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  1. Book ; Online: PoE

    Zhang, Chen / D'Haro, Luis Fernando / Zhang, Qiquan / Friedrichs, Thomas / Li, Haizhou

    a Panel of Experts for Generalized Automatic Dialogue Assessment

    2022  

    Abstract: Chatbots are expected to be knowledgeable across multiple domains, e.g. for daily chit-chat ... To tackle the multi-domain dialogue evaluation task, we propose a Panel of Experts (PoE), a multitask ... domain dialogue dataset leveraging data augmentation and pseudo-labeling. The PoE network is ...

    Abstract Chatbots are expected to be knowledgeable across multiple domains, e.g. for daily chit-chat, exchange of information, and grounding in emotional situations. To effectively measure the quality of such conversational agents, a model-based automatic dialogue evaluation metric (ADEM) is expected to perform well across multiple domains. Despite significant progress, an ADEM that works well in one domain does not necessarily generalize to another. This calls for a dedicated network architecture for domain generalization. To tackle the multi-domain dialogue evaluation task, we propose a Panel of Experts (PoE), a multitask network that consists of a shared transformer encoder and a collection of lightweight adapters. The shared encoder captures the general knowledge of dialogues across domains, while each adapter specializes in one specific domain and serves as a domain expert. To validate the idea, we construct a high-quality multi-domain dialogue dataset leveraging data augmentation and pseudo-labeling. The PoE network is comprehensively assessed on 16 dialogue evaluation datasets spanning a wide range of dialogue domains. It achieves state-of-the-art performance in terms of mean Spearman correlation over all the evaluation datasets. It exhibits better zero-shot generalization than existing state-of-the-art ADEMs and the ability to easily adapt to new domains with few-shot transfer learning.

    Comment: Currently under review at TASLP, upload to arxiv for easy cross-reference
    Keywords Computer Science - Computation and Language
    Subject code 006
    Publishing date 2022-12-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Curcumin-Eudragit® E PO solid dispersion: A simple and potent method to solve the problems of curcumin.

    Li, Jinglei / Lee, Il Woo / Shin, Gye Hwa / Chen, Xiguang / Park, Hyun Jin

    European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V

    2015  Volume 94, Page(s) 322–332

    Abstract: Using a simple solution mixing method, curcumin was dispersed in the matrix of Eudragit® E PO ... polymer. Water solubility of curcumin in curcumin-Eudragit® E PO solid dispersion (Cur@EPO) was greatly ...

    Abstract Using a simple solution mixing method, curcumin was dispersed in the matrix of Eudragit® E PO polymer. Water solubility of curcumin in curcumin-Eudragit® E PO solid dispersion (Cur@EPO) was greatly increased. Based on the results of several tests, curcumin was demonstrated to exist in the polymer matrix in amorphous state. The interaction between curcumin and the polymer was investigated through Fourier transform infrared spectroscopy and (1)H NMR which implied that OH group of curcumin and carbonyl group of the polymer involved in the H bonding formation. Cur@EPO also provided protection function for curcumin as verified by the pH challenge and UV irradiation test. The pH value influenced curcumin release profile in which sustained release pattern was revealed. Additionally, in vitro transdermal test was conducted to assess the potential of Cur@EPO as a vehicle to deliver curcumin through this alternative administration route.
    MeSH term(s) Calorimetry, Differential Scanning ; Curcumin/administration & dosage ; Curcumin/chemistry ; Curcumin/pharmacokinetics ; Curcumin/radiation effects ; Drug Compounding ; Drug Liberation ; Drug Stability ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Nanoparticles/chemistry ; Particle Size ; Polymethacrylic Acids/administration & dosage ; Polymethacrylic Acids/chemistry ; Polymethacrylic Acids/pharmacokinetics ; Polymethacrylic Acids/radiation effects ; Solubility ; Spectroscopy, Fourier Transform Infrared ; Surface Properties ; Ultraviolet Rays ; X-Ray Diffraction
    Chemical Substances Polymethacrylic Acids ; Eudragit E PO (905HNO1SIH) ; Curcumin (IT942ZTH98)
    Language English
    Publishing date 2015-06-12
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1065368-5
    ISSN 1873-3441 ; 0939-6411
    ISSN (online) 1873-3441
    ISSN 0939-6411
    DOI 10.1016/j.ejpb.2015.06.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Aspiratsionnaia pH-metriia zheludka po E.Iu. Linaru--optima'lnyĭ metod izucheniia zheludochnoĭ sekretsii.

