Bioinformatics in pandemic
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This document summarizes a seminar presentation on using bioinformatics in pandemics. The presentation was given by Puneeth V G at Sahyadri Science College and discussed how bioinformatics can help shorten the time needed to identify drug and vaccine targets during a pandemic. It explained that bioinformatics tools like genome sequencing and comparative genomics can be used to find overlapping genes between host and pathogen genomes, identify unique pathogen sequences, and ultimately find protein targets that could be used for vaccines or drugs. The presentation highlighted that bioinformatics allows for more rapid identification of targets with fewer resources during a pandemic compared to traditional methods.
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We have demonstrated that the exposition of colon cancer cells cultured in BIOMIMESYS® Oncology matrix to an anti-proliferative drug showed a closer in vitro/in vivo correlation in the EC50 curve compared to 2D culture. Cancer cells can be advantageously grown in BIOMIMESYS® for several weeks in multiwell plates and in microfluidic chips for more advanced models. We also observed that modifications in the matrix composition and stiffness modify the cell behavior. Moreover, thanks to collaborations with academic laboratories, we demonstrated that BIOMIMESYS® allows to reproduce in vitro the behavior of cancerous cells in vivo, like mutation effects and metastasis propagation, and could be a relevant alternative to animal models. These results showed that the matricial microenvironment modifies the cell behavior in vitro and should be considered carefully in drug discovery. BIOMIMESYS® hydroscaffold™ is adapted to High Content Screening and represented a powerful tool to better select drug candidate.
CV_Vaibhav
Vaibhav Shinde has over 10 years of experience in experimental biology. He has contributed to the development of targeted molecules for cancer and stem cell models for developmental toxicity. His education includes a Ph.D. from the University of Cologne in stem cell biology and establishment of a stem cell-based teratogenicity prediction system. He has over 10 publications and expertise in stem cell biology, cancer biology, and drug discovery. Currently, he is seeking new opportunities to apply his skills in leading scientific discoveries into clinical cures.
Marsh pers strat-mednov2014
Talk delivered at Warwick Biomedical Engineering Seminar series 27 November 2014. Develops a theme emerging from a review in 2010:
J Watkins, A Marsh, P C Taylor, D R J Singer
Therapeutic Delivery, 2010, 1, 651-665
"Continued adherence to a single-drug single-target paradigm will limit the ability of chemists to contribute to advances in personalized medicine, whether they be in discovery or delivery"
Principles organization and_operation_of_a_dna_bank
This document describes the principles, organization, and operation of a DNA bank established by the Department of Veterans Affairs Cooperative Studies Program. The DNA bank was created to facilitate genetic research using DNA samples collected from participants in clinical trials and studies. Key aspects discussed include obtaining informed consent from participants, ensuring privacy and confidentiality, resolving issues around ownership and future use of genetic material, and providing an infrastructure to support linking genetic and clinical data. The DNA bank is intended to be a shared resource that can support future genetic research across multiple clinical studies in different disease areas over time.
Human Disease Ontology Project presented at ISB's Biocurator meeting April 2014
The Human Disease Ontology (DO), organized as a directed acyclic graph, represents a knowledge base of inherited, environmental, infectious diseases (http://www.disease-ontology.org). DO's textual definition model incorporates a semi-structured format describing the disease etiology built to capture the complex nature of human disease etiology within a is_a hierarchy. DO includes disease concepts for cancer, metabolic disease, infectious disease, mental disorders, genetic disease and syndromes. DO contains disease definitions, external references to resources including ICD, NCI-metathesaurus, SNOMED, MeSH and OMIM and extended relationships that conform to OBO guidelines. DO provides a central ‘switchboard’ for connecting resources, datasets, and computational tools that include disease terms or relationships.
Extracellular vesicles as drug delivery systems.pptx
Extracellular vesicles (EVs) are cell-derived membrane vesicles, and represent an endogenous mechanism for intercellular communication. Since the discovery that EVs are capable of functionally transferring biological information, the potential use of EVs as drug delivery vehicles has gained considerable scientific interest. EVs may have multiple advantages over currently available drug delivery vehicles. Here, we review and discuss development of EVs as drug delivery vehicles.
PBSS sf 10-28-2016 flyer
This document announces a one-day symposium on biomarkers for immuno-oncology therapeutics to be held on October 28, 2016 in Foster City, CA. The symposium will introduce fundamentals, technologies, and applications of biomarkers in research, translational, and clinical development of immune-oncology treatments. Nine speakers from academia and biotech/pharma companies will present on topics such as maximizing anti-PD1 therapy, biomarker strategies for combination immunotherapy, biomarkers for novel checkpoint inhibitors, analysis of the tumor microenvironment, and prediction of tumor response to checkpoint inhibitors. The goal is for participants to learn the latest advancements and network with others in the field.
