BiP-derived HLA-DR4 Epitopes Differentially Recognized by T cells in RA
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This study identified different T cell stimulatory and immunoregulatory epitopes derived from the human BiP protein. Specifically, it identified the BiP336-355 peptide as an immunogenic HLA-DR4-restricted epitope that stimulates SE+ T cells in a dose-dependent manner, linking it to genetic associations with abnormal immune responses. Additionally, it identified the BiP456-475 peptide as an epitope that induces regulatory T cells in both healthy donors and rheumatoid arthritis patients. Administration of the BiP456-475 peptide was shown to suppress inflammatory arthritis in a collagen-induced arthritis model, suggesting BiP may be a therapeutic target for rheumatoid arthritis treatment.
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This research article studied the effects of personalized probiotic intake on natural killer (NK) cell cytotoxicity. Researchers screened 6 probiotics to identify those with the highest ratio of interferon-gamma (IFN-γ) to interleukin-10 (IL-10) or vice versa for 100 volunteers. Volunteers taking probiotics with high IFN-γ/IL-10 showed significantly increased NK cytotoxicity compared to those taking probiotics with high IL-10/IFN-γ or no probiotics. Certain probiotic strains were better inducers of either IFN-γ or IL-10 dominated immune responses. This highlights personalized probiotic approaches to potentially increase NK cell activity.
Management and treatment of auto immune hemolytic anemia
This document summarizes a presentation on the management and treatment of autoimmune hemolytic anemia (AIHA). It discusses the challenges in diagnosing and treating AIHA due to incomplete understanding of its pathophysiology and lack of standardized therapies. It then covers the types of autoantibodies involved in warm AIHA and cold agglutinin disease, and how they are diagnosed. The document outlines first-line glucocorticoid treatment and alternatives like rituximab or splenectomy. It discusses evaluating treatment response and managing relapsed or refractory cases. Various pharmacologic options are presented along with their response rates and durations. The conclusion emphasizes the heterogeneity of AIHA and need to define subtypes to guide appropriate management.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells. When studying the molecular mechanism, it was found that TRIM35 interacted with IRF5, promoting the ubiquitination and degradation of IRF5. In the clinical specimens of HCC, TRIM35 was negatively correlated with the expression of IRF5. These observations reveal the oncogenic function of IRF5 in the progression of HCC, suggesting that IRF5 is a promising target for the therapy of HCC.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells. When studying the molecular mechanism, it was found that TRIM35 interacted with IRF5, promoting the ubiquitination and degradation of IRF5. In the clinical specimens of HCC, TRIM35 was negatively correlated with the expression of IRF5. These observations reveal the oncogenic function of IRF5 in the progression of HCC, suggesting that IRF5 is a promising target for the therapy of HCC.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells. When studying the molecular mechanism, it was found that TRIM35 interacted with IRF5, promoting the ubiquitination and degradation of IRF5. In the clinical specimens of HCC, TRIM35 was negatively correlated with the expression of IRF5. These observations reveal the oncogenic function of IRF5 in the progression of HCC, suggesting that IRF5 is a promising target for the therapy of HCC.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells. When studying the molecular mechanism, it was found that TRIM35 interacted with IRF5, promoting the ubiquitination and degradation of IRF5. In the clinical specimens of HCC, TRIM35 was negatively correlated with the expression of IRF5. These observations reveal the oncogenic function of IRF5 in the progression of HCC, suggesting that IRF5 is a promising target for the therapy of HCC.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells. When studying the molecular mechanism, it was found that TRIM35 interacted with IRF5, promoting the ubiquitination and degradation of IRF5. In the clinical specimens of HCC, TRIM35 was negatively correlated with the expression of IRF5. These observations reveal the oncogenic function of IRF5 in the progression of HCC, suggesting that IRF5 is a promising target for the therapy of HCC.
