Researchers at the University of Toronto developed a novel clustering algorithm called affinity propagation that is able to cluster large amounts of data without predetermining the number of groups or examples. The algorithm works by sending messages between data points to maximize similarity within groups. It was shown to cluster various types of data like gene expressions, images, and network data much faster than traditional clustering methods. The affinity propagation algorithm provides an intuitive way to cluster complex data and could be useful for analyzing biological data.
Dr Kad's talk summarized his lab's work using single molecule approaches to study nucleotide excision repair in prokaryotes. While prokaryotic nucleotide excision repair involves only 6 proteins compared to 30+ in eukaryotes, the interactions between the 6 proteins are complex. His lab uses DNA "tightropes" stretched between beads to observe individual repair protein interactions, finding that the UvrA protein does not slide along DNA as expected but instead binds and dissociates across the strand, while UvrAB complex slides to scan for damage.
This document is a slideshow presentation by Dr. Ken Biegeleisen on topologically non-linked ("TN") DNA. It discusses the history of the double helix model of DNA and alternative theories proposing that DNA may take non-helical structures inside cells. It notes that early researchers like Cairns, who discovered circular bacterial chromosomes, did not adequately consider issues like how circular DNA could replicate without unwinding and rewinding thousands of twists each replication cycle. The presentation examines evidence supporting the idea that DNA may take non-helical, topologically non-linked conformations in vivo.
The nucleus is the largest organelle in eukaryotic cells, taking up about 10% of the cell volume. It houses most of the cell's DNA and controls its metabolic and hereditary activities. The nucleus is enclosed by a double membrane with nuclear pores that regulate transport between the nucleus and cytoplasm. Inside the nucleus are nucleoplasm, nucleolus, and chromatin containing the cell's chromosomes. The nuclear envelope, nuclear lamina, and nuclear pores play important roles in controlling nuclear structure and transport.
The document summarizes key points about the origin of cells:
1. Cell theory states that all living things are made of cells, the cell is the smallest unit of life, and cells only come from pre-existing cells.
2. Pasteur's experiments in 1864 disproved spontaneous generation and provided evidence that cells only arise from other cells.
3. Miller and Urey's experiments in 1953 simulated early Earth conditions and formed simple organic molecules like amino acids, providing evidence that the first cells could have originated from non-living materials.
4. The endosymbiotic theory explains the origin of eukaryotic cells, proposing that organelles like mitochondria and chloroplasts originally came from
This document discusses the discovery of the DNA double helix structure in 1953 by James Watson and Francis Crick. It describes how earlier research on DNA structure using X-ray diffraction, conducted by Maurice Wilkins, Rosalind Franklin, and Raymond Gosling at King's College London, provided key data that enabled Watson and Crick to deduce the double helix model. The document also discusses the early investigations into DNA structure, reactions to the double helix model when it was announced, and how later work confirmed that DNA is the genetic material.
This document summarizes a lecture about DNA replication. It discusses why DNA needs to be replicated to pass genetic information from one generation of cells or organisms to the next. It introduces the three proposed models of DNA replication - conservative, dispersive, and semi-conservative - and describes the famous Meselson-Stahl experiment that used nitrogen isotopes to prove that DNA replicates in a semi-conservative manner, where each new double strand contains one original strand and one newly synthesized strand. The experiment demonstrated that DNA replication follows the semi-conservative model.
The RNA world hypothesis proposes that RNA, not DNA or proteins, was the first self-replicating molecule and the central player in early life. RNA can both store genetic information and catalyze chemical reactions, acting as both the genome and enzymes. Evidence for this includes the discovery that some RNA molecules can self-replicate and that the ribosome, the cell's protein-building machinery, has RNA as its key component. While still debated, the RNA world hypothesis provides a plausible explanation for how life could have originated and evolved prior to the development of DNA and proteins.
Dr Kad's talk summarized his lab's work using single molecule approaches to study nucleotide excision repair in prokaryotes. While prokaryotic nucleotide excision repair involves only 6 proteins compared to 30+ in eukaryotes, the interactions between the 6 proteins are complex. His lab uses DNA "tightropes" stretched between beads to observe individual repair protein interactions, finding that the UvrA protein does not slide along DNA as expected but instead binds and dissociates across the strand, while UvrAB complex slides to scan for damage.
This document is a slideshow presentation by Dr. Ken Biegeleisen on topologically non-linked ("TN") DNA. It discusses the history of the double helix model of DNA and alternative theories proposing that DNA may take non-helical structures inside cells. It notes that early researchers like Cairns, who discovered circular bacterial chromosomes, did not adequately consider issues like how circular DNA could replicate without unwinding and rewinding thousands of twists each replication cycle. The presentation examines evidence supporting the idea that DNA may take non-helical, topologically non-linked conformations in vivo.
The nucleus is the largest organelle in eukaryotic cells, taking up about 10% of the cell volume. It houses most of the cell's DNA and controls its metabolic and hereditary activities. The nucleus is enclosed by a double membrane with nuclear pores that regulate transport between the nucleus and cytoplasm. Inside the nucleus are nucleoplasm, nucleolus, and chromatin containing the cell's chromosomes. The nuclear envelope, nuclear lamina, and nuclear pores play important roles in controlling nuclear structure and transport.
The document summarizes key points about the origin of cells:
1. Cell theory states that all living things are made of cells, the cell is the smallest unit of life, and cells only come from pre-existing cells.
2. Pasteur's experiments in 1864 disproved spontaneous generation and provided evidence that cells only arise from other cells.
3. Miller and Urey's experiments in 1953 simulated early Earth conditions and formed simple organic molecules like amino acids, providing evidence that the first cells could have originated from non-living materials.
4. The endosymbiotic theory explains the origin of eukaryotic cells, proposing that organelles like mitochondria and chloroplasts originally came from
This document discusses the discovery of the DNA double helix structure in 1953 by James Watson and Francis Crick. It describes how earlier research on DNA structure using X-ray diffraction, conducted by Maurice Wilkins, Rosalind Franklin, and Raymond Gosling at King's College London, provided key data that enabled Watson and Crick to deduce the double helix model. The document also discusses the early investigations into DNA structure, reactions to the double helix model when it was announced, and how later work confirmed that DNA is the genetic material.
This document summarizes a lecture about DNA replication. It discusses why DNA needs to be replicated to pass genetic information from one generation of cells or organisms to the next. It introduces the three proposed models of DNA replication - conservative, dispersive, and semi-conservative - and describes the famous Meselson-Stahl experiment that used nitrogen isotopes to prove that DNA replicates in a semi-conservative manner, where each new double strand contains one original strand and one newly synthesized strand. The experiment demonstrated that DNA replication follows the semi-conservative model.
