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  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2010
    In:  Natural Computing Vol. 9, No. 1 ( 2010-3), p. 173-181
    In: Natural Computing, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2010-3), p. 173-181
    Type of Medium: Online Resource
    ISSN: 1567-7818 , 1572-9796
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2010
    detail.hit.zdb_id: 2065639-7
    SSG: 12
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  • 2
    In: Communications Medicine, Springer Science and Business Media LLC, Vol. 2, No. 1 ( 2022-01-19)
    Abstract: Approximately 2.4 million patients in Japan would benefit from treatment for thyroid disease, including Graves’ disease and Hashimoto’s disease. However, only 450,000 of them are receiving treatment, and many patients with thyroid dysfunction remain largely overlooked. In this retrospective study, we aimed to develop and conduct preliminary testing on a machine learning method for screening patients with hyperthyroidism and hypothyroidism who would benefit from prompt medical treatment. Methods We collected electronic medical records and medical checkup data from four hospitals in Japan. We applied four machine learning algorithms to construct classification models to distinguish patients with hyperthyroidism and hypothyroidism from control subjects using routine laboratory tests. Performance evaluation metrics such as sensitivity, specificity, and the area under receiver operating characteristic (AUROC) were obtained. Techniques such as feature importance were further applied to understand the contribution of each feature to the machine learning output. Results The results of cross-validation and external evaluation indicated that we achieved high classification accuracies (AUROC = 93.8% for hyperthyroidism model and AUROC = 90.9% for hypothyroidism model). Serum creatinine (S-Cr), mean corpuscular volume (MCV), and total cholesterol were the three features that were most strongly correlated with the hyperthyroidism model, and S-Cr, lactic acid dehydrogenase (LDH), and total cholesterol were correlated with the hypothyroidism model. Conclusions We demonstrated the potential of machine learning approaches for diagnosing the presence of thyroid dysfunction from routine laboratory tests. Further validation, including prospective clinical studies, is necessary prior to application of our method in the clinic.
    Type of Medium: Online Resource
    ISSN: 2730-664X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 3096949-9
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  • 3
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2007
    In:  Journal of Mathematical Biology Vol. 56, No. 1-2 ( 2007-11-21), p. 201-214
    In: Journal of Mathematical Biology, Springer Science and Business Media LLC, Vol. 56, No. 1-2 ( 2007-11-21), p. 201-214
    Type of Medium: Online Resource
    ISSN: 0303-6812 , 1432-1416
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2007
    detail.hit.zdb_id: 1421292-4
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Japanese Society for Artificial Intelligence ; 2017
    In:  Transactions of the Japanese Society for Artificial Intelligence Vol. 32, No. 2 ( 2017), p. F-AI30Ge_1-10
    In: Transactions of the Japanese Society for Artificial Intelligence, Japanese Society for Artificial Intelligence, Vol. 32, No. 2 ( 2017), p. F-AI30Ge_1-10
    Type of Medium: Online Resource
    ISSN: 1346-0714 , 1346-8030
    Uniform Title: 訂正記事: 医師国家試験を自動解答するプログラムの構築
    Language: English , Japanese
    Publisher: Japanese Society for Artificial Intelligence
    Publication Date: 2017
    detail.hit.zdb_id: 2045823-X
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 1997
    In:  New Generation Computing Vol. 15, No. 1 ( 1997-03), p. 59-83
    In: New Generation Computing, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 1997-03), p. 59-83
    Type of Medium: Online Resource
    ISSN: 0288-3635 , 1882-7055
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 1997
    detail.hit.zdb_id: 797870-4
    detail.hit.zdb_id: 2164639-9
    SSG: 11
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  • 6
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2019-09-03)
    Abstract: Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled production of target-gene knock-out (KO) NHP models. Target-gene-KO/knock-in (KI) efficiency of CRISPR/Cas9 has not been extensively investigated in marmosets. In this study, optimum conditions for target gene modification efficacies of CRISPR/mRNA and CRISPR/nuclease in marmoset embryos were examined. CRISPR/nuclease was more effective than CRISPR/mRNA in avoiding mosaic genetic alteration. Furthermore, optimal conditions to generate KI marmoset embryos were investigated using CRISPR/Cas9 and 2 different lengths (36 nt and 100 nt) each of a sense or anti-sense single-strand oligonucleotide (ssODN). KIs were observed when CRISPR/nuclease and 36 nt sense or anti-sense ssODNs were injected into embryos. All embryos exhibited mosaic mutations with KI and KO, or imprecise KI, of c-kit . Although further improvement of KI strategies is required, these results indicated that CRISPR/Cas9 may be utilized to produce KO/KI marmosets via gene editing.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2615211-3
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  • 7
    Online Resource
    Online Resource
    MDPI AG ; 2021
    In:  Life Vol. 11, No. 11 ( 2021-10-25), p. 1135-
    In: Life, MDPI AG, Vol. 11, No. 11 ( 2021-10-25), p. 1135-
    Abstract: Protein–RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein–RNA structures, various computational methods have been developed to predict PRIs. However, most of these methods focus on predicting only RNA-binding regions in proteins or only protein-binding motifs in RNA. Methods for predicting entire residue–base contacts in PRIs have not yet achieved sufficient accuracy. Furthermore, some of these methods require the identification of 3D structures or homologous sequences, which are not available for all protein and RNA sequences. Here, we propose a prediction method for predicting residue–base contacts between proteins and RNAs using only sequence information and structural information predicted from sequences. The method can be applied to any protein–RNA pair, even when rich information such as its 3D structure, is not available. In this method, residue–base contact prediction is formalized as an integer programming problem. We predict a residue–base contact map that maximizes a scoring function based on sequence-based features such as k-mers of sequences and the predicted secondary structure. The scoring function is trained using a max-margin framework from known PRIs with 3D structures. To verify our method, we conducted several computational experiments. The results suggest that our method, which is based on only sequence information, is comparable with RNA-binding residue prediction methods based on known binding data.
    Type of Medium: Online Resource
    ISSN: 2075-1729
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2662250-6
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  • 8
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2011
    In:  BMC Bioinformatics Vol. 12, No. S1 ( 2011-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 12, No. S1 ( 2011-12)
    Abstract: Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several hierarchical clustering methods have been developed using similarity measures based on the scores of structural alignment. However, the high computational cost of exact structural alignment requires these methods to employ approximate algorithms. Such heuristics degrade the quality of clustering results, especially when the similarity among family members is not detectable at the primary sequence level. Results We describe a new similarity measure for the hierarchical clustering of ncRNAs. The idea is that the reliability of approximate algorithms can be improved by utilizing the information of suboptimal solutions in their dynamic programming frameworks. We approximate structural alignment in a more simplified manner than the existing methods. Instead, our method utilizes all possible sequence alignments and all possible secondary structures, whereas the existing methods only use one optimal sequence alignment and one optimal secondary structure. We demonstrate that this strategy can achieve the best balance between the computational cost and the quality of the clustering. In particular, our method can keep its high performance even when the sequence identity of family members is less than 60%. Conclusions Our method enables fast and accurate clustering of ncRNAs. The software is available for download at http://bpla-kernel.dna.bio.keio.ac.jp/clustering/ .
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 9
    In: BMC Chemical Biology, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2012-12)
    Abstract: Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. Results We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system. As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. Conclusions This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.
    Type of Medium: Online Resource
    ISSN: 1472-6769
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2059860-9
    SSG: 12
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  • 10
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 21, No. S3 ( 2020-04)
    Abstract: The common marmoset ( Callithrix jacchus ) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. Results Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. Conclusions Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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