Small molecule antiviral compound collection (SMACC): A comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules

Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential threat to global human health. By identifying and solving several challenges related to data annotation accuracy, we developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic and target-based assays for these viruses that we dubbed SMACC (Small Molecule Antiviral Compound Collection). The pilot version of the SMACC database contains over 32,500 entries for 13 viruses. By analyzing data in SMACC, we have identified ∼50 compounds with polyviral inhibition profile, mostly covering flavi- and coronaviruses. The SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks. SMACC is publicly available at https://smacc.mml.unc.edu.

Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules.. [PMID: 35860225 PMCID: PMC9298133 DOI: 10.1101/2022.07.09.499397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Diseases caused by new viruses costs thousands if not millions of human lives and trillions of dollars in damage to the global economy. Despite the rapid development of vaccines for SARS-CoV-2, the lack of small molecule antiviral drugs that work against multiple viral families (broad-spectrum antivirals; BSAs) has left the entire world’s human population vulnerable to the infection between the beginning of the outbreak and the widespread availability of vaccines. Developing BSAs is an attractive, yet challenging, approach that could prevent the next, inevitable, viral outbreak from becoming a global catastrophe. To explore whether historical medicinal chemistry efforts suggest the possibility of discovering novel BSAs, we (i) identified, collected, curated, and integrated all chemical bioactivity data available in ChEMBL for molecules tested in respective assays for 13 emerging viruses that, based on published literature, hold the greatest potential threat to global human health; (ii) identified and solved the challenges related to data annotation accuracy including assay description ambiguity, missing cell or target information, and incorrect BioAssay Ontology (BAO) annotations; (iii) developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic (21,392 entries) and target-based (11,123 entries) assays for these viruses; and (iv) identified a subset of compounds showing BSA activity. For the latter task, we eliminated inconclusive and annotated duplicative entries by checking the concordance between multiple assay results and identified eight compounds active against 3–4 viruses from the phenotypic data, 16 compounds active against two viruses from the target-based data, and 35 compounds active in at least one phenotypic and one target-based assay. The pilot version of our SMACC (Small Molecule Antiviral Compound Collection) database contains over 32,500 entries for 13 viruses. Our analysis indicates that previous research yielded very small number of BSA compounds. We posit that focused and coordinated efforts strategically targeting the discovery of such agents must be established and maintained going forward. The SMACC database publicly available at https://smacc.mml.unc.edu may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks.

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

Defining clinical outcome pathways

Here, we propose a broad concept of 'Clinical Outcome Pathways' (COPs), which are defined as a series of key molecular and cellular events that underlie therapeutic effects of drug molecules. We formalize COPs as a chain of the following events: molecular initiating event (MIE) → intermediate event(s) → clinical outcome. We illustrate the concept with COP examples both for primary and alternative (i.e., drug repurposing) therapeutic applications. We also describe the elucidation of COPs for several drugs of interest using the publicly accessible Reasoning Over Biomedical Objects linked in Knowledge-Oriented Pathways (ROBOKOP) biomedical knowledge graph-mining tool. We propose that broader use of COP uncovered with the help of biomedical knowledge graph mining will likely accelerate drug discovery and repurposing efforts.

Knowledge-based approaches to drug discovery for rare diseases

The conventional drug discovery pipeline has proven to be unsustainable for rare diseases. Herein, we discuss recent advances in biomedical knowledge mining applied to discovering therapeutics for rare diseases. We summarize current chemogenomics data of relevance to rare diseases and provide a perspective on the effectiveness of machine learning (ML) and biomedical knowledge graph mining in rare disease drug discovery. We illustrate the power of these methodologies using a chordoma case study. We expect that a broader application of knowledge graph mining and artificial intelligence (AI) approaches will expedite the discovery of viable drug candidates against both rare and common diseases.

COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19

The COVID-19 pandemic has catalyzed a widespread effort to identify drug candidates and biological targets of relevance to SARS-COV-2 infection, which resulted in large numbers of publications on this subject. We have built the COVID-19 Knowledge Extractor (COKE), a web application to extract, curate, and annotate essential drug-target relationships from the research literature on COVID-19. SciBiteAI ontological tagging of the COVID Open Research Data set (CORD-19), a repository of COVID-19 scientific publications, was employed to identify drug-target relationships. Entity identifiers were resolved through lookup routines using UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of the target protein and drug terms, and confidence scores were calculated for each entity pair. COKE processing of the current CORD-19 database identified about 3000 drug-protein pairs, including 29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical trials for COVID-19. The COKE repository and web application can serve as a useful resource for drug repurposing against SARS-CoV-2. COKE is freely available at https://coke.mml.unc.edu/, and the code is available at https://github.com/DnlRKorn/CoKE.

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database

SUMMARY

In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP) biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to generate new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19 by establishing respective confirmatory pathways of drug action.

AVAILABILITY AND IMPLEMENTATION

COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.

COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19

Objective: The COVID-19 pandemic has catalyzed a widespread effort to identify drug candidates and biological targets of relevance to SARS-COV-2 infection, which resulted in large numbers of publications on this subject. We have built the COVID-19 Knowledge Extractor (COKE), a web application to extract, curate, and annotate essential drug-target relationships from the research literature on COVID-19 to assist drug repurposing efforts. Materials and Methods: SciBiteAI ontological tagging of the COVID Open Research Dataset (CORD-19), a repository of COVID-19 scientific publications, was employed to identify drug-target relationships. Entity identifiers were resolved through lookup routines using UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of protein and drug terms, and confidence scores were calculated for each entity pair. Results: COKE processing of the current CORD-19 database identified about 3,000 drug-protein pairs, including 29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical trials for COVID-19. Discussion: The rapidly evolving situation concerning the COVID-19 pandemic has resulted in a dramatic growth of publications on this subject in a short period. These circumstances call for methods that can condense the literature into the key concepts and relationships necessary for insights into SARS-CoV-2 drug repurposing. Conclusion: The COKE repository and web application deliver key drug - target protein relationships to researchers studying SARS-CoV-2. COKE portal may provide comprehensive and critical information on studies concerning drug repurposing against COVID-19. COKE is freely available at https://coke.mml.unc.edu/ and the code is available at https://github.com/DnlRKorn/CoKE.

Learning from history: do not flatten the curve of antiviral research!

Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus Disease 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. All six prior epidemics studied [bird flu, severe acute respiratory syndrome (SARS), swine flu, Middle East Respiratory Syndrome (MERS), Ebola, and Zika] were characterized by an initial spike of research response that flattened shortly thereafter. Unfortunately, no antiviral medications have been discovered to date as treatments for any of these diseases. By contrast, the HIV/AIDS pandemic has garnered consistent research investment since it began and resulted in drugs being developed within 7 years of its start date, with many more to follow. We argue that, to develop effective treatments for COVID-19 and be prepared for future epidemics, long-term, consistent investment in antiviral research is needed.

QSAR Modeling of SARS-CoV Mpro Inhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and other Drugs as Candidates for Repurposing against SARS-CoV-2

The main protease (M^pro) of the SARS-CoV-2 has been proposed as one of the major drug targets for COVID-19. We have identified the experimental data on the inhibitory activity of compounds tested against the closely related (96 % sequence identity, 100 % active site conservation) M^pro of SARS-CoV. We developed QSAR models of these inhibitors and employed these models for virtual screening of all drugs in the DrugBank database. Similarity searching and molecular docking were explored in parallel, but docking failed to correctly discriminate between experimentally active and inactive compounds, so it was not relied upon for prospective virtual screening. Forty-two compounds were identified by our models as consensus computational hits. Subsequent to our computational studies, NCATS reported the results of experimental screening of their drug collection in SARS-CoV-2 cytopathic effect assay (https://opendata.ncats.nih.gov/covid19/). Coincidentally, NCATS tested 11 of our 42 hits, and three of them, cenicriviroc (AC₅₀ of 8.9 μM), proglumetacin (tested twice independently, with AC₅₀ of 8.9 μM and 12.5 μM), and sufugolix (AC₅₀ 12.6 μM), were shown to be active. These observations support the value of our modeling approaches and models for guiding the experimental investigations of putative anti-COVID-19 drug candidates. All data and models used in this study are publicly available via Supplementary Materials, GitHub (https://github.com/alvesvm/sars-cov-mpro), and Chembench web portal (https://chembench.mml.unc.edu/).

SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules

Small, colloidally aggregating molecules (SCAMs) are the most common source of false positives in high-throughput screening (HTS) campaigns. Although SCAMs can be experimentally detected and suppressed by the addition of detergent in the assay buffer, detergent sensitivity is not routinely monitored in HTS. Computational methods are thus needed to flag potential SCAMs during HTS triage. In this study, we have developed and rigorously validated quantitative structure-interference relationship (QSIR) models of detergent-sensitive aggregation in several HTS campaigns under various assay conditions and screening concentrations. In particular, we have modeled detergent-sensitive aggregation in an AmpC β-lactamase assay, the preferred HTS counter-screen for aggregation, as well as in another assay that measures cruzain inhibition. Our models increase the accuracy of aggregation prediction by ∼53% in the β-lactamase assay and by ∼46% in the cruzain assay compared to previously published methods. We also discuss the importance of both assay conditions and screening concentrations in the development of QSIR models for various interference mechanisms besides aggregation. The models developed in this study are publicly available for fast prediction within the SCAM detective web application (https://scamdetective.mml.unc.edu/).

COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database.. [PMID: 32601612 PMCID: PMC7316095 DOI: 10.26434/chemrxiv.12462623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing ROBOKOP biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to test new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19. COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.

Computational Models Identify Several FDA Approved or Experimental Drugs as Putative Agents Against SARS-CoV-2

The outbreak of a novel human coronavirus (SARS-CoV-2) has evolved into global health emergency, infecting hundreds of thousands of people worldwide. We have identified experimental data on the inhibitory activity of compounds tested against closely related (96% sequence identity, 100% active site conservation) protease of SARS-CoV and employed this data to build QSAR models for this dataset. We employed these models for virtual screening of all drugs from DrugBank, including compounds in clinical trials. Molecular docking and similarity search approaches were explored in parallel with QSAR modeling, but molecular docking failed to correctly discriminate between experimentally active and inactive compounds. As a result of our studies, we recommended 41 approved, experimental, or investigational drugs as potential agents against SARS-CoV-2 acting as putative inhibitors of Mpro. Ten compounds with feasible prices were purchased and are awaiting the experimental validation.
.

Cytokines in the Nasal Washes of Children with Respiratory Syncytial Virus Bronchiolitis

Although respiratory syncytial (RS) virus is the major cause of bronchiolitis and pneumonia in young children, the factors that regulate the associated lung inflammation have not been defined. The levels of interleukin (IL)10, IL-12, and interferon (IFN) were determined in the nasal wash samples from 20 infants with a clinical diagnosis of bronchiolitis, seven with confirmed RS virus infections and 9 control children without respiratory illnesses. IL-10 levels were significantly higher in acute nasal wash samples (1–4 d post-hospitalization) from RS virus- infected infants than in convalescent samples from these children (14–21 d post-hospitalization), from children with other forms of bronchiolitis and from control children. In contrast, only one RS virus-infected infant had detectable IL-12 in an acute nasal wash sample. IFN activity was not detected in any samples from RS virus-infected children. RS virus infection stimulates IL-10 expression but not IL-12 and IFN, possibly contributing to an ineffective cell-mediated immune response.