The RNA world hypothesis proposes that RNA, not DNA or proteins, was the first self-replicating molecule and the central player in early life. RNA can both store genetic information and catalyze chemical reactions, acting as both the genome and enzymes. Evidence for this includes the discovery that some RNA molecules can self-replicate and that the ribosome, the cell's protein-building machinery, has RNA as its key component. While still debated, the RNA world hypothesis provides a plausible explanation for how life could have originated and evolved prior to the development of DNA and proteins.
The document discusses Yoshinori Ohsumi winning the 2016 Nobel Prize in Physiology or Medicine for his decades of research elucidating autophagy, the process by which cells recycle their own contents. Ohsumi's work changed the understanding of this fundamental cellular process and has implications for developing potential treatments for chronic diseases. As a researcher, Ohsumi focused solely on science rather than accolades, though he had dreamed of receiving the Nobel Prize as a child.
Peter Agre discovered the first water channel protein (aquaporin) in the early 1990s. Aquaporins allow water to pass through cell membranes while preventing the passage of ions or other molecules. Roderick MacKinnon succeeded in determining the atomic structure of ion channels in 1998, opening up new areas of research. Together, their discoveries of water and ion channels helped explain how cells regulate the transport of water and ions, fundamental to cellular functions and communication between cells. Defects in these channels can cause diseases.
Biotecnika Times Newspaper 6th December 2018shekhar suman
This summary provides the key details from the multi-page document in 3 sentences:
The document reports on recent scientific studies, including the development of a new type of biological data recorder using genetically modified E. coli bacteria. It also describes new "kill switch" mechanisms engineered into bacteria to ensure they self-destruct under certain conditions. Additionally, the document summarizes a study that found the process of clearing dying cancer cells (efferocytosis) can unexpectedly promote tumor growth in bone metastases of prostate cancer by stimulating the release of a pro-inflammatory protein.
This document discusses two main theories for how enzyme systems evolved: retrograde evolution and patchwork evolution. Retrograde evolution proposes that pathways evolve backwards, with newer reactions preceding existing ones. Patchwork evolution suggests that enzymes initially had broad specificities and specialized over time through gene duplication. While some evidence supports retrograde evolution, more data favors patchwork evolution. However, the CS2 hydrolase enzyme appears to be an exception, as its structure and function indicate it did not evolve but was purposefully designed. In conclusion, the theories of enzyme evolution are still being refined as exceptions are discovered.
The presentation deals with evolution of enzyme systems especially retrograde and patchwork.The presentation also deals with the case study on enzyme CS2 hydrolase and its evolution hypothesis
This document summarizes a paper on computational modeling of astrocytes. It discusses:
1) The biological roles of astrocytes in the brain and evidence they play a role in complexity.
2) Existing models of artificial neural-astrocyte networks (ANAN) that aim to model astrocyte functions, including penultimate ANAN, genetic ANAN, and self-organized map ANAN.
3) Challenges in constructing adequate learning algorithms for ANAN given their complexity.
Robert Hooke discovered cells in 1665 using an early microscope. He observed the structures of cork cells. The development of electron microscopes in the 1930s allowed scientists to view cells and organelles at much higher magnifications. Key discoveries included the nucleus by Brown in 1831, living cells by Van Leeuwenhoek in 1674, and the proposal of the cell theory by Schleiden, Schwann, and Virchow from 1838-1858 stating that cells are the fundamental unit of life. Plant cells have additional structures like a cell wall and chloroplasts. The main components of plant cells are the cell membrane, cytoplasm, and nucleus. The nucleus contains DNA and controls the cell.
The document discusses synapses, the connections between neurons that allow neuronal communication. It begins by discussing the history and etymology of the term "synapse", which was coined in 1897. It then defines synapses and describes their basic anatomical components. The rest of the document classifies synapses based on various properties like location, effect, basis of process, transmitter, and junction type. It also discusses the synaptic vesicle cycle of trafficking neurotransmitters and fusing with the neuronal membrane. Debate around different modes of vesicle fusion like "kiss-and-run" is also summarized.
INTRODUCTION TO CELLS
INTRODUCTION TO CELL THEORY
HISTORY
FORMULATION OF CELL THEORY
CLASSICAL CELL THEORY
DRAWBACKS OF CLASSICAL THEORY
MORDEN CELL THEORY
EXCEPTION OF CELL THEORY
SIGNIFICANCE OF CELL THEORY
HOW HAS THE CELL THEORY BEEN USED
CONCLUSION
This document discusses the ethical issues surrounding human cloning. It provides a brief history of cloning, noting that the concept originated from botany but now refers to identical genetic copies of organisms produced artificially. The document outlines the differences between sexual reproduction and cloning by nuclear transfer. Recent advances in cloning research on animals are also examined. The ethical issues of research cloning versus reproductive cloning, and the potential for adult stem cells to replace embryonic stem cells, are explored. The international community's discussion on regulating cloning is also summarized.
Review and development of techniques for studying cellular biophysics with hi...Michael Butler
This thesis investigates techniques for studying cellular biophysics with high frequency ultrasound. It reviews theories of acoustic wave interactions at the molecular level and cellular scale. Experimental work develops thin film aluminum nitride and lithium niobate crystal transducers for generating broadband ultrasound up to 140 MHz. Preliminary testing of these transducers is presented along with the design of a broadband acoustic spectrometry system to study the effects of high frequency sound on actin polymerization in vitro.
Can a biologist fix a radio or what i learned while studying apoptosisSantosh Kathwate
This document summarizes a biologist's experience studying apoptosis and his realization that the lack of a standardized language to describe biological systems contributes to increasing confusion in the field despite accumulating data. The biologist uses the analogy of trying to fix an old radio without an engineering approach to illustrate how biologists approach complex biological problems in an experimental rather than quantitative way. He argues that developing a standardized, quantitative language for biology similar to what engineers use could help overcome increasing complexity and paradoxes in rapidly advancing fields.
The document discusses the cell theory, which states that all living things are made up of cells, cells carry out functions needed to support life, and cells only come from pre-existing cells. It describes how the cell theory was developed over 200 years through the work of scientists like Hooke, Pasteur, and Virchow. The cell theory gives us a foundation for understanding living things and cells. It has endured and remained largely unchanged for over 150 years despite new details being discovered. The cell theory helped develop a better understanding of how cells work.