New laboratory markers for the management of Rheumatoid Arthritis
This is a journal club presentation where we present good quality papers from leading journals of the world. This particular paper deals with new biomarkers for Rheumatoid Arthritis.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
The IRF family of proteins involves in the tumor progression. However, but the functions of IRF5 in the tumorigenesis are largely unknown. Here, IRF5 was found to be up-regulated in hepatocellular carcinoma (HCC). Interfering with IRF5 inhibited the growth and tumorigenic ability of HCC cells.
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
1. The study found that IRF5 was upregulated in hepatocellular carcinoma (HCC) tissues compared to normal tissues based on mRNA and protein levels.
2. Overexpression of IRF5 promoted the growth and colony formation of HCC cells in vitro, while silencing IRF5 inhibited HCC cell growth and proliferation.
3. TRIM35 was found to interact with and promote the degradation of IRF5. TRIM35 expression was negatively correlated with IRF5 levels in HCC clinical samples.
2015 BioMedTracker Pre-ASH Report
This document provides a summary and schedule for presentations at the 57th Annual Meeting of the American Society of Hematology (ASH) being held from December 5-8, 2015 in Orlando, FL. Key highlights mentioned include presentations on venetoclax for CLL, KTE-C19 CAR-T therapy for NHL, Zydelig for CLL, Ninlaro for multiple myeloma, Keytruda for CLL, and Imbruvica for CLL. The document also includes full schedules of presentations for each day of the conference divided by topic.
Targeted therapy psoriasis
This document summarizes several newer targeted therapies for psoriasis. It discusses therapies that target T-cells, cytokines, leukocyte adhesion, signal transduction and transcription pathways, and chemokine receptors. Specific therapies mentioned include co-stimulation inhibitors that target T-cell activation; vitamin D derivatives that suppress the function of antigen presenting cells; fumaric acid esters that downregulate cytokine production by T-cells; antibodies targeting inflammatory cytokines like IL-12/IL-23 and IL-17; and leukocyte adhesion inhibitors like efalizumab that target the interaction of CD11a with ICAM molecules. The document also discusses protein kinase C inhibitors, Janus kinase inhibitors, mitogen activated protein kinase inhibitors
CML: What's New at EHA? Tim Brümmendorf, EHA Capacity Building Session, EHA c...
"CML: What's New at EHA?", presented by Prof Tim Brümmendorf, EHA Patient Advocacy Capacity Building Session, EHA congress June 2017
Storage of the Recombinant Protein hPDGF-BB in the Culture of Pichia pastoris
Storage of the Recombinant Protein hPDGF-BB in the Culture of Pichia pastorisSSR Institute of International Journal of Life Sciences
ABSTRACT Human platelet-derived growth factor-BB (hPDGF-BB), a proliferation factor, has been successfully manufactured and approved by FDA as the treatment for diabetic foot ulcer and self bone grafting. There have been no reports on the storage of the recombinant hPDGF-BB (rhPDGF-BB) in the Pichia pastoris fermentation broth although during the research of process development and the production manufacture it needs to be stored at low temperature. The concentration of rhPDGF-BB protein in the fed-batch fermentation broth of P. pastoris was stable during 3-week storage at -20oC, but its bioactivity was reduced by 20%. The addition of a mixture of 50% glycerol with either 1 mM EDTA or 1 mM PMSF into the fermentation broth could fully preserve the bioactivity of rhPDGF-BB until 3 weeks at -20oC. The addition of 50% glycerol with either 1 mM EDTA or 1 mM PMSF was found no affection on the protein purification process.
Key-words: rhPDGF-BB, Pichia pastoris, Fed-batch fermentation, Protein stability, Bioactivity, StorageSimilar to BiP-derived HLA-DR4 Epitopes Differentially Recognized by T cells in RA (20)
Disruptive technologies in the manufacture of plasma protein therapies
Disruptive technologies in the manufacture of plasma protein therapies
Envisioning the Future of Emerging Nonfactor Therapies in Hemophilia A and B:...
Envisioning the Future of Emerging Nonfactor Therapies in Hemophilia A and B:...
Daily Intake of Probiotics with High IFN-γ IL-10 Ratio Increases the Cytotoxi...
