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1. Speech rate calculations with short utterances:A study from a speech-to-speech, machine translation mediated map task

Author

Akira, H., Carl Vogel, Luz, S., Campbell, N., Isahara, Hitoshi, Maegaard, Bente, Piperidis, Stelios, Cieri, Christopher, Declerck, Thierry, Hasida, Koiti, Mazo, Helene, Choukri, Khalid, Goggi, Sara, Mariani, Joseph, Moreno, Asuncion, Calzolari, Nicoletta, Odijk, Jan, and Tokunaga, Takenobu

Subjects
Linguistics and Language, Utterance duration comparison, Speech rate, Task oriented dialogues, Library and Information Sciences, Language and Linguistics, Education
Abstract

The motivation for this paper is to present a way to verify if an utterance within a corpus is pronounced at a fast or slow pace. An alternative method to the well-known Word-Per-Minute (wpm) method for cases where this approach is not applicable. For long segmentations, such as the full introduction section of a speech or presentation, the measurement of wpm is a viable option. For short comparisons of the same single word or multiple syllables, Syllables-Per-Second (sps) is also a viable option. However, when there are multiple short utterances that are frequent in task oriented dialogues or natural free flowing conversation, such as those of the direct Human-to-Human dialogues of the HCRC Map Task corpus or the computer mediated inter-lingual dialogues of the ILMT-s2s corpus, it becomes difficult to obtain a meaningful value for the utterance speech rate. In this paper we explain the method used to provide a alternative speech rate value to the utterance of the ILMT-s2s corpus and the HCRC Map Task corpus.

Published
2018

2. Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

Author

Masahito, Y., Hiroko, O., Susumu, H., Satoshi, K., Alistair R, R.F., Hideya, K., Michael, R., J Kenneth Baillie, Michiel J, L.D.H., Vanja, H., Timo, L., Ivan, V.K., Marina, L., Masayoshi, I., Robin, A., Christopher, J.M., Terrence, F.M., Sebastian, S., Nicolas, B., Mette, J., Emmanuel, D., Erik, A., Christian, S., Ulf, S., Yulia, A.M., Charles, P., Morana, V., Jessica, S., Colin, A.S., Yuri, I., Margherita, F., Intikhab, A., Davide, A., Gabriel, M.A., John A, C.A., Peter, A., Magda, B., Sarah, B., Piotr, J.B., Anthony, G.B., Swati, P., Judith, A.B., Antje, B., Bodega, B., Alessandro, B., James, B., Frank, B., A Maxwell Burroughs, Andrea, C., Carlo, V.C., Daniel, C., Yun, C., Marco, C., Yari, C., Hans, C.C., Emiliano, D., Carrie, A.D., Michael, D., Alexander, D.D., Taeko, D., Finn, D., Albert S, B.E., Matthias, E., Karl, E., Mitsuhiro, E., Hideki, E., Michela, F., Lynsey, F., Hai, F., Mary, C.F., Geoffrey, J.F., Alexander, V.F., Malcolm, E.F., Martin, C.F., Rie, F., Shiro, F., Cesare, F., Masaaki, F., Jun-ichi, F., Teunis, B.G., Andrew, G., Thomas, G., Daniel, G., Julian, G., Sven, G., Reto, G., Stefano, G., Thomas, J.H., Masahide, H., Mitsuko, H., Matthias, H., Jayson, H., Akira, H., Yuki, H., Takehiro, H., Meenhard, H., Kelly, J.H., Shannan, J.H.S., Oliver, M.H., Ilka, H., Fumi, H., Lukasz, H., Kei, I., Tomokatsu, I., Boris, R.J., Hui, J., Anagha, J., Giuseppe, J., Bogumil, K., Chieko, K., Kaoru, K., Kaiho, A., Kazuhiro, K., Mutsumi, K., Artem, S.K., Takeya, K., Shintaro, K., Sachi, K., Shuji, K., Hiroshi, K., Yuki, I.K., Tsugumi, K., Judith, S.K., Tony, J.K., Juha, K., Levon, M.K., Toshio, K., S