Low-power silicon-organic hybrid (SOH) modulators for advanced modulation formats

We demonstrate silicon-organic hybrid (SOH) electro-optic modulators that enable quadrature phase-shift keying (QPSK) and 16-state quadrature amplitude modulation (16QAM) with high signal quality and record-low energy consumption. SOH integration combines highly efficient electro-optic organic materials with conventional silicon-on-insulator (SOI) slot waveguides, and allows to overcome the intrinsic limitations of silicon as an optical integration platform. We demonstrate QPSK and 16QAM signaling at symbol rates of 28 GBd with peak-to-peak drive voltages of 0.6 V(pp). For the 16QAM experiment at 112 Gbit/s, we measure a bit-error ratio of 5.1 × 10⁻⁵ and a record-low energy consumption of only 19 fJ/bit.

Silicon-organic hybrid (SOH) frequency comb sources for terabit/s data transmission

We demonstrate frequency comb sources based on silicon-organic hybrid (SOH) electro-optic modulators. Frequency combs with line spacings of 25 GHz and 40 GHz are generated, featuring flat-top spectra with less than 2 dB power variations over up to 7 lines. The combs are used for WDM data transmission at terabit/s data rates and distances of up to 300 km.

Second-order nonlinear silicon-organic hybrid waveguides

We describe a concept for second-order nonlinear optical processes in silicon photonics. A silicon-organic hybrid (SOH) double slot waveguide is dispersion-engineered for mode phase-matching (MPM). The proposed waveguide enables highly efficient nonlinear processes in the mid-IR range. With a cladding nonlinearity of χ(2) = 230 pm/V and 20 dBm pump power at a CW wavelength of 1550 nm, we predict a gain of 14.7 dB/cm for a 3100 nm signal. The suggested structure enables for the first time efficient second-order nonlinear optical mixing in silicon photonics with standard technology.

Reduced propagation loss in silicon strip and slot waveguides coated by atomic layer deposition

When silicon strip and slot waveguides are coated with a 50 nm amorphous titanium dioxide (TiO2) film, measured losses at a wavelength of 1.55 μm can be as low as (2 ± 1)dB/cm and (7 ± 2)dB/cm, respectively. We use atomic layer deposition (ALD), estimate the effect of ALD growth on the surface roughness, and discuss the effect on the scattering losses. Because the gap between the rails of a slot waveguide narrows by the TiO2 deposition, the effective slot width can be back-end controlled. This is useful for precise adjustment if the slot is to be filled with, e. g., a nonlinear organic material or with a sensitizer for sensors applications.

42.7 Gbit/s electro-optic modulator in silicon technology

CMOS-compatible optical modulators are key components for future silicon-based photonic transceivers. However, achieving low modulation voltage and high speed operation still remains a challenge. As a possible solution, the silicon-organic hybrid (SOH) platform has been proposed. In the SOH approach the optical signal is guided by a silicon waveguide while the electro-optic effect is provided by an organic cladding with a high χ(2)-nonlinearity. In these modulators the optical nonlinear region needs to be connected to the modulating electrical source. This requires electrodes, which are both optically transparent and electrically highly conductive. To this end we introduce a highly conductive electron accumulation layer which is induced by an external DC "gate" voltage. As opposed to doping, the electron mobility is not impaired by impurity scattering. This way we demonstrate for the first time data encoding with an SOH electro-optic modulator. Using a first-generation device at a data-rate of 42.7 Gbit/s, widely open eye diagrams were recorded. The measured frequency response suggests that significantly larger data rates are feasible.

Cytokines in the nasal washes of children with respiratory syncytial virus bronchiolitis

Although respiratory syncytial (RS) virus is the major cause of bronchiolitis and pneumonia in young children, the factors that regulate the associated lung inflammation have not been defined. The levels of interleukin (IL)10, IL-12, and interferon (IFN) were determined in the nasal wash samples from 20 infants with a clinical diagnosis of bronchiolitis, seven with confirmed RS virus infections and 9 control children without respiratory illnesses. IL-10 levels were significantly higher in acute nasal wash samples (1-4 d post hospitalization) from RS virus-infected infants than in convalescent samples from these children (14-21 d post-hospitalization), from children with other forms of bronchiolitis and from control children. In contrast, only one RS virus-infected infant had detectable IL-12 in an acute nasal wash sample. IFN activity was not detected in any samples from RS virus-infected children. RS virus infection stimulates IL-10 expression but not IL-12 and IFN, possibly contributing to an ineffective cell-mediated immune response.

