The document summarizes key findings from the 2010 Global Burden of Disease Study, which assessed the prevalence of 291 diseases and injuries and 67 risk factors across 187 countries from 1990 to 2010. It found that ischemic heart disease, HIV/AIDS, and lower respiratory infections caused the most disability-adjusted life years lost globally. The study applied consistent estimation methods to comprehensively measure the health burden and trends in both communicable and non-communicable diseases. It represents an improvement over previous analyses by strengthening statistical methods and expanding the scope of conditions and risk factors considered.
This document provides an overview and syllabus for a course on bioinformatics. It discusses the goals of learning about available bioinformatics programs and tools, and interpreting their outputs. The course will cover topics like sequence alignment, phylogenetics, genome comparison and using databases. Assessment will include homework, exams, a report, and participation. The document contrasts the "old" and "new" biology, noting how the new biology generates large datasets that require computational analysis to make sense of the data. It emphasizes that bioinformatics uses algorithms and databases to organize, analyze and interpret biological data at large scales.
Dr Yousef Elshrek is One co-authors in this study >>>> Global, regional, and...Univ. of Tripoli
Global, regional, and national age–sex specifi c all-cause and cause-specifi c mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013
GBD 2013 Mortality and Causes of Death Collaborators*
Dr. Yousef Elshrek is Coauthors in this study
Life expectancy has increased greatly over the past 100 years. Increased wealth, sanitation, and access to pharmaceutical innovation have contributed to our health, allowing us to live longer and healthier lives. We are on a tipping-point of healthcare mostly related to new technologies - big data and genomics, robotics, immunotherapy, remote monitoring, 3D printing, among others, will bring forth a new era in health and standards of care.
This study analyzed cancer mortality rates in older Mexican individuals (aged 65+) from 2000 to 2010 using data from cancer registries. The key findings were:
1) The overall cancer mortality rate significantly declined from 630 to 573 per 100,000 inhabitants. Rates declined in both men and women.
2) The highest mortality rates were from lung, stomach, and liver cancers. Rates of these cancers significantly declined over the study period.
3) Colorectal cancer mortality rates significantly increased while rates of most other cancer types did not significantly change.
4) Men had higher cancer mortality rates than women, with the highest rates in prostate and breast cancers respectively.
GHME 2013 Conference
Session: Global Burden of Diseases, Injuries, and Risk Factors Study 2010: workshop on methods and key findings
Date: June 18 2013
Presenter: Rafael Lozano
Institute:
Institute for Health Metrics and Evaluation (IHME), University of Washington
Opportunities in technology and connected health for population science Warren Kibbe
AACR Modernizing Population Science in the Digital Age MEG meeting.Keynote on Opportunities in technology and connected health for population science from February 2019
NDGISUC2017 - GIS and Public Health: The Economic Geography of DiseaseNorth Dakota GIS Hub
The document discusses how GIS can be used in public health to better understand the economic geography of disease. It provides background on rising US healthcare costs and the need to shift to population health. It then outlines different determinants of health like epidemiology, demography, and genetics that can be analyzed using GIS. The document presents a case study from Providence Health and Services on how they used location analytics and other data to understand adverse childhood experiences and their link to later health issues in Montana. It concludes by thanking the audience.
AN MFA APPLICATION IN TUBERCULOSIS PREVALENCE ANALYSISChaoyi WU
This document describes using multiple factor analysis (MFA) to analyze factors that affect tuberculosis (TB) prevalence using estimated data. MFA was used to analyze observations across several groups of variables. Vertices method symbolic PCA (V-SPCA) was employed to deal with interval data in MFA. The analysis found HIV and TB to be highly correlated and identified two key dimensions: one related to economics and one distinguishing TB, HIV, and tobacco use. While V-SPCA made little difference, further improvement of variable selection and model validation were recommended.
This document provides an overview and syllabus for a course on bioinformatics. It discusses the goals of learning about available bioinformatics programs and tools, and interpreting their outputs. The course will cover topics like sequence alignment, phylogenetics, genome comparison and using databases. Assessment will include homework, exams, a report, and participation. The document contrasts the "old" and "new" biology, noting how the new biology generates large datasets that require computational analysis to make sense of the data. It emphasizes that bioinformatics uses algorithms and databases to organize, analyze and interpret biological data at large scales.
Dr Yousef Elshrek is One co-authors in this study >>>> Global, regional, and...Univ. of Tripoli
Global, regional, and national age–sex specifi c all-cause and cause-specifi c mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013
GBD 2013 Mortality and Causes of Death Collaborators*
Dr. Yousef Elshrek is Coauthors in this study
Life expectancy has increased greatly over the past 100 years. Increased wealth, sanitation, and access to pharmaceutical innovation have contributed to our health, allowing us to live longer and healthier lives. We are on a tipping-point of healthcare mostly related to new technologies - big data and genomics, robotics, immunotherapy, remote monitoring, 3D printing, among others, will bring forth a new era in health and standards of care.
This study analyzed cancer mortality rates in older Mexican individuals (aged 65+) from 2000 to 2010 using data from cancer registries. The key findings were:
1) The overall cancer mortality rate significantly declined from 630 to 573 per 100,000 inhabitants. Rates declined in both men and women.
2) The highest mortality rates were from lung, stomach, and liver cancers. Rates of these cancers significantly declined over the study period.
3) Colorectal cancer mortality rates significantly increased while rates of most other cancer types did not significantly change.
