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现代生物医学进展 2017年第15期17卷 I0003-I0003页

作者： Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan Shyam Prabhakar Elise T Courtois, Yuliana Tan Paul Robson Debarka Sengupta Kok Hao Chen, Jolene Jie Lin Goh Paul Jongjoon Choi Say Li Kong, Axel M Hillmer Iain Beehuat Tan Clarinda Chua Iain Beehuat Tan Lim Kiat Hon Wah Siew Tan Mark Wong Lawrence J K Wee Iain Beehuat Tan Paul Robson Paul Robson Paul Robson Computational and Systems Biology Genome Institute of Singapore Singapore Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India Synthetic Biology Genome Institute of Singapore Singapore Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Department of Medical Oncology National Cancer Centre Singapore Singapore Department of Pathology Singapore General Hospital Singapore Department of Colorectal Surgery Singapore General Hospital Singapore Data Analytics Department Institute for Infocomm Research Singapore Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA Department of Biological Sciences National University of Singapore Singapore.

结合单细胞基因组学和计算机技术，一个研究团队（包括来自杰克逊实验室（JAx）单细胞生物学主任Paul Robson博士在内）鉴定出了11种结直肠癌肿瘤的癌细胞组成及邻近的非癌细胞。这对于更好的肿瘤靶向诊断和治疗很重要。”使用单细胞测... 详细信息

结合单细胞基因组学和计算机技术，一个研究团队（包括来自杰克逊实验室（JAx）单细胞生物学主任Paul Robson博士在内）鉴定出了11种结直肠癌肿瘤的癌细胞组成及邻近的非癌细胞。这对于更好的肿瘤靶向诊断和治疗很重要。”使用单细胞测序。”JAX科学家、这篇发表在Nature Genetics上的文章共同第一作者Elise Courtois说道。”我们可以根据肿瘤中的细胞组成将结直肠癌进一步分类。因为每种亚型的肿瘤病人生存率存在差别，我们的方法将为肿瘤医生提供更多的关于肿瘤预后和治疗的信息。”

关键词：单细胞分析结直肠癌癌细胞 Nat 细胞组成肿瘤病计算机技术细胞生物学

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Quantum simulation of an extended Dicke model with a magnetic solid

Communications Materials

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Communications Materials 2024年第1期5卷 42页

作者： Marquez Peraca, Nicolas Li, Xinwei Moya, Jaime M. Hayashida, Kenji Kim, Dasom Ma, Xiaoxuan Neubauer, Kelly J. Fallas Padilla, Diego Huang, Chien-Lung Dai, Pengcheng Nevidomskyy, Andriy H. Pu, Han Morosan, Emilia Cao, Shixun Bamba, Motoaki Kono, Junichiro Department of Physics and Astronomy Rice University HoustonTX United States Department of Physics California Institute of Technology PasadenaCA United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX United States Division of Applied Physics Graduate School of Engineering Hokkaido University Hokkaido Japan Department of Electrical and Computer Engineering Rice University HoustonTX United States Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University Shanghai China Department of Physics and Center for Quantum Frontiers of Research and Technology National Cheng Kung University Tainan Taiwan Department of Chemistry Rice University HoustonTX United States Department of Physics I Kyoto University Kyoto Japan The Hakubi Center for Advanced Research Kyoto University Kyoto Japan PRESTO Japan Science and Technology Agency Saitama Japan Department of Physics Yokohama National University Yokohama Japan Department of Materials Science and NanoEngineering Rice University HoustonTX United States

The Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO3, where the role of atoms (photons) is played by Er3+ spins (Fe3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems. © The Author(s) 2024.

