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.
1. Nephron sparing surgery (NSS), also known as partial nephrectomy, aims to remove renal tumors while preserving as much healthy kidney tissue as possible.
2. NSS has similar oncologic outcomes as radical nephrectomy but offers advantages like preserving renal function and reducing risks of chronic kidney disease.
3. While NSS was historically more complex and risky than radical nephrectomy, advances in surgical techniques like laparoscopic and robotic partial nephrectomy have reduced risks and made NSS a viable option for more patients with renal cell carcinoma.
14 5-13 ipmr approach to cancer diagnosisSimba Syed
This document discusses different approaches to cancer diagnosis, including clinical suspicion based on symptoms and history, physical examination to find signs, screening examinations for early diagnosis, and various diagnostic techniques. It covers cytologic diagnosis using samples from various sites and tissues, histologic diagnosis through biopsy methods, specialized staining, immunohistochemistry, electron microscopy, and flow cytometry. Radiologic imaging and serologic tests are also discussed for diagnostic or staging purposes. The pathology report provides information on tumor type, behavior, grade, invasion extent, pathologic stage, and other details to guide treatment and prognosis.
This document discusses treatment approaches for locally advanced breast cancer (LABC). It describes inflammatory breast cancer (IBC) as an aggressive variant of LABC. Nearly all cases of LABC warrant neoadjuvant chemotherapy followed by surgery. For some patients, breast-conserving surgery may be an option after chemotherapy reduces the tumor size. Mastectomy remains the standard surgical treatment for LABC. Axillary lymph node assessment involves sentinel lymph node biopsy or axillary lymph node dissection depending on clinical response to neoadjuvant therapy. The residual cancer burden score provides a standardized way to report tumor response after neoadjuvant treatment and correlate with patient outcomes.
O documento classifica o carcinoma hepatocelular (CHC) em estágios de A a D com base no tamanho e número de nódulos, invasão vascular e função hepática. Quanto mais avançado o estágio, pior o prognóstico e menor a sobrevida. O estágio influencia o tratamento, variando entre cuidados paliativos, ablação, ressecção e transplante hepático.
Luc Rotenberg : US guided vacuum breast biopsy and minimal Invasive Intervent...breastcancerupdatecongress
This document summarizes minimal invasive interventional procedures for breast lesions. It discusses ultrasound-guided breast biopsy procedures and whether they can provide minimal invasive diagnosis and treatment of benign and malignant lesions. Various biopsy methods and devices are reviewed, including vacuum-assisted biopsy. Indications, risks, sample size, and follow up after biopsy are addressed. Underestimation rates of ductal carcinoma in situ and atypical lesions with biopsy are discussed. Radiological-pathological concordance and determining appropriate management of biopsy results is also covered. Radiofrequency ablation is presented as a potential minimal invasive treatment option.
1. Nephron sparing surgery (NSS), also known as partial nephrectomy, aims to remove renal tumors while preserving as much healthy kidney tissue as possible.
2. NSS has similar oncologic outcomes as radical nephrectomy but offers advantages like preserving renal function and reducing risks of chronic kidney disease.
3. While NSS was historically more complex and risky than radical nephrectomy, advances in surgical techniques like laparoscopic and robotic partial nephrectomy have reduced risks and made NSS a viable option for more patients with renal cell carcinoma.
14 5-13 ipmr approach to cancer diagnosisSimba Syed
This document discusses different approaches to cancer diagnosis, including clinical suspicion based on symptoms and history, physical examination to find signs, screening examinations for early diagnosis, and various diagnostic techniques. It covers cytologic diagnosis using samples from various sites and tissues, histologic diagnosis through biopsy methods, specialized staining, immunohistochemistry, electron microscopy, and flow cytometry. Radiologic imaging and serologic tests are also discussed for diagnostic or staging purposes. The pathology report provides information on tumor type, behavior, grade, invasion extent, pathologic stage, and other details to guide treatment and prognosis.
This document discusses treatment approaches for locally advanced breast cancer (LABC). It describes inflammatory breast cancer (IBC) as an aggressive variant of LABC. Nearly all cases of LABC warrant neoadjuvant chemotherapy followed by surgery. For some patients, breast-conserving surgery may be an option after chemotherapy reduces the tumor size. Mastectomy remains the standard surgical treatment for LABC. Axillary lymph node assessment involves sentinel lymph node biopsy or axillary lymph node dissection depending on clinical response to neoadjuvant therapy. The residual cancer burden score provides a standardized way to report tumor response after neoadjuvant treatment and correlate with patient outcomes.