Romain Banchereau - Resume
Romain Banchereau is a computational biologist and translational immunologist focused on analyzing immune cell populations and transcriptional profiles from human disease cohorts. He has expertise in genomics analysis of blood and immune cells from infectious and autoimmune disease patients. Through bioinformatics analysis, he identifies biomarkers for disease diagnosis, prognosis, and response to treatment. He currently works as a research associate applying these skills to study lupus, juvenile arthritis, and complications during pregnancy with SLE.
Similar to Bioinformatics in pandemic (20)
Application of Biomedical Informatics in Clinical Problem Solving
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Integrating network pharmacology and in silico analysis.pdf
Integrating network pharmacology and in silico analysis.pdf
Poster - Including the matricial tumoral microenvironment in 3D in vitro mode...
Poster - Including the matricial tumoral microenvironment in 3D in vitro mode...
Principles organization and_operation_of_a_dna_bank
Principles organization and_operation_of_a_dna_bank
Human Disease Ontology Project presented at ISB's Biocurator meeting April 2014
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Extracellular vesicles as drug delivery systems.pptx
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Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...Abdul Wali Khan University Mardan,kP,Pakistan
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsPhenomics assisted breeding in crop improvement
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Bob Reedy - Nitrate in Texas Groundwater.pdf
Presented at June 6-7 Texas Alliance of Groundwater Districts Business Meeting
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
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3D Particle-In-Cell (PIC) algorithm,
Plasma expansion in the dipole magnetic field.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
Equivariant neural networks and representation theory
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样
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本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
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留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
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Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
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Compexometric titration/Chelatorphy titration/chelating titration
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Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
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Equivariant neural networks and representation theory
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Bioinformatics in pandemic
- 1. Seminar on BIOINFORMATICS IN PANDEMIC Guided by: Dr. Jamuna K S Lecturer, Department of Biotechnology Sahyadri Science College Shimoga. SAHYADRI SCIENCE COLLEGE Presented by: Puneeth V G I M.Sc Biotechnology Sahyadri Science College Shimoga.
- 3. in silico molecular biology
- 4. “disease occurring worldwide, or over a very wide area crossing international boundaries and usually affecting a large number of people”. Bulletin of the World Health Organization, doi: 10.2471/BLT.11.088815
- 5. Vaccine Drug Both of them takes longer path
- 6. Vaccine Drug Bioinformatics cut shorts this longer path
- 7. Identification of drug / vaccine target plays more important role than identifying drug / vaccine itself
- 8. Genome/Proteome Sequencing plays a critical role
- 10. Movie – villain = Hero Host genome or proteome Pathogen genome or proteome Drug or vaccine target - = Reductive Genomics
- 11. Host genome/proteome Pathogen genome/proteome Identifying overlapping genes/proteins with similarity at sequence level, pathway level and flux level Annotation of unique and unknown sequences, their sub-cellular localization and their availability for drug.
- 12. Host genome/proteome Pathogen genome/proteome Ultimately, few proteins remain that may be treated as vaccine or drug targets
- 13. Bioinformatics can aid in identification of drug or vaccine targets at the earliest with least resources and economy. “ ”
- 14. Barh, D., Tiwari, S., Jain, N., Ali, A., Santos, A. R., Misra, A. N., … Kumar, A. (2011). In silico subtractive genomics for target identification in human bacterial pathogens. Drug Development Research, 72(2), 162–177 Bulletin of the World Health Organization, doi: 10.2471/BLT.11.088815 Chawley, P., Samal, H. B., Prava, J., Suar, M., & Mahapatra, R. K. (2014). Comparative genomics study for identification of drug and vaccine targets in Vibrio cholerae: MurA ligase as a case study. Genomics, 103(1), 83–93. Chowdhury, M. R. H., Bhuiyan, M. I., Saha, A., Mosleh, I. M., Mondol, S., & Ahmed, C. M. S. (2014). Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis. Advances and Applications in Bioinformatics and Chemistry : AABC, 7, 45–54. Damte, D., Suh, J.-W., Lee, S.-J., Yohannes, S. B., Hossain, M. A., & Park, S.-C. (2013). Putative drug and vaccine target protein identification using comparative genomic analysis of KEGG annotated metabolic pathways of Mycoplasma hyopneumoniae. Genomics, 102(1), 47–56. Vetrivel, U., Subramanian, G., & Dorairaj, S. (2011). A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens. The HUGO Journal, 5(1–4), 25–34.