Daily Intake of Probiotics with High IFN-γ IL-10 Ratio Increases the Cytotoxi...
Management and treatment of auto immune hemolytic anemia
Management and treatment of auto immune hemolytic anemia
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
New laboratory markers for the management of Rheumatoid Arthritis
New laboratory markers for the management of Rheumatoid Arthritis
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
IRF5 Promotes the Progression of Hepatocellular Carcinoma and is Regulated by...
CML: What's New at EHA? Tim Brümmendorf, EHA Capacity Building Session, EHA c...
CML: What's New at EHA? Tim Brümmendorf, EHA Capacity Building Session, EHA c...
Storage of the Recombinant Protein hPDGF-BB in the Culture of Pichia pastoris
Storage of the Recombinant Protein hPDGF-BB in the Culture of Pichia pastoris
More from Thi K. Tran-Nguyen, PhD
CHAMP1-family-conference-Oct-2022.pptx
Presenting a MediKanren-based drug repurposing approach utilizing transcriptome data from patients with CHAMP1 disorder.
IL-21 promotes pulmonary fibrosis through the induction of profibrotic CD8+ T...
IL-21 promotes pulmonary fibrosis through the induction of profibrotic CD8+ T...Thi K. Tran-Nguyen, PhD
IL-21 promotes pulmonary fibrosis by inducing profibrotic CD8+ T cells. The study found that (1) IL-21 is upregulated in response to bleomycin-induced lung injury and IL-21R signaling is required for optimal recruitment of CD8+ T cells and development of fibrosis, (2) IL-21 differentiates CD8+ T cells into profibrotic Tc2 cells that produce high levels of IL-13, a key driver of fibrosis, and (3) adoptive transfer of IL-21-responsive CD8+ Tc2 cells can restore fibrosis in IL-21R-deficient mice, demonstrating that IL-21-induced CD8+ Tc2 cellsFibrotic Diseases
This document summarizes information about fibrotic diseases and idiopathic pulmonary fibrosis (IPF). It discusses how fibrosis occurs as an evolutionary response to injury but can become pathological. Factors that drive persistent fibrosis include ongoing pathogens/antigens, autoimmunity, impaired regeneration, and pleiotropic gene actions. IPF is a chronic lung disease caused by lung scarring and has no known cause or animal model. It presents with loss of lung function and median 3-year survival. Recent clinical trials found pifinidone and nintedanib can slow IPF progression by anti-fibrotic and anti-inflammatory mechanisms.
Histology Exam
This document provides instructions for a histology take-home exam. Students are asked to log onto a virtual microscopy website and identify various tissue structures from slides. They must capture screenshots of the structures, label them, and submit the completed PowerPoint file by email. Sample questions are provided asking students to identify specific structures like ciliated columnar epithelium, squamous epithelium, exocrine glands, islets of Langerhans, bronchi, bile ducts, goblet cells, glomeruli, proximal tubules, neurons, and white matter from slides of different tissues and pathology cases.
Goblet Cells Deliver Luminal Antigen to CD103+ DCs
The document describes a mechanism called goblet-cell associated antigen passage (GAP) by which goblet cells in the intestine deliver soluble luminal antigens to CD103+ dendritic cells. GAP allows CD103+ dendritic cells, which promote tolerance, to preferentially acquire innocuous food antigens from the intestinal lumen. This identifies a pathway for inducing tolerance to foods and suggests how the immune system distinguishes harmless from pathogenic antigens.
Induction of Protective IgA by intestinal DC
This document summarizes research on the induction of protective IgA antibodies by intestinal dendritic cells carrying commensal bacteria. It finds that dendritic cells can capture and transport intact antigens from commensal bacteria to mesenteric lymph nodes. Within the lymph nodes, the antigen-loaded dendritic cells can then transfer the antigens to B cells and induce antibody production, including IgA, even without T cell help. This IgA production helps prevent the commensal bacteria from penetrating the mucosal barrier and restricts the immune response locally to the mesenteric lymph nodes.
Fibrosis- Why and How?