4) Men had higher cancer mortality rates than women, with the highest rates in prostate and breast cancers respectively.
GHME 2013 Conference
Session: Global Burden of Diseases, Injuries, and Risk Factors Study 2010: workshop on methods and key findings
Date: June 18 2013
Presenter: Rafael Lozano
Institute:
Institute for Health Metrics and Evaluation (IHME), University of Washington
Opportunities in technology and connected health for population science Warren Kibbe
AACR Modernizing Population Science in the Digital Age MEG meeting.Keynote on Opportunities in technology and connected health for population science from February 2019
NDGISUC2017 - GIS and Public Health: The Economic Geography of DiseaseNorth Dakota GIS Hub
The document discusses how GIS can be used in public health to better understand the economic geography of disease. It provides background on rising US healthcare costs and the need to shift to population health. It then outlines different determinants of health like epidemiology, demography, and genetics that can be analyzed using GIS. The document presents a case study from Providence Health and Services on how they used location analytics and other data to understand adverse childhood experiences and their link to later health issues in Montana. It concludes by thanking the audience.
AN MFA APPLICATION IN TUBERCULOSIS PREVALENCE ANALYSISChaoyi WU
This document describes using multiple factor analysis (MFA) to analyze factors that affect tuberculosis (TB) prevalence using estimated data. MFA was used to analyze observations across several groups of variables. Vertices method symbolic PCA (V-SPCA) was employed to deal with interval data in MFA. The analysis found HIV and TB to be highly correlated and identified two key dimensions: one related to economics and one distinguishing TB, HIV, and tobacco use. While V-SPCA made little difference, further improvement of variable selection and model validation were recommended.
CT AND SPECT ANALYSIS1CT and SPECT ProceduresA statistic.docxannettsparrow
CT AND SPECT ANALYSIS 1
CT and SPECT Procedures
A statistical comparison of usage in MN hospitals
INTRODUCTION
Over the last few decades, the usage of diagnostic imaging in United States hospitals has been increasing. This rise in medical imaging contributes to both the increasing costliness of medicine and the amount of radiation patients are being exposed to while undergoing medical treatments. Of the many forms of medical imaging, computerized tomography (CT) and Single-photon emission computed tomography (SPECT) scans are some of the most prevalent. However, some studies have begun to show the use of SPECT procedures are slightly declining. (Smith-Bindman, Miglioretti, & Larson, 2008; Mettler, Wiest, Locken, & Kelsey, 2000; Muschlitz, 2011)
One study by Smith-Bindman, Miglioretti & Larson (2008) showed that CT usage has increased 14 percent per year, from 81 to 181 examinations, per 1000 patients. Subsequently, CT usage doubled over the ten year period in which the study was conducted. This increase was noted for all tested groups regardless of age, anatomic area scanned, and modality. Another report concluded that “in most large hospitals in the United States, CT scanning likely accounts for more than ten percent of diagnostic radiology examinations.” (Mettler, Wiest, Locken, & Kelsey, 2000) Mettler, Wiest, Locken and Kelsey (2000) noted that they found the largest percentage of scans was done in the 36-50-year-old age group. According the Minnesota Department of Health (MDH), the abundance of CT usage in the state is due to its ease of use during emergent situations; a CT scan can be provided within 25-45 minutes depending on positive or negative readings (Alberts et al., 2013).
While SPECT imaging has a well-defined role in medical diagnostic imaging, it tends to be most useful for Cardiovascular, stem cells, oncologic, neuroimaging applications. (Khalil, Tremoleda, Bayomy & Gsell, 2011) This may account fewer overall procedures performed. One study by Druz, Phillips and Sharifova (2011) evaluated 2005 SPECT appropriateness criteria in a diverse patient and physician population from a large regional medical center. An important finding was that appropriateness of SPECT was “strongly influenced by presence of symptoms, pre-test likelihood of disease, and Framingham risk scores.” (Druz, Phillips & Sharifova, sec 4, 2011) There was a strong trend for more appropriate studies in symptomatic patients and those at a greater likelihood of coronary artery disease (CAD), which is a recurring theme in SPECT usage analyzations. This study also showed that Cardiac Medical Doctors tend to refer fewer inappropriate SPECT procedures than do their counterparts in other specialties. Amen (b) et al (2011) further investigates the use of SPECT by limited numbers of clinicians and presents rationale for a more widespread use of SPECT in clinical practice for complex cases such as traumatic brain injury mapping and assessing other forms of cog.
King Holmes, MD, PhD: Present and Future Challenges in Global Public HealthUWGlobalHealth
King Holmes, MD, PhD: Present and Future Challenges in Global Public Health, Interscience Conference on Antimicrobial Agents and Chemotherapy, Sept. 12, 2009.
Used for Medical Grand Rounds at several hospitals, this is data based comprehensive review of the shortcomings of the American Medical System and dysfunctional political attempts at reform. Single payer, Medicare for all, with elimination of for profit insurance companies is the best answer.
Predictive analysis WHO's life expectancy dataset using Tableau data visualis...Tarun Swarup
This document discusses a statistical analysis of factors influencing life expectancy using data from the World Health Organization and United Nations. It describes the dataset, variables considered, and objectives of analyzing relationships between life expectancy and factors like immunization rates, mortality rates, economics, and demographics. Four dashboards are proposed to analyze trends in adult mortality rates, compare life expectancy and infant death rates in populated countries, forecast adult mortality and hepatitis rates in Brazil, and compare GDP in developed and developing countries.
