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Deep learning framework for material design space exploration using active transfer learning and data augmentation

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npj Computational Materials 2021年第1期7卷 1261-1267页

作者： Yongtae Kim Youngsoo Kim charles Yang Kundo Park Grace X.Gu Seunghwa ryu Department of Mechanical Engineering&KI for the NanoCentury Korea Advanced Institute of Science and Technology(KAIST)Yuseong-guDaejeonRepublic of Korea Department of Nature-Inspired System and Application Korea Institute of Machinery and MaterialsDaejeonRepublic of Korea Department of Mechanical Engineering University of CaliforniaBerkeleyCAUSA

Neural network-based generative models have been actively investigated as an inverse design method for finding novel materials in a vast design ***,the applicability of conventional generative models is limited because they cannot access data outside the range of training *** generative models that were devised to overcome the limitation also suffer from the weak predictive power on the unseen *** this study,we propose a deep neural network-based forward design approach that enables an efficient search for superior materials far beyond the domain of the initial training *** approach compensates for the weak predictive power of neural networks on an unseen domain through gradual updates of the neural network with active transfer learning and data augmentation *** demonstrate the potential of our framework with a grid composite optimization problem that has an astronomical number of possible design *** show that our proposed framework can provide excellent designs close to the global optima,even with the addition of a very small dataset corresponding to less than 0.5%of the initial training dataset size.

关键词： neural Deep network

OPTICAL MEASUrEMENT OF PHOTOSENSITIZEr CONCENTrATION IN VIVO

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Journal of Innovative Optical Health Sciences 2011年第2期4卷 97-111页

作者： MArTIN r.AUSTWICK JOSEPHINE H.WOODHAMS VADZIM CHALAU charles A.MOSSE CArOLINE ELIOT LAUrENCE LOVAT ALEXANDEr J.MACrOBErT IrVING J.BIGIO STEPHEN G.BOWN National Medical Laser Centre charles Bell House 67-73 Riding House Street University College London London W1W 7EJUK Boston University BME44 Cummington Street BostonMA 02215USA

Most techniques for measuring tissue concentrations of drugs are invasive,time-consuming,and often require the removal of tissue or *** pharmacokinetics(OP)is a minimally invasive alternative giving an immediate *** of white light are directed at the tissue of interest using afiber optic *** light is detected by a secondfiber immediately adjacent to thefirst in the same probe(separation 1.7 mm).Using the photosensitizer disulfonated aluminium phthalocyanine(AlS_(2)Pc),OP measurements were made in phantoms and on the mouth,stomach,colon,skin,and liver of normal rats 1 and 24 h after intravenous AlS_(2)Pc ***_(2)Pc concentration was determined by calculating the area under the curve(AUC)in the spectral region around the peak drug absorption or measuring the height of the *** baseline interpolation removed the need for pre-drug,control optical *** measurements correlated well with values from alkali chemical extraction(CE)of the corresponding tissues,(r^(2)0.87=0.97).OP measurements in the mouth also correlated with CE of less accessible internal organs(r^(2)0.77-0.88).In phantoms,the lowest detectable concentration was 0.1μg/*** vivo,results were limited by the lower accuracy in the CE measurements but were almost certainly *** incidentalfinding was a 12-15nm red shifted component in the spectra observed 1 h after drug administration,suggesting partitioning of the drug in different microenvironment compartments,which could prove to be of considerable interest in future *** conclusion,OP shows promise for real-time measurement of concentrations of drugs with suitable absorption peaks.

关键词： Optical pharmacokinetics chemometrics photodynamic therapy noninvasive measurement

The sperm-interacting proteome in the bovine isthmus and ampulla during the periovulatory period

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Journal of Animal Science and Biotechnology 2023年第3期14卷 980-1000页

作者： Coline Mahe regis Lavigne Emmanuelle Com charles Pineau Aleksandra Maria Zlotkowska Guillaume Tsikis Pascal Mermillod Jennifer Schoen Marie Saint-Dizier CNrS IFCEINRAEUniversite de ToursPRC37380 NouzillyFrance Univ rennes InsermEHESPIrset(Institut de Recherche en SanteEnvironnement Et Travail)-UMR-S 1085F‑35000 RennesFrance Univ rennes CNRSInsermBiosit UAR 3480 US_S 018Protim Core Facility35000 RennesFrance Institute of reproductive Biology Leibniz Institute for Farm Animal BiologyFBNDummerstorfGermany Present Address:Department of reproduction Biology Leibniz Institute for Zoo and Wildlife Research(IZW)BerlinGermany

Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely *** objectives were to identify an exhaustive list of sperm-interacting proteins(SIPs)in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region(isthmus ***)and time relative to ovulation(pre-ovulatory ***-ovulatory)on SIPs number and *** Pools of oviduct fluid(OF)from the pre-ovulatory ampulla,pre-ovulatory isthmus,post-ovulatory ampulla,and post-ovulatory isthmus in the side of ovulation were collected from the ***-thawed bull sperm were incubated with OF or phosphate-buffered saline(control)for 60 min at 38.5℃.After protein extraction and digestion,sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein *** A quantitative comparison between proteins identified in sperm and OF samples(2333 and 2471 proteins,respectively)allowed for the identification of 245 *** highest number(187)were found in the pre-ovulatory isthmus,i.e.,time and place of the sperm *** total,41 SIPs(17%)were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs(31%)were identified in only one region×stage *** analysis of SIPs predicted roles in cell response to stress,regulation of cell motility,fertilization,and early embryo *** This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatiotemporal changes in sperm-oviduct interactions around ovulation ***,these data provide protein candidates to improve sperm conservation and in vitro fertilization media.

关键词： Ampulla Fallopian tube Interactome Isthmus Oviduct Ovulation Post-ovulatory Pre-ovulatory Proteomics Spermatozoa

Inflammatory bowel disease patient profiles are related to specific information needs: A nationwide survey

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World Journal of Gastroenterology 2019年第30期25卷 4246-4260页

作者： Saleh Daher Tawfik Khoury Ariel Benson John r Walker Oded Hammerman ron Kedem Timna Naftali rami Eliakim Ofer Ben-Bassat charles N Bernstein Eran Israeli Institute of Gastroenterology and Liver Diseases Hadassah-Hebrew University Medical CenterJerusalem 91120Israel Department of Gastroenterology Galilee Medical CenterFaculty of Medicine in the GalileeBar-Ilan UniversityNahariya 22100Israel IBD Clinical and research Centre University of ManitobaWinnipegMB R3E3P4Canada research Branch IDF Medical CorpsTel-HashomerRamat Gan 52630Israel Institute of Gastroenterology Meir Medical CenterKfar-saba 4428164Israel Sackler School of Medicine Tel-Aviv UniversityTel-Aviv 6997801Israel Institute of Gastroenterology Sheba Medical CenterRamat-Gan 52630Israel Institute of Gastroenterology Rabin Medical CenterPetach-Tikva 49100Israel

BACKGrOUND Inflammatory bowel diseases(IBD) is a heterogenous, lifelong disease, with an unpredictable and potentially progressive course, that may impose negative psychosocial impact on *** informed patients with chronic illness have improved adherence and outcomes, previous research showed that the majority of IBD patients receive insufficient information regarding their *** large heterogeneity of IBD and the wide range of information topics makes a one-size fits all knowledge resource overwhelming and *** hypothesized that different patient profiles may have different and specific information needs, the identification of which will allow building personalized computer-based information resources in the *** To evaluate the scope of disease-related knowledge among IBD patients and determine whether different patient profiles drive unique information *** We conducted a nationwide survey addressing hospital-based IBD clinics.A Total of 571 patients completed a 28-item questionnaire, rating the amount of information received at time of diagnosis and the importance of information, as perceived by participants, for a newly diagnosed patient, and for the participants themselves, at current *** performed an exploratory factor analysis of the crude responses aiming to create a number of representative knowledge domains(factors), and analyzed the responses of a set of 15 real-life patient profiles generated by the study *** Participants gave low ratings for the amount of information received at disease onset(averaging 0.9/5) and high ratings for importance, both for the newly diagnosed patients(mean 4.2/5) and for the participants themselves at current time(mean 3.5/5).Factor analysis grouped responses into six *** responses of selected profiles, compared with the rest of the participants, yielded significant associations(defined as a difference in rating of >0.5 points with a P < 0.05).Patients w