关键词： Atoms

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Two-Step Activated Carbon Cloth Enhances Microbial Interactions and Methane Production During Anaerobic Digestion of Municipal Sludge

SSRN

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SSRN 2022年

作者： Kumar, Vikas Kieft, Brandon Devi, Parmila Hallam, Steven J. Eskicioglu, Cigdem UBC Bioreactor Technology Group School of Engineering University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Department of Microbiology and Immunology University of British Columbia VancouverBCV6T 1Z4 Canada Department of Microbiology and Immunology University of British Columbia VancouverBC Canada Graduate Program in Bioinformatics University of British Columbia VancouverBCV6T 1Z4 Canada Genome Science and Technology Program University of British Columbia 2329 West Mall VancouverBCV6T 1Z4 Canada Life Sciences Institute University of British Columbia VancouverBCV6T 1Z3 Canada ECOSCOPE Training Program University of British Columbia VancouverBCV6T 1Z3 Canada

This study investigated the effects of two-step activated carbon cloth (CC) on the syntrophic microbial association during anaerobic digestion (AD) of municipal sludge. A simple two-step activation, acid pretreatment (H2SO4/HNO3) followed by air calcination (550°C), was used to convert commercial untreated CC (U-CC) into high performance activated CC (A-CC). Biochemical methane potential (BMP) assays conducted at different CC dosages indicated that A-CC, at a dose of 0.80 g A-CC {1.48 g A-CC/g-VS (volatile solids)substrate}, enhanced methane yield from by 3.7 times and reduced the lag phase up to 15.6-fold, compared to non-CC control within 3 days. Characterization of CC surfaces and kinetic modeling indicated a 435-times increased A-CC pore size area (Barrett, Joyner, and Halenda, BJH) with the potential to promote electron transfer and accelerate kinetic rates of methane production. Consistent with these results, microbial community structure analysis of CC surfaces indicated rapid adherence of methanogenic archaea and bacterial syntrophs to A-CC within 3 days. Multi-variate statistical analyses indicated that these populations were highly enriched on 0.80 g A-CC dosage compared to controls. Based on these results it can be concluded that A-CC provides a robust selective environment for syntrophic energy metabolism driving enhanced methane production from municipal sludge. © 2022, The Authors. All rights reserved.

关键词： Anaerobic digestion

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C-Terminal-Truncating ASXL1 Mutations Induce MDS Via Inhibition Of PRC2

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BLOOD 2013年第21期122卷 471-471页

作者： Inoue, Daichi Kitaura, Jiro Togami, Katsuhiro Nishimura, Koutarou Enomoto, Yutaka Uchida, Tomoyuki Kagiyama, Yuki Kawabata, Kimihito Cojin Nakahara, Fumio Oki, Toshihiko Harada, Hironori Ochiya, Takahiro Aburatani, Hiroyuki Kimura, Hiroshi Thol, Felicitas Heuser, Michael Levine, Ross L. Abdel-Wahab, Omar Kitamura, Toshio Division of Cellular Therapy The Institute of Medical Science The University of Tokyo Tokyo Japan Division of Hematological Malignancy National Cancer Center Research Institute Tokyo Japan Department of Hematology Juntendo University School of Medicine Tokyo Japan Sec. Meta. National Cancer Center Research Institute Tokyo Japan Genome Science Division Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Graduate School of Frontier Biosciences Osaka University Suita Japan Department of Hematology Hemostasis Oncology and Stem Cell Transplantation Hannover Medical School Hannover Germany Department of Medicine Memorial Sloan-Kettering Cancer Center New York NY USA Leukemia Service and Human Oncology and Pathogenesis Program Memorial Sloan-Kettering Cancer Center New York City NY USA

471

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Serendipitous discoveries in microarray analysis

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BMC Bioinformatics 2010年第4期11卷 1-1页

作者： Sally R Ellingson Charles A Phillips Michael A Langston Randy Glenn Douglas Swanson Thomas Ha Daniel Goldowitz Genome Science and Technology Program University of Tennessee Knoxville TN 37996 USA Department of Electrical Engineering and Computer Science University of Tennessee Knoxville TN 37996 USA Centre for Molecular Medicine and Therapeutics University of British Columbia Vancouver BC V5Z 4H4 Canada

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Publisher Correction: IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis

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Scientific reports 2018年第1期8卷 10367页

