This document summarizes research on a two-component nanoparticle system that uses communication to amplify targeting of nanoparticles to tumors. The system consists of "signalling" nanoparticles that first target tumors and activate the coagulation cascade locally, and "receiving" nanoparticles that target areas of coagulation activation to deliver diagnostic or therapeutic agents. Two types of signalling nanoparticles are investigated - gold nanorods that activate coagulation when heated with near-infrared light, and engineered tissue factor proteins that activate coagulation upon binding to tumor receptors. Both are shown to induce localized fibrin deposition in tumors. Receiving nanoparticles containing imaging or drug payloads are then able to target the coagulated tumor sites for enhanced delivery.
Nanoparticles that communicate in vivo to amplify tumour targetingEdwin Alvarado
This document describes a new approach for targeted cancer therapy using communicating nanoparticles. Signaling nanoparticles are designed to first target tumors and then activate the body's coagulation cascade locally. This amplification broadcasts the location of the tumor to receiving nanoparticles circulating in the blood that can then deliver diagnostic or therapeutic agents to the tumor in much higher doses than non-communicating nanoparticles. The system takes advantage of the body's natural coagulation pathway to transmit signals between nanoparticles. In experiments, signaling gold nanorods were able to precisely induce coagulation when heated in tumors, demonstrating the ability of the system to activate coagulation specifically at tumor sites.
Immune Escape Mechanisms of Cancers and High Grade Glial TumorsNeuroAcademy
The document discusses immune escape mechanisms of cancers and high grade gliomas. It describes how dendritic cell treatment can be used for glioblastomas, using glioblastoma associated antigens, glioblastoma stem cell antigens, tumor lysates, tumor RNA, or peptides. The optimal dosage of dendritic cells for treatment ranges from 1 million to 10 billion cells. It also discusses how the expression of coinhibitory molecules on tumor cell surfaces limits antitumor responses and the efficacy of dendritic cell vaccination. Finally, it outlines multiple approaches for cancer immunotherapy, including cytokine secreting tumor cells, ex vivo tumor loaded dendritic cells, antibodies targeting costimulatory lymphocyte receptors, and depletion of regulatory T cells and myeloid-derived suppress
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
This document summarizes research on analyzing differential miRNA-mRNA co-expression networks in colorectal cancer. The researchers analyzed paired expression data from cancer and normal tissues to identify changes in interactions. They found that cancer networks have decreased connectivity and identified differentially connected genes, including known cancer genes. Pathway analysis revealed an alteration in colorectal cancer tissues in the interplay between miRNAs and the eukaryotic translation initiation factor 3 complex, which is important for translation. Certain miRNAs were also identified as having many differentially co-expressed target mRNAs.
CRISPR as a potential tool for malaria eradicationMatthias Samwald
Why avoiding delays to gene-drive based mosquito eradication should be the most important goal of the global community right now, and why it is not.
Presentation at the Vienna Rationality Meetup 14.05.2016
1. The document discusses how most current cancer treatments work by generating reactive oxygen species, but metastatic cancers have heightened antioxidant levels making them resistant. It suggests focusing on inhibiting cancer cell proliferation rather than growth.
2. Epithelial-mesenchymal transitions that occur during cancer metastasis change gene expression patterns and make cancers resistant to targeted drugs. Cytokines like IL6 may drive proliferation of mesenchymal cancers.
3. The gene transcription activator Myc is a key driver of proliferation in many incurable cancers but has been difficult to directly target with drugs. Inhibiting bromodomain protein 4 lowers Myc levels and kills some leukemia cells.
This document discusses a presentation on microbiome identification and characterization technologies. It begins with an introduction to the human microbiome and catalogs our "second genome". It then discusses how technologies like 16S rRNA sequencing and metagenomics have unlocked the ability to study the microbiome. Population studies of microbiome composition and disease associations are also reviewed. The presentation goes on to provide examples of how to design assays to identify and profile relevant microbiome targets, and discusses solutions for identification and profiling in microbiome research.
Nanoparticles that communicate in vivo to amplify tumour targetingEdwin Alvarado
This document describes a new approach for targeted cancer therapy using communicating nanoparticles. Signaling nanoparticles are designed to first target tumors and then activate the body's coagulation cascade locally. This amplification broadcasts the location of the tumor to receiving nanoparticles circulating in the blood that can then deliver diagnostic or therapeutic agents to the tumor in much higher doses than non-communicating nanoparticles. The system takes advantage of the body's natural coagulation pathway to transmit signals between nanoparticles. In experiments, signaling gold nanorods were able to precisely induce coagulation when heated in tumors, demonstrating the ability of the system to activate coagulation specifically at tumor sites.
Immune Escape Mechanisms of Cancers and High Grade Glial TumorsNeuroAcademy
The document discusses immune escape mechanisms of cancers and high grade gliomas. It describes how dendritic cell treatment can be used for glioblastomas, using glioblastoma associated antigens, glioblastoma stem cell antigens, tumor lysates, tumor RNA, or peptides. The optimal dosage of dendritic cells for treatment ranges from 1 million to 10 billion cells. It also discusses how the expression of coinhibitory molecules on tumor cell surfaces limits antitumor responses and the efficacy of dendritic cell vaccination. Finally, it outlines multiple approaches for cancer immunotherapy, including cytokine secreting tumor cells, ex vivo tumor loaded dendritic cells, antibodies targeting costimulatory lymphocyte receptors, and depletion of regulatory T cells and myeloid-derived suppress
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
This document summarizes research on analyzing differential miRNA-mRNA co-expression networks in colorectal cancer. The researchers analyzed paired expression data from cancer and normal tissues to identify changes in interactions. They found that cancer networks have decreased connectivity and identified differentially connected genes, including known cancer genes. Pathway analysis revealed an alteration in colorectal cancer tissues in the interplay between miRNAs and the eukaryotic translation initiation factor 3 complex, which is important for translation. Certain miRNAs were also identified as having many differentially co-expressed target mRNAs.
CRISPR as a potential tool for malaria eradicationMatthias Samwald
Why avoiding delays to gene-drive based mosquito eradication should be the most important goal of the global community right now, and why it is not.
