Revol, N., Makino, K., Berz, M.
The goal of this paper is to prove that the implementation of Taylor models in COSY, based on floating-point arithmetic, computes results satisfyin- g the «containment property», i.e. guaranteed...
Revol, N., Makino, K., Berz, M.
The goal of this paper is to prove that the implementation of Taylor models in COSY, based on floating-point arithmetic, computes results satisfyin- g the «containment property», i.e. guaranteed...
Sugimoto, K, Nishida, M, Otsuka, M, Makino, K, Ohkubo, K, Mori, Y, ...
Unit Mixte, N. Revol, K. Makino, M. Berz
The goal of this paper is to prove that the implementation of Taylor models in COSY, based on oating-point arithmetic, computes results satisfying the containment property, i.e. guaranteed results.
Revol, N., Makino, K., Berz, M.
The goal of this paper is to prove that the implementation of Taylor models in COSY, based on floating-point arithmetic, computes results satisfyin- g the «containment property», i.e. guaranteed...
On Maximal Frequent and Minimal Infrequent Sets (2002)
E. Boros, V. Gurvich, L. Khachiyan, K. Makino
Given an m n binary matrix A, a subset C of the columns is called t-frequent if there are at least t rows in A in which all entries belonging to C are nonzero. Let us denote by # the number of...
Dual-Bounded Generating Problems: Weighted Transversals of a Hypergraph (2002)
E. Boros, V. Gurvich, L. Khachiyan, K. Makino
We consider a generalization of the notion of transversal to a finite hypergraph, so called weighted transversals. Given a non-negative weight vector assigned to each hyperedge of an input hypergraph...
Recent progress in neutrino factory and muon collider research within the Muon collaboration (2002)
Neutrino Factory Collaboration, Alsharoa, MM, Ankenbrandt, CM, Atac, M, Autin, BR, Balbekov, VI, ...
A new fluorescent biosensor for inositol trisphosphate (2002)
Morii, T, Sugimoto, K, Makino, K, Otsuka, M, Imoto, K, Mori, Y
Structure-based design of a leucine zipper protein with new DNA contacting region (2002)
Morii, T, Sato, S, Hagihara, M, Mori, Y, Imoto, K, Makino, K
E. Boros, K. Elbassioni, V. Gurvich, L. Khachiyan, K. Makino
We consider the problem of enumerating all minimal integer solutions of a monotone system of linear inequalities. We first show that for any monotone system of r linear inequalities in n variables,...
A Satisfiability Formulation of Problems on Level Graphs (2001)
B. Randerath, E. Speckenmeyer, E. Boros, P. Hammer, A. Kogan, K. Makino, ...
In this note we present a formulation of two related combinatorial embedding problems concerning level graphs in terms of CNF -formulas. The rst problem is known as level planar embedding and the...
Feasibility study 2 of a muon based neutrino source (2001)
Ozaki, S, Palmer, RB, Zisman, MS, Gallardo, JC, Goodman, M, Hassanein, A, ...
F. Zimmermann, C. Johnstone, M. Berz, B. Erdelyi, K. Makino, W. Wan
Quadrupole fringe fields can limit the dynamic aperture of muon storage rings. Using the computer code COSY INFINITY for particle tracking and normal-form analysis, we evaluate the importance of...
Fringe Fields and Dynamic Aperture in the FNAL Muon Storage Ring (2000)
Zimmermann, Frank, Berz, M, Erdélyi, B, Johnstone, C, Makino, K, Wan, W
Quadrupole fringe fields can limit the dynamic aperture of muon storage rings.Using the computer code COSY INFINITY for particle tracking and normal-form analysis, we evaluate the importance of...
A Feasibility study of a neutrino source based on a muon storage ring (2000)
Holtkamp, N, Finley, D A, Anderson, T, Andreev, N, Ankenbrandt, C M, Assadi, S, ...
Sakakura, C, Yamaguchi-Iwai, Y, Satake, M, Bae, S C, Takahashi, A, Ogawa, E, ...
The translocation from chromosome 8 to chromosome 21, t(8;21), associated with acute myeloid leukemia results in production of an AML1/MTG8(ETO) fusion transcript. The product of the AML1 gene...
Igarashi, K, Hanamura, A, Makino, K, Aiba, H, Aiba, H, Mizuno, T, ...
