A short talk for Space Week given at Maynooth University on October 6th 2022 about cosmology, the large-scale structure of the Universe and the European Space Agency's Euclid Mission.
Open Access Publishing in Astrophysics and the Open Journal of AstrophysicsPeter Coles
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Open Access Publishing in Astrophysics and the Open Journal of AstrophysicsPeter Coles
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Open Access Publishing and the Open Journal of AstrophysicsPeter Coles
A short talk given at the 'Astronomy Tea' at the University of Sydney, Australia, on February 19th 2024.
Abstract:
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Talk given at the Institut de Physique Théorique, Paris-Saclay, 28th November 2023.
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s, thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I discuss the environment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Slides for seminar given at Cardiff University on 1st November 2023, covering Open Access publishing in astrophysics with reference to the Open Journal of Astrophysics.
Public evening talk given on 6th September 2023 at an event called "Weird Matter at Maynooth University". Euclid is the name of a new scientific mission from the European Space Agency, launched on July 1st, designed to explore the composition and evolution of the Universe. The Euclid mission takes its name from the ancient Greek mathematician regarded by many as the Father of geometry. Until the last century, Euclid’s theorems were assumed not just to be mathematical notions, but to describe the geometrical structure of the physical Universe. Einstein’s general theory of relativity swept that idea aside and gave us new ways of describing space, by unifying it with time, and by allowing it to be affected by matter in a manner very different from that formulated by Euclid. Over the past century, this theory has proved to be very effective at describing the properties of the Universe as observed by modern astronomical telescopes, while also suggesting the existence of dark matter and dark energy.
The Euclid telescope will create an enormous map of the large-scale structure of the Universe across space and time by observing billions of galaxies out to 10 billion light-years, across more than a third of the sky. Euclid will explore how the Universe has expanded and how galaxies and clusters of galaxies have formed over cosmic history, and how space itself is distorted by these structures.
This talk discusses our modern ideas of space and time, how the Euclid mission will try to test whether or not they are correct and shed light on the nature of dark matter and dark energy.
Talk given at the Irish National Astronomy Meeting: a discussion of recent developments in Open Access Publishing, with particular reference to Astrophysics and the Open Journal of Astrophysics
Talk given at ITP 2022 at the Dublin Institute for Advanced Study on May 26th 2022. In this talk I discuss some applications of the Schrodinger-Poisson wave-mechanical approach to
cosmological structure formation. The most obvious use of this formalism is to "fuzzy" dark matter,
i.e. dark matter consisting of extremely light particles whose eective de Broglie wavelength is
suciently large to be astrophysically relevant, but it can be used to model more general scenarios
and has a number of advantages over standard methods based on Eulerian perturbation theory. I
illustrate the formalism with some calculations for cosmic voids and discuss its application to the
cosmological reconstruction problem(s).
Open Access Publishing in Astrophysics and the Open Journal of AstrophysicsPeter Coles
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Open Access Publishing in Astrophysics and the Open Journal of AstrophysicsPeter Coles
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Open Access Publishing and the Open Journal of AstrophysicsPeter Coles
A short talk given at the 'Astronomy Tea' at the University of Sydney, Australia, on February 19th 2024.
Abstract:
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I shall discuss the ennvironment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I will also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Talk given at the Institut de Physique Théorique, Paris-Saclay, 28th November 2023.
Over the past decade, the landscape of academic publishing has changed dramatically, with publishers moving from subscription-based models to "open access" in which papers are available to read free of charge. Many journals have made the decision to maintain revenue by charging authors for this, via so-called "Article Processing Charges" (APCs) which can run to $1000s, thereby closing the door on those without funds to pay. More recently, there have been moves to encourage researchers to publish using "Diamond" Open Access wherein papers are published without charge to the authors and without cost to the reader. In this talk I discuss the environment for Open Access Publishing in Astrophysics with reference to the Open Journal of Astrophysics (OJAp), which offers a not-for-profit service of this kind using an arXiv-overlay model. I also offer a possible vision of the future of truly "Open Access" publishing based on a global network of institutional and/or subject-based repositories.
