- Last 7 days
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www.biorxiv.org www.biorxiv.org
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explore an alternative index design based on k-mer minimizers and integer compression methods
Summary: Compression is achieved by merging the colour sets of k-mers by "similarity"
(from Our contribution section)
In short, our solution merges the color sets of k-mers in a coherent way, e.g., those that share the same minimizer (smallest substring). This allows to save storage space (as the number of indexed sets reduces dramatically).Unlike Bloom- filter based solutions, where approximate color sets are created by merging the color sets of k-mers drawn at random (k-mers that hash to the same bit positions in the filter), we merge them based on their “similarity”.
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en.wikipedia.org en.wikipedia.org
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we obtain the expression for terminal speed of a spherical object moving under creeping flow conditions
what is d in this equation?
characteristic length scale
ordiameter of object
- creeping flow = stokes flow ; low reynold's number / high viscousity conditions
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royalsocietypublishing.org royalsocietypublishing.org
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we develop a proof of concept framework for training a machine learning (ML) algorithm to model bacterial genome composition
Bag of genes model
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www.cell.com www.cell.com
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Summary: human mitochondrial DNA is harder to remove than nuclear DNA from metagenomic datasets meant to house microbial sequences. Stool, oral and skin are especially prone to this mtDNA contamination - Removal by mapping paired reads to a reference genome - Reference genomes lacking mtDNA implicated in leaving them in the databases? - Stringency in having both pairs of read map don't work for small & circular mtDNA (16.5 kb) - + having a single end map to the reference increases spurious matches off-target reads reducing microbial reads
Therefore, extensive validation of the available pipelines is still required.
In our view, the most reliable approach to systematically minimize human DNA and mtDNA contamination in public metagenomic samples would be for the maintainers of public archives to routinely check for this information prior to making records public.
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human mtDNA is an extranuclear molecule of ∼16.5 kilobases
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mtDNA is an informative matrilineal uniparental marker that can be used to trace the ancestry of an individual
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scanned all the assembled contigs from each sample for human mtDNA by running homology search (i.e., BLASTn)
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Positive cases were derived from stool, oral, and skin samples
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it is now considered mandatory to remove human DNA (or RNA) sequencing reads before depositing metagenomes in public repositories
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Human DNA could be considered personal identifying information
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there is not a consensus on which version of the human reference genome to use for human DNA decontamination
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studies that reported exclusion of only reads where both paired-end reads are mapped still detected mtDNA
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small, circular nature of the mitochondrial genome allows reads to span the start and end positions, leading to incomplete exclusion of mtDNA
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nuclear DNA is linear and much larger, so this approach effectively removes most nuclear DNA reads, leaving only minimal traces
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exclude more off-target reads
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using single-end mapping
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extensive validation of the available pipelines is still required.
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academic.oup.com academic.oup.com
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How is this paper different from StrainPhlAn? - What makes it more sensitive for closely related genomes?
Also how does this compare to LoFreq
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he likens freedom to income. He states, “Someone with very limited income has little freedom to choose.”
Do you disagree with this statement then?
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driving beats walking
Does it really? In a place enabled with public transport?
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but they provide benefits to consumers who buy them
?
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- May 2025
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www.researchsquare.com www.researchsquare.com
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we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community
The mock community data is that of whole genomes of ~20 organisms
Reference genomes of 14 bacterial species frequently observed in AGS and activated sludge microbial communities were downloaded from NCBI RefSeq ... + - genomes of Candidatus Moranbacteria and Solirubrobacter bacterium 67 − 14 (reported in AGS and activated sludge studies), retrieved from GenBank, -- as these genera lack official reference genomes. - To incorporate microbial eukaryotes and bacteriophages, the reference genomes of Diploscapter spp., Paramecium spp. and a T4 bacteriophage species were also included. Notably, Paramecium spp. were selected
Simulated untargeted sequencing of these genomes was performed using InSilicoSeq (ISS) v2.01 [27], emulating sequencing via Illumina NovaSeq
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link.springer.com link.springer.com
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hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance
This is confusing. Do you mean had lower sensitivity / higher LOD?
From Discussion
This globally aligns with previously reported detection limits of 90 CFU/mL for Gram positive S. aureus and 15 CFU/mL for Gram negative E. coli [16].
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www.biorxiv.org www.biorxiv.org
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benefit of plasmid-borne CRISPR-Cas is severely reduced against TA-encoding competitor plasmids, but only when plasmid-borne CRISPR-Cas is horizontally transferred
Interesting. Good paper with a well setup experiments. It is intuitive that the long term effect of the toxin-antitoxin (TA) system would outselect any efforts to degrade a plasmid carrying it by any means, including CRISPR-cas.
It is nice to see that this this toy example system has been validated in a broader ecosystem with bioinformatic analysis.
Finally, we further tested our theory and generalized our experimental results by bioinformatically analysing plasmids carrying CRISPR-Cas systems and their target plasmids and found that these targeted plasmids did not typically encode TA systems.
CRISPR-Cas systems are common on bacterial chromosomes (∼42% of chromosomes carry a CRISPR-Cas system), but are also found on ∼3% of plasmids. (Pinilla-Redondo et al., 2022). Plasmid-borne CRISPR-Cas systems can be nucleolytic or silence gene expression, and have been implicated in plasmid warfare (reviewed in (Koonin and Makarova, 2024)): plasmids’ CRISPR spacers tend to match other, competing plasmids – particularly those of similar size which occupy the same niche (Pinilla-Redondo et al., 2022; Benz et al., 2024).