Peter Klinken, Alan, J.K., Miki, K., Soichi, K., Naoto, K., Haruhiko, K., Shigeo, K., Sarah, K., Atsutaka, K., Andrew, T.K., Jeroen F, J.L., Weonju, L., Andreas, L., Kang, L., Berit, L., Leonard, L., Alan, M., Ri-ichiroh, M., Jessica, C.M., Benoit, M., Anthony, M., Niklas, M., Alison, M., Yosuke, M., David, A.D.L.M., Hiromasa, M., Mitsuru, M., Kazuyo, M., Efthymios, M., Hozumi, M., Christine, L.M., Mitsuyoshi, M., Sayaka, N., Yutaka, N., Fumio, N., Toshiyuki, N., Yukio, N., Kenichi, N., Erik van Nimwegen, Noriko, N., Hiromi, N., Shohei, N., Tadasuke, N., Soichi, O., Naganari, O., Hiroshi, O., Mitsuhiro, O., Mariko, O., Yasushi, O., Valerio, O., Dmitry, A.O., Arnab, P., Robert, P., Margaret, P., Helena, P., Silvano, P., James G, D.P., Owen J, L.R., Jordan, A.R., Mamoon, R., Timothy, R., Patrizia, R., Marco, R., Sugata, R., Morten, B.R., Eri, S., Antti, S., Akiko, S., Shimon, S., Mizuho, S., Hiroki, S., Hironori, S., Suzana, S., Alka, S., Claudio, S., Erik, A.S., Gundula, G.S., Anita, S., Thierry, S., Guojun, S., Hisashi, S., Yishai, S., Jay, W.S., Christophe, S., Daisuke, S., Takaaki, S., Masanori, S., Rolf, K.S., Peter A, C.'.H., Michihira, T., Naoko, T., Jun, T., Hiroshi, T., Hideki, T., Zuotian, T., Mark, T., Hiroo, T., Tetsuro, T., Eivind, V., Marc van de Wetering, Linda, M.V.D.B., Roberto, V., Dipti, V., Ilya, E.V., Wyeth, W.W., Shoko, W., Christine, A.W., Louise, N.W., Ernst, W., Emily, J.W., Yoko, Y., Masayuki, Y., Misako, Y., Yohei, Y., Shigehiro, Y., Suzan, E.Z., Peter, G.Z., Xiaobei, Z., Silvia, Z., Kim, M.S., Harukazu, S., Carsten, O.D., Jun, K., Peter, H., Winston, H., Tom, C.F., Boris, L., Vladimir, B.B., Martin, S.T., Vsevolod, J.M., Albin, S., David, A.H., Piero, C., Yoshihide Hayashizaki Yoshihide, H., Motokazu, T., Kohji, N., Hubrecht Institute for Developmental Biology and Stem Cell Research, Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Cell type, Corneal endothelium, Pathology, medicine.medical_specialty, medicine.medical_treatment, lcsh:Medicine, Settore BIO/11 - Biologia Molecolare, Nerve Tissue Proteins, Context (language use), Biology, Zona Pellucida Glycoproteins, Receptors, G-Protein-Coupled, Cornea, Corneal Transplantation, medicine, Humans, Regeneration, Endothelial dysfunction, lcsh:Science, Corneal transplantation, Membrane Glycoproteins, Multidisciplinary, Tissue Engineering, Regeneration (biology), lcsh:R, Egg Proteins, Endothelium, Corneal, Endothelial Cells, Membrane Proteins, Correction, Middle Aged, medicine.disease, medicine.anatomical_structure, Receptor, Serotonin, 5-HT1D, Bullous keratopathy, cardiovascular system, lcsh:Q, Carrier Proteins, Biomarkers, Research Article
Abstract

