Stefan Edlund

IBM · Public Health Research

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic mat...

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix...

Foodborne diseases are a longstanding worldwide public health concern. Modeling the transmission pathways of foodborne pathogens accurately and effectively can aid in understanding the spread of pathogens and facilitate decision making for intervention. A new compartmental model is reported that integrates the effects of both direct and indirect tr...

Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA se...

Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into questi...

The Spatiotemporal Epidemiologic Modeler (STEM) is an open source software project supported by the Eclipse Foundation and used by a global community of researchers and public health officials working to track and, when possible, control outbreaks of infectious disease in human and animal populations. STEM is not a model or a tool designed for a sp...

To investigate the feasibility of using freeware to model and forecast disease on a local scale, we report the results of modeling measles using a spatial patch model centered around 73 clinics in the North West London Borough of Ealing. MMR1 and MM2 immunization data was extracted for three cohorts, age 1-3, 4-6 and 7-19 and patient population was...

The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associa...

The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation an...

Under intense scrutiny for safety and authenticity, our food supply encompasses probiotic supplementation, fermentation organisms, pathogenic bacteria, and microbial toxins - in short, the microbiome and metabolome of food. Recent claims regarding probiotic supplements, additives, and cultured foods highlight the need for widely accepted protocols...

Foodborne disease is a global public health problem that affects millions of people every year. During a foodborne illness outbreak, rapid identification of contaminated food is vital to minimize illness, loss and impact on society. Public health officials face a significant challenge and long delays in obtaining critical information to help identi...

Food safety procedures are critical to reducing pathogen caused food-borne disease (FBD). However there is no way to completely eliminate the risk of consuming contaminated products. When prevention efforts fail, rapid identification of the contaminated product is essential. The medical and economic losses incurred grow with the duration of the out...

The current outbreak of Ebola virus disease (EVD) in West Africa has caused around 23000 infections by middle of February 2015, with a death rate of 40%. The cases have been imported into developed countries, e.g., Spain and US, through travelers and returning healthcare workers. It is clear that the virus is a threat to public health worldwide. Gi...

Described are a dynamic interest profile (DIP) system and method for dynamically tracking interests of a user based on personal information. The DIP system obtains electronic documents of the user from a document stream and processes the documents to obtain certain information therefrom. Based on the information obtained from the documents, the DIP...

Current SEC and NASD rules require securities brokers and dealers to maintain, supervise, and periodically review electronic communications. We present a solution called Galaxy that provides automatic supervision and in-depth discovery of email, instant messages, and other electronic communications to enable compliance with these rules. Galaxy's su...

Foodborne disease outbreaks of recent years demonstrate that due to increasingly interconnected supply chains these type of crisis situations have the potential to affect thousands of people, leading to significant healthcare costs, loss of revenue for food companies, and-in the worst cases-death. When a disease outbreak is detected, identifying th...

Food safety procedures, such as the recommendations recently published by the FDA, are critical to reducing foodborne illness. However there is no way to completely eliminate the risk of receiving contaminated food. When prevention efforts fail, rapid identification of the source product is essential. The medical and economic losses incurred grow w...

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of th...

The system and method of the present invention provide for automatic on-demand replication in a replication cluster of content management servers. A replication manager of a content management server receives newly created, modified, and deleted application item types along with their associated physical tables and automatically forwards the receiv...

Dengue is a major international public health concern that impacts one-third of the world's population. There are four serotypes of the dengue virus (DENV). Infection with one serotype affords life-long immunity to that serotype but only temporary cross immunity (CI) to other serotypes. The risk of lethal complications is elevated upon re-infection...

Over the last decades the globalization of trade has significantly altered the topology of food supply chains. Even though food-borne illness has been consistently on the decline, the hazardous impact of contamination events is larger [1-3]. Possible contaminants include pathogenic bacteria, viruses, parasites, toxins or chemicals. Contamination ca...

This paper describes the Spatiotemporal Epidemiological Modeler (STEM), an open source disease modeling application available through the Eclipse Foundation. The most distinguishing aspect of STEM is that it provides an open platform for researchers to build, run, share, and reuse models of infectious disease. We give a motivation why we believe an...

Background The role of the Anopheles vector in malaria transmission and the effect of climate on Anopheles populations are well established. Models of the impact of climate change on the global malaria burden now have access to high-resolution climate data, but malaria surveillance data tends to be less precise, making model calibration problematic...

A community resource for spatial, temporal and food chain epidemiological modelling to assess risks in bio-terroristic or agro-terroristic crisis situations Falenski, A.1, Thoens, C.1, Filter, M.1, Kaesbohrer, A.1, Appel, B.1, Kaufman, J.H.2, Edlund, S.2, Davis,M.2, Douglas, J.V.2, and Hu, K.2, 1Federal Institute for Risk Assessment, Department Bio...

