arXiv subjects

David Fajardo-Ortiz

Publications and source records attributed to David Fajardo-Ortiz.

9 recordsLinked to original sources

arXiv2026

Evolution of funding for collaborative health research towards higher-level patient-oriented research. A comparison of the European Union Framework Programmes to the program funding by the United States National Institutes of Health

Public research funding agencies increasingly seek to steer health research toward higher levels of translation and societal relevance. Yet it remains unclear to what extent such policy shifts are effectively implemented and reflected in funded projects and scientific outputs. This study examines evolution and changes in the orientation of health research portfolios since 2008 within European funding (Framework Programmes FP7 and Horizon 2020 funding for collaborative health research, FP-HR, and ERC Life Sciences grants), in comparison to NIH funding for collaborative research (P01, U01, and UM1). Using large-scale text analysis and supervised classification, we analyze both project descriptions and the associated scientific publications. At the project level, the EU FP-HR show pronounced shifts toward population-level, diagnostic, and health systems-oriented research, whereas investigator-driven ERC life sciences, NIH P01 and U01, display greater stability with a predominance of basic biomedical research. Publication-level analyses reveal more moderate changes, with basic biomedical research remaining a central component including in EU FP-HR, indicating partial translation of funding priorities into outputs. By jointly analyzing projects and publications, this study identifies and distinguishes between changes in funder expectations and realized research trajectories, highlighting how strategic funding shapes research portfolios within enduring epistemic and institutional constraints.

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arXiv2022

Funding CRISPR: Understanding the role of government and philanthropic institutions in supporting academic research within the CRISPR innovation system

CRISPR/Cas has the potential to revolutionize medicine, agriculture, and biology. Understanding the trajectory of CRISPR research, how it is influenced and who pays for it, is an essential research policy question. We use a combination of methods to map, via quantitative content analysis of CRISPR papers, the research funding profile of major government agencies and organizations philanthropic, and the networks involved in supporting key stages of high-influence research, namely basic biological research and technological development. The results of the content analysis show how the research supported by the main US government agencies focus both on the study of CRISPR as a biological phenomenon and on its technological development and use as a biomedical research tool. US philanthropic organizations with the exception of HHMI, tend, by contrast, to specialize in funding CRISPR as a genome editing technology. We present a model of co-funding networks at the two most prominent institutions for CRISPR/Cas research, the University of California and the Harvard/MIT/Broad Institute, to illuminate how philanthropic organizations have articulated with government agencies to co-finance the discovery and development of CRISPR/Cas. Our results raise fundamental questions about the role of the state and the influence of philanthropy over the trajectory of transformative technologies.

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arXiv2018

Team assembly mechanisms and the knowledge produced in the Mexico's National Institute of Geriatrics: a network analysis and agent-based modelling approach

Mexico's National Institute of Geriatrics (INGER) is the national research center of reference for matters related to human aging. INGER scientists perform basic, clinical and demographic research which may imply different scientific cultures working together in the same specialized institution. In this paper, by a combination of text mining, co-authorship network analysis and agent-based modeling we analyzed and modeled the team assembly practices and the structure of the knowledge produced by scientists from INGER. Our results showed a weak connection between basic and clinical research, and the emergence of a highly connected academic leadership. Importantly, basic and clinical-demographic researchers exhibited different team assembly strategies: Basic researchers tended to form larger teams mainly with external collaborators while clinical and demographic researchers formed smaller teams that very often incorporated internal (INGER) collaborators. We showed how these two different ways to form research teams impacted the organization of knowledge produced at INGER. Following these observations, we modeled, via agent-based modeling, the coexistence of different scientific cultures (basic and clinical research) exhibiting different team assembly strategies in the same institution. Our agent model successfully reproduced the current situation of INGER. Moreover, by modifying the values of homophily we obtain alternative scenarios in which multidisciplinary and interdisciplinary research could be done.

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arXiv2017

Emerging basic, clinical and translational research fronts in dental biomaterials R&D

The current (2007-2007) structure and content of dental materials research has been investigated by identifying and describing the emergent research fronts which can be related to basic, translational and clinical observation research. By a combination of network analysis and text mining of the literature on dental materials indexed in the Web of Science, we have identified eleven emerging research fronts. These fronts are related to different dental materials applications which are at different levels in the knowledge translation and biomedical innovation process. We identified fronts related to dominant designs like titanium implants, competing technologies like ceramics and composites applications to prothesis and restauration, and disruptive technologies like nanomaterials and mineral trioxide aggregates. Our results suggest the possible relation between the technological complexity of the dental materials and the level of advance in terms of knowledge translation. This is the first time the structure and content of research on dental materials research is analyzed.