Presentation at the Vienna Rationality Meetup 14.05.2016
1. The document discusses how most current cancer treatments work by generating reactive oxygen species, but metastatic cancers have heightened antioxidant levels making them resistant. It suggests focusing on inhibiting cancer cell proliferation rather than growth.
2. Epithelial-mesenchymal transitions that occur during cancer metastasis change gene expression patterns and make cancers resistant to targeted drugs. Cytokines like IL6 may drive proliferation of mesenchymal cancers.
3. The gene transcription activator Myc is a key driver of proliferation in many incurable cancers but has been difficult to directly target with drugs. Inhibiting bromodomain protein 4 lowers Myc levels and kills some leukemia cells.
This document discusses a presentation on microbiome identification and characterization technologies. It begins with an introduction to the human microbiome and catalogs our "second genome". It then discusses how technologies like 16S rRNA sequencing and metagenomics have unlocked the ability to study the microbiome. Population studies of microbiome composition and disease associations are also reviewed. The presentation goes on to provide examples of how to design assays to identify and profile relevant microbiome targets, and discusses solutions for identification and profiling in microbiome research.
This document discusses the development of models for predicting toxicity after radiotherapy for prostate cancer. Early models focused only on dosimetric variables but were limited. Later models incorporated clinical variables and improved predictions. Current research aims to include genetic and biomolecular factors to account for variability in individual radiosensitivity. While some models exist for acute and late rectal toxicity, validation and inclusion of additional variables is still needed. Future multifactorial models integrating dosimetric, clinical, and genetic data may enable more individualized risk assessments and isotoxic treatment planning.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Conferencia de la Dra. Ana María Roa, Bióloga Molecular, sobre Epigenética, impartida en la Universidad Popular Carmen de Michelena de Tres Cantos el 1 de marzo de 2013.
Más información en:
http://www.universidadpopularc3c.es/index.php/actividades/conferencias/event/448-conferencia-una-revision-de-los-conocimientos-fundamentales-de-la-biologia-de-la-celula-la-epigenetica
Dendritic cell vaccines show potential for treating high grade glial tumors. Dendritic cells can present tumor antigens to activate CD8 and CD4 T cells. They undergo a maturation process where they migrate to lymph nodes, interact with T cells and release cytokines to stimulate an immune response. Dendritic cells can be obtained from patients and loaded with tumor antigens ex vivo before being reinfused to induce anti-tumor immunity. Multiple methods are being studied to enhance dendritic cell vaccines including combination with other immunotherapies.
Review of Adoptive T-Cell ImmunotherapyLuke Brennan
1) Adoptive T-cell immunotherapy (ACT) involves extracting a patient's T-cells, modifying them to better recognize cancer cells, and reintroducing them to attack the cancer. Two main types are tumor-infiltrating lymphocytes (TILs) and engineered T-cells.
2) While promising, ACT faces challenges including T-cell inhibition by the immune system and cancer, toxicity from off-target autoimmunity, and short longevity of the modified T-cells. Additional research is needed to address these issues before ACT can become widely used.
3) The lengthy and resource-intensive cell culture and testing required for each patient also makes ACT costly currently, limiting its application to rare cancers
1) Researchers genetically modified cytokine-induced killer (CIK) cells to express chimeric antigen receptors (CARs) targeting CD123 or CD19 antigens on leukemia cells using the Sleeping Beauty transposon system.
2) The optimized transfection and expansion protocol resulted in over 30-fold increases in CAR-modified CIK cells suitable for adoptive cell therapy.
3) The CAR-modified CIK cells specifically recognized and killed leukemia cells and promoted cytokine secretion and proliferation upon antigen exposure, suggesting they could target and activate upon encountering leukemia in patients.
My presentation at the 2014 MetaCenter symposium in Eugene, OR entitled "High-throughput annotation of metagenomes reveals community physiological variation in the mammalian microbiome"
Oncolytic viruses are a unique class of cancer therapeutics that target viral replication and lysis specifically to tumor cells. They work through three mechanisms: 1) cell lysis within tumors, 2) immune recognition of viral particles tagging tumor cells as foreign, and 3) presentation of tumor antigens to stimulate antitumor immunity. Phase II trials of the oncolytic adenovirus ONYX-015 as a single agent showed responses in recurrent head and neck cancer patients who had failed other treatments. Intravenous delivery of the engineered oncolytic virus JX-594 leads to high cancer-selective amplification and spread within tumors through multiple anticancer mechanisms. JX-594 has shown tumor eradication in
Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: ...GigaScience, BGI Hong Kong
This document discusses challenges in comparing metagenomic data from different environments and studies. It argues that when exploring a new environment, multiple methodological approaches should be used to capture natural and methodological variations. When performing global comparisons, methodological variations should be considered for all environments. Defining ecosystems precisely at the microorganism level is important. The author's vision is for projects like the Earth Microbiome Project to use flexible experimental designs informed by different experts to best represent microbial communities.
Metagenomics research is a vast field which studies about the genetic system of the
environmental samples. Binning is a bioinformatics tool. Binning tool helps to analyses the
genomic analysis of the environmental samples.The
Bioengineered 3D Co culture Lung In Vitro Models: Platforms to Integrate Cell...Ken Rogan
Cian O'Leary and his lab are developing 3D bioengineered in vitro models of the lung and other tissues using scaffolds.
[1] They have created bilayered collagen-hyaluronate scaffolds that support a mucociliary epithelial phenotype in lung cell culture models.
[2] The lab is also working on 3D hydrogel models of pancreatic cancer to study cell-matrix interactions and cancer progression.
[3] Future work includes developing dynamically stiffening hydrogel models and applying these platforms to study lung cancer and the pre-metastatic niche.
