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IEEE International Symposium on Biomedical Imaging

作者： Mengqi Xing Reza Tadayonnejad Annmarie MacNamara Olusola Ajilore K. Luan Phan Heide Klumpp Alex Leow Department of Bioengineering University of Illinois at Chicago Chicago IL Department of Psychiatry Chicago IL Department of Anatomy and Cell Biology and Psychology The Graduate Program in Neuroscience Chicago IL Mental Health Service Line Jesse Brown VA Medical Center Chicago IL

ISBN: (纸本)9781479923519

Patients suffering from anxiety disorders commonly have difficulties in emotion regulation. Understanding underlying brain network dysfunction can provide insight into their pathophysiology. Electroencephalography (EEG)-based functional connectivity contains high temporal information of brain network dynamics. We acquired EEG recordings in the resting state and during a series of emotion regulation tasks (ERT) from a sample of 20 subjects with anxiety disorders and 20 healthy controls. To generate EEG-based functional connectomes, we used the weighted phase lag index (WPLI), a phase based connectivity metric. Graph theory measures of clustering coefficient (CC) and characteristic path length (CPL) were computed to characterize properties of these complex functional networks. Results showed that in the theta band network integration measured using CPL increased as the cognitive load during the emotion regulation task increased, with a complementary trend in the CC. In summary, the EEG-based functional connectome is highly dynamic and task dependent, thus may serve as a promising non-invasive biomarker for diagnosis and treatment evaluation.

关键词： Electroencephalography Pollution measurement Market research Graph theory Atmospheric measurements Particle measurements Time-frequency analysis

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

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Nature genetics 2021年第12期53卷 1722页

作者： Yang Luo Masahiro Kanai Wanson Choi Xinyi Li Saori Sakaue Kenichi Yamamoto Kotaro Ogawa Maria Gutierrez-Arcelus Peter K Gregersen Philip E Stuart James T Elder Lukas Forer Sebastian Schönherr Christian Fuchsberger Albert V Smith Jacques Fellay Mary Carrington David W Haas Xiuqing Guo Nicholette D Palmer Yii-Der Ida Chen Jerome I Rotter Kent D Taylor Stephen S Rich Adolfo Correa James G Wilson Sekar Kathiresan Michael H Cho Andres Metspalu Tonu Esko Yukinori Okada Buhm Han Paul J McLaren Soumya Raychaudhuri Center for Data Sciences Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Division of Rheumatology Immunology and Immunity Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Division of Genetics Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Department of Biomedical Informatics Harvard Medical School Boston MA USA. yangluo@***. Broad Institute of MIT and Harvard Cambridge MA USA. yangluo@***. Department of Biomedical Informatics Harvard Medical School Boston MA USA. Broad Institute of MIT and Harvard Cambridge MA USA. Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA. Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Department of Biomedical Sciences Seoul National University College of Medicine Seoul South Korea. Committee on Genetics Genomics and Systems Biology University of Chicago Chicago IL USA. Center for Data Sciences Brigham and Women's Hospital Harvard Medical School Boston MA USA. Division of Rheumatology Immunology and Immunity Brigham and Women's Hospital Harvard Medical School Boston MA USA. Division of Genetics Brigham and Women's Hospital Harvard Medical School Boston MA USA. Department of Pediatrics Osaka University Graduate School of Medicine Osaka Japan. Department of Neurology Osaka University Graduate School of Medicine Osaka Japan. The Robert S. Boas Center for Genomics and Human Genetics Feinstein Institute for Medical ResearchNorth Short LIJ Health System Manhasset NY USA. Department of Dermatology University of Michigan Ann Arbor MI USA. Ann Arbor Veterans Affairs Hospital Ann Arbor MI USA. Institute of Genetic Epidemiology Department of Genetics and Pharmacology Medical University of Innsbruck Innsbruck Austria. Department of Biostatistics

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Corrigendum: Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue

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Letters in applied microbiology 2017年第4期65卷 343页

作者： I Choopara N Arunrut W Kiatpathomchai D Dean N Somboonna Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok Thailand. Bioengineering and Sensing Technology Laboratory National Center for Genetic Engineering and Biotechnology Khlong Nueng Khlong Luang Pathum Thani Thailand. Center for Immunobiology and Vaccine Development UCSF Benioff Children's Hospital Oakland Research Institute Oakland CA USA. Department of Medicine University of California San Francisco CA USA. Joint Graduate Program in Bioengineering University of California Berkeley CA USA. Department of Microbiology Faculty of Science Chulalongkorn University Bangkok Thailand.