O documento classifica o carcinoma hepatocelular (CHC) em estágios de A a D com base no tamanho e número de nódulos, invasão vascular e função hepática. Quanto mais avançado o estágio, pior o prognóstico e menor a sobrevida. O estágio influencia o tratamento, variando entre cuidados paliativos, ablação, ressecção e transplante hepático.
Luc Rotenberg : US guided vacuum breast biopsy and minimal Invasive Intervent...breastcancerupdatecongress
This document summarizes minimal invasive interventional procedures for breast lesions. It discusses ultrasound-guided breast biopsy procedures and whether they can provide minimal invasive diagnosis and treatment of benign and malignant lesions. Various biopsy methods and devices are reviewed, including vacuum-assisted biopsy. Indications, risks, sample size, and follow up after biopsy are addressed. Underestimation rates of ductal carcinoma in situ and atypical lesions with biopsy are discussed. Radiological-pathological concordance and determining appropriate management of biopsy results is also covered. Radiofrequency ablation is presented as a potential minimal invasive treatment option.
Colorectal Cancer Detection: Fact vs FictionJarrod Lee
Colorectal cancer is the most common cancer in Singapore. It can be prevented by timely screening. Yet there are many misconceptions about colorectal cancer screening. This talk addresses some of the common perceptions about colorectal cancer screening. This talk was first presented to the public at Feel Fab Fest 2018.
Newer advances in diagnosis of Lung Cancer biomarkers provide a more comprehensive perspective. Molecular pathology now supplements traditional histologic classification, with biomarkers like EGFR, ALK, ROS1, and PD-L1 expression level guiding targeted therapy selection. Biomarker testing is important for identifying actionable mutations to help select appropriate targeted therapies and improve patient outcomes. However, barriers remain like insufficient tissue samples, long turnaround times, and lack of universal testing. Efforts are ongoing to address disparities and expand the use of liquid biopsy and next-generation sequencing to overcome challenges and improve personalized treatment of lung cancer.
The document summarizes the UWCCC/WON Molecular Tumor Board (MTB) and Registration Protocol. The MTB is a panel of experts that provides treatment recommendations based on pathology or genomics analysis. Physicians can submit cases for review to receive recommendations for clinical trials, off-label drugs, or standard treatment. The Registration Protocol collects genomic, clinical, and outcome data to evaluate the effectiveness of targeted therapies recommended by the MTB.
This document describes a research study that used laser capture microdissection to isolate distinct cell populations from mouse and human inner ear tissue for gene expression analysis. The researchers were able to extract RNA from formalin-fixed paraffin-embedded tissue sections, amplify it, and detect cell-type specific gene expression by RT-PCR. This technique allows targeted analysis of gene expression in specific inner ear structures, and could be applied to archived human temporal bone samples preserved in formalin. The researchers validated the method by detecting housekeeping genes and cell markers in laser-captured cells from mouse and human inner ear tissue.
The RAPIDO trial compared short-course radiotherapy followed by chemotherapy and surgery to preoperative chemoradiotherapy, surgery, and optional adjuvant chemotherapy in locally advanced rectal cancer. It found that short-course radiotherapy followed by chemotherapy reduced the risk of disease-related treatment failure at 3 years compared to standard chemoradiotherapy. At 3 years, the probability of distant metastases was 20.0% in the experimental group versus 26.8% in the standard care group. The trial demonstrated that incorporating chemotherapy between short-course radiotherapy and surgery decreased distant metastases and improved outcomes for patients with locally advanced rectal cancer.
1) O documento discute a seqüência adenoma-carcinoma no desenvolvimento do câncer colorretal, com evidências mostrando que adenomas precursoras evoluem para carcinoma após sucessivas alterações genéticas.
2) A detecção e remoção endoscópica de adenomas pode prevenir o câncer colorretal, reduzindo sua incidência em até 85%.
3) A polipose adenomatosa familiar é uma doença genética dominante que causa inúmeros pólipos e quase sempre leva ao câncer colorretal na quarta dé
This document provides an overview of the principles of immunotherapy. It begins by describing the cancer-immunity cycle and how the adaptive anticancer immune response is initiated. It then discusses how tumors can evade the immune system, such as by overexpressing inhibitory receptors like PD-L1. The document reviews different approaches to immunotherapy, including passive approaches using checkpoint inhibitors and active approaches like cancer vaccines. It also covers topics like evaluating the efficacy of immunotherapy, biomarkers, combination immunotherapy, and immune-related adverse events.
