Volume 221
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Seminar Report
iTHEMS Biology Seminar by Dr. Lazaro-Guevara Jose Miguel on October 6, 2022
2022-10-14
On October 6th, 2022, we had the pleasure to have José Miguel Lázaro-Guevara, a postdoctoral researcher at the University of British Columbia, in our Biology seminar. His talk was related to pharmacogenomics. The idea behind the field of pharmacogenomics is that the effectiveness of drugs in medical treatments is partially determined by the genetic variation of patients, but producing genome-wide data for one patient is costly and not affordable for many patients or insurance companies. For these cases, Lázaro-Guevara proposes using an extreme-low coverage genotyping, which consists on sequencing random sections of the genome of on a patient. By doing so, it is possible to later use a background reference (the genome of other genetically related people) to apply an imputation method to infer the parts of the genome that were not directly sequenced. By showing clinical cases on patients from a population from Utah, USA, the extreme-low coverage method seems to be a reliable and effective method to detect associations between genetic variation and the effectiveness of drug treatment.
Reported by José Said Gutiérrez-Ortega
Extremely low-coverage whole genome sequencing (XLC-WGS) as a cost-effective tool for pharmacogenomic profiling: Advantages and Challenges
October 6 (Thu) at 10:00 - 11:00, 2022
Upcoming Events
Seminar
iTHEMS Math Seminar
Measuring diversity: the axiomatic approach
October 21 (Fri) at 16:00 - 17:00, 2022
Tom Leinster (Professor, University of Edinburgh, UK)
Ecologists have been debating the best way to measure diversity for more than 50 years. The concept of diversity is relevant not only in ecology, but also in other fields such as genetics and economics, as well as being closely related to entropy. The question of how best to quantify diversity has surprising mathematical depth. I will argue that the best approach is axiomatic: to enable us to reason logically about diversity, the measures we use must satisfy certain mathematical conditions, and those conditions dramatically limit the choice of measures. This point will be illustrated with a theorem: using a simple model of ecosystems, the only diversity measures that behave logically are the Hill numbers, which are very closely related to the Rényi entropies of information theory.
Venue: via Zoom
Event Official Language: English
Seminar
iTHEMS Biology Seminar
Migration dynamics and model of cells crawling on a matrix with cell-scale stiffness heterogeneity
October 27 (Thu) at 16:00 - 17:00, 2022
Hiroyuki Ebata (Assistant Professor, Graduate School of Science, Kyushu University)
In living tissues where cells migrate, spatial distribution of mechanical properties, especially matrix stiffness, are generally heterogenous with cell-scales ranging from 10 to 1000 μm. Since the cell migration in our body plays critical role in morphogenesis, wound healing, and cancer metastasis, it is essential to understand the migratory dynamics on the matrix with cell-scale stiffness heterogeneity. However, while cellular responses to homogeneous matrix have been extensively explored, studies of the cell motility with stiffness heterogeneity have been limited to the directional movement (durotaxis) driven by a simple stiffness gradient. Thus, we need to elucidate how cell migration is determined through the interaction among cell-scale stiffness heterogeneity and cellular responses such as dynamics of the cell-matrix adhesion site, the intracellular prestress, and cell shape.
In this talk, we introduce our experiments on cell motility, shaping, adhesion, and traction forces at long time scales using microelastically patterned hydrogels that enable us to systematically control the cell-scale heterogeneity of the matrix-stiffness. Using microelastically patterned hydrogels, we showed that the cell exhibited a general mode of durotaxis depending on the shape and size of the stiff domains, which was coincided with the extraordinarily large fluctuation of the traction force. We proposed a cell migration model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. By considering the cellular response to stiffness gradients, the model can reproduce general durotaxis driven by cell-scale heterogeneity of the matrix-stiffness.
Venue: via Zoom
Event Official Language: English
Seminar
iTHEMS Math Seminar
Measuring diversity: species similarity
October 28 (Fri) at 16:00 - 17:00, 2022
Tom Leinster (Professor, University of Edinburgh, UK)
Traditional measures of the diversity of an ecological community depend only on how abundant the species are, not the similarities or differences between them. To better reflect biological reality, species similarity should be incorporated. Mathematically, this corresponds to moving from probability distributions on sets to probability distributions on metric spaces. I will explain how to do this and how it can change ecological judgements. Finally, I will describe a surprising theorem on maximum diversity (joint with Meckes and Roff), which reveals close connections between maximum diversity and invariants of geometric measure.
Venue: via Zoom
Event Official Language: English
Seminar
DMWG Seminar
Gamma-ray emission from the Sagittarius Dwarf Spheroidal galaxy due to millisecond pulsars
October 28 (Fri) at 17:00 - 18:00, 2022
Oscar Macias (Faculty of Science, University of Amsterdam, Netherlands)
The Fermi Bubbles are giant, gamma-ray emitting lobes emanating from the nucleus of the Milky Way discovered in ~1-100 GeV data collected by the Fermi Gamma-Ray Space Telescope. Previous work has revealed substructure within the Fermi Bubbles that has been interpreted as a signature of collimated outflows from the Galaxy's super-massive black hole. In this talk, I will show that much of the gamma-ray emission associated to the brightest region of substructure -- the so-called cocoon -- is likely due to the Sagittarius dwarf spheroidal (Sgr dSph) galaxy. This large Milky Way satellite is viewed through the Fermi Bubbles from the position of the Solar System. As a tidally and ram-pressure stripped remnant, the Sgr dSph has no on-going star formation, but I will demonstrate that the dwarf's millisecond pulsar (MSP) population can plausibly supply the observed gamma-ray signal. This finding plausibly suggests that MSPs produce significant gamma-ray emission amongst old stellar populations, potentially confounding indirect dark matter searches in regions such as the Galactic Centre, the Andromeda galaxy, and other massive Milky Way dwarf spheroidals.
Venue: via Zoom
Event Official Language: English
Lecture
An Introduction to Quantum Measurement Theory for Physicists
November 10 (Thu) - 12 (Sat), 2022
Masahiro Hotta (Assistant Professor, Department of Physics, Graduate School of Science, Tohoku University)
In this lecture, basic concepts in quantum measurement theory are introduced, including measurement operators and POVM's. The related topics are also picked up.
Lecture 1: Nov. 10, 10:30 - 12:00
Lecture 2: Nov. 10, 13:30 - 15:00
Lecture 3: Nov. 10, 15:30 - 17:00
Lecture 4: Nov. 11, 10:30 - 12:00
Lecture 5: Nov. 11, 13:30 - 15:00
Lecture 6: Nov. 12, 10:30 - 12:00
Venue: #345-347, 3F, Main Research Building, RIKEN / via Zoom
Event Official Language: English
Paper of the Week
Week 4, October 2022
2022-10-20
Title: Competition between pairing and tripling in one-dimensional fermions with coexistent s- and p-wave interactions
Author: Yixin Guo, Hiroyuki Tajima
arXiv: http://arxiv.org/abs/2210.07042v1
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