SARS-CoV-2 genome clusters analyzed by Deep Learning

We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large number of genotypes, an appropriate method for understanding the entire population is required. The method using autoencoder meets this requirement and is suitable for understanding how and when the variants emarge and disappear. For the over 30,000 SARS-CoV-2 ORF1ab gene sequences sampled globally from December 2019 to February 2021, we were able to represent a summary of their characteristics in a 3D plot and show the expansion, decline, and transformation of the virus types over time and by region. Based on ORF1ab genes, the SARS-CoV-2 viruses were classified into five major types (A, B, C, D, and E in the order of appearance): the virus type that originated in China at the end of 2019 (type A) practically disappeared in June 2020; two virus types (types B and C) have emerged in the United States and Europe since February 2020, and type B has become a global phenomenon. Type C is only prevalent in the U.S. and is suspected to be associated with high mortality, but this type also disappeared at the end of June. Type D is only found in Australia. Currently, the epidemic is dominated by types B and E

Spinal Aspergillosis of the Thoracic Spine : Case Report

OBJECTIVE AND IMPORTANCE : Fungal infection of the spine is a rare entity, and is usually associated with opportunistic infection in immuno-compromised patients. The authors present a case of spinal aspergillosis in a diabetic patient. CLINICAL PRESENTATION : The subject was a 74-year-old man with a history of left lung tuberculosis who was diagnosed as having diabetes mellitus 20 years ago. His diabetes was controlled by diet and insulin therapy. On admission, he suffered from a moderate fever, paraparesis and sensory impairment of the bilateral lower extremities. A thoracic MRI showed a mass lesion was constricting the dural sac in the T6-9 thoracic spine region. INTERVENTION : A laminectomy was performed and antifungal agents (fluconazole and amphotericin B) were administered, but the treatment was ineffective, with the patient dying of multiple organ failure about three months after the operation. CONCLUSION : The outcome in cases of Aspergillus spinal infection is generally poor, in spite of the recent progress of medical treatment or surgical technique, so the importance of early diagnosis and initiation of treatment for this intractable disease are emphasized

Increase in Cellulose Accumulation and Improvement of Saccharification by Overexpression of Arabinofuranosidase in Rice

Cellulosic biomass is available for the production of biofuel, with saccharification of the cell wall being a key process. We investigated whether alteration of arabinoxylan, a major hemicellulose in monocots, causes an increase in saccharification efficiency. Arabinoxylans have β-1,4-D-xylopyranosyl backbones and 1,3- or 1,4-α-l-arabinofuranosyl residues linked to O-2 and/or O-3 of xylopyranosyl residues as side chains. Arabinose side chains interrupt the hydrogen bond between arabinoxylan and cellulose and carry an ester-linked feruloyl substituent. Arabinose side chains are the base point for diferuloyl cross-links and lignification. We analyzed rice plants overexpressing arabinofuranosidase (ARAF) to study the role of arabinose residues in the cell wall and their effects on saccharification. Arabinose content in the cell wall of transgenic rice plants overexpressing individual ARAF full-length cDNA (OsARAF1-FOX and OsARAF3-FOX) decreased 25% and 20% compared to the control and the amount of glucose increased by 28.2% and 34.2%, respectively. We studied modifications of cell wall polysaccharides at the cellular level by comparing histochemical cellulose staining patterns and immunolocalization patterns using antibodies raised against α-(1,5)-linked l-Ara (LM6) and β-(1,4)-linked d-Xyl (LM10 and LM11) residues. However, they showed no visible phenotype. Our results suggest that the balance between arabinoxylan and cellulose might maintain the cell wall network. Moreover, ARAF overexpression in rice effectively leads to an increase in cellulose accumulation and saccharification efficiency, which can be used to produce bioethanol

Surgical Treatment of Tentorial Meningiomas ? Based on Our Classification Related to Venous Sinuses ?

We report our experience and long-term results in the surgical treatment of 27 tentorial meningiomas (TMs). These cases were operated on between 1980 to 2000.5 and represented 9.8% of all 275 surgically treated intracranial meningiomas in that period. Of the total 29 TMs (additional 2 non-surgically treated TMs), 25 were women and 4 were men ranging in age from 26 to 75 years (mean 55.2 years). According to the site of tumor attachment and the venous sinuses, these 29 TMs were divided into 6 subgroups: central (C; 3), anterolateral (AL; 3), posterolateral (PL; 6), free edge (FE; 6), anteromedial (AM; 3), and posteromedial (PM; 8). Various surgical approaches were selected on the tumor location and extension, however, these are divided into 2 approaches. One is anterior or posterior petrosal approach, selected in AL and FE cases and the other is combined occipital-suboccipital approach, selected in C, PL, AM, and PM cases. In 17 patients, total removal (Simpson Grade 1 : 8, II : 9) was achieved, subtotal removal (SG III) in 4, and partial removal (SG IV) in 6. Four patients had surgical complications. Gamma knife radiosurgery was performed in 4 residual and 3 recurrent meningiomas. In all these 7 meningiomas, tumor sizes have been well controlled. With a mean follow-up of 70 months (2 to 157 months), recurrences occurred in 5 patients (21.7%), which were subtotal and partial removal cases. Glasgow Outcome Scale scores were GR in 21 patients (77.8%), MD in 3 (11.1%), VS in 1 (3.7%), and D in 2 (7.4%)