The SOFT trial investigated the role of ovarian function suppression (OFS) and aromatase inhibitors (AIs) in premenopausal breast cancer patients. It found that adding OFS to tamoxifen (TAM) improved 5-year disease-free survival from 84.7% to 86.6%, though the difference was not statistically significant. The SOFT+TEXT analysis found that substituting exemestane for TAM when combined with OFS improved 5-year disease-free survival from 87.3% to 91.1%, with a statistically significant difference. For patients who received chemotherapy, exemestane+OFS provided an absolute 5-year breast cancer-free rate improvement of 3.
Revisão da literatura sobre o assunto, incluindo:
1) Epidemiologia do CaP
2) O que dizem as Diretrizes
3) Por que fazer linfadenectomia pélvica estendida (eLND)?
4) Quais áreas podem ser incluídas na eLND?
5) Morbidade e prevenção de complicações
6) Padronização da dissecção
7) Conclusões
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.
InSyBio is developing an integrated cloud platform for biomarker discovery to improve precision medicine and clinical trials. Their platform performs end-to-end biomarker analysis from raw biological data through extraction, interpretation and applications. This is more efficient than existing fragmented methods. InSyBio's biomarkers are highly accurate with small sample sizes and can reduce clinical trial costs and times. Their platform has applications in nutrition, pharma and diagnostics.
Oncology Discoveries, University of Chicagouchicagotech
The University of Chicago Comprehensive Cancer Center (UCCCC) uses cooperative, multidisciplinary initiatives to support innovative cancer research. It has over 320 active clinical trials spanning various phases, as well as core facilities that support research efforts. Research is organized into six scientific programs, including Molecular Mechanisms of Cancer and Hematopoiesis and Hematological Malignancies. These programs work to define the genetic causes of cancer and develop targeted therapies through translational research that moves between basic science and clinical applications. Representative technologies described include methods for inhibiting cancer metastasis and developing novel antibodies.
5th Tumor Models Boston July 2017 BrochureDiane McKenna
Tumor Models Boston 2017 will address the preclinical & clinical developments of the most promising therapies including targeted therapies, check-point inhibitors & CAR-T therapies and how these findings can be utilized to bridge the gap between preclinical and clinical studies.
Kerry Robinson works as an Associate Practitioner (Band 4) in histopathology. Some of their key responsibilities include specimen reception and labeling, macroscopic tissue descriptions during dissection, tissue embedding, trimming and microtomy using a microtome, and tissue staining. They work in several areas of the laboratory including the main lab, histopathology, non-gynae, cytology, andrology, and secondary staining. Kerry aims to develop skills in teamwork, communication, independence, attention to detail, and using various equipment and software. Their career goals are to complete their degree and IBMS portfolio to become a Band 5 Trainee Biomedical Scientist and eventually a Band 6 Biomedical Scientist in hist
Presented at American Association for Cancer Research (AACR) at New Orleans 2016 annual conference. Fight Colorectal Cancer and Cancer Research Institute joint effort.
Presented by
Al B. Benson III, MD FACP FASCO
Professor of Medicine
Associate Director for Cooperative Groups Robert H. Lurie Comprehensive Cancer Center of Northwestern University
Please share this webinar with anyone who may be interested!
Watch all our webinars: https://www.youtube.com/playlist?list=PL4dDQscmFYu_ezxuxnAE61hx4JlqAKXpR
Cancer care is increasingly tailored to individual patients, who can undergo genetic or biomarker testing soon after diagnosis, to determine which treatments have the best chance of shrinking or eliminating tumours.
In this webinar, a pathologist and clinical oncologist discuss:
● how they are using these new tests,
● how they communicate results and treatment options to patients and caregivers, and
● how patients can be better informed on the kinds of tests that are in development or in use across Canada
View the video: https://youtu.be/_Wai_uMQKEQ
Follow our social media accounts:
Twitter - https://twitter.com/survivornetca
Facebook - https://www.facebook.com/CanadianSurvivorNet
Pinterest - https://www.pinterest.com/survivornetwork
YouTube - https://www.youtube.com/user/Survivornetca
Introduction to Cancer: Focus on Solid Tumors Course, organized by Healthcare...James Prudhomme
Delegates attending this course will benefit from an introductory overview of the terminology and classification of cancer and the principle issues in its treatment. Commonly available anti-cancer drugs will be reviewed, including immunotherapies. The range of side-effects of cancer treatments will be studied in detail. Quality-of-life issues in terms of overall assessment and result interpretation will also be discussed.
