NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!
Download release 15.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. What’s New? Release 15.0 contains: 16,667 HMMs maintained by NCBI 279 new HMMs since release 14.0 Several … Continue reading NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!
Bruker Wins NanoString Auction
NanoString declaring bankruptcy on the eve of 2024's edition of AGBT was a shock to many at the meeting and then there was confusion: would one of the sponsors have a dark booth? The aggressive 10X Genomics legal strategy that forced the bankruptcy raised a degree of polite ire. But NanoString marketing carried on and CSO Joe Beecham delivered a fiery speech saying "we're not going anywhere". Then an investment firm, Patient Square Capital, appeared to be the front runner for acquiring the assets, with speculation they would combine NanoString with their other spatial omics portfolio company, Resolve Biosciences. But last week, as the genomics world was still processing PacBio's turmoil, news broke that Bruker had significantly outbid Patient Square - $392.6M vs $220M. So Bruker takes NanoString home - and I gives me an entree to float an ontology of spatial technologies I've been fermenting, as Bruker will now have instruments in the four major spatial approaches. And 10X now has a more formidable opponent in the ongoing patent wars.
Read more » Posted by in Uncategorized
Climate change in your lifetime and the next
One of the challenges of understanding the weight of climate change is that it’s a slow process. You likely won’t see the full effect in your lifetime. So, for The Tardigrade, Julia Janicki and Daisy Chung placed your timeline against others to show how your future and others’ futures differ.
Projections are from the Intergovernmental Panel on Climate Change and show the timeline up until you turn 100 years old. You might recognize the visual form, which is based on Ed Hawkins’ climate stripes.
Tags: climate change, future, Tardigrade
Posted by in climate change, future, Infographics, Tardigrade
Cleaner BLAST Databases for More Accurate Results
Removing contaminated sequences using NCBI quality assurance tools Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance … Continue reading Cleaner BLAST Databases for More Accurate Results
Israel uses Iron Dome as defense against rockets
Using a series of graphics, Reuters explains Israel’s defense against rockets, also known as Iron Dome.
A key part of Iron Dome is its control system’s ability to discern what incoming targets pose a threat. If an adversary’s rocket will land harmlessly – in an unpopulated area or in the sea, for instance – it will not be intercepted. That makes it ideal for “saturation” scenarios in which an enemy tries to fire so many missiles that not all of them will be shot down, said Uzi Rubin, a senior researcher at the Jerusalem Institute for Strategy and Security.
Weekend reads: Deans out following Retraction Watch reporting; making sense of retractions; why one university is having grants withheld
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The week at Retraction Watch featured:
Our list of retracted or withdrawn COVID-19 papers is up past 400. There are more than 48,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 250 titles. And have you seen our leaderboard of authors with the most retractions lately — or our list of top 10 most highly cited retracted papers? What about The Retraction Watch Mass Resignations List — or our list of nearly 100 papers with evidence they were written by ChatGPT?
Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):
- A dean of engineering in Nevada is out following allegations about “bizarre publishing” and plagiarism in a grant report.
- “Making Sense of Retractions and Tackling Research Misconduct.”
- “One Scientist Neglected His Grant Reports. Now U.S. Agencies Are Withholding Grants for an Entire University.”
- “Shrouded in secrecy: how science is harmed by the bullying and harassment rumour mill.”
- PLOS ONE retracts a paper with clear but undisclosed evidence of ChatGPT use. Nearly 100 such papers here.
- “Dana-Farber retracts string of studies in systematic review of data integrity.”
- “Errors, omissions, potential bias: Why some ME experts are calling for a retraction of the NIH intramural study.”
- “Researchers need ‘open’ bibliographic databases, new declaration says.”
- “Congress pushes NIH to review reproducibility and ‘near-misses.’”
- “Researchers want a ‘nutrition label’ for academic-paper facts.”
- “US COVID-origins hearing puts scientific journals in the hot seat.”
- “2 top Chinese academics named and shamed by graft-busters for ‘saying hello.’
- “Arise robot overlords! A synergy of artificial intelligence in the evolution of scientific writing and publishing.”
