This document proposes and evaluates different approaches for performing real-time 3D wavelet lifting. It finds that a true 3D approach that processes all dimensions within a single loop outperforms naive approaches that process each dimension sequentially. This true 3D approach achieves an 11.7x speedup on Intel Core2 and 8x speedup on AMD Opteron CPUs compared to the best naive approach due to being more CPU cache and SIMD friendly.
Poster presentation at Zienkiewicz Centre for Computational Engineering (ZCCE) annual workshop 2018.
Best poster award!
http://www.swansea.ac.uk/engineering/zcce/conferences/postgraduate-workshop-2018/
1H/31P 3D MRSI at 3T with Novel Rosette k-space Trajectory with compressed se...Uzay Emir
1H/31P 3D MRSI at 3T with Novel Rosette k-space Trajectory with compressed sensing reconstruction
Bozymski B, Shen X, Özen A, Ilbey S, Thomas MA, Chiew M, Dydak U, Emir UE. Ultra-Short Echo Time 31P 3D MRSI at 3T with Novel Rosette k-space Trajectory, International Society for Magnetic Resonance in Medicine Annual Meeting 2022
Lifting Scheme Cores for Wavelet TransformDavid Bařina
The thesis focuses on efficient computation of the two-dimensional discrete wavelet transform. The state-of-the-art methods are extended in several ways to perform the transform in a single loop, possibly in multi-scale fashion, using a compact streaming core. This core can further be appropriately reorganized to target the minimization of certain platform resources. The approach presented here nicely fits into common SIMD extensions, exploits the cache hierarchy of modern general-purpose processors, and is suitable for parallel evaluation. Finally, the approach presented is incorporated into the JPEG 2000 compression chain, in which it has proved to be fundamentally faster than widely used implementations.
Modified Adaptive Lifting Structure Of CDF 9/7 Wavelet With Spiht For Lossy I...idescitation
We present a modified structure of 2-D cdf 9/7 wavelet
transforms based on adaptive lifting in image coding. Instead
of alternately applying horizontal and vertical lifting, as in
present practice, Adaptive lifting performs lifting-based
prediction in local windows in the direction of high pixel
correlation. Hence, it adapts far better to the image orientation
features in local windows. The predicting and updating signals
of Adaptive lifting can be derived even at the fractional pixel
precision level to achieve high resolution, while still
maintaining perfect reconstruction. To enhance the
performance of adaptive based modified structure of 2-D CDF
9/7 is coupled with SPIHT coding algorithm to improve the
drawbacks of wavelet transform. Experimental results show
that the proposed modified scheme based image coding
technique outperforms JPEG 2000 in both PSNR and visual
quality, with the improvement up to 6.0 dB than existing
structure on images with rich orientation features .
SVD and Lifting Wavelet Based Fragile Image WatermarkingIDES Editor
Creation and distribution of digital multimedia, by
copying and editing, has both advantages and disadvantages.
These can facilitate unauthorized usage, misappropriation,
and misrepresentation. Therefore the content providers have
become more concerned. So image watermarking, which is the
act of embedding another signal (the watermark) into an
image, have been proposed for copyright protection and
authentication by robust and fragile methodologies
respectively. So for various applications, there are different
watermarking algorithms, but here this work is mainly for
authentication as the watermarking scheme is fragile. The
discrete lifting based wavelet transform and the singular value
decomposition (SVD) algorithms are used in this scheme. The
former for the carrier or the image to be authenticated, while
the latter for the logo which is embedded in the carrier. The
distribution of SVD compressed pixel values are distributed in
the wavelet domain based on a pseudorandom sequence. This
has been observed to test the integrity of the stego image and
its authentication. Moreover due to usage of lifting based
wavelet transform and SVD the hardware implementability is
better.
The two-dimensional discrete wavelet transform (DWT) can be applied in the heart of many image-processing algorithms.
Until recently, several studies have compared the performance of such transform on parallel architectures, for example, on graphics
processing units (GPUs). All these studies however considered only separable calculation schedules.
Poster presentation at Zienkiewicz Centre for Computational Engineering (ZCCE) annual workshop 2018.