This document summarizes research on cellular transforming genes in cancer. Experiments found that genes from normal cells, when abnormally expressed, can transform cells at high efficiencies. High molecular weight DNA from cancer cells also transforms cells at high efficiencies, suggesting the genes are no longer properly controlled. Various carcinogens were found to activate the same transforming genes within cancers of particular cell types. Cloning of these genes revealed they are evolutionarily conserved between species. The research aims to identify transforming genes activated at different stages of immune cell differentiation to examine genetic events in cancer development.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Metagenomics is the study of genomic material obtained directly from environmental samples rather than from isolated cultures. It allows researchers to study the 99% of microorganisms that cannot be cultured using traditional methods. There are two main approaches - sequence-driven metagenomics sequences environmental DNA and compares taxonomic relationships, while function-driven metagenomics expresses cloned genes to compare metabolic relationships and discover new enzymes/chemicals. Metagenomics has been applied to study microbes in ocean water, human gut, acid mine drainage and more extreme habitats, identifying novel genes and furthering understanding of microbial communities. Future applications include discovering new antibiotics and enzymes, studying human microbiomes and antibiotic resistance.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
Programmatic detection of spatial behaviour in an agent-based modelITIIIndustries
The automated detection of aspects of spatial behaviour in an agent-based model is necessary for model testing and analysis. In this paper we compare four predictors of herding behaviour in a model of a grazing herbivore. We find that a) the mean number of neighbours adjusted to account for population variation and b) the mean Hamming distance between rows of the two-dimensional environment can be used to detect herding. Visual inspection of the model behaviour revealed that herding occurs when the herbivore mobility reaches a threshold level. Using this threshold we identify a limits for these predictors to use in the program code. These results apply only to one set of parameters and environment size; future research will involve a wider parameter space.
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
This pilot study examined the combination of high-dose zidovudine and valganciclovir for the treatment of Kaposi sarcoma herpesvirus (KSHV)-associated multicentric Castleman disease (MCD) in 14 HIV-infected patients. The rationale was that these drugs target KSHV lytic genes ORF36 and ORF21, selectively killing KSHV-infected plasmablasts expressing these genes. A total of 86% of patients achieved a major clinical response and 50% a major biochemical response. Median progression-free survival was 6 months and overall survival at 43 months of follow-up was 86%. This virus-activated cytotoxic therapy showed activity in KSHV-
14.anaeli and nicolle. mycobacteriophages paper.anaelishockey
Two mycobacteriophages were isolated from a soil sample collected in Gurabo, Puerto Rico. Following enrichment and plaque purification, two distinct phages (named Shockage and Zombage) were isolated based on differences in morphology and protein band patterns. Shockage had a distinct protein profile while Zombage and another initially isolated phage had nearly identical protein bands, indicating they were the same phage. Further DNA sequencing would help fully characterize these newly isolated phages and determine if they represent unique viruses. Overall, this experiment demonstrated a method for isolating new mycobacteriophages from environmental samples.
This document discusses the development of models for predicting toxicity after radiotherapy for prostate cancer. Early models focused only on dosimetric variables but were limited. Later models incorporated clinical variables and improved predictions. Current research aims to include genetic and biomolecular factors to account for variability in individual radiosensitivity. While some models exist for acute and late rectal toxicity, validation and inclusion of additional variables is still needed. Future multifactorial models integrating dosimetric, clinical, and genetic data may enable more individualized risk assessments and isotoxic treatment planning.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Conferencia de la Dra. Ana María Roa, Bióloga Molecular, sobre Epigenética, impartida en la Universidad Popular Carmen de Michelena de Tres Cantos el 1 de marzo de 2013.
Más información en:
http://www.universidadpopularc3c.es/index.php/actividades/conferencias/event/448-conferencia-una-revision-de-los-conocimientos-fundamentales-de-la-biologia-de-la-celula-la-epigenetica
Dendritic cell vaccines show potential for treating high grade glial tumors. Dendritic cells can present tumor antigens to activate CD8 and CD4 T cells. They undergo a maturation process where they migrate to lymph nodes, interact with T cells and release cytokines to stimulate an immune response. Dendritic cells can be obtained from patients and loaded with tumor antigens ex vivo before being reinfused to induce anti-tumor immunity. Multiple methods are being studied to enhance dendritic cell vaccines including combination with other immunotherapies.
Review of Adoptive T-Cell ImmunotherapyLuke Brennan
1) Adoptive T-cell immunotherapy (ACT) involves extracting a patient's T-cells, modifying them to better recognize cancer cells, and reintroducing them to attack the cancer. Two main types are tumor-infiltrating lymphocytes (TILs) and engineered T-cells.
2) While promising, ACT faces challenges including T-cell inhibition by the immune system and cancer, toxicity from off-target autoimmunity, and short longevity of the modified T-cells. Additional research is needed to address these issues before ACT can become widely used.
3) The lengthy and resource-intensive cell culture and testing required for each patient also makes ACT costly currently, limiting its application to rare cancers
1) Researchers genetically modified cytokine-induced killer (CIK) cells to express chimeric antigen receptors (CARs) targeting CD123 or CD19 antigens on leukemia cells using the Sleeping Beauty transposon system.
2) The optimized transfection and expansion protocol resulted in over 30-fold increases in CAR-modified CIK cells suitable for adoptive cell therapy.
3) The CAR-modified CIK cells specifically recognized and killed leukemia cells and promoted cytokine secretion and proliferation upon antigen exposure, suggesting they could target and activate upon encountering leukemia in patients.
My presentation at the 2014 MetaCenter symposium in Eugene, OR entitled "High-throughput annotation of metagenomes reveals community physiological variation in the mammalian microbiome"
Oncolytic viruses are a unique class of cancer therapeutics that target viral replication and lysis specifically to tumor cells. They work through three mechanisms: 1) cell lysis within tumors, 2) immune recognition of viral particles tagging tumor cells as foreign, and 3) presentation of tumor antigens to stimulate antitumor immunity. Phase II trials of the oncolytic adenovirus ONYX-015 as a single agent showed responses in recurrent head and neck cancer patients who had failed other treatments. Intravenous delivery of the engineered oncolytic virus JX-594 leads to high cancer-selective amplification and spread within tumors through multiple anticancer mechanisms. JX-594 has shown tumor eradication in
Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: ...GigaScience, BGI Hong Kong
This document discusses challenges in comparing metagenomic data from different environments and studies. It argues that when exploring a new environment, multiple methodological approaches should be used to capture natural and methodological variations. When performing global comparisons, methodological variations should be considered for all environments. Defining ecosystems precisely at the microorganism level is important. The author's vision is for projects like the Earth Microbiome Project to use flexible experimental designs informed by different experts to best represent microbial communities.
