Recommendable!
Boeing needs a new slogan! 😊
Sunday, January 28, 2024
Astronomers detect oldest black hole ever observed. It's size and age challenge existing theories
Amazing stuff!
The Big Bang is a dubious, quite implausible theory. What came before the Big Bang? Perhaps, God was just twiddling its thumbs for many eons of years, before it pointed its finger to create the universe? Did the universe come into being out of nothing?
"... detect the black hole, which dates from 400 million years after the big bang ... That this surprisingly massive black hole – a few million times the mass of our Sun – even exists so early in the universe challenges our assumptions about how black holes form and grow. Astronomers believe that the supermassive black holes found at the centre of galaxies like the Milky Way grew to their current size over billions of years. But the size of this newly-discovered black hole suggests that they might form in other ways: they might be ‘born big’ or they can eat matter at a rate that’s five times higher than had been thought possible. ..."
From the abstract:
"Multiple theories have been proposed to describe the formation of black hole seeds in the early Universe and to explain the emergence of very massive black holes observed in the first billion years after Big Bang. Models consider different seeding and accretion scenarios, which require the detection and characterisation of black holes in the first few hundred million years after Big Bang to be validated. Here we present an extensive analysis of the JWST-NIRSpec spectrum of GN-z11, an exceptionally luminous galaxy at z = 10.6, revealing the detection of the [NeIV]λ2423 and CII*λ1335 transitions (typical of Active Galactic Nuclei, AGN), as well as semi-forbidden nebular lines tracing gas densities higher than 109 cm−3, typical of the Broad Line Region of AGN. These spectral features indicate that GN-z11 hosts an accreting black hole. The spectrum also reveals a deep and blueshifted CIVλ1549 absorption trough, tracing an outflow with velocity 800 − 1000 km s−1, likely driven by the AGN. Assuming local virial relations, we derive a black hole mass of log (MBH/M⊙) = 6.2 ± 0.3, accreting at about 5 times the Eddington rate. These properties are consistent with both heavy seeds scenarios, or scenarios envisaging intermediate/ light seeds experiencing episodic super-Eddington phases. Our finding naturally explains the high luminosity of GN-z11 and can also provide an explanation for its exceptionally high nitrogen abundance."
A small and vigorous black hole in the early Universe (no public access)
Nuclear power generation to reach record high in 2025, IEA forecasts
Good news! China & India (and other Asia) are significantly expanding their nuclear power generation in the coming years, while Western countries remain rather stagnant!
So called renewable energy (in particular wind power) is the greatest boondoggle and scandal of our time
"... Output from nuclear power plants is expected to rise by about 3 per cent both this year and next to 2,915TWh, overtaking the previous peak of 2,809TWh in 2021, and by a further 1.5 per cent in 2026, the IEA said.
Growth will be driven by new reactors in China and India as well as the return of plants in France that were shut down last year for maintenance. ..."
"... with more consumers using technologies such as electric vehicles and heat pumps. Electricity accounted for 20% of final energy consumption in 2023, up from 18% in 2015, though meeting the world’s climate goals would require electrification to advance significantly faster in the coming years. ..."
Clean sources of generation are set to cover all of the world’s additional electricity demand over the next three years (IEA) Renewables are growing rapidly and nuclear power is on track to reach new all-time high next year, enabling low-emissions generation to outpace robust electricity demand growth
Newly discovered virus kills dormant bacteria in superbug breakthrough
Good news!
"... In hostile environments – such as when they’re exposed to antibiotics – bacteria can go into a form of hibernation, where they stop growing and dividing until things calm down. This makes it difficult to fully wipe them out and contributes to the growing problem of antibiotic resistance, which threatens to eventually make even basic infections deadly. ...
Scientists at ETH Zurich hypothesized that there must be some [bacteriophage] species that can attack bacteria in this dormant state. Now, after years of searching, they’ve identified just such a phage, which they’ve named Paride. The team found that Paride was able to infect the bacteria species Pseudomonas aeruginosa, which is responsible for a range of common infections like pneumonia and UTIs, and is increasingly becoming drug-resistant. ..."
"In brief
- For the first time, ETH Zurich researchers have isolated a bacteriophage from rotting plant material that can attack and kill bacteria in a dormant state.
- How the phage manages this is still unclear.
- Combination therapy with this phage and an antibiotic eradicates many dormant germs in pure culture and in the mouse model.
In nature, most bacteria live on the bare minimum. If they experience nutrient deficiency or stress, they shut down their metabolism in a controlled manner and go into a resting state. In this stand-by mode, certain metabolic processes still take place that enable the microbes to perceive their environment and react to stimuli, but growth and division are suspended. ..."
From the abstract:
"Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates (“hibernation”). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions."
A virus that kills sleepers (ETH Zurich) ETH Zurich researchers have found a virus that kills dormant bacteria. This rare discovery could help to combat germs that can’t be treated with antibiotics alone.
The paride phage (purple) is one of the few phages to attack dormant bacteria.
Fig. 1: Most bacteriophages cannot replicate on deep-dormant E. coli or P. aeruginosa.
