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description Publicationkeyboard_double_arrow_right Article 2019 Australia, France, United StatesPublisher:Springer Science and Business Media LLC Funded by:NIH | Adapter-Layer RTK Signali..., EC | MYELOSHOCK, NIH | Design of Antibody Fragme... +1 projectsNIH| Adapter-Layer RTK Signaling: Basic Understanding & Targeted DrugResistance ,EC| MYELOSHOCK ,NIH| Design of Antibody Fragments Specific For Amyloidogenic Aggregates ,NSF| Collaborative Research: GOALI: Nanoparticle analysis of antibody colloidal interactions and their influence on viscoelastic properties of concentrated antibody solutionsChang-Han Lee; Tae Hyun Kang; Ophélie Godon; Makiko Watanabe; George Delidakis; Caitlin M. Gillis; Delphine Sterlin; David Hardy; Michel Cogné; Macdonald Lynn; Andrew J. Murphy; Naxin Tu; Jiwon Lee; Jonathan R. McDaniel; Emily K. Makowski; Peter M. Tessier; Aaron S. Meyer; Pierre Bruhns; George Georgiou;pmc: PMC6834678 , PMC6877538
handle: 10453/140049
The pharmacokinetic properties of antibodies are largely dictated by the pH-dependent binding of the IgG fragment crystallizable (Fc) domain to the human neonatal Fc receptor (hFcRn). Engineered Fc domains that confer a longer circulation half-life by virtue of more favorable pH-dependent binding to hFcRn are of great therapeutic interest. Here we developed a pH Toggle switch Fc variant containing the L309D/Q311H/N434S (DHS) substitutions, which exhibits markedly improved pharmacokinetics relative to both native IgG1 and widely used half-life extension variants, both in conventional hFcRn transgenic mice and in new knock-in mouse strains. engineered specifically to recapitulate all the key processes relevant to human antibody persistence in circulation, namely: (i) physiological expression of hFcRn, (ii) the impact of hFcγRs on antibody clearance and (iii) the role of competing endogenous IgG. DHS-IgG retains intact effector functions, which are important for the clearance of target pathogenic cells and also has favorable developability. International audience
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6877538Data sources: PubMed CentralNature CommunicationsArticle . 2019 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC6834678Data sources: PubMed CentraleScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 49 citations 49 popularity Top 1% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6877538Data sources: PubMed CentralNature CommunicationsArticle . 2019 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC6834678Data sources: PubMed CentraleScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2018 FrancePublisher:Elsevier BV Funded by:NIH | Together: Transforming an..., NIH | Together: Transforming an..., NSF | A Person-Centric Predicti...NIH| Together: Transforming and Translating Discovery to Improve Health ,NIH| Together: Transforming and Translating Discovery to Improve Health ,NSF| A Person-Centric Prediction Model of Job Loss based on Social MediaLossio-Ventura, Juan Antonio, A; Bian, Jiang; Jonquet, Clement; Roche, Mathieu; Teisseire, Maguelonne;[Departement_IRSTEA]Territoires [TR1_IRSTEA]SYNERGIE [Axe_IRSTEA]TETIS-SISO [ADD1_IRSTEA]Dynamiques spatiales d'anthropisation; International audience; Background: Rapid advancements in biomedical research have accelerated the number of relevant electronic documents published online, ranging from scholarly articles to news, blogs, and user-generated social media content. Nevertheless, the vast amount of this information is poorly organized, making it difficult to navigate. Emerging technologies such as ontologies and knowledge bases (KBs) could help organize and track the information associated with biomedical research developments. A major challenge in the automatic construction of ontologies and KBs is the identification of words with its respective sense(s) from a free-text corpus. Word-sense induction (WSI) is a task to automatically induce the different senses of a target word in the This paper is a significant extension of our previous studies published in the proceedings of: 1) The 10th International Conference on Language Resources and Evaluation (LREC'2016) titled, " Automatic biomedical term polysemy detection " ; and 2) The 19th International Conference on Extending Database Technology (EDBT'2016) titled, " A way to automatically enrich biomedical ontologies " , with new scientific methodologies and results. 2 Juan Antonio Lossio-Ventura et al. different contexts. In the last two decades, there have been several efforts on WSI. However, few methods are effective in biomedicine and life sciences. Methods: We developed a framework for biomedical entity sense induction using a mixture of natural language processing, supervised, and unsupervised learning methods with promising results. It is composed of three main steps: 1) a polysemy detection method to determine if a biomedical entity has many possible meanings; 2) a clustering quality index-based approach to predict the number of senses for the biomedical entity; and 3) a method to induce the concept(s) (i.e., senses) of the biomedical entity in a given context. Results: To evaluate our framework, we used the well-known MSH WSD polysemic dataset that contains 203 annotated ambiguous biomedical entities, where each entity is linked to 2 to 5 concepts. Our polysemy detection method obtained an F-measure of 98%. Second, our approach for predicting the number of senses achieved an F-measure of 93%. Finally, we induced the concepts of the biomedical entities based on a clustering algorithm and then extracted the keywords of reach cluster to represent the concept. Conclusions: We have developed a framework for biomedical entity sense induction with promising results. Our study results can benefit a number of downstream applications, for example, help to resolve concept ambiguities when building Semantic Web KBs from biomedical text.
