Publications

Supplementary Figure 4 from Collaborative Cancer Epidemiology in the 21st Century: The Model of Cancer Consortia

<p>PDF - 132KB, Fraction of small and large CEC and non-CEC associated grants by year.</p>

023 META-ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES OF OSTEOARTHRITIS

Data for aggregate statistics in "Hundreds of extreme self-citing scientists revealed in new database"

Data supporting the charts in https://www.nature.com/articles/d41586-019-02479-7. Based on a snapshot of Scopus dated July 2019, across around the 7 Million author profiles that have 5 or more publications in Scopus. Information about the compilation of the dataset of which this aggregate is derived is available with the article dataset: https://data.mendeley.com/datasets/btchxktzyw/1

Association of Collagen Iα 1 Sp1 Polymorphism with the Risk of Prevalent Fractures: A Meta-Analysis

Abstract Several studies have addressed the effect of the Sp1 polymorphism of the collagen Iα 1 (COLIA1) gene on the prevalence of fractures. The results are not in full agreement on whether this polymorphism is associated with fracture risk. To clarify this uncertainty, we performed a meta-analysis including 13 eligible studies with 3641 subjects. The COLIA1 Sp1 polymorphism showed a dose-response relationship with the prevalence of fractures. The risk was 1.25-fold (95% CI, 1.09–1.45) in Ss heterozygotes versus SS homozygotes, 1.68-fold (95% CI, 1.35–2.10) in ss homozygotes versus SS> homozygotes, and 1.35 (95% CI, 1.04–1.75) for ss homozygotes versus Ss heterozygotes by random effects calculations. There was modest heterogeneity for these three effect estimates (p value for heterogeneity, 0.17, 0.16, and 0.08, respectively). The Sp1 polymorphism effects possibly were larger when the analysis was limited to studies considering only vertebral fractures (pooled risk ratios [RR], 1.30, 2.07, and 1.46, respectively). Conversely, the Sp1 polymorphism effects tended to be smaller in studies with mean patient age ≥65 years than in studies with younger patients on average, but the differences were not formally significant. We estimated the total average attributable fraction (AF) of fractures due to the s allele in European/U.S. populations as 9.4%. The meta-analysis suggests an important role for the Sp1 polymorphism in the regulation of fracture risk; however, potential heterogeneity across ethnic groups, age groups, and skeletal sites may be important to clarify in future studies. Very large studies or meta-analyses are required to document subtle genetic differences in fracture risk.

JAMA

Using texture mapping with mipmapping to render a VLSI layout

This paper presents a method of using texture mapping with mipmapping to render a VLSI layout. Texture mapping is used to save already rasterized areas of the layout from frame to frame, and to take advantage of any hardware accelerated capabilities of the host platform. Mipmapping is used to select which textures to display so that the amount of information sent to the display is bounded, and the image rendered on the display is filtered correctly. Additionally, two caching schemes are employed. The first, used to bound memory consumption, is a general purpose cache that holds textures spatially close to the user's current viewpoint. The second, used to speed up the rendering process, is a cache of heavily used sub-designs that are precomputed so rasterization on the fly is not necessary.