Detailed consideration will be given to the treatment of major tumor types: breast, lung, upper gastrointestinal (GI), colorectal, melanoma, ovarian and prostate cancer.
This document summarizes an upcoming Cancer Diagnosis & Therapy Congress organized by MnM Conferences on September 3-4, 2015 in London. The two-day conference will bring over 150 experts from around the world to discuss advances in cancer diagnosis technologies and novel targeted cancer therapies. Key discussion topics will include interventional radiology techniques, immunotherapy, biomarkers, nanotechnology, biosensors, and functional genomics. Over 30 distinguished international speakers will present, including researchers from industry, academia, and hospitals. The conference aims to provide a platform for knowledge sharing between researchers, pharmaceutical companies, and doctors to collaborate and stay updated on the latest discoveries and technologies for cancer diagnosis and treatment.
Data sharing drivers in precision oncology, biomedical research, and healthcare. Accelerating discovery, innovation, providing credit for all stakeholders - patients, researchers, care providers, payers.
This curriculum vitae summarizes the qualifications and experience of Dr. Sandeep Kumar. It outlines his educational background, including degrees from universities in India and the UK. It describes his doctoral thesis which focused on the role of the tumor suppressor PDCD4 in pancreatic cancer under hypoxic conditions. It lists his professional experience in research roles in universities and research institutions in the UK, India, and Ukraine. It also outlines his skills in various laboratory techniques and areas of research expertise.
Colorectal Cancer Detection: Fact vs FictionJarrod Lee
Colorectal cancer is the most common cancer in Singapore. It can be prevented by timely screening. Yet there are many misconceptions about colorectal cancer screening. This talk addresses some of the common perceptions about colorectal cancer screening. This talk was first presented to the public at Feel Fab Fest 2018.
Newer advances in diagnosis of Lung Cancer biomarkers provide a more comprehensive perspective. Molecular pathology now supplements traditional histologic classification, with biomarkers like EGFR, ALK, ROS1, and PD-L1 expression level guiding targeted therapy selection. Biomarker testing is important for identifying actionable mutations to help select appropriate targeted therapies and improve patient outcomes. However, barriers remain like insufficient tissue samples, long turnaround times, and lack of universal testing. Efforts are ongoing to address disparities and expand the use of liquid biopsy and next-generation sequencing to overcome challenges and improve personalized treatment of lung cancer.
The document summarizes the UWCCC/WON Molecular Tumor Board (MTB) and Registration Protocol. The MTB is a panel of experts that provides treatment recommendations based on pathology or genomics analysis. Physicians can submit cases for review to receive recommendations for clinical trials, off-label drugs, or standard treatment. The Registration Protocol collects genomic, clinical, and outcome data to evaluate the effectiveness of targeted therapies recommended by the MTB.
This document describes a research study that used laser capture microdissection to isolate distinct cell populations from mouse and human inner ear tissue for gene expression analysis. The researchers were able to extract RNA from formalin-fixed paraffin-embedded tissue sections, amplify it, and detect cell-type specific gene expression by RT-PCR. This technique allows targeted analysis of gene expression in specific inner ear structures, and could be applied to archived human temporal bone samples preserved in formalin. The researchers validated the method by detecting housekeeping genes and cell markers in laser-captured cells from mouse and human inner ear tissue.
The RAPIDO trial compared short-course radiotherapy followed by chemotherapy and surgery to preoperative chemoradiotherapy, surgery, and optional adjuvant chemotherapy in locally advanced rectal cancer. It found that short-course radiotherapy followed by chemotherapy reduced the risk of disease-related treatment failure at 3 years compared to standard chemoradiotherapy. At 3 years, the probability of distant metastases was 20.0% in the experimental group versus 26.8% in the standard care group. The trial demonstrated that incorporating chemotherapy between short-course radiotherapy and surgery decreased distant metastases and improved outcomes for patients with locally advanced rectal cancer.
1) O documento discute a seqüência adenoma-carcinoma no desenvolvimento do câncer colorretal, com evidências mostrando que adenomas precursoras evoluem para carcinoma após sucessivas alterações genéticas.