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Human Bone Xenografts: from Preclinical Testing for Regenerative Medicine to Modeling of Diseases

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Current Molecular Biology Reports 2016年第3期2卷 158-170页

作者： Mark Seow Khoon Chong Chaolemeng Bao King Pan Ng Jing Lim Jerry Kok Yen Chan Division of Bioengineering School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore Department of Obstetrics and Gynaecology Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Cancer and Stem Cell Biology Program Duke-NUS Graduate Medical School Singapore Singapore Department of Reproductive Medicine KK Women’s and Children’s Hospital Singapore Singapore

Xenografting involves the transplantation of human tissue or cells into animal models and is an important tool for regenerative medicine research. Implantation of engineered human bone tissues into animal models, for example, is performed in preclinical evaluations of product safety and efficacy. With the advent of improved experimental methodologies, these models are further being exploited to interrogate molecular mechanisms and physiological interactions in vivo. In parallel to these developments, patient-derived xenograft murine models of cancer are increasingly being studied for various applications in cancer research and therapy; it follows that xenograft models in tissue engineering may be adapted for such approaches. In this review, we first discuss the development of human bone xenograft models to recapitulate physiological states in regenerative medicine. Subsequently, we discuss the use of these techniques for applications in modeling pathological states in skeletal oncology, namely, hematopoietic malignancies, bone metastatic disease, and primary bone malignancy.

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Ultrafast photonic PCR

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Light(Science & Applications) 2015年第1期4卷 267-273页

作者： Jun Ho Son Byungrae Cho SoonGweon Hong Sang Hun Lee Ori Hoxha Amanda J Haack Luke P Lee Department of Bioengineering University of CaliforniaBerkeleyCA 94720USA Berkeley Sensor and Actuator Center University of CaliforniaBerkeleyCA 94720USA Department of Electrical Engineering and Computer Sciences University of CaliforniaBerkeleyCA 94720USA Biophysics Graduate Program University of CaliforniaBerkeleyCA 94720USA

Nucleic acid amplification and quantification via polymerase chain reaction(PCR)is one of the most sensitive and powerful tools for clinical laboratories,precision medicine,personalized medicine,agricultural science,forensic science and environmental *** multiplex PCR,characterized by low power consumption,compact size and simple operation,is ideal for timely diagnosis at the point-of-care(POC).Although several fast/ultrafast PCR methods have been proposed,the use of a simple and robust PCR thermal cycler remains challenging for POC ***,we present an ultrafast photonic PCR method using plasmonic photothermal light-to-heat conversion via photon–electron–phonon *** demonstrate an efficient photonic heat converter using a thin gold(Au)film due to its plasmon-assisted high optical absorption(approximately 65%at 450 nm,the peak wavelength of heat source light-emitting diodes(LEDs)).The plasmon-excited Au film is capable of rapidly heating the surrounding solution to over 150℃ within 3 *** this method,ultrafast thermal cycling(30 cycles;heating and cooling rate of 12.7960.93℃ s^(-1) and 6.660.29℃ s^(-1),respectively)from 55℃(temperature of annealing)to 95℃(temperature of denaturation)is accomplished within 5 *** photonic PCR thermal cycles,we demonstrate here successful nucleic acid(λ-DNA)*** simple,robust and low cost approach to ultrafast PCR using an efficient photonic-based heating procedure could be generally integrated into a variety of devices or procedures,including on-chip thermal lysis and heating for isothermal amplifications.