The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro.

Published
2015

3. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

Author

Arner, E., Forrest, A.R.R., Hideya, K., Michael, R., J Kenneth Baillie, Michiel J, L.D.H., Vanja, H., Timo, L., Ivan, V.K., Marina, L., Masayoshi, I., Robin, A., Christopher, J.M., Terrence, F.M., Sebastian, S., Nicolas, B., Mette, J., Emmanuel, D., Erik, A., Christian, S., Ulf, S., Yulia, A.M., Charles, P., Morana, V., Jessica, S., Colin, A.S., Yuri, I., Margherita, F., Intikhab, A., Davide, A., Gabriel, M.A., John A, C.A., Peter, A., Magda, B., Sarah, B., Piotr, J.B., Anthony, G.B., Swati, P., Judith, A.B., Antje, B., Bodega, B., Alessandro, B., James, B., Frank, B., A Maxwell Burroughs, Andrea, C., Carlo, V.C., Daniel, C., Yun, C., Marco, C., Yari, C., Hans, C.C., Emiliano, D., Carrie, A.D., Michael, D., Alexander, D.D., Taeko, D., Albert S, B.E., Matthias, E., Karl, E., Mitsuhiro, E., Hideki, E., Michela, F., Lynsey, F., Hai, F., Mary, C.F., Geoffrey, J.F., Alexander, V.F., Malcolm, E.F., Martin, C.F., Rie, F., Shiro, F., Cesare, F., Masaaki, F., Jun-ichi, F., Teunis, B.G., Andrew, G., Thomas, G., Daniel, G., Julian, G., Sven, G., Reto, G., Stefano, G., Thomas, J.H., Masahide, H., Mitsuko, H., Matthias, H., Jayson, H., Akira, H., Yuki, H., Takehiro, H., Meenhard, H., Kelly, J.H., Shannan, J.H.S., Oliver, M.H., Ilka, H., Fumi, H., Lukasz, H., Kei, I., Tomokatsu, I., Boris, R.J., Hui, J., Anagha, J., Giuseppe, J., Bogumil, K., Chieko, K., Kaoru, K., Kaiho, A., Kazuhiro, K., Mutsumi, K., Artem, S.K., Takeya, K., Shintaro, K., Sachi, K., Shuji, K., Hiroshi, K., Yuki, I.K., Tsugumi, K., Judith, S.K., Tony, J.K., Juha, K., Levon, M.K., Toshio, K., S Peter Klinken, Alan, J.K., Miki, K., Soichi, K., Naoto, K., Haruhiko, K., Shigeo, K., Sarah, K., Atsutaka, K., Andrew, T.K., Jeroen F, J.L., Weonju, L., Andreas, L., Kang, L., Berit, L., Leonard, L., Alan, M., Ri-ichiroh, M., Jessica, C.M., Benoit, M., Anthony, M., Niklas, M., Alison, M., Yosuke, M., David, A.D.L.M., Hiromasa, M., Mitsuru, M., Kazuyo, M., Efthymios, M., Hozumi, M., Christine, L.M., Mitsuyoshi, M., Sayaka, N., Yutaka, N., Fumio, N., Toshiyuki, N., Yukio, N., Kenichi, N., Erik van Nimwegen, Noriko, N., Hiromi, N., Shohei, N., Tadasuke, N., Soichi, O., Naganari, O., Hiroko, O., Hiroshi, O., Mitsuhiro, O., Mariko, O., Yasushi, O., Valerio, O., Dmitry, A.O., Arnab, P., Robert, P., Margaret, P., Helena, P., Silvano, P., James G, D.P., Owen J, L.R., Jordan, A.R., Mamoon, R., Timothy, R., Patrizia, R., Marco, R., Sugata, R., Morten, B.R., Eri, S., Antti, S., Akiko, S., Shimon, S., Mizuho, S., Hiroki, S., Hironori, S., Suzana, S., Alka, S., Claudio, S., Erik, A.S., Gundula, G.S., Anita, S., Thierry, S., Guojun, S., Hisashi, S., Yishai, S., Jay, W.S., Christophe, S., Daisuke, S., Takaaki, S., Masanori, S., Rolf, K.S., Peter A, C.'.H., Michihira, T., Naoko, T., Jun, T., Hiroshi, T., Hideki, T., Zuotian, T., Mark, T., Hiroo, T., Tetsuro, T., Eivind, V., Marc van de Wetering, Linda, M.V.D.B., Roberto, V., Dipti, V., Ilya, E.V., Wyeth, W.W., Shoko, W., Christine, A.W., Louise, N.W., Ernst, W., Emily, J.W., Yoko, Y., Masayuki, Y., Misako, Y., Yohei, Y., Shigehiro, Y., Suzan, E.Z., Peter, G.Z., Xiaobei, Z., Silvia, Z., Kim, M.S., Harukazu, S., Carsten, O.D., Jun, K., Peter, H., Winston, H., Tom, C.F., Boris, L., Vladimir, B.B., Martin, S.T., Vsevolod, J.M., Albin, S., David, A.H., Piero, C., Yoshihide HayashizakiEhrlund, A., Mejhert, N., Itoh, M., Kawaji, H., Lassmann, T., Laurencikiene, J., Ryden, M., Arner, P., Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Male, Angiogenesis, lcsh:Medicine, Adipose tissue, Gene Expression, Endocrinology, Neoplasms, Molecular Cell Biology, Basic Cancer Research, Databases, Genetic, Medicine and Health Sciences, Adipocytes, lcsh:Science, Multidisciplinary, biology, Cancer Risk Factors, Ceruloplasmin, Genomics, Middle Aged, Genomic Databases, Functional Genomics, Oncology, Adipose Tissue, Female, Transcriptome Analysis, Network Analysis, Research Article, Signal Transduction, Adult, medicine.medical_specialty, Computer and Information Sciences, Adipose tissue macrophages, Adipokine, Settore BIO/11 - Biologia Molecolare, Adipokines, Internal medicine, Cell Line, Tumor, medicine, Genetics, Cancer Genetics, Humans, Obesity, Sweden, business.industry, Gene Expression Profiling, lcsh:R, Cancer, Biology and Life Sciences, Computational Biology, Cell Biology, medicine.disease, Genome Analysis, Signaling Networks, Cell culture, Genetic Loci, Metabolic Disorders, Case-Control Studies, Cancer cell, biology.protein, lcsh:Q, business, Genome Expression Analysis
Abstract