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www.nature.com www.nature.com
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Summary
- Uses marker gene list to differentiate between strains ; could it work will a full core genome alignment?
ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples
define a ‘strain’ as a cluster of marker sequences (subsequences from reference genomes) where the threshold used to define these clusters is an arbitrary user-specified variable.
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www.nature.com www.nature.com
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hundreds of experiments
How many eggs have they used for this!?
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www.tomsguide.com www.tomsguide.com
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unlike regions such as the US or the UK, a very small number of VPNs are actually fit for use within the UAE, which is why choosing a VPN for this particular part of the world can be tricky
why?
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www.bsiranosian.com www.bsiranosian.com
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A more advanced and easier to use workflow manager will be developed that overtakes nextflow in popularity and community support
Does snakemake fit?
Redun satisfies many of these criteria Desirable criteria - python, cloud support, GUI for monitoring
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learn.flowdeploy.com learn.flowdeploy.com
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around 40% of bioinformatics pipelines are written in Snakemake
This is from a twitter poll of 230 people 😒
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learn.flowdeploy.com learn.flowdeploy.com
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pipeline is based on output files for each step, which is clunky for steps which don't produce files.
Seen dummy files used here?
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www.man7.org www.man7.org
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The new session is attached to the current terminal unless -d is given.
Issue with running this
Tmux sessions persist only as long as at least one window or pane remains open (usually with a running shell or a long-lived process). If the command finishes instantly, the session will terminate right away and won't appear in the session list (source: perplexity)
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www.biorxiv.org www.biorxiv.org
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PanTax, a pangenome graph-based taxonomic profiler
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pangenome graphs possess the capability to depict the full range of genetic variability present across multiple
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genomes
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taxonomic classification for strain resolution
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academic.oup.com academic.oup.com
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Summary - ANI is good for closely related microbial species - For distant ones, Amino acid is better (AAI)
Implementation: - Identify markers among the 122 single copy proteins with HMMs - Break protein sequence into k-mers, k = 4 amino acids - Find jacard distance between 2 organisms as an estimator of AAI! - Process done very fast and comparable accuracy to rRNA phylogeny!
Briefly, FastAAI performs, (i) identification of marker proteins in each genome using a set of 122 universal SCP represented by hidden Markov models (HMMs) (Supplementary Table S6, and below), (ii) extraction of tetramers for each protein per genome, (iii) estimation of Jaccard indices based on the tetramers extracted from proteins shared by a genome pair, (iv) estimation of the average Jaccard index ( ) followed by its translation to estimated AAI values
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- Apr 2025
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academic.oup.com academic.oup.com
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Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes
How does this compare to IGV?
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Bakta is reported to find sligthly more of everything compare to prokka
Bakta
: improved accuracy toProkka
, in finding short ORFs - assigns cross-refs to RefSeq, UniProt - higher memory footprint, database size
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Phylogenetics Primer
by Dr. An Dinh (Houston methodist)
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Snippy
Variant calling tool default settings are robust ; good for bacteria.
Underneath the hood, it simply is a pipeline that utilizes a short-read alignment using bwa mem followed by variant calling using FreeBayes. It works incredibly well for multiple tasks
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genomebiology.biomedcentral.com genomebiology.biomedcentral.com
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visualization tool Gingr allows for interactive exploration of trees and alignments
Any alternative to this for Windows?
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qcb.illinois.edu qcb.illinois.edu
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faculty support letter
how is this letter different from the
letter of recommendation
?
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magazine.rice.edu magazine.rice.edu
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By writing a paper, you’re going to have to take all these bits of evidence into account, weigh them and figure out how to articulate them correctly. That’s a process of character building
Why chatGPT can't replace writing
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Annotators
URL
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www.irs.gov www.irs.gov
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Resident aliens, in general, have the same liability for Social Security and Medicare Taxes that U.S. Citizens have.
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www.biorxiv.org www.biorxiv.org
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Cornetto enables us to generate highly complete diploid human genome assemblies using only a single LRS platform
no need to polish assembly with higher accuracy illumina or PacBio?
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www.builder.io www.builder.io
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One other really cool feature of Cursor is automatically generated commit messages with one click.
This is a very useful feature. Windsurf can also do this now?
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www.howtogeek.com www.howtogeek.com
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To move a window to a display oriented to the right of your current display, press Windows + Shift + Right Arrow.
use for top display as well
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Local file Local file
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Micromonas has a flagellum and is motile, with an estimated swimming speed of 100mm/s (i.e., 75 body lengths/s) and is strongly phototactic
Micromonas pusilla
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atio impacts the efficiency of nutrient acquisition
surface area to volume ratio
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Because of their low Re picoplanktondo not sink through the water column as individual cells; they can sink only if pack-aged into larger material (e.g., through predation, fecal pellet, and marine snow for-mation)
Check for similar affirmations from other sources
due to their tiny size, all picoplankton, whether eukaryotic or prokaryotic, have low Reynolds numbers (Re), indicating that their movement is dominated by viscous forces, rather than inertial force
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www.science.org www.science.org
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cell size, density, and nutrient dependency of sinking velocities
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Annotators
URL
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www-annualreviews-org.ezproxy.rice.edu www-annualreviews-org.ezproxy.rice.edu
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When nutrients run out they will often aggregate into flocs that sink quickly out of the photic zone
for small celled diatom species ~ 5 - 50 um size range. - What is the physical effect that causes the flocs to sink? - Higher density vs larger size?
This might work the same for microalgae as well?