关键词： Inflammatory bowel diseases Information needs Patient education Knowledge resources Patient profiles

An evaluation of the role played by remote sensing technology following the World Trade Center attack

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Earthquake Engineering and Engineering Vibration 2003年第1期2卷 159-168页

作者： charles K.Huyck Beverley J.Adams David I.Kehrlein ImageCat Inc.400 OceangateSuite 1050Long BeachCA90802USA Senior Vice President ImageCat Inc.400 OceangateSuite 1050Long BeachCA90802USA Project Scientist ImageCat Inc.6047 Woodhaven AvenueCarmichaelCA95608USA Vice PresidentGIS Operations

remote sensing technology has been widely recognized for contributing to emergency response efforts after the World Trade Center attack on September 11th, 2001. The need to coordinate activities in the midst of a dense, yet relatively small area, made the combination of imagery and mapped data strategically useful. This paper reviews the role played by aerial photography, satellite imagery, and LIDAr data at Ground Zero. It examines how emergency managers utilized these datasets, and identifies significant problems that were encountered. It goes on to explore additional ways in which imagery could have been used, while presenting recommendations for more effective use in future disasters and Homeland Security applications. To plan adequately for future events, it was important to capture knowledge from individuals who responded to the World Trade Center attack. In recognition, interviews with key emergency management and geographic information system (GIS) personnel provide the basis of this paper. Successful techniques should not be forgotten, or serious problems dismissed. Although widely used after September 11th, it is important to recognize that with better planning, remote sensing and GIS could have played an even greater role. Together with a data acquisition timeline, an expanded discussion of these issues is available in the MCEEr/NSF report “Emergency response in the Wake of the World Trade Center Attack; The remote Sensing Perspective” (Huyck and Adams, 2002) Keywords World Trade Center (WTC) - terrorism - emergency response - emergency management - ground zero - remote sensing - emergency operations - disasters - geographic information systems (GIS) - satellite imagery - synthetic aperture radar (SAr) - light detection and ranging imagery (LIDAr)

关键词： World Trade Center (WTC) terrorism emergency response emergency management ground zero remote sensing emergency operations disasters geographic information systems (GIS) satellite imagery synthetic aperture radar (SAr) light detection and ranging imagery (LIDAr)

Some Challenges of Deep Mining

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Engineering 2017年第4期3卷 527-537页

作者： charles Fairhurst University of Minnesota Minneapolis MN 55455 USA Itasca International Inc. Minneapolis MN 55401 USA

An increased global supply of minerals is essential to meet the needs and expectations of a rapidly rising world population. This implies extraction from greater depths. Autonomous mining systems, developed through sustained r＆D by equipment suppliers, reduce miner exposure to hostile work environments and increase safety. This places increased focus on ＂ground control＂ and on rock mechanics to define the depth to which minerals may be extracted economically. Although significant efforts have been made since the end of World War II to apply mechanics to mine design, there have been both technological and organizational obstacles. rock in situ is a more complex engineering material than is typically encountered in most other engineering disciplines. Mining engineering has relied heavily on empirical procedures in design for thousands of years. These are no longer adequate to address the challenges of the 21st century, as mines venture to increasingly greater depths. The development of the synthetic rock mass （SrM） in 2008 provides researchers with the ability to analyze the deformational behavior of rock masses that are anisotropic and discontinuous-attributes that were described as the defining characteristics of in situ rock by Leopold Mfiller, the president and founder of the International Society for rock Mechanics （ISrM）, in 1966. recent developments in the numerical modeling of large-scale mining operations （e.g., caving） using the SrM reveal unanticipated deformational behavior of the rock. The application of massive parallelization and cloud computational techniques offers major opportunities： for example, to assess uncertainties in numerical predictions： to establish the mechanics basis for the empirical rules now used in rock engineering and their validity for the prediction of rock mass behavior beyond current experience： and to use the discrete element method （DEM） in the optimization of deep mine design. For the first time, mining-and rock engineering-wi

关键词： Deep mining rock discontinuities Synthetic rock mass Mineral resources rock mechanics

rapid and Cost-Effective Gene Targeting in rat Embryonic Stem Cells by TALENs

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Journal of Genetics and Genomics 2012年第6期39卷 275-280页