Medical information privacy and the conduct of biomedical research

Profound changes in the health care delivery system, the increasing pervasiveness of information technology, and dramatic advancements in research in human genetics are intensifying public concerns about the privacy of medical information. The author argues that some of these concerns, such as the fear that medical data could be used to deny health insurance or employment, are "pragmatic" and can be dealt with through the political process. But other, "ideologic" concerns tend to generate strong emotions and political positions that impede rational discourse and confound attempts to seek workable compromises. He stresses that the progress of medicine has long depended on studies of collections of empirical data about individuals, and discusses the federal oversight of research involving human subjects, including provisions in place to protect their privacy and maintain the confidentiality of data while at the same time permitting necessary access to data for research. He suggests that since every individual benefits from the accumulated medical knowledge base, everyone should contribute to the ongoing expansion and renewal of that base. The author then states nine principles crafted at the Association of American Medical Colleges to guide its thinking and advocacy efforts regarding medical-information privacy issues. (For example, "the free flow of identifiable medical information within the boundaries of the health care system is essential to the optimum provision of patient care and its payment.") He acknowledges that the flows and uses of identifiable patient information within our complex health care and research systems are bewildering and hard to explain to the public, which is deeply concerned about privacy in general, and especially medical information privacy. How to address this concern and at the same time protect the completeness, accuracy, and integrity of the medical record? The author offers no specific answers beyond those embodied in the AAMC principles, but maintains that a satisfactory solution will come only from carefully crafted federal legislation that creates a comprehensive, uniform, and effective system of workable protections of the confidentiality of medical information, while protecting the access needed to puruse the nation's ambitious agenda in health research.

Impact of a program to diminish gender insensitivity and sexual harassment at a medical school

PURPOSE

To measure the effect of an intervention to reduce gender insensitivity and sexual harassment at one medical school.

METHOD

Stanford University School of Medicine undertook a multifaceted program to educate faculty and students regarding gender issues and to diminish sexual harassment. The authors developed a survey instrument to assess the faculty's perceptions regarding environment (five scales) and incidences of sexual harassment. Faculty were surveyed twice during the interventions (1994 and 1995).

RESULTS

Between the two years, the authors measured significant improvements in mean ratings for positive climate (p = .004) and cohesion (p = .006) and decreases in the faculty's perceptions of sexual harassment (p = 0006), gender insensitivity (p = .001), and gender discrimination (p = .004). The faculty also reported fewer observations of harassing behavior during the study period.

CONCLUSIONS

An intervention program to diminish gender insensitivity and sexual harassment can measurably improve a medical school's environment.

Measuring contributions to the research mission of medical schools

The authors of this article, who were the members and staff of a research panel formed by the AAMC as part of its mission-based management initiative, reflect on the growing interest in quantitative information in the management of the research mission of medical schools. They note the serious limitations of any such system of measures for research, particularly its inability to represent directly the quality of the research effort. Despite these concerns, the authors acknowledge that leaders in academic medicine have always used quantitative measures in one form or another to compare performance or assess progress. Two factors appear to be driving increases in this practice: (1) the need to demonstrate to institutional stakeholders that resources are being used wisely and that the school's performance justifies continued investment in the research mission; and (2) the need to fashion an economic strategy to manage precious institutional resources, particularly research space. Given these realities, the authors offer guidelines for the proper development and use of measures to assess contributions by faculty, departments, and institutions to the research mission. They also comment on the measures most commonly used in four areas: grants and other revenue-generating activities; publications; faculty members' research reputation and contributions to the national research enterprise; and support to the general research mission of the school. The authors conclude that quantitative information can help institutional leaders in important management decisions. However, the potential for misuse is great. The key is always to regard this information as an aid to judgment, not a substitute for it.