关键词： genomics light-emitting diodes(LEDs) molecular diagnostics personalized medicine plasmonics point-of-care(POC)diagnostics polymerase chain reaction(PCR)

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A miniaturized brain-machine-spinal cord interface (BMSI) for closed-loop intraspinal microstimulation

A miniaturized brain-machine-spinal cord interface (BMSI) fo...

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IEEE Biomedical Circuits and Systems (BIOCAS)

作者： Shahab Shahdoost Shawn Frost David Guggenmos Jordan Borrell Caleb Dunham Scott Barbay Randolph Nudo Pedram Mohseni Electrical Engineering and Computer Science Dept Case Western Reserve University Cleveland OH USA Rehabilitation Medicine Dept University of Kansas Medical Center Kansas City KS USA University of Kansas Medical Center Kansas City KS US Bioengineering Graduate Program University of Kansas Lawrence KS USA

ISBN: (纸本)9781509029600

This paper reports on a fully miniaturized brain-machine-spinal cord interface (BMSI) for closed-loop cortical control of intraspinal microstimulation (ISMS). The system incorporates two identical 4-channel modules, with each module comprising a neural recording front-end, embedded digital signal processing (DSP) unit, and programmable stimulating back-end. The DSP unit is capable of generating multichannel trigger signals for a wide array of ISMS triggering patterns based upon online discrimination of a programmable number of intracortical neural spikes within a pre-specified time bin via thresholding and time-amplitude windowing. The BMSI system is validated experimentally in a rat model of contusion spinal cord injury (SCI) by converting in real-time multichannel neural spikes recorded from the cerebral cortex into electrical stimuli delivered to the lumbar spinal cord below the level of the injury, resulting in distinct patterns of hindlimb muscle activation in the SCI rat.

关键词： Blanking Digital signal processing Rats Injuries Voltage measurement Spinal cord injury

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Theoretical design and evaluation of endoluminal ultrasound applicators for thermal therapy of pancreatic cancer under image guidance

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AIP Conference Proceedings 2017年第1期1821卷

作者： Matthew Adams Serena Scott Vasant Salgaonkar Graham Sommer Chris Diederich 1Thermal Therapy Research Group University of California San Francisco 2340 Sutter Street S341 San Francisco CA 94109 USA 2Joint Graduate Program in Bioengineering UC Berkeley and UC San Francisco USA 3Stanford Medical Center 300 Pasteur Drive Stanford CA 94305 USA

An image-guided endoluminal ultrasound applicator has been proposed for palliative and potential curative thermal therapy of pancreatic tumors. By considering a directional transducer array of planar, tubular, or curvilinear transducers, this design offers the potential for fast volumetric therapy and 3D spatial control over the energy deposition profile. Treatment of pancreatic tumor tissue would be performed in a minimally invasive fashion with the applicator positioned in the gastrointestinal (GI) lumen, and sparing of the luminal wall would be achieved with a water-cooled balloon surrounding the transducers. A theoretical evaluation of this design was performed by developing a 3D acoustic and bioheat transfer model, with temperature and thermal dose solutions obtained using a FEM solver (COMSOL Multiphysics). Parametric studies were performed on a generalized anatomical model of the pancreas, tumor, and adjacent luminal wall to determine preferred transducer configurations and frequencies for maximizing lesion volume and penetration while sparing the luminal wall. Patient-specific models of pancreatic tumors were generated from CT studies and used to assess the feasibility of performing thermal ablation or hyperthermia on small (∼2 cm diameter) pancreatic head tumors with an endoluminal applicator positioned within the duodenum. Simulation results indicate lower transducer operating frequencies (1-3 MHz) are necessary to mitigate damage to the luminal wall, and a tradeoff between penetration depth and lesion volume emerges as the degree of focusing increases. For patient-specific ablation modeling of tumors within 30 mm of the luminal wall, approximately 95% of the volume could be ablated within 15 min using a planar or lightly focused transducer configuration without duodenal damage. Over 90% of the volume could be elevated above 40°C at steady state for hyperthermia applications (e.g., radiation sensitization, drug delivery) using a tubular transducer. For tum

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Education for the future

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Science 2018年第6396期360卷 1409-1412页

