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Author Correction: Genetic drivers and cellular selection of female mosaic X chromosome loss

Nature 2024年第8043期636卷 E7页

作者： Aoxing Liu Giulio Genovese Yajie Zhao Matti Pirinen Seyedeh M Zekavat Katherine A Kentistou Zhiyu Yang Kai Yu Caitlyn Vlasschaert Xiaoxi Liu Derek W Brown Georgi Hudjashov Bryan R Gorman Joe Dennis Weiyin Zhou Yukihide Momozawa Saiju Pyarajan Valdislav Tuzov Fanny-Dhelia Pajuste Mervi Aavikko Timo P Sipilä Awaisa Ghazal Wen-Yi Huang Neal D Freedman Lei Song Eugene J Gardner Vijay G Sankaran Aarno Palotie Hanna M Ollila Taru Tukiainen Stephen J Chanock Reedik Mägi Pradeep Natarajan Mark J Daly Alexander Bick Steven A McCarroll Chikashi Terao Po-Ru Loh Andrea Ganna John R B Perry Mitchell J Machiela Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland. liuaoxin@***. Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA. liuaoxin@***. Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. liuaoxin@***. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA. liuaoxin@***. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA. liuaoxin@***. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA. giulio@***. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA. giulio@***. Department of Genetics Harvard Medical School Boston MA USA. giulio@***. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland. Department of Public Health University of Helsinki Helsinki Finland. Department of Mathematics and Statistics University of Helsinki Helsinki Finland. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA. Cardiovascular Research Center Massachusetts General Hospital Boston MA USA. Department of Ophthalmology Massachusetts Eye and Ear Harvard Medical School Boston MA USA. Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville MD USA. Department of Medicine Queen's University Kingston Ontario Canada. Laboratory for Statistical and Translational Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Cancer Prevention Fellowship Program Division of Cancer Prevention National Cancer Institute Rockville MD USA. Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia. Center for Data and Computational Sciences (C-DACS) VA Cooperative Studies Program VA Boston Health

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Correction to: Optimal deterministic algorithm generation

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Journal of Global Optimization 2018年第2期73卷 465-465页

作者： Mitsos, Alexander Najman, Jaromił Kevrekidis, Ioannis G. AVT Process Systems Engineering (SVT) RWTH Aachen University Aachen Germany Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics Princeton University Princeton USA IAS-TUM Garching and Zuse Institut FU Berlin Berlin Germany Departments of Chemical and Biomolecular Engineering Applied Mathematics and Statistics and Urology Johns Hopkins University Baltimore USA

Unfortunately, the copyright information of the article in Springerlink appears as “©  Springer Science+Business Media, LLC, part of Springer Nature 2018” this has been corrected to “©  ...

Unfortunately, the copyright information of the article in Springerlink appears as “© Springer Science+Business Media, LLC, part of Springer Nature 2018” this has been corrected to “© The Author(s) 2018.”

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A new phase-field approach to variational implicit solvation of charged molecules with the coulomb-field approximation

arXiv

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arXiv 2017年

作者： Zhao, Yanxiang Ma, Yanping Sun, Hui Li, Bo Du, Qiang Department of Mathematics George Washington University 801 22nd St. NW Phillips 739 WashingtonDC20052 United States Department of Mathematics Loyola Marymount University 1 LMU drive Los AngelesCA90045 United States Department of Mathematics and Statistics California State University Long BeachCA90840-1001 United States Department of Mathematics and Quantitative Biology Graduate Program University of California San Diego 9500 Gilman Drive Mail code: 0112 La JollaCA92093-0112 United States Department of Applied Physics and Applied Mathematics Columbia University NY10027 United States

We construct a new phase-field model for the solvation of charged molecules with a variational implicit solvent. Our phase-field free-energy functional includes the surface energy, solute-solvent van der Waals dispersion energy, and electrostatic interaction energy that is described by the Coulomb-field approximation, all coupled together self-consistently through a phase field. By introducing a new phase-field term in the description of the solute-solvent van der Waals and electrostatic interactions, we can keep the phase-field values closer to those describing the solute and solvent regions, respectively, making it more accurate in the free-energy estimate. We first prove that our phase-field functionals Γ-converge to the corresponding sharp-interface limit. We then develop and implement an efficient and stable numerical method to solve the resulting gradient-flow equation to obtain equilibrium conformations and their associated free energies of the underlying charged molecular system. Our numerical method combines a linear splitting scheme, spectral discretization, and exponential time differencing Runge-Kutta approximations. Applications to the solvation of single ions and a two-plate system demonstrate that our new phase-field implementation improves the previous ones by achieving the localization of the system forces near the solute-solvent interface and maintaining more robustly the desirable hyperbolic tangent profile for even larger interfacial width. This work provides a scheme to resolve the possible unphysical feature of negative values in the phase-field function found in the previous phase-field modeling (cf. H. Sun, et al. J. Chem. Phys., 2015) of charged molecules with the Poisson-Boltzmann equation for the electrostatic interaction. Copyright © 2017, The Authors. All rights reserved.

