New tech could soon let you test whether your lettuce carries E. coli

Popular Science

For months this past spring, the public was exposed to frightening news and a potentially deadly pathogen due to an outbreak of E. coli in romaine lettuce. The epidemic was the largest in over a decade, affecting nearly 200 people in 35 states, and killing five. Despite the Food and Drug Administration's (FDA) best efforts, the source of the infection was never detected, although the agency believes it came from the Yuma region of Arizona. Romaine harvest season ended in April, and the shelf-life for lettuce is limited, so the danger is likely over. However, new salmonella infections in eggs and melon have already cropped up, and another infection is almost certain to happen in the future.


Your Chicken's Salmonella Problem Is Worse Than You Think

WIRED

This story originally appeared on Mother Jones and is part of the Climate Desk collaboration. We eat way more of it than any other meat, and it triggers more foodborne disease outbreak-related illnesses than any other food, according to a recent report from the Centers for Disease Control and Prevention. The main reason it makes people sick is because it carries salmonella. Back in 2015, the government agency that oversees the safety of the nation's meat supply, the US Department of Agriculture's Food Safety and Inspection Service, introduced a new testing regime at slaughterhouses to try and reduce the amount of salmonella consumers encounter on their chicken. But the program doesn't appear to be working very well.


Your Chicken's Salmonella Problem Is Worse Than You Think

Mother Jones

The main reason it makes people sick is because it carries salmonella. Back in 2015, the government agency that oversees the safety of the nation's meat supply, the US Department of Agriculture's Food Safety and Inspection Service (FSIS), introduced a new testing regime at slaughterhouses to try and reduce the amount of salmonella consumers encounter on their chicken. But the program doesn't appear to be working very well. According to data released in June, more than a third of the country's slaughterhouses are currently failing to meet safety standards developed to try and prevent salmonella contamination on the chicken we buy. For years, the FSIS's salmonella-testing program focused on carcasses--whole chickens that have been slaughtered, plucked, and cleaned but not yet cut into parts.


Negative Example Aided Transcription Factor Binding Site Search

arXiv.org Machine Learning

Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of negative examples in binding site search is still very limited. We propose the 2-centroid and optimal discriminating vector methods, taking into account negative examples. Cross-validation results on E. coli transcription factors show that the proposed methods benefit from negative examples, outperforming the centroid and position-specific scoring matrix methods. We further show that our proposed methods perform better than a state-of-the-art method. We characterize the proposed methods in the context of the other compared methods and show that, coupled with motif subtype identification, the proposed methods can be effectively applied to a wide range of transcription factors. Finally, we argue that the proposed methods are well-suited for eukaryotic transcription factors as well. Software tools are available at: http://biogrid.engr.uconn.edu/tfbs_search/.


AI Identifies Patients at Highest Risk of Cholera Infection

#artificialintelligence

Image has been cropped and resized. Scientists have developed machine-learning algorithms that can identify patterns in the bacteria of a patient's gut to determine whether the patient is likely to get infected if exposed to cholera. The researchers believe such artificial intelligence (AI) could be critical in areas of high cholera risk, since it can analyze trillions of bacteria, much more than can be done by humans. The study also demonstrates the power of machine learning to uncover medical insights that would otherwise remain obscure. READ: AI's Ethical Concerns Go Beyond Data Security and Quality The research is a collaboration between Duke University, Massachusetts General Hospital, and the International Centre for Diarrheal Disease Research, in Bangladesh.