作者： Cheung, Man Kit Schwendimann, Beat A. Ward, Adrian Pietrzak, Barbara Mollaoglu, Gurkan Duong, Michael Tran Allareddy, Veerasathpurush Ulltveit-Moe, Nils Dutton-Regester, Ken Zhang, Jian Scult, Matthew A. Singh, Poonam C. Yan, Hong Young Naz, Saima Isaacson, Kyle Dennis, Allison F. Beardsley, Felicia Rounds Al-Humaidan, Eyad Ibrahim Lo, Cody Jones, Tyler Sood, Prashant Nieuwenhuis, Rense Ali, Basant A. Yu, Kun-Hsing Arthur, Patrick Kobina Kumar, Brijesh Buschke, Falko Chen, Alexander Cingl, Lubomír O’Mullane, Anthony Peter Coetzee, Vinet Zaidi, Syed Shan-e-Ali Konstantinides, Nikos School of Life Sciences Chinese University of Hong Kong Shatin New Territories Hong Kong Graduate School of Education University of California Berkeley Berkeley 94720 CA United States University of Queensland St. Lucia 4072 QLD Australia Department of Hydrobiology Faculty of Biology Biological and Chemical Research Centre University of Warsaw Warsaw 02-089 Poland Department of Oncological Sciences University of Utah School of Medicine Salt Lake City 84112 UT United States Perelman School of Medicine University of Pennsylvania Philadelphia 19104 PA United States University of Illinois College of Dentistry Chicago 60612 IL United States Department of Information and Communication Technology University of Agder 4879 Grimstad Norway Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane 4006 QLD Australia School of Safety and Environmental Engineering Hunan Institute of Technology Hengyang Hunan 421002 China Lahore 54000 Punjab Pakistan Department of Psychology and Neuroscience Duke University Durham 27708 NC United States National Museum of Marine Biology and Aquarium Chercheng Pingtung County 94450 Taiwan Division of Plant Microbe Interactions CSIR–National Botanical Research Institute Lucknow 226001 Uttar Pradesh India Program in Cell Molecular Developmental Biology and Biophysics (CMDB) Johns Hopkins University Baltimore 21218 MD United States Stem Cell and Tissue Re-Engineering Program King Faisal Specialist Hospital and Research Centre Riyadh Saudi Arabia Department of Sociology and Anthropology University of La Verne La Verne 91750 CA United States Department of Bioengineering University of Utah Salt Lake City 84112 UT United States MRC Centre for Medical Mycology University of Aberdeen Aberdeen AB25 2ZD United Kingdom Faculty of Medicine University of British Columbia Vancouver V6T 1Z2 BC Canada School of Engineering Brown University Providence 02912 RI United States

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Modeling delayed processes in biological systems

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Physical Review E 2016年第3期94卷 032408-032408页

作者： Jingchen Feng Stuart A. Sevier Bin Huang Dongya Jia Herbert Levine Department of Bioengineering and Center for Theoretical Biological Physics Rice University Houston Texas 77251-1892 USA Department of Physics and Center for Theoretical Biological Physics Rice University Houston Texas 77251-1892 USA Department of Chemistry and Center for Theoretical Biological Physics Rice University Houston Texas 77251-1892 USA Graduate Program in Systems Synthetic and Physical Biology and Center for Theoretical Biological Physics Rice University Houston Texas 77251-1892 USA

Delayed processes are ubiquitous in biological systems and are often characterized by delay differential equations (DDEs) and their extension to include stochastic effects. DDEs do not explicitly incorporate intermediate states associated with a delayed process but instead use an estimated average delay time. In an effort to examine the validity of this approach, we study systems with significant delays by explicitly incorporating intermediate steps. We show that such explicit models often yield significantly different equilibrium distributions and transition times as compared to DDEs with deterministic delay values. Additionally, different explicit models with qualitatively different dynamics can give rise to the same DDEs revealing important ambiguities. We also show that DDE-based predictions of oscillatory behavior may fail for the corresponding explicit model.

关键词： Gene regulatory networks Nonlinear time-delay systems Stochastic analysis

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