Metagenomics research is a vast field which studies about the genetic system of the
environmental samples. Binning is a bioinformatics tool. Binning tool helps to analyses the
genomic analysis of the environmental samples.The
Bioengineered 3D Co culture Lung In Vitro Models: Platforms to Integrate Cell...Ken Rogan
Cian O'Leary and his lab are developing 3D bioengineered in vitro models of the lung and other tissues using scaffolds.
[1] They have created bilayered collagen-hyaluronate scaffolds that support a mucociliary epithelial phenotype in lung cell culture models.
[2] The lab is also working on 3D hydrogel models of pancreatic cancer to study cell-matrix interactions and cancer progression.
[3] Future work includes developing dynamically stiffening hydrogel models and applying these platforms to study lung cancer and the pre-metastatic niche.
This document summarizes research on cellular transforming genes in cancer. Experiments found that genes from normal cells, when abnormally expressed, can transform cells at high efficiencies. High molecular weight DNA from cancer cells also transforms cells at high efficiencies, suggesting the genes are no longer properly controlled. Various carcinogens were found to activate the same transforming genes within cancers of particular cell types. Cloning of these genes revealed they are evolutionarily conserved between species. The research aims to identify transforming genes activated at different stages of immune cell differentiation to examine genetic events in cancer development.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Metagenomics is the study of genomic material obtained directly from environmental samples rather than from isolated cultures. It allows researchers to study the 99% of microorganisms that cannot be cultured using traditional methods. There are two main approaches - sequence-driven metagenomics sequences environmental DNA and compares taxonomic relationships, while function-driven metagenomics expresses cloned genes to compare metabolic relationships and discover new enzymes/chemicals. Metagenomics has been applied to study microbes in ocean water, human gut, acid mine drainage and more extreme habitats, identifying novel genes and furthering understanding of microbial communities. Future applications include discovering new antibiotics and enzymes, studying human microbiomes and antibiotic resistance.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
Programmatic detection of spatial behaviour in an agent-based modelITIIIndustries
The automated detection of aspects of spatial behaviour in an agent-based model is necessary for model testing and analysis. In this paper we compare four predictors of herding behaviour in a model of a grazing herbivore. We find that a) the mean number of neighbours adjusted to account for population variation and b) the mean Hamming distance between rows of the two-dimensional environment can be used to detect herding. Visual inspection of the model behaviour revealed that herding occurs when the herbivore mobility reaches a threshold level. Using this threshold we identify a limits for these predictors to use in the program code. These results apply only to one set of parameters and environment size; future research will involve a wider parameter space.
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
This pilot study examined the combination of high-dose zidovudine and valganciclovir for the treatment of Kaposi sarcoma herpesvirus (KSHV)-associated multicentric Castleman disease (MCD) in 14 HIV-infected patients. The rationale was that these drugs target KSHV lytic genes ORF36 and ORF21, selectively killing KSHV-infected plasmablasts expressing these genes. A total of 86% of patients achieved a major clinical response and 50% a major biochemical response. Median progression-free survival was 6 months and overall survival at 43 months of follow-up was 86%. This virus-activated cytotoxic therapy showed activity in KSHV-
14.anaeli and nicolle. mycobacteriophages paper.anaelishockey
Two mycobacteriophages were isolated from a soil sample collected in Gurabo, Puerto Rico. Following enrichment and plaque purification, two distinct phages (named Shockage and Zombage) were isolated based on differences in morphology and protein band patterns. Shockage had a distinct protein profile while Zombage and another initially isolated phage had nearly identical protein bands, indicating they were the same phage. Further DNA sequencing would help fully characterize these newly isolated phages and determine if they represent unique viruses. Overall, this experiment demonstrated a method for isolating new mycobacteriophages from environmental samples.
Bacteriophage Zombage was isolated and characterized using electron microscopy. Pictures were taken of the phage using electron microscopy to view its structure and morphology at high magnification. The electron microscopy images provide detailed views of Zombage's capsid, tail fibers, and other viral structures.
Bacteriophage Shockage was isolated and characterized. Electron microscopy pictures were taken of the phage particles. The pictures show the structure of Shockage, which includes an icosahedral capsid and long, non-contractile tail.
This document summarizes three research articles on the use of cannabis to treat Crohn's disease. The first article finds that 21 out of 30 Crohn's patients saw improved symptoms after treatment with cannabis. It also found reductions in drug usage and surgeries. The second article determines that cannabidiol selectively inhibits inflammatory hypermotility in mice when an inflammatory stimulus is present. The third article surveys Crohn's and ulcerative colitis patients and finds that cannabis helped relieve common symptoms like abdominal pain and diarrhea for most users.
1. This laboratory focused on practicing proper micropipetting techniques. Students mixed solutions of water and dyes to practice using micropipettes accurately and safely. This helped prepare them for upcoming labs requiring precise measurements.
2. Students learned different microscopy techniques, including fluorescence and bright field microscopy. They took photomicrographs using a camera attached to the microscope.
3. Over three days, students extracted their own DNA from mouth cells, ran PCR tests to determine if a patient sample had diabetes, and used gel electrophoresis to analyze protein biomarkers and diagnose a lysosomal storage disorder.
This document describes the isolation of mycobacteriophages from soil samples in Puerto Rico. Two students isolated three unique phages and characterized them through plaque assays, enrichment techniques, and SDS-PAGE gel electrophoresis. Two distinct phages, named Shockage and Zombage, were identified based on their protein band patterns and plaque morphology. Further sequencing of the phage genomes was proposed to better characterize the newly discovered viruses.