The role of the alpha subunit of Escherichia coli RNA polymerase in transcription activation by positive factors was investigated using two reconstituted mutant RNA polymerases (containing...
Shimizu, H, Yagi, R, Kimura, Y, Makino, K, Terato, H, Ohyama, Y, ...
alpha-2'-Deoxyadenosine (alpha) is a major adenine lesion produced by gamma-ray irradiation of DNA under anoxic conditions. In this study, single-stranded recombinant M13 vectors containing alpha...
Yoshida, M, Makino, K, Morita, H, Terato, H, Ohyama, Y, Ide, H
5-Formyluracil (fU) is one of the thymine lesions produced by reactive oxygen radicals in DNA and its constituents. In this work, 5-formyl-2'-deoxyuridine 5'-triphosphate (fdUTP) was chemically...
Hiratsu, K, Amemura, M, Nashimoto, H, Shinagawa, H, Makino, K
In vitro transcription analysis has shown that only RNA polymerase containing an alternative sigma subunit, sigma E, activates transcription from one of the rpoH promoters and the htrA promoter. The...
Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli.
Kim, S K, Makino, K, Amemura, M, Shinagawa, H, Nakata, A
By making operon fusions with lambda placMu53, we identified, cloned, and analyzed the phoH gene belonging to the phosphate (pho) regulon. We mapped the phoH gene at 23.6 min in the Escherichia coli...
Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters.
Kasahara, M, Makino, K, Amemura, M, Nakata, A, Shinagawa, H
The ugp operon of Escherichia coli includes genes involved in the uptake of sn-glycerol-3-phosphate and glycerophosphoryl diesters and belongs to the pho regulon which is induced by phosphate...
Makino, K, Kim, S K, Shinagawa, H, Amemura, M, Nakata, A
We cloned the cryptic phn operon of a K-12 strain, phn(EcoK), and analyzed the nucleotide sequence of the phn region (11,672 bp). An mRNA start site upstream of the phnC gene was identified by S1...
Lee, T Y, Makino, K, Shinagawa, H, Nakata, A
A DNA fragment of Escherichia coli cloned on pBR322 elevated the production of alkaline phosphatase and phosphate-binding protein in a phoR phoM strain. Nucleotide sequence analysis and enzyme assays...
Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome.
Nakata, A, Amemura, M, Makino, K
Between 59 and 60 min on the Escherichia coli genetic map, there is a highly conserved sequence of 29 base pairs, containing an inverted repeat of seven base pairs that appears 14 times, 32 or 33...
Iwasaki, H, Shiba, T, Makino, K, Nakata, A, Shinagawa, H
The ruvA and ruvB genes of Escherichia coli constitute an operon which belongs to the SOS regulon. Genetic evidence suggests that the products of the ruv operon are involved in DNA repair and...
Yamada, M, Makino, K, Amemura, M, Shinagawa, H, Nakata, A
The phoB gene product of Escherichia coli is the transcriptional activator for the genes in the phosphate regulon as well as for phoB itself, all of which are induced by phosphate starvation. The...
Lee, T Y, Makino, K, Shinagawa, H, Amemura, M, Nakata, A
The structure and function of the phoB and phoR genes of Shigella dysenteriae strains and Klebsiella pneumoniae, which are involved in regulation of the phosphate regulon, were analyzed....
Shinagawa, H, Makino, K, Amemura, M, Kimura, S, Iwasaki, H, Nakata, A
The ruv gene of Escherichia coli, which is involved in DNA repair and recombination, was cloned on a plasmid vector. The DNA of the ruv region was sequenced; it had two open reading frames in tandem...
Amemura, M, Makino, K, Shinagawa, H, Nakata, A
The phoM gene is one of the positive regulatory genes for the phosphate regulon of Escherichia coli. We analyzed the nucleotide sequence of a 4.7-kilobase chromosomal DNA segment that encompasses the...
Ishino, Y, Shinagawa, H, Makino, K, Amemura, M, Nakata, A
The iap gene in Escherichia coli is responsible for the isozyme conversion of alkaline phosphatase. We analyzed the 1,664-nucleotide sequence of a chromosomal DNA segment that contained the iap gene...
Amemura, M, Shinagawa, H, Makino, K, Otsuji, N, Nakata, A
The regulatory genes of alkaline phosphatase, phoS and phoT, of Escherichia coli were cloned on pBR322, initially as an 11.8-kilobase EcoRI fragment. A restriction map of the hybrid plasmid was...