Central nervous system neurons are unable to regenerate unlike peripheral nervous system neurons due to inhibitory factors and low cAMP levels in the central nervous system. However, if peripheral and central nervous system branches are separated, the peripheral branch can cause cAMP levels to rise and allow the central branch to regrow. This research aims to develop a genetically manipulable model to identify molecules regulating axon regeneration. Caenorhabditis elegans is a suitable model as it has a simple nervous system with identifiable axon paths and synapses, as well as being small and transparent, and its genes, regeneration patterns, and mechanisms are similar to vertebrates.
Evolution Vs Macroevolution Research PaperKatie Parker
The document discusses the theories of evolution and intelligent design as explanations for the origin of life. It provides definitions of key concepts like creation, intelligent design, and natural processes. The document also notes some of the perspectives Christians have regarding the origin of life based on accounts in the Bible, as well as examples evolutionists use regarding traits evolving through natural selection over time.
This document summarizes recent research on action potential initiation and propagation in neurons. It discusses how direct recordings from axons have provided new insights beyond what is known from somatic recordings alone. Specifically, it finds that axons contain distinct collections of ion channels compared to somatodendritic compartments. This allows axons to exhibit more computational power in determining spike threshold and waveform than traditionally thought. The document reviews sodium channel subtypes, localization, development, and roles in shaping firing properties and ensuring reliable propagation.
DNA
its Discovery
Who Discovered DNA?
Credit for who first identified DNA is often mistakenly given to James Watson and Francis Crick, who just furthered Miescher’s discovery with their own groundbreaking research nearly 100 years later. Watson and Crick contributed largely to our understanding of DNA in terms of genetic inheritance, but much like Miescher, long before their work, others also made great advancements in and contributions to the field.
In 1866, before many significant discoveries and findings, Gregor Mendel was the first to suggest that characteristics are passed down from generation to generation. Mendel coined the terms as recessive and dominant.
In 1869, Friedrich Miescher identified the “nuclein” by isolating a molecule from a cell nucleus that would later become known as DNA.
In 1881, Nobel Prize winner and German biochemist Albrecht Kossel, who is credited with naming DNA, identified nuclein as a nucleic acid. He also isolated those five nitrogen bases that are now considered to be the basic building blocks of DNA and RNA: adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U) in case of RNA).
In 1882, Walther Fleming devoted research and time to cytology, which is the study of chromosomes. He discovered mitosis in 1882 when he was the first biologist to execute a wholly systematic study of the division of chromosomes. His observations that chromosomes double is significant to the later discovered theory of inheritance.
In Early 1900s, Theodor Boveri and Walter Sutton were independently working on what’s now known as the Boveri-Sutton chromosome theory, or the chromosomal theory of inheritance. Their findings are fundamental in our understanding of how chromosomes carry genetic material and pass it down from one generation to the next.
In 1902, Mendel’s theories were finally associated with a human disease by Sir Archibald Edward Garrod, who published the first findings from a study on recessive inheritance in human beings in 1902. Garrod opened the door for our understanding of genetic disorders resulting from errors in chemical pathways in the body.
In 1944, Oswald Avery first outlined DNA as the transforming principle, which essentially means that DNA transform cell properties.
The document is Michael Järvå's thesis for a Doctor of Philosophy degree in Natural Sciences from the University of Gothenburg, in which he studies the structure and function of the spinach aquaporin SoPIP2;1 using X-ray crystallography and scattering techniques to better understand how it is regulated by factors like pH, calcium, and mercury. The thesis includes 4 papers on topics like the pH-gating mechanism, calcium binding sites, mercury's activating effect, and using nanodiscs and scattering to study the protein's structure.
Aquaporins are integral membrane proteins that form pores to transport water molecules across cell membranes. They are essential for water transport in plants, allowing for rapid movement of water and tolerance to drought. Aquaporin proteins form tetramers and contain six transmembrane helices arranged in a bundle, with loops containing highly conserved amino acid motifs like NPA that help orient water molecules as they pass through the narrow pore. Aquaporins are found in many organisms including plants, bacteria, and humans where they play important roles in tissue hydration and fluid transport.
This document contains two news articles from ScienceDaily discussing recent scientific findings. The first article describes research from UTMB that identified an enzyme called NEIL1 that fixes single-stranded DNA during cell replication. The second article discusses a study finding that biomolecules like DNA and proteins can spontaneously cluster together to form protocells in salty solutions, providing insight into how early cells may have originated. The student provides observations on the potential medical applications of this research, such as using synthetic cells for tissue regeneration and treating diseases through improved gene editing.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
The document discusses Yoshinori Ohsumi winning the 2016 Nobel Prize in Physiology or Medicine for his decades of research elucidating autophagy, the process by which cells recycle their own contents. Ohsumi's work changed the understanding of this fundamental cellular process and has implications for developing potential treatments for chronic diseases. As a researcher, Ohsumi focused solely on science rather than accolades, though he had dreamed of receiving the Nobel Prize as a child.
Peter Agre discovered the first water channel protein (aquaporin) in the early 1990s. Aquaporins allow water to pass through cell membranes while preventing the passage of ions or other molecules. Roderick MacKinnon succeeded in determining the atomic structure of ion channels in 1998, opening up new areas of research. Together, their discoveries of water and ion channels helped explain how cells regulate the transport of water and ions, fundamental to cellular functions and communication between cells. Defects in these channels can cause diseases.
Biotecnika Times Newspaper 6th December 2018shekhar suman
This summary provides the key details from the multi-page document in 3 sentences:
The document reports on recent scientific studies, including the development of a new type of biological data recorder using genetically modified E. coli bacteria. It also describes new "kill switch" mechanisms engineered into bacteria to ensure they self-destruct under certain conditions. Additionally, the document summarizes a study that found the process of clearing dying cancer cells (efferocytosis) can unexpectedly promote tumor growth in bone metastases of prostate cancer by stimulating the release of a pro-inflammatory protein.
This document discusses two main theories for how enzyme systems evolved: retrograde evolution and patchwork evolution. Retrograde evolution proposes that pathways evolve backwards, with newer reactions preceding existing ones. Patchwork evolution suggests that enzymes initially had broad specificities and specialized over time through gene duplication. While some evidence supports retrograde evolution, more data favors patchwork evolution. However, the CS2 hydrolase enzyme appears to be an exception, as its structure and function indicate it did not evolve but was purposefully designed. In conclusion, the theories of enzyme evolution are still being refined as exceptions are discovered.
The presentation deals with evolution of enzyme systems especially retrograde and patchwork.The presentation also deals with the case study on enzyme CS2 hydrolase and its evolution hypothesis
This document summarizes a paper on computational modeling of astrocytes. It discusses:
1) The biological roles of astrocytes in the brain and evidence they play a role in complexity.