Obesity confers an increased risk of developing specific cancer forms. Although the mechanisms are unclear, increased fat cell secretion of specific proteins (adipokines) may promote/facilitate development of malignant tumors in obesity via cross-talk between adipose tissue(s) and the tissues prone to develop cancer among obese. We searched for novel adipokines that were overexpressed in adipose tissue of obese subjects as well as in tumor cells derived from cancers commonly associated with obesity. For this purpose expression data from human adipose tissue of obese and non-obese as well as from a large panel of human cancer cell lines and corresponding primary cells and tissues were explored. We found expression of ceruloplasmin to be the most enriched in obesity-associated cancer cells. This gene was also significantly up-regulated in adipose tissue of obese subjects. Ceruloplasmin is the body's main copper carrier and is involved in angiogenesis. We demonstrate that ceruloplasmin is a novel adipokine, which is produced and secreted at increased rates in obesity. In the obese state, adipose tissue contributed markedly (up to 22%) to the total circulating protein level. In summary, we have through bioinformatic screening identified ceruloplasmin as a novel adipokine with increased expression in adipose tissue of obese subjects as well as in cells from obesity-associated cancers. Whether there is a causal relationship between adipose overexpression of ceruloplasmin and cancer development in obesity cannot be answered by these cross-sectional comparisons.

Published
2014

4. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

Author

Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A.R.R., Hideya, K., Michael, R., J Kenneth Baillie, Michiel J, L.D.H., Vanja, H., Timo, L., Ivan, V.K., Marina, L., Masayoshi, I., Robin, A., Christopher, J.M., Terrence, F.M., Sebastian, S., Nicolas, B., Mette, J., Emmanuel, D., Erik, A., Christian, S., Ulf, S., Yulia, A.M., Charles, P., Morana, V., Jessica, S., Colin, A.S., Yuri, I., Robert, S.Y., Margherita, F., Intikhab, A., Davide, A., Gabriel, M.A., Takahiro, A., John A, C.A., Peter, A., Magda, B., Sarah, B., Piotr, J.B., Anthony, G.B., Swati, P., Judith, A.B., Antje, B., Bodega, B., Alessandro, B., James, B., Frank, B., A Maxwell Burroughs, Andrea, C., Carlo, V.C., Daniel, C., Yun, C., Marco, C., Yari, C., Hans, C.C., Emiliano, D., Carrie, A.D., Michael, D., Alexander, D.D., Taeko, D., Finn, D., Albert S, B.E., Matthias, E., Karl, E., Mitsuhiro, E., Hideki, E., Michela, F., Lynsey, F., Hai, F., Mary, C.F., Geoffrey, J.F., Alexander, V.F., Malcolm, E.F., Martin, C.F., Rie, F., Shiro, F., Cesare, F., Masaaki, F., Jun-ichi, F., Teunis, B.G., Andrew, G., Thomas, G., Daniel, G., Julian, G., Sven, G., Reto, G., Stefano, G., Thomas, J.H., Masahide, H., Mitsuko, H., Matthias, H., Jayson, H., Akira, H., Yuki, H., Takehiro, H., Meenhard, H., Kelly, J.H., Shannan, J.H.S., Oliver, M.H., Ilka, H., Fumi, H., Lukasz, H., Kei, I., Tomokatsu, I., Boris, R.J., Hui, J., Anagha, J., Giuseppe, J., Bogumil, K., Chieko, K., Kaoru, K., Kaiho, A., Kazuhiro, K., Mutsumi, K., Artem, S.K., Takeya, K., Shintaro, K., Sachi, K., Shuji, K., Hiroshi, K., Yuki, I.K., Tsugumi, K., Judith, S.K., Tony, J.K., Juha, K., Levon, M.K., Toshio, K., S Peter Klinken, Alan, J.K., Miki, K., Soichi, K., Naoto, K., Haruhiko, K., Shigeo, K., Sarah, K., Atsutaka, K., Andrew, T.K., Jeroen F, J.L., Weonju, L., Andreas, L., Kang, L., Berit, L., Leonard, L., Alan, M., Ri-ichiroh, M., Jessica, C.M., Benoit, M., Anthony, M., Niklas, M., Alison, M., Yosuke, M., David, A.D.L.M., Hiromasa, M., Mitsuru, M., Kazuyo, M., Efthymios, M., Hozumi, M., Christine, L.M., Mitsuyoshi, M., Sayaka, N., Yutaka, N., Fumio, N., Toshiyuki, N., Yukio, N., Kenichi, N., Erik van Nimwegen, Noriko, N., Hiromi, N., Shohei, N., Tadasuke, N., Soichi, O., Naganari, O., Hiroko, O., Hiroshi, O., Mitsuhiro, O., Mariko, O., Yasushi, O., Valerio, O., Dmitry, A.O., Arnab, P., Robert, P., Margaret, P., Helena, P., Silvano, P., James G, D.P., Owen J, L.R., Jordan, A.R., Mamoon, R., Timothy, R., Patrizia, R., Marco, R., Sugata, R., Morten, B.R., Eri, S., Antti, S., Akiko, S., Shimon, S., Mizuho, S., Hiroki, S., Hironori, S., Suzana, S., Alka, S., Claudio, S., Erik, A.S., Gundula, G.S., Anita, S., Thierry, S., Guojun, S., Hisashi, S., Yishai, S., Jay, W.S., Christophe, S., Daisuke, S., Takaaki, S., Masanori, S., Naoko, S., Rolf, K.S., Peter A, C.'.H., Michihira, T., Naoko, T., Jun, T., Hiroshi, T., Hideki, T., Zuotian, T., Mark, T., Hiroo, T., Tetsuro, T., Eivind, V., Marc van de Wetering, Linda, M.V.D.B., Roberto, V., Dipti, V., Ilya, E.V., Wyeth, W.W., Shoko, W., Christine, A.W., Louise, N.W., Ernst, W., Emily, J.W., Yoko, Y., Masayuki, Y., Misako, Y., Yohei, Y., Shigehiro, Y., Suzan, E.Z., Peter, G.Z., Xiaobei, Z., Silvia, Z., Kim, M.S., Harukazu, S., Carsten, O.D., Jun, K., Peter, H., Winston, H., Tom, C.F., Boris, L., Vladimir, B.B., Martin, S.T., Vsevolod, J.M., Albin, S., David, A.H., Piero, C., Yoshihide HayashizakSuzuki, H., Hjelt Institute (-2014), Forensic Medicine, PaleOmics Laboratory, Amsterdam institute for Infection and Immunity, Infectious diseases, Experimental Immunology, and Hubrecht Institute for Developmental Biology and Stem Cell Research