Journal of Biomedica... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-InsermArticle . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 6 citations 6 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Journal of Biomedica... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-InsermArticle . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.jbi.2018.06.007&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2016 France, United KingdomPublisher:Frontiers Media SA Funded by:NIH | Scientific and Statistica..., WT | Transforming statistical ..., WTNIH| Scientific and Statistical Computing Core ,WT| Transforming statistical methodology for neuroimaging meta-analysis. ,WTPauli, R; Bowring, A; Reynolds, R; Chen, G; Nichols, T; Maumet, C;International audience; Data sharing is becoming a priority in functional Magnetic Resonance Imaging (fMRI) research, but the lack of a standard format for shared data is an obstacle (Poline et al., 2012; Poldrack and Gorgolewski, 2014). This is especially true for information about data provenance, including auxiliary information such as participant characteristics and task descriptions. The three most commonly used analysis software packages [AFNI1 (Cox, 1996), FSL2 (Jenkinson et al., 2012), and SPM3 (Penny et al., 2011)] broadly conduct the same analysis, but differ in how fundamental concepts are described, and have a myriad of differences in the pre-processing and modeling steps. The practical consequence is that sharing analyzed data is further complicated by the idiosyncrasies of the particular software used.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4932120Data sources: PubMed CentralOxford University Research ArchiveArticle . 2018License: CC BYData sources: Oxford University Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.3389/fninf.2016.00024&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 26 citations 26 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!visibility 3visibility views 3 download downloads 227 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4932120Data sources: PubMed CentralOxford University Research ArchiveArticle . 2018License: CC BYData sources: Oxford University Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.3389/fninf.2016.00024&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 France, United StatesPublisher:American Medical Association (AMA) Funded by:NIH | MOLECULAR DEFECTS IN ORAL..., NIH | Cancer Center Support (CO..., NIH | CLONAL CHANGES IN ORAL LE... +2 projectsNIH| MOLECULAR DEFECTS IN ORAL CARCINOGENESIS ,NIH| Cancer Center Support (CORE) Grant ,NIH| CLONAL CHANGES IN ORAL LESIONS OF HIGH-RISK PATIENTS ,NIH| CHEMOPREVENTION OF SECOND PRIMARY TUMORS WITH 13-CIS RETINOIC ACID ,NIH| CA: Administrative CoreWilliam N. William; Vassiliki A. Papadimitrakopoulou; J. Jack Lee; Li Mao; Ezra E.W. Cohen; Heather Lin; Ann M. Gillenwater; Jack W. Martin; Mark W. Lingen; Jay O. Boyle; Dong M. Shin; Nadarajah Vigneswaran; Nancy Shinn; John V. Heymach; Ignacio I. Wistuba; Ximing Tang; Edward S. Kim; Pierre Saintigny; Elizabeth A. Blair; Timothy F. Meiller; J. Silvio Gutkind; Jeffrey N. Myers; Adel K. El-Naggar; Scott M. Lippman;pmc: PMC4771491
International audience; IMPORTANCE: Standard molecularly based strategies to predict and/or prevent oral cancer development in patients with oral premalignant lesions (OPLs) are lacking. OBJECTIVE: To test if the epidermal growth factor receptor inhibitor erlotinib would reduce oral cancer development in patients with high-risk OPLs defined by specific loss of heterozygosity (LOH) profiles. Secondary objectives included prospective determination of LOH as a prognostic marker in OPLs. DESIGN: The Erlotinib Prevention of Oral Cancer (EPOC) study was a randomized, placebo-controlled, double-bind trial. Accrual occurred from November 2006 through July 2012, with a median follow-up time of 35 months in an ambulatory care setting in 5 US academic referral institutions. Patients with OPLs were enrolled in the protocol, and each underwent LOH profiling (N = 379); they were classified as high-risk (LOH-positive) or low-risk (LOH-negative) patients based on their LOH profiles and oral cancer history. The randomized sample consisted of 150 LOH-positive patients. INTERVENTIONS: Oral erlotinib treatment (150 mg/d) or placebo for 12 months. MAIN OUTCOMES AND MEASURES: Oral cancer-free survival (CFS). RESULTS: A total of 395 participants were classified with LOH profiles, and 254 were classified LOH positive. Of these, 150 (59%) were randomized, 75 each to the placebo and erlotinib groups. The 3-year CFS rates in placebo- and erlotinib-treated patients were 74% and 70%, respectively (hazard ratio [HR], 1.27; 95% CI, 0.68-2.38; P = .45). The 3-year CFS was significantly lower for LOH-positive compared with LOH-negative groups (74% vs 87%, HR, 2.19; 95% CI, 1.25-3.83; P = .01). Increased EGFR gene copy number correlated with LOH-positive status (P \\textless .001) and lower CFS (P = .01). The EGFR gene copy number was not predictive of erlotinib efficacy. Erlotinib-induced skin rash was associated with improved CFS (P = .01). CONCLUSIONS AND RELEVANCE: In this trial, LOH was validated as a marker of oral cancer risk and found to be associated with increased EGFR copy number (the target of the intervention). Erlotinib did not, however, improve CFS in high-risk patients with LOH-positive or high-EGFR-gene-copy-number OPLs. These results support incorporation of LOH testing as a prognostic tool in routine clinical practice but do not support erlotinib use in this setting. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00402779
JAMA Oncology arrow_drop_down eScholarship - University of CaliforniaArticle . 2016Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 122 citations 122 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert JAMA Oncology arrow_drop_down eScholarship - University of CaliforniaArticle . 2016Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 United States, United States, FrancePublisher:Springer Science and Business Media LLC Funded by:NIH | Population mixture in evo..., NIH | African Odyssey: An Integ..., NSF | Collaborative Research: G... +2 projectsNIH| Population mixture in evolutionary and medical genetics ,NIH| African Odyssey: An Integrative Genomics Analysis of Complex Physiologic Traits ,NSF| Collaborative Research: Genetic Bases for the Evolution of Human Diet ,NIH| Variation at Malaria Resistance Genes in Africans ,NSF| A new history and geography of human genes informed by ancient DNAJoseph K. Pickrell; Nick Patterson; Chiara Barbieri; Falko Berthold; Linda Gerlach; Tom Güldemann; Blesswell Kure; Sununguko Wata Mpoloka; Hirosi Nakagawa; Christfried Naumann; Mark Lipson; Po-Ru Loh; Joseph Lachance; Joanna L. Mountain; Carlos Bustamante; Bonnie Berger; Sarah A. Tishkoff; Brenna M. Henn; Mark Stoneking; David Reich; Brigitte Pakendorf;pmid: 23072811
pmc: PMC3493647
Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their relationships are poorly understood. Here, we report data from 23 populations analyzed at over half a million single nucleotide polymorphisms, using a genome-wide array designed for studying human history. The southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. We find that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began approximately 1,200 years ago. In addition, the east African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa To appear in Nature Communications
HAL-Inserm; Mémoires... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3493647Data sources: PubMed CentralarXiv.org e-Print ArchiveOther literature type . Preprint . 2012Data sources: arXiv.org e-Print ArchiveeScholarship - University of CaliforniaArticle . 2012Data sources: eScholarship - University of Californiahttps://doi.org/10.48550/arxiv...Article . 2012License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/ncomms2140&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 247 citations 247 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert HAL-Inserm; Mémoires... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3493647Data sources: PubMed CentralarXiv.org e-Print ArchiveOther literature type . Preprint . 2012Data sources: arXiv.org e-Print ArchiveeScholarship - University of CaliforniaArticle . 2012Data sources: eScholarship - University of Californiahttps://doi.org/10.48550/arxiv...Article . 2012License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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description Publicationkeyboard_double_arrow_right Article 2019 Australia, France, United StatesPublisher:Springer Science and Business Media LLC Funded by:NIH | Adapter-Layer RTK Signali..., EC | MYELOSHOCK, NIH | Design of Antibody Fragme... +1 projectsNIH| Adapter-Layer RTK Signaling: Basic Understanding & Targeted DrugResistance ,EC| MYELOSHOCK ,NIH| Design of Antibody Fragments Specific For Amyloidogenic Aggregates ,NSF| Collaborative Research: GOALI: Nanoparticle analysis of antibody colloidal interactions and their influence on viscoelastic properties of concentrated antibody solutionsChang-Han Lee; Tae Hyun Kang; Ophélie Godon; Makiko Watanabe; George Delidakis; Caitlin M. Gillis; Delphine Sterlin; David Hardy; Michel Cogné; Macdonald Lynn; Andrew J. Murphy; Naxin Tu; Jiwon Lee; Jonathan R. McDaniel; Emily K. Makowski; Peter M. Tessier; Aaron S. Meyer; Pierre Bruhns; George Georgiou;pmc: PMC6834678 , PMC6877538
handle: 10453/140049