Transient and local weakening of surface winds observed above the Kuroshio front in the winter East China Sea

To confirm whether surface winds strengthen above warm waters around oceanic fronts using in situ data, a field measurement was conducted using both expendable bathythermographs and Global Positioning System sondes released concurrently across the Kuroshio front in the East China Sea in December 2010. In contrast to previous studies mainly based on satellite observations, the finding of the present field survey is the local weakening of surface winds at the northern flank of the Kuroshio front. From the above field observation in conjunction with a regional numerical model experiment, it is suggested that the northwesterly winds crossing the Kuroshio front from the cooler side first weaken at the northern flank of the front because of the onset of upward transfer of the "nonslip" condition at the sea surface. Thereafter, as the atmospheric mixed layer with warm and humid air mass develops gradually downwind over the Kuroshio region, the surface winds are gradually accelerated by the momentum mixing with strong winds aloft. The surface winds remain strong over the cool East China Sea shelf, and it is thus considered that the surface winds only weaken at the northern flank of the Kuroshio front. However, numerical modeling indicates that this local weakening of the surface winds occurs as a transient state with a short duration and such a structure has thus rarely been detected in the long-term averaged wind fields observed by satellites. Key Points An XBT/GPS sonde observation was conducted across the Kuroshio front Local weakening of surface winds was found just above the Kuroshio front The weakening occurs at the onset of cross-frontal winds transientl

Manifestation of the Pacific Decadal Oscillation in the Kuroshio

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 36 (2009): L16602, doi:10.1029/2009GL039216.Pacific Decadal Oscillation (PDO) index is strongly correlated with vertically integrated transport carried by the Kuroshio through the East China Sea (ECS). Transport was determined from satellite altimetry calibrated with in situ data and its correlation with PDO index (0.76) is highest at zero lag. Total PDO-correlated transport variation carried by the ECS-Kuroshio and Ryukyu Current is about 4 Sv. In addition, PDO index is strongly negatively correlated, at zero lag, with NCEP wind-stress-curl over the central North Pacific at ECS latitudes. Sverdrup transport, calculated from wind-stress-curl anomalies, is consistent with the observed transport variations. Finally, PDO index and ECS-Kuroshio transport are each negatively correlated with Kuroshio Position Index in the Tokara Strait; this can be explained by a model in which Kuroshio path is steered by topography when transport is low and is inertially controlled when transport is high.MA, MW and JP were supported by ONR grant N000140210271. XZ was supported by the National Natural Science Foundation of China under grant 40776021 and the National Basic Research Programs of China under grant 2006CB400603. KK and KC were supported by the Korea EAST-I Program

Characterization of pullulanase (PUL)-deficient mutants of rice (Oryza sativa L.) and the function of PUL on starch biosynthesis in the developing rice endosperm

Rice (Oryza sativa) allelic sugary1 (sug1) mutants defective in isoamylase 1 (ISA1) accumulate varying levels of starch and phytoglycogen in their endosperm, and the activity of a pullulanase-type of a debranching enzyme (PUL) was found to correlate closely with the severity of the sug1 phenotype. Thus, three PUL-deficient mutants were generated to investigate the function of PUL in starch biosynthesis. The reduction of PUL activity had no pleiotropic effects on the other enzymes involved in starch biosynthesis. The short chains (DP ≤13) of amylopectin in PUL mutants were increased compared with that of the wild type, but the extent of the changes was much smaller than that of sug1 mutants. The α-glucan composition [amylose, amylopectin, water-soluble polysaccharide (WSP)] and the structure of the starch components (amylose and amylopectin) of the PUL mutants were essentially the same, although the average chain length of the B2-3 chains of amylopectin in the PUL mutant was ∼3 residues longer than that of the wild type. The double mutants between the PUL-null and mild sug1 mutants still retained starch in the outer layer of endosperm tissue, while the amounts of WSP and short chains (DP ≤7) of amylopectin were higher than those of the sug1 mutant; this indicates that the PUL function partially overlaps with that of ISA1 and its deficiency has a much smaller effect on the synthesis of amylopectin than ISA1 deficiency and the variation of the sug1 phenotype is not significantly dependent on the PUL activities

A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system

Funding Information: Acknowledgements This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Green Technology Project EF-1004). We are grateful to Dr. Takuji Sasaki for his encouragement throughout the project and his excellent advice on the improvement of this manuscript, and to Dr. Shoshi Kikuchi for providing useful information on rice FL-cDNAs. We thank Professors Kokichi Hinata, Atsushi Hirai, Hiroshi Kamada and Masashi Ugaki for their encouragement, critical comments and helpful suggestions, and Drs. Hisato Okuizumi and Hiroyuki Kawahigashi for their administrative support throughout the project. We also thank Mayumi Akagawa, Hiroko Abe, Keiko Mori, Etsuko Sugai, Yumiko Nakane, Ken-ichi Watanabe, Mayumi Takeya, and Kana Miyata for their technical assistance; the members of the Technical Support Section of the National Institute of Agrobiological Sciences for their help in the care of the FOX-rice plants; Haruko Onodera and Kazuko Ono for their technical assistance and advice on rice transformation; Inplanta Innovations Inc. for their technical help on the construction of theThe latest report has estimated the number of rice genes to be ∼32 000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13 980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12 000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene, confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.publishersversionPeer reviewe