2) Existing models of artificial neural-astrocyte networks (ANAN) that aim to model astrocyte functions, including penultimate ANAN, genetic ANAN, and self-organized map ANAN.
3) Challenges in constructing adequate learning algorithms for ANAN given their complexity.
Robert Hooke discovered cells in 1665 using an early microscope. He observed the structures of cork cells. The development of electron microscopes in the 1930s allowed scientists to view cells and organelles at much higher magnifications. Key discoveries included the nucleus by Brown in 1831, living cells by Van Leeuwenhoek in 1674, and the proposal of the cell theory by Schleiden, Schwann, and Virchow from 1838-1858 stating that cells are the fundamental unit of life. Plant cells have additional structures like a cell wall and chloroplasts. The main components of plant cells are the cell membrane, cytoplasm, and nucleus. The nucleus contains DNA and controls the cell.
The document discusses synapses, the connections between neurons that allow neuronal communication. It begins by discussing the history and etymology of the term "synapse", which was coined in 1897. It then defines synapses and describes their basic anatomical components. The rest of the document classifies synapses based on various properties like location, effect, basis of process, transmitter, and junction type. It also discusses the synaptic vesicle cycle of trafficking neurotransmitters and fusing with the neuronal membrane. Debate around different modes of vesicle fusion like "kiss-and-run" is also summarized.
INTRODUCTION TO CELLS
INTRODUCTION TO CELL THEORY
HISTORY
FORMULATION OF CELL THEORY
CLASSICAL CELL THEORY
DRAWBACKS OF CLASSICAL THEORY
MORDEN CELL THEORY
EXCEPTION OF CELL THEORY
SIGNIFICANCE OF CELL THEORY
HOW HAS THE CELL THEORY BEEN USED
CONCLUSION
This document discusses the ethical issues surrounding human cloning. It provides a brief history of cloning, noting that the concept originated from botany but now refers to identical genetic copies of organisms produced artificially. The document outlines the differences between sexual reproduction and cloning by nuclear transfer. Recent advances in cloning research on animals are also examined. The ethical issues of research cloning versus reproductive cloning, and the potential for adult stem cells to replace embryonic stem cells, are explored. The international community's discussion on regulating cloning is also summarized.
Review and development of techniques for studying cellular biophysics with hi...Michael Butler
This thesis investigates techniques for studying cellular biophysics with high frequency ultrasound. It reviews theories of acoustic wave interactions at the molecular level and cellular scale. Experimental work develops thin film aluminum nitride and lithium niobate crystal transducers for generating broadband ultrasound up to 140 MHz. Preliminary testing of these transducers is presented along with the design of a broadband acoustic spectrometry system to study the effects of high frequency sound on actin polymerization in vitro.
Can a biologist fix a radio or what i learned while studying apoptosisSantosh Kathwate
This document summarizes a biologist's experience studying apoptosis and his realization that the lack of a standardized language to describe biological systems contributes to increasing confusion in the field despite accumulating data. The biologist uses the analogy of trying to fix an old radio without an engineering approach to illustrate how biologists approach complex biological problems in an experimental rather than quantitative way. He argues that developing a standardized, quantitative language for biology similar to what engineers use could help overcome increasing complexity and paradoxes in rapidly advancing fields.
The document discusses the cell theory, which states that all living things are made up of cells, cells carry out functions needed to support life, and cells only come from pre-existing cells. It describes how the cell theory was developed over 200 years through the work of scientists like Hooke, Pasteur, and Virchow. The cell theory gives us a foundation for understanding living things and cells. It has endured and remained largely unchanged for over 150 years despite new details being discovered. The cell theory helped develop a better understanding of how cells work.
Central nervous system neurons are unable to regenerate unlike peripheral nervous system neurons due to inhibitory factors and low cAMP levels in the central nervous system. However, if peripheral and central nervous system branches are separated, the peripheral branch can cause cAMP levels to rise and allow the central branch to regrow. This research aims to develop a genetically manipulable model to identify molecules regulating axon regeneration. Caenorhabditis elegans is a suitable model as it has a simple nervous system with identifiable axon paths and synapses, as well as being small and transparent, and its genes, regeneration patterns, and mechanisms are similar to vertebrates.
Evolution Vs Macroevolution Research PaperKatie Parker
The document discusses the theories of evolution and intelligent design as explanations for the origin of life. It provides definitions of key concepts like creation, intelligent design, and natural processes. The document also notes some of the perspectives Christians have regarding the origin of life based on accounts in the Bible, as well as examples evolutionists use regarding traits evolving through natural selection over time.
This document summarizes recent research on action potential initiation and propagation in neurons. It discusses how direct recordings from axons have provided new insights beyond what is known from somatic recordings alone. Specifically, it finds that axons contain distinct collections of ion channels compared to somatodendritic compartments. This allows axons to exhibit more computational power in determining spike threshold and waveform than traditionally thought. The document reviews sodium channel subtypes, localization, development, and roles in shaping firing properties and ensuring reliable propagation.
DNA
its Discovery
Who Discovered DNA?
Credit for who first identified DNA is often mistakenly given to James Watson and Francis Crick, who just furthered Miescher’s discovery with their own groundbreaking research nearly 100 years later. Watson and Crick contributed largely to our understanding of DNA in terms of genetic inheritance, but much like Miescher, long before their work, others also made great advancements in and contributions to the field.
In 1866, before many significant discoveries and findings, Gregor Mendel was the first to suggest that characteristics are passed down from generation to generation. Mendel coined the terms as recessive and dominant.
In 1869, Friedrich Miescher identified the “nuclein” by isolating a molecule from a cell nucleus that would later become known as DNA.
In 1881, Nobel Prize winner and German biochemist Albrecht Kossel, who is credited with naming DNA, identified nuclein as a nucleic acid. He also isolated those five nitrogen bases that are now considered to be the basic building blocks of DNA and RNA: adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U) in case of RNA).
In 1882, Walther Fleming devoted research and time to cytology, which is the study of chromosomes. He discovered mitosis in 1882 when he was the first biologist to execute a wholly systematic study of the division of chromosomes. His observations that chromosomes double is significant to the later discovered theory of inheritance.
In Early 1900s, Theodor Boveri and Walter Sutton were independently working on what’s now known as the Boveri-Sutton chromosome theory, or the chromosomal theory of inheritance. Their findings are fundamental in our understanding of how chromosomes carry genetic material and pass it down from one generation to the next.