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genome.cshlp.org genome.cshlp.org
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formal equation for the action of coding mutations on fitness
Action of coding mutation on fitness = evolutionary importance of site \(*\) amino acid similarity
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www.biorxiv.org www.biorxiv.org
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each unique k-mer is stored only once
Do you also store the counts of each k-mer then?
k-mer counting is quite resource-intensive, as storing large numbers of k-mers along with their counts is expensive in terms of both memory and time.
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almob.biomedcentral.com almob.biomedcentral.com
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Comparing a set of given sequences is a common task
Find homology, construct phylogenetic tree, overlap detection + graphs (for genome assembly) etc.
Comparing a set of given sequences is a common task involved in many bioinformatics applications, such as homology detection [1], overlap detection and the construction of overlap graphs [2,3,4], phylogenetic tree reconstruction, and isoform detection from circular consensus sequence (CCS) reads [5], to name a few.
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www.npr.org www.npr.org
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I just love the look of amazement when anyone looks into the Foldscope for the first time, particularly little kids," Pandiarajan says. "When their eyes light up, I know that's the moment they will embrace science and learning for the rest of their lives."
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www.nature.com www.nature.com
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Oxford Nanopore (older chemistry with 90% mean identity)
is this R9?
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We show that sylph’s ANI estimation is accurate and apply it to species-level profiling through a principled 95% ANI cutoff
Read this paper to figure out why 95% cutoff is called "Principled"
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This tool is good for taxonomic assignment of low abundance organisms from metagenome sequencing data. - low abundance makes it harder to assemble genomes, which is the standard way to assign taxonomy confidently?
Key innovation
key innovation in sylph is a statistical model based on zero-inflated Poisson statistics to debias containment ANI under low coverage
How does this differ from kraken2? - Kraken 2 uses short exact matches to a database (causes false positives) which are controlled by abundance cutoffs and confidence thresholds
Differ from sourmash? - k-mer sketching approaches have ANI estimation bias for low-abundance genomes due to incomplete read coverage - Will need arbitrary thresholds to work for low abundance micro-organisms
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‘marker gene methods’ and not to be confused with 16S sequencing
I guess universal marker gene methods use shortgun/metagenomic sequencing data so is not comparable to amplicon sequencing of 16S?
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However, such methods usually use databases that are difficult to build and hard for users to customize.
such methods =
Species-specific or universal marker gene methods (hereafter denoted as ‘marker gene methods’
Tags
Annotators
URL
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www.nature.com www.nature.com
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maximum growth rates were collected
Is the antibiotic treatment hitting the cells at the maximum growth rate stage? Or can we assume the proportion of current growth rate to maximum observed is the same across all clones?
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- Mar 2025
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www.biorxiv.org www.biorxiv.org
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Each overlapping primer pair is checked to see if it can be added to any pool other than the leading primer pair’s pool.
It gives higher primacy to primers of earlier amplicons?
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www.biorxiv.org www.biorxiv.org
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for k-mer-based tools like Kraken 2, there is no single value of k that consistently yields optimal results across all scenarios
This isn't an issue if k-mer size can be tweaked automatically? Don't know if there is any tool doing this?
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genomebiology.biomedcentral.com genomebiology.biomedcentral.com
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our ensemble machine learning model can label protein-coding sequences with FunSoCs
Functions of Sequences of Concern (FunSoCs)
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You have well-curated data, relevant to your task, already labeled with preferred outputs. You need this data for effective fine-tuning.
Use fine tuning when
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www.biorxiv.org www.biorxiv.org
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the deep learning method D-SCRIPT (a deep learning PPI prediction method shown to have state-of-the-art performance [86] in non-model organisms) to infer the initial, noisy PPI network.
What is the input to this network?
requires only the amino acid sequences of two proteins and predicts a probability of interaction
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academic.oup.com academic.oup.com
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A clear statement of the nature of the intrusive judicial inquiry a parent company could be subjected to in such cases was provided by Lord Bingham when the litigation reached the House of Lords as follows:
Intrusive Judicial Inquiry into Parent Company Liability Lord Bingham’s statement in the House of Lords highlights the level of scrutiny that a parent company may face in transnational tort claims. Courts assess whether the parent company played an active role in controlling the subsidiary’s operations, particularly in matters of health, safety, and environmental standards. This includes an inquiry into:
Corporate Oversight – The extent to which the parent company exercised control over subsidiaries. Knowledge and Responsibility – What the parent company’s directors and employees knew or ought to have known about the subsidiary’s activities. Decision-Making and Action – Whether the parent company took positive steps to ensure compliance or failed to act, leading to harm. Documentary Evidence – Courts examine internal company records, including: Board meeting minutes Reports from directors and employees Correspondence related to oversight of the subsidiary Jurisdiction and Access to Justice The House of Lords upheld jurisdiction in the UK by applying the Connelly principle, which states that English courts should hear cases if there is a real risk that justice would not be accessible in the foreign jurisdiction. This was based on:
The complexity of the litigation, making it difficult to fund and pursue in South Africa. The need for extensive corporate records, which were primarily located in the UK parent company’s offices. Precedents in Parent Company Liability By 2001, English courts had ruled on three key cases affirming parent company liability, establishing that:
The legal principle was not controversial. UK courts should retain jurisdiction under forum non conveniens grounds when justice could not be obtained abroad. Impact on Transnational Litigation This judicial approach set an important precedent, paving the way for future cases like Chandler v Cape (2012) and Okpabi v Shell (2021), reinforcing the principle that parent companies may owe a duty of care to individuals harmed by the actions of their foreign subsidiaries.