Analysis for the global burden of disease study 2016 lancet 2017Luis Sales
This document summarizes the findings of the Global Burden of Disease Study 2016, which assessed prevalence, incidence, and years lived with disability for 328 diseases and injuries from 1990 to 2016 for 195 countries. Some key findings were:
1) Low back pain, migraine, hearing loss, iron-deficiency anemia, and major depressive disorder were the top five causes of years lived with disability globally in 2016.
2) Age-standardized rates of years lived with disability decreased by 2.7% between 1990 and 2016, but the number of years lived with disability from non-communicable diseases has risen due to population growth and aging.
3) Years lived with disability rates were 10.4% higher
This document summarizes health spending and outcomes data from 13 countries. It finds that the US spends much more per capita on health care than other countries, but has poorer outcomes including higher rates of mortality amenable to health care and lower life expectancy. The US also has the highest prices for pharmaceuticals, diagnostic imaging, and hospital care. However, the US performs well on some measures of health care supply and utilization, conducting more diagnostic tests and surgeries per capita than most other countries.
Data Science Meets Healthcare: The Advent of Personalized Medicine - Jacomo C...CityAge
Healthcare spending is growing unsustainably as a proportion of GDP. The advent of big data and personalized medicine enabled by electronic health records, rich sensor data from devices, and advances in machine learning algorithms provides an opportunity to make healthcare more efficient and effective. Two case studies are described: 1) Using machine learning to develop more targeted preventive screening policies that balance benefits and harms better than current demographic-based guidelines. 2) Analyzing surgical team performance data to optimize team assignment and forecast outcomes, finding experience factors like dyadic team experience matter more than conventional views of individual experience alone. Effective use of data requires asking the right questions, joining diverse data sources, iterative testing, and a focus on real-world impact.
The document outlines the Global Burden of Diseases, Injuries, and Risk Factors Study. It describes the study's goal of producing new estimates of disease burden. It details the organizational structure, including expert groups organized into clusters. Mortality is estimated through various data sources using Gaussian Process Regression to synthesize estimates. Causes of death are analyzed using over 5,000 country-years of data from various sources, which are cleaned and mapped to different classification lists.
The document discusses several key topics related to scaling up health systems and achieving universal access:
1. Evidence is important for implementing sustainable change, but the right questions must be asked and appropriate models/assumptions used.
2. Much of the variation in health outcomes between countries is due to differences in technological progress, not income levels. More research is needed to address developing country needs.
3. Scaling up health systems is an experiment in itself. Different types of evidence are needed from individual, institutional, and systems-level research on scaling up programs.
4. Research and innovation systems must work together across sectors and levels to develop and disseminate new health technologies, processes and knowledge globally.
Survey on Plastics and its Adverse Effects on Environment with quite simple s...dbpublications
Abstract : Environmentally, plastic is a growing disaster. Most plastics are made from petroleum or natural gas, nonrenewable
resources extracted and processed using energy-intensive techniques that destroy fragile ecosystems. The
manufacture of plastic, as well as its destruction by incineration, pollutes air, land and water and exposes workers to
toxic chemicals, including carcinogens. Plastic packaging – especially the ubiquitous plastic bag – is a significant
source of landfill waste and is regularly eaten by numerous marine and land animals, to fatal consequences. Synthetic
plastic does not biodegrade. It just sits and accumulates in landfills or pollutes the environment. Plastics have become a
municipal waste nightmare, prompting local governments all over the world to implement plastic bag, and increasingly
polystyrene (styrofoam), bans.
Keywords: Carcinogens, Workflow Management, Plastic packaging.
This document discusses several key concepts related to epigenetics and environmental influences on health. It begins with an overview of fetal programming, in which the environment during early development can influence cell differentiation through epigenetic changes. It then discusses developmental plasticity and how the same genome can result in different cell types based on environmental information processed epigenetically. The document also highlights the role of the environment in health, noting that many diseases have increased dramatically in recent decades and exploring possible environmental contributions, such as endocrine disrupting chemicals, heavy metals, and other pollutants that can influence the epigenome even at low levels. Overall, the document emphasizes that the epigenome acts as an interface between the environment and genome,
Digital and technological advancements and how they have impacted health. From data, IoT & wearables, 3D printing, personalized medicine, all of these trends can be levers to help with demographic shifts, increased access to healthcare and rising costs.
Lessons from COVID-19: How Are Data Science and AI Changing Future Biomedical...Jake Chen
: COVID-19 has profoundly impacted all our lives. Not all such impacts in science are negative. For example, how we adapt to online learning, remote mentorship, and online teamwork may become new “norms” of future scientific collaborations, breaking down institutional boundaries to communication. The COVID-19 pandemic has united the scientific community more than ever, through more than 3600 clinical trials, 60,000 peer-reviewed publications, 80,000 SARS-CoV-2 genome sequences, 100,000 COVID-19 open software tools, and a global community of scientists, with which all of us are working hard to find epidemiological patterns, diagnosis, therapeutics, and vaccines in a “War Against COVID-19”. In this talk, I will define and characterize data-driven medicine primarily through my personal journey in the past ten months, having witnessed the rapid “weaponizing of data science tools” in our community’s fight against COVID-19 (including ours, at http://covid19.ubrite.org/). I will review up-to-date COVID-19 literature, especially those related to how biomedical informatics, data science, and artificial intelligence have been applied in accelerating COVID-19 breakthrough discoveries, from basic research to clinical practice. I will end by sharing my thoughts on how the future of medicine in cancer and other translational areas can benefit from the proactive incorporation of new “data science engines.”