Study reveals how some bacterial infections become chronic
Good news!
"... A new study ... sheds light on the biological mechanisms that enable another kind of Salmonella to evade the immune system and cause long-term infections. The team focused on the “nontyphoidal” forms of Salmonella, which cause food-borne illness and, like the typhoidal form, can linger in the body long after the initial infection. By examining the genomes of bacteria collected from hundreds of people with persistent Salmonella infections, they discovered genetic mutations that both reduce the bacteria’s “virulence,” or ability to infect, and dampen the host’s immune responses, creating a kind of molecular camouflage that shields the bacteria from the immune system’s gaze. This insight could one day lead to new diagnostic approaches or treatments that prevent these infections from becoming chronic. ...
they found that while most people cleared the infection after a week or so without treatment, roughly 2.2 percent of the cases became persistent infections that lingered for months to years. ...
They confirmed that most of the cases were due to chronic infection by the same strain, rather than reinfection by different strains of the same bacteria. After analyzing the genomes of Salmonella in patient samples at various time points, the team highlighted mutations in two genes, barA and sirA, that arose in the bacteria repeatedly during chronic infection. ...
The mutated genes had different misspellings in different patients, suggesting that the bacteria evolve independently to lower the host immune response. ..."
they found that while most people cleared the infection after a week or so without treatment, roughly 2.2 percent of the cases became persistent infections that lingered for months to years. ...
They confirmed that most of the cases were due to chronic infection by the same strain, rather than reinfection by different strains of the same bacteria. After analyzing the genomes of Salmonella in patient samples at various time points, the team highlighted mutations in two genes, barA and sirA, that arose in the bacteria repeatedly during chronic infection. ...
The mutated genes had different misspellings in different patients, suggesting that the bacteria evolve independently to lower the host immune response. ..."
From the highlights and abstract:
"Highlights
• Salmonella global regulators are frequently mutated during persistent human infection
• The barA/sirA virulence regulatory pathway was most frequently mutated
• barA/sirA mutants were less virulent and elicited a weakened host immune response
• barA/sirA mutants colonized mice and were shed during persistent salmonellosis
Summary
Several bacterial pathogens, including Salmonella enterica, can cause persistent infections in humans by mechanisms that are poorly understood. By comparing genomes of isolates longitudinally collected from 256 prolonged salmonellosis patients, we identified repeated mutations in global regulators, including the barA/sirA two-component regulatory system, across multiple patients and Salmonella serovars. Comparative RNA-seq analysis revealed that distinct mutations in barA/sirA led to diminished expression of Salmonella pathogenicity islands 1 and 4 genes, which are required for Salmonella invasion and enteritis. Moreover, barA/sirA mutants were attenuated in an acute salmonellosis mouse model and induced weaker transcription of host immune responses. In contrast, in a persistent infection mouse model, these mutants exhibited long-term colonization and prolonged shedding. Taken together, these findings suggest that selection of mutations in global virulence regulators facilitates persistent Salmonella infection in humans, by attenuating Salmonella virulence and inducing a weaker host inflammatory response."
Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway (no public access)
Graphical abstract
Syphilis-like diseases were already widespread in America before the arrival of Columbus, new study finds
So were the conquistadors actually infected by indigenous women not vice versa? (Caution: Facetious question)
"Researchers at the Universities of Basel and Zurich have discovered the genetic material of the pathogen Treponema pallidum in the bones of people who died in Brazil 2,000 years ago. This is the oldest verified discovery of this pathogen thus far, and it proves that humans were suffering from diseases akin to syphilis—known as treponematoses—long before Columbus's discovery of America. ...
The researchers used dentists' drilling tools to remove minuscule samples of bone under sterile conditions. From those samples they isolated prehistoric genetic material (ancient DNA) belonging to the syphilis pathogen. Their study demonstrates that all the bacterial genomes that have been investigated can be attributed to the Treponema pallidum endemicum strain—that is, the pathogen that leads to bejel. ...
Intense debates are still ongoing today among specialists and medical historians concerning whether Christopher Columbus's sailors and soldiers brought sexually transmitted syphilis from the New World to the Old upon their return in 1492. The illness spread rapidly from the end of the 15th century onwards, particularly in harbor towns. ...
The DNA comparison also allows the date of the Treponema pallidum family's emergence to be deduced. The team's investigations show that these pathogens arose at some point between 12,000 and 550 BCE. The history of these pathogens therefore stretches much further back than previously assumed. ..."
From the abstract:
"The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus’ expeditions. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses."
Syphilis-like diseases were already widespread in America before the arrival of Columbus (University of Basel)
Professor Verena Schünemann isolates ancient DNA in the laboratory.
Fig. 1: The archaeological site and the T. pallidum-positive samples that yielded the reconstructed genomes.
Laboratory-acquired infections and pathogen escapes worldwide between 2000 and 2021
Maybe lab leaks are not so rare as want to believe! These events seem to be rare, but they could also be underreported.
There is a high probability that the SARS-CoV-2/Covid-19 escaped from a lab possibly the Wuhan Institute of Virology.