This document summarizes a case presentation of a patient with progressive neurological deficits and HIV. Over several weeks, the patient developed numbness that spread across his face and limbs, as well as other neurological symptoms. Imaging and spinal fluid testing did not reveal any abnormalities. A biopsy showed diffuse large B-cell lymphoma that was HHV8-positive but EBV-negative. This type of lymphoma is associated with Kaposi's sarcoma-associated herpesvirus (KSHV), which can cause various malignancies in HIV/AIDS patients such as multicentric Castleman's disease, primary effusion lymphoma, and diffuse large B-cell lymphoma.
Moving from Big Data to Better Models of Disease and Drug Response - Joel DudleyCityAge
Joel Dudley is the director of biomedical informatics and an assistant professor of genetics and genomic sciences at Mount Sinai School of Medicine. The document discusses moving from big data to better disease models through integrating diverse data types and building predictive network models. It highlights several projects using this approach, including identifying new drug indications for existing drugs to treat diseases like inflammatory bowel disease. The goal is to leverage "big data" from sources like genomics, clinical data, and electronic health records to generate testable predictions to improve disease diagnosis and treatment through precision medicine approaches.
The document describes an experiment using microfluidic devices to quantify the migration of prostate cancer cells in response to conditioned media. Microfluidic devices provided physical confinement and a controllable microenvironment to monitor cell movement over multiple days. Results showed no migration with standard media, some migration with conditioned media, and highest migration when conditioned media was in the reagent channel, indicating it acted as a chemoattractant. The microfluidic model provided a way to accurately measure and analyze cancer cell metastasis.
CXCL1, CCL20, STAT1 was Identified and Validated as a Key Biomarker Related t...semualkaira
Growing evidence suggests a correlation between ulcerative colitis (UC) and immune markers. Pathogenesis of UC was not yet been clearly elucidated, and few researches on immune-related biomarkers published.
CXCL1, CCL20, STAT1 was Identified and Validated as a Key Biomarker Related t...semualkaira
Growing evidence suggests a correlation between ulcerative colitis (UC) and immune markers. Pathogenesis
of UC was not yet been clearly elucidated, and few researches on
immune-related biomarkers published.
Nanotechnology is being used in the field of nanomedicine to develop targeted drug delivery systems, diagnostic tools, and regenerative medicine applications at the molecular scale. Nanomedicine exploits the unique properties of nanomaterials to enable early disease detection, improved diagnosis and imaging, and more effective treatments. Some examples include using nanoparticles to specifically deliver anti-cancer drugs to tumor cells, developing magnetic nanoparticles that can be used to track stem cells via MRI, and creating smart biomaterials that promote tissue self-healing. Nanomedicine shows promise for solving health issues like cancer, diabetes, and neurodegenerative diseases.
This document discusses several microfluidic separation methods for isolating circulating tumor cells (CTCs) from blood. It describes how microfluidics can accurately manipulate flow conditions to efficiently separate CTCs from blood cells based on differences in their biophysical properties such as size and deformability. Using these microfluidic approaches, viable CTCs can be retrieved from cancer patient blood samples with high isolation efficiency and purity. Identification of CTCs aids in cancer detection, disease monitoring, and insights into metastasis. The document also discusses using magnetic nanoparticles coupled with doxorubicin chemotherapy drug and an external magnetic field to more effectively deliver the drug to breast cancer cells and increase mortality rates.
Objective: To probe into the influence of miR-21 on the proliferation as well as apoptosis of oral squamous cell carcinoma (OSCC) and its causative role.
Study Design: We adopted microarray for detecting the differentially expressed genes in OSCC tumor tis-sues and paracancerous tissues. We assessed the link of miR-21 expression with tumor size, lymph node metastasis, and tumor differentiation. We employed CCK-8 and EdU assay for detecting the impact of miR-21 inhibitor and miR-21 mimic on Cal-27 cell proliferation, as well as TUNEL and AnnexinV-FITC/PI double staining for detecting miR-21 expression on cell apoptosis. We forecasted the possible target of miR-21 via TargetScan, as well as detected the interaction of miR-21 with PTEN via luciferase reporter experiment. The function of miR-21 expression in PTEN signaling pathway was monitored via western blot. We constructed PTEN overexpression plasmid and conducted rescue experiment to evaluate overexpressed PTEN on miR-21–induced proliferation.
Results: Microarray and RT-qPCR indicated that miR-21 expression increased demonstrably in OSCC. Subsequently, statistical analysis showed that miR-21 expression was plainly correlated with tumor size, lymph node metastasis, tumor differentiation, and smoking history. CCK-8 and EdU method exhibited that miR-21 mimics manifestly promoted Cal-27 cell proliferation, while miR-21 inhibitor blatantly inhibited Cal-27 cell proliferation. TUNEL and V-FITC/PI double staining assay showed that miR-21 inhibitor conspicuously promoted Cal-27 cell apoptosis. CCK-8 and EdU assay exhibited that overexpressed PTEN abolished the pro-proliferation influence of miR-21 mimic. TUNEL and V-FITC/PI experiments pointed out that knocking down PTEN abrogated the pro-apoptosis impact of miR-21 inhibitor.
Conclusion: miR-21 contributes to OSCC cell proliferation via targeting PTEN and inhibits its apoptosis.
Keywords: Akt/PKB signaling pathway; apoptosis; biomarkers, tumor; carcinoma, squamous cell; cell line, tumor; cell proliferation; microRNAs; miR-21; miRNA-21; mouth neoplasms; oral cancer; oral squamous cell carcinoma; proliferation; real time PCR
Radiotherapy promotes the polarization of tumor-associated macrophages (TAMs) in mice with Lewis lung cancer into anti-tumor M1 macrophages. This is accompanied by increased expression of the long non-coding RNA lincRNA-p21 in the TAMs. TAMs exposed to radiation therapy suppress the viability and invasion of Lewis lung cancer cells in culture. Overexpression of lincRNA-p21 in TAMs enhances their anti-tumor effects, while decreasing lincRNA-p21 reduces the effects of radiation therapy, suggesting lincRNA-p21 plays a key role in the anti-tumor actions of radiotherapy in lung cancer.