Morphologomics - Challenges for Surgical Pathology in the Genomic Age by Dr. ...Cirdan
This presentation introduces and discussesthe concept of ‘morphologomics’ that is omics approaches critically reimagined and reappraised from the viewpoint of classic morphology.
It was delivered by Dr. Anthony Gill at the Pathology Horizons 2017 conference in Cairns, Australia.
introduce and discuss the concept of ‘morphologomics’ that is omics approaches critically reimagined and reappraised from the viewpoint of classic morphology.
The role of genetic factors in Hypertension among Iraqi citizensAI Publications
This document summarizes a study examining the role of genetic factors in hypertension among Iraqi citizens. The study included 140 patients divided into a case group of 120 hypertensive patients and a control group of 30 normotensive patients. Data on demographics, family history, blood pressure, and other medical variables were collected and analyzed. Statistical analysis found a significant relationship between genetic factors and hypertension, with a p-value of 0.001. Patients with a positive family history of hypertension in a first-degree relative had 3.98 times higher odds of having hypertension themselves. The study concluded that genetics play an important role in hypertension risk among Iraqi citizens.
Opportunities for computing in cancer researchWarren Kibbe
- Data generation is no longer the bottleneck in oncology research - data management, analysis, and reasoning present greater challenges due to the pace of data and technology growth.
- Computing and data science are enabling researchers to move beyond simple observations to predictive modeling and interventions based on understanding complex patient trajectories over time using diverse real-world data sources.
- Machine learning and data analytics applied at scale can support tasks like tumor board decision making, identifying high-risk patients, and understanding disease at multiple levels, but require significant computing power.
The 2007 AIDS Epidemic Update from UNAIDS and WHO provides revised estimates of the global HIV/AIDS epidemic due to improvements in estimation methodologies. Key findings include:
- The estimated number of people living with HIV decreased 16% to 33.2 million, largely due to changes in India's estimates.
- Global HIV prevalence has stabilized at around 0.8% since 2001, though localized declines are occurring in some countries.
- Estimated new HIV infections in 2007 were 2.5 million, declining from a peak of over 3 million in the late 1990s likely due to prevention efforts.
- AIDS deaths in 2007 were estimated at 2.1 million, showing declines in recent years partly
Why collect and use health data? Professor Peter Bradley, Director of Knowl...NHS England
Professor Bradley outlines the importance of population based studies, the development of data science and what is needed for the efficient use of data.
CT AND SPECT ANALYSIS1CT and SPECT ProceduresA statistic.docxannettsparrow
CT AND SPECT ANALYSIS 1
CT and SPECT Procedures
A statistical comparison of usage in MN hospitals
INTRODUCTION
Over the last few decades, the usage of diagnostic imaging in United States hospitals has been increasing. This rise in medical imaging contributes to both the increasing costliness of medicine and the amount of radiation patients are being exposed to while undergoing medical treatments. Of the many forms of medical imaging, computerized tomography (CT) and Single-photon emission computed tomography (SPECT) scans are some of the most prevalent. However, some studies have begun to show the use of SPECT procedures are slightly declining. (Smith-Bindman, Miglioretti, & Larson, 2008; Mettler, Wiest, Locken, & Kelsey, 2000; Muschlitz, 2011)
One study by Smith-Bindman, Miglioretti & Larson (2008) showed that CT usage has increased 14 percent per year, from 81 to 181 examinations, per 1000 patients. Subsequently, CT usage doubled over the ten year period in which the study was conducted. This increase was noted for all tested groups regardless of age, anatomic area scanned, and modality. Another report concluded that “in most large hospitals in the United States, CT scanning likely accounts for more than ten percent of diagnostic radiology examinations.” (Mettler, Wiest, Locken, & Kelsey, 2000) Mettler, Wiest, Locken and Kelsey (2000) noted that they found the largest percentage of scans was done in the 36-50-year-old age group. According the Minnesota Department of Health (MDH), the abundance of CT usage in the state is due to its ease of use during emergent situations; a CT scan can be provided within 25-45 minutes depending on positive or negative readings (Alberts et al., 2013).
While SPECT imaging has a well-defined role in medical diagnostic imaging, it tends to be most useful for Cardiovascular, stem cells, oncologic, neuroimaging applications. (Khalil, Tremoleda, Bayomy & Gsell, 2011) This may account fewer overall procedures performed. One study by Druz, Phillips and Sharifova (2011) evaluated 2005 SPECT appropriateness criteria in a diverse patient and physician population from a large regional medical center. An important finding was that appropriateness of SPECT was “strongly influenced by presence of symptoms, pre-test likelihood of disease, and Framingham risk scores.” (Druz, Phillips & Sharifova, sec 4, 2011) There was a strong trend for more appropriate studies in symptomatic patients and those at a greater likelihood of coronary artery disease (CAD), which is a recurring theme in SPECT usage analyzations. This study also showed that Cardiac Medical Doctors tend to refer fewer inappropriate SPECT procedures than do their counterparts in other specialties. Amen (b) et al (2011) further investigates the use of SPECT by limited numbers of clinicians and presents rationale for a more widespread use of SPECT in clinical practice for complex cases such as traumatic brain injury mapping and assessing other forms of cog.