The changing landscape for clinical research

The authors review the history of U.S. clinical research and identify the profound changes stemming from advancements in the biomedical sciences, the recent transformation in the organization and financing of health care delivery, and the increasing application of information technologies. They observe that the enterprise must reorganize to account for the changed landscape, but there is a lack of the data necessary to monitor change and determine the extent to which clinical research is successfully realigning and sustaining itself. The authors discuss the evolving definition, scope, and venues for clinical research, and review previous analyses of clinical research's difficulties and remedies proposed: shared responsibility in the financing of academic medicine, support by federal and private health insurers for routine costs of patient care in clinical trials, and strengthened collaboration between and among industry, academia, insurers, and government. The authors conclude by describing two major initiatives to foster clinical investigation in the new landscape. The first is the Clinical Research Summit Project, a convocation of representative stakeholders from the health care system with an interest in clinical research, whose charge will be to formulate a national agenda for clinical research that has the broad-based support of the stakeholders. Among the challenges of this undertaking are the needs to identify new and stable sources of support for clinical research infrastructure, assess the future workforce needs for clinical investigation, and devise new methods to ensure the continued vitality and account-ability of clinical research. The second is the Clinical Research Task Force, an initiative of the Association of American Medical Colleges (AAMC), which is already exploring and advising on how AAMC member organizations can best strengthen their capacity to support clinical research programs in the current scientific, health care delivery, and financial environment.

Study of interface phenomena between bone and titanium and alumina surfaces in the case of monolithic and composite dental implants

The interface between mandibular bone and dental implants was examined with the in vivo dog model. Implant/bone interfaces were investigated for three types of materials: Ti-30 wt% Ta/Al2O3, titanium and Al2O3 using microscopy techniques covering a large magnification range: scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray analysis and Auger spectroscopy. During the interaction of the Al2O3 ceramic with bone, an interfacial layer about 15 microm thick is formed. The same phenomenon was observed at the titanium bone interface, where the thickness of the layer was about 10 microm. In all cases, interface layers were sharp with well-defined borders between bone tissue and implant materials. No calcification took place inside the interface layer. A chemical analysis performed on this layer shows the presence of titanium, calcium and phosphorus in the case of titanium implants, and aluminium, calcium and phosphorus in the case of alumina implants. A rapid decrease in metal composition with increasing distances from the implant surface is correlated to a slow increase in calcium and phosphorus in the direction of the bone. Direct contact between implant and bone was observed. No biocorrosive effects were detected at the Ti-30 wt% Ta/Al2O3 metal-ceramic interface.

Medical school funding

Letters from:

Although medical schools might appear to be robust enterprises, with aggregate annual expenditures in 1995 of more than $30 billion, the fact is that on average only about 10 to 20% of their annual revenues comes from such secure sources as tuition and fees, endowment earnings and gifts, or (mainly for the public schools) state support. About 20% of their annual revenues comes from the NIH (National Institutes of Health), nearly 35% from fees generated by the faculty physicians' practice of medicine, and another roughly 15% in direct payments from teaching hospital partners. In other words, about 50% of the schools' aggregate revenues is derived from the provision of medical care; these revenues have provided surpluses that have been used by the medical schools as flexible funds for academic investments. In fiscal year 1994, the Association of American Medical Colleges survey indicated that revenues from the faculty physicians' practice alone contributed $2.4 billion to medical schools for support of education and research. Although the majority of the funds were expended for clinical education and research, not all of them were, and the fact that the funds were discretionary is their critically important feature. It is these clinical surpluses that are being wrung out of the health care system by a managed care enterprise that has demonstrated little willingness to contribute to the costs of education and research. And just as the teaching hospitals are threatened by this new environment and require additional stabilization funds, so, too, are the medical schools.

The purpose of a new Medical School Fund (K. I. Shine, Editorial, 3 Jan., p. 9 ) is to replace these clinical revenues and provide the schools with flexible funds for the support of their academic objectives. Some of the new funds would go toward the support of curricular innovation, others to the support of the research infrastructure (or capacity) that enables the medical schools to partner with NIH in sharing the costs of sustaining the world's leading biomedical research enterprise. A good fraction of the funds would undoubtedly go to the support of clinical research, but that should be by choice and not by mandate. The schools must certainly be held accountable for the expenditure of any monies that might be received from a new public fund, but the overriding need of the medical schools at this time of convulsive change is for new monies that are flexible, not earmarked by prescription to overly specific applications.