- Perceptions of research integrity in three different European countries: Estonia, France, and Spain.
- “Navigating the Science System: Research Integrity and Academic Survival Strategies.”
- “Hyper-ambition and the Replication Crisis: Why Measures to Promote Research Integrity can Falter.”
- “Make peer review great (again?)“
- “Our ‘publish-or-perish’ culture is breaking the academy.”
- “The war on error: A new project seeks to root out fraud in academia.”
- “A Study on the Knowledge, Attitude, and Practice of Research Integrity among Medical Professionals in Ningxia, China.”
- “How Should We Fund Scientific Error Detection?” asks sleuth James Heathers. “I have a place to start.”
- “‘A Mess’: Harvard Med School Professor Plagiarized in Expert Report, Judge Says.”
- “Revealed: the ten research papers that policy documents cite most.”
- “Navigating the Science System: Research Integrity and Academic Survival Strategies.”
- “Structure peer review to make it more robust.”
- “Journals and publishers facing issues from fraudulent sites.”
- A doctor who took on drug companies and publishers has died.
- “The Replication Database: Documenting the Replicability of Psychological Science.”
- “To figure out whether an accusation of plagiarism is serious, apply the counterfactual test.”
- “Mistakes and misconduct in science are not synonymous; there are remedies for both.”
- “There Are Mistakes, And There Are Mistakes.”
- “Whistleblower professor accused of ‘serious misconduct’ sues Sydney Uni.”
- “Should researchers use AI to write papers? Group aims for community-driven standards.”
Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly update, follow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.
Posted by in weekend reads
Climate Change Affects Communities and the Labs That Serve Them. How Prepared Is Yours?
By Donna Campisano, specialist, Communications, APHL
According to the World Health Organization (WHO), “Climate change is directly contributing to humanitarian emergencies from heatwaves, wildfires, floods, tropical storms and hurricanes, and they are increasing in scale, frequency and intensity.”
WHO reports that 3.6 billion people live in areas susceptible to the impacts of climate change and between 2030-2050, climate change is predicted to cause an additional 250,000 deaths per year due to impacts like heat stress and undernutrition.
Climate change is the result of many interconnected factors that require a wide array of data to understand so that potential solutions can be found. Fortunately, environmental and public health laboratories have established testing infrastructure and data collection that will help meet existing and future climate-change related needs.
Climate Change and Your Laboratory
Climate change not only affects our lives, it also affects our labs—especially when it comes to the type and volume of testing you do. Consider these statistics:
- The US Environmental Protection Agency (EPA) notes that Lyme disease has nearly doubled since 1991, in part because the ticks that carry it thrive in our increasingly warmer temperatures.
- Heavy downpours and flooding can cause sewage overflows as well as polluted storm water runoff and agricultural runoff. In 2021, WHO reported that 1.7 billion people used a water source contaminated with feces. These polluted water sources can lead to diseases such as cholera, dysentery and hepatitis A, among others.
- Puerto Rico recently declared a public health emergency over rising cases of dengue, a disease carried by warm-weather, moisture-loving mosquitos.
Top 8 APHL Climate Change Resources
The climate crisis is a public health emergency. In recognition of Earth Day, we’ve compiled this list of APHL resources to help guide your lab to respond to the impacts and challenges of climate change.
- Leveraging Public Health Laboratory Science to Understand and Address Climate Change Health Impacts: This document provides information on areas of public health laboratory work that will likely be impacted by climate change.
- So, You Want to Make Your Laboratory More Sustainable…: This webinar outlines practical approaches laboratories can take to minimize unintended impacts to public health and the environment.
- Environmental Justice in Our Communities: Strategies for Laboratory Involvement: This webinar describes how public health labs can integrate environmental justice into their work.
- Cyanotoxins: A Guidance Document for Public Health Laboratories: Factors that lead to harmful algal blooms are exacerbated by climate change. This document provides laboratories guidance and resources on implementing cyanotoxin testing.
- Naegleria fowleri: Public Health Response to Municipal Water-Associated Cases in Texas and Louisiana: Increasing temperatures and water system damage may increase contamination of treated drinking water with pathogens. This webinar discusses how two different health departments responded to water-associated Naegleria fowleri cases.