Makino, K, Morimoto, M, Nishi, M, Sakamoto, S, Tamura, A, Inooka, H, ...
This paper describes elucidation of the conformation of the human epidermal growth factor (hEGF) in an aqueous environment, using one- and two-dimensional proton nuclear magnetic resonance methods....
Ide, H, Murayama, H, Sakamoto, S, Makino, K, Honda, K, Nakamuta, H, ...
DNA polymerase preferentially incorporate dAMP opposite abasic sites (A-rule). The mechanism of the A-rule can be studied by analyzing three dissected stages of the reaction including (i) initial...
Yamamoto, K, Ichinose, Y, Shinagawa, H, Makino, K, Nakata, A, Iwanaga, M, ...
Vibrio cholerae O1 biotype El Tor produces and secretes a 65-kDa cytolysin/hemolysin into the culture medium. We cloned the structural gene (hlyA) for the cytolysin from the total DNA of a V....
Murakami, A, Nakaura, M, Nakatsuji, Y, Nagahara, S, Tran-Cong, Q, Makino, K
Fluorescein-labeled oligonucleotides as DNA-probes were synthesized and used to monitor hybrid formation, namely to detect DNA or oligonucleotide sequence in solution. The introduction of fluorescein...
DNA bending and binding factors of the human beta-actin promoter.
Kawamoto, T, Makino, K, Orita, S, Nakata, A, Kakunaga, T
Transcription of the beta-actin gene is rapidly inducible in response to serum stimulation. To determine the regions responsible for serum inducible and basal level expression, the human beta-actin...
Identification of the human beta-actin enhancer and its binding factor.
Kawamoto, T, Makino, K, Niwa, H, Sugiyama, H, Kimura, S, Amemura, M, ...
An enhancer of the human beta-actin gene and a factor that specifically interacts with it were detected. A mobility shift assay showed that the factor bound to the 25-base-pair sequence (between +759...
Mechanistic studies on depurination and apurinic site chain breakage in oligodeoxyribonucleotides.
Suzuki, T, Ohsumi, S, Makino, K
Products formed from defined oligodeoxyribonucleotide tetramers (oligonucleotides) by depurination at pH 5.0 and 90 degrees C followed by chain breakage at the resulting apurinic sites (AP sites)...
Amemura, M, Makino, K, Shinagawa, H, Nakata, A
Transcription of the genes in the phosphate regulon in Escherichia coli is activated by PhoB protein, which is phosphorylated by PhoR protein under phosphate-limiting conditions. In the absence of...
Oda, T, Makino, K, Yamashita, I, Namba, K, Maéda, Y
We examined factors that affect the filament orientation in F-actin sols to prepare highly well-oriented liquid crystalline sols suitable for x-ray fiber diffraction structure analysis. Filamentous...
Oda, T, Makino, K, Yamashita, I, Namba, K, Maéda, Y
Lowering pH or raising salt concentration stabilizes the F-actin structure by increasing the free energy change associated with its polymerization. To understand the F-actin stabilization mechanism,...
Sakakura, C, Yamaguchi-Iwai, Y, Satake, M, Bae, S C, Takahashi, A, Ogawa, E, ...
The translocation from chromosome 8 to chromosome 21, t(8;21), associated with acute myeloid leukemia results in production of an AML1/MTG8(ETO) fusion transcript. The product of the AML1 gene...
Igarashi, K, Hanamura, A, Makino, K, Aiba, H, Aiba, H, Mizuno, T, ...
The role of the alpha subunit of Escherichia coli RNA polymerase in transcription activation by positive factors was investigated using two reconstituted mutant RNA polymerases (containing...
Shimizu, H, Yagi, R, Kimura, Y, Makino, K, Terato, H, Ohyama, Y, ...
alpha-2'-Deoxyadenosine (alpha) is a major adenine lesion produced by gamma-ray irradiation of DNA under anoxic conditions. In this study, single-stranded recombinant M13 vectors containing alpha...
Yoshida, M, Makino, K, Morita, H, Terato, H, Ohyama, Y, Ide, H
5-Formyluracil (fU) is one of the thymine lesions produced by reactive oxygen radicals in DNA and its constituents. In this work, 5-formyl-2'-deoxyuridine 5'-triphosphate (fdUTP) was chemically...