Subjects
Stage-Specific Embryonic Antigens, Chromosomal Proteins, Non-Histone, Cellular differentiation, Basic fibroblast growth factor, Gene Expression, LINES, OXYGEN, chemistry.chemical_compound, 0302 clinical medicine, Piperidines, Phosphorylation, STAT3, Induced pluripotent stem cell, Cells, Cultured, Chemokine CCL2, 0303 health sciences, Multidisciplinary, biology, Reverse Transcriptase Polymerase Chain Reaction, PROLIFERATION, Cell Differentiation, 319 Forensic science and other medical sciences, Nanog Homeobox Protein, Immunohistochemistry, Cell Hypoxia, Cell biology, HUMAN EMBRYONIC STEM, GROUND-STATE, Fibroblast Growth Factor 2, INACTIVATION, Signal transduction, Stem cell, Signal Transduction, Pluripotent Stem Cells, STAT3 Transcription Factor, EXPRESSION, Immunoblotting, Induced Pluripotent Stem Cells, Kruppel-Like Transcription Factors, Settore BIO/11 - Biologia Molecolare, Alkenes, Article, Kruppel-Like Factor 4, 03 medical and health sciences, Humans, Janus Kinases, 030304 developmental biology, Homeodomain Proteins, Proteins, Janus Kinase 1, CAP ANALYSIS, SELF-RENEWAL, chemistry, Epiblast, INDUCIBLE FACTOR-I, Immunology, biology.protein, 030217 neurology & neurosurgery
Abstract

Standard culture of human induced pluripotent stem cells (hiPSCs) requires basic Fibroblast Growth Factor (bFGF) to maintain the pluripotent state, whereas hiPSC more closely resemble epiblast stem cells than true naïve state ES which requires LIF to maintain pluripotency. Here we show that chemokine (C-C motif) ligand 2 (CCL2) enhances the expression of pluripotent marker genes through the phosphorylation of the signal transducer and activator of transcription 3 (STAT3) protein. Moreover, comparison of transcriptomes between hiPSCs cultured with CCL2 versus with bFGF, we found that CCL2 activates hypoxia related genes, suggesting that CCL2 enhanced pluripotency by inducing a hypoxic-like response. Further, we show that hiPSCs cultured with CCL2 can differentiate at a higher efficiency than culturing with just bFGF and we show CCL2 can be used in feeder-free conditions in the absence of LIF. Taken together, our finding indicates the novel functions of CCL2 in enhancing its pluripotency in hiPSCs.

Published
2014
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5. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