This study investigated the effects of serotonin on congenital melanocytic nevus cells. The results showed that serotonin treatment increased nevus cell migration in a scratch assay by upregulating expression of the EMT genes Twist1 and Twist2. This suggests that serotonin may promote nevus cell migration and proliferation, potentially increasing the risk of malignant transformation. The research provides insight into molecular mechanisms underlying nevus progression and identifies serotonin as a potential target for future treatments.
DDW Biomarkers of Polyp Recurrence in Colon Cancer PatientsSean Maden
1. The study aimed to identify DNA methylation markers in normal colon tissue that are associated with increased risk of metachronous polyp formation after colorectal cancer (CRC) resection.
2. DNA methylation analysis of normal colon samples from 41 CRC patients identified 5 differentially methylated loci between those with and without subsequent polyps. These mapped to genes implicated in cancer development.
3. Characterizing a pre-malignant field through aberrant DNA methylation could help identify high-risk individuals for CRC prevention and lend insight into CRC pathogenesis.
This document describes an automated robotic platform developed for the high-throughput production of induced pluripotent stem cells (iPSCs) with minimal manual intervention. Some key points:
- The platform automates the reprogramming of skin fibroblasts into iPSCs using mRNA, as well as purification of iPSCs using immunomagnetic beads to isolate TRA-1-60+ cells.
- Automated reprogramming resulted in the generation of over 200 iPSC lines from adult fibroblasts with a reprogramming efficiency of 0.001-0.16%. A modified reprogramming strategy using gradual serum reduction improved success rates.
- Polyclonal iPSC lines produced through the automated process expressed plurip
This research article demonstrates the use of Wavelength Modulated Raman Spectroscopy (WMRS) to identify major immune cell subsets in an unlabeled and non-fixed state. Using WMRS, the researchers were able to distinguish between CD4+ T lymphocytes, CD8+ T lymphocytes, and CD56+ Natural Killer cells from multiple donors with up to 96% specificity. They also distinguished between CD303+ plasmacytoid and CD1c+ myeloid dendritic cell subsets. This label-free method opens new opportunities for analyzing immune systems and developing diagnostic technologies without altering or damaging the cells.
This document describes a label-free method for cell counting using paramagnetic bead aggregation. When cells are lysed in a chaotropic solution, the released DNA causes paramagnetic beads to aggregate. The extent of aggregation correlates with the amount of DNA and cell number. This allows direct enumeration of cells from crude samples. The method is demonstrated by monitoring bacterial growth and obtaining white blood cell counts from whole blood samples, showing good agreement with standard methods. Specific cell types like CD4+ T cells can also be enumerated using bead-based immunocapture prior to the aggregation step. The method requires only inexpensive equipment and could provide an accessible alternative to more expensive cell counting techniques.
This research article describes a novel method using high-density peptide microarrays and computational analysis to identify B-cell epitopes in patients with celiac disease. Overlapping peptide sequences from native and deamidated gliadin proteins were synthesized onto silicon wafers. Serum samples from celiac patients and controls were tested on the microarrays. Computational analysis identified distinct epitope sets that differentiated celiac patients from controls with high accuracy. The identified epitopes have potential for developing improved diagnostic tests for celiac disease.
Application of Biomedical Informatics in Clinical Problem Solvingimprovemed
1) The document discusses several use cases for applying data mining and machine learning techniques to biomedical problems.
2) One use case aims to enable early diagnosis of cancers like lung cancer through predictive modeling of patient data.
3) Another use case examines predicting patient responses to drug therapies for breast cancer by analyzing genomic and other molecular profiling data using machine learning algorithms.
4) Other use cases discussed include using imaging data and time series analysis of patient information to aid in early detection and risk assessment of chronic diseases.
This study performed a genome-wide analysis of DNA methylation in colorectal carcinoma (CRC) tissue samples from 24 Bangladeshi patients. The researchers found a total of 627 differentially methylated loci covering 513 genes when comparing CRC tissue to normal adjacent tissue, with 535 loci covering 465 genes being newly identified. Gene set enrichment analysis showed hypermethylation in CRC of gene sets related to inhibition of adenylate cyclase activity, Rac guanyl-nucleotide exchange factor activity, regulation of retinoic acid receptor signaling, and estrogen receptor activity. Predictive models based on differentially methylated loci showed potential for CRC diagnosis with around 89% sensitivity and specificity.
The document discusses several use cases for applying data mining and machine learning techniques in healthcare and biomedical research. Three examples are:
1) Early diagnosis of cancers like lung cancer and breast cancer through predictive modeling of patient data to detect cancers at earlier stages when survival rates are higher.
2) Predicting patient responses to drug therapies for cancers like breast cancer by combining different types of molecular profiling data using techniques like support vector machines and random forests.
3) Using imaging data and temporal analysis of metrics like medication purchases to better understand and predict chronic diseases like diabetes and associated health complications.
CHI's Targeting Stromal Cells in Cancer and Inflammatory Diseases Conference ...James Prudhomme
This virtual meeting will highlight cutting-edge science and provide insight into recent developments towards therapeutic stromal cell targeting in cancer and chronic inflammatory diseases. View full details and register: https://www.healthtech.com/stroma-conference
Discovering Yourself with Computational BioinformaticsLarry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on his self-experimentation with quantifying biomarkers and 'omics data to gain insights into his health. Smarr has tracked over 100 blood biomarkers, sequenced his microbiome, and analyzed over 1 million SNPs from his genome. Computational analysis of this data helped diagnose Smarr with Crohn's disease and revealed shifts in his microbiome from healthy to diseased states. Smarr advocates integrating multi-omics data to achieve predictive, preventative and participatory medicine.
Chimeric Antigen Receptors (paper with corresponding power point)Kevin B Hugins
Gene therapy was first conceptualized to alter debilitating fates of genetic diseases. Gene therapy technology can help introduce new functional DNA to replace mutated genes. The idea first arose in 1972 when Friedmann and Roblin authored a paper, “Gene therapy for human genetic disease?”, demonstrating that exogenous DNA can be taken up by mammalian cells (1). They proposed that the same procedure could be done on humans to correct genetic defects by introducing therapeutic DNA. Currently, genetic modification of T lymphocytes has been the major area of research for treating malignant tumors. This technique seeks to create chimeric antigen receptor (CAR) in T cells by genetically modifying them in vitro and reintroduce them back into blood circulation. The T cells are unique to every patient and the chimeric antigen receptors are unique to the tumor that it is targeting.