关键词： Free energy

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Analysis of Lead (Pb) and Zinc (Zn) Content in Sediments and Faunus ater at Bale Lhoknga Aceh Besar District

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Journal of Physics: Conference Series 2019年第1期1232卷

作者： Rahmi Agustina M. Ali Sarong Fredinan Yulianda Suhendrayatna Rahmadi Lelifajri Graduate School of Mathematics and Applied Sciences Syiah Kuala University Banda Aceh Indonesia 23111 Departement of Biology Faculty of Teacher Training and Education Jabal Ghafur University Sigli Indonesia 24171 Departement of Biology Faculty of Teacher Training and Education Syiah Kuala University Banda Aceh Indonesia 23111 Departement of Water Resources Management Faculty of Fisheries and Marine Sciences Bogor Agricultural University Bogor Indonesia 16680 Department of Chemical Engineering Faculty of Engineering Syiah Kuala University Banda Aceh Indonesia 23111 Department of Chemistry Faculty of Mathematics and Science Post Graduate Program Syiah Kuala University Banda Aceh Indonesia 23111

Faunus ater is a favoritemollusca that is often found on the Bale River. Local people use these snails as food for consumption along with their main food. Bale River itself is located adjacent to the cement factory, used water washing machines distributed to the river is feared to support the presence of lead (Pb) and zinc (Zn) metals in the river. This study aims to analyze the relationship of Pb and Zn content in sediments to the content of Pb and Zn in Faunus ater. Data collection was carried out in Februari until April 2018. The relationship between Pb and Zn content in sediments with Pb and Zn content in the body of Faunus ater was analyzed by correlation analysis. The results of the data analysis showed that the metal content of Pb and Zn in sediment and Faunus aterwere found to vary. The highest Pb content in sediment was found at station 2 in March, amounting to 32.87 mg / kg. while the highest Zn content was found at station 1 in March amounting to 84 mg / kg. The relationship of heavy metals Pb and Zn in sediments to the content of Pb and Zn in the body of Faunus ater showed a negative correlation. The conclusion of this study is that there is no correlation between the content of Pb and Zn heavy metals in sediments on the content of lead Pb and Zn in the body of Faunus ater at the Bale Lhoknga River in Aceh Besar District.

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Optimization of second order spatially distributed systems with multiple interconnected actuator/sensor pairs

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IFAC-PapersOnLine 2016年第18期49卷 476-481页

作者： Demetriou, Michael A. Fahroo, Fariba Aerospace Engineering Program Mechanical Engineering Department Worcester Polytechnic Institute WorcesterMA01609 United States Department of Applied Mathematics Naval Postgraduate School MontereyCA93943 United States

This work considers the economic aspects in control implementation of second order spatially distributed systems. By opting to use multiple actuator/sensor pairs with limited capacity, instead of a single actuator/sensor pair with higher price and larger capacity, this work provides a first view into the economic, computational and communication aspects. Considering a large number of actuator/sensor pairs and the a priori defined controller architecture of static output feedback along with the collocation assumption of the actuators and sensors, the resulting closed-loop system is expressed in terms of a static output feedback gain matrix that defines the communication amongst the actuator/sensor pairs. The design problem is then to find the values of the static feedback gain matrix in order to optimize a performance measure. Using the energy of the second order infinite dimensional system as the performance measure, the resulting optimization is expressed in terms of the solution to a parameterized operator Lyapunov equation. Simulation studies of the wave PDE in one spatial dimension for different communication topologies, reveal the effects of communication on the performance of the closed loop system. © 2016