Author

Alistair R, R.F., Hideya, K., Michael, R., J Kenneth Baillie, Michiel J, L.D.H., Vanja, H., Timo, L., Ivan, V.K., Marina, L., Masayoshi, I., Robin, A., Christopher, J.M., Terrence, F.M., Sebastian, S., Nicolas, B., Mette, J., Emmanuel, D., Erik, A., Christian, S., Ulf, S., Yulia, A.M., Charles, P., Morana, V., Jessica, S., Colin, A.S., Yuri, I., Margherita, F., Intikhab, A., Davide, A., Gabriel, M.A., John A, C.A., Peter, A., Magda, B., Sarah, B., Piotr, J.B., Anthony, G.B., Swati, P., Judith, A.B., Antje, B., Bodega, B., Alessandro, B., James, B., Frank, B., A Maxwell Burroughs, Andrea, C., Carlo, V.C., Daniel, C., Yun, C., Marco, C., Yari, C., Hans, C.C., Emiliano, D., Carrie, A.D., Bart, D., Michael, D., Alexander, D.D., Taeko, D., Finn, D., Albert S, B.E., Matthias, E., Karl, E., Mitsuhiro, E., Hideki, E., Michela, F., Lynsey, F., Hai, F., Mary, C.F., Geoffrey, J.F., Alexander, V.F., Malcolm, E.F., Martin, C.F., Rie, F., Shiro, F., Cesare, F., Masaaki, F., Jun-ichi, F., Teunis, B.G., Andrew, G., Thomas, G., Daniel, G., Julian, G., Sven, G., Reto, G., Stefano, G., Thomas, J.H., Masahide, H., Mitsuko, H., Matthias, H., Jayson, H., Akira, H., Yuki, H., Takehiro, H., Meenhard, H., Kelly, J.H., Shannan, J.H.S., Oliver, M.H., Ilka, H., Fumi, H., Lukasz, H., Kei, I., Tomokatsu, I., Boris, R.J., Hui, J., Anagha, J., Giuseppe, J., Bogumil, K., Chieko, K., Kaoru, K., Kaiho, A., Kazuhiro, K., Mutsumi, K., Artem, S.K., Takeya, K., Shintaro, K., Sachi, K., Shuji, K., Hiroshi, K., Yuki, I.K., Tsugumi, K., Judith, S.K., Tony, J.K., Juha, K., Levon, M.K., Toshio, K., S Peter Klinken, Alan, J.K., Miki, K., Soichi, K., Naoto, K., Haruhiko, K., Shigeo, K., Sarah, K., Atsutaka, K., Andrew, T.K., Jeroen F, J.L., Weonju, L., Andreas, L., Kang, L., Berit, L., Leonard, L., Alan, M., Ri-ichiroh, M., Jessica, C.M., Benoit, M., Anthony, M., Niklas, M., Alison, M., Yosuke, M., David, A.D.L.M., Hiromasa, M., Mitsuru, M., Kazuyo, M., Efthymios, M., Hozumi, M., Christine, L.M., Mitsuyoshi, M., Sayaka, N., Yutaka, N., Fumio, N., Toshiyuki, N., Yukio, N., Kenichi, N., Erik van Nimwegen, Noriko, N., Hiromi, N., Shohei, N., Tadasuke, N., Soichi, O., Naganari, O., Hiroko, O., Hiroshi, O., Mitsuhiro, O., Mariko, O., Yasushi, O., Valerio, O., Dmitry, A.O., Arnab, P., Robert, P., Margaret, P., Helena, P., Silvano, P., James G, D.P., Owen J, L.R., Jordan, A.R., Mamoon, R., Timothy, R., Patrizia, R., Marco, R., Sugata, R., Morten, B.R., Eri, S., Antti, S., Akiko, S., Shimon, S., Mizuho, S., Hiroki, S., Hironori, S., Suzana, S., Alka, S., Claudio, S., Erik, A.S., Gundula, G.S., Anita, S., Thierry, S., Guojun, S., Hisashi, S., Yishai, S., Jay, W.S., Christophe, S., Daisuke, S., Takaaki, S., Masanori, S., Rolf, K.S., Peter A, C.'.H., Michihira, T., Naoko, T., Jun, T., Hiroshi, T., Hideki, T., Zuotian, T., Mark, T., Hiroo, T., Tetsuro, T., Eivind, V., Marc van de Wetering, Linda, M.V.D.B., Roberto, V., Dipti, V., Ilya, E.V., Wyeth, W.W., Shoko, W., Christine, A.W., Louise, N.W., Ernst, W., Emily, J.W., Yoko, Y., Masayuki, Y., Misako, Y., Yohei, Y., Shigehiro, Y., Suzan, E.Z., Peter, G.Z., Xiaobei, Z., Silvia, Z., Kim, M.S., Harukazu, S., Carsten, O.D., Jun, K., Peter, H., Winston, H., Tom, C.F., Boris, L., Vladimir, B.B., Martin, S.T., Vsevolod, J.M., Albin, S., David, A.H., Piero, C., Yoshihide Hayashizaki Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A.R.R., Carninci, P., Hayashizaki, Y., Daub, C.O., Okada-Hatakeyama, M., Mar, J.C., Hubrecht Institute for Developmental Biology and Stem Cell Research, Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
MAP Kinase Signaling System, Neuregulin-1, Cellular differentiation, lcsh:Medicine, Gene Expression, Settore BIO/11 - Biologia Molecolare, Apoptosis, Breast Neoplasms, Cell fate determination, Biology, Cell Line, Promoter Regions, Genetic, Cell Line, Tumor, Humans, Cell Cycle, Cell Differentiation, Cell Proliferation, Enzyme Activation, Epidermal Growth Factor, ErbB Receptors, Extracellular Signal-Regulated MAP Kinases, Female, Focal Adhesions, Gene Expression Profiling, Gene Expression Regulation, MCF-7 Cells, Promoter Regions, Genetic, Tumor Suppressor Protein p53, lcsh:Science, Transcription factor, Genetics, Regulation of gene expression, Tumor, Multidisciplinary, lcsh:R, Promoter, FHL2, Cell biology, Gene expression profiling, lcsh:Q, Signal transduction, Research Article
Abstract