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academic.oup.com academic.oup.com
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CD8-depletion antibodies
DOI: 10.1093/infdis/jiad149
Resource: (NIH Nonhuman Primate Reagent Resource Cat# PR-0817, RRID:AB_2716320)
Curator: @giovanni.decastro
SciCrunch record: RRID:AB_2716320
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academic.oup.com academic.oup.comHarlem1
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When I began my work, jazz was a stunt,” was Duke Ellington’s later critique of some of this music11Close—but the slick professionalism of the Harlem stride style also served to expand the audience for African American music in the face of discrimination from cultural elites, both within and without the black community, and despite a severe economic downturn.
for final
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academic.oup.com academic.oup.com
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within the internal perspective. They are first-order claims about what is right or wrong in specific counterfactual conditions, and can thus be glossed in expressivist terms. This is underpinned by the fact that our moral attitudes respond to natural features of the world. We judge that kicking dogs is wrong because of the pain they suffer when kicked, not because we happen to disapprove of such behaviour. Quasi-realists can therefore hold that kicking dogs remains wrong in worlds at which our counterparts approve of it, for o
.kjgjjhk
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academic.oup.com academic.oup.com
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Moreover, just like cognitive disinhibition, schizotypy is correlated with creativity, verbal and visual, with one caveat: Desiring isolation, being introvertive, lacking a capacity for pleasure—these do not predict creativity. They don’t make you more creative, according to the studies.
??
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hey made themselves schizotypal
??
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that he purposefully overrode,
can induce?
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with no regard for the truth of the assertion. To others and to himself, he willfully defied reality. He’d reverse himself, too. If particular lines of argument failed to persuade, he’d advocate others. He’d throw people off by adopting their position as his own. He’d say an idea was crazy, then a week later call it great.
this sounds horrible
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And since you can’t connect what never gets in, art is enhanced potential for connectivity.
!!
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genome.cshlp.org genome.cshlp.org
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Despite the short history of bioinformatics, several software efforts have evolved into a pipeline model
history of toolchaining for bioinformatics
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Seems to be an early paper on toolchaining for bioinformatic workflows. Would be a good reference for introduction when talking about the modern
Nextflow
andSnakemake
workflows
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Annotators
URL
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academic.oup.com academic.oup.com
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the advantages of computational pipelines over ad hoc scripts, even for simple tasks, are all more apparent with increasingly complex datasets and the use of parallel processing.
why pipelines vs ad hoc scripts - track dependencies (statically inferred, DAGs) - rules reused for many files (parallelization) - data tracking (rapid development in subsets of pipeline ~ changing parameters,ie. avoid duplicate work when resuming workflows.)
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genomebiology.biomedcentral.com genomebiology.biomedcentral.com
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the installation, integration, and tuning of multiple software packages, which is not trivial even for groups with extensive bioinformatics expertise.
laborious work of setting up multiple packages
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www.biorxiv.org www.biorxiv.org
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capable of identifying the common markers for each cell type and furnishing encyclopedic explanations rooted in domain expertise
Where is this domain expertise coded? RAG?
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obtain scRNAseq bioinformatics analysis use cases
what does a use case mean?
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BIA builds the Anndata from the sequence read data following standard practice, i.e., aligning public FASTQ files with Cell Ranger software
Would be useful to store the Anndata into some cache for papers that are reused? assuming this generation is an intensive process
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learn.flowdeploy.com learn.flowdeploy.com
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Nextflow's advantages are a broad network of integrations
where do I find these?
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www.biorxiv.org www.biorxiv.org
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healthy individuals contained higher abundances of sugars, myo-inositol, and ellagic acid
Sugars here is a proxy for vegetable fibres?
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www.nature.com www.nature.com
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This should be done for each biological unit
means Genus vs order etc.
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www.theregister.com www.theregister.com
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says that US tech companies are losing "billions" through having to comply with regulations such as the Digital Markets Act (DMA), and having to obtain user consent for their data to be used for advertising purposes
These things are more important than billions in the long term
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US companies face "substantial financial burdens" due to the European Union's digital regulations
Can the EU provide something short term to compensate the cost of digital regulations for companies that are smaller/struggling?
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mastertechvpp.com mastertechvpp.com
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How do I use Roadside Assistance? For all vehicles except Motor Homes & Travel Trailers, dial 866.300.8579
Master tech roadside assistance
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Local file Local file
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Phage T4 was genetically engineered with the optimized nanoluc gene
"codon-optimized"
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The performance of the enhanced bioluminescent reporterphagosensor was carefully evaluated under conditions with target bacteria at differentphases
Did you mean different "concentrations", because I couldn't find any figure that shows different growth phases of bacteria.
It might be useful to discuss that coli forms that contaminate drinking water or other low nutrient samples might typically be in the stationary phase. You can cite this paper for evidence of phage T4 infecting stationary phase bacteria -
Bryan, D., El-Shibiny, A., Hobbs, Z., Porter, J., & Kutter, E. M. (2016). Bacteriophage T4 infection of stationary phase E. coli: life after log from a phage perspective. Frontiers in microbiology, 7, 1391.
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(D) Dose-response curves
fig 6D: did you test without any bacteria or not? Could indicate with a non-detected (ND) label in the chart and clarify in the legend
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(B-C) Specificity of reporter phage-based methodsfor the detection of viable E.coli;
fig 6B: x-axis should list organism names instead of the ATCC numbering for understandability. Organism name could be shortened as P. putida etc. the ATCC numbers can be clarified in the figure legend or methods section as a table/list. Clarify what Mix means in legend
fig 6C: mention in legend what the non-viable E. coli is such as heat killed E. coli etc.