In 1902, Mendel’s theories were finally associated with a human disease by Sir Archibald Edward Garrod, who published the first findings from a study on recessive inheritance in human beings in 1902. Garrod opened the door for our understanding of genetic disorders resulting from errors in chemical pathways in the body.
In 1944, Oswald Avery first outlined DNA as the transforming principle, which essentially means that DNA transform cell properties.
The document is Michael Järvå's thesis for a Doctor of Philosophy degree in Natural Sciences from the University of Gothenburg, in which he studies the structure and function of the spinach aquaporin SoPIP2;1 using X-ray crystallography and scattering techniques to better understand how it is regulated by factors like pH, calcium, and mercury. The thesis includes 4 papers on topics like the pH-gating mechanism, calcium binding sites, mercury's activating effect, and using nanodiscs and scattering to study the protein's structure.
Aquaporins are integral membrane proteins that form pores to transport water molecules across cell membranes. They are essential for water transport in plants, allowing for rapid movement of water and tolerance to drought. Aquaporin proteins form tetramers and contain six transmembrane helices arranged in a bundle, with loops containing highly conserved amino acid motifs like NPA that help orient water molecules as they pass through the narrow pore. Aquaporins are found in many organisms including plants, bacteria, and humans where they play important roles in tissue hydration and fluid transport.
This document contains two news articles from ScienceDaily discussing recent scientific findings. The first article describes research from UTMB that identified an enzyme called NEIL1 that fixes single-stranded DNA during cell replication. The second article discusses a study finding that biomolecules like DNA and proteins can spontaneously cluster together to form protocells in salty solutions, providing insight into how early cells may have originated. The student provides observations on the potential medical applications of this research, such as using synthetic cells for tissue regeneration and treating diseases through improved gene editing.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/
DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
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- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
Best 20 SEO Techniques To Improve Website Visibility In SERPPixlogix Infotech
Boost your website's visibility with proven SEO techniques! Our latest blog dives into essential strategies to enhance your online presence, increase traffic, and rank higher on search engines. From keyword optimization to quality content creation, learn how to make your site stand out in the crowded digital landscape. Discover actionable tips and expert insights to elevate your SEO game.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Things to Consider When Choosing a Website Developer for your Website | FODUUFODUU
Choosing the right website developer is crucial for your business. This article covers essential factors to consider, including experience, portfolio, technical skills, communication, pricing, reputation & reviews, cost and budget considerations and post-launch support. Make an informed decision to ensure your website meets your business goals.
In his public lecture, Christian Timmerer provides insights into the fascinating history of video streaming, starting from its humble beginnings before YouTube to the groundbreaking technologies that now dominate platforms like Netflix and ORF ON. Timmerer also presents provocative contributions of his own that have significantly influenced the industry. He concludes by looking at future challenges and invites the audience to join in a discussion.
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During this demo, the founders of Secludy will demonstrate how their system utilizes Milvus to store and manipulate embeddings for generating privacy-protected synthetic data. Their approach not only maintains the confidentiality of the original data but also enhances the utility and scalability of LLMs under privacy constraints. Attendees, including machine learning engineers, data scientists, and data managers, will witness first-hand how Secludy's integration with Milvus empowers organizations to harness the power of LLMs securely and efficiently.
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GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
Have you ever been confused by the myriad of choices offered by AWS for hosting a website or an API?
Lambda, Elastic Beanstalk, Lightsail, Amplify, S3 (and more!) can each host websites + APIs. But which one should we choose?
Which one is cheapest? Which one is fastest? Which one will scale to meet our needs?
Join me in this session as we dive into each AWS hosting service to determine which one is best for your scenario and explain why!
Monitoring and Managing Anomaly Detection on OpenShift.pdfTosin Akinosho
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
- Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices.
4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
- Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions.
6. Viewing Kafka Messages in the Data Lake
- Learn how to view and analyze Kafka messages stored in a data lake for better insights.
7. What is Prometheus?
- Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices.
8. Monitoring Application Metrics with Prometheus
- Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system.
9. What is Camel K?
- Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes.
10. Configuring Camel K Integrations for Data Pipelines
- Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow.
11. What is a Jupyter Notebook?
- Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text.
12. Jupyter Notebooks with Code Examples
- Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
1. NewsBytes
Aquaporin Simulations exchange experimentally for about ten
years. To him, aquaporins are a likely
De-Bunk Gas Exchange suspect for gas conduction because they
Assumptions exist in places where oxygen must go in
Biologists have long taken gas and carbon dioxide must come out. For
exchange for granted, assuming that example they are plentiful in cells that
gases simply seep through the cell’s lipid line the lung, in red blood cells, and in
membrane. Since 1998, however, evi- astrocytes—cells at the blood-brain barri-
dence has been building that gases er. But it’s very hard to measure small
might also be exchanged through pores changes in oxygen concentration at the
created by specialized proteins. surface of a membrane experimentally.
Now molecular dynamics simulations So Tajkhorshid’s team pitched in
of aquaporins have weighed in on the with molecular dynamics simulations.
question. The result: “It’s now well Aquaporins occur in groups of four
established that these proteins can con- (tetramers), with four pores that con-
duct gas molecules,” says Emad duct water (one through each aquapor-
Tajkhorshid, PhD, co-author of the in molecule) and one central pore
work and assistant professor of bio- where the molecules meet. The latter,
chemistry, pharmacology and biophysics until now, had no known function.
at the University of Illinois at Urbana- When simulated using two comple-
Champaign. But, he says, some uncer- mentary methods—explicit sampling
tainty remains: “Whether or not it’s with full gas permeation and implicit Simulations of the aquaporin tetramer
important in the human body, that’s the ligand sampling—the team found both found that carbon dioxide and oxygen are
controversial part.” The work was pub- oxygen and carbon dioxide were exchanged through the central pore—a site
lished in the March 2007 issue of the exchanged through that central pore. of previously unknown function. Image
Journal of Structural Biology. Carbon dioxide was also transmitted courtesy of Emad Tajkhorshid, a faculty
Fifteen to twenty years ago, scientists through the four water pores, while oxy- associate of the NIH Resource for
believed that water permeation through gen passed through those pores only Macromolecular Modeling and
lipid bilayers was enough for water trans- rarely. The research also found, howev- Bioinformatics, and his UIUC colleagues
port into and out of cells. Gradually, er, that a plain lipid bilayer conducts Klaus Schulten, Yi Wang, and Jordi Cohen.