This document discusses fibrosis, including both the beneficial and pathological aspects. It notes that fibrosis is an evolutionary response to wound healing, protecting against blood loss and pathogens. However, fibrotic diseases contribute to many deaths worldwide by affecting organs like the lungs, liver, heart, and skin. The document then examines factors that can drive persistent fibrotic responses, such as the persistence of pathogens/antigens, autoimmune reactions, impaired regeneration due to genetic/epigenetic factors or aging, and pleiotropic genes involved in development and wound healing.
Vietnam
Vietnam is located in Southeast Asia. Some key facts about Vietnam presented in the document include:
- Inflation has increased the value of the Vietnamese currency significantly from 1990 to recent years, with 1 USD equal to 23,000 Vietnamese dong currently.
- Approximately 80% of Vietnam's population are farmers.
- Many Vietnamese people share the same last names.
- Motorbikes are a major form of transportation in Vietnam.
- Fish sauce, a fermented fish condiment, is widely used in Vietnamese cooking.
- Vietnam is known for its coffee.
Transcriptional Responses to Anti-cancer Drugs in vitro
This document summarizes a study that used high throughput transcript profiling to analyze common and cell-type specific responses to anti-cancer drugs across 6 breast cancer cell lines treated with 109 drugs. The researchers used the L1000 assay to generate gene expression signatures from the cell lines in response to drug treatments at different doses and time points. They analyzed the signatures using the characteristic direction method and clustered the signatures based on cosine distance to identify different response patterns among the cell lines. Their results provide insights into variable drug responses in breast cancer subtypes.
CancerSeek
Early detection of cancer is very important to cure cancers because when the tumor burden is small and localized, they can be surgically removed. This paper describes a new strategy for early cancer detection, aiming at screening multiple different cancers within the general population using blood based test, both the protein component as well as the circulating DNA.
Deep Learning for EHR Data
Presented a fantastic cutting-edge paper about using deep learning approach to learn from EHR (electronic health record) data in a clinical informatics journal club at UAB, October 2018.
PSN for Precision Medicine
Presented a paper: "Patient Similarity Networks for Precision Medicine" in Clinical Informatics Journal Club, October 2018.
Extract Stressors for Suicide from Twitter Using Deep Learning
The document describes a deep learning pipeline to extract psychiatric stressors from Twitter data related to suicide. It uses a convolutional neural network classifier to filter tweets, then a recurrent neural network to extract stressors. Transfer learning from pre-trained clinical models helped reduce annotation costs and improve performance. Key results included an 83% F1 score for tweet classification and 53-68% F1 for stressor recognition. Limitations included a lack of ground truth data and context from single tweets.
Big Data Programming-Final Project
This document analyzes League of Legends match data from a big data project. It summarizes the performance of players and champions, finding that active players with over 50 games have a win ratio around 60% and champion win ratios are balanced around 50%. It also finds that killing more minions may decrease the chance of winning and ward positioning patterns do not distinguish between winning and losing teams.
Predictive Features of TCR Repertoire
This document summarizes the characterization of 10 epitope-specific CD8+ T cell receptor repertoires from over 4,600 single cells. Key findings include quantifying gene segment usage, epitope selection, TCR similarity using TCRdist, repertoire diversity with TCRdiv, and developing a distance-based classifier to assign unobserved TCR. The work demonstrates that predictive models for TCR-pMHC recognition may be possible despite tremendous TCR diversity, with potential applications to analyze clinical T cell receptor repertoire data.
Cancer Immunotherapy
This document summarizes a presentation on molecular basis of disease and cancer immunotherapy. It outlines tumor-immune system interactions and different types of immunotherapy, including passive and active approaches. Passive non-specific immunotherapy includes immune checkpoint blockade drugs like Ipilimumab and Nivolumab. Active non-specific immunotherapy includes cytokine therapy and BCG vaccine used to treat non-muscular invasive bladder cancer. Passive specific immunotherapy uses antibodies against tumor antigens or CAR-T cells. Active specific immunotherapy includes tumor vaccines using tumor antigens administered through DNA, proteins, dendritic cells or autologous tumor extracts. Challenges to cancer immunotherapy include tumor resistance, requirements for strong immune responses, and high costs.