King Holmes, MD, PhD: Present and Future Challenges in Global Public HealthUWGlobalHealth
King Holmes, MD, PhD: Present and Future Challenges in Global Public Health, Interscience Conference on Antimicrobial Agents and Chemotherapy, Sept. 12, 2009.
Used for Medical Grand Rounds at several hospitals, this is data based comprehensive review of the shortcomings of the American Medical System and dysfunctional political attempts at reform. Single payer, Medicare for all, with elimination of for profit insurance companies is the best answer.
Predictive analysis WHO's life expectancy dataset using Tableau data visualis...Tarun Swarup
This document discusses a statistical analysis of factors influencing life expectancy using data from the World Health Organization and United Nations. It describes the dataset, variables considered, and objectives of analyzing relationships between life expectancy and factors like immunization rates, mortality rates, economics, and demographics. Four dashboards are proposed to analyze trends in adult mortality rates, compare life expectancy and infant death rates in populated countries, forecast adult mortality and hepatitis rates in Brazil, and compare GDP in developed and developing countries.
Analysis for the global burden of disease study 2016 lancet 2017Luis Sales
This document summarizes the findings of the Global Burden of Disease Study 2016, which assessed prevalence, incidence, and years lived with disability for 328 diseases and injuries from 1990 to 2016 for 195 countries. Some key findings were:
1) Low back pain, migraine, hearing loss, iron-deficiency anemia, and major depressive disorder were the top five causes of years lived with disability globally in 2016.
2) Age-standardized rates of years lived with disability decreased by 2.7% between 1990 and 2016, but the number of years lived with disability from non-communicable diseases has risen due to population growth and aging.
3) Years lived with disability rates were 10.4% higher
This document summarizes health spending and outcomes data from 13 countries. It finds that the US spends much more per capita on health care than other countries, but has poorer outcomes including higher rates of mortality amenable to health care and lower life expectancy. The US also has the highest prices for pharmaceuticals, diagnostic imaging, and hospital care. However, the US performs well on some measures of health care supply and utilization, conducting more diagnostic tests and surgeries per capita than most other countries.
Data Science Meets Healthcare: The Advent of Personalized Medicine - Jacomo C...CityAge
Healthcare spending is growing unsustainably as a proportion of GDP. The advent of big data and personalized medicine enabled by electronic health records, rich sensor data from devices, and advances in machine learning algorithms provides an opportunity to make healthcare more efficient and effective. Two case studies are described: 1) Using machine learning to develop more targeted preventive screening policies that balance benefits and harms better than current demographic-based guidelines. 2) Analyzing surgical team performance data to optimize team assignment and forecast outcomes, finding experience factors like dyadic team experience matter more than conventional views of individual experience alone. Effective use of data requires asking the right questions, joining diverse data sources, iterative testing, and a focus on real-world impact.
The document outlines the Global Burden of Diseases, Injuries, and Risk Factors Study. It describes the study's goal of producing new estimates of disease burden. It details the organizational structure, including expert groups organized into clusters. Mortality is estimated through various data sources using Gaussian Process Regression to synthesize estimates. Causes of death are analyzed using over 5,000 country-years of data from various sources, which are cleaned and mapped to different classification lists.
The document discusses several key topics related to scaling up health systems and achieving universal access:
1. Evidence is important for implementing sustainable change, but the right questions must be asked and appropriate models/assumptions used.
2. Much of the variation in health outcomes between countries is due to differences in technological progress, not income levels. More research is needed to address developing country needs.
3. Scaling up health systems is an experiment in itself. Different types of evidence are needed from individual, institutional, and systems-level research on scaling up programs.
4. Research and innovation systems must work together across sectors and levels to develop and disseminate new health technologies, processes and knowledge globally.
Survey on Plastics and its Adverse Effects on Environment with quite simple s...dbpublications
Abstract : Environmentally, plastic is a growing disaster. Most plastics are made from petroleum or natural gas, nonrenewable
resources extracted and processed using energy-intensive techniques that destroy fragile ecosystems. The
manufacture of plastic, as well as its destruction by incineration, pollutes air, land and water and exposes workers to
toxic chemicals, including carcinogens. Plastic packaging – especially the ubiquitous plastic bag – is a significant
source of landfill waste and is regularly eaten by numerous marine and land animals, to fatal consequences. Synthetic
plastic does not biodegrade. It just sits and accumulates in landfills or pollutes the environment. Plastics have become a
municipal waste nightmare, prompting local governments all over the world to implement plastic bag, and increasingly
polystyrene (styrofoam), bans.
Keywords: Carcinogens, Workflow Management, Plastic packaging.
This document discusses several key concepts related to epigenetics and environmental influences on health. It begins with an overview of fetal programming, in which the environment during early development can influence cell differentiation through epigenetic changes. It then discusses developmental plasticity and how the same genome can result in different cell types based on environmental information processed epigenetically. The document also highlights the role of the environment in health, noting that many diseases have increased dramatically in recent decades and exploring possible environmental contributions, such as endocrine disrupting chemicals, heavy metals, and other pollutants that can influence the epigenome even at low levels. Overall, the document emphasizes that the epigenome acts as an interface between the environment and genome,
Digital and technological advancements and how they have impacted health. From data, IoT & wearables, 3D printing, personalized medicine, all of these trends can be levers to help with demographic shifts, increased access to healthcare and rising costs.