作者： charles Ashton Eli and Edythe Broad Center for regenerative Medicine and Stem Cell research at USC Department of Cell and NeurobiologyKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA

The rat is the preferred animal model in many areas of biomedical research and drug development. Genetic manipulation in rats has lagged behind that in mice due to the lack of efficient gene targeting tools. Previously, we generated a knockout rat via conventional homologous recombination in rat embryonic stern （ES） cells. Here, we show that efficient gene targeting in rat ES cells can be achieved quickly through transcription activator-like effector nuclease （TALEN）-mediated DNA double-strand breaks. Using the Golden Gate cloning technique, we constructed a pair of TALEN targeting vectors for the gene of interest in 5 days. After gene transfection, the targeted rat ES cell colonies were isolated, screened, and confirmed by PCr without the need of drug selection. Our results suggest that TALEN-mediated gene targeting is a superior means of establishing genetically modified rat ES cell lines with high efficiency and short turnaround time.

关键词： TAL effector BMPr2 rat ES cells Gene-targeting

The Development of a Framework for CFD Validation and Best Practice: The QNET-CFD Knowledge Base

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Chinese Journal of Aeronautics 2006年第2期19卷 105-113页

作者： charles HIrSCH Vrije Universiteit Brussel Pleinlaan 21050 BrusselsBelgium

QNET-CFD is a thematic network on quality and trust for the industrial applications of Computational Fluid Dynamics （CFD）, developed under the European Union r＆D program. The main objectives of QNET-CFD were to collect CFD and experimental data in a systematic and quality controlled way and to set the basis for a consistent Knowledge Base in support of CFD guidance and validation. The QNET-CFD activity was organized around six Thematic Areas （TAs） covering the following industry sectors： external aerodynamics; combustion ＆ heat transfer; chemical process, thermal hydraulics and nuclear safety; civil construction ＆ HVAC; environment; turbomachinery internal flows. The main outcome of the QNET-CFD actions is the Knowledge Base （KB） with contains in a user oriented interface, extensive experimental and CFD data for a large number of test cases subdivided into 53 Application Challenges （AC） and 43 Underlying Flow regimes （UFr）. The KB contains, in addition to state-of-the-art reviews for each of the six thematic areas, Best Practice Advice （BPA） in the use of CFD for most of AC. This is considered as a significant contribution form the QNET-CFD activities and it is expected that the level of the thrust and quality in CFD will hereby be improved.

关键词： QNET-CFD CFD thematic network knowledge base

AUTOMATIC PATENT DOCUMFNT SUMMArIZATION FOr COLLABOrATIVE KNOWLEDGE SYSTEMS AND SErVICES

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Journal of Systems Science and Systems Engineering 2009年第1期18卷 71-94页

作者： Amy J.C. TrAPPEY charles V. TrAPPEY Chun-Yi WU Dept. of Industrial Engineering and Management National Taipei University of Technology Taiwan China Dept. of lndustrial Engineering and Engineering Management National Tsing Hua University Taiwan China Dept. of Management Science National Chiao Tung University Taiwan China

Engineering and research teams often develop new products and technologies by referring to inventions described in patent databases. Efficient patent analysis builds r＆D knowledge, reduces new product development time, increases market success, and reduces potential patent infringement. Thus, it is beneficial to automatically and systematically extract information from patent documents in order to improve knowledge sharing and collaboration among r＆D team members. In this research, patents are summarized using a combined ontology based and TF-IDF concept clustering approach. The ontology captures the general knowledge and core meaning of patents in a given domain. Then, the proposed methodology extracts, clusters, and integrates the content of a patent to derive a summary and a cluster tree diagram of key terms. Patents from the International Patent Classification （IPC） codes B25C, B25D, B25F （categories for power hand tools） and B24B, C09G and H011 （categories for chemical mechanical polishing） are used as case studies to evaluate the compression ratio, retention ratio, and classification accuracy of the summarization results. The evaluation uses statistics to represent the summary generation and its compression ratio, the ontology based keyword extraction retention ratio, and the summary classification accuracy. The results show that the ontology based approach yields about the same compression ratio as previous non-ontology based research but yields on average an 11% improvement for the retention ratio and a 14% improvement for classification accuracy.

关键词： Semantic knowledge service key phrase extraction document summarization text mining,patent document analysis