Direct submission system and literature annotation of rice genes in Oryzabase

Oryzabase ("http://www.shigen.nig.ac.jp/rice/oryzabase/":http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date, literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown genes from journals. The machine extraction followed by manual annotation achieved promising results and increased efficiency in manual annotation. Furthermore a direct submission system where rice researchers can deposit new genes according to the standardized nomenclature ^2^ became operational in 2008. Recent advances will be introduced.

[1] Kurata, N. and Y. Yamazaki., Oryzabase, An Integrated Biological and Genome 
 Information Database for Rice. _Plant Physiology_ (2006) 140, 12-17 
[2] Susan R. McCouch, Gene Nomenclature System for Rice, Rice (2008) 1:72-8

Features of the Dubowitz neurologic examination of preterm infants : Comparison with neonatal encephalopathy infants

低出生体重児57名と,新生児期に明らかな脳障害が確認された11名を対象に,出産予定日頃にDubowitz の神経学的評価を行った.発達に影響を及ぼす因子として報告されている,在胎週数,出生体重を考慮し,評価結果の比較検討を行った.評価したすべてのカテゴリーとtotal score において低出生体重児では早産・低体重の程度による影響を受けず,出産予定日での発達に差はなかった.tone,reflexes,behavior のカテゴリーでは早産児は脳障害児のスコアと比べて有意に高かった.また,tone patterns,abnormal signs では早産児と脳障害児でスコアに違いはみられず,このカテゴリーにおいて異常性との判別は難しいと考えられる.total score でみると早産児のスコアはDubowitz により報告されたカットオフ値の30 より低いスコアであり,低出生体重児での新たな基準を設定する必要が示唆された.Fifty-seven preterm infants and eleven infants in whom neonatal encephalopathy had been confirmed were examined by Dubowitz neurologic examination at term age. The results were compared based on their gestational age and birthweight, both of which are reported as factors which influence development. No influence of premature delivery and low weight was seen in preterm infants in the evaluated total score of the Dubowitz neurologic examination, and there was no difference in development at term age. There were significant differences in the scores in the categories of tone, reflexes, and behavior in the preterm infants compared with the neonatal encephalopathy infants. Moreover, no difference was seen in the score of the preterm infants and the neonatal encephalopathy infants in tone patterns and abnormal signs. Therefore, it is difficult to distinguish premature infants from abnormal infants in these categories. In this study, the total score reported by Dubowitz for preterm infants was lower than that for full-term infants, and the necessity for establishing a new standard for preterm infants is proposed

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

BACKGROUND: Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan. RESULTS: Fifteen insect species inhabited the plant accessions, with the insect community composition significantly attributed to variations among plant accessions. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both field sites, while glucosinolates had variable effects on leaf chewers between the sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than on their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers; flea beetles and turnip sawflies. CONCLUSIONS: Overall, our results indicate that insect community composition significantly varies among A. thaliana accessions across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide effect of a single plant gene on crucifer-feeding insects in the field

A Comprehensive Study of Short Bursts from SGR 1806-20 and SGR 1900+14 Detected by HETE-2

We present the results of temporal and spectral studies of the short burst (less than a few hundred milliseconds) from the soft gamma repeaters (SGRs) 1806-20 and 1900+14 using the HETE-2 samples. In five years from 2001 to 2005, HETE-2 detected 50 bursts which were localized to SGR 1806-20 and 5 bursts which were localized to SGR 1900+14. Especially SGR 1806-20 was active in 2004, and HETE-2 localized 33 bursts in that year. The cumulative number-intensity distribution of SGR 1806-20 in 2004 is well described by a power law model with an index of -1.1+/-0.6. It is consistent with previous studies but burst data taken in other years clearly give a steeper distribution. This may suggest that more energetic bursts could occur more frequently in periods of greater activity. A power law cumulative number-intensity distribution is also known for earthquakes and solar flares. It may imply analogous triggering mechanisms. Although spectral evolution during bursts with a time scale of > 20 ms is not common in the HETE-2 sample, spectral softening due to the very rapid (< a few milliseconds) energy reinjection and cooling may not be excluded. The spectra of all short bursts are well reproduced by a two blackbody function (2BB) with temperatures ~4 and ~11 keV. From the timing analysis of the SGR 1806-20 data, a time lag of 2.2+/-0.4 ms is found between the 30-100 keV and 2-10 keV radiation bands. This may imply (1) a very rapid spectral softening and energy reinjection, (2) diffused (elongated) emission plasma along the magnetic field lines in pseudo equilibrium with multi-temperatures, or (3) a separate (located at < 700 km) emission region of softer component (say, ~4 keV) which could be reprocessed X-rays by higher energy (> 11 keV) photons from an emission region near the stellar surface.Comment: 50 pages, 14 figures, accepted for publication in PAS

