Archive for the 'SciLit' Category

graph genome applied in Rice pan-genome

October 17, 2021

Cell
2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28.
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
https://www.sciencedirect.com/science/article/abs/pii/S009286742100581X

motif discovery on personal genomes

October 9, 2021

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009444

Navigating the new era of assisted suicide and execution drugs | Journal of Law and the Biosciences | Oxford Academic

October 2, 2021

https://academic.oup.com/jlb/article/4/2/424/4265564
QT:{{”
Meanwhile, the standard PAS protocol in the USA involves the prescription of a lethal dose of a barbiturate, typically
pentobarbital or secobarbital, to be consumed by the patient in liquid form. Often, the dose is mixed with juice, in what is often called a ‘potion’, to combat the bitter taste of the drugs. The patient is legally required to drink the potion by themselves, to ensure the decision remains autonomous. Physicians are free to prescribe, off-label, any drug they deem fit for these lethal purposes, under protection from prosecution. Only three lethal medications
(secobarbital, pentobarbital, and phenobarbital) have been used, according to state statistics, aside from anti-nausea and anti-anxiety medications to combat side effects.5 In the Netherlands and Belgium, physicians typically rely on sodium thiopental and pancuronium bromide when euthanizing patients at their behest.13
“}}

Oral delivery of systemic monoclonal antibodies, peptides and small molecules using gastric auto-injectors | Nature Biotechnology

September 25, 2021

https://www.nature.com/articles/s41587-021-01024-0

An easily swallowed capsule injects drugs straight into the gut https://www.nature.com/articles/d41586-021-02443-4

Using deep learning to model the hierarchical structure and function of a cell | Nature Methods

September 18, 2021

https://www.nature.com/articles/nmeth.4627

interpretable deep learning model

Expanding Access to Large-Scale Genomic Data While Promoting Privacy: A Game Theoretic Approach: The American Journal of Human Genetics

August 29, 2021

https://www.cell.com/ajhg/fulltext/S0002-9297(16)30526-2

Expanding Access to Large-Scale Genomic Data While Promoting Privacy: A Game Theoretic Approach

Zhiyu Wan
Yevgeniy Vorobeychik
Weiyi Xia
Ellen Wright Clayton
Murat Kantarcioglu
Bradley Malin

Published:January 05, 2017
DOI:https://doi.org/10.1016/j.ajhg.2016.12.002

fermented foods

August 28, 2021

How Fermented Foods May Alter Your Microbiome and Improve Your Health
https://www.nytimes.com/2021/08/13/well/eat/yogurt-kimchi-kombucha-microbiome.html

Foods like yogurt, kimchi, sauerkraut and kombucha increased the diversity of gut microbes and led to lower levels of inflammation.

ARTICLE| VOLUME 184, ISSUE 16, P4137-4153.E14, AUGUST 05, 2021

https://www.cell.com/cell/fulltext/S0092-8674(21)00754-6

Gut-microbiota-targeted diets modulate human immune status

Hannah C. Wastyk 7
Gabriela K. Fragiadakis 7
Dalia Perelman
Dylan Dahan
Bryan D. Merrill
Feiqiao B. Yu
Madeline Topf
Carlos G. Gonzalez
William Van Treuren
Shuo Han
Jennifer L. Robinson
Joshua E. Elias
Erica D. Sonnenburg
Christopher D. Gardner
Justin L. Sonnenburg 8

Published:July 12, 2021

DOI:https://doi.org/10.1016/j.cell.2021.06.019

Visualizing 3D imagery by mouth using candy-like models | Science Advances

August 20, 2021

https://advances.sciencemag.org/content/7/22/eabh0691

Bioanalogous Properties of Blockchains

August 14, 2021

https://link.springer.com/article/10.1007/s11084-021-09608-1

Emergent Bioanalogous Properties of Blockchain-based Distributed Systems

Oleg Abramov, Kirstin L. Bebell & Stephen J. Mojzsis

Origins of Life and Evolution of Biospheres (2021)

Frontiers | InferBERT: A Transformer-Based Causal Inference Framework for Enhancing Pharmacovigilance | Artificial Intelligence

July 31, 2021

Nice talk by W Tong at #ISMBECCB21 (CAMDA session) discussing the FDA perspective on how to do AI for regulatory science. He presents the TRIAL framework: transparency, reliability, interpretability, applicability & liability. #ISMBECCB2021

In relation to interpretability, he discusses InferBert
(https://www.frontiersin.org/articles/10.3389/frai.2021.659622/full) which builds a Bayesian causality framework (using the Do-calculus) for interpreting the BERT transformer based model. #ISMBECCB21 #ISMBECCB2021