From the abstract:
"Laboratory-acquired infections (LAIs) and accidental pathogen escape from laboratory settings (APELS) are major concerns for the community. A risk-based approach for pathogen research management within a standard biosafety management framework is recommended but is challenging due to reasons such as inconsistency in risk tolerance and perception. Here, we performed a scoping review using publicly available, peer-reviewed journal and media reports of LAIs and instances of APELS between 2000 and 2021. We identified LAIs in 309 individuals in 94 reports for 51 pathogens. Eight fatalities (2·6% of all LAIs) were caused by infection with Neisseria meningitidis (n=3, 37·5%), Yersinia pestis (n=2, 25%), Salmonella enterica serotype Typhimurium (S Typhimurium; n=1, 12·5%), or Ebola virus (n=1, 12·5%) or were due to bovine spongiform encephalopathy (n=1, 12·5%). The top five LAI pathogens were S Typhimurium (n=154, 49·8%), Salmonella enteritidis (n=21, 6·8%), vaccinia virus (n=13, 4·2%), Brucella spp (n=12, 3·9%), and Brucella melitensis (n=11, 3·6%). 16 APELS were reported, including those for Bacillus anthracis, SARS-CoV, and poliovirus (n=3 each, 18·8%); Brucella spp and foot and mouth disease virus (n=2 each, 12·5%); and variola virus, Burkholderia pseudomallei, and influenza virus H5N1 (n=1 each, 6·3%). Continual improvement in LAI and APELS management via their root cause analysis and thorough investigation of such incidents is essential to prevent future occurrences. The results are biased due to the reliance on publicly available information, which emphasises the need for formalised global LAIs and APELS reporting to better understand the frequency of and circumstances surrounding these incidents."
Credits: Die unterschätzte Gefahr
Figure 1 Laboratory-acquired infection case reports, including causal pathogens for each geographical region for the period from 2000 to 2021. Note that in 1 instance the geographic location of the LAI case was not stated.
Harvard University: Migrant children in U.S. detention face physical, mental harms. Really!
What about the physical, mental harms inflicted on these children by human trafficking, long journeys, separation from parents and so on.
Instead of voting with their feet, immigrants should have voted for a better life in their respective countries!
"Children detained for a prolonged period in family immigration detention centers in the U.S. are experiencing mental and physical harm due to inadequate and inappropriate medical care, according to a new report. ...
“Detention is never in the best interest of children,” said Vasileia Digidiki, an instructor and director of FXB’s Summer Program on Migration and Refugee Studies, in an FXB press release. “The conditions that we documented in this study evidence a lack of some fundamental protections owed to children, whatever their immigration status.” ..."
“Detention is never in the best interest of children,” said Vasileia Digidiki, an instructor and director of FXB’s Summer Program on Migration and Refugee Studies, in an FXB press release. “The conditions that we documented in this study evidence a lack of some fundamental protections owed to children, whatever their immigration status.” ..."
House GOP reveals articles of impeachment against Homeland Security Secretary Alejandro Mayorkas. Really!
The GOP waited three years until next election before impeachment! They are not serious. This a bad joke!
When the GOP was not in the majority, they should still have tried it! They would have exposed the Dimocrats that way!
"... The first article alleges Mayorkas participated in a "willful and systemic refusal to comply with the law," while the second article says he breached the public's trust for his handling of the southern border amid record illegal immigration numbers. ..."
Professional musician plays guitar while undergoing brain surgery in Florida
Amazing stuff! What would you do?
Saturday, January 27, 2024
Former French colony in India expresses pride in city’s multicultural history
Recommendable! History is full of surprises! Want to eat a fresh baked croissant for breakfast in India?
How BYD killed Tesla! But can they stay on top?
Recommendable! Certainly a significant challenge for Western electrical vehicle manufacturers. This report omitted to specify what the Chinese government subsidies etc. are for BYD.
Is Facial Recognition a Useful Public Safety Tool or Something Sinister? Benefits outweigh concerns!
This article below is kind of a book review!
Facial recognition is another topic prone to alarmism and hysteria!
Facial recognition in the hands of dictatorial regimes like Russia, China, and Iran are dangerous! However, these regimes will use this technology anyway. "The Chinese government has deployed over 700 million surveillance cameras; in many cases, artificial intelligence analyzes their output in real time. Chinese authorities have used it to police behavior like jaywalking and to monitor racial and religious minorities and political dissidents. Hill reports there is a "red list" of VIPs who are invisible to facial recognition systems. "In China, being unseen is a privilege," ... Meanwhile, Iranian authorities are using facial recognition tech to monitor women protesting for civil rights by refusing to wear hijabs in public. ..."
As far as forensics is concerned face recognition is an addition to dactyloscopy (finger print identification).
Face recognition may also help e.g. find abducted children, exonerate innocent people and much more.
Claims of racial bias are as spurious as usual:
"Some privacy activists argue that facial recognition technologies are racially biased and do not work as well on some groups. But as developers continued to train their algorithms, they mostly fixed that problem; the software's disparities with respect to race, gender, and age are now so negligible as to be statistically insignificant."