2) A detecção e remoção endoscópica de adenomas pode prevenir o câncer colorretal, reduzindo sua incidência em até 85%.
3) A polipose adenomatosa familiar é uma doença genética dominante que causa inúmeros pólipos e quase sempre leva ao câncer colorretal na quarta dé
This document provides an overview of the principles of immunotherapy. It begins by describing the cancer-immunity cycle and how the adaptive anticancer immune response is initiated. It then discusses how tumors can evade the immune system, such as by overexpressing inhibitory receptors like PD-L1. The document reviews different approaches to immunotherapy, including passive approaches using checkpoint inhibitors and active approaches like cancer vaccines. It also covers topics like evaluating the efficacy of immunotherapy, biomarkers, combination immunotherapy, and immune-related adverse events.
The SOFT trial investigated the role of ovarian function suppression (OFS) and aromatase inhibitors (AIs) in premenopausal breast cancer patients. It found that adding OFS to tamoxifen (TAM) improved 5-year disease-free survival from 84.7% to 86.6%, though the difference was not statistically significant. The SOFT+TEXT analysis found that substituting exemestane for TAM when combined with OFS improved 5-year disease-free survival from 87.3% to 91.1%, with a statistically significant difference. For patients who received chemotherapy, exemestane+OFS provided an absolute 5-year breast cancer-free rate improvement of 3.
Revisão da literatura sobre o assunto, incluindo:
1) Epidemiologia do CaP
2) O que dizem as Diretrizes
3) Por que fazer linfadenectomia pélvica estendida (eLND)?
4) Quais áreas podem ser incluídas na eLND?
5) Morbidade e prevenção de complicações
6) Padronização da dissecção
7) Conclusões
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.
InSyBio is developing an integrated cloud platform for biomarker discovery to improve precision medicine and clinical trials. Their platform performs end-to-end biomarker analysis from raw biological data through extraction, interpretation and applications. This is more efficient than existing fragmented methods. InSyBio's biomarkers are highly accurate with small sample sizes and can reduce clinical trial costs and times. Their platform has applications in nutrition, pharma and diagnostics.
Oncology Discoveries, University of Chicagouchicagotech
The University of Chicago Comprehensive Cancer Center (UCCCC) uses cooperative, multidisciplinary initiatives to support innovative cancer research. It has over 320 active clinical trials spanning various phases, as well as core facilities that support research efforts. Research is organized into six scientific programs, including Molecular Mechanisms of Cancer and Hematopoiesis and Hematological Malignancies. These programs work to define the genetic causes of cancer and develop targeted therapies through translational research that moves between basic science and clinical applications. Representative technologies described include methods for inhibiting cancer metastasis and developing novel antibodies.
5th Tumor Models Boston July 2017 BrochureDiane McKenna
Tumor Models Boston 2017 will address the preclinical & clinical developments of the most promising therapies including targeted therapies, check-point inhibitors & CAR-T therapies and how these findings can be utilized to bridge the gap between preclinical and clinical studies.
Kerry Robinson works as an Associate Practitioner (Band 4) in histopathology. Some of their key responsibilities include specimen reception and labeling, macroscopic tissue descriptions during dissection, tissue embedding, trimming and microtomy using a microtome, and tissue staining. They work in several areas of the laboratory including the main lab, histopathology, non-gynae, cytology, andrology, and secondary staining. Kerry aims to develop skills in teamwork, communication, independence, attention to detail, and using various equipment and software. Their career goals are to complete their degree and IBMS portfolio to become a Band 5 Trainee Biomedical Scientist and eventually a Band 6 Biomedical Scientist in hist
Presented at American Association for Cancer Research (AACR) at New Orleans 2016 annual conference. Fight Colorectal Cancer and Cancer Research Institute joint effort.
Presented by
Al B. Benson III, MD FACP FASCO
Professor of Medicine
Associate Director for Cooperative Groups Robert H. Lurie Comprehensive Cancer Center of Northwestern University
Please share this webinar with anyone who may be interested!
Watch all our webinars: https://www.youtube.com/playlist?list=PL4dDQscmFYu_ezxuxnAE61hx4JlqAKXpR
Cancer care is increasingly tailored to individual patients, who can undergo genetic or biomarker testing soon after diagnosis, to determine which treatments have the best chance of shrinking or eliminating tumours.