“It’s now well established that [aquaporins] can conduct gas
molecules,” says Emad Tajkhorshid. “Whether or not it’s
important in the human body, that’s the controversial part.”
though, researchers realized that some two and a half times as much gas as one properties of the central pore.
cells need to control water permeability, embedded with aquaporin tetramers. Meanwhile, Boron’s group is looking for
and other cells have lipid bilayers that “The question is whether this pathway a system in which gas conduction
aren’t very permeable to water. is significant and makes any difference through aquaporins is a major pathway.
Aquaporins, it turned out, carry water in in terms of total permeability of the Says Tajkhorshid: “Even if it’s 30 per-
and out in a controllable fashion. “I membrane,” says Tajkhorshid. cent of total gas permeability, it becomes
think the same might be true for gas per- The researchers hypothesize that, as physiologically relevant because then
meability,” says Tajkhorshid. “Gas perme- with water permeability, aquaporins may you can control it.”
ability of a lipid bilayer is like an open be physiologically relevant to gas According to Nazih Nakhoul, PhD,
free highway where everything can go exchange when cells have dense, rigid research associate professor in biochem-
through. With a protein, you can have a lipid bilayers or when aquaporins occu- istry at Tulane University, “This idea of
gating mechanism and some regulation.” py a major fraction of the membrane. gas transport through membrane proteins
One of Tajkhorshid’s collaborators, Tajkhorshid plans to introduce point is really gaining support. It’s interesting to
Walter Boron, MD, PhD, professor of mutations inside the central pore and see molecular dynamics simulations con-
cellular and molecular physiology at Yale manipulate the behavior of a gating loop firm some of the earliest findings.”
University, has been working on gas to see how that changes the conducting —By Katharine Miller
2 BIOMEDICAL COMPUTATION REVIEW Summer 2007 www.biomedicalcomputationreview.org
2. NewsBytes
Parkinson’s Culprit its hexamer interacting with the cell mediate and each may last only as long
membrane required juggling around a as half of a nanosecond. Nevertheless,
Modeled million atoms, Tsigelny says. Tsigelny says, even such fleeting inter-
Under a microscope, the curious pro-
Yet more than the size of alpha-synu- mediates may aggregate. The pore-
tein clumps that dot the brains of
clein, what made it difficult to model like aggregates, they found, are far
Parkinson’s patients stick out like the
was its lack of structure. Alpha-synucle- more stable than single molecules of
culprits they are. But no one has yet
in is an intrinsically unstructured pro- alpha-synuclein.
caught the protein—alpha-synuclein—in
tein—one without a distinct three- Having this model “is one step for-
the act of causing disease. Now, investi-
dimensional shape. Most proteins con- ward,” says Hilal Lashuel, PhD, profes-
gators report in an April 2007 issue of
sistently fold into a favored shape to do sor at the Swiss Federal Institute of
FEBS Journal that they’re getting closer:
their jobs, a form that can be crystal- Technology in Lausanne, Switzerland.
they’ve modeled alpha-synuclein’s early
lized, imaged, and pored over. But The UCSD model provides a structural
aggregation and offered a detailed mech-
unstructured proteins flop this way and basis for testing the hypothesis that
anism for its participation in neuron
that, even while performing their spe- alpha-synuclein forms toxic pores, he
death.
cific tasks, making them very difficult adds. But Lashuel also cautions that
“This is not just the first computa-
to pin down and study. only biochemical and in vivo studies can
tional model of alpha-synuclein,” says
“We were not scared by an unstable prove whether alpha-synuclein pokes
Igor Tsigelny, PhD, an author of the
protein,” Tsigelny states. And he and holes in neurons. “Isolating the toxic
paper and a computational biologist at
his coworkers developed an unusual species is really the most difficult ques-
the San Diego Supercomputer Center.
“all-dynamic” approach to modeling tion we are dealing with. You have to
“Up to now, there was no molecular
the protein. None of the conformations catch it in the act.”
concept of the aggregation going on.”
are final—they are all considered inter- —By Louisa Dalton
In the brain cells of Parkinson’s
patients, alpha-synuclein first starts to
cluster as a proto-fibril. It then forms fib-
ril chains, and finally ends up in the
dense clumps of fibrils called Lewy bod-
ies. Some researchers have suggested in
the past few years that alpha-synuclein
knocks off neurons right at the begin-
ning of aggregation, long before it can be
detected as a Lewy body. Biochemical
and structural evidence hints that when
a few alpha-synuclein molecules first self-
assemble into proto-fibrils, they can
form pore-like ring structures. These
may interact with the cell membrane
and allow ions to enter the cell. The
entrance of ions such as Ca2+ could
lead to neuron death.
The computer model created by
Tsigelny and his colleagues at the
University of California, San Diego, sup-
ports this theory, providing detailed
dynamics of alpha-synuclein hexamers
and pentamers and their interaction
with the cell membrane. What’s more,
the model shows that another synuclein
in the cell—beta-synuclein—blocks alpha-
synuclein’s ring-making, suggesting at
least one avenue for future inhibitory
drug development.
Modeling such a complex aggregation
wasn’t simple. Alpha-synuclein is a large Alpha-synuclein poses as a pentamer, pore-like, on the surface of a cell membrane. Courtesy
protein (140 amino acids), and to model of Igor Tsigelny
www.biomedicalcomputationreview.org Summer 2007 BIOMEDICAL COMPUTATION REVIEW 3
3. NewsBytes
Clustering Without Limits “Part of the
Starting in preschool we all learn how
to get organized. Typically, we start with
pre-determined categories (dolls, trains, attraction of the
blocks); pre-set ideas about what belongs
in each category (Barbie: doll; Thomas [affinity propagation]
the Tank Engine: train) and a fixed num-
ber of bins to put things in. algorithm is that,
But what if you started with none of
those initial limitations? Could you still although it was
group the toys? It turns out that, in a
computer, such sorting is not only possi-
ble, but extremely efficient. Using a
complicated to
Frey and Dueck use affinity propagation
novel algorithm called affinity propaga-
tion, researchers at the University of
derive, it’s quite to cluster data around “exemplars”—
data points that best represent their
Toronto found that they can not only
cluster lots of different kinds of data simple to implement compatriots. In this graphic, after start-
ing with an equal chance of serving as an
appropriately, but do it better and faster
than other methods. The work was and to get an exemplar, candidates for that job have
already emerged (red dots). Each data
published in the February 16 issue of
Science. intuitive feel for it,” point sends messages to each candidate
exemplar conveying how well it repre-
“Almost all existing techniques work
on a hypothesis refinement basis: they says Brendan Frey. sents the blue point compared to other
candidate exemplars. And candidate
start off with a set of assumed groups
exemplars send messages conveying
and iteratively refine them,” says
their availability to serve as an exemplar
Brendan Frey, PhD, associate professor
for particular data points.
of electrical and computer engineering The task sounds mind-boggling: There
at the University of Toronto, co-author are a huge number of possible groupings.
of the paper. “To our knowledge, ours is But affinity propagation handles that says Dueck. Indeed the algorithm is so
the first algorithm to consider all possi- problem by sending messages between generic that Frey and Dueck used it to
ble groupings at once.” data points—pair-wise—so as to maximize analyze gene expression data, facial
the net similarity in images, and airline routes, while other
each group. “Each mes- researchers have found applications in
sage encapsulates or basketball statistics, the stock market and
summarizes a whole dis- computer vision. And many tasks in com-
tribution of possible putational biology require a computer to
groupings for one of the organize the data before using it to make
data points,” says predictions.