There is an old adage in medical school lore which says that any policy that would gratuitously restrict a previously unrestricted source of funds is bad policy. From this perspective, and with deeper understanding of the schools' historic dependence on flexible clinical revenues to support a broad array of educational and research objectives, one should oppose the suggestion by Shine that funds to be raised from a new all-payer assessment be restricted by policy to support clinical investigation.

How medical schools can maintain quality while adapting to resource constraints

To gain a better understanding of the effects on medical schools of ongoing transformations in medical practice, science, and public expectations, the Association of American Medical Colleges (AAMC) formed the Advisory Panel on the Mission and Organization of Medical Schools (APMOMS) in 1994. Six working groups were appointed to address different issues of importance. This article is a report of the findings and recommendations of the Working Group on Adapting to Resource Constraints. That group was charged to consider how leaders in academic medicine can respond to the challenges of external forces and the anticipated diminishing of resources, and to focus on medical schools and how they can maintain quality while reengineering to effect needed changes. The group members developed their thinking within four categories: size of the academic enterprise; organizational models and their relationships to the clinical enterprise; faculty tenure and compensation; and partnerships with capital-intensive entities. Three recommendations for action, to which the APMOMS unanimously agreed, were made to the AAMC, which has already acted upon them in ways described in the article. The group also developed a series of "ideas for consideration," which represent a range of the members' perspectives. The working group did not seek (and probably could not have obtained) unanimous agreement on many of the issues that these ideas focus upon. The ideas are presented as a series of resolutions designed to stimulate discussion and foster better-informed planning.

On the cost of educating a medical student

The cost of educating a medical student has been an issue of intermittent public concern for most of the twentieth century, beginning in 1910 with the Flexner Report. The issue is now reemerging as a topic of high public and political interest, for several reasons, including concern about medical schools and their financing. Estimates of medical student education costs appear to vary widely; but such variations derive from the different ways the question has been framed. Costs can be categorized as instructional costs and total educational resource costs. Instructional costs, which can be distinguished further as marginal costs or proportionate-share costs, are those costs that can be related directly to the teaching program and its support. Total educational resource costs are those costs supporting all faculty deemed necessary to conduct undergraduate medical education in all their activities of teaching, research, scholarship, and patient care. The authors review studies spanning a period of more than 20 years and find that instructional cost estimates of medical student education, when adjusted to a standard base year (1996 dollars), fall within a fairly narrow range: most are between $40,000 and $50,000 per student per year. Estimates of total educational resource costs show greater variation, but four of six estimates fall between approximately $72,000 and $93,000 per student per year. The authors note that present directions of curricular innovation-small-group learning, investment in information technology, and clinical education in ambulatory sites-offer little solace to those concerned with mitigating the costs of medical student education. Several proposals have been advanced to restructure medical student education in the name of efficiency and cost-effectiveness, but many are simply maneuvers to transfer responsibility for costs to other entities. Only by a net reduction of the medical school curriculum might costs truly be reduced. Yet the medical knowledge base continues to increase, as does the range of information and skills required of medical students. Unless society is prepared to change dramatically its concept of the well-educated physician, opportunities for significant reductions in the costs of medical student education are difficult to visualize.