作者： Daichi Shigemizu Fuyuki Miya Shintaro Akiyama Shujiro Okuda Keith A Boroevich Akihiro Fujimoto Hidewaki Nakagawa Kouichi Ozaki Shumpei Niida Yonehiro Kanemura Nobuhiko Okamoto Shinji Saitoh Mitsuhiro Kato Mami Yamasaki Tatsuo Matsunaga Hideki Mutai Kenjiro Kosaki Tatsuhiko Tsunoda Department for Medical Genome Sciences Medical Genome Center National Center for Geriatrics and Gerontology Aichi Japan. daichi@ncgg.go.jp. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. daichi@ncgg.go.jp. RIKEN Center for Integrative Medical Sciences Yokohama Japan. daichi@ncgg.go.jp. Medical Sciences Innovation Hub Program Cluster for Science and Technology Hub RIKEN Yokohama Japan. daichi@ncgg.go.jp. CREST JST Japan. daichi@ncgg.go.jp. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department for Medical Genome Sciences Medical Genome Center National Center for Geriatrics and Gerontology Aichi Japan. Niigata University Graduate School of Medical and Dental Sciences Niigata Japan. Department of Drug Discovery Medicine Graduate School of Medicine Kyoto University Kyoto Japan. Division of Regenerative Medicine Institute for Clinical Research Osaka National Hospital National Hospital Organization Osaka Japan. Department of Neurosurgery Osaka National Hospital National Hospital Organization Osaka Japan. Department of Medical Genetics Osaka Medical Center and Research Institute for Maternal and Child Health Osaka Japan. Department of Pediatrics and Neonatology Nagoya City University Graduate School of Medical Sciences Nagoya Japan. Department of Pediatrics Showa University School of Medicine Tokyo Japan. Department of Pediatric Neurosurgery Takatsuki General Hospital Osaka Japan. Division of Hearing and Balance Research National Institute of Sensory Organs National Hospital Organization Tokyo Medical Center Tokyo Japan. Center for Medical Genetics Keio University School of Medicine Tokyo Japan. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. tsunoda.mesm@mri.tmd.a

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

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Synthesis and Evaluation of Metal-Impregnated Carbon Cloth Supplementation to Improve Anaerobic Digestion Performance from Municipal Sludge

SSRN

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SSRN 2023年

作者： Kumar, Vikas Devi, Parmila Patil, Abhishek Santana, Juan Camilo Bobowski, Jake S. Hallam, Steven J. Eskicioglu, Cigdem UBC Bioreactor Technology Group School of Engineering University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Department of Microbiology and Immunology University of British Columbia VancouverBCV6T 1Z4 Canada Department of Physics University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Graduate Program in Bioinformatics University of British Columbia VancouverBCV6T 1Z4 Canada Genome Science and Technology Program University of British Columbia 2329 West Mall VancouverBCV6T 1Z4 Canada Life Sciences Institute University of British Columbia VancouverBCV6T 1Z3 Canada Ecoscope Training Program University of British Columbia VancouverBCV6T 1Z3 Canada

This study investigated the effect of metal-impregnated carbon cloth (CC) supplementation on thermophilic anaerobic digestion (AD) improvement utilizing municipal sludge as a biomass input. Four types of metal-impregnated CC nanocomposites (Fe/CC, Ni/CC, Ni/Fe/CC, NiPcS/Fe/CC) were synthesized from activated CC (A-CC) using hydrothermal synthesis and compared with untreated CC (U-CC) to evaluate their functional significance for enhanced AD. The main factors inspected were electrical conductivity (EC) and Brunauer–Emmett–Teller (BET) surface area. A-CC had the highest surface area of 386.15 m2/g, followed by Fe/CC, NiPcS/Fe/CC, Ni/CC and Ni/Fe/CC with 140.96, 52.27, 43.52 and 36.07 m2/g, respectively. The A-CC and Fe/CC reactors produced 3.45 and 2.70 times more methane than Control (without CC) in the first 9 days. In contrast, the methane production for U-CC, Ni/CC, Ni/Fe/CC and NiPcS/Fe/CC was only 0.87, 1.26, 1.01 and 1.29 times, respectively, compared to Control. At a higher BET surface (>350 m2/g), the surface area becomes a more dominant factor, and the increase of EC value (>2.9*104 1/Ω.m) does not have an impact on methane enhancement. Microbial community analysis revealed that A-CC had the highest abundances of Syntrophomonas, Coprothermobacter and methanogenic populations, including Methanothermobacter and Methanosarcina, within 3 days compared to Control and metal-impregnated CC. There were minimal changes in microbial community composition in metal-impregnated CC compared to the U-CC. The result implies that the efficacy of CC supplementation for AD upgrading largely depends on the higher surface area compared to metal impregnation or conductivity. © 2023, The Authors. All rights reserved.