Delbert Dueck, a PhD “Part of the attraction of the algo-
candidate in Frey’s lab. rithm is that, although it was complicat-
“No one has done that ed to derive, it’s quite simple to imple-
before.” ment and to get an intuitive feel for it,”
Affinity propagation says Frey. There are basically only two
is based on an algo- equations to it. “Sometimes we’ll give a
rithm called belief prop- talk and get emails from people who’ve
agation, which has been implemented it the day after,” he says.
around in various incar- When the researchers looked at how
nations for many years. well the algorithm performed compared
But, say the authors, it’s to other clustering methods they found
an approach that has it remarkably efficient. “A problem our
never been applied to algorithm could solve in about five min-
If asked to cluster facial images, a standard clustering method
clustering. “Certainly utes on one computer would take other
(k-means clustering) would take up to a million years on a sin-
not to generic clustering methods up to one million years to solve
gle computer to achieve the accuracy achieved by affinity prop-
of any type of data,” on that same computer,” says Frey.
agation after five minutes.
4 BIOMEDICAL COMPUTATION REVIEW Summer 2007 www.biomedicalcomputationreview.org
4. NewsBytes
Tim Hughes, PhD, of the Center for lished out of the lab run by Tomaso was able to classify pictures of a busy
Cellular and Biomolecular Research at Poggio, PhD, at MIT’s McGovern street scene as well as other leading
the University of Toronto, is considering Institute for Brain Research. mathematics-based computer vision sys-
using affinity propagation in his For decades, scientists have struggled tems, as described in the March 2007
research. “It seems like it would do best to create computer programs that can rec- issue of IEEE Transactions on Pattern
when things really do form independent ognize visual objects as well as humans Analysis and Machine Intelligence.
groups, and when the data are can. Some computer systems excel at rec- Serre’s team then built a more com-
fairly sparse, so most of the correlation ognizing one particular object, but none plex system, consisting of many S and C
matrix can be dropped in early are anywhere close to recognizing the wide layers designed to closely match the flow
cycles,” he says. “I think it will work well range of objects observed by the human of information in a human brain during
with exon-profiling data or brain. Visual the first 100-200
genome-tiling data, where there is also a recognition is milliseconds of
constraint that the groups complicated by “We’ve built a model perception. This
have to correspond to regions near each two conflicting enhanced system
other on the chromosome.” goals: a program to be as close as performed as well
—By Katharine Miller must be specific as humans on a
enough to discrim- possible to what is rapid object recog-
inate between nition task: distin-
Computer Vision that different objects,
such as a person
known about the guishing animals
from non-animals
Mimics Human Vision
Our brains can recognize most of the
or a car, yet flexi-
ble enough to rec-
human visual when images were
flashed in front of
things we pass on an evening stroll: ognize the same humans and com-
Cars, buildings, trees, and people all reg- type of object in system,” says puters. The work
ister even at a great distance or from an different sizes, appeared in the
odd angle. Now, a new computer vision poses, and light- Thomas Serre. April 2007 issue of
program can do the same thing. It suc- ing. the Proceedings of
cessfully rivals the human ability to rap- To achieve these goals, Serre and col- the National Academy of Sciences. The
idly recognize objects in a complex pic- leagues used data recorded from real computer system even made errors simi-
ture because it mimics how information neurons in the visual system to program lar to the errors made by humans, sug-
flows during the initial stages of visual two fundamentally different kinds of vir- gesting that the model recapitulates the
perception. tual neurons called S (simple) and C early processes of the human visual sys-
“We’ve built a model to be as close as (complex) units. S units recognize specif- tem.
possible to what is known about the ic features of an image; C units monitor The model will be used as a tool by
human visual system,” explains Thomas a range of S units in one area and allow neuroscientists to better understand the
Serre, PhD, a postdoctoral associate in for variation in position and size. human visual system, and also has prac-
the Center for Biological and The researchers were surprised to tical applications for surveillance, driv-
Computational learning at MIT and find that a simple system, consisting of ing assistance, and autonomous robot-
lead author of two papers recently pub- four alternating layers of S and C units, ics. According to Poggio, the team’s next
When presented with a real-world
street scene (left), Serre’s computer
vision system successfully recog-
nized pedestrians, cars, buildings,
trees, sky, and the street (right).
Although not pictured, the model
also successfully identified bicycles.
Note the error in this example: the
model mistakenly classified a street
sign as a pedestrian. Graphic cour-
tesy of Stanley Bileschi, PhD,
McGovern Institute for Brain
Research at MIT.
www.biomedicalcomputationreview.org Summer 2007 BIOMEDICAL COMPUTATION REVIEW 5
5. NewsBytes
goal is to extend the model to include
the “back projections” from other parts
of the brain that allow feedback process-
ing of visual information after 200 mil-
liseconds. Agent-based computer models predict the
“This is the first demonstration that pattern (left) produced when genetically
a purely bottom up approach to visual identical cells have an inherent probability
object recognition, inspired by record- of changing (from green to red and vice
ings from the neurons in the brain, is versa), and the pattern (right) produced
effective as a practical computer vision when cells are triggered to change by an
system,” says Terry Sejnowski, PhD, extrinsic factor, such as cell density. Top
head of the Computational Neuro- images represent exponential growth;
biology Lab at the Salk Institute. “There bottom are at equilibrium. Courtesy of
is much more work to do, both to Andras Paldi.
improve its performance, and also to use
it to better understand how our own
visual system works.” agent based models of a tissue culture can affect the differentiation process.
