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

TAK1 maintains the survival of immunoglobulin λ‐chain‐positive B cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135064/1/gtc12442-sup-0001-FigS1-S6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135064/2/gtc12442.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135064/3/gtc12442_am.pd

ダウン症候群児の咀嚼機能獲得に関連する要因の検討

Down syndrome (DS) has the highest prevalence of any chromosomal abnormality identified in newborns. DS children have specific eating and swallowing difficulties such as poor tongue control, mouth opening, swallowing food without chewing, and both facial and occlusal abnormalities. DS children are also at high risk of aspiration, and swallowing food without chewing is considered to be a factor associated with increased risk of aspiration and eating problems. This study aimed to identify factors preventing the acquisition of masticatory function in DS children. The subjects were 75 outpatient DS children (44 males, age range 12 to 36 month-old, mean age 33.0 ± 7.0 month­-old; 31 females, age 12 to 36 month-old, mean age 20.8 ± 8.0 month-old), who had not yet acquired masticatory function, out of 319 who visited the clinic between October 2012 and October 2017. The information necessary for assessment was retrospectively extracted from the medical records of the subjects. The items examined included age, birth weight, nutritional intake, picky eating, tactile hyperesthesia, cognitive development assessed by Ohta stage, gross motor function, occlusal condition by Hellman's dental age, and tongue thrust/lip closure/mastication while eating. The relationships between the acquisition of masticatory function and these items were investigated after one year of rehabilitation. The revealed age, low birth weight, picky eating, and gross motor function to be relevant factors. Among these, gross motor function was found to be the factor most strongly associated with acquisition of masticatory function

Laser-induced fine structures on silicon exposed to THz-FEL

We found the irradiation of focused linearly polarized terahertz (THz)-waves emitted from THz free-electron laser (THz-FEL) engraved fine periodic stripe structures on the surfaces of single-crystal Si wafers. The experiments were performed at several wavelengths ranging from 50 to 82 μm with a macro-pulse fluence up to 32 J/cm2. The engraved structures are considered equivalent to the laser-induced periodic surface structures (LIPSS) produced by the irradiation of a femtosecond (fs)-pulsed laser in the near-infrared (NIR) region. However, the minimum period of ∼1/25 of the wavelength in the present case of THz-FEL is surely much smaller than those reported so far by use of fs-lasers and no more explicable by the so far proposed mechanisms. The finer LIPSS confirmed by longer-wavelength laser excitation by means of THz-FEL motivates investigation into the universal mechanism of LIPSS formation, which has been under a hot debate for decades

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

Directional linearly polarized terahertz emission from argon clusters irradiated by noncollinear double-pulse beams

It has been demonstrated that the interaction between argon clusters and intense femtosecond double laser pulses with appropriate intervals in time and space provides important properties for terahertz electromagnetic wave generation, namely, high forward directivity, power enhancement, and linear polarization with a variable direction. Irradiating argon clusters with double pulses (1 and 3 mJ, 40 fs, 810 nm) in 133-ps and 40-μm intervals results in terahertz wave emission in the forward direction that is 10 times greater than that for a single pulse. The polarization direction of terahertz electromagnetic waves can be varied by changing the relative focal positions of the first and second pulses