The pharmacokinetic properties of antibodies are largely dictated by the pH-dependent binding of the IgG fragment crystallizable (Fc) domain to the human neonatal Fc receptor (hFcRn). Engineered Fc domains that confer a longer circulation half-life by virtue of more favorable pH-dependent binding to hFcRn are of great therapeutic interest. Here we developed a pH Toggle switch Fc variant containing the L309D/Q311H/N434S (DHS) substitutions, which exhibits markedly improved pharmacokinetics relative to both native IgG1 and widely used half-life extension variants, both in conventional hFcRn transgenic mice and in new knock-in mouse strains. engineered specifically to recapitulate all the key processes relevant to human antibody persistence in circulation, namely: (i) physiological expression of hFcRn, (ii) the impact of hFcγRs on antibody clearance and (iii) the role of competing endogenous IgG. DHS-IgG retains intact effector functions, which are important for the clearance of target pathogenic cells and also has favorable developability. International audience
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6877538Data sources: PubMed CentralNature CommunicationsArticle . 2019 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC6834678Data sources: PubMed CentraleScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41467-019-13108-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 49 citations 49 popularity Top 1% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6877538Data sources: PubMed CentralNature CommunicationsArticle . 2019 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC6834678Data sources: PubMed CentraleScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41467-019-13108-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2018 FrancePublisher:Elsevier BV Funded by:NIH | Together: Transforming an..., NIH | Together: Transforming an..., NSF | A Person-Centric Predicti...NIH| Together: Transforming and Translating Discovery to Improve Health ,NIH| Together: Transforming and Translating Discovery to Improve Health ,NSF| A Person-Centric Prediction Model of Job Loss based on Social MediaLossio-Ventura, Juan Antonio, A; Bian, Jiang; Jonquet, Clement; Roche, Mathieu; Teisseire, Maguelonne;[Departement_IRSTEA]Territoires [TR1_IRSTEA]SYNERGIE [Axe_IRSTEA]TETIS-SISO [ADD1_IRSTEA]Dynamiques spatiales d'anthropisation; International audience; Background: Rapid advancements in biomedical research have accelerated the number of relevant electronic documents published online, ranging from scholarly articles to news, blogs, and user-generated social media content. Nevertheless, the vast amount of this information is poorly organized, making it difficult to navigate. Emerging technologies such as ontologies and knowledge bases (KBs) could help organize and track the information associated with biomedical research developments. A major challenge in the automatic construction of ontologies and KBs is the identification of words with its respective sense(s) from a free-text corpus. Word-sense induction (WSI) is a task to automatically induce the different senses of a target word in the This paper is a significant extension of our previous studies published in the proceedings of: 1) The 10th International Conference on Language Resources and Evaluation (LREC'2016) titled, " Automatic biomedical term polysemy detection " ; and 2) The 19th International Conference on Extending Database Technology (EDBT'2016) titled, " A way to automatically enrich biomedical ontologies " , with new scientific methodologies and results. 2 Juan Antonio Lossio-Ventura et al. different contexts. In the last two decades, there have been several efforts on WSI. However, few methods are effective in biomedicine and life sciences. Methods: We developed a framework for biomedical entity sense induction using a mixture of natural language processing, supervised, and unsupervised learning methods with promising results. It is composed of three main steps: 1) a polysemy detection method to determine if a biomedical entity has many possible meanings; 2) a clustering quality index-based approach to predict the number of senses for the biomedical entity; and 3) a method to induce the concept(s) (i.e., senses) of the biomedical entity in a given context. Results: To evaluate our framework, we used the well-known MSH WSD polysemic dataset that contains 203 annotated ambiguous biomedical entities, where each entity is linked to 2 to 5 concepts. Our polysemy detection method obtained an F-measure of 98%. Second, our approach for predicting the number of senses achieved an F-measure of 93%. Finally, we induced the concepts of the biomedical entities based on a clustering algorithm and then extracted the keywords of reach cluster to represent the concept. Conclusions: We have developed a framework for biomedical entity sense induction with promising results. Our study results can benefit a number of downstream applications, for example, help to resolve concept ambiguities when building Semantic Web KBs from biomedical text.