In this webinar, a pathologist and clinical oncologist discuss:
● how they are using these new tests,
● how they communicate results and treatment options to patients and caregivers, and
● how patients can be better informed on the kinds of tests that are in development or in use across Canada
View the video: https://youtu.be/_Wai_uMQKEQ
Follow our social media accounts:
Twitter - https://twitter.com/survivornetca
Facebook - https://www.facebook.com/CanadianSurvivorNet
Pinterest - https://www.pinterest.com/survivornetwork
YouTube - https://www.youtube.com/user/Survivornetca
Introduction to Cancer: Focus on Solid Tumors Course, organized by Healthcare...James Prudhomme
Delegates attending this course will benefit from an introductory overview of the terminology and classification of cancer and the principle issues in its treatment. Commonly available anti-cancer drugs will be reviewed, including immunotherapies. The range of side-effects of cancer treatments will be studied in detail. Quality-of-life issues in terms of overall assessment and result interpretation will also be discussed.
Detailed consideration will be given to the treatment of major tumor types: breast, lung, upper gastrointestinal (GI), colorectal, melanoma, ovarian and prostate cancer.
This document summarizes an upcoming Cancer Diagnosis & Therapy Congress organized by MnM Conferences on September 3-4, 2015 in London. The two-day conference will bring over 150 experts from around the world to discuss advances in cancer diagnosis technologies and novel targeted cancer therapies. Key discussion topics will include interventional radiology techniques, immunotherapy, biomarkers, nanotechnology, biosensors, and functional genomics. Over 30 distinguished international speakers will present, including researchers from industry, academia, and hospitals. The conference aims to provide a platform for knowledge sharing between researchers, pharmaceutical companies, and doctors to collaborate and stay updated on the latest discoveries and technologies for cancer diagnosis and treatment.
Data sharing drivers in precision oncology, biomedical research, and healthcare. Accelerating discovery, innovation, providing credit for all stakeholders - patients, researchers, care providers, payers.
This curriculum vitae summarizes the qualifications and experience of Dr. Sandeep Kumar. It outlines his educational background, including degrees from universities in India and the UK. It describes his doctoral thesis which focused on the role of the tumor suppressor PDCD4 in pancreatic cancer under hypoxic conditions. It lists his professional experience in research roles in universities and research institutions in the UK, India, and Ukraine. It also outlines his skills in various laboratory techniques and areas of research expertise.
The University of Chicago has significant expertise and resources in microbiome research across multiple departments. Key areas of focus include the human microbiome and its relationship to health conditions like diabetes, IBD, and autism. They have unique clinical and research facilities for studying the microbiome, as well as computational and data analytics capabilities. Notable initiatives led by UChicago researchers include the Earth, Home, and Hospital Microbiome Projects which analyze microbiome samples from various environmental and clinical settings. The university welcomes partnerships with industry to advance microbiome research and translate findings to applications that improve human health and the environment.
Join us in Boston this coming Fall to attend Cambridge Healthtech Institute's (CHI) 2nd Annual FAST: Functional Analysis & Screening Technologies Congress on November 17-19, 2014 and meet with a community of 250+ biologists, screening managers, assay developers, engineers and pharmacologists dedicated to improving in vitro cell models and phenotypic screening to advance drug discovery and development at 6 conferences: Phenotypic Drug Discovery (Part I & II), Engineering Functional 3D Models, Screening and Functional Analysis of 3D Models, Organotypic Culture Models for Toxicology and Physiologically-Relevant Cellular Tumor Models for Drug Discovery. Delegates have the opportunity to share insights in interactive panel discussions and connect during networking breaks. View innovative technologies and scientific research revolutionizing early-stage drug discovery in the exhibit/poster hall.
Downloadable slides highlighting key concepts in colorectal cancer screening and appropriate therapy selection and application in the adjuvant setting and beyond.
International Journal of Biometrics and Bioinformatics(IJBB) Volume (3) Issue...CSCJournals
This document reviews approaches for predicting breast cancer prognosis using both clinical data and gene expression profiles. Traditional prognosis models rely mainly on clinical factors like age, tumor size, and lymph node status, but can fail to distinguish molecularly distinct subgroups. Gene expression profiling via microarray technology has improved molecular classification and shown promise for prognosis. However, most studies have focused on gene signatures without fully leveraging clinical data. Integrating clinical and gene expression data may enhance accuracy by accounting for their complementary nature. The review discusses feature selection and classification methods applied to both data types, as well as related work on data integration. The goal is to develop an improved prognosis model that incorporates both clinical and molecular factors.
