Saturday, May 9, 2020

Folding@home with unused laptop resources for science

Protein Folding, or how to predict the 3D structure of proteins from 1D sequence, is a key task in molecular biology which is not yet resolved.

Folding@home is an oldest citizen science project i know. The project has started in October 2000 and now approaches its 20th anniversary.

Anyone can fold at home with a personal computer. The Folding@home software will run in the background, eat some free resources and fold the proteins for several projects including Oncology and COVID-19.

It does not slow down my laptop as i writing this post running The Folding@home in the background.

Software installation is here: https://foldingathome.org/start-folding/
Scientific part & publications of results: https://foldingathome.org/category/science/
Competing (donating resources) teams: https://stats.foldingathome.org/teams

Sunday, March 8, 2020

How to learn about Blockchain?-> try it!

Photomania.net
The best way to learn about Blockchain is to try it.

One possible option is this:
  1. Create free Ether wallet on Ether website or with Ether app . Make sure to back up passwords and keys.
  2. Earn some tokens with Publish0x or Brave browser (if you have a website) .
  3. Transfer tokens to Ether or other wallet.

This post is not a financial or investment advice. 


Links:

Other funny projects @ your own risk:
1. Cryptolab Browser websitehttps://cryptotabbrowser.com/11790497
2. Banano.cc https://powerplant.banano.cc/?r=18599
3. Uptrennd: https://www.uptrennd.com/signup/Njg2MzA 

Wednesday, February 26, 2020

Direct-to-Consumer Genetic Testing: Pros and Cons


Millions of people worldwide have taken the at-home genetic test (1,2). Ancestry tests are very popular, plus there is a growing offering of health-related tests.


There is still a fair amount of uncertainty about test results and the use of personal data. In table below, there is an attempt to summarize arguments in favor or against private testing.  (This is not a recommendation in favor of taking a test). 


Pros
Cons
Useful information (Ancestry, Relatives, Health).
Privacy. Others can use your information in the way you do not know or do not want.
Some tests can be done anonymously (without providing personal details).
Privacy. Anonymous tests sound impossible. 
Help Scientific research / Benefit from scientific results
Privacy. Possible discrimination (5), possible psychological Implications 
Financial incentive for sharing data
Privacy. Not clear regulation / GDPR 
Intriguing part of the decision making around taking or not taking DTC tests is that individuals can be still identified by DNA, even if not taking DNA tests. Either genetic databases or DNA markers can be used to learn about anonymous DNA and locate an individual.
Literature:
1. More than 270 Direct-to-Consumer Genetic Testing services are examined, their business models are classified in January 2020 publication of .'Valuable Genomes: Taxonomy and Archetypes of Business Models in Direct-to-Consumer Genetic Testing'. Comprehensive list of 448 DTC genetic companies is available @ publication sitehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001042/bin/jmir_v22i1e14890_app1.xlsx
2. More than 26 million people have taken an at-home ancestry test. The genetic genie is out of the bottle. And it’s not going back. https://www.technologyreview.com/s/612880/more-than-26-million-people-have-taken-an-at-home-ancestry-test/
3.Opportunities and challenges of Distributed Ledger Technology in genomics: a call for Europe are summarized in the article of . Opportunities are : flexibility and access advantaged to data exchange for research, Increased security, further democratization of data. Challenges are: size of genomic data set, uncertain regulatory especially GDPR, awareness of public towards genetic data.
4. A Ledger of Me: Personalizing Healthcare Using Blockchain Technology  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668357/
5. What is genetic discrimination? https://ghr.nlm.nih.gov/primer/testing/discrimination
6. A Systematic Review of the Psychological Implications of Genetic Testing: A Comparative Analysis Among Cardiovascular, Neurodegenerative and Cancer Diseases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295518/
8. What is anonymous sequencing? https://nebula.org/anonymous-sequencing/
9. Facial recognition from DNA using face-to-DNA classifiers https://www.nature.com/articles/s41467-019-10617-y
10. Identification of Anonymous DNA Using Genealogical Triangulation https://www.biorxiv.org/content/10.1101/531269v1


12. The law of genetic privacy: applications, implications, and limitations
https://academic.oup.com/jlb/article/6/1/1/5489401

Sunday, January 26, 2020

Dog Aging Project -> Nominate your dog

The Dog Aging Project is a long-term biological study of aging in dogs, centered at the University of Washington.


