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Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software.

Extract

In 2021, the World Health Organization (WHO) issued recommendations for the use of artificial intelligence (AI), affirming the technology could be used instead of human readers for the interpretation of chest radiograph (CXR) images for the screening and triage of tuberculosis (TB), marking a historic precedent for a guideline on AI in health [1]. The forward-looking guidance highlights the utility of CXR in TB, despite past reluctance from WHO to use it in TB programmes [2]. Employing CXR in a diagnostic algorithm can identify people with subclinical TB who are asymptomatic but have lung pathology suggestive of TB, and refer them for testing and diagnosis [3].

Background

Computer-aided detection (CAD) systems hold promise for improving tuberculosis (TB) detection on digital chest radiographs. However, data on their performance in exclusively paediatric populations are scarce.

BACKGROUND AND PURPOSE:

Hemangioblastoma is a rare vascular tumor that occurs within the central nervous system in children. Differentiating hemangioblastoma from other posterior fossa tumors can be challenging on imaging, and preoperative diagnosis can change the neurosurgical approach. We hypothesize that a "lightbulb sign" on the arterial spin-labeling (ASL) sequence (diffuse homogeneous intense hyperperfusion within the solid component of the tumor) will provide additional imaging finding to differentiate hemangioblastoma from other posterior fossa tumors.

Secretary of State Rex Tillerson speaks at the Center for Strategic and International Studies on Wednesday.

WASHINGTON — Secretary of State Rex Tillerson is condemning reported atrocities committed against Rohingya Muslims in Myanmar, and he says those responsible — perhaps the country’s military — will be held accountable.

Tillerson says accounts of the suffering of the Rohingya are “heartbreaking” — and that if those reports are true, then “someone is going to be held to account for that.”

Tillerson — who’s set to visit South Asia next week — is urging the Myanmar government to improve humanitarian access to the population in western Rakhine state.

Amnesty International has accused Myanmar’s security forces of killing hundreds of men, women and children during a systematic campaign to expel the Rohingya. More than 580,000 refugees have fled to neighboring Bangladesh since late August.

“We really hold the military leadership accountable for what’s happening,” Tillerson said at the Center for Strategic and International Studies, a Washington think tank. “What’s most important to us is that the world can’t just stand idly by and be witness to the atrocities that are being reported in that area.”

He also called Wednesday for the U.S. and India to expand strategic ties. He pointedly criticized China, which he accused of challenging international norms needed for global stability.

He said the world needed the U.S. and India to have a strong partnership. The two nations share goals of security, free navigation, free trade and fighting terrorism in the Indo-Pacific, and serve as “the eastern and western beacons” for an international rules-based order which is increasingly under strain, he said.

Both India and China had benefited from that order, but Tillerson said India had done so while respecting rules and norms, while China had “at times” undermined them. To make his point, he alluded to China’s island building and expansive territorial claims in seas where Beijing has long-running disputes with Southeast Asian neighbors.

“China’s provocative actions in the South China Sea directly challenge the international law and norms that the United States and India both stand for,” Tillerson said in an address at the Center for Strategic and International Studies, a Washington think tank.

He added that the U.S. seeks constructive relations with China but “won’t shrink” from the challenges it poses when it “subverts the sovereignty of neighboring countries, and disadvantages the U.S. and our friends.”

U.S.-India relations have generally prospered in the past decade, in part because of their shared concerns about the rise of China. While President Donald Trump has looked to deepen cooperation with China on addressing the nuclear threat from North Korea, he’s also sought a closer relationship with India, which shares U.S. worries on Islamic extremism.

“In this period of uncertainty and angst, India needs a reliable partner on the world stage. I want to make clear: with our shared values and vision for global stability, peace and prosperity, the United States is that partner,” Tillerson said.

Tillerson said the U.S. wants to help improve India’s military capabilities, and also improve security cooperation among the region’s major democracies, which included Japan and Australia.

Tillerson said the U.S. and India were leading regional efforts on counterterrorism. He called for India’s archrival Pakistan “to take decisive action against terrorist groups based within their own borders that threaten its own people and the broader region.”

The post Tillerson: ‘Heartbreaking’ reports of suffering in Myanmar appeared first on PBS NewsHour.

Health Secretary Neil Gray will address concerns around his use of a ministerial car to attend football games at Hampden.

Many people enjoy the experience of using AIs like ChatGPT or voice assistants like Alexa to find out information, but it turns out doing so makes it less likely you will spot inaccurate information

To address the problem of AIs generating inaccurate information, a team of ethicists says there should be legal obligations for companies to reduce the risk of errors, but there are doubts about whether it would work

AI chatbots from Google and Microsoft sometimes parrot disinformation when answering questions about Russia’s invasion of Ukraine – but their performance depends on language and changes over time

The controversies surrounding football’s video assistant referee (VAR) system highlight our troubled relationship with uncertainty – and point to potential solutions

A mum-of-four was tragically found dead at her home following a fire.