关键词： Anaerobic digestion

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Author Correction: Examining the healthy human microbiome concept

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Nature reviews. Microbiology 2025年第3期23卷 206页

作者： Raphaela Joos Katy Boucher Aonghus Lavelle Manimozhiyan Arumugam Martin J Blaser Marcus J Claesson Gerard Clarke Paul D Cotter Luisa De Sordi Maria G Dominguez-Bello Bas E Dutilh Stanislav D Ehrlich Tarini Shankar Ghosh Colin Hill Christophe Junot Leo Lahti Trevor D Lawley Tine R Licht Emmanuelle Maguin Thulani P Makhalanyane Julian R Marchesi Jelle Matthijnssens Jeroen Raes Jacques Ravel Anne Salonen Pauline D Scanlan Andrey Shkoporov Catherine Stanton Ines Thiele Igor Tolstoy Jens Walter Bo Yang Natalia Yutin Alexandra Zhernakova Hub Zwart Joël Doré R Paul Ross APC Microbiome Ireland University College Cork Cork Ireland. School of Microbiology University College Cork Cork Ireland. Department of Anatomy and Neuroscience University College Cork Cork Ireland. Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark. Center for Advanced Biotechnology and Medicine Rutgers University Piscataway NJ USA. Department of Psychiatry and Neurobehavioural Science University College Cork Cork Ireland. Teagasc Food Research Centre and VistaMilk SFI Research Centre Moorepark Fermoy Moorepark Ireland. Centre de Recherche Saint Antoine Sorbonne Université INSERM Paris France. Department of Biochemistry and Microbiology Rutgers University New Brunswick NJ USA. Institute of Biodiversity Faculty of Biological Sciences Cluster of Excellence Balance of the Microverse Friedrich Schiller University Jena Jena Germany. Theoretical Biology and Bioinformatics Department of Biology Science for Life Utrecht University Utrecht The Netherlands. Université Paris-Saclay INRAE MetaGenoPolis (MGP) Jouy-en-Josas France. Department of Clinical and Movement Neurosciences University College London London UK. Department of Computational Biology Indraprastha Institute of Information Technology Delhi (IIIT-Delhi) New Delhi India. Département Médicaments et Technologies pour La Santé (DMTS) Université Paris-Saclay CEA INRAE MetaboHUB Gif-sur-Yvette France. Department of Computing University of Turku Turku Finland. Host-Microbiota Interactions Laboratory Wellcome Sanger Institute Hinxton UK. National Food Institute Technical University of Denmark Kgs. Lyngby Denmark. Université Paris-Saclay INRAE AgroParisTech MICALIS Jouy-en-Josas France. Department of Microbiology Faculty of Science Stellenbosch University Stellenbosch South Africa. Division of Digestive Diseases Department of Metabolism Digestion and Reproduction Imperial College London London UK. K

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Magnetically tuned continuous transition from weak to strong coupling in terahertz magnon polaritons

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Physical Review Research 2023年第1期5卷 L012039-L012039页