Images on the Internet are in the public domain:
"... As Hill documents, the billions of photos in Clearview AI's ever-growing database were scraped without permission [???] from Facebook, TikTok, Instagram, and other social media sites. The company argues that what it is doing is no different than the way Google catalogs links and data for its search engine, only that theirs is for photographs. The legal memo leaked to Hill was part of the company's defense against numerous lawsuits filed by social media companies and privacy advocates who objected to the data scraping. ..."
"This book traces the longer history of attempts to deploy accurate and pervasive facial recognition technology, but it chiefly focuses on the quixotic rise of Clearview AI. Hill first learned of this company's existence in November 2019, when someone leaked a legal memo to her in which the mysterious company claimed it could identify nearly anyone on the planet based only on a snapshot of their face. ...
"We have developed a revolutionary, web-based intelligence platform for law enforcement to use as a tool to help generate high-quality investigative leads," explains the company's website. "Our platform, powered by facial recognition technology, includes the largest known database of 40+ billion facial images sourced from public-only web sources, including news media, mugshot websites, public social media, and other open sources." ..."
Researchers Claim First Functioning Graphene-Based Chip
Good news!
"... The research ... focuses on leveraging epitaxial graphene, a crystal structure of carbon chemically bonded to silicon carbide (SiC). This novel semiconducting material, dubbed semiconducting epitaxial graphene (SEC) —or alternatively, epigraphene—boasts enhanced electron mobility compared with that of traditional silicon, allowing electrons to traverse with significantly less resistance. The outcome is transistors capable of operating at terahertz frequencies, offering speeds 10 times as fast as that of the silicon-based transistors used in current chips. ...
While it has been known since 2008 that it’s possible to make graphene behave like a semiconductor by heating it in a vacuum with SiC, it’s the method ... that makes the difference in the bandgap. ..."
While it has been known since 2008 that it’s possible to make graphene behave like a semiconductor by heating it in a vacuum with SiC, it’s the method ... that makes the difference in the bandgap. ..."
"Researchers at the Georgia Institute of Technology have created the world’s first functional semiconductor made from graphene, a single sheet of carbon atoms held together by the strongest bonds known. ..."
From the abstract:
"Semiconducting graphene plays an important part in graphene nanoelectronics because of the lack of an intrinsic bandgap in graphene. In the past two decades, attempts to modify the bandgap either by quantum confinement or by chemical functionalization failed to produce viable semiconducting graphene. Here we demonstrate that semiconducting epigraphene (SEG) on single-crystal silicon carbide substrates has a band gap of 0.6 eV and room temperature mobilities exceeding 5,000 cm2 V−1 s−1, which is 10 times larger than that of silicon and 20 times larger than that of the other two-dimensional semiconductors. It is well known that when silicon evaporates from silicon carbide crystal surfaces, the carbon-rich surface crystallizes to produce graphene multilayers. The first graphitic layer to form on the silicon-terminated face of SiC is an insulating epigraphene layer that is partially covalently bonded to the SiC surface. Spectroscopic measurements of this buffer layer demonstrated semiconducting signatures, but the mobilities of this layer were limited because of disorder. Here we demonstrate a quasi-equilibrium annealing method that produces SEG (that is, a well-ordered buffer layer) on macroscopic atomically flat terraces. The SEG lattice is aligned with the SiC substrate. It is chemically, mechanically and thermally robust and can be patterned and seamlessly connected to semimetallic epigraphene using conventional semiconductor fabrication techniques. These essential properties make SEG suitable for nanoelectronics."
Researchers Create First Functional Semiconductor Made From Graphene (Georgia Tech) The technology could allow for smaller and faster devices and may have applications for quantum computing.
Ultrahigh-mobility semiconducting epitaxial graphene on silicon carbide (no public access, but article above contains link to PDF)
ECB trade union says staff feel Lagarde not right person to lead European Central Bank
I have blogged here several times about Christine Lagarde! She is a joke with nice earrings and spectacle frames!
"Summary
IPSO union runs mid-term survey of staff
Lagarde performs worse than predecessors
Trust in entire Executive Board falls
53.5% of respondents say Lagarde not the right president
ECB says survey flawed ...
ECB trade union says staff feel Lagarde not right person to lead central bank | ReutersHowever, IPSO said around half of those who responded expressed some doubts about Lagarde's track record on fighting inflation, the ECB's primary objective.
"
Scientists Find Evidence of a Universal, Non-Verbal Communication System in silent gestures between very young children and adults
Amazing stuff! Getting to the very essence and beginnings of human language?
"... new research hints at a shared, universal non-verbal communication system that comes to life when we gesture without talking. ...
However, when describing the same scenes without speaking, the sequences of the children's hand gestures were remarkably similar. The language-specific differences in gestures had seemingly evaporated.
... also found similarly in earlier work with adults: blind English and Turkish speakers organized their gestures the same as sighted speakers did when they refrained from speaking.
Past studies in German and English-speaking children have also found silent gestures don't necessarily follow the structure of a person's native language, however those studies didn't directly compare different language speakers like this new one did.