Lessons from COVID-19: How Are Data Science and AI Changing Future Biomedical...Jake Chen
: COVID-19 has profoundly impacted all our lives. Not all such impacts in science are negative. For example, how we adapt to online learning, remote mentorship, and online teamwork may become new “norms” of future scientific collaborations, breaking down institutional boundaries to communication. The COVID-19 pandemic has united the scientific community more than ever, through more than 3600 clinical trials, 60,000 peer-reviewed publications, 80,000 SARS-CoV-2 genome sequences, 100,000 COVID-19 open software tools, and a global community of scientists, with which all of us are working hard to find epidemiological patterns, diagnosis, therapeutics, and vaccines in a “War Against COVID-19”. In this talk, I will define and characterize data-driven medicine primarily through my personal journey in the past ten months, having witnessed the rapid “weaponizing of data science tools” in our community’s fight against COVID-19 (including ours, at http://covid19.ubrite.org/). I will review up-to-date COVID-19 literature, especially those related to how biomedical informatics, data science, and artificial intelligence have been applied in accelerating COVID-19 breakthrough discoveries, from basic research to clinical practice. I will end by sharing my thoughts on how the future of medicine in cancer and other translational areas can benefit from the proactive incorporation of new “data science engines.”
Morphologomics - Challenges for Surgical Pathology in the Genomic Age by Dr. ...Cirdan
This presentation introduces and discussesthe concept of ‘morphologomics’ that is omics approaches critically reimagined and reappraised from the viewpoint of classic morphology.
It was delivered by Dr. Anthony Gill at the Pathology Horizons 2017 conference in Cairns, Australia.
introduce and discuss the concept of ‘morphologomics’ that is omics approaches critically reimagined and reappraised from the viewpoint of classic morphology.
The role of genetic factors in Hypertension among Iraqi citizensAI Publications
This document summarizes a study examining the role of genetic factors in hypertension among Iraqi citizens. The study included 140 patients divided into a case group of 120 hypertensive patients and a control group of 30 normotensive patients. Data on demographics, family history, blood pressure, and other medical variables were collected and analyzed. Statistical analysis found a significant relationship between genetic factors and hypertension, with a p-value of 0.001. Patients with a positive family history of hypertension in a first-degree relative had 3.98 times higher odds of having hypertension themselves. The study concluded that genetics play an important role in hypertension risk among Iraqi citizens.
Opportunities for computing in cancer researchWarren Kibbe
- Data generation is no longer the bottleneck in oncology research - data management, analysis, and reasoning present greater challenges due to the pace of data and technology growth.
- Computing and data science are enabling researchers to move beyond simple observations to predictive modeling and interventions based on understanding complex patient trajectories over time using diverse real-world data sources.
- Machine learning and data analytics applied at scale can support tasks like tumor board decision making, identifying high-risk patients, and understanding disease at multiple levels, but require significant computing power.
The 2007 AIDS Epidemic Update from UNAIDS and WHO provides revised estimates of the global HIV/AIDS epidemic due to improvements in estimation methodologies. Key findings include:
- The estimated number of people living with HIV decreased 16% to 33.2 million, largely due to changes in India's estimates.
- Global HIV prevalence has stabilized at around 0.8% since 2001, though localized declines are occurring in some countries.
- Estimated new HIV infections in 2007 were 2.5 million, declining from a peak of over 3 million in the late 1990s likely due to prevention efforts.
- AIDS deaths in 2007 were estimated at 2.1 million, showing declines in recent years partly
Why collect and use health data? Professor Peter Bradley, Director of Knowl...NHS England
Professor Bradley outlines the importance of population based studies, the development of data science and what is needed for the efficient use of data.
Similar to Welcoming to incoming bioinformatics students at UCSF (20)
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
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.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
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.
Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...Travis Hills MN
By harnessing the power of High Flux Vacuum Membrane Distillation, Travis Hills from MN envisions a future where clean and safe drinking water is accessible to all, regardless of geographical location or economic status.
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.
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...PsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
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.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...
Welcoming to incoming bioinformatics students at UCSF
1. Biological & Medical
Informatics:!
the beginning
Daniel Himmelstein!
September 24, 2014
Hand Drawn Map of SF!
by Jenni Sparks
Before the Money Came!
Bettye LaVette
8. The exponential rise of ‘omics’
Andrew Su
on Twitter
‘omics’ — collective characterization and
quantification of biomolecules
9. Data Scientist:
The Sexiest Job of the 21st Century
Meet the people who
can coax treasure out of
messy, unstructured data.
by Thomas H. Davenport
and D.J. Patil
hen Jonathan Goldman ar-
rived for work in June 2006
at LinkedIn, the business
networking site, the place still
felt like a start-up. The com-
pany had just under 8 million
accounts, and the number was
growing quickly as existing mem-
bers invited their friends and col-
leagues to join. But users weren’t
seeking out connections with the people who were already on the site
at the rate executives had expected. Something was apparently miss-
ing in the social experience. As one LinkedIn manager put it, “It was
Meet the people who
can coax treasure out of
messy, unstructured data
by Thomas H. Davenport
and D.J. Patil
70 Harvard Business Review October 2012
70 Harvard Business Review October 2012 Harvard Business Review October 201
Artwork: Tamar Cohen, Andrew J Buboltz, 2011
Definition (wikipedia):
!
