James Lyons-Weiler, PhD
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Author, CEO, President, Scientist, Editor-in-Chief and President at Institute for Pure and Applied Knowledge http://ipaknowledge.org

Editor in chief of the Journal Science, Public Health Policy and the Law http://publichealthpolicyjournal.com
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Sequence-based COVID19 testing is here. NAATEC consortium member Dr. Sin Hang Lee's lab has won CLIA certification to use Sanger sequencing to detect COVID19 in a more accurate manner. No more Ct threshold baloney. Dr. Lee show other lab how this is done. https://www.wtnh.com/news/health/coronavirus/new-type-of-covid-test-developed-in-milford-lab-samples-virus-infected-cells-for-more-accuracy/ #Science
Registration is still open - first bioinformatics class is today @ 1PM ET. Get some bioinformatics skills from an expert. Here's the syllabus. Register here - > https://ipak-edu.org/old-home-2/

SYLLABUS (Subject to change)

Biology 202

Bioinformatics

with Dr. Lyons-Weiler

Classes Start June 1, 2021

Amaze and astound your friends and family! Imagine if you could analyze any DNA, RNA or protein sequence and run analyses on it to determine its likely identity, function, structure, relationships to other nucleotide sequence. If it's an RNA sequence, what is its likely structure? If it's DNA, does it encode a protein? Does the protein have a likely special function, or cellular location? Does the protein have conserved domains? If it’s a viral or bacterial protein, does it have any immunogenic epitopes? If so, what are they, and do they match human proteins in a manner that might lead to pathogenic priming? Plus much, much more.

Course Description: This course will provide students with an introduction to some of the important fundamental skill sets in Bioinformatics. In-depth description of methods and algorithms will provide background and hands-on experience with software will provide practical experience. Concepts and approaches to DNA and amino acid sequence alignment, homology, conserved domain identification, phylogenetic inference, array-based transcriptomics, quantitative PCR analysis and peptide identification searches will be presented. Basic computing skills are required.

Learning Outcomes:

Students will

· Understand molecular biology of genes, transcription and translation beyond central dogma

· Search biological databases containing sequences, clinical, and structural information

· Retrieve information from these biological databases

· Perform structure/function analysis of biological molecules

· Perform DNA/protein sequence alignment and analysis

· Identify homologs and conserved domains

· Perform a basic phylogenetic inference from a multiple sequence alignment

· Identify differentially expressed genes in a microarray data set

· Be able to interpret the output of a quantitative RT-PCR experiment

· Understand peptide identification search algorithms given proteomics profiles

· Be able to detect structure in small RNAs

Time Tuesdays 1:00PM-3:00PM (usually lasts an hour or so)

Instructor: James Lyons-Weiler

Required Materials: Students will make extensive use of computers and the internet. PC software to be used includes various web applications.

Recommended Text(s): Recommended readings will be sent each week. The book that most closely parallels our in-class experiences is David Mount’s Bioinformatics: Sequence and Genome Analysis. However, every student of Biotechnology should get and read a copy of Campbell & Heyer’s Discovering Genomics, Proteomics and Bioinformatics.

Directed Study: Data analysis using web-based database searches, sequence analysis, protein structure analysis, phylogenetic trees, transcriptomics, proteomic peptide identification, qPCR. Interpretation of current journal articles involving bioinformatics and QA/QC.

Teaching Methods:

Emphasis on learning by doing – directed exercises in 1) use of a variety of web applications, 2) interpretation of results from those applications, 3) in-class/take-home exercises that build on past experiences, 4) in-class quizzes and exams.

The assignments and content will rely on web-based tutorials and specific assignments from bioinformatics websites. The tools and resources for bioinformatics are generally free to the public. They lend themselves to exploration, so students are encouraged to ask and seek answers for impromptu questions.

Course Plan:

1 Beyond the Central Dogma Course Overview.

Lecture on transcription, translation, alternative splicing, RNA editing, post-translational modification. Find splice variants (isoforms) of sequences with the same gene name in Genbank. Homework Assignment #1

2 Overview of Bioinformatics Resources.
General description of bioinformatics resources, introduction to NCBI, Genbank, Pubmed, Nucleotide, Protein Identify a gene of interest related to a disease or disease state of interest to the student. Find the nucleotide sequence in the Nucleotide database. Find the protein sequence in the Nucleotide entry and in the Protein database. Homework Assignment #2

