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Context effects produced by question orders reveal quantum nature of human judgments


Via Arjen ten Have
Mel Melendrez-Vallard's insight:

Great Insight from Arjen ten Have's:

"So do you still believe in free will? I must say, this flabbergasts me but this is just sooooooooooo nice. Good start of the week! In recent years, quantum probability theory has been used to explain a range of seemingly irrational human decision-making behaviors. The quantum models generally outperform traditional models in fitting human data, but both modeling approaches require optimizing parameter values. However, quantum theory makes a universal, nonparametric prediction for differing outcomes when two successive questions (e.g., attitude judgments) are asked in different orders. Quite remarkably, this prediction was strongly upheld in 70 national surveys carried out over the last decade (and in two laboratory experiments) and is not one derivable by any known cognitive constraints. The findings lend strong support to the idea that human decision making may be based on quantum probability"
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Arjen ten Have's curator insight, June 16, 9:26 PM
So do you still believe in free will? I must say, this flabbergasts me but this is just sooooooooooo nice. Good start of the week! In recent years, quantum probability theory has been used to explain a range of seemingly irrational human decision-making behaviors. The quantum models generally outperform traditional models in fitting human data, but both modeling approaches require optimizing parameter values. However, quantum theory makes a universal, nonparametric prediction for differing outcomes when two successive questions (e.g., attitude judgments) are asked in different orders. Quite remarkably, this prediction was strongly upheld in 70 national surveys carried out over the last decade (and in two laboratory experiments) and is not one derivable by any known cognitive constraints. The findings lend strong support to the idea that human decision making may be based on quantum probability
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Reagent contamination can critically impact sequence-based microbiome analyses

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Mel Melendrez-Vallard's insight:

Interesting discussion in comment section Reagent contamination can impacts microbiome analyses

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Was John Snow more of an empiricist than the miasmatists?

Was John Snow more of an empiricist than the miasmatists? | Tools and tips for scientific tinkers and tailors | Scoop.it
If you know anything about epidemiology, you know that the iconic Broad Street pump in the Soho district of London is the site of what is considered to have been the first modern, epidemiological study.
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The Ebola Number You Haven't Heard: 80% Of U.S. Ebola Patients Have Survived

The Ebola Number You Haven't Heard: 80% Of U.S. Ebola Patients Have Survived | Tools and tips for scientific tinkers and tailors | Scoop.it
Ebola's a death sentence — or at least, that's the popular wisdom. And in the current West Africa outbreak, that's not far from the truth. The Ebola survival rate in Guinea might be somewhere around 30%.

Via Technical Dr. Inc.
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Rescooped by Mel Melendrez-Vallard from Virology and Bioinformatics from Virology.ca
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Omics Find Chinks in Ebola Armor for Vaccine and Drug Development

On October 12, the Ebola crisis hit home in a new way, as the first case of person-to-person transmission of the virus was reported in Texas. A nurse who helped treat the Liberian man who died from the virus has tested positive for the disease, despite wearing a gown, gloves, mask, and other protective gear while in contact with the victim.

Ebola (EBOV), a single-stranded RNA filovirus, causes infections characterized by immune suppression and a systemic inflammatory response. This results in impairment of the vascular, coagulation, and immune systems, leading to multiorgan failure and shock (in some ways resembling septic shock).

But while overwhelming challenges in controlling and treating this disease remain, the availability of genomic and proteomic data accumulated and shared by researchers since the virus’ discovery in 1976 has already translated into invaluable knowledge about the deadly RNA virus, pinpointing potential targets for diagnostics, vaccines, and therapeutics.


Via Ed Rybicki
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Ed Rybicki's curator insight, October 21, 11:29 AM

Of COURSE 'omics will solve the problem.  It can solve EVERYTHING B-)

Rescooped by Mel Melendrez-Vallard from Systems biology and bioinformatics
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Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group

Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group | Tools and tips for scientific tinkers and tailors | Scoop.it

Via Dmitry Alexeev
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Dmitry Alexeev's curator insight, Today, 4:12 AM

biogeography and reference free

 

we are getting deeper

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Crucial gene for Malaria Transmission

How can malaria be exterminated? This is a vital question, because 200 million people worldwide are currently affected by this deadly disease. Unfortunately, answering this big question was a bridg...
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Study reveals how deadly MERS virus enters human cells | Cornell Chronicle

Cornell Chronicle: Daily news from Cornell University
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A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer

Background: The MinIONTM is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies.It measures four inches in length and is powered from the USB 3.0 port of a laptop computer.The MinIONTM measures the change in current...
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Rescooped by Mel Melendrez-Vallard from Amazing Science
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UCSC Ebola genome browser now online to aid researchers' response to crisis

UCSC Ebola genome browser now online to aid researchers' response to crisis | Tools and tips for scientific tinkers and tailors | Scoop.it

The UC Santa Cruz Genomics Institute late Tuesday (September 30) released a new Ebola genome browser to assist global efforts to develop a vaccine and antiserum to help stop the spread of the Ebola virus.

The team led by University of California, Santa Cruz researcher Jim Kent worked around the clock for the past week, communicating with international partners to gather and present the most current data. The Ebola virus browser aligns five strains of Ebola with two strains of the related Marburg virus. Within these strains, Kent and other members of the UC Santa Cruz Genome Browser team have aligned 148 individual viral genomes, including 102 from the current West Africa outbreak.