Allogeneic IgG Enhances Antitumor T-cell Immunity
I presented a fascinating Nature paper about the potential use of allogenic IgG in cancer immunotherapy.
CD28null T-cells in Autoimmune Disease
This study characterized a unique subset of CD4+ T cells that lack the CD28 co-stimulatory receptor found in patients with chronic inflammatory diseases. The study found that these CD4+CD28null T cells: 1) Are antigen-experienced cells with limited antigen diversity that may develop from repeated antigen stimulation; 2) Highly express inflammatory cytokines and cytolytic enzymes; 3) Have a higher tissue-infiltrating property and undergo autologous proliferation when exposed to antigens; 4) Are more strongly reactive to CMV than known auto-antigens, suggesting CMV exposure may drive their clonal expansion.
Gut Microbiome Composition Influences Responses to immunotherapy
I presented a Science paper about how gut microbiome composition may affect response to immunotherapy in an Immunology Journal Club at UAB on November 15th, 2017.
Single-Cell RNAseq in IPF
In a special seminar organized by the Pulmonary Division at UAB, I presented 2 novel preprint studies about scRNAseq in IPF lungs.
More from Thi K. Tran-Nguyen, PhD (20)
IL-21 promotes pulmonary fibrosis through the induction of profibrotic CD8+ T...
IL-21 promotes pulmonary fibrosis through the induction of profibrotic CD8+ T...
Goblet Cells Deliver Luminal Antigen to CD103+ DCs
Goblet Cells Deliver Luminal Antigen to CD103+ DCs
Transcriptional Responses to Anti-cancer Drugs in vitro
Transcriptional Responses to Anti-cancer Drugs in vitro
Extract Stressors for Suicide from Twitter Using Deep Learning
Extract Stressors for Suicide from Twitter Using Deep Learning
Gut Microbiome Composition Influences Responses to immunotherapy
Gut Microbiome Composition Influences Responses to immunotherapy
Recently uploaded
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/
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
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.
Cytokines and their role in immune regulation.pptx
This presentation covers the content and information on "Cytokines " and their role in immune regulation .
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.
Phenomics 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.
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
3D Particle-In-Cell (PIC) algorithm,
Plasma expansion in the dipole magnetic field.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
20240520 Planning a Circuit Simulator in JavaScript.pptx
Evaporation step counter work. I have done a physical experiment.
(Work in progress.)
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
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)”
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.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Recently uploaded (20)
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Cytokines and their role in immune regulation.pptx
Cytokines and their role in immune regulation.pptx
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
8.Isolation of pure cultures and preservation of cultures.pdf
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BiP-derived HLA-DR4 Epitopes Differentially Recognized by T cells in RA
- 1. Molecular and Cellular Immunology JC April 13th, 2016 Autoantigen BiP-Derived HLA–DR4 Epitopes Differentially Recognized by Effector and Regulatory T Cells in Rheumatoid Arthritis Hirofumi Shoda, Keishi Fujio, Keiichi Sakurai, Kazuyoshi Ishigaki, Yasuo Nagafuchi, Mihoko Shibuya, Shuji Sumitomo, Tomohisa Okamura, and Kazuhiko Yamamoto ARTHRITIS & RHEUMATOLOGY Vol. 67, No. 5, May 2015, pp 1171–1181 Presented by: Thi Tran
- 2. BiP/GRP78/hsp 70 kDa 5 – a member of heat shock protein family
- 3. Hydropathicity transmembrane model of GRP78 ANTIOXIDANTS & REDOX SIGNALING Volume 11, Number 9, 2009
- 4. A proposed model of membrane-bound GRP78 topology ANTIOXIDANTS & REDOX SIGNALING Volume 11, Number 9, 2009
- 5. Immune responses to BiP in RA • BiP is highly expressed in the inflamed RA synovium. • 60% RA patients have significant level of autoab to BiP (some have cit BiP). • RA patients T cells respond to BiP stimulation. • However, several studies indicate BiP can induce Treg and antibody to BiP is anti-inflammatory.