Best poster award!
http://www.swansea.ac.uk/engineering/zcce/conferences/postgraduate-workshop-2018/
1H/31P 3D MRSI at 3T with Novel Rosette k-space Trajectory with compressed se...Uzay Emir
1H/31P 3D MRSI at 3T with Novel Rosette k-space Trajectory with compressed sensing reconstruction
Bozymski B, Shen X, Özen A, Ilbey S, Thomas MA, Chiew M, Dydak U, Emir UE. Ultra-Short Echo Time 31P 3D MRSI at 3T with Novel Rosette k-space Trajectory, International Society for Magnetic Resonance in Medicine Annual Meeting 2022
Lifting Scheme Cores for Wavelet TransformDavid Bařina
The thesis focuses on efficient computation of the two-dimensional discrete wavelet transform. The state-of-the-art methods are extended in several ways to perform the transform in a single loop, possibly in multi-scale fashion, using a compact streaming core. This core can further be appropriately reorganized to target the minimization of certain platform resources. The approach presented here nicely fits into common SIMD extensions, exploits the cache hierarchy of modern general-purpose processors, and is suitable for parallel evaluation. Finally, the approach presented is incorporated into the JPEG 2000 compression chain, in which it has proved to be fundamentally faster than widely used implementations.
Modified Adaptive Lifting Structure Of CDF 9/7 Wavelet With Spiht For Lossy I...idescitation
We present a modified structure of 2-D cdf 9/7 wavelet
transforms based on adaptive lifting in image coding. Instead
of alternately applying horizontal and vertical lifting, as in
present practice, Adaptive lifting performs lifting-based
prediction in local windows in the direction of high pixel
correlation. Hence, it adapts far better to the image orientation
features in local windows. The predicting and updating signals
of Adaptive lifting can be derived even at the fractional pixel
precision level to achieve high resolution, while still
maintaining perfect reconstruction. To enhance the
performance of adaptive based modified structure of 2-D CDF
9/7 is coupled with SPIHT coding algorithm to improve the
drawbacks of wavelet transform. Experimental results show
that the proposed modified scheme based image coding
technique outperforms JPEG 2000 in both PSNR and visual
quality, with the improvement up to 6.0 dB than existing
structure on images with rich orientation features .
SVD and Lifting Wavelet Based Fragile Image WatermarkingIDES Editor
Creation and distribution of digital multimedia, by
copying and editing, has both advantages and disadvantages.
These can facilitate unauthorized usage, misappropriation,
and misrepresentation. Therefore the content providers have
become more concerned. So image watermarking, which is the
act of embedding another signal (the watermark) into an
image, have been proposed for copyright protection and
authentication by robust and fragile methodologies
respectively. So for various applications, there are different
watermarking algorithms, but here this work is mainly for
authentication as the watermarking scheme is fragile. The
discrete lifting based wavelet transform and the singular value
decomposition (SVD) algorithms are used in this scheme. The
former for the carrier or the image to be authenticated, while
the latter for the logo which is embedded in the carrier. The
distribution of SVD compressed pixel values are distributed in
the wavelet domain based on a pseudorandom sequence. This
has been observed to test the integrity of the stego image and
its authentication. Moreover due to usage of lifting based
wavelet transform and SVD the hardware implementability is
better.
The two-dimensional discrete wavelet transform (DWT) can be applied in the heart of many image-processing algorithms.
Until recently, several studies have compared the performance of such transform on parallel architectures, for example, on graphics
processing units (GPUs). All these studies however considered only separable calculation schedules.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
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 .
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.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
6. Naive Approaches
Naive Vertical
foreach dimension do /* X, Y, Z axis */
foreach sample do
foreach lifting do
step;
end
end
end
huge amount of cache misses
three passes through the data
8. 2-D Approach
2-D Slices
foreach slice do
foreach sample do
foreach lifting do step; /* X axis */
foreach lifting do step; /* Y axis */
end
end
/* Z axis */
foreach sample do
foreach lifting do step;
end
42 core with SIMD
10. 3-D Approach
True 3-D
foreach sample do
foreach lifting do step; /* X axis */
foreach lifting do step; /* Y axis */
foreach lifting do step; /* Z axis */
end
23 cube
43 with SIMD