Journal of Biomedica... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-InsermArticle . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.jbi.2018.06.007&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 6 citations 6 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Journal of Biomedica... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-InsermArticle . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.jbi.2018.06.007&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2016 France, United KingdomPublisher:Frontiers Media SA Funded by:NIH | Scientific and Statistica..., WT | Transforming statistical ..., WTNIH| Scientific and Statistical Computing Core ,WT| Transforming statistical methodology for neuroimaging meta-analysis. ,WTPauli, R; Bowring, A; Reynolds, R; Chen, G; Nichols, T; Maumet, C;International audience; Data sharing is becoming a priority in functional Magnetic Resonance Imaging (fMRI) research, but the lack of a standard format for shared data is an obstacle (Poline et al., 2012; Poldrack and Gorgolewski, 2014). This is especially true for information about data provenance, including auxiliary information such as participant characteristics and task descriptions. The three most commonly used analysis software packages [AFNI1 (Cox, 1996), FSL2 (Jenkinson et al., 2012), and SPM3 (Penny et al., 2011)] broadly conduct the same analysis, but differ in how fundamental concepts are described, and have a myriad of differences in the pre-processing and modeling steps. The practical consequence is that sharing analyzed data is further complicated by the idiosyncrasies of the particular software used.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4932120Data sources: PubMed CentralOxford University Research ArchiveArticle . 2018License: CC BYData sources: Oxford University Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.3389/fninf.2016.00024&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 26 citations 26 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!visibility 3visibility views 3 download downloads 227 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4932120Data sources: PubMed CentralOxford University Research ArchiveArticle . 2018License: CC BYData sources: Oxford University Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.3389/fninf.2016.00024&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 France, United StatesPublisher:American Medical Association (AMA) Funded by:NIH | MOLECULAR DEFECTS IN ORAL..., NIH | Cancer Center Support (CO..., NIH | CLONAL CHANGES IN ORAL LE... +2 projectsNIH| MOLECULAR DEFECTS IN ORAL CARCINOGENESIS ,NIH| Cancer Center Support (CORE) Grant ,NIH| CLONAL CHANGES IN ORAL LESIONS OF HIGH-RISK PATIENTS ,NIH| CHEMOPREVENTION OF SECOND PRIMARY TUMORS WITH 13-CIS RETINOIC ACID ,NIH| CA: Administrative CoreWilliam N. William; Vassiliki A. Papadimitrakopoulou; J. Jack Lee; Li Mao; Ezra E.W. Cohen; Heather Lin; Ann M. Gillenwater; Jack W. Martin; Mark W. Lingen; Jay O. Boyle; Dong M. Shin; Nadarajah Vigneswaran; Nancy Shinn; John V. Heymach; Ignacio I. Wistuba; Ximing Tang; Edward S. Kim; Pierre Saintigny; Elizabeth A. Blair; Timothy F. Meiller; J. Silvio Gutkind; Jeffrey N. Myers; Adel K. El-Naggar; Scott M. Lippman;pmc: PMC4771491
International audience; IMPORTANCE: Standard molecularly based strategies to predict and/or prevent oral cancer development in patients with oral premalignant lesions (OPLs) are lacking. OBJECTIVE: To test if the epidermal growth factor receptor inhibitor erlotinib would reduce oral cancer development in patients with high-risk OPLs defined by specific loss of heterozygosity (LOH) profiles. Secondary objectives included prospective determination of LOH as a prognostic marker in OPLs. DESIGN: The Erlotinib Prevention of Oral Cancer (EPOC) study was a randomized, placebo-controlled, double-bind trial. Accrual occurred from November 2006 through July 2012, with a median follow-up time of 35 months in an ambulatory care setting in 5 US academic referral institutions. Patients with OPLs were enrolled in the protocol, and each underwent LOH profiling (N = 379); they were classified as high-risk (LOH-positive) or low-risk (LOH-negative) patients based on their LOH profiles and oral cancer history. The randomized sample consisted of 150 LOH-positive patients. INTERVENTIONS: Oral erlotinib treatment (150 mg/d) or placebo for 12 months. MAIN OUTCOMES AND MEASURES: Oral