the study of the generalizable
extraction of knowledge from data
13. • Aggregate microbial rDNA
content of a seawater sample
• richness of operational
taxonomic units (OTUs)
• species distribution modeling
Diversity of the Marine Metagenome
Ladau et al. (2013) ISME
doi:10.1038/ismej.2013.37
Katie Pollard
-180° -150° -120° -90° -60° -30° 0° 30° 60° 90° 120° 150° 180°
-180° -150° -120° -90° -60° -30° 0° 30° 60° 90° 120° 150° 180°
-90°
-60°
-30°
0°
30°
60°
90°
-90°
-60°
-30°
0°
30°
60°
90°
MICROBIS
FUHRMAN2008
POMMIER2007
GOS
Figure S1: Sampling locations for data used in constructing maps. Models with
zero to eight parameters were fitted using MICROBIS data. Predictive performance of
the models was evaluated using both internal measures of model performance (AIC, BIC,
and PRESS) and three independent data sets, collected at the locations shown in red,
green, and yellow (see Table S1). Analyses were based on 377 samples (234 MICROBIS,
30 GOS, 9 POMMIER2007, 103 FUHRMAN2008) collected from 164 distinct locations.
-180° -150° -120° -90° -60° -30° 0° 30° 60° 90° 120° 150° 1
-180° -150° -120° -90° -60° -30° 0° 30° 60° 90° 120° 150° 1
-90°
-60°
-30°
0°
30°
60°
90°
MICROBIS
FUHRMAN2008
POMMIER2007
GOS
Figure S1: Sampling locations for data used in constructing maps. Mode
zero to eight parameters were fitted using MICROBIS data. Predictive performa
the models was evaluated using both internal measures of model performance (AIC
and PRESS) and three independent data sets, collected at the locations shown
green, and yellow (see Table S1). Analyses were based on 377 samples (234 MICR
30 GOS, 9 POMMIER2007, 103 FUHRMAN2008) collected from 164 distinct loca
14. Diversity in June
Ladau et al. (2013) ISME
doi:10.1038/ismej.2013.372.05 2.20 2.35 2.50 2.65
Log10(OTU Richness)
-9
-6
-3
0
30
60
90
-9
-6
-3
0
30
Log10(OTU Richness)
15. Diversity in December
Ladau et al. (2013) ISME
doi:10.1038/ismej.2013.372.05 2.20 2.35 2.50 2.65
Log10(OTU Richness)
-9
-6
-3
0
30
60
90
-9
-6
-3
0
30
16. Slime Mold & the
Greater Tokyo
Rail System
Tero et al (2010) Science
DOI: 10.1126/science.1177894http://youtu.be/GwKuFREOgmo
• 17 cm (7 in) agar-
filled petri dish
• plasmodium for
Tokyo
• quaker oats for
cities
• vegetate for a day
• decentralized,
distributed
planning
17. Tero et al (2010) Science
DOI: 10.1126/science.1177894
aftermath: no illumination
aftermath: geographic
constraint using illumination
18. The SlimeNet was comparable or
preferable to the RealNet in terms of:!
• efficiency
• fault tolerance
• cost
Actual Rail Network Slime Tubule Network
Tero et al (2010) Science
DOI: 10.1126/science.1177894
19. Human Evolution & Population Genetics
John Novembre
Ryan Hernandez
• 3,192 Europeans
• 500,568 SNPs
• Reduced to 2d (PCA)
Veeramah & Hammer (2014) Nat Rev Genet
doi:10.1038/nrg3625
out-of-Africa
bottleneck
• Europeans have less
genetic diversity
than Africans
Novembre et al (2008) Nature
doi:10.1038/nature07331
20. Genes mirror geography within Europe
Novembre et al (2008) Nature
doi:10.1038/nature07331
• Despite the low diversity in Europeans, 500 thousand common
variants discriminate population diversity with high resolution.
21. Medical Informatics
- An invited segment by Antoine Lizée -
How to build
intelligence around
patient medical
records
Adriana Karembeu & Antoine Lizee
at Sandler Neurosciences Center, UCSF
22. 4500 visits - 600 patients – 10th year (UCSF EPIC STUDY)
Images ~200MB/visit
Brain MRI
T1, T2,
proton density
Processed MRI
Cortical Thickness,
Myelin
Overlays
CT, Myelin,
Anatomical labels
GWAS
500,000+ SNPs
HLA
A,B,C,
DRB1, DQB1
Patient data Age, sex, history, etc.