Federal Funding and Citation Metrics of US Biomedical Researchers, 1996 to 2022

Importance Both citation and funding metrics converge in shaping current perceptions of academic success. Objective To evaluate what proportion of the most-cited US-based scientists are funded by biomedical federal agencies and whether funded scientists are more cited than nonfunded ones. Design, Setting, and Participants This survey study used linkage of a Scopus-based database on top-cited US researchers (according to a composite citation metric) and the National Institutes of Health RePORTER database of federal funding (33 biomedical federal agencies). Matching was based on name and institution. US-based top-cited scientists who were allocated to any of 69 scientific subfields highly related to biomedicine were considered in the main analysis. Data were downloaded on June 11, 2022. Main Outcomes and Measures Proportion of US-based top-cited biomedical scientists who had any (1996-2022), recent (2015-2022), and current (2021-2022) funding. Comparisons of funded and nonfunded scientists assessed total citations and a composite citation index. Results There were 204 603 records in RePORTER (1996-2022) and 75 316 US-based top-cited scientists in the career-long citation database; 40 887 scientists were included in the main analysis. The proportion of US-based top-cited biomedical scientists (according to career-long citation impact) who had received any federal funding from biomedical research agencies was 62.7% (25 650 of 40 887) for any funding (1996-2022), 23.1% (9427 of 40 887) for recent funding (2015-2022), and 14.1% (5778 of 40 887) for current funding (2021-2022). Respective proportions were 64.8%, 31.4%, and 20.9%, for top-cited scientists according to recent single-year citation impact. There was large variability across scientific subfields (eg, current funding: 31% of career-long impact top-cited scientists in geriatrics, 30% in bioinformatics and 29% in developmental biology, but 0% in legal and forensic medicine, general psychology and cognitive sciences, and gender studies). Funded top-cited researchers were overall more cited than nonfunded top-cited scientists (median [IQR], 9594 [5650-1703] vs 5352 [3057-9890] citations; P < .001) and substantial difference remained after adjusting for subfield and years since first publication. Differences were more prominent in some specific biomedical subfields. Conclusions and Relevance In this survey study, biomedical federal funding had offered support to approximately two-thirds of the top-cited biomedical scientists at some point during the last quarter century, but only a small minority of top-cited scientists had current federal biomedical funding. The large unevenness across subfields needs to be addressed with ways that improve equity, efficiency, excellence, and translational potential.

Comparison of pandemic excess mortality in 2020-2021 across different empirical calculations

Different modeling approaches can be used to calculate excess deaths for the COVID-19 pandemic period. We compared 6 calculations of excess deaths (4 previously published and two new ones that we performed with and without age-adjustment) for 2020-2021. With each approach, we calculated excess deaths metrics and the ratio R of excess deaths over recorded COVID-19 deaths. The main analysis focused on 33 high-income countries with weekly deaths in the Human Mortality Database (HMD at mortality.org) and reliable death registration. Secondary analyses compared calculations for other countries, whenever available. Across the 33 high-income countries, excess deaths were 2.0-2.8 million without age-adjustment, and 1.6-2.1 million with age-adjustment with large differences across countries. In our analyses after age-adjustment, 8 of 33 countries had no overall excess deaths; there was a death deficit in children; and 0.478 million (29.7%) of the excess deaths were in people <65 years old. In countries like France, Germany, Italy, and Spain excess death estimates differed 2 to 4-fold between highest and lowest figures. The R values’ range exceeded 0.3 in all 33 countries. In 16 of 33 countries, the range of R exceeded 1. In 25 of 33 countries some calculations suggest R>1 (excess deaths exceeding COVID-19 deaths) while others suggest R<1 (excess deaths smaller than COVID-19 deaths). Inferred data from 4 evaluations for 42 countries and from 3 evaluations for another 98 countries are very tenuous Estimates of excess deaths are analysis-dependent and age-adjustment is important to consider. Excess deaths may be lower than previously calculated. 

Convolution engine

General-purpose processors, while tremendously versatile, pay a huge cost for their flexibility by wasting over 99% of the energy in programmability overheads. We observe that reducing this waste requires tuning data storage and compute structures and their connectivity to the data-flow and data-locality patterns in the algorithms. Hence, by backing off from full programmability and instead targeting key data-flow patterns used in a domain, we can create efficient engines that can be programmed and reused across a wide range of applications within that domain. We present the Convolution Engine (CE)---a programmable processor specialized for the convolution-like data-flow prevalent in computational photography, computer vision, and video processing. The CE achieves energy efficiency by capturing data-reuse patterns, eliminating data transfer overheads, and enabling a large number of operations per memory access. We demonstrate that the CE is within a factor of 2--3× of the energy and area efficiency of custom units optimized for a single kernel. The CE improves energy and area efficiency by 8--15× over data-parallel Single Instruction Multiple Data (SIMD) engines for most image processing applications.<!-- END_PAGE_1 -->

Energy-performance tunable logic

An externally static, internally dynamic topology creates a new logic family that enables the user to tune effective transistor thresholds post-fabrication by adjusting a few power supplies. These gates can therefore be programmed for higher speed or for lower power based on the system requirements. An application of this logic to programmable interconnect circuits is shown in this paper. In a 90-nm test chip, the circuit achieves the same performance as conventional static circuits at 65% energy and has a 2X wider energy-performance tuning range. This property enables building in-field energy-performance tunable FPGAs.