作者： Andrey Baydin Kenji Hayashida Takuma Makihara Fuyang Tay Xiaoxuan Ma Wei Ren Guohong Ma G. Timothy Noe, II Ikufumi Katayama Jun Takeda Hiroyuki Nojiri Shixun Cao Motoaki Bamba Junichiro Kono Department of Electrical and Computer Engineering Rice University Houston Texas 77005 USA Smalley-Curl Institute Rice University Houston Texas 77005 USA Division of Applied Physics Graduate School of Engineering Hokkaido University Sapporo Hokkaido 060-8628 Japan Department of Physics and Astronomy Rice University Houston Texas 77005 USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas 77005 USA Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University 200444 Shanghai China Department of Physics Graduate School of Engineering Science Yokohama National University Yokohama 240-8501 Japan Institute for Materials Research Tohoku University Sendai 980-8577 Japan The Hakubi Center for Advanced Research Kyoto University Kyoto 606-8502 Japan Department of Physics I Kyoto University Kyoto 606-8502 Japan PRESTO Japan Science and Technology Agency Kawaguchi 332-0012 Japan Department of Materials Science and NanoEngineering Rice University Houston Texas 77005 USA

Depending on the relative rates of coupling and dissipation, a light-matter coupled system is either in the weak- or strong-coupling regime. Here, we present a unique system where the coupling rate continuously increases with an externally applied magnetic field while the dissipation rate remains constant, allowing us to monitor a weak-to-strong coupling transition as a function of magnetic field. We observed a Rabi splitting of a terahertz magnon mode in yttrium orthoferrite above a threshold magnetic field of ∼14 T. Based on a microscopic theoretical model, we show that with increasing magnetic field the magnons transition into magnon polaritons through an exceptional point, which will open up new opportunities for in situ control of non-Hermitian systems.

关键词： Antiferromagnetism High magnetic fields Magneto-optics Magnons Polaritons Non-Hermitean systems Terahertz time-domain spectroscopy Transfer matrix method

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71 Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

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Journal of Biomolecular Structure and Dynamics 2013年第SUPP 1期31卷 45-46页

作者： Raluca Gordan[a][b][*] Ning Shen[c] Iris Dror[d] Tianyin Zhou[d] John Horton[b] Remo Rohs[d] & Martha L. Bulyk[e][f] [a] Departments of Biostatistics and Bioinformatics Computer Science and Molecular Genetics and Microbiology Duke University Durham NC USA [b] Institute for Genome Sciences and Policy Duke University Durham NC 27708 USA Phone: Phone: +1 (919) 667-8673 Fax: Phone: +1 (919) 667-8673 [c] Department of Pharmacology and Cancer Biology Duke University Durham NC 27708 USA [d] Molecular and Computational Biology Program Departments of Biological Sciences Chemistry and Physics and Astronomy University of Southern California 1050 Childs Way Los Angeles CA 90089 USA [e] Division of Genetics Departments of Medicine and Pathology Brigham and Women’s Hospital and Harvard Medical School Boston MA 02115 USA [f] Harvard-MIT Division of Health Sciences and Technology (HST) Harvard Medical School Boston MA 02115 USA

Transcriptional regulation of gene expression is enacted mainly through binding of transcription factors (TFs) to specific, short DNA sites in cis-regulatory regions of genes. Most TFs are members of protein families that share a common DNA-binding domain and thus recognize similar DNA-binding sequences. It is not well understood why paralogous TFs often bind different genomic target sitesin vivoto effect different regulatory programs, despite apparently recognizing the same sequence motifs. Here, we designed custom protein-binding microarrays (PBMs) to analyze the DNA-binding specificities of twoSaccharomyces cerevisiaebasic helix-loop-helix (bHLH) proteins, Tye7 and Cbf1, as a model system. Our data reveal that E-box DNA-binding sequences (CAnnTG), when tested in the context of their native genomic flanking sequences, are bound differently by Cbf1 and Tye7. Computational models of the PBM data indicate that DNA sequence features located in the genomic sequences outside the E-box contribute to DNA-binding specificityin vitro. Our analyses suggest that these flanking regions affect DNA-binding specificity indirectly by influencing the three-dimensional structure of the E-box binding sites. Finally, we show that these subtle differences in intrinsic sequence preferences of Cbf1 and Tye7in vitrohelp to explain their differential DNA-binding preferencesin vivo. Our results provide further evidence that the local shape of DNA-binding sites may be an important feature in distinguishing the DNA-binding preferences among paralogous TFs and thus may play a widespread role in determining how transcriptional regulatory specificity within TF families is achieved.

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