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arXiv2017

The evolution and structure of biomedical knowledge on cytochrome P450

Cytochrome P450 are fundamental proteins to the metabolism of drugs and other relevant processes. through a combination of text mining and network analysis of the P450 literature we mapped the emergence and evolution of the biomedical research communities working on this family of proteins. Our results suggest that the historical research communities that worked on P450 emerged and were organized mainly around methodological achievements like the induction of animal liver microsomal P450 by drugs, the use of chemical inhibitors of P450 enzymes in in-vitro metabolism studies and the development of E. coli expression systems. We found clear evidence that P450 research indeed constitutes a material scientific culture, as we discuss in the text.

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arXiv2017

The emergence and evolution of the research fronts in HIV/AIDS research

In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus", "HIV-1" and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Then, a sub-network of the papers with the highest number of inter-citations (with a minimal in-degree of 28) was selected to perform a combination of network clustering and text mining to identify the paradigmatic research fronts and analyze their dynamics. Thirteen research fronts were identified in this sub-network. The biggest and oldest front is related to the clinical knowledge on the disease in the patient. Nine of the fronts are related to the study of specific molecular structures and mechanisms and two of these fronts are related to the development of drugs. The rest of the fronts are related to the study of the disease at the cellular level. Interestingly, the emergence of these fronts occurred in successive "waves" over the time which suggest a transition in the paradigmatic focus. The emergence and evolution of the biomedical fronts in HIV/AIDS research is explained not just by the partition of the problem in elements and interactions leading to increasingly specialized communities, but also by changes in the technological context of this health problem and the dramatic changes in the epidemiological reality of HIV/AIDS that occurred between 1993 and 1995.

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arXiv2016

Mapping knowledge translation and innovation processes in Cancer Drug Development: the case of liposomal doxorubicin

We explored how the knowledge translation and innovation processes are structured when they result in innovations, as in the case of liposomal doxorubicin research. In order to map the processes, a literature network analysis was made through Cytoscape and semantic analysis was performed by GOPubmed which is based in the controlled vocabularies MeSH (Medical Subject Headings) and GO (Gene Ontology). We found clusters related to different stages of the technological development (invention, innovation and imitation) and the knowledge translation process (preclinical, translational and clinical research), and we were able to map the historic emergence of Doxil as a paradigmatic nanodrug. This research could be a powerful methodological tool for decision-making and innovation management in drug delivery research.

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arXiv2016

Hegemonic structure of basic, clinical and patented knowledge on Ebola research: a US army reductionist initiative

Background: In this paper, we present an approach to understand how the basic, clinical and patent knowledge on Ebola is organized and intercommunicated and what leading factor could be shaping the evolution of the knowledge translation process for this disease. Methodology: A combination of citation network analysis; analysis of Medical heading Subject (MeSH) and Gene Ontology (GO) terms, and quantitative content analysis for patents and scientific literature, aimed to map the organization of Ebola research was carried out. Results: We found six putative research fronts (i.e. clusters of high interconnected papers). Three research fronts are basic research on Ebola virus structural proteins: glycoprotein, VP40 and VP35, respectively. There is a fourth research front of basic research papers on pathogenesis, which is the organizing hub of Ebola research. A fifth research front is pre-clinical research focused on vaccines and glycoproteins. Finally, a clinical-epidemiology research front related to the disease outbreaks was identified. The network structure of patent families shows that the dominant design is the use of Ebola virus proteins as targets of vaccines and other immunological treatments. Therefore, patents network organization resembles the organization of the scientific literature. Specifically, the knowledge on Ebola would flow from higher (clinical-epidemiology) to intermediated (cellular-tissular pathogenesis) to lower (molecular interactions) levels of organization. Conclusion: Our results suggest a strong reductionist approach for Ebola research probably influenced by the lethality of the disease. On the other hand, the ownership profile of the patent families network and the main researches relationship with the United State Army suggest a strong involvement of this military institution in Ebola research.

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arXiv2016

Liposomes versus metallic nanostructures: differences in the process of knowledge translation in cancer

This research maps the knowledge translation process for two different types of nanotechnologies applied to cancer: liposomes and metallic nanostructures (MNs). We performed a structural analysis of citation networks and text mining supported in controlled vocabularies. In the case of liposomes, our results identify subnetworks (invisible colleges) associated with different therapeutic strategies: nanopharmacology, hyperthermia, and gene therapy. Only in the pharmacological strategy was an organized knowledge translation process identified, which, however, is monopolized by the liposomal doxorubicins. In the case of MNs, subnetworks are not differentiated by the type of therapeutic strategy, and the content of the documents is still basic research. Research on MNs is highly focused on developing a combination of molecular imaging and photothermal therapy.

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