Pumping up genomics: how to engineer better NGS sample prep systems

DAVID WOLD | July 4, 2019 | 101 views

With high-throughput genomics impacting every corner of biology, the demand for more efficient Next-generation sequencing (NGS) workflows is growing rapidly. Automating the process of NGS sample preparation is crucial to avoid inaccuracies due to human error, bottlenecks that delay sequencing results, and the additional expense of re-running sequences. What are the most important factors for an engineer to consider when selecting a pump to meet the stringent performance required for an automated NGS library preparation system?

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Saolta University Health Care Group

Saolta University Health Care Group comprises of 6 hospitals across 7 sites: Letterkenny University Hospital (LUH) Mayo University Hospital (MUH) Merlin Park University Hospital (MPUH) Portiuncula University Hospital (PUH) Roscommon University Hospital (RUH) Sligo University Hospital (SUH) University Hospital Galway (UHG)

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MEDTECH

Top 10 biotech IPOs in 2019

Article | September 22, 2022

The big question at the start of 2019 was whether the IPO window would stay open for biotech companies, particularly those seeking to pull off ever-larger IPOs at increasingly earlier stages of development. The short answer is yes—kind of. Here’s the long answer: In the words of Renaissance Capital, the IPO market had “a mostly good year.” The total number of deals fell to 159 from 192 the year before, but technology and healthcare companies were standout performers. The latter—which include biotech, medtech and diagnostics companies—led the pack, making up 43% of all IPOs in 2019. By Renaissance’s count, seven companies went public at valuations exceeding $1 billion, up from five the year before

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MEDTECH

Cell Out? Lysate-Based Expression an Option for Personalized Meds

Article | July 16, 2022

Cell-free expression (CFE) is the practice of making a protein without using a living cell. In contrast with cell line-based methods, production is achieved using a fluid containing biological components extracted from a cell, i.e., a lysate. CFE offers potential advantages for biopharma according to Philip Probert, PhD, a senior scientist at the Centre for Process Innovation in the U.K.

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MEDICAL

Closing bacterial genomes from the human gut microbiome using long-read sequencing

Article | August 16, 2022

In our lab, we focus on the impact of the gut microbiome on human health and disease. To evaluate this relationship, it’s important to understand the particular functions that different bacteria have. As bacteria are able to exchange, duplicate, and rearrange their genes in ways that directly affect their phenotypes, complete bacterial genomes assembled directly from human samples are essential to understand the strain variation and potential functions of the bacteria we host. Advances in the microbiome space have allowed for the de novo assembly of microbial genomes directly from metagenomes via short-read sequencing, assembly of reads into contigs, and binning of contigs into putative genome drafts. This is advantageous because it allows us to discover microbes without culturing them, directly from human samples and without reference databases. In the past year, there have been a number of tour de force efforts to broadly characterize the human gut microbiota through the creation of such metagenome-assembled genomes (MAGs)[1–4]. These works have produced hundreds of thousands of microbial genomes that vastly increase our understanding of the human gut. However, challenges in the assembly of short reads has limited our ability to correctly assemble repeated genomic elements and place them into genomic context. Thus, existing MAGs are often fragmented and do not include mobile genetic elements, 16S rRNA sequences, and other elements that are repeated or have high identity within and across bacterial genomes.

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Selexis Cell Line Development Strategies

Article | February 11, 2020

In today’s biotechnology landscape, to be competitive, meet regulations, and achieve market demands, “we must apply Bioprocessing 4.0,” said Igor Fisch, PhD, CEO, Selexis. In fact, in the last decade, “Selexis has evolved from cloning by limiting dilution to automated cell selection to nanofluidic chips and from monoclonality assessment by statistical calculation to proprietary bioinformatic analysis,” he added. Single-use processing systems are an expanding part of the biomanufacturing world; as such, they are a major component of Bioprocessing 4.0. “At Selexis, we use single use throughout our cell line development workflow. Currently, we have incorporated single-use automated bioprocessing systems such as ambr® and the Beacon® optofluidic platform for accelerated cell line development. By using these systems and optimizing our parameters, we were able to achieve high titers in shake flasks. Additionally, the Beacon systems integrate miniaturized cell culture with high-throughput liquid handling automation and cell imaging. This allows us to control, adjust, and monitor programs at the same time,” noted Fisch.

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Spotlight

Saolta University Health Care Group

Saolta University Health Care Group comprises of 6 hospitals across 7 sites: Letterkenny University Hospital (LUH) Mayo University Hospital (MUH) Merlin Park University Hospital