... suggest their findings, although tentative, hint at the possibility that we all share some rudimentary non-verbal communication system that gets overridden or altered once we start learning language. ..."
"... all the studies have produced very similar results. In fact, many of the gestures used by participants resemble what are known as “home sign systems,” which are informal sign language systems that are created spontaneously by deaf children, who have not been exposed to a conventional sign language by their hearing parents. ..."
From the abstract:
"Adults display cross-linguistic variability in their speech in how they package and order semantic elements of a motion event. These differences can also be found in speakers’ co-speech gestures (gesturing with speech), but not in their silent gestures (gesturing without speech). Here, we examine when in development children show the differences between co-speech gesture and silent gesture found in adults. We studied speech and gestures produced by 100 children learning English or Turkish (n = 50/language) – equally divided into 5 age-groups: 3–4, 5–6, 7–8, 9–10, and 11–12 years. Children were asked to describe three-dimensional spatial event scenes (e.g., a figure crawling across carpet) first with speech and then without speech using their hands. We focused on physical motion events that elicit, in adults, cross-linguistic differences in co-speech gesture and cross-linguistic similarities in silent gesture. We found the adult pattern even in the youngest children: (1) Language shaped co-speech gesture beginning at age 3 years, showing an early effect of language on thinking for speaking (as measured by gestures that occur during the speech act). (2) Language did not affect silent gesture at any age, highlighting early limits on the effects language has on thinking and revealing a language of gesture that shows similarities across languages."
Dana-Farber top scientists retract papers: meet the blogger who spotted problems in dozens of cancer papers
One man on a mission! See also my earlier bog post on this topic here.
As of today (1/27/2024), the official news of the Dana-Farber Institute do not mention the scandal!
"The prestigious Dana-Farber Cancer Institute (DFCI) in Boston, Massachusetts, acknowledged this week that it would seek retractions for 6 papers and corrections for an additional 31 — some co-authored by DFCI chief executive Laurie Glimcher, chief operating officer William Hahn and several other prominent cancer researchers. The news came after scientific-image sleuth Sholto David posted his concerns about more than 50 manuscripts to a blog on 2 January.
... It was not the first time that some of these irregularities had been noted; some were flagged years ago on PubPeer, a website where researchers comment on and critique scientific papers. ..."
As of today (1/27/2024), Laurie H. Glimcher is still President and Chief Executive Officer o Dana-Farber Cancer Institute
Molecular biologist Sholto David scans the scientific literature for problematic images
The Forces That Drive Evolution May Not Be as Random as We Thought
Amazing stuff!
"... They were able to test renowned evolutionary biologist Stephen J. Gould's thought experiment: replaying a tape of evolutionary history would result in a different, unpredictable outcome each time, since evolutionary paths depend on unpredictable events. ..."
"A groundbreaking study has found that evolution is not as unpredictable as previously thought, which could allow scientists to explore which genes could be useful to tackle real-world issues such as antibiotic resistance, disease and climate change. ...
The study ... has found that the evolutionary trajectory of a genome may be influenced by its evolutionary history, rather than determined by numerous factors and historical accidents. ..."
Using a machine learning approach known as Random Forest, along with a dataset of 2,500 complete genomes from a single bacterial species, the team carried out several hundred thousand hours of computer processing to address the question. ...
In effect, the researchers discovered an invisible ecosystem where genes can cooperate or can be in conflict with one another. ..."
From the significance and abstract:
"Significance
Different strains of the same prokaryotic species often show significant variation in gene content. Whether this variation is due to genetic drift or selection is not well understood. If the latter, we expect sets of genes to be consistently and repeatedly gained or lost together, or sequentially. We used machine learning to predict the presence of variable genes in a large set of Escherichia coli strains, using other variable genes as predictors. We find a large proportion of genes are predictable, suggesting selection plays a role in their acquisition, loss, and maintenance. We show that some genes are consistently associated with the presence or absence of others. These results have implications for understanding evolutionary dynamics in prokaryotic genomes.
Abstract
Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene–gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem’s set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene–gene relationships across the pangenome."
Evolution is not as random as previously thought, finds a new study (Nottingham University)
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome (open access)
Fig. 2 Relationships between selected presence–absence patterns in the E. coli pangenome. On the top are a network of nodes that represent the presence–absence patterns of the columns directly beneath, as well as the connections between the nodes that represent significant co-occurrence and avoidance relationships. Below left, the backbone phylogeny of the genomes in this study is positioned such that the rows of the heatmap to its right represent the presence or absence of nodes according to the label above each column.
In 2024, the nuclear Doomsday Clock remains at 90 seconds to midnight. Yawn!
This clock has been published since 1947 beginning at 7 minutes!
"The Bulletin has reset the minute hand on the Doomsday Clock 25 times since its debut in 1947, most recently in 2023 when we moved it from 100 seconds to midnight to 90 seconds to midnight."
English for trippers: Condemn condoms in condominiums
Makes sense when the population is shrinking or aging or both!