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detection of viable E. coliin juice (1-6), water (7-12), milk (13-18), lettuce (19-24), beef (25-30) samples.
fig 6H: mention the type of sample in the x-axis label. Clarify the colour map title, is it CFU/ml?
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For E.coli, the limit of detection (LOD) was approximately 5 CFU/mL
mention which figure panel shows the 5 CFU/ml detection limit
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4 Conclusions
Extensions to this work should be added to the discussions 1. Detecting different concentrations of E. coli among a mixture of other bacteria would be interesting to know about the specificity. 2. Detecting contamination in real samples or when spiked with unknown contaminating source such as sewage wastewater would be a useful extension to this work.
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E. coli at various concentrations was subjected to different concentrations of E.coli in food samples.
fix sentence
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samples including water, juice and milk was inoculated with E. coli at variousconcentrations.
Does the detection depend on the growth phase of E. coli and how does this correspond to the real world scenario?
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Therefore,T4 phages with short latency times and high burst sizes are promising reporter phagecandidates.
For perspective, you could mention an estimate of the quickest possible detection with this method using short latency, high burst size T4 phages with citations
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Optimization of (A) capture time, (B)phage concentration, and (C) detection time of reporter phages.
Fig 5A: figure legend is too short. Add a short one line description of capture efficiency / how it was measured. This is useful to make the figure self explanatory without referring to methods
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(B)T4Δsoc::nluc and (C) T4 wild type;
fig 3B,C: Use bars of a single colour to improve readability and minimize distraction with multiple colours
fig 3B-E: Describe what the a, b, c, d above the bars are in the figure legend
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To quantify E. coli incomplex food matrices, the samples were incubated with phage-magnetic nanocarriers
need to mention what samples were used
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H) Lysis properties of reporter T4 phage.
? / fig 3H: Needs a negative control of phage without E. coli cells to confirm that the luminiscence happens only upon infection
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A system forassessing EOP value to present the success of infection by the phage:
fig 2E: explain the 1-72 numbers in the y-axis briefly in the legend
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Selection and cleavage efficiency of T4 phage crRNA targeting;
Fig 2B: Avoid the use of bars on a log plot. Show raw data points with dots and use a line to show the mean. - re-order the x axis in descending order and shorten the x-axis labels to just the numbers to minimize redundancy
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Construction of the T4phage CRISPR system in E. coli;
Fig 1 image could be improved for better understanding 1. Avoid yellow which is hard to see 2. show much fewer particles and phages for more clarity (2-3 only) 3. could merge C, D and E and Zoom into B
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nluc gene with twohomologous sequences (S1 and S2)
need to mention everywhere (except abstract) that editing was carried out by homologous recombination with CRISPR based counter-selection.
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Average values are shown foreach experiment. The error bars represent the standard deviations of the data.
Please show individual data points as well
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www.nytimes.com www.nytimes.com
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women are more likely to seek preventive care, visit doctors and follow health recommendations
This might not be applicable for frugal South Asian women who are likely to spend less on non-essential purchases and delay their health check-ups and anything preventative until things get serious. - Will look for a good citation for this..
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Why not instead give each institution a lump sum of money for research and attach reproducibility and replication and scientific integrity requirements to the funds.
Is this somewhat the German model of funding?
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It would put the burden on the institution to figure out the best way to spend the money
There might be downsides to this too
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Local file Local file
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Graph Neural Networks
discussion tomorrow / > 11/Mar/25
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www.sciencedaily.com www.sciencedaily.com
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Anshumali's prime research work on SLIDE algorithms.
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events.rice.edu events.rice.edu
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Rice Cinema
Sewall Hall 301
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bitesizebio.com bitesizebio.com
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Practicing is a double-edged sword. Of course, you want to rehearse your talk, but if you rehearse it too much and have a ‘script’ memorized, it can sound robotic. It can also backfire because if you screw up one little bit of the script, it can cause a sort of domino effect and you can end up totally lost.
I am concerned about this and hence default towards impromptu presentation delivery all the time.
This works great if there's no hard time constraint, such as in casual settings such as lab meetings, but for talks, there needs to be some hybrid strategy?
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- Feb 2025
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www.bakerinstitute.org www.bakerinstitute.org
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Slow the transition to clean energy
Interesting, I would disagree as a gut feeling. Read more
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help.obsidian.md help.obsidian.md
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You can change the image dimensions, by adding |640x480 to the link destination, where 640 is the width and 480 is the height.![[Engelbart.jpg|100x145]]
changing an image size syntax
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timesofindia.indiatimes.com timesofindia.indiatimes.com
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the joint committee’s report to the National Green Tribunal (NGT) pointed out that the RO purifiers also waste almost double the water that they actually purify as ‘reject water’.
This seems likely to be inaccurate
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RO is a simple, yet effective method for filtering out harmful contaminants like TDS (total dissolved solids), host of toxins, arsenic, fluoride, silica, etc. from water
TDS is not a harmful substance. This is misleading
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reverse osmosis filter (RO filter) channels water through a semi-permeable membrane to remove dissolved solids. These dissolved solids include harmful contaminants like lead, mercury, chromium-6, chlorine, etc
need to do a pre-test to see if the water actually contains any of these in concerning levels before hasting into an RO setup
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forum.obsidian.md forum.obsidian.md
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or a Wikilink (using double square brackets) ![[my-image.jpg]]
insert image
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statisticsbyjim.com statisticsbyjim.com
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Consider using the Mann Whitney U test when your data follow a nonnormal distribution, and you have a small sample size. Learn more about the Normal Distribution.
small sample size ~ < 30 (source?) - (logic) If the sample size is large, central limit theorem will rescue non-normal data to apply t-test
If you have more than 15 observations in each group, you might want to use the t-test even when you have nonnormal data. The central limit theorem causes the sampling distributions to converge on normality, making the t-test an appropriate choice.