- SARS-CoV-2 Wastewater Surveillance Testing Guide for Public Health Laboratories: As climate change brings an increase in diseases, wastewater surveillance can be a useful tool to detect community disease burden.
- Citizen Science Toolkit: Citizen science—also known as community science, volunteer monitoring and public participation in scientific research, among other terms—uses the collective strength and knowledge of the public to gather and analyze data to answer environmental and public health questions. This toolkit can be used for potential testing for climate change effects.
- EH Lab Communications Toolkit: This toolkit can help laboratory directors advocate for and promote the role of environmental health testing.
What Happens After April 22?
Creating a healthier environment is a 24/7, 365-days-a-year endeavor. APHL will continue to work with laboratories around the country and the world to address issues related to climate change and advocate for ways to make the world a healthier place.
The post Climate Change Affects Communities and the Labs That Serve Them. How Prepared Is Yours? appeared first on APHL Blog.
Posted by in All Posts, earth day, Environmental Health
Dean in Indonesia resigns following Retraction Watch report
Kumba Digdowiseiso, the dean of the economics and business faculty at Universitas Nasional in Jakarta, Indonesia, resigned on Thursday after a firestorm of criticism over the past week.
The move, reported widely in the Indonesian media, came eight days after Retraction Watch reported that researchers at Universiti Malaysia Terengganu alleged that Digdowiseiso had added dozens of their colleagues’ names to papers without their permission.
“This resignation is a form of my academic responsibility to the Chancellor of Unas and the academic community so as not to burden the campus in carrying out investigations into the problems I am facing,” Digdowiseiso told Kompas yesterday.
Digdowiseiso “denied the accusation of including his name in his scientific publication, calling it baseless,” Kompas reported. “In fact, he considered, there was an impression of bringing down his good name and character assassination, aka destroying his reputation.”
As we reported last week:
Digdowiseiso has published at least 160 papers in 2024 alone, according to his Google Scholar profile, which casts a wider net for publications than other indexing services such as Web of Science.
The dean had visited the Malaysian university last year, according to the deputy dean of Academic and Student Affairs, Azwadi Ali. Ali said Digdowiseiso met with management to discuss student mobility, guest lectures and potential research collaboration. “But we did not know that this might happen,” Ali said.
Digdowiseiso told Retraction Watch:
In connection with the news issued by retractionwatch.com on April 11 2024, which in my opinion is one-sided information and there is no determination as to whether what has been accused of me has been proven to be true or false, this news has made the public in Indonesia, the alma mater where I work and my family feel the consequences. Namely, getting accusations, the perception that I had made a very big academic mistake. Therefore, regarding this matter, I, who was not given the opportunity to explain, chose to take intellectual responsibility, namely resigning from my academic position.
We note that Digdowiseiso was given the chance to respond to the allegations before our April 11 post.
The choice to withdraw was a choice of conscience that I carried out so that what was accused of me did not involve other people. And as a citizen, academician, and head of the family, I will fight to restore the beliefs that I believe to be true by proving that what I have been accused of has not been proven.
I will go through a legitimate and legal process to fight for this belief. In relation to this issue, a Fact Finding Team has been formed consisting of several UNAS Internal Professors and Independent Professors from other Universities in Indonesia to find the facts and truth regarding the things that have been accused of me. And, I hope this team can be a “place” for me to fight for my rights fairly.
I also hope that retractionwatch.com will be more professional, objective and fair in its reporting, even though this has made me a victim who has to bear the consequences of this reporting.
Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly update, follow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.
Existing mortgages with lower rates than new ones
For The Upshot, Emily Badger and Francesca Paris compare the rates of existing mortgages against current rates for new loans. A stacked area chart shows the large share of existing rates that are lower, which means a lot of people aren’t so eager to move, relative to the past 20 years.
I’m in that dark maroon group. Higher mortgage rates, higher listing prices, and higher property taxes. Doesn’t seem fun.
Posted by in mortgage, Statistical Visualization, Upshot