Don't they say having sex in nature is more pleasure? (Caution: Satire)
What is behind the obvious, stark imbalance between the publicity of transgender men and transgender women?
We still live in a male dominated world? Patriarchy is alive and kicking?
Women transgendering to men are of little interest to those promoting transgenderism?
It suggests women do transgender less often than men. If correct, why?
Where are the usual (transgender) women rights activists when you need them?
Cui bono? From a male perspective it is probably more beneficial to be transgender than from a female perspective. Just think of e.g. male prisoners.
Rare decay of the Higgs boson may point to physics beyond the Standard Model
Amazing minute stuff! The publication of this research is a bit dated as it was discovered already in May 2023.
"... But one Higgs decay mode that had yet to be investigated was a theoretical prediction that a Higgs boson would occasionally decay and produce a photon, the quantum of light, and a Z boson, which is an uncharged particle that together with the two W bosons conveys the weak force. ...
Theory predicts that about 15 times per 10,000 decays, the Higgs boson should decay into a Z boson and a photon, the rarest decay in the Standard Model. It does so by first producing a pair of top quarks, or a pair of W bosons, which themselves then decay into the Z and photon.
The Atlas/CMS collaboration ... found a "branching ratio," or fraction of decays of 34 times per 10,000 decays, plus or minus 11 per 10,000—2.2 times the theoretical value. ...
One possibility for physics beyond the Standard Model is supersymmetry, the theory that posits a symmetry—a relationship—between particles of a half-spin, called fermions, and integer spin, called bosons, with every known particle having a partner with a spin differing by a half-integer.
Many theoretical physicists have long been advocates of supersymmetry as it would solve many conundrums that plague the Standard Model, such as the large difference (1024) between the strengths of the weak force and gravity, or why the mass of the Higgs boson, about 125 gigaelectron-volts (GeV), is so much less than the grand unification energy scale of about 1016 GeV. ..."
From the abstract:
"The first evidence for the Higgs boson decay to a Z boson and a photon is presented, with a statistical significance of 3.4 standard deviations. The result is derived from a combined analysis of the searches performed by the ATLAS and CMS Collaborations with proton-proton collision datasets collected at the CERN Large Hadron Collider (LHC) from 2015 to 2018. These correspond to integrated luminosities of around 140 fb − 1 for each experiment, at a center-of-mass energy of 13 TeV. The measured signal yield is 2.2±0.7 times the standard model prediction, and agrees with the theoretical expectation within 1.9 standard deviations."
Evidence for the Higgs Boson Decay to a Z Boson and a Photon at the LHC (open access)
The ATLAS and CMS collaborations have joined forces to establish the first evidence of the rare decay of the Higgs boson into a Z boson and a photon
FIG. 1. Examples of Feynman diagrams for H→Zγ decay.
Greg Kelly: The Trump accuser E. Jean Carroll has 'serious issues'
Very recommendable! Why this trial against Trump was a farce! Greg mentions this woman never reported her alleged sexual assault to the police. The alleged assault is only published in one of her books.
The judge in this case prevented exculpatory evidence to be presented.
How South Africa Became a Failed State
Recommendable! That is the country that recently accused Israel of genocide in the Gaza Strip! One party rule! ANC mismanagement!
Friday, January 26, 2024
Researchers establish brain pathway linking motivation, addiction and disease
Amazing stuff! There you have it, one single pathway!
""We are exploring a direct communication between two major components of our brain's movement system, which is absent from neuroscience textbooks. These systems are traditionally thought to function independently," ...
In their study ... reported the first direct evidence that the two systems are intertwined—showing the cerebellum modulates basal ganglia dopamine levels that influence movement initiation, vigor of movement and reward processing. ..."
From the abstract:
"Evidence of direct reciprocal connections between the cerebellum and basal ganglia has challenged the long-held notion that these structures function independently. While anatomical studies have suggested the presence of cerebellar projections to the substantia nigra pars compacta (SNc), the nature and function of these connections (Cb–SNc) is unknown. Here we show, in mice, that Cb–SNc projections form monosynaptic glutamatergic synapses with dopaminergic and non-dopaminergic neurons in the SNc. Optogenetic activation of Cb–SNc axons in the SNc is associated with increased SNc activity, elevated striatal dopamine levels and increased locomotion. During behavior, Cb–SNc projections are bilaterally activated before ambulation and unilateral lever manipulation. Cb–SNc projections show prominent activation for water reward and higher activation for sweet water, suggesting that the pathway also encodes reward value. Thus, the cerebellum directly, rapidly and effectively modulates basal ganglia dopamine levels and conveys information related to movement initiation, vigor and reward processing."
Researchers Establish Brain Pathway Linking Motivation, Addiction and Disease (New Jersey Institute of Technology)
The cerebellum directly modulates the substantia nigra dopaminergic activity (no public access)
Afghanistan: Taliban Tighten Leash on Women Who Work, buy contraceptives, or wear improper clothing
May the women of Afghanistan fight for their rights as women did in Western countries. Freedom is not free.
"Hundreds of Afghan women were forced to quit their jobs or have been arrested and denied access to essential services in the last quarter of 2023, a UN Assistance Mission in Afghanistan report revealed on Monday [1/22/2024]. ..."