Slides for seminar given at Cardiff University on 1st November 2023, covering Open Access publishing in astrophysics with reference to the Open Journal of Astrophysics.
Public evening talk given on 6th September 2023 at an event called "Weird Matter at Maynooth University". Euclid is the name of a new scientific mission from the European Space Agency, launched on July 1st, designed to explore the composition and evolution of the Universe. The Euclid mission takes its name from the ancient Greek mathematician regarded by many as the Father of geometry. Until the last century, Euclid’s theorems were assumed not just to be mathematical notions, but to describe the geometrical structure of the physical Universe. Einstein’s general theory of relativity swept that idea aside and gave us new ways of describing space, by unifying it with time, and by allowing it to be affected by matter in a manner very different from that formulated by Euclid. Over the past century, this theory has proved to be very effective at describing the properties of the Universe as observed by modern astronomical telescopes, while also suggesting the existence of dark matter and dark energy.
The Euclid telescope will create an enormous map of the large-scale structure of the Universe across space and time by observing billions of galaxies out to 10 billion light-years, across more than a third of the sky. Euclid will explore how the Universe has expanded and how galaxies and clusters of galaxies have formed over cosmic history, and how space itself is distorted by these structures.
This talk discusses our modern ideas of space and time, how the Euclid mission will try to test whether or not they are correct and shed light on the nature of dark matter and dark energy.
Talk given at the Irish National Astronomy Meeting: a discussion of recent developments in Open Access Publishing, with particular reference to Astrophysics and the Open Journal of Astrophysics
Talk given at ITP 2022 at the Dublin Institute for Advanced Study on May 26th 2022. In this talk I discuss some applications of the Schrodinger-Poisson wave-mechanical approach to
cosmological structure formation. The most obvious use of this formalism is to "fuzzy" dark matter,
i.e. dark matter consisting of extremely light particles whose eective de Broglie wavelength is
suciently large to be astrophysically relevant, but it can be used to model more general scenarios
and has a number of advantages over standard methods based on Eulerian perturbation theory. I
illustrate the formalism with some calculations for cosmic voids and discuss its application to the
cosmological reconstruction problem(s).
Astrophysics & Cosmology Masterclass November 2021Peter Coles
Slides used during a Science Week event at Maynooth University on 12th November 2021. These are the slides for the Cosmology part of the event which was run by Peter Coles and John Regan of the Department of Theoretical Physics at Maynooth University.
The O-level Latin examinations I took in 1979. There are three papers altogether, Paper 1 which was a language examination, and Paper 2 (in two Sections A and B) which were about set books: we did Book II of Virgil's Aeneid and Book V of Caesar's De Bello Gallico.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Astrophysics & Cosmology Masterclass November 2021Peter Coles
Slides used during a Science Week event at Maynooth University on 12th November 2021. These are the slides for the Cosmology part of the event which was run by Peter Coles and John Regan of the Department of Theoretical Physics at Maynooth University.
The O-level Latin examinations I took in 1979. There are three papers altogether, Paper 1 which was a language examination, and Paper 2 (in two Sections A and B) which were about set books: we did Book II of Virgil's Aeneid and Book V of Caesar's De Bello Gallico.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
17. Dark Matter…..
• Most of the matter in the Universe
is dark..
• “Dark Matter” can be detected in
galaxies and galaxy clusters…
• ..and in the space between them
18.
19.
20.
21.
22.
23. Dark Energy
• The “Cosmological Constant” () was
introduced by Einstein to make a static
universe (his “biggest blunder”)
• Now we think of as “vacuum energy”
that causes the expansion Universe to
speed up..
• The vacuum energy is directly
connected to the microscopic physics of
elementary particles.