Effective Antivirals in Pandemic Preparedness: Past Mistakes, Future Needs

Abstract The next pandemic may demand faster, more flexible responses with better risk-benefit and cost-benefit ratios than current systems can deliver. During COVID-19, R&D funding allocation strongly favored vaccines over antivirals and regulatory approvals of vaccines far exceeded approvals for antivirals. Moreover, early evidence on antiviral effectiveness was often limited or even misleading. Antivirals may have advantages in early outbreak control, high-risk populations, and settings with delayed vaccine uptake. For future pandemics, we propose a dedicated antiviral agenda to coordinate R&D for broad-spectrum agents, fund phase 2/3 trials for high-severity pathogens, enable rapid manufacturing scale-up for demonstrably effective interventions, and secure equitable global access through tiered pricing, stockpiling, and technology transfer. This platform would fill the critical therapeutic blind spot in existing pandemic vaccine-centric strategies. The proposed approach should ensure transparency, strengthen equity, and provide rigorous evidence for both vaccines and antivirals, dissecting their relative benefits, limitations, complementarity, and cost–benefit.

Energy-Efficient Processor Design

 Acknowledgments  This work was performed in collaboration with Aqeel Mahesri and Sanjay Patel from the University of Illinois at Urbana-Champaign  Related References  Omid Azizi; Mahesri, A.; Patel, S.; Horowitz, M., “Area-Efficiency in CMP Core Design: Co-optimization of Circuits and Microarchitecture,” Workshop on Design, Architecture, and Simulation of Chip Multiprocessors (dasCMP), 41st International Symposium on Microarchitecture, November 2008.  Omid Azizi; Collins, J.; Patil, D.; Wang, H.; Horowitz, M., “Processor Performance Modeling using Symbolic Simulation, IEEE International Symposium on Performance Analysis of Systems & Software, 2007. ISPASS 2008. 20-22 April 2008. Architectural Performance Modeling and Optimization

Bringing Source-Level Debugging Frameworks to Hardware Generators

High-level hardware generators have significantly increased the productivity of design engineers. They use software engineering constructs to reduce the repetition required to express complex designs and enable more composability. However, these benefits are undermined by a lack of debugging infrastructure, requiring hardware designers to debug generated, usually incomprehensible, RTL code. This paper describes a framework that connects modern software source-level debugging frameworks to RTL created from hardware generators. Our working prototype offers an Integrated Development Environment (IDE) experience for generators such as RocketChip (Chisel), allowing designers to set breakpoints in complex source code, relate RTL simulation state back to source-level variables, and do forward and backward debugging, with almost no simulation overhead (less than 5%).

Routinely collected data for randomized trials: promises, barriers, and implications

Future research should be directed toward such issues and specifically focus on data quality validation, alternative research designs and how they affect outcome assessment, and aspects of reporting and transparency.

Just fast keying

We describe Just Fast Keying (JFK), a new key-exchange protocol, primarily designed for use in the IP security architecture. It is simple, efficient, and secure; we sketch a proof of the latter property. JFK also has a number of novel engineering parameters that permit a variety of tradeoffs, most notably the ability to balance the need for perfect forward secrecy against susceptibility to denial-of-service attacks.

Is Molecular Profiling Ready for Use in Clinical Decision Making?

Learning Objectives After completing this course, the reader will be able to: Discuss the current status of translational research on molecular profiling for cancer.Highlight the steps and difficulties and biases involved in moving molecular profiling from the bench to the bedside.Propose potential solutions to the challenges of clinical use of this new technology. CME Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com

Network meta-analyses performed by contracting companies and commissioned by industry

There is a prolific sector of professional contracting companies that perform network meta-analyses. Industry commissions many network meta-analyses, but most are not registered before or published after analyses in the scientific literature. Mechanisms to improve publication rates of network meta-analysis commissioned by industry are warranted.

JAMA

Biomedical research: increasing value, reducing waste