying Snake's Glide

We have developed a toy model of flying snake's glide [J.J. Socha, Nature vol. 418 (2002) 603.] by modifying a model for a falling paper. We have found that asymmetric oscillation is a key about why snake can glide. Further investigation for snake's glide will provide us details about how it can glide without a wing.Comment: 6 pages, to be submitted to J. Phys. Soc. Jpn. Revised Version submitted to the abov

Instrumental and Initial Experimental Testing of Solar Habitat I

This report presents a description of the analytical and experimental procedures used to determine the performance of all subsystems and models for Solar Habitat I. It includes a description of the instrumentation necessary for evaluating all subsystems and models and the corresponding test methods used. Experimental test data is presented and compared with the results based on previously developed analytical models

Mn-euvering Manganese: The Role of Transporter Gene Family Members in Manganese Uptake and Mobilization in Plants

Manganese (Mn), an essential trace element, is important for plant health. In plants, Mn serves as a cofactor in essential processes such as photosynthesis, lipid biosynthesis and oxidative stress. Mn deficient plants exhibit decreased growth and yield and are more susceptible to pathogens and damage at freezing temperatures. Mn deficiency is most prominent on alkaline soils with approximately one third of the world’s soils being too alkaline for optimal crop production. Despite the importance of Mn in plant development, relatively little is known about how it traffics between plant tissues and into and out of organelles. Several gene transporter families have been implicated in Mn transport in plants. These transporter families include NRAMP (natural resistance associated macrophage protein), YSL (yellow stripe-like), ZIP (zinc regulated transporter/iron-regulated transporter [ZRT/IRT1]-related protein), CAX (cation exchanger), CCX (calcium cation exchangers), CDF/MTP (cation diffusion facilitator/metal tolerance protein), P-type ATPases and VIT (vacuolar iron transporter). A combination of techniques including mutant analysis and Synchrotron X-ray Fluorescence Spectroscopy can assist in identifying essential transporters of Mn. Such knowledge would vastly improve our understanding of plant Mn homeostasis

Prediction of qualitative parameters of slab steel ingot using numerical modelling

The paper describes the verification of casting and solidification of heavy slab ingot weighing 40 t from tool steel by means of numerical modelling with use of a finite element method. The pre-processing, processing and post-processing phases of numerical modelling are outlined. Also, the problems with determination of the thermodynamic properties of materials and with determination of the heat transfer between the individual parts of the casting system are discussed. The final porosity, macrosegregation and the risk of cracks were predicted. The results allowed us to use the slab ingot instead of the conventional heavy steel ingot and to improve the ratio, the chamfer and the external shape of the wall of the new design of the slab ingot

Determination of solidus and liquidus temperatures for S34MnV steel grade by thermal analysis and calculations

The paper is devoted to the comparison of the results in the frame of solidus and liquidus temperatures obtained by thermo analytical methods with the generally used empirically based formulas and thermo dynamical Computherm software. The series of thermal analysis measurements of high temperature phase transformations of real steel grade (S34MnV) under conditions of two analytical devices (Netzsch STA 449 F3 Jupiter; Setaram Multi High Temperature Calorimeter (MHTC)) were carried out. Two thermo analytical methods were used (DSC and Direct Thermal Analysis). The different weight of samples was used (2,6 g; 23 g). The liquidus and solidus temperatures for close to equilibrium conditions during heating (DSC: 1 °C/min; 2 °C/min) and during cooling (Direct Thermal Analysis: 1 °C/min) were determined and compared. Then, the discussion on the different values obtained by experiments and empirically based calculation is realised

Reduction of copper slag with the use of carbon granulates

The investigation results on the reduction of slag from flash smelting furnace and the use of carbon granulates obtained from fine-grained waste materials of both the coal enrichment and coking processes have been presented in the paper. The investigation results on the reduction of slag from flash furnace and the use of carbon granulates obtained from fine-grained waste materials of both the coal enrichment and coking processes have been presented in the paper