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www.biorxiv.org www.biorxiv.org
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quick thoughts glancing the paper - Why are you flipping the gene instead of the promoter? :
Better efficiency with a larger flipping region.. - Why did you choose integrase12?
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smartasset.com smartasset.com
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you will owe regular income tax when you make qualified withdrawals
401(a)
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- Jan 2025
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medium.com medium.com
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Take aways: AI will become cheaper and more efficient. - closed source models can cache responses and save computations for repetitive queries - closed source also has possibility of iterative improvements using constant reinforcement learning. - Prioritizing capabilities and deliberate strategy in data selection, carefully designed training objectives.
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We’ve always advocated that our AI processes are orders of magnitude inefficient.
read this paper. AI improvements
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knowledgecafe.rice.edu knowledgecafe.rice.edu
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Car Insurance Special offers by AAA. Please see the flyer for more information.
AAA website has 60% discount right now so it's cheaper to get directly
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blogs.nvidia.com blogs.nvidia.com
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The court clerk of AI is a process called retrieval-augmented generation, or RAG for short.
great example! RAG's => special expertise that is domain specific that is retrieved from a well curated library of text.
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www.consumerreports.org www.consumerreports.org
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The low rolling resistance tires tend to transmit road-induced impacts into the cabin
Does replacing tires improve this? these are fuel efficient though!
Source: discounttire
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www.autotrader.com www.autotrader.com
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Test drive with sellers. Buy cars online. Clean title. No hassle. Free AutoCheck report, fraud protection, financing, vehicle service contracts and GAP insurance available.
Autotrader private seller exchange
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www.man7.org www.man7.org
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-t sort by time, newest first; see --time
ls
sorted output by time ; use-d
for descending order
Tags
Annotators
URL
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bitesizebio.com bitesizebio.com
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identical alignments when searching different databases may not receive the same e-value
difference in the number of sequences across databases
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aiml.rice.edu aiml.rice.eduCourses1
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introductory AI courses at Rice University
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www.consumerreports.org www.consumerreports.org
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If the battery ever did need to be replaced, it would run between $2,200 and $2,600 from a Toyota dealer, but it's doubtful that anyone would purchase a new battery for such an old car. Most will probably choose to buy a low-mileage unit from a salvage yard, just as they would with an engine or transmission. We found many units available for around $500.
battery tips,
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www.pnas.org www.pnas.org
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addition of IPTG should induce high expression of Cas1 and Cas2 in nongrowing bacteria since they have kept a high copy number of pSCRATCH, while growing bacteria should not express the Cas proteins in sufficient quantities for spacer acquisition
Any issues with expressing new proteins when non-growing?
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qiime2.org qiime2.orgQIIME 21
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Your analysis is complex - QIIME 2 records the steps you took to be sure that your work will be reproducible by you or others
- Does this provenance record the parameters used for reach step?
- Is there also a way of sharing the whole recipe with others that enables something like a one-click reproducibility?
Because dadasnake has these features which will make it a better tool for particular NGS sequence analysis
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www.caranddriver.com www.caranddriver.com
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the brand's novel ProPilot Assist semi-autonomous driving mode is available on SV, SV Plus, and SL trims as part of the Technology package; it's standard on the SL Plus
2021 Nissan leaf
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Annotators
URL
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Local file Local file
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Locked primary admin user accounts can now be unlocked remotely with respective user ID and aone-time password (OTP) (see Section 5.12.4 Resetting a user password of the QIAcube ConnectUser Manual)
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www.biorxiv.org www.biorxiv.org
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This paper is too specific to transcriptomic analysis but it has some inspiration. - This seems more of a substitute for R and python workflows as opposed to a complete tool-chain philosophy that could put together mature command line tools like Nextflow. So this is more relevant for final polishing etc. - They don't mention what backend they are using as the LLM. Is it just making API calls to chatGPT or something they coded themselves? this would be most relevant to know for Omi
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users can copy and paste it to create the figures
can automate running the code too?
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advances in prompt engineering1, agents2, retrieval-augmented generation (RAG)3, and fine-tuning4
LLM advances
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result documentation: the copilot now supports the generation of PDFs that include images and detailed analysis
useful. Need to have customizable sections and added explanations of terms and meanings of measures if user requires.
How does a html work with clickable/hover hyperlinks for defining key complex terms for first time users?
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pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov
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we demonstrate intragenerational genetic biocontrol, wherein mating with engineered males reduces female lifespan
how does this persist evolutionarily - would this have higher selective pressure to mutate away?
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oiss.rice.edu oiss.rice.edu
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There are several reporting requirements that apply to you while you are on your STEM extension to ensure that you are maintaining your F-1 status.
STEM OPT recipients must make a "validation report" to their school every six months starting from the date the 24-month extension begins - Regardless of change in employment
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stackoverflow.com stackoverflow.com
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Meta-f Move forward a word, where a word is composed of letters and digits.
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cutadapt.readthedocs.io cutadapt.readthedocs.io
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This is usually how forward PCR primers are found in the read in amplicon sequencing, for instance
anchored 5' adapters
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stackoverflow.com stackoverflow.com
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Show activity on this post. Use Esc + D or Alt + D to delete the word on the right.
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itsfoss.com itsfoss.com
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Ctrl + WDelete the word before the cursor.
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Ctrl + UDelete from the cursor to the start of the line.