Gene-therapy breakthrough allows congenitally deaf children to hear and respond to speech in China
Good news! "may yield other treatments for more of the 30 million kids with genetic hearing loss"
"A novel gene therapy approach has given five children who were born deaf the ability to hear. The method, which overcomes a roadblock presented by large genes, may be useful in other treatments, according to researchers. ...
treated six children aged 1 to 7 who were suffering from an inherited mutation of the OTOF gene, which manufactures a protein important in transmitting signals from the ear to the brain.
Five of the six children showed improvement in hearing over the 26-week trial, with four outcomes described by researchers as “robust.” ...
The three older children, with cochlear implants turned off, could understand and respond to speech by 26 weeks, with two able to recognize speech in a noisy room and have a telephone conversation. ...
Before the trial began, researchers had to tackle a significant technical problem related to the size of the OTOF gene. The procedure called for the gene to be inserted into the cochlea using a type of virus researchers commonly use for this purpose.
The virus inserts the gene into the DNA of target cells, which then begin to manufacture the missing protein. The problem in this case is that the OTOF gene is too big for the virus to hold. Researchers got past this by dividing the gene into two, encapsulating the halves into separate viruses, and then injecting a mixture with both halves of the gene into the cochlea. ..."
"... the researchers found the novel gene therapy to be an effective treatment for patients with a specific form of autosomal recessive deafness caused by mutations of the OTOF (otoferlin) gene, called DFNB9. With its first patient treated in December 2022, this research represents the first human clinical trial to administer gene therapy for treating this condition ..."
From the abstract:
"Background
Autosomal recessive deafness 9, caused by mutations of the OTOF gene, is characterised by congenital or prelingual, severe-to-complete, bilateral hearing loss. However, no pharmacological treatment is currently available for congenital deafness. In this Article, we report the safety and efficacy of gene therapy with an adeno-associated virus (AAV) serotype 1 carrying a human OTOF transgene (AAV1-hOTOF) as a treatment for children with autosomal recessive deafness 9.
Methods
This single-arm, single-centre trial enrolled children (aged 1–18 years) with severe-to-complete hearing loss and confirmed mutations in both alleles of OTOF, and without bilateral cochlear implants. A single injection of AAV1-hOTOF was administered into the cochlea through the round window. The primary endpoint was dose-limiting toxicity at 6 weeks after injection. Auditory function and speech were assessed by appropriate auditory perception evaluation tools. All analyses were done according to the intention-to-treat principle. This trial is registered with Chinese Clinical Trial Registry, ChiCTR2200063181, and is ongoing.
Findings
Between Oct 19, 2022, and June 9, 2023, we screened 425 participants for eligibility and enrolled six children for AAV1-hOTOF gene therapy (one received a dose of 9 × 1011 vector genomes [vg] and five received 1·5 × 1012 vg). All participants completed follow-up visits up to week 26. No dose-limiting toxicity or serious adverse events occurred. In total, 48 adverse events were observed; 46 (96%) were grade 1–2 and two (4%) were grade 3 (decreased neutrophil count in one participant). Five children had hearing recovery, shown by a 40–57 dB reduction in the average auditory brainstem response (ABR) thresholds at 0·5–4·0 kHz. In the participant who received the 9 × 1011 vg dose, the average ABR threshold was improved from greater than 95 dB at baseline to 68 dB at 4 weeks, 53 dB at 13 weeks, and 45 dB at 26 weeks. In those who received 1·5 × 1012 AAV1-hOTOF, the average ABR thresholds changed from greater than 95 dB at baseline to 48 dB, 38 dB, 40 dB, and 55 dB in four children with hearing recovery at 26 weeks. Speech perception was improved in participants who had hearing recovery.
Interpretation
AAV1-hOTOF gene therapy is safe and efficacious as a novel treatment for children with autosomal recessive deafness 9. ..."
Unveiling dynamic superconductivity or phase III
Amazing stuff! Looks like superconductivity is more complicated!
"... Instead of dealing with actual superconducting materials, the scientists harnessed the behavior of strontium atoms, laser-cooled to 10 millionths of a degree above absolute zero and levitated within an optical cavity built out of mirrors.
In this simulator, the presence or absence of a Cooper pair was encoded in a two-level system or qubit. In this unique setup, photon-mediated interactions between electrons were realized between the atoms within the cavity.
Thanks to their simulation, the researchers observed three distinct phases of superconducting dynamics, including a rare "Phase III" featuring persistent oscillatory behavior predicted by condensed matter physics theorists but never before observed. ...
In the past few decades, condensed matter theorists have predicted three distinct dynamical phases for a superconductor to experience when it evolves. In Phase I, the strength of superconductivity decays rapidly to zero. In contrast, Phase II represents a steady state in which superconductivity is preserved.
However, the previously unobserved Phase III is the most intriguing. "The idea of phase III is that the strength of superconductivity has persistent oscillations with no damping," ..."