    Geller, L I / Geller, A L

    Klinicheskaia meditsina

    1989  Volume 67, Issue 5, Page(s) 140–141

    Abstract: Discussion is devoted to the advantages of intragastric pH-metry and gastric probe study in aspiration pH-metry of the stomach. Data are given on the means of decoding the results of pH-metry. Aspects of the examination of gastric secretion that ... ...

    Title translation Aspiration pH-metry of the stomach by the Linar technic--an optimal method of studying gastric secretion.
    Abstract Discussion is devoted to the advantages of intragastric pH-metry and gastric probe study in aspiration pH-metry of the stomach. Data are given on the means of decoding the results of pH-metry. Aspects of the examination of gastric secretion that contribute both to research and clinical practice are discussed.
    MeSH term(s) Gastric Acid/secretion ; Gastric Acidity Determination/instrumentation ; Gastric Mucosa/secretion ; Humans ; Hydrogen-Ion Concentration ; Intubation, Gastrointestinal/instrumentation ; Latvia ; Methods
    Language Russian
    Publishing date 1989-05
    Publishing country Russia (Federation)
    Document type Journal Article
    ZDB-ID 391034-9
    ISSN 0023-2149
    ISSN 0023-2149
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Po povodu stat'i A.D. Frolovoĭ, E.L. Dolgopolovoĭ, T.G. Martinson "K uskorennomu prognozirovaniiu bezopasnykh urovneĭ vozdeĭstviia malorastvorimykh pyleĭ".

    Katsnel'son, B A / Privalova, L I

    Gigiena i sanitariia

    1992  , Issue 5-6, Page(s) 74–75

    Title translation Concerning the article by A.D. Frolova, E.L. Dolgopolova and T.G. Martinson "Rapid prediction of the safe degree of action of poorly soluble dusts".
    MeSH term(s) Air Pollutants/toxicity ; Dose-Response Relationship, Drug ; Dust/adverse effects ; Humans ; Maximum Allowable Concentration ; Phagocytosis/immunology ; Prognosis ; Pulmonary Alveoli/drug effects ; Pulmonary Alveoli/immunology ; Quartz/administration & dosage ; Quartz/immunology ; Quartz/standards ; Quartz/toxicity ; Solubility ; Time Factors
    Chemical Substances Air Pollutants ; Dust ; Quartz (14808-60-7)
    Language Russian
    Publishing date 1992-05
    Publishing country Russia (Federation)
    Document type Comparative Study ; Journal Article
    ZDB-ID 410437-7
    ISSN 0016-9900
    ISSN 0016-9900
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Osnovnye itogi i perspektivy nauchnykh issledovaniĭ po voprosam meditsiny truda i promyshlennoĭ ékologii v Srednem Povolzh'e.

    Karkhanin, N P / Sukhacheva, I F / Tkach, A N / Razveĭkin, S V / Shumilina, A V / Kaz'mina, N P / Udovitskaia, E A / Bedareva, L I / Zhuravleva, N V