UC Santa Cruz has established the UCSC Ebola Genome Portal, with links to the new Ebola genome browser as well as links to all the relevant scientific literature on the virus. 

“Ebola has been one of my biggest fears ever since I learned about it in my first microbiology class in 1997," said Kent, who 14 years ago created the first working draft of the human genome.  "We need a heroic worldwide effort to contain Ebola. Making an informatics resource like the genome browser for Ebola researchers is the least we could do.”

Scientists around the world can access the open-source browser to compare genetic changes in the virus genome and areas where it remains the same. The browser allows scientists and researchers from drug companies, other universities, and governments to study the virus and its genomic changes as they seek a solution to halt the epidemic. 


Via Dr. Stefan Gruenwald
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De Novo Transcriptome Sequencing Analysis and Comparison of Differentially Expressed Genes (DEGs) in Macrobrachium rosenbergii in China

by Hai Nguyen Thanh, Liangjie Zhao, Qigen Liu
Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture.
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Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures | RNA-Seq Blog

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures | RNA-Seq Blog | Tools and tips for scientific tinkers and tailors | Scoop.it
There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression
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TWiV 307: Ebola aetiology

Tara Smith joins the TWiEBOVsters to discuss the Ebola virus outbreak, spread of the disease to and within the US, transmission of the virus, and more.
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Here's What It Looks Like When Ebola Fear Comes to the Heartland

How one American university is handling a brush with the deadly disease.
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One opinion on writing an NSF preproposal

After last year's inaugural round of NSF Bio preproposals there was a flurry of discussion regarding what made a successful application. After attending a panel, I've expressed what I thought made ...
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NPR: When Women Stopped Coding

For decades, the share of women majoring in computer science was rising. Then, in the 1980s, something changed.
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Oxford MinION at ASHG 2014: Updates on MinION and Promethion

Oxford Nanopore at ASHG 2014
It is almost two years ago at ASHG 2012, Oxford Nanopore showed off Oxford MinION at ASHG 2012.
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Rescooped by Mel Melendrez-Vallard from Amazing Science
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Using monoclonal antibodies produced in plants to fight off a lethal virus like Ebola


Kevin Whaley, the CEO at Mapp Bio isn't much given to publicly discussing ZMapp, the remarkable new treatment for Ebola, at all. At a time when every public biotech company with a preclinical program for Ebola is clamoring for attention, Whaley has given precious few interviews. And when he has talked about ZMapp, he's been careful to say that the company doesn't know whether it works and has lots more work to do. If anything, the air of mystery has only heightened the lurid 24/7 cable news attention given to ZMapp, which could help revolutionize the way in which outbreaks are treated in years to come.


Via Dr. Stefan Gruenwald
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How Firestone controlled Ebola virus disease in Liberia

When the first case of Ebola virus infection was detected at Firestone Liberia, Inc. the company needed to prevent the virus from spreading.
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WHO | Nigeria is now free of Ebola virus transmission

WHO officially declares that Nigeria is now free of Ebola virus transmission.
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Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

Background:
Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities.
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Rescooped by Mel Melendrez-Vallard from Bioinformatics, Comparative Genomics and Molecular Evolution
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Origins of major archaeal clades correspond to gene acquisitions from bacteria : Nature : Nature Publishing Group

Origins of major archaeal clades correspond to gene acquisitions from bacteria : Nature : Nature Publishing Group | Tools and tips for scientific tinkers and tailors | Scoop.it
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms[mdash]ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

Via Arjen ten Have
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Arjen ten Have's curator insight, October 20, 3:04 PM

HGT is for prokaryotes as sex is for eukaryotes. They form the  most interesting emergent property of evolution. But this goes beyond the fact that HGT is pretty normal in prokaryotes: This paper actually shows it drives evolution and speciation, and indirectly substantiates the hypothesis that early and prokaryote evolution is communal, which explains the evolution of the genetic code. Oh my, this is YUMMIIE!

Rescooped by Mel Melendrez-Vallard from Systems biology and bioinformatics
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Genome Medicine | Abstract | Modules, networks and systems medicine for understanding disease and aiding diagnosis

Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.

Via Dmitry Alexeev
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Dmitry Alexeev's curator insight, October 21, 5:59 AM

systems medicine in translation

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PacBio Blog: SMRT Sequencing for the HLA Complex: PacBio Goes to ASHI

Attend our #ASHI2014 workshop w speakers from @AnthonyNolan, Histogenetics & the National Bone Marrow Donor Program http://t.co/WQZNEKrN2S
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The NewYorker: Inside the Ebola Wars

As the epidemic widens, the virus is mutating. Geneticists are racing to keep up. Richard Preston reports.
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Can Ebola virus infect via the skin?

The outer layer of the skin is dead, and viruses landing on skin cannot simply replicate. However they can enter the body via cuts or abrasions.
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Removing Disease from the Genome

Removing Disease from the Genome | Tools and tips for scientific tinkers and tailors | Scoop.it
Scientists removed and replaced gene causing muscular dystrophy in mice. Most diseases are really complex. Not just when it comes to symptoms and outward appearance, but also considering their tang...
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