3 BLAST Searching sequence databases.

Performing BLAST comparisons between two sequences. BLASTing one sequence against a chosen database In-class/take-home exercise. BLAST a sequence of interest against Nucleotide database @ NCBI and BLAST 2 Sequences. Homework Assignment #3

4 Pairwise Sequence Alignment

Principles of sequence alignment algorithm In-class/take-home exercise with alignment of two sequences. Homework Assignment #4

5 Studying Your Sequence Open Reading Frames and the Conserved Domain Database In-class/take-home exercise of finding open reading frames in nucleotide sequences using ORF, and finding conserved domains in protein sequences via the CDD. Homework Assignment #5

6 Identifying Immunogenic Epitopes in Pathogen Proteins

7 Identifying Potentially Autoreactogenic Epitopes in Pathogen Proteins

8 Conserved Domains Conserved Domain Database part 2 and Homologene

In-class/take-home exercise on identification of conserved domains in amino acid coding sequences and finding homologs. Homework Assignment #6

9 Phylogenetic Inference ClustalW multiple sequence alignment tools.

Tools for estimating phylogenetic trees. Derive a multiple alignment and a phylogenetic tree for homologs of the student’s sequence of interest.

Homework Assignment #7

10 Transcriptomics with Microarrays 1 The Basics Read an overview on transcriptomics with microarrays. None.

11 Transcriptomics with Microarrays 2

Normalization/Transformation; Identifying Differentially Expressed Genes Implement a simple analysis comparing gene expression in two clinical groups using a web application. Homework Assignment #8

12 Quantitative

PCR Interpretation of qRT-PCR results Given qRT-PCR output, perform interpretation of CT values. Homework Assignment #9

13 Proteomics

Peptide identification Mass-spec profile peptide identification/Mascot/Sequest/X-Tandem/Consensus Perform an online peptide fingerprint search Homework Assignment #10

14 Small RNAs

Computational Analysis of Small RNAs Use web tools to predict small RNA structure/function Homework Assignment #11

15 Summing it All Up
COVID-19 Diagnosis Numbers and Deaths Fiasco Continues

Dr. Jack and Dr. Henry Ealy get into the question of whether CDC changed their criterion for considering COVID-19 cases in the vaccinated compared to those in use since April 2020 - and they review the startling statistics on deaths and vaccine adverse events being reported following COVID-19 vaccination. Fact-checkers beware: We're fact-checking you AGAIN.
(IPAK CEO & Director Accuses CDC of Fraud) FACT-CHECKING THE FACT-CHECKERS: In a live #UNBREAKINGSCIENCE podcast today with guest Dr. Henry Ealy, IPAK CEO & Director Dr. James Lyons-Weiler, upon reviewing the facts of whether CDC changed the criteria for surveilling and reporting COVID-19 cases in persons vaccinated against COVID-19, realized that the CDC had changed the outcome measure during a post-market "pharmacovigilence" COVID-19 vaccine safety & efficacy trials. Dr. Lyons-Weiler (aka Dr. Jack) called the change "scientific fraud". Dr. Ealy and Dr. Jack debunk so-called "fact-checker" claims that CDC did not change the criteria for tracking COVID-19 cases among the vaccinated, and review recent data on deaths reported in the VAERS database. Dr. Ealy reported an anomaly where the number of deaths following the COVID-19 vaccine DECREASED this week compared to last.

Don't miss this episode of #UnbreakingScience - and please heed Dr. Jack's call to get this information to your Congressional Representatives and Senators. The video is currently available on YouTube - we'll see for how long!

https://www.youtube.com/watch?v=Rn5B9HBx3io
STOP to end
One-third of sites contaminated is somehow "not widespread"??? #envtox Sign up for my Certificate Course in Environmental Toxicology now, get educated and fight for clean air, water, food.... classes start in the fall. Http://ipak-edu.org

https://www.wgal.com/article/pfas-chemicals-found-in-a-third-of-water-samples-pennsylvania-says/36635708
Registration is now OPEN at IPAK-EDU.org for our FOUNDATIONAL LAW COURSE, "HISTORY OF LAW IN THE WEST & THE US" - Instructor Robert Rigny. This course is a required prerequisite for all future courses in the law curriculum. {Note: These courses are designed to teach key principles of law TO THE PUBLIC and are NOT meant to substitute law training toward a law degree}.