The World Health Organization has declared mpox a public health emergency of international concern – a new variant of the virus has caused an outbreak in Central and West Africa and spread to Sweden

After an mRNA vaccine for mpox achieved promising results in monkeys, researchers say it could have several advantages over existing vaccines – but cold storage requirements mean it will be hard to roll out in some hard-hit countries

Genetic testing on samples collected during the earliest days of the covid-19 outbreak suggests it is likely that the virus spread from animals to humans at the Huanan seafood market

A vaccination campaign targeting ducks, the farm birds most at risk of getting and spreading bird flu, succeeded in greatly reducing outbreaks of the virus on poultry farms in France

Federal officials are investigating a new outbreak of E. coli O121:H19. A source of the pathogen has not yet been identified. The investigation is in its early stages, and 33 patients have been discovered. The Food and Drug Administration has not released any patient information, such as where the patients... Continue Reading

Germany has reported a decline in outbreaks for 2023, but more people were sick than in the previous year. In 2023, the Federal Office of Consumer Protection and Food Safety (BVL) and the Robert Koch Institute (RKI) received 190 reports of foodborne outbreaks that caused 2,248 illnesses, 283 hospitalizations, and... Continue Reading

An investigation into a Salmonella outbreak in Sweden has been restarted after more people fell sick. From August to October, 81 people from 18 regions contracted Salmonella Typhimurium with sequence type (ST) 36. Where information about the country of infection is available, all cases were infected in Sweden. Folkhälsomyndigheten (the Public... Continue Reading

The Centers for Disease Control and Prevention typically coordinates between 17 and 36 investigations of foodborne illnesses involving multiple states each week.  A report is posted weekly, but does not include any information about where the outbreaks are occurring, what foods are involved, or how many patients have been identified.... Continue Reading

Montana public health officials are investigating an outbreak of infections caused by Salmonella. The Cascade City-County Health Department in Great Falls is reporting that six students at Sacajawea and Valley View elementary schools have tested positive for the pathogen. A staff member at another school has also tested positive. There... Continue Reading

A multi-country Salmonella outbreak in Europe linked to tomatoes from Italy has sickened more than 250 people. From January 2023 to November 2024, 266 confirmed cases of Salmonella Strathcona have been identified in 16 European countries and the United Kingdom. Croatia, Czech Republic, Denmark, Estonia, Finland, France, Ireland, Luxembourg, the... Continue Reading

Stock and bond markets are already reacting in anticipation of the changes

Georgia's loss to Ole Miss Saturday brought a wild shakeup to the college football rankings, and the Bulldogs find themselves out of the playoff picture.

Country music star Darius Rucker paid the East Tennessee State University's NIL fund $10 for every minute he was on the field Saturday after what he called an "awkward" appearance.

Donald Trump and the Republicans have a mandate for new economic policy.

The post Breitbart Business Digest: The Trump Economic Mandate appeared first on Breitbart.

Mobile games don’t have to make sense, as evidenced by the enduring popularity of a franchise that sees players catapulting …

Continue reading "‘Foxy’s Football Islands’ Offers Up Something Very Different on Mobile"

SYDNEY FC headed to Barker College last week to promote their upcoming school holiday bootcamps which they hope will uncover the next Ronaldo.

At a time when FDA’s responsibilities continue to grow rapidly, the agency has been caught in an across-the-board reduction (sequester) in federal discretionary spending, effective March 2, 2013. Although Congress may yet reverse course and restore money to affected federal agencies, this is not considered a high probability. Altogether, FDA will lose about $209 million between now and September 30, 2013. This will reduce inspections, slow drug and device approvals, and restrict implementation of the Food Safety Modernization Act and other recent legislation. Because of the many questions about the process and outcome, this is FDA Matters’ primer on the sequester of FDA funds.

NEW YORK — McDonald's on Sunday (Oct 27) ruled out beef patties as a source of the E. coli outbreak linked to Quarter Pounder hamburgers, which has killed at least one person and sickened nearly 75 others. "We remain very confident that any contaminated product related to this outbreak has been removed from our supply chain and is out of all McDonald's restaurants," the fast-food chain's chief supply chain officer Cesar Pina said in a statement. The Colorado Department of Agriculture said that all subsamples from multiple lots of McDonald's brand fresh and frozen beef patties had tested negative for E. coli, adding that it had completed beef testing and does not anticipate receiving further samples. McDonald's said it would resume distribution of fresh supplies of the Quarter Pounder and that it is expected to be available in all restaurants in the coming week, according to the statement.

The US Centers for Disease Control and Prevention said on Wednesday that slivered onions served on McDonald's, opens new tab Quarter Pounder hamburgers and other menu items were the likely source of an E. coli outbreak that sickened 90 people. The outbreak linked to Quarter Pounder was first reported on Oct 22, and slivered onions were suspected to be the source of the infections. The US Food and Drug Administration and the company have confirmed that Taylor Farms was the supplier for the affected locations, and it has since recalled several batches of yellow onions produced in a Colorado facility. The FDA on Wednesday said it had initiated inspections at a Taylor Farms processing center in Colorado, a state where 29 people have fallen ill due to the outbreak. An onion grower of interest in Washington state is also being investigated, the FDA added. The CDC said the number of infected people has risen by 15 people from 75 and 27 persons have been hospitalised due to the illness, which has already killed one person.

Jul 4, 2024

Massachusetts has set aggressive targets for heat pump installations for over 100,000 homes by 2025 and over 500,000 homes by 2030. But the high price of electricity in Massachusetts — the fourth highest in the nation — relative to natural gas or oil makes achieving these targets very challenging unless there is a major change in electricity policy.

Enjoy Life with Clayton Homes and you could be going to the Big Game!

Flatbed Cider Co. offers two all new hand-crafted ciders made from the apples and pears that made the Northwest famous. Look for our Crisp Apple Cider and Pear Cider at restaurants and retailers throughout Washington State and Oregon.

Commercial for the new JetBlue Card