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Annotators
URL
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ecm.capitalone.com ecm.capitalone.com
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questions about a specific vehicle’s coverageor organization where the vehicle is being reserved, callthe Benefit Administrator at 1-800-825-4062
Check if Zipcar works as a valid rental car
-
Trip Cancellation and Interruption benefits pay up to twothousand dollars ($2,000.00) per Insured Person for the non-refundable Common Carrier ticket(s) that You paid for withYour covered Account and/or rewards programs associatedwith Your covered Account.
only applicable in narrow cases - death, injury, illness or insolvency
-
Wear and tear, gradual deterioration, or mechanicalbreakdown
not covered
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www.americanexpress.com www.americanexpress.com
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Damage which is due and confined to freezing, mechanical or electrical breakdownor failure unless such Damage results from a Theft Covered Event
not covered
-
Benefits are provided to Eligible Renters up to $50,000 per Rental Agreement forDamage to or Theft of a Rental Vehicle
Amex, blue cash preferred
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www.capitalone.com www.capitalone.com
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Report your covered event to your card’s benefits administrator as soon as possible. To open a claim with Mastercard, go online or call 877-288-6784; with Visa, go online or call 1-800-825-4062.
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ecm.capitalone.com ecm.capitalone.com
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Roadside Dispatch is a pay-per-use roadside assistance program. The programprovides you with security and convenience wherever your travels take you.For roadside assistance, call 1-800-847-2869.
is this applicable for
visa infinite
as well?
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- Dec 2024
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scienceadvance.com scienceadvance.com
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A 2007 study published in PLOS ONE confirmed this unique energy mechanism, showing that fungi exposed to high radiation levels grow faster than those in non-radioactive conditions.
Find this paper and speculate on the mechanism of energy conversion
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en.wikipedia.org en.wikipedia.org
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Melanin may also be able to help the fungus metabolize radiation, but more evidence and research is still needed.[1]
Would be interesting to see hypotheses as to the mechanism in which energy could be harvested by melanin and any experiments that could test it?
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Annotators
URL
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www.sciencedirect.com www.sciencedirect.com
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It is known that all plasmids transmissible by conjugation contain a known relaxase [42].
This is debatable. OriT is enough if Mob relaxase is supplied in trans.
Kiara wants a fact-check on this
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pubs.acs.org pubs.acs.org
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yeast assembly has been used
Is there a good way to remove the yeast selection regions and yeast Ori after the assembly?
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RP4 plasmid (also known as RK2, RP1, and the Birmingham plasmid) stands not only as a model of bacterial conjugation studied over the past 40 years, but also as one of the most conspicuous, broad-host range conjugative plasmids described in the literature. It mediates mating and plasmid transfer between a wide variety of Gram– donors/recipients (8) and is also capable of efficiently conjugating with Gram+, (9) yeast (10,11) and mammalian cells. (12)
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Annotators
URL
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www.mdpi.com www.mdpi.com
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Optimization parameters included: (i) molten agar media temperature, (ii) molten agar media agar concentration, and (iii) volumes of E. coli and S. cerevisiae cell suspensions harvested at various optical densities (ODs)
Best protocol : 60C, 2% agar ; 100 ul each of donor and recipient at OD of 1. - Use 20 - 60% of the mix for fewer and larger colonies
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Some conjugation systems, such as IncF, IncH, and IncI plasmids, transfer DNA efficiently in liquid media, while others, including the IncN, IncM, IncP, and IncW plasmids, achieve higher DNA transfer frequencies on solid media [28]. It is suspected that the ability to transfer DNA in different environmental conditions is related to variation in pilus formation, structure, and stability of cells during the conjugation process.
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such a protocol may permit more accurate enumeration of transconjugants by avoiding the use of a spreader while plating cells on selective media
How will this conjugation protocol allow enumeration of only transconjugants by excluding the donors in the mix?
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may enhance the ability to transfer plasmids and chromosomes greater than 100 kbp
This is testable easily ; with a fluorescence carrying plasmid and flow cytometry counting
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we developed a procedure for conjugation within solid media. Such a protocol may expand conjugation as a tool for DNA transfer to species that require semi-solid or solid media for growth
embedded inside soft agar
Tags
Annotators
URL
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- Nov 2024
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A. thaliana (hereafter referred to as Arabidopsis)
Good choice instead of an acronym..
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www.nature.com www.nature.com
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Over the last 25 years, shotgun metagenomic sequencing1 and associated computational methods have developed as robust, efficient ways to study the taxonomic composition
Read to figure out benefits compared to marker genes profiling such as 16S?
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Annotators
URL
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huttenhower.sph.harvard.edu huttenhower.sph.harvard.edu
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MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins
This same dataset might be handy to find and parse for better universal marker genes across phyla or all bacteria?
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biotium.com biotium.com
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Template Buffer should be at 1X inthe final reaction
effectively, 0.5 ul of the tempalate buffer per 20 ul reaction
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- Oct 2024
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journals.plos.org journals.plos.org
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not compatible with real-time PCR due to the presence of unnatural nucleotides in their sequence
This is an unfounded argument ; Inosine bases are perfectly fine to use in qPCR primers
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journals.plos.org journals.plos.org
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removal of sequences containing nonsense mutations was found to be a valuable filter in addition to flowgram-based denoising
stop codons and frameshifts
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biotium.com biotium.com
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1.8 uL diluted ROX per 20 uL
Note that 20 ul reaction is equivalent to 10 ul of the master mix..
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- Sep 2024
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www.nature.com www.nature.com
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We found a distinctive wheel-shaped arrangement of the cells
Is this arrangement dependent on the 100 kb collapse or the UMAP dimensionality reduction algorithm used?