Understanding how cells use complex transcriptional programs to alter their fate in response to specific stimuli is an important question in biology. For the MCF-7 human breast cancer cell line, we applied gene expression trajectory models to identify the genes involved in driving cell fate transitions. We modified trajectory models to account for the scenario where cells were exposed to different stimuli, in this case epidermal growth factor and heregulin, to arrive at different cell fates, i.e. proliferation and differentiation respectively. Using genome-wide CAGE time series data collected from the FANTOM5 consortium, we identified the sets of promoters that were involved in the transition of MCF-7 cells to their specific fates versus those with expression changes that were generic to both stimuli. Of the 1,552 promoters identified, 1,091 had stimulus-specific expression while 461 promoters had generic expression profiles over the time course surveyed. Many of these stimulus-specific promoters mapped to key regulators of the ERK (extracellular signal-regulated kinases) signaling pathway such as FHL2 (four and a half LIM domains 2). We observed that in general, generic promoters peaked in their expression early on in the time course, while stimulus-specific promoters tended to show activation of their expression at a later stage. The genes that mapped to stimulus-specific promoters were enriched for pathways that control focal adhesion, p53 signaling and MAPK signaling while generic promoters were enriched for cell death, transcription and the cell cycle. We identified 162 genes that were controlled by an alternative promoter during the time course where a subset of 37 genes had separate promoters that were classified as stimulus-specific and generic. The results of our study highlighted the degree of complexity involved in regulating a cell fate transition where multiple promoters mapping to the same gene can demonstrate quite divergent expression profiles.

Published
2015
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9. Adaptive Multi-View Semi-Supervised Nonnegative Matrix Factorization

Author

Akira, H., Seiichi, O., Doya, K., Kazushi, I., Minho, L., Derong, L., Wang, Jing, Wang, X., Tian, Feng, Liu, Chang Hong, Yu, Hongchuan, Liu, Yanbei, Akira, H., Seiichi, O., Doya, K., Kazushi, I., Minho, L., Derong, L., Wang, Jing, Wang, X., Tian, Feng, Liu, Chang Hong, Yu, Hongchuan, and Liu, Yanbei

Abstract

Multi-view clustering, which explores complementary information between multiple distinct feature sets, has received considerable attention. For accurate clustering, all data with the same label should be clustered together regardless of their multiple views. However, this is not guaranteed in existing approaches. To address this issue, we propose Adaptive Multi-View Semi-Supervised Nonnegative Matrix Factorization (AMVNMF), which uses label information as hard constraints to ensure data with same label are clustered together, so that the discriminating power of new representations are enhanced. Besides, AMVNMF provides a viable solution to learn the weight of each view adaptively with only a single parameter. Using L2,1-norm, AMVNMF is also robust to noises and outliers. We further develop an efficient iterative algorithm for solving the optimization problem. Experiments carried out on five well-known datasets have demonstrated the effectiveness of AMVNMF in comparison to other existing state-of-the-art approaches in terms of accuracy and normalized mutual information.

12. Adaptive Multi-View Semi-Supervised Nonnegative Matrix Factorization

Author

Hongchuan Yu, Chang Hong Liu, Feng Tian, Jing Wang, Xiao Wang, Yanbei Liu, Akira, H., Seiichi, O., Doya, K., Kazushi, I., Minho, L., and Derong, L.

Subjects
QA75, Optimization problem, business.industry, Iterative method, 020207 software engineering, Pattern recognition, 02 engineering and technology, Semi-supervised learning, Non-negative matrix factorization, Power (physics), Feature (computer vision), Outlier, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Artificial intelligence, business, Cluster analysis, Mathematics
Abstract

Multi-view clustering, which explores complementary \ud information between multiple distinct feature sets, has received considerable attention. For accurate clustering, all data with the same label should be clustered together regardless of their multiple views. However, this is not guaranteed in existing approaches. To address this issue, we propose Adaptive Multi-View Semi-Supervised Nonnegative Matrix Factorization (AMVNMF), which uses label information as hard constraints to ensure data with same label are clustered together, so that the discriminating power of new representations are enhanced. Besides, AMVNMF provides a viable solution to learn the weight of each view adaptively\ud with only a single parameter. Using L2,1-norm, AMVNMF is also robust to noises and outliers. We further develop an efficient iterative algorithm for solving the optimization problem. Experiments carried out on five well-known datasets have demonstrated the effectiveness of AMVNMF\ud in comparison to other existing state-of-the-art approaches in terms of accuracy and normalized mutual information.