Biodefense in the Age of Synthetic Biology – Tom SlezakCatalyst Biosummit
This document summarizes a report from the National Academies of Sciences on biodefense challenges posed by advances in synthetic biology. The report developed a framework to assess security vulnerabilities associated with synthetic biology and applied it to 12 capabilities, like pathogen synthesis. It found that synthetic biology expands what can be produced and decreases production time and actors. It recommends continued monitoring of biotechnology advances that may lower barriers. The report also identifies challenges for biodefense like unpredictability and the need for new preparedness and response strategies. It explores opportunities to advance mitigation like detection of unusual weapons and using synthetic biology for countermeasures.
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
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 cells
BiP-derived HLA-DR4 Epitopes Differentially Recognized by T cells in RAThi K. Tran-Nguyen, PhD
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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
The document discusses the Gene Expression Omnibus (GEO) database, which is a public repository maintained by the National Center for Biotechnology Information that archives and freely distributes gene expression and other high-throughput functional genomics data submitted by the research community. It outlines the background and purpose of GEO, describes the types of data it contains including platforms, samples, and series. It also lists 10 ways that researchers can utilize and analyze data from GEO, such as performing searches, downloading data files, and using online analysis tools to visualize and compare gene expression data.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
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.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
The binding of cosmological structures by massless topological defectsSérgio Sacani
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.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
6. cfDNA vs ctDNA
cfDNA (cell-free DNA)
• Non-encapsulated DNA fragments of 100-300bp
• t1/2 ~ 2h for ctDNA and 1h for fetal-derived cfDNA
• Source: death, dying, necrosis/apoptosis cells
• Used in noninvasive prenatal diagnostics and cancer assessment
• Concentration in blood varies, increase with the size of fetus/ tumor
ctDNA (circulating tumor DNA)
• How is it specific to tumor? Cancer-specific mutations.
• As a biomarker: real time, non-invasive, multi-lesions, potentially cheaper (>biopsies)
• Often low concentration mutant DNA in the sea of wild type DNA, especially in early stage of
cancer. Eg. Early stage has <1 mutant template/ml plasma -> beyond detection limit (0.1%)
• But mutation information alone is not enough to predict the location of origin -> challenge
for follow-up tests
7. Study cohortTable S11. Cancer patients evaluated in this
study by tumor type and stage.
Tumor Type AJCC Stage
Patients
(n)
Proportion
of cases
(%)
Breast
I 32 15
II 114 55
III 63 30
I-III 209 --
Colorectum
I 77 20
II 191 49
III 120 31
I-III 388 --
Esophagus
I 5 11
II 29 64
III 11 24
I-III 45 --
Liver
I 5 11
II 19 43
III 20 45
I-III 44 --
Lung
I 46 44
II 27 26
III 31 30
I-III 104 --
Ovary
I 9 17
II 4 7
III 41 76
I-III 54 --
Pancreas
I 4 4
II 83 89
III 6 6
I-III 93 --
Stomach
I 21 31
II 30 44
III 17 25
I-III 68 --
• 1005 patients
• 8 types of cancer stage II (49%), stage III (31%)
and stage I (20%)
• Neoadjuvant chemo/ metastasis excluded
• Median age = 64 (range 22-93)
Control group:
• 812 “healthy” controls
• Median age = 55 (range 17-88)
• Criteria: no known history of cancer, high-grade dysplasia,
autoimmune or chronic kidney disease.
11. Mutation detection and analysis
Mutation detection
• Read was matched to reference sequence using custom scripts :
• https://github.com/InSilicoSolutions/SafeSeqS
• Reads from a common template molecule were grouped based on UID
• Artefactual mutations removed by requiring a mutation to be presen tin > 90% reads in
each UID family
• Redundant reads from optical duplication were removed by requiring reads to be at least
5000 pixels apart when located on the same file.
• Mutations must meet either one of these 2 criteria to be considered (1) present in the
COSMIC databases or (2) predicted to be inactivating in tumor suppressor genes.
• Synonymous mutation (except those at exon ends) and intronic mutations (except for
those at splice sites) were excluded.
Mutation analysis
• Mutant allele frequency (MAF) = mutant fraction per well.