Hiratsu, K, Amemura, M, Nashimoto, H, Shinagawa, H, Makino, K
In vitro transcription analysis has shown that only RNA polymerase containing an alternative sigma subunit, sigma E, activates transcription from one of the rpoH promoters and the htrA promoter. The...
Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli.
Kim, S K, Makino, K, Amemura, M, Shinagawa, H, Nakata, A
By making operon fusions with lambda placMu53, we identified, cloned, and analyzed the phoH gene belonging to the phosphate (pho) regulon. We mapped the phoH gene at 23.6 min in the Escherichia coli...
Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters.
Kasahara, M, Makino, K, Amemura, M, Nakata, A, Shinagawa, H
The ugp operon of Escherichia coli includes genes involved in the uptake of sn-glycerol-3-phosphate and glycerophosphoryl diesters and belongs to the pho regulon which is induced by phosphate...
Makino, K, Kim, S K, Shinagawa, H, Amemura, M, Nakata, A
We cloned the cryptic phn operon of a K-12 strain, phn(EcoK), and analyzed the nucleotide sequence of the phn region (11,672 bp). An mRNA start site upstream of the phnC gene was identified by S1...
Lee, T Y, Makino, K, Shinagawa, H, Nakata, A
A DNA fragment of Escherichia coli cloned on pBR322 elevated the production of alkaline phosphatase and phosphate-binding protein in a phoR phoM strain. Nucleotide sequence analysis and enzyme assays...
Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome.
Nakata, A, Amemura, M, Makino, K
Between 59 and 60 min on the Escherichia coli genetic map, there is a highly conserved sequence of 29 base pairs, containing an inverted repeat of seven base pairs that appears 14 times, 32 or 33...
Iwasaki, H, Shiba, T, Makino, K, Nakata, A, Shinagawa, H
The ruvA and ruvB genes of Escherichia coli constitute an operon which belongs to the SOS regulon. Genetic evidence suggests that the products of the ruv operon are involved in DNA repair and...
Yamada, M, Makino, K, Amemura, M, Shinagawa, H, Nakata, A
The phoB gene product of Escherichia coli is the transcriptional activator for the genes in the phosphate regulon as well as for phoB itself, all of which are induced by phosphate starvation. The...
Lee, T Y, Makino, K, Shinagawa, H, Amemura, M, Nakata, A
The structure and function of the phoB and phoR genes of Shigella dysenteriae strains and Klebsiella pneumoniae, which are involved in regulation of the phosphate regulon, were analyzed....
Shinagawa, H, Makino, K, Amemura, M, Kimura, S, Iwasaki, H, Nakata, A
The ruv gene of Escherichia coli, which is involved in DNA repair and recombination, was cloned on a plasmid vector. The DNA of the ruv region was sequenced; it had two open reading frames in tandem...
Amemura, M, Makino, K, Shinagawa, H, Nakata, A
The phoM gene is one of the positive regulatory genes for the phosphate regulon of Escherichia coli. We analyzed the nucleotide sequence of a 4.7-kilobase chromosomal DNA segment that encompasses the...
Ishino, Y, Shinagawa, H, Makino, K, Amemura, M, Nakata, A
The iap gene in Escherichia coli is responsible for the isozyme conversion of alkaline phosphatase. We analyzed the 1,664-nucleotide sequence of a chromosomal DNA segment that contained the iap gene...
Amemura, M, Shinagawa, H, Makino, K, Otsuji, N, Nakata, A
The regulatory genes of alkaline phosphatase, phoS and phoT, of Escherichia coli were cloned on pBR322, initially as an 11.8-kilobase EcoRI fragment. A restriction map of the hybrid plasmid was...
Makino, K, Morimoto, M, Nishi, M, Sakamoto, S, Tamura, A, Inooka, H, ...
This paper describes elucidation of the conformation of the human epidermal growth factor (hEGF) in an aqueous environment, using one- and two-dimensional proton nuclear magnetic resonance methods....
Ide, H, Murayama, H, Sakamoto, S, Makino, K, Honda, K, Nakamuta, H, ...
DNA polymerase preferentially incorporate dAMP opposite abasic sites (A-rule). The mechanism of the A-rule can be studied by analyzing three dissected stages of the reaction including (i) initial...