Clinical data
Clinical Scores, treatments
Patient reported
Quality of Life questionnaires
Processed data
MRI-based
ReferenceData
Genotypes
~1MB/patient
(Para-) Clinical Data
~250 variables/visit
27. Highschool
Camp
College
Kin
UCSF
Research
Debate
1,278 nodes (1 type)
40,255 edges (1 type)
http://dhimmel.com
Facebook Friends
Genes
DiseasesPathophysiologies
Tissues
Genomic
Positions
Perturbations
Canonical
Pathways
BioCarta
KEGG
Reactome
miRNA
TFBS
Cancer
Hoods
Cancer
Modules
GO: BP
GO: MF
GO: CC
Oncogenic
Immunologic
Complex Diseases
29,241 nodes (19 types)
1,608,168 edges (20 types)
http://het.io
28. Multiple
SclerosisRF1 IL2RA
4 1 1 4
Multiple
SclerosisRF1 IRF8
4 1 1 4
Multiple
SclerosisRF1 CXCR4
4 2 1 4
Multiple
SclerosisRF1 Leukocyte
2 1 1 1
paths path
degree
product
degree
weighted
path count
0.707
0.25
0.25
0.177
0.677
0.707
ITCH
Lung
SUMO1
Multiple
Sclerosis
IRF1
Leukocyte
Crohn’s
Disease
IL2RA
IRF8
CXCR4
STAT3
expression
interaction
association
localization
association
association
association
interaction
Graph SubsetC
PDP(path) =
Y
d2Dpath
d w
metaedge-specific degrees
Network
G T De l
G G Di a
a aG D G Da
G Da
MetaPaths
GTDelGGDia
Multiple
SclerosisIRF1 IL2RA
4 1 1 4
Multiple
SclerosisIRF1 IRF8
4 1 1 4
Multiple
SclerosisIRF1 CXCR4
4 2 1 4
Multiple
SclerosisIRF1 Leukocyte
2 1 1 1
metapath paths path
degree
product
degree
weighted
path count
0.707
0.25
0.25
0.177
0.677
0.707
ITCHSUMO1
IL2RA
IRF8
CXCR4
interaction
a mG D P Dm
i iG G G Da
a lG D T Dl
e eG T G Da
physiology
B
D
PDP(path) =
Y
d2Dpath
d wm mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Da
m mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Dam mG M G Da
DWPC(metapath) =
X
path2P aths
PDP(path)
metaedge-specific degrees
Feature Computation
{Cancer Hood}
{Positional}
GeTeGaDGiGeTlDGeTlD
{GO
Function}
{GO
Component}
{miRNA Target}
{BioCarta}
{Oncogenic}
{TF Target}
GaD
(any gene)
{Cancer Module}
GiGiGaD
{GO
Process}GiGaD{KEGG}
{Immunologic}
{Reactome}
{Perturbation}
GaDmPmD
GaD
(any disease)
GaDlTlD
GaDaGaD
2 0 2 4
Standardized Coe cient
Method (AUROC)
ridge (0.829)
lasso (0.823)
Machine Learning
0.0
0.2
0.4
0.6
0.8
1.0
0.0 0.2 0.4 0.6 0.8 1.0
False Positive Rate
Recall
Partition (AUROC)
Testing (0.829)
Training (0.810)
Performance
0.2
0.6
1.0
1.4
1.8
Meta2.5
0.0 0.2 0.4 0.6 0.8 1.0
P-value
Density
Combine Predictions
& Statistical Evidence
15
Gene Meta2.5 HNLP WTCCC2
JAK2 0.047 0.102 0.0015
REL 0.001 0.040 0.0003
SH2B3 0.012 0.034 0.0130
RUNX3 0.016 0.025 0.0073
Table 5. Multiple sclerosis gene discovery.
Discover Novel
Susceptibility Genes
30. Mechanisms of Pathogenesis
Gene—{MSigDB Collection}—Gene—Disease DWPC Model
—
—
—
———
—
—
——
— — —
—
—
—
—
———
—
—
——
— — —
—
— —
—
—
0.4
0.6
0.8
1.0
Positional
C
ancerH
oodBioC
arta
G
O
C
om
ponent
m
iR
N
A
Target
G
O
FunctionR
eactom
eO
ncogenicTF
Target
KEG
G
G
O
Process
C
ancerM
odule
Im
m
unologic
Perturbation
Lasso
R
idge
AUROC
— ——
— ——
— ——
—
—— ——
— —
—
—
—
—
— —
—
—
0.4
0.6
0.8G
iG
aDG
eTeG
aD
G
eTlD
G
iG
eTlDG
aD
aG
aDG
aD
m
Pm
D
G
iG
iG
aD
G
aD
lTlD
G
aD
(any
gene)
G
aD
(any
disease)
Lasso
R
idge
AUROC
Pathophysiology
degenerative
immunologic
metabolic
neoplastic
psychiatric
unspeci c
37. Per Article Cost
from "Open Access: Market Size, Share, Forecast, and Trends"
Outsell. January 31, 2013
!
Subscription: $4,000.00
Open Access: $950.00
UCSF Open Access Fund
http://www.library.ucsf.edu/services/scholpub/oa/fund/eligibility
Fully OA Journal: $2,000
Hybrid OA: $1,000
• PeerJ — Lifetime publishing
plan for $99
• eLife — currently no APC,
“pain free publication”
• PLOS, BMC, Specialty Pubs
• F1000 Research, pre-review
publication
• preprints, arRxiv & bioRxiv
38. Article-level metrics
doi:10.1371/journal.pone.0013636.g005
Open Access increases Citations
Gargouri et al. PLOS One. 2010
• Alternative to journal impact
factor
• Citations, downloads, views,
social media
• Accelerates science —
impact factor = rejection
• Expands the audience
evaluating article importance
and quality
• Already used: h-index
Grow in importance
39. Public Data increases Citations
citations
Piwowar & Vision (2013)
DOI: 10.7717/peerj.175
• 10,555 microarray
studies
• Classified studies
by data availability
• 8 categories of
covariates
40. Availability & Reuse
• only applies to
original research
articles
• journals often
withhold the typeset
version
• does not affect reuse
Creative Commons Attribution Alone
Mandatory Archiving
!
NIH: PubMed Central
UC: eScholarship
• subscription journal
require the transfer of
article ownership
• enforce the article
copyright
• require licensing for
reuse
41. Tools for Efficiency & Reproducibility
Version control:
Online code repositories:
Interactive programming
environments:
ipython notebook