The document discusses in silico drug discovery methods including identifying potential drug targets, generating pharmacophore models, screening compound databases, and analyzing top hits through molecular docking simulations. A drug discovery strategy is outlined involving primary and secondary screening to identify lead compounds. The work plan describes using AutoDock Vina to dock and rank compounds, selecting the top 14 hits, and analyzing their binding interactions with HIV proteases. Nilotinib, lopinavir, ergoloid, and zafirlukast were evaluated in more detail and found to have high binding affinity to the target proteins.
This document contains 4 images of the blue-green algae Nostoc viewed under a microscope using Bright Field techniques at magnifications of 200x and 400x. The images show Nostoc in its natural state as well as using a squash technique to better view its structure.
This article discusses a study that surveyed patients with inflammatory bowel diseases like Crohn's disease and ulcerative colitis about their use of cannabis. The researchers hypothesized that cannabis works as an anti-inflammatory through receptors called endocannabinoids. The survey found that in most cases, patients reported cannabis helped relieve abdominal pain, diarrhea and reduced appetite. While cannabis has side effects, it improved quality of life for these patients and could be a viable treatment option.
This research paper studied whether cannabidiol inhibits inflammatory hypermotility in mice. Researchers induced intestinal inflammation in mice using croton oil, then tested the effects of different doses of cannabidiol. They found that cannabidiol effectively reduced hypermotility when inflammation was present, and higher doses produced greater inhibition. The study concluded that cannabidiol can help normalize intestinal motility during inflammation.
This article describes a study of 30 Crohn's disease patients who used cannabis as a treatment. Cannabis is known to have anti-inflammatory properties, and a symptom of Crohn's is bowel inflammation. The study found that 21 of the 30 patients experienced great improvement in their condition after using cannabis. The results show that cannabis treatment can reduce symptoms of Crohn's disease like bowel inflammation.
Galsulfase is a recombinant form of human N-acetylgalactosamine 4-sulfatase that was approved by the FDA in May 2005 for the treatment of mucopolysaccharidosis type VI (MPS-VI), a rare lysosomal storage disorder. MPS-VI is caused by a deficiency of N–acetylgalactosamine 4-sulfatase, which leads to the accumulation of dermatan sulfate. Clinical trials found that patients treated with galsulfase showed improvements in walking and stair-climbing ability compared to placebo. Galsulfase represents the first approved treatment for MPS-VI and provides an important new therapy for patients suffering from this rare disease.
The Biology Honor Society will provide refreshments from 10:30-10:40 in room 106 MMM on Thursday. Yadilette Rivera, an alumna from Univ. of Massachusetts Amherst, will then give a seminar from 10:40-11:20 in room 106 MMM about the challenges of protein crystallography and graduate school.
Yadilette's research focuses on treating lysosomal storage disorders, which cause bone abnormalities, through enzyme replacement therapy rather than bone marrow transplantation. Her treatment involves purifying proteins through crystallization and x-ray analysis to determine the replacement enzyme, then injecting patients weekly and monitoring their progress through tests, with some patients showing increased mobility based on walking and climbing tests. This research helps improve the lives of those suffering from these diseases and creates more awareness.
This document discusses incorporating unnatural amino acids into proteins to expand their functions. It describes how pyrrolysine is used as an orthogonal system to incorporate unnatural amino acids specified by an amber stop codon. Various unnatural amino acids containing alkene and norbornene functional groups were successfully incorporated into GFP and other proteins in E. coli and mammalian cells. These modified proteins could then be site-specifically labeled using bioorthogonal reactions like the thiol-ene and Diels-Alder reactions. This allows proteins to be labeled and studied in live cells with new functions.
This document describes a new method for site-specifically labeling proteins using genetically encoded norbornene and rapidly reactive tetrazine probes. Key points:
1) A norbornene-containing amino acid is genetically encoded in E. coli and mammalian cells using the pyrrolysyl tRNA synthetase system.
2) A series of tetrazine probes are developed that react rapidly and specifically with norbornene via an inverse electron demand Diels-Alder reaction.
3) The tetrazine-norbornene reaction is shown to be much faster than established bioorthogonal reactions, allowing specific labeling of proteins both in vitro and on mammalian cell surfaces.
Jessica Torres from North Carolina State University will give a seminar on incorporating unnatural amino acids into proteins. Unnatural amino acids allow the expression of proteins with new functions and enable a wide range of studies by using diverse functional groups beyond the 20 common amino acids. Examples include incorporating fluorescent and spectroscopic probes to study biological processes in live cells. The seminar will discuss how introducing unnatural amino acids into proteins, both in vitro and in vivo, is a promising technique that can provide insights into answering biomedical questions relevant to human health. Refreshments will be provided before the talk at 10:30am on Thursday September 20 in room MMM 106.
An improved method of protein labeling uses unnatural amino acids inserted during protein synthesis, which do not interfere with the organism's natural systems. The unnatural amino acids are chosen for their similarity to natural amino acids but are distinct enough to avoid incorporation elsewhere. By adding a stop codon to the unnatural amino acid and inserting it into tRNA, only the desired protein will be labeled without affecting other proteins.
Rta is a key transcriptional activator that is required for reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) from latency. Rta stimulates DNA binding of the transcription factor RBP-Jk to KSHV promoter regions containing RBP-Jk binding sites. The interaction between Rta and RBP-Jk leads to recruitment of additional factors and transactivation of immediate early and delayed early genes, establishing the lytic replication cycle. Precise cis-elements including CANT repeats and [A/T]3 motifs that flank the RBP-Jk site contribute to the strength of Rta/RBP-Jk mediated transactivation. Understanding this molecular mechanism of
Ms. Olga González presented on the Kaposi sarcoma-associated herpesvirus (KSHV). KSHV has two stages - the lytic cycle where infection occurs, and the lysogenic cycle where the virus establishes latency. It infects people through saliva, blood or sexual contact, and only causes harm in those with weak immune systems, allowing the virus to reactivate, switch cycles, and reproduce to create cancerous tumors. Her research aims to find and stop the molecular trigger of reactivation, which could help other scientists attack the virus at its source without killing healthy cells, as well as create awareness for those susceptible to infection.