The project engages the general public to register their dogs in the studies, and therefore the project is an example of citizen science..... A small subset of those dogs (approximately 500) will be enrolled in a double-blind, placebo-controlled study of the pharmaceutical rapamycin, which has shown signs of extending longevity in species such as mice.


Life Span <-> Health Span

Wednesday, December 25, 2019

Free Promethease reports & SNPedia

SNPedia is a wiki-based bioinformatics web site, a database of single nucleotide polymorphisms (SNPs).

Promethease is to compare personal genetics results from Myheritage, 23andme, Ancestry, FamilyTreeDNA, others gainst the SNPedia database.

Sample reports are available @ https://promethease.com/

Be sure to read privacy and data protection policy on websites of the companies, more on regulations of testings:

Friday, December 20, 2019

Crypto Social


Brave is a free and open-source web browser ...blocks ads and website trackers. The company has proposed adopting a pay-to-surf business model in a future version of the browser.

Brave allows users to support the sites they visit with BAT.[11] Users may earn BAT by watching ads or by funding their BAT wallet. Users are paid 70% of the revenue they generate. The remaining 30% is split between Brave and the advertisement's publisher.[12]

BAT token is traded on crypto exchanges and several major websites are registered as Brave publishers. Once Brave Browser (here with swca.ch referral) is installed, one can earn some BAT and share it with publishers. 
Coil.com enables users to pay websites and creators directly.
Swissborg community (Predict, learn and earn Bitcoin with zero risk) with it's own CHSB coin.  SWCA referral code: 4JNW5RA

Steemit (steemit.com) is a blockchain-based blogging and social media website, which rewards its users with the cryptocurrency STEEM for publishing and curating content, and is owned by Steemit Inc., a privately held company based in New York City and a headquarters in Virginia.



Sunday, November 10, 2019

Amanita muscaria

The toxins in Amanita muscaria are water-soluble ... the consumption of detoxified A. muscaria has been practiced in some parts of Europe (notably by Russian settlers in Siberia) since at least the 19th century, and likely earlier. 






This observation may imply that A. fulva under typical geochemical site conditions is able to regulate the accumulation of many of the elements mentioned in fruiting bodies :  Ag, Al, As, Ba, Ca, Cd, Co, Cu, Cr, Fe, K, Mg, Mn, Na, Ni, P, Pb, Rb, Sr, Tl, V, U and Zn



.... accumulation of U, Th, Pb and Ag in macrofungal fruit-bodies apparently does not depend on total content and chemical

fractionation of these metals in soils (tested by the BCR sequential extraction in this study).



Friday, October 4, 2019

Anonymous Sequencing & Oral Microbiome

Nebula Genomics offers anonymous sequencing with oral microbiome analysis, storing data on blockchain-based storage but yet in US only. (https://nebula.org/anonymous-sequencing)
Dante Labs performs tests in Italy and recently announced 10'000 Oral Microbiome project to improve oral care.

More on Oral Microbiome:



Wednesday, September 25, 2019

Whole Genome Sequencing for ... USD 600 = Unbelievable!

https://neural-labs.com/en/arti/Whole genome sequencing (WGS) is ostensibly the process of determining the complete DNA sequence of an organism's genome at a single time. 

The "$1,000 genome" phrase neatly highlighted the chasm between the actual cost of the Human Genome Project, estimated at $2.7 billion over a decade, and the benchmark for routine, affordable personal genome sequencing.

In 2010, Illumina introduced its individual genome sequencing service for consumers, who were required to present a doctor's note. The initial price was $50,000/person. One of the first clients was former Solexa CEO John West, who had his entire family of four sequenced.[22]
Now "$1,000 genome" is in past as there are number of companies offering WGS starting from USD 600.... 
Additional reading:
WGS should not be confused with Exome sequencing (WES) - a genomic technique for sequencing all of the protein-coding region of genes in a genome (known as the exome). 


Friday, September 20, 2019

Fighting Plastic waste with ...Kefir?