• MAF in a sample = SUM of supermutant in 6 wells / total number of UID in 6 wells
12. Bioplex-200
• xMAP technology to multiplex up to 100 different analytes/ sample
• 100 colored magnetic beads created by the use of 2 fluorescent dyes
at distinct ratios of concentrations.
Houser, B. (2012). Bio-Rad’s Bio-Plex® suspension array system, xMAP technology overview.
Archives of Physiology and Biochemistry,
Magnetic bead
Charge-coupled device
CCD technology
13. Approach
• CancerSEEK approach: Combined gene + protein biomarkers
• Features
1. Gene: 61 amplicons panel of 16 genes: NRAS, CTNNB1, PIK3CA,
FBXW7, APC, EGFR, BRAG, CDKN2A, PTEN, FGFR2, HRAS, AKT1,
TP53, PPP2R1A, GNAS
2. Protein: Literature search to find protein that detect at least 1/8
cancer types with >10% sensitivity and 99% specificities : list of 41
proteins (39 can be reproducibly evaluated) -> narrow down the test
to 8 proteins
15. CancerSEEK algorithm-1
1. Mutant allelle frequency (MAF) normalization:
• MAF = # supermutants/ # UID in the same well
• Normalized by observed MAFs (for each mutation) in training set composed of normal
controls + 256 healthy WBC .
• MAF < 100 UID : set to zero
• Average MAF = ave_i for each mutation i = 1,… n
• 25th percentile of this ave_i distribution -> ave_ref
• Normalized MAF = MAF * (ave_ref/ave_i)
2. Reference distribution and p-values:
• UID was split in 10 intervals (<1000, 1000 - 2000, … , >9000)
• Corresponding to the range of UIDs, MAF was compared to 2 reference distributions:
(normal + 256 WBC healthy) or cancer patients in training set using 10-fold cross
validation-> pN and pC values.
“The classification of a sample's ctDNA status was obtained from a statistical test comparing
the normalized mutation frequencies of the sample of interest to the distributions of the
normalized mutation frequencies of, respectively, normal and cancer samples in the training
set.”
16. CancerSEEK algorithm-2
3. Log ratios and omega scores
• pC/pN for each mutation was calculated (Min and Max of 6 wells was omitted):
where Wi = #UID/ total UID for mutation i
Example for KRAS mutation:
Ø The number of supermutants and UIDs in each of the six wells were
(161, 3755), (78, 2198), (99, 2966), (84, 2013), (177, 3694), (117,3427), respectively.
Ø 6 MAFs (0.043, 0.035, 0.033, 0.042, 0.048, 0.034),
or (0.0057, 0.0047, 0.0044, 0.0056, 0.0064, 0.0045) after normalization.
Ø pC = (1.06E-06, 5.70E-06, 1.02E-05, 1.03E-06, 3.09E-07, 8.83E-06)
Ø pN = (0.100, 0.124, 0.128, 0.114, 0.094, 0.112)
Ø pC / pN = (94243, 21716, 12510,110752, 305090, 12680).
Ø Eliminate min and max
19. CancerSEEK algorithm-3
5. Logistic Regression:
• omega score + 8 protein concentration (CA-125, CA19-9, CEA, HGF, MPO, OPN, PRL, TIMP-1)
• Selection of 8/ 39 proteins:
1/ eliminate any proteins with higher median values in normal samples: 39->26 left
2/ Forward selection: each protein was dropped, and the decrease in accuracy of the test was
Checked -> importance of each protein
3/ Perform 10 rounds of 10-fold cross-validations
6. Tissue localization:
• Random forest to predict cancer types using omega score + 8 protein + 31 other proteins +
gender.
• Classification calls were obtained in an average round of 10-fold CV.
• Concordance between mutations in plasma vs tumor was considered only when omega> 3
and primary tumor contain any mutation with MAF> 5%
4. Protein normalization and transformation:
• Set all values < limits of detection : m
• Set all values > limits of detection : M
• Further transformation: if a protein concentration < 95th percentile of normal samples in
training set, then protein concentration = 0, otherwise, protein concentration = original value
28. Conclusion
• CancerSEEK = multi-analyte blood
test that can detect the presence of 8
common solid tumors (60%
estimated cancer death in the US) by
combining 8 protein biomarkers with
genetic biomarkers (61 amplicons of
16 genes)
• Estimate cost ~< $500
This study lays a foundation for a single multi-analyte blood test that combine other blood
biomarkers (metabolites, mRNA, miRNA and methylated DNA) to detect cancer for early
intervention.