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Studying gene–gene correlations on a local scale, we observed the expected high correlations between the expression profiles of genes residing in the same operon
How did you chose these few operons/ this chromosomal region for this analysis?
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Principal component analysis (PCA) at the gene level
read up: why PCA pattern differs from UMAP?
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Two-dimensional projection by uniform manifold approximation and projection (UMAP) of LB-grown E. coli
why UMAP vs other dimensionality reduction methods? - read methods?
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bmcmicrobiol.biomedcentral.com bmcmicrobiol.biomedcentral.com
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Degenerate consensual pairs of rpoB primers called Univ_rpoB_F_deg (forward primer) and Univ_rpoB_R_deg (reverse primer) were manually designed from clustalW alignments
How small was this alignment that you manually design primers?
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we constructed a reference database including ~ 45000 sequences; this database is available from the FROGS website (http://frogs.toulouse.inra.fr/).
Does database have full rpoB or only 434 bp region?
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royalsocietypublishing-org.ezproxy.rice.edu royalsocietypublishing-org.ezproxy.rice.edu
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In many cases, such variations reflect differences in the essentiality of genes. Genes with higher connectivity are often more essential for the reproductive success of a cell or organism
This assumption will not hold true for auxiallary genes or genes not in the core genome but still contribute to essential functions conditional to certain circumstances? for example: antibiotic resistance genes?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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poses challenges for many classical methods, such as parametric statistical tests (for example, Student’s t-test and ANOVA) and measures of correlation, including Spearman’s rank correlation, often leading to completely unacceptable false discovery rates above 90%
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We recommend that these methods replace OTU-based approaches for all applications, except when it is necessary to combine sequence data that were generated using different technologies (that is, Illumina sequencing and 454 pyrosequencing) or with different primer sets, when mapping to a common reference database of full-length sequences is often still needed
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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The number of k-mers in each hash bin is tabulated
across all input sequences I assume?
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If rearrangement events and horizontal transfers are rare for the 16S rRNA gene, as is widely believed to be the case, then its true gene tree is likely to be a good approximation to the true phylogenetic tree based on vertically inherited traits, assuming that the latter tree can be meaningfully defined
Is this really true? If so, it must be true for every gene right?
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If an environmental sequence is annotated as belonging to a taxon which is defined by traits, then this is a prediction which can always be checked in principle
taxonomy by phenotype~?
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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highly multiplexed ribosomal (r)RNA-FISH
Why chose rRNA vs other phylogenetic marker genes?
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link.springer.com link.springer.com
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The diversity of bacteria can also be accessed by using COI, rpoB, cpn60 (encodes for chaperonin protein), tuf (elongation factor), RIF (Replication initiation factor), and gnd (Gluconate-6-phosphate dehydrogenase) gene as barcode
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www.sciencedirect.com www.sciencedirect.com
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The origin of the rain is not clear. Rain often is attributed to delayed PCR onset [3] or partial PCR inhibition in individual droplets [4]. However, it could also be a consequence of damaged positive droplets with corresponding reduced fluorescence, or damaged negative droplets with increased background fluorescence, or a mixture of both [5].
Tags
Annotators
URL
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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we found that the clouds can become more compact and produce substantially less rain upon: (i) reducing the ramp rate to 1 °C/sec in every PCR step (Fig. 10a), (ii) increasing the annealing/extension time to 2 minutes (up from 1 minute; Fig. 10b), and (iii) increasing the number of cycles to 50 (Fig. 10c)28
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rnajournal.cshlp.org rnajournal.cshlp.org
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Trans-splicing ribozymes can, in principle, target every uridine residue of a substrate RNA, but the target sites need to be accessible.
Can RNA folding prediction tools be used to predict accessibility?
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In this assay, the mRNA is incubated with trans-splicing ribozymes that carry a randomized internal guide sequence (IGS). This enables the ribozyme population to splice on every accessible site on the mRNA. The sites at which trans-splicing occurred were identified by RT-PCR, cloning, and sequencing
This might be a way to test for accessibility of the site for splicing from a secondary structure point of view?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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we performed RT-qPCR on the high-performing RENDR design, split site 15. We observed a 93-fold increase in the abundance of spliced mRNA in cells expressing both RENDR and RNA input compared to control cells lacking the RNA input
This split site 15 from Fig 2 was used in the RAM paper as well (RAM = Ribozyme addressable memory)
- 15 corresponds to: (IGS / 6 bp + P1_loop_01 / 9 bp)
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RENDR variants sensing different RNA inputs from RFP
These are all based on splice site 15 from fig 2. This should have been explicitly mentioned :😞
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best design delivers a 93-fold dynamic range of splicing with RENDR controlling fluorescent protein production in response to an RNA input
wasn't the dynamic range much higher (10^4 fold?!) when we checked with qPCR?
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Local file Local file
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P1_loop_03 TAGTTACCTTT
Why was this
T>G
mutation used here?
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P1_loop_03 TAGTTACCTTT
Look for the reasoning for this T>G substitution
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AAATAGCAATATTTACCTTTGGGTCA
WT P1 loop and IGS annotated here
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www.sciencedirect.com www.sciencedirect.com
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adjustments must be made in the IGS to allow the formation of a stable P10 helix
How can you adjust the IGS when there are two constrains on it from both P1 and P10?
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- Aug 2024
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oiss.rice.edu oiss.rice.edu
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Here is the information you may need in order to complete page 2 of the Form I-983:
If your employer is Rice University, here's the E-verify info -
Employer's Name as Listed in E-Verify: Rice University Rice's E-Verify ID: 698729
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