Here are the things I discovered this week that fascinates me.
- Computer science
- Computational Biology
- Error types
- Other gems
The StellarGraph Machine Learning Library
StellarGraph is a python library for machine learning on graphs and networks.
Typical applications include
- Representation learning for nodes and edges, used for visualization and down-stream machine-learning tasks
- Node or edge class prediction
- Classification of graphs
- Link prediction
I could install the library. Now I am looking for opportunities to test it.
Inferring spatial and signaling relationships from single-cell data
Cang and Nie reported their effect to use tools from optimal transport, a mathematical branch that gained much attention recently in many fields including biology, to recover spatial relationship from single-cell data using spatial measurements of a small number of genes.
The method may be useful to integrate non-spatial with spatial data, and to infer dynamic signalling events using spatial data.
Other interesting papers in computational biology
- The software Souporcell, covered in the Nature Methods publication by Heaton et al., clusters mixed-genotype single-cell RNA sequencing data by individual.
Structure of RNA-dependent RNA polymerase of SARS-Cov-2 bound to remdesivir
There is quite some debating ongoing about the clinical efficacy of remdesivir against the new corona virus (SARS-Cov-2). While the study by Yin et al, published online on May 1st on Science, does not end the debate, it gives us some hint how remdesivir binds to its supposed target, RNA-dependent RNA polymerase (RdRp).
The structure, collected by cryo-EM imaging at the resolution of about ~2.5 Angstrom ($10^-10$m), reveals that remdesivir inserts itself into the primer strand of RNA synthesis at the first base and terminates chain elongation. The insights may help to make more specific and efficacious RdRp inhibitors.
SARS-Cov-2 infects human gut enterocytes
Lamers et al. reported on Science that the new corona virus infects human gut enterocytes. They used human intestinal organoid systems and both confocal- and electron-microscopy to demonstrate the infection. The authors also used bulk RNA-seq to show that cytokines and interferon response genes are positively regulated by viral infection, which fits our understanding of a generic viral response.
The bulk RNA-seq data is available at Gene Expression Omnibus, with the accession ID GSE149312.
A 3D brain model infected by HSV develops Alzheimer-Disease-like phenotypes
There has been a few studies suggesting a correlation between viral infection and the Alzheimer Disease (AD). A definitive causal link is missing. It may take a few years, when not decades, until a causal link can be confirmed or rejected.
An alternative way to support the viral hypothesis is to build a viral infection model that mimics the pathogenesis and phenotypes of AD in human brain. Cairns et al. reported on Science Advances such a model using stem cells.
They built a 3D model using human-induced neural stem cells infected by Herpes Simplex Virus Type I (HSV-1). They reported phenotypes that resemble AD, including amyloid plaque-like formations, gliosis, neuroinflammation, and decreased functionality.
While the model does not prove the viral hypothesis, it provides a platform to identify drugs that reverse HSV-1 induced phenotype. Whether such drugs can indeed halt or stop the progression of AD is another tough question that needs to be addressed.
Other interesting papers in biology
- Gordon et al. reported on Nature a protein interaction map of SARS-Cov-2. The work is supervised among others by Brian Shoichet and Nevan Krogan.
- Eshraghi et al. reported their findings on Science Advances that RasGRP1 (RAS guanyl release protein factor 1) controls the development of L-DOPA induced dyskenisia (involuntary muscle movements). Inhibiting RasGRP1 may reduce the side effects associated with L-DOPA treatment.
- Brook et al. reported that Bacille Calmette-Guerin (BCG) vaccination induced granulocyte colony-stimulating factor (G-CSF) within hours of administration. It drove de novo generation of neutrophils in the process known as emergency granulopoiesis (EG, reviewed by Manz and Boettcher in Nature Reviews Immunology, 2014). Increased neutrophils protects from sepsis in mice. And increased neutrophils were observed in human infants as well. Previous studies reported an interesting negative correlation between BCG vaccination status and nCov-19 mortality in many countries. Whether EG plays a role there is not known.
- Wireless recording from unrestrained monkeys reveals motor goal encoding beyond immediate reach in frontoparietal cortex: reach goals beyond immediate reach by thoughts? That works at least on two rhesus monkeys.
This week I finished a draft proposal for a new book, Multiscale Modelling in Drug Discovery: An Introduction (working title). The book complements the course Applied mathematics and informatics in drug discovery that I teach at the University of Basel.
I tried the python tool proselint to check my writing styles, and liked it. It is not a grammar checker. Instead, it checks the writing style using predefine rules. For instance, it suggests to delete every instance of the word ‘very’ and to limit the use of proclamation (!) to 3 ppm.
Unfortunately, proselint seem to stop being actively developed since a few years ago according to the commits.
Proselint is an example of so-called linters. I discovered an interface
to various of linters in vim:
vim-syntastic. I used it and liked
it, too. Different from proselint, which checks only writing,
allows file checking with any external tools. For markdown files, the syntastic
about checkers listed following linters:
mdl (markdown lint tool),
Another vim plug-in I found useful for writing prose is reedes/vim-pencil.
Another great xkcd!
- Raspberry Pi High-Quality Camera is available for 50$. It supports interchangeable lenses and offers a 12.3 mega-pixel sensor. The base and the HQ camera cost about 120 Swiss francs and are available in Switzerland from Pi-Shop.ch.
- JukeBox by OpenAI, a neural network that generates both music and voice. The songs sounded indeed like being generated by AI, but the idea is interesting.
- Ionic gelatin as a wearable energy source.
- Following last week’s reading on Ruan Yiweng’s blog, I tried and installed pi-hole at home. I am excited about it. It is a DNS sinkhole, which provides network-wide ad blocking via my own Linux hardware. Please consider donation and spreading the word if you find the tool useful, too.
- leeoniya/uPlot on GitHub: a small and fast chart for time series, lines, etc. MIT licensed.
- I migrated from keepassx to keepassxc to manage my passwords and credentials. So far it looks good. Synchronization with Google Drive is a pain point in Linux. Though Gnome supports mounting Google Drive, keepassxc opens the database file only as ‘Read-Only’. The software insync may solve the problem, it costs though 30 dollars.
- House concert at the Palace Bellevue Berlin, Ludwid van Beethoven: Waldstein Sonata op.53 by Igor Levit on Youtube. It calmed some part in me while excited other parts. An amazing performance.
- Fullstackopen.com offers an open and free course on full-stack development of single-page applications. It was written by Matti Luukkainen and many other open-source developers. I discovered it from the blog of Ruan Yifeng.
Have a nice weekend!