    Meditsina truda i promyshlennaia ekologiia

    1998  , Issue 7, Page(s) 22–26

    Title translation The basic results of and outlook for scientific research on the problems of occupational medicine and industrial ecology in the central Volga region.
    MeSH term(s) Ecology ; Female ; Humans ; Male ; Occupational Diseases/etiology ; Occupational Diseases/prevention & control ; Occupational Medicine/trends ; Pregnancy ; Research/trends ; Russia ; Women, Working
    Language Russian
    Publishing date 1998
    Publishing country Russia (Federation)
    Document type Journal Article
    ZDB-ID 1169087-2
    ISSN 1026-9428 ; 1727-5903 ; 0016-9919
    ISSN 1026-9428 ; 1727-5903 ; 0016-9919
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Bibliograficheskiĭ ukazatel' izobreteniĭ po radionuklidnoĭ diagnostike i luchevoĭ terapii za 2-e polugodie 1979 g.; po materialam ofitsial'nykh biulleteneĭ patentnykh vedomstv SSSR, Velikobritanii, SShA, FRG, Iaponii, Frantsii.

    Menzhinskaia, G V / Moiseeva, L I

    Meditsinskaia radiologiia

    1980  Volume 25, Issue 11, Page(s) 86–92

    Title translation Bibliographic index of inventions for radionuclide diagnosis and radiation therapy for the 2d half of 1979; based on data from the official bulletins of the patent services of the USSR, Great Britain, USA, Federal Republic of Germany, Japan and France.
    MeSH term(s) Bibliography as Topic ; France ; Germany, West ; Japan ; Patents as Topic ; Radionuclide Imaging/instrumentation ; Radiotherapy/instrumentation ; USSR ; United Kingdom ; United States
    Language Russian
    Publishing date 1980-11
    Publishing country Russia (Federation)
    Document type Bibliography ; Journal Article
    ZDB-ID 1189930-x
    ISSN 0025-8334
    ISSN 0025-8334
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

    Lo, Chien-Chi / Shakya, Migun / Connor, Ryan / Davenport, Karen / Flynn, Mark / Gutiérrez, Adán Myers Y / Hu, Bin / Li, Po-E / Jackson, Elais Player / Xu, Yan / Chain, Patrick S G

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 10, Page(s) 2700–2704

    Abstract: Summary: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with ... ...

    Abstract Summary: Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences.
    Availability and implementation: https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) COVID-19 ; Genome, Viral ; Genomics ; Humans ; Pandemics ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-05-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac176
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.

    Bartlow, Andrew W / Stromberg, Zachary R / Gleasner, Cheryl D / Hu, Bin / Davenport, Karen W / Jakhar, Shailja / Li, Po-E / Vosburg, Molly / Garimella, Madhavi / Chain, Patrick S G / Erkkila, Tracy H / Fair, Jeanne M / Mukundan, Harshini

    PLOS global public health

    2022  Volume 2, Issue 7, Page(s) e0000811

    Abstract: Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory ... ...

    Abstract Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.
    Language English
    Publishing date 2022-07-20
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0000811
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

    Connor, Ryan / Shakya, Migun / Yarmosh, David A / Maier, Wolfgang / Martin, Ross / Bradford, Rebecca / Brister, J Rodney / Chain, Patrick S G / Copeland, Courtney A / di Iulio, Julia / Hu, Bin / Ebert, Philip / Gunti, Jonathan / Jin, Yumi / Katz, Kenneth S / Kochergin, Andrey / LaRosa, Tré / Li, Jiani / Li, Po-E /
    Lo, Chien-Chi / Rashid, Sujatha / Maiorova, Evguenia S / Xiao, Chunlin / Zalunin, Vadim / Purcell, Lisa / Pruitt, Kim D

    Viruses

    2024  Volume 16, Issue 3

    Abstract: Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 ... ...

    Abstract Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Pandemics ; Workflow ; Computational Biology
    Language English
    Publishing date 2024-03-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v16030430
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.

    Andrew W Bartlow / Zachary R Stromberg / Cheryl D Gleasner / Bin Hu / Karen W Davenport / Shailja Jakhar / Po-E Li / Molly Vosburg / Madhavi Garimella / Patrick S G Chain / Tracy H Erkkila / Jeanne M Fair / Harshini Mukundan

    PLOS Global Public Health, Vol 2, Iss 7, p e

    2022  Volume 0000811

    Abstract: Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory ... ...

    Abstract Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.
    Keywords Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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