Published
2016

13. Early post-traumatic splenic arteriovenous fistula in the pancreatic arcade: Diagnosis by volume-rendered 3D reconstruction images.

Author

Tsurukiri J, Sano H, Akira H, and Kaneko N

Subjects
Accidents, Traffic, Aged, Arteriovenous Fistula diagnostic imaging, Arteriovenous Fistula etiology, Arteriovenous Fistula surgery, Diagnosis, Differential, Female, Humans, Imaging, Three-Dimensional, Tomography, X-Ray Computed, Abdominal Injuries complications, Arteriovenous Fistula diagnosis, Lymphoma, Spleen injuries, Wounds, Nonpenetrating complications
Abstract

Arteriovenous fistula (AVF) of splenic vessels is rare. It is most commonly caused by spontaneous rupture of an extant splenic artery aneurysm into an adjacent vein, or by traumatic or iatrogenic pseudoaneurysm. Blunt abdominal trauma can sometimes lead to vascular damage to spleen, resulting in AVF formation. Presently described is case of an elderly patient with high-grade splenic injury. Early post-traumatic AVF was detected by volume-rendered 3D reconstruction using fused arterial and venous phase computed tomography (CT) images.

Published
2016
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14. Development of an assay of seven biochemical items, HbA1c, and hematocrit using a small amount of blood collected from the fingertip.

Author

Shinya S, Masaru A, Akira H, Eisaku H, and Susumu O

Subjects
Calibration, Humans, Uncertainty, Choline blood, Clinical Chemistry Tests, Fingers, Glycated Hemoglobin analysis, Hematocrit, Tyramine blood
Abstract

Background: Lifestyle-related diseases in Japan account for 30% of the entire medical expenditure of the country and cause 60% of all deaths. For the prevention of lifestyle-related diseases, medical examination by laboratory tests on metabolic syndrome is important., Methods: To undertake examination by collection of blood from a fingertip, we developed the "Well Kit". About 65 μl of blood collected from a fingertip was diluted with buffer solution, which contained two internal standard materials. The kit also separated corpuscles and diluted plasma with a special filter. It measured the obtained diluted plasma using the JCA-BM2250., Results: This measurement system was evaluated for the quantitative analysis of 8 items. The uncertainties of tested items of this measurement system were 1.7% to 6.4%. The coefficients of correlation of all tested items between this measurement value and the venous plasma sample value were 0.876-0.991, and hematocrit was 0.958., Conclusions: This system for testing blood collected from a fingertip is simple to use and can be applied in testing for metabolic syndrome. In addition, this testing system is useful in the medical examination of the personal healthcare and inhabitants., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Published
2012
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15. Induction of atrial fibrillation and nerve sprouting by prolonged left atrial pacing in dogs.

Author

Hamabe A, Chang CM, Zhou S, Chou CC, Yi J, Miyauchi Y, Okuyama Y, Fishbein MC, Karagueuzian HS, Chen LS, and Chen PS

Subjects
Animals, Autonomic Nervous System, Dogs, Heart Atria pathology, Atrial Fibrillation etiology, Cardiac Pacing, Artificial, Heart Atria innervation
Abstract

The authors hypothesized that rapid electrical stimulation can induce nerve sprouting in canine atria, and that LA pacing is more effective than RA pacing in inducing sustained AF. Chronic rapid (20 Hz) LA epicardial pacing was performed in six dogs. Sustained AF (>48 hours) was induced within 23 +/- 8 days, which was much faster than that with RA endocardial pacing using the same protocol (139 +/- 84 days, P < 0.05). Nerves were identified by immunocytochemical techniques. In all dogs, growth-associated protein 43-positive (sprouting) nerve density was highest near the pacing site, and the rapid LA pacing resulted in differential nerve sprouting among the LA, left superior pulmonary vein (LSPV), interatrial septum (IAS), and RA (5521 +/- 1496, 3154 +/- 2355, 3953 +/- 1164, 1559 +/- 1077 microm2/mm2, respectively, P = 0.0032). Tyrosine hydroxylase-positive (sympathetic) nerve density were not significantly different among groups (2726 +/- 1165, 1586 +/- 558, 2156 +/- 1741, 1509 +/- 1242 microm2/mm2, respectively). The nerves were inhomogeneously distributed. LA epicardial pacing induced sustained AF much faster than RA endocardial pacing and rapid electrical stimulation can induce inhomogeneous nerve sprouting near the pacing site.

Published
2003
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