An educated public is an empowered public!

https://ipak-edu.org/old-home-2/?store-page=History-of-Law-in-the-West-and-the-US-p364517198

#IPAEDU #LEARN
Tired of toxins? Sign up to take this course in the fall and you will learn what you need to learn to participate in ending corporate toxins.

https://ipak-edu.org/old-home-2/?store-page=Environmental-Toxicology-A-p360046326

https://civileats.com/2021/06/15/dead-bees-sick-residents-from-pesticide-pollution-in-a-nebraska/
For more info, email info@ipak-edu.org, subject line #COVIDCOURSE

We're planning an annual Key Readings in Public Health course at IPAK-EDU in which teams of students read specific published studies and reports and then share w/the class their overview, incl. strengths & weaknesses. This way everyone can be solid on what resources exist for their positions and knowledge. Here's the draft syllabus. I have collected and will be organizing most of the studies and reports for reading.

Key Studies in Public Health - Topic – COVID19
Syllabus
Instructor: James Lyons-Weiler, PhD

In this class, instructor-led discussions of readings of key studies and reports on COVID-19 published at the beginning of the pandemic will be discussed. Studies and reports will be critically examined by all class participants for the level-of-evidence and quality-of-evidence. Students will work in teams to read, evaluate and summarize the study or reports and provide the rest of the class with typed notes and summaries describing the strengths and weaknesses of the study and report.

1. The SARS-CoV-2 Virus
2. COVID19 as a Disease
3. MIS-C
4. Pathogenic Priming and ADE
5. Diagnosis & RT-PCR
6. Diagnosis & Reporting
7. Transmission
8. Mitigation, Tracking
9. Lockdowns
10. Supplements & Herbal Remedies - Vitamin D
11. Treatment 1 – Ivermectin
12. Treatment 2 – Hydroxychloroquine
13. Treatment 3 – Fluvoxamine
14. Treatment 4 – Other (Nitric Oxide) – Phase 1,2,3 studies 15. Treatment – Rational Workflow
16. Vaccines Phase 1, 2/3 Studies – Moderna
17. Vaccines Phase 1, 2/3 Studies – Pfizer
18. Vaccines - J&J, GSK, Novavax
19. Vaccines Post-EUA Studies
20. Pathophysiology of the Spike Protein
21. Variants – Test escape, Vaccine Escape, Current State of Knowledge
22. Natural Immunity vs. Vaccination immunity
23. Public Health Policies and Science, Regulatory Capture
#IPAKEDU
The NAATEC Consortium has submitted the IRB application, and the lab is CLIA-certified. It will be time soon to start the actual study of what's really infecting people w/"COVID-19". That's where you come in. Check us out at http://ipaknowledge.org

https://www.businesswire.com/news/home/20210621005496/en/%E2%80%9CReplace-bogus-PCR-tests-to-avoid-unnecessary-Coronavirus-lockdowns%E2%80%9D-Urges-Milford-Molecular-Diagnostics-Director-Dr.-Sin-Hang-Lee
We have just opened up registration for the Fall term for our most popular LIVE ONLINE course, "Anatomy of a Scientific Study" (HOW TO READ & INTERPRET A SCIENTIFIC STUDY; Analytics 100). Learn the landscape and what to expect to find in valid studies! Reserve your spot today! https://bit.ly/3jhDZx1 #science #IPAKEDU Time and Day TBD; all lectures are recorded for later access.
Agreed.

“We need to reclassify SIDS as VIDS: Vaccine Induced Death Syndrome. “

New study FINALLY published looking into SIDS and vaccinations.
Highlights to study:

Additive or synergistic toxicity may occur following multivalent vaccination.

Infant deaths post-vaccination are often misclassified as SIDS or suffocation in bed.

Of all reported SIDS cases post-vaccination, 75 % occurred within 7 days (p < 0.00001).

Inflammatory cytokines in the infant medulla act as neuromodulators causing prolonged apneas.

Adjuvants that cross the BBB may induce fatal
https://www.sciencedirect.com/science/article/pii/S2214750021001268?via%3Dihub
The Most Important Vaccine Study EVER

Dr. Jack and Dr. Neil Miller discuss Dr. Miller's new study on data on the occurrence of SIDS in preterm infants following vaccination. The study can be found here and should be sent to every OB/GYN and pediatrician, along with Dr. Jack's studies on aluminum clearance and retention under the CDC's vaccination schedule. https://www.sciencedirect.com/science/article/pii/S2214750021001268?via=ihub

The report - https://ipaknowledge.org/NDRR-IPAK-Tech-Report-20171.php
SaNOtize Nasal Spray Prevention Treatment for COVID19

Dr. Jack interviews Dr. Chris Miller of SaNOtize on their nasal spray for COVID19.

https://www.facebook.com/jamesLweiler/videos/552463352738093/