From the abstract:
"In conventional Bardeen–Cooper–Schrieffer superconductors, electrons with opposite momenta bind into Cooper pairs due to an attractive interaction mediated by phonons in the material. Although superconductivity naturally emerges at thermal equilibrium, it can also emerge out of equilibrium when the system parameters are abruptly changed. The resulting out-of-equilibrium phases are predicted to occur in real materials and ultracold fermionic atoms, but not all have yet been directly observed. Here we realize an alternative way to generate the proposed dynamical phases using cavity quantum electrodynamics (QED). Our system encodes the presence or absence of a Cooper pair in a long-lived electronic transition in 88Sr atoms coupled to an optical cavity and represents interactions between electrons as photon-mediated interactions through the cavity. To fully explore the phase diagram, we manipulate the ratio between the single-particle dispersion and the interactions after a quench and perform real-time tracking of the subsequent dynamics of the superconducting order parameter using nondestructive measurements. We observe regimes in which the order parameter decays to zero (phase I), assumes a non-equilibrium steady-state value (phase II) or exhibits persistent oscillations (phase III). This opens up exciting prospects for quantum simulation, including the potential to engineer unconventional superconductors and to probe beyond mean-field effects like the spectral form factor, and for increasing the coherence time for quantum sensing."
Deaths of U.S. Citizens Undergoing Cosmetic Surgery in the Dominican Republic between 2009–2022
If you are obese, you may not want to undergo cosmetic surgery in the Dominican Republic or go on weight loss first!
"... The number of deaths after cosmetic surgery among U.S. citizens in the Dominican Republic increased from a mean of 4.1 per year during 2009–2018 to a mean of 13.0 during 2019–2022 with a peak in of 17 in 2020. A review of the 29 deaths during 2019–2020 revealed that the deaths were associated with fat or venous thromboembolism. A high proportion of patients who died had risk factors for embolism, including obesity and having multiple procedures performed during the same operation. ..."
OpenAI responds to Congressional Black Caucus about lack of diversity on its board. Very disturbing!
This is pretty disturbing news! And OpenAI responded to this extortion attempt by some racist U.S. Representatives?
"... In mid-December, CBC Chairs Rep. Emanuel Cleaver and Rep. Barbara Lee sent a letter to OpenAI asking it to “move expeditiously” in diversifying its board. It noted how important a Black perspective is while building machine learning tools in order to help mitigate AI bias. The letter was addressed to Altman, Taylor, and board members Larry Summers and Adam D’Angelo. The CBC letter then asked five questions to OpenAI, including whether the company had any DEI goals for the board and how it was ensuring women and people of color were being considered for the roles. It initially gave OpenAI a December 29 response deadline.
“The board of OpenAI, a non-profit public institution created to ensure that AI benefits all of humanity, is now composed exclusively of white men,” the CBC letter read. ..."
English for trippers: Dying dyes. To die or not to dye
What happens to unpopular dyes? They eventually die.
U.S. Secretly Alerted Iran Ahead of Islamic State Terrorist Attack with specific information about location and timing
Amazing stuff! What! This could be a political bombshell!
Will the people of Iran finally get rid of their theocratic dictatorship since 1979?
"The U.S. secretly warned Iran that Islamic State was preparing to carry out the terrorist attack early this month that killed more than 80 Iranians in a pair of coordinated suicide bombings, U.S. officials said. ..."
"The confidential intelligence was specific enough about the location and sufficiently timely that it might have helped thwart the Jan. 3 pair of coordinated suicide bombings or decrease the number of casualties. Iran failed to prevent the attack, which targeted a crowd in the town of Kerman commemorating the anniversary of the death of the commander of the Islamic Revolutionary Guard Corps’ Quds force. Qassem Soleimani was killed in a 2020 drone attack near the Baghdad airport that then-President Donald Trump had ordered. Officials with Iran’s mission to the U.N. didn’t immediately respond to a request for comment."
Young Russian woman sentenced to 27 years for handing a bomb to and killing a pro-war military blogger, who was a former bank robber
Will the next Russian woman hand a bomb to Putin the Terrible! A sigh of relieve would be heard around the world.
"A young Russian woman was jailed for 27 years on Thursday for delivering a bomb that exploded in the hands of a pro-war military blogger last year and killed him on the spot.
Darya Trepova, 26, was convicted by a St Petersburg court of terrorism, handling explosives and using forged documents in connection with the death of blogger Vladlen Tatarsky.
She showed no visible emotion in response to the sentence, which Russian media said was the [longest] given to any woman in the country's modern history. ...
Trepova said she had been set up, and had thought the statuette contained a listening device, not a bomb. ...
The defence said Trepova too was a victim because, sitting only several metres from Tatarsky, she could herself have been killed or wounded. ..."
"... The former bank robber-turned blogger died when a bomb concealed in a statuette of his likeness that was handed to him in a St. Petersburg, Russia, cafe last April exploded. More than 50 people were injured in the blast, authorities said. ..."
Woman Given 27 Years for the Killing of Pro-War Blogger in Russian Cafe Bombing Attack strikes at the heart of Kremlin’s unofficial wartime propaganda machine
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