- 6. The shared epitope (SE) hypothesis in RA
- 7. 42 peptides 20 aa long Overlap by 5aa • [3H] incorporation (SI) • Cytokines (IL-17 and IFNg) RA +/+, +/-, -/- Healthy Donor +/- SLE +/- BiP Identify SE-restricted BiP epitopes
- 8. Fig.1. BiP336-355 peptide as the immunogenic HLA-DR4 - restricted epitope
- 9. Fig.2 BiP336-355 binds to HLA-DR4 molecule HA Inhibition assay Binding activity to HLA-DRB*0405 Alanine substitution assay Gel Filtration assay
- 10. Fig.3 Correlation of BiP336-355 induced PBMC proliferation with RA clinical measures
- 11. Fig.4 BiP456-576 induce IL-10 production in PBMC in both RA and Healthy Donor (HD)
- 12. Fig.5. BiP 456-475 strongly suppresses BiP 336-355 - induced PBMC proliferation
- 13. Fig.6. Therapeutics: BiP 456-475 oral administration in CIA model
- 14. Fig.6B. Therapeutics: BiP 456-475 oral administration in CIA model
- 15. Conclusions • This study identify different T cells stimulatory and immunoregulatory epitopes derived from human BiP protein. • Identify the autoag that stimulate SE+ T cells in a dose dependent manner-> a link for genetic association with abnormal immune responses . • Identify BiP 456-475 as epitope of Tregs (natural or induced?) in both HD and RA. • Oral administration of immunoregulatory BiP suppresses inflammatory arthritis in CIA, suggesting BiP as therapeutic target for treatment of RA.
- 16. Discussion • Circulating hsp->Necrosis/apoptosis tissue homeostasis? Balance of effector and reg T cells/ B cells. • In what circumstances (genes, viral infection, chronic inflammation) will tolerance to HSP/GRP78 be broken? • What is the general role of antibody to HSP/GRP78 in normal/ autoimmune/cancer patients? • Since HLA polymorphism deterines patterns of presented peptides and fates of epitope specific T cells->different repertoire of autoabs to hsp in RA vs normal? (different specificities/different isotypes/glycosylation…)
Editor's Notes
- BiP = Binding Immunoglobulin protein Function in Ig assembly Member of Hsp70 heat shock protein family, In the ER, HSP direct protein transport and assembly of multimeric complexes. Inactive state, HSP is a ER stress sensor. BiP is involved in both HLA class I and class II antigen processing.
- ER stress response overlaps with inflammatory pathways in cancer, infection and autoimmunity. ER stress can lead to epitope spreading=> break tolerance
- Susceptibility to rheumatoid arthritis (RA) maps to residues QKRAA/QRRAA in the third hypervariable region of the HLA DRI31 chain. Amino acid sequences (using the one letter amino acid code) of the third hypervariable regions of the 131 chain of different HLA-DR4 subtypes. HLA DR4Dw4, HLA-DR4Dwl4, HLA-DR4Dwl5, and HLA-DR1 are associated with RA, whereas HLA-DR4Dwl0 and HLADR4Dwl3 are not.
- -Previously, they show RA peripheral T cells proliferate in response to whole BiP protein in an HLA-DR-dependent manner compared to healthy donor T cells. In this study, they break the whole BiP protein into peptides 20mers long, overlap by 5 mers and use these peptide to screen for PBMNC activity by thymidine incorporation. To identify SE-restricted, RA-associated epitopes of BiP, we screened 42 BiP-derived epitopes for ex vivo peptide reactivity using PBMCs from SE-positive RA patients
- inhibitory concentration (IC) Concentration of a substance that causes a defined inhibition of a given system: IC50 is the median concentration that causes 50% inhibition.
- BiP456–475 as a Treg cell epitope that induces IL-10.
- Splenic CD4+ T cells
- Splenic CD4+ T cells => insights to resolve the conflicts among literature.
- Splenic CD4+ T cells