关键词： Actuators Closed loop systems Feedback control Lyapunov functions Spatial distribution Actuator/sensor Communication topologies Controller architectures Distributed parameter systems Infinite dimensional system Second order systemss Spatially distributed system Static output feedback

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Classical many-particle systems with unique disordered ground states

arXiv

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arXiv 2017年

作者： Zhang, G. Stillinger, F.H. Torquato, S. Department of Chemistry Princeton University PrincetonNJ08544 Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544

Classical ground states (global energy-minimizing configurations) of many-particle systems arefitypically unique crystalline structures, implying zero enumeration entropy of distinct patterns (aside from trivial symmetry operations). By contrast, the few previously known disordered classical ground states of many-particle systems are all high-entropy (highly degenerate) states. Here we show computationally that our recently-proposed \perfect-glass" many-particle model [Sci. Rep., 6, 36963 (2016)] possesses disordered classical ground states with a zero entropy: a highly counterintuitive situation. For all of the system sizes, parameters, and space dimensions that we have numerically investigated, the disordered ground states are unique such that they can always be superposed onto each other or their mirror image. At low energies, the density of states obtained from simulations matches those calculated from the harmonic approximation near a single ground state, further confirming ground-state uniqueness. Our discovery provides singular examples in which entropy and disorder are at odds with one another. The zero-entropy ground states provide a unique perspective on the celebrated Kauzmann-entropy crisis in which the extrapolated entropy of a supercooled liquid drops below that of the crystal. We expect that our disordered unique patterns to be of value infields beyond glass physics, including applications in cryptography as pseudo-random functions with tunable computational complexity. Copyright © 2017, The Authors. All rights reserved.

关键词： Ground state

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The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

arXiv

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arXiv 2024年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Gandhi, Deep Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Franson, Andrea Gottipati, Anurag Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Khalili, Neda Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Sheth, Nakul Tu, Wenxin Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Zapaishchykova, Anna Bornhorst, Miriam Deutsch, Michelle Fouladi, Maryam Lazow, Margot Mikael, Leonie Hummel, Trent Kann, Benjamin de Blank, Peter Hoffman, Lindsey Aboian, Mariam Nabavizadeh, Ali Packer, Roger Bakas, Spyridon Resnick, Adam Rood, Brian Vossough, Arastoo Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center DurhamNC United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States C. S. Mott Children’s Hospital University of Michigan MI United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center OH United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of De

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2024, CC BY.

关键词： Deep learning

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Corrigendum to ``A model for effects of adaptive immunity on tumor response to chemotherapy and chemoimmunotherapy'' [Journal of Theoretical Biology 380 (2015) 569-584]

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Journal of theoretical biology 2019年 464卷 181页

作者： Mark Robertson-Tessi Ardith El-Kareh Alain Goriely Program in Applied Mathematics University of Arizona Tucson AZ 85721 United States Integrated Mathematical Oncology Moffitt Cancer Center Tampa FL 33612 United States. Electronic address: mark.robertsontessi@***. ARL-Microcirculation Division University of Arizona Tucson AZ 85724 United States. Mathematical Institute University of Oxford Woodstock Road OX2 6GG UK.

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Peripheral fishes in the Estuary of Simeulue Island, Indonesia

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IOP Conference Series: Earth and Environmental Science 2018年第1期216卷

作者： A S Batubara M Abdan Z Muhammad N F Putra Z A Muchlisin Department of Aquaculture Faculty of Marine and Fisheries Syiah Kuala University Banda Aceh 23111 Indonesia. Doctorate Program of Mathematics and Applied Sciences Syiah Kuala University Banda Aceh 23111 Indonesia

The objective of the present study was to inventory of peripheral water fishes were conducted in several estuaries of Simeulue Island, Aceh Province, Indonesia. The sampling was done at seven river mouths in August 2017 and May 2018. The fish samples were collected using fishhooks, casting net and gill net. The sampled fishes were taxonomic identified based on several references at the Laboratory of Ichthyology, Faculty of Marine and Fisheries, Syiah Kuala University. The results showed that there were 356 individual of fishes were recorded during the survey, its belong to 10 orders, 25 families, 41 genera and 52 species. The Perciformes was a predominant with a total of 15 families, 27 genera and 35 species. Furthermore, Gobiidae was predominant with the highest number of genera and species (7 genera and 10 species), followed by Eleotridae (4 genera and 4 species), Mugilidae (3 genera and 4 species), and Carangidae (3 genera and 4 species).

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