14.anaeli.review paper.final draft.the use of cannabis sativa as an antianaelishockey
This document summarizes research on using Cannabis sativa (marijuana) to treat Crohn's disease. Crohn's is a chronic inflammatory bowel disease. The author reviews studies showing that cannabinoids in cannabis reduce bowel inflammation in mice with induced colitis. Surveys of human patients also found cannabis relieved abdominal pain and diarrhea from Crohn's. While legal issues surround cannabis, synthetic cannabinoids are being developed that may have similar medical benefits. The document concludes that cannabis appears to be an effective treatment for reducing intestinal inflammation in Crohn's disease patients.
This document discusses the use of Cannabis sativa as an anti-inflammatory for Crohn's Disease. It first provides background on Crohn's Disease, describing its symptoms and current treatments. It then discusses the composition of Cannabis sativa, including cannabinoids such as THC and CBD. Studies in mice and humans are summarized that show Cannabis reduces inflammation and symptoms of Crohn's such as abdominal pain and diarrhea. The document concludes that cannabinoids may provide protection against gut inflammation for Crohn's patients.
The first seminar attended as part of the RISE Fall program 2012 discussed the Kaposi sarcoma-associated herpesvirus (KSHV). The presenter explained that KSHV is one of eight known herpes viruses that infects people through saliva, blood or sexual contact. However, it only causes illness in those with weak immune systems, as it reproduces and creates cancerous tumors. The presenter effectively communicated details about how KSHV works and the importance of further research on the virus.
Herpesviruses like KSHV have the ability to establish lifelong latent infections and periodically reactivate. During reactivation, the viruses undergo full gene expression and produce new virus particles. Reactivation is a key step in disease development for many herpesviruses, including KSHV which is associated with Kaposi's sarcoma cancer. The researcher's lab focuses on understanding the molecular mechanisms that drive KSHV reactivation in order to develop new therapies and diagnostics for KSHV infection.
The document discusses Anaeli Shockey's experience in the RISE (Research Initiative Science Experience) summer program between high school and university. The six-week program involved taking a general biology course and lab, which helped Shockey realize her strong interest in science and learn key lab skills and safety procedures. She also learned how to develop a research proposal by choosing a topic, researching problems, and proposing hypotheses. This educational experience helped Shockey grow as a young scientist by gaining fundamental knowledge and skills in several important areas.
The document compares two forests in Puerto Rico: Bosque Seco de Guánica and El Yunque National Forest. It discusses differences between the forests in areas, canopy layers and height, flora, fauna, buffer zones, and problems faced. The key information provided includes descriptions of the different forest types in each area based on rainfall levels, canopy structure variations, distinctive plant and animal species present, and environmental challenges affecting the forests.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Building Production Ready Search Pipelines with Spark and MilvusZilliz
Spark is the widely used ETL tool for processing, indexing and ingesting data to serving stack for search. Milvus is the production-ready open-source vector database. In this talk we will show how to use Spark to process unstructured data to extract vector representations, and push the vectors to Milvus vector database for search serving.
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Best 20 SEO Techniques To Improve Website Visibility In SERPPixlogix Infotech
Boost your website's visibility with proven SEO techniques! Our latest blog dives into essential strategies to enhance your online presence, increase traffic, and rank higher on search engines. From keyword optimization to quality content creation, learn how to make your site stand out in the crowded digital landscape. Discover actionable tips and expert insights to elevate your SEO game.
GraphRAG for Life Science to increase LLM accuracyTomaz Bratanic
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
Maruthi Prithivirajan, Head of ASEAN & IN Solution Architecture, Neo4j
Get an inside look at the latest Neo4j innovations that enable relationship-driven intelligence at scale. Learn more about the newest cloud integrations and product enhancements that make Neo4j an essential choice for developers building apps with interconnected data and generative AI.
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/
DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
- Verstehen des DLAU-Tools und wie man es am besten nutzt
- Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw.
- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/building-and-scaling-ai-applications-with-the-nx-ai-manager-a-presentation-from-network-optix/
Robin van Emden, Senior Director of Data Science at Network Optix, presents the “Building and Scaling AI Applications with the Nx AI Manager,” tutorial at the May 2024 Embedded Vision Summit.
In this presentation, van Emden covers the basics of scaling edge AI solutions using the Nx tool kit. He emphasizes the process of developing AI models and deploying them globally. He also showcases the conversion of AI models and the creation of effective edge AI pipelines, with a focus on pre-processing, model conversion, selecting the appropriate inference engine for the target hardware and post-processing.
van Emden shows how Nx can simplify the developer’s life and facilitate a rapid transition from concept to production-ready applications.He provides valuable insights into developing scalable and efficient edge AI solutions, with a strong focus on practical implementation.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
AI 101: An Introduction to the Basics and Impact of Artificial IntelligenceIndexBug
Imagine a world where machines not only perform tasks but also learn, adapt, and make decisions. This is the promise of Artificial Intelligence (AI), a technology that's not just enhancing our lives but revolutionizing entire industries.
How to Get CNIC Information System with Paksim Ga.pptxdanishmna97
Pakdata Cf is a groundbreaking system designed to streamline and facilitate access to CNIC information. This innovative platform leverages advanced technology to provide users with efficient and secure access to their CNIC details.
Infrastructure Challenges in Scaling RAG with Custom AI modelsZilliz
Building Retrieval-Augmented Generation (RAG) systems with open-source and custom AI models is a complex task. This talk explores the challenges in productionizing RAG systems, including retrieval performance, response synthesis, and evaluation. We’ll discuss how to leverage open-source models like text embeddings, language models, and custom fine-tuned models to enhance RAG performance. Additionally, we’ll cover how BentoML can help orchestrate and scale these AI components efficiently, ensuring seamless deployment and management of RAG systems in the cloud.