Home production of kefir requires kefir grains, Milk and 5 minutes time daily. Home production of Kefir may reduce consumption of packaged product and does not require plastic.

Where to get kefir grains? from friends making kefir already or from on-line shop
How to produce kefir @home?
Some Scientific articles on kefir research: 
and about plastic waste:




Some Room for -> Mushroom

Mushrooms as a source of Vitamin D:





Articles on Mushrooms vs. Immune System and/or Cancer:



Mushrooms in Clinical Trials:






More on Mushrooms:



Sunday, June 30, 2019

Favorite Photo Pages and Photo Commerce Sites


Get your photos exhibited in galleries around the world: Gurushots Exibitions.

Etsy: Millions of shoppers can’t wait to see what you have in store. My favorite store on Etsy: KindStoryArt.

Photomyne:  scan dozens of photos in minutes

Snapseed from Google: on-line and Android/iPhone apps

AI Editors: https://www.swca.ch/2019/03/best-photo-editing-applications.html

Friday, June 21, 2019

MOOD: to track or not to track?

Mood tracking is a positive psychology technique for improving mental health where a person records their mood, usually at set time intervals, in order to help identify patterns in how their mood varies.



Sunday, April 14, 2019

Circadian Rhythms, Biological Clock and Health



A circadian (24-hour) rhythms are driven by a circadian clock, and they have been widely observed in plants, animals, fungi, and cyanobacteria.

Biological clock humanThere is strong data to suggest CR disturbances, due to either shift work, sleep disorders or frequent travel between time zones, has negative impact on health. 
Circadian Rhythms: Will It Revolutionise the Management of Diseases? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425903/)


Currently, in developed countries, nights are excessively illuminated (light at night), whereas daytime is mainly spent indoors, and thus people are exposed to much lower light intensities than under natural conditions. In spite of the positive impact of artificial light, we pay a price for the easy access to light during the night: disorganization of our circadian system or chronodisruption (CD), including perturbations in melatonin rhythm. Epidemiological studies show that CD is associated with an increased incidence of diabetes, obesity, heart disease, cognitive and affective impairment, premature aging and some types of cancer.  Protecting the Melatonin Rhythm through Circadian Healthy Light Exposure (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284776/)
NIGMS, the National Institutes of Health resources on Circadian Rhythms and sleep: https://www.nigms.nih.gov/education/pages/factsheet_circadianrhythms.aspx 


Saturday, April 13, 2019

Science of attention, cognition, meditation.

brotThere are many information sources related to meditation. Below is result of my search in scientific publications and lectures that address some aspects of meditation and consciousness: 

Michael Posner's articles on attention networks highlight three meanings that capture aspects of consciousness: 
(1) the neurology of the state of mind allowing coherent orientation to time and place 
(2) the selection of sensory or memorial information for awareness 
(3) the voluntary control over overt responses.

Attentional Networks and Consciousness
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298960/)

The three attention networks are 
(1) alerting network, which focused on brain stem arousal systems along with right hemisphere systems related to sustained vigilance
(2) an orienting network focused on, among other regions, parietal cortex
(3) an executive network, which included midline frontal/anterior cingulate cortex

These are described in great details in the work: The Attention System of the Human Brain: 20 Years After (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413263/)

Developing Brain Networks of Attention
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5257020/)
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5257020/figure/F1/)

There are two forms of training:
(1) practice in tasks that involve particular networks
(2) changes in brain state through such practices as meditation that may influence many networks.
The developing brain in a multitasking world (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371544/)







Sunday, March 17, 2019

Best Photo-Editing Apps with AI, Deep learning and neural network algorithms

Prisma (http://prisma-ai.com/)  - transforms images into artistic effects by utilizing neural network and artificial intelligence algorithms. Prisma is based on open source programming that underlies DeepArt (https://deepart.io/).


ARTi (https://neural-labs.com/en/arti/)  transforms photos into fine art paintings with artificial intelligence algorithms. App analyses pictures and produced hashtags for social networks

Deeparteffects (https://www.deeparteffects.com/) transforms photos with AI and deep learning algorithms. 

It is important to read Privacy Policy and End User Agreements before using image processing apps.

Not only on Instagram, popular photo game and competition app - Gurushots.