Associations in tumor infiltrating lymphocytes between clinicopathological factors and clinical outcomes in estrogen receptor-positive/human epidermal growth factor receptor type 2 negative breast cancer

The value of assessing tumor infiltrating lymphocytes (TILs) in estrogen receptor (ER) positive/human epidermal growth factor receptor type 2 (HER2) negative breast cancer has yet to be determined. In the present study, a total of 184 cases with early distant recurrence detected within 5 years following the primary operation, 134 with late distant recurrence diagnosed following 5 years or longer and 321 controls without recurrence for >10 years following starting the initial treatment for ER-positive/HER2 negative breast cancer, registered in 9 institutions, were analyzed. The distributions of TILs and their clinical relevance were investigated. TIL distributions did not differ significantly among the early, late and no recurrence groups, employing a 30% cut-off point as a dichotomous variable. In those who had received adjuvant chemotherapy as well as endocrine therapy, a trend toward higher TIL proportions was detected when the early recurrence group was compared with the no recurrence group employing the 30% cut-off point (P=0.064). The TIL distributions were significantly associated with nodal metastasis (P=0.004), ER status (P=0.045), progesterone receptor (PgR) status (P=0.002), tumor grade (P=0.021), and the Ki67 labeling index (LI) (P=0.002) in the no recurrence group and with the Ki67 LI in the recurrence groups (P=0.002 in early recurrence group, P=0.023 in late recurrence group). High TIL distributions also predicted shorter survival time following the detection of recurrence (P=0.026). However, these prognostic interactions were not significant in multivariate analysis (P=0.200). The present retrospective study demonstrated no significant interaction between TIL proportions and the timing of recurrence. However, higher TIL proportions were observed in breast cancer patients with aggressive biological phenotypes, which tended to be more responsive to chemotherapy. The clinical relevance of stromal TILs for identifying patients who would likely benefit from additional therapies merits further investigation in a larger patient population

Hansen\u27s disease (leprosy) in Japan, 1947-2020: an epidemiologic study during the declining phase to elimination

Objectives: Leprosy, or Hansen’s disease was a major public health problem in Japan in the early 20th century. Today, the number of new cases has decreased significantly. We aimed to investigate the trends of leprosy in Japan over the past 73 years and the challenges faced in recent years. Methods: We assessed the data on newly registered cases of leprosy from 1947 to 2020. Results: A total of 10,796 newly registered cases of leprosy were reported during the study period, of which 7573 were registered in mainland Japan, 2962 in Okinawa, and 250 were of foreign origin. Most autochthonous cases were born before 1950 in mainland Japan and before 1975 in Okinawa. The number of nonautochthonous cases surpassed that of autochthonous cases in 1992. Nonautochthonous cases orig- inated from 26 countries, particularly Brazil and the Philippines. Three cases of antimicrobial resistance have been detected among nonautochthonous cases since 2004. Conclusion: Our data suggest that ongoing transmission of leprosy likely ceased in the 1940s in mainland Japan and in the 1970s in Okinawa. With the recent rise of nonautochthonous cases with globalization, continuous surveillance and effort s to maint ain leprosy services within the country are necessary even after reaching the state of elimination