The SpatioTemporal Epidemiological Modeler: An open source framework for modeling food-borne disease Authors: JH Kaufman*, M Davis, JV Douglas, S Edlund, and K Hu IBM Research Division, Almaden Research Center, San Jose, CA M Filter, J-F Wigger, C Thoens, AA Weiser, A Kaesbohrer, and B Appel Federal Institute for Risk Assessment, Dep. Biologica...

In recent decades, dengue becomes a major international public health concern. Dengue Fever (DF) is now endemic in more than 100 countries and impact one-third of the world's population1. This vector-borne disease is transmitted by the bite of an infectious Aedes mosquito. No specific vaccine and treatment are available. There are four serotypes of...

In this paper we report the use of the open source Spatiotemporal Epidemiological Modeler (STEM, www.eclipse.org/stem) to compare three basic models for seasonal influenza transmission. The models are designed to test for possible differences between the seasonal transmission of influenza A and B. Model 1 assumes that the seasonality and magnitude...

This paper describes an attempt to model seasonal influenza using the SpatioTemporal Epidemiological Modeler (STEM). Ten years of influenza data collected at 49 locations in Israel by the Israeli Center for Disease Control was used to fit the model, and a deterministic SIR(S) compartmental disease model was extended to account for seasonal variatio...

In this paper, we give an overview of the Spatiotemporal Epidemiological Model (STEM), an open source disease modeling application available for free under the Eclipse Public License. We explain why applications such as STEM can benefit from being open and available to the general research community, and describe the design and architecture of STEM...

In March 2009, deaths from influenza like illness began to mount in Mexico and the United States. In April, the National Respiratory Disease Institute [1] reported a 100 percent increase in patients checking in for atypical pneumonia. Samples were sent to laboratories in Canada and the United States. On April 17, a national influenza alert was anno...

Faced with limited financial and personnel resources, public health researchers and policy makers are increasingly relying on computer modeling systems to investigate complex phenomena such as disease outbreaks both natural and manmade at the local, national and global levels. With multiple possible disease scenarios, multiple possible intervention...

The rise of global economies in the 21st century, the rapid national and international movement of people, and the increased reliance of developed countries on global trade, all greatly increase the potential and possible magnitude of a worldwide pandemic. New epidemics may be the result of global climate change, vector-borne diseases, food-borne i...

The elevated moon usually appears smaller than the horizon moon of equal angular size. This is the moon illusion. Distance cues may enable the perceptual system to place the horizon moon at an effectively greater distance than the elevated moon, thus making it appear as larger. This explanation is related to the size-distance invariance hypothesis....

The relationship between distance and size perception is unclear because of conflicting results of tests investigating the size-distance invariance hypothesis (SDIH), according to which perceived size is proportional to perceived distance. We propose that response bias with regard to measures of perceived distance is at the root of the conflict. Ra...

While applications built on top of groupware systems are capable of managing mundane tasks such as scheduling and email, they are not optimised for certain kinds of applications, for instance generating aggregated summaries of scheduled activities. Groupware systems are primarily designed with online transaction processing in mind, and are highly f...

The information age has brought with it the promise of unprecedented economic growth based on the efficiencies made possible by new technology. This same greater efficiency has left society with less and less time to adapt to technological progress. Perhaps the greatest cost of this progress is the threat to privacy we all face from unconstrained e...

With a growing trend toward a world where people, computers, vehicles, and other mobile objects are interconnected at all times, it is no surprise that tracking the location of these objects and performing computation on such location data are also attracting interest. The idea of location-based services has captured the imagination of application...

Tempus Fugit ("Time Flies") is the first of a new generation of Personal Information Management (PIM) systems. A PIM system incorporates an electronic calendar, "to-do" list and address book. The premise behind Tempus Fugit is that information stored in electronic calendars, to-do lists and address books can be given richer semantic interpretation...

Tracking the location of people, computers, vehicles, and other mobile objects and performing computation on such location data are quickly gaining interest. The idea of location-based services has captured the imagination of application developers, wireless service providers, and content providers alike. However, the location of people, the most i...

The information age has brought with it the promise of unprecedented economic growth based on the efficiencies made possible by new technology. This same greater efficiency has left society with less and less time to adapt to technological progress. Perhaps the greatest cost of this progress is the threat to privacy we all face from unconstrained e...

By the use of declarative rules, automation of tasks can be performed through an electronic personal information management (PIM) application. Rules can be used in a variety of different scenarios, for instance to trigger information retrieval tasks or to send out notifications when a pre-determined set of conditions are satisfied. The technology d...

Tempus Fugit ("Time Flies") is the first of a new generation of Personal Information Management (PIM) systems. A PIM system incorporates an electronic calendar, "to-do" list and address book. The premise behind Tempus Fugit is that information stored in electronic calendars, to-do lists and address books can be given richer semantic interpretation...

The consumer's view of a universal information appliance (UIA) is a personal device, such as a PDA (personal digital assistant) or a wearable computer that can interact with any application, access any information store, or remotely operate any electronic device. The technologist's view of the UIA is a portable computer, communicating over a bi-dir...