—By Matthew Busse, PhD plate. In each model, all cells act inde- “The stem cell nature is not an intrinsic
pendently and can switch between two property of the cell,” he says. “It is a prop-
cell types: A or B. In the “extrinsic” erty of the whole cell population.” Paldi
model, A cells turn into B cells when it further believes the work supports the
Nature Versus gets crowded, and back to A cells when effort to find a way of converting adult,
Nurture In Silico they have more space. In the “intrinsic” differentiated cells into stem cells (and
Every generation, a few noncon- model, each cell has fixed probabilities of avoid the need for harvesting embryonic
formists crop up in tissue cultures of switching from A to B and back again. stem cells)—a possibility that has not just
genetically identical cells. The question is: When the scientific,
are the wayward simply born that way, or scientists ran the Why, in the same warm but social
did something in the environment affect models, they and political
them? “You have these two possibilities—
intrinsic or extrinsic, nature or nurture,”
found each pro-
duces a stable,
spot, getting the same implications
as well.
says Andras Paldi, PhD, a biologist at heterogeneous
Genethon in France. population, yet
rich media, do some cells Christa
Muller-
Now, Paldi and his colleagues have they differ in the Sieburg,
modeled such cultured cells to deter- cell patterns. differentiate and others PhD, how-
mine whether extrinsic or intrinsic The intrinsic ever, dis-
influences play a key role in the sponta- model predicts stay stem cells? putes that
neous emergence of phenotypic varia- lone A cells dis- scientific
tion. It turns out that for spatial patterns tributed evenly throughout a largely B conclusion. “The idea that mature cells
beyond randomness to arise, there has population. Extrinsic predicts that the A can turn into stem cells is very attractive
to be some effect of sensing neighboring cells will cluster. The result held even to many modelers but has little support
cells—i.e., extrinsic factors must play a though the cells were allowed to migrate. through experimental data,” says the
role. And the extrinsic model resembles This pattern difference allowed the professor at the Sidney Kimmel Cancer
results seen in real cells. The work researchers to compare their computa- Center.
appears in April in PLoS One. tional simulation with real cells. Using a Sui Huang, MD, PhD, at
Paldi’s work was motivated in part by muscle cell line that can switch between Children’s Hospital Boston, would
the open question among stem cell biol- two distinct phenotypes, a stem-cell like have liked to see Paldi’s group perturb
ogists of what triggers a stem cell to dif- progenitor state and a differentiated state, the cell line or the culture to confirm
ferentiate. Why, in the same warm spot, they found that the cell pattern mostly their model. But both he and Muller-
getting the same rich media, do some resembles that of the extrinsic model. Sieburg believe the study addressed an
cells differentiate and others stay stem Many of the rare, stem-cell like cells clus- important question, that of heterogene-
cells? It is commonly assumed that this is ter; a few are solitary. ity of a genetically identical population
because the decision to differentiate is What’s important here, Paldi says, is of cells. And, says Huang, it certainly
intrinsic—that is, purely random. that they find environment playing a “contributes to the discussion in the
To test that assumption, Paldi’s group role—a significant one. In the case of stem community.”
started by designing two simple, multi- (progenitor) cells, it means neighbor cells —By Louisa Dalton
6 BIOMEDICAL COMPUTATION REVIEW Summer 2007 www.biomedicalcomputationreview.org
6. Simulating Populations But that technique is not without its based on Python. The software is freely
problems. When a population evolves for- available at http://simupop.sourceforge.net,
with Complex Diseases ward in time, there are simply too many under a GPL license.
Diabetes, breast cancer, multiple When Peng and his colleagues used
possible outcomes. Most notably, when
sclerosis, Alzheimer’s disease. All are their method to compare several gene map-
you introduce a disease allele, it can rapid-
associated with several genes’ alleles ping techniques they found that certain
ly be eliminated and replaced with new
interacting in complex ways with one methods worked better for loci that were
alleles. So Peng came up with a trick: He
another and the environment. Now, located distantly from one another; and
pre-sets desired disease allele frequencies in
using a computationally intensive other methods were
method known as forward-time simula- more effective when
tion of human populations, researchers loci were close together.
are hoping to gain a better understand- Overall, though, says
ing of how such complex diseases Kimmel, “We’re mildly
become established. pessimistic” about cur-
“In a real population you just see peo- rent gene mapping
ple with the disease,” says Marek approaches. “When
Kimmel, PhD, professor of statistics at the number of loci
Rice University and co-author of the CANCER
involved in complex
work. “You don’t see who in the popula- disease is greater than
tion has the disease genes because peo- two, the methods rap-
ple carrying these genes do not necessar- MULTIPLE
SCLEROSIS idly lose their power.”
ily become diseased.” But in the model Until recently, gene
population, he says, “you see both.” And mapping for complex
the researchers’ approach allows them to diseases has been disap-
simulate a very complicated scenario— pointing, he says. Loci
including changes in types of selection identified in such
pressure. efforts have later
“This lets us evaluate how well statis- DIABETES
turned out to be statis-
tical genetics tests determine what genes tical artifacts. “Our
are responsible for the symptoms of a modeling could figure
disease and how frequently those genes out if this is inevitable,”
appear in the population.” That’s a he says—and help guide
non-trivial exercise, he says, because it people toward more
has been impossible, until now, to effective approaches.
compare the many existing gene-map- David Balding,
ping methods head-to-head. The work PhD, a professor of
was published in PLoS Genetics in “In a real population, you just see statistical genetics at
March 2007. Imperial College in
Before now, the most commonly people with the disease,” says
London, does similar
used approach to simulating diseases in
human populations—called the “coales-
Marek Kimmel. “You don't see work using forward-
time simulations of
cent” method—worked by coalescing who in the population has the large genomic
backward in time to a most-recent com- regions. He has
mon ancestor. But it’s extremely diffi- disease genes...” become pessimistic
cult to take selection into account using
the current generation, extrapolates them about the method’s usefulness for
the coalescent method, says co-author
backward, and starts the simulation from understanding complex diseases because
Bo Peng, PhD, a postdoctoral fellow at
there. As Kimmel puts it, “We are restrict- no one really knows what kind of selec-
the University of Texas MD Anderson
ing potential variability in one aspect of tion is going on. Nevertheless, he says,
Cancer Center. Moreover, that
the present in order to produce a simula- this work can be useful for studying
approach gets too complicated if more
tion that resembles something close to the selection itself. “People tend to look at
than one disease gene is involved. So selection one allele at a time,” he says,
actual variability that exists now.”
Peng and his colleagues turned to for-
The simulation uses a scripting lan- “But forward-time simulation lets us do
ward-time simulation, an approach
guage called simuPOP, a general-purpose it with complex interactions.”
that’s been around for about one hun-
forward-time simulation environment —By Katharine Miller ■
dred years.
www.biomedicalcomputationreview.org Summer 2007 BIOMEDICAL COMPUTATION REVIEW 7