Preserving medical schools' academic mission in a competitive marketplace

To gain a better understanding of the effects on medical schools of transformations in medical practice, science, and public expectations, the AAMC in 1994 formed the Advisory Panel on the Mission and Organization of Medical Schools and appointed six working groups to address relevant issues. This article is a report of the findings of the Working Group on Preserving Medical Schools' Academic Mission in a Competitive Marketplace, which was charged with exploring how medical schools could acquire and/or preserve an adequate patient base for teaching, research, and income generation in a competitive marketplace. The other groups' reports will appear in future issues of Academic Medicine. To understand the diversity of approaches that schools have taken to achieve this goal and to preserve their missions, the group interviewed representatives of nine medical schools, selected to represent a cross section of U.S. medical schools. The interviews took place on four occasions between June 1995 and March 1996. The information and comments shared by participants helped the working group gain insight into the fundamental issues it had been charged to address, including those of new delivery structures, what value schools offer to delivery structures, how education and research can be incorporated and supported financially, possible new pressures on relationships between medical schools and teaching hospitals, changes in faculty physicians' employment relationships and terms, and the role of the medical school in graduate medical education. In collecting and analyzing the data, the working group focused on the distinction between protecting an institution's existing enterprise and preserving an institution's core mission. This article gives a detailed overview of the information and comments each school presented, organized under the appropriate question. The working group's conclusions and commentaries on the findings follow. An appendix presents more detailed summaries of the schools' presentations, organised as case studies. The picture that emerges is complex. The working group concluded that medical schools will take a variety of approaches to define and preserve their missions. Most, but not all, medical schools will be able to secure the patient bases necessary to fulfill their missions even in a competitive marketplace. However, the nature of many of the schools is likely to change, and it is not clear whether the core missions of education and research will continue at their present levels at all schools.

Reengineering academic medical centers: reengineering academic values?

Academic medicine is entering an era of profound, unsettling change resulting not simply from the drastic transformation of the health care marketplace but more fundamentally from the chronic, growing gap between academic medicine's seemingly insatiable demand for total resources and the supply of resources that society is willing to provide. To examine this problem, the author reviews the major factors that have shaped the development of academic medical centers (AMCs) since World War II and are now the roots of their vulnerability. The first was the major federal investment in university-based programs of science research and education that began in the 1940s; the second was the enactment in the 1960s of the Medicare/Medicaid legislation that established federal responsibility for the support of graduate medical education. After describing important characteristics (e.g., number of faculty, number of students, dollars spent on research) of the growth and accomplishment that resulted from this massive infusion of federal funds over the last few decades, the author discusses several adverse consequences, such as the de-emphasis on education in favor of research and clinical service delivery and the serious disjunction between the internal labor markets of the AMCs and the external labor markets of the real world that AMCs' graduates enter. The author then analyzes the severe challenges being faced by academic medicine in research, education, and clinical practice in the emerging resource-limited environment. Of particular concern are the fate of the clinical investigator and the future of clinical research. The author concludes with a list of four feasible strategic options for AMCs (e.g., "build one's own system") and an extensive list of what he believes AMCs will do to respond to the stresses now upon them (e.g., capitalize on unique strengths rather than trying to compete in all areas). He concludes that it will take courage for AMCs to preserve their core values in the new era, but that this can be done if AMCs craft new adaptive structures that are better attuned to the new environment and not wedded to one that is vanishing.

Effects of various hygiene procedures on the surface characteristics of titanium abutments

The use of cleaning instruments on titanium implants may cause undesired surface alterations. In a qualitative and quantitative assessment of these alterations, 5 titanium implant abutments were treated with a steel curet, a prototype pure titanium curet, an air abrasive polishing system, and an ultrasonic system. Custom-made polymer templates, used to secure the curet to a vertical guide bar and a spring scale to maintain a constant instrument pressure, guaranteed a standardized procedure and reproducible results. The ultrasonic and the air abrasive polishing method were also standardized. Evaluation by scanning electron microscopy (SEM) revealed surface alterations for all instruments and systems except the plastic curet, which did not roughen the surface at all. The confocal laser-scanning microscope allows a 3-dimensional reproduction of these surface alterations and their direct measurement. The profilometric tracing was not sensitive enough to register the minor effects caused by the titanium curet and the air abrasive polishing system. Dimensions of the resulting surface microstructure could be determined with the laser-scanning microscope. Since the influence of such surface defects on the peri-implant tissue reaction is unpredictable, the titanium curet and the air abrasive system can only be recommended with restrictions. The steel curet and the ultrasonic system proved to be totally unsuitable for cleaning titanium implants.