cancer-free survival (CFS). RESULTS: A total of 395 participants were classified with LOH profiles, and 254 were classified LOH positive. Of these, 150 (59%) were randomized, 75 each to the placebo and erlotinib groups. The 3-year CFS rates in placebo- and erlotinib-treated patients were 74% and 70%, respectively (hazard ratio [HR], 1.27; 95% CI, 0.68-2.38; P = .45). The 3-year CFS was significantly lower for LOH-positive compared with LOH-negative groups (74% vs 87%, HR, 2.19; 95% CI, 1.25-3.83; P = .01). Increased EGFR gene copy number correlated with LOH-positive status (P \\textless .001) and lower CFS (P = .01). The EGFR gene copy number was not predictive of erlotinib efficacy. Erlotinib-induced skin rash was associated with improved CFS (P = .01). CONCLUSIONS AND RELEVANCE: In this trial, LOH was validated as a marker of oral cancer risk and found to be associated with increased EGFR copy number (the target of the intervention). Erlotinib did not, however, improve CFS in high-risk patients with LOH-positive or high-EGFR-gene-copy-number OPLs. These results support incorporation of LOH testing as a prognostic tool in routine clinical practice but do not support erlotinib use in this setting. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00402779
JAMA Oncology arrow_drop_down eScholarship - University of CaliforniaArticle . 2016Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1001/jamaoncol.2015.4364&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 122 citations 122 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert JAMA Oncology arrow_drop_down eScholarship - University of CaliforniaArticle . 2016Data sources: eScholarship - University of CaliforniaHAL Descartes; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1001/jamaoncol.2015.4364&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 United States, United States, FrancePublisher:Springer Science and Business Media LLC Funded by:NIH | Population mixture in evo..., NIH | African Odyssey: An Integ..., NSF | Collaborative Research: G... +2 projectsNIH| Population mixture in evolutionary and medical genetics ,NIH| African Odyssey: An Integrative Genomics Analysis of Complex Physiologic Traits ,NSF| Collaborative Research: Genetic Bases for the Evolution of Human Diet ,NIH| Variation at Malaria Resistance Genes in Africans ,NSF| A new history and geography of human genes informed by ancient DNAJoseph K. Pickrell; Nick Patterson; Chiara Barbieri; Falko Berthold; Linda Gerlach; Tom Güldemann; Blesswell Kure; Sununguko Wata Mpoloka; Hirosi Nakagawa; Christfried Naumann; Mark Lipson; Po-Ru Loh; Joseph Lachance; Joanna L. Mountain; Carlos Bustamante; Bonnie Berger; Sarah A. Tishkoff; Brenna M. Henn; Mark Stoneking; David Reich; Brigitte Pakendorf;pmid: 23072811
pmc: PMC3493647
Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their relationships are poorly understood. Here, we report data from 23 populations analyzed at over half a million single nucleotide polymorphisms, using a genome-wide array designed for studying human history. The southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. We find that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began approximately 1,200 years ago. In addition, the east African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa To appear in Nature Communications
HAL-Inserm; Mémoires... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3493647Data sources: PubMed CentralarXiv.org e-Print ArchiveOther literature type . Preprint . 2012Data sources: arXiv.org e-Print ArchiveeScholarship - University of CaliforniaArticle . 2012Data sources: eScholarship - University of Californiahttps://doi.org/10.48550/arxiv...Article . 2012License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/ncomms2140&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 247 citations 247 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert HAL-Inserm; Mémoires... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3493647Data sources: PubMed CentralarXiv.org e-Print ArchiveOther literature type . Preprint . 2012Data sources: arXiv.org e-Print ArchiveeScholarship - University of CaliforniaArticle . 2012Data sources: eScholarship - University of Californiahttps://doi.org/10.48550/arxiv...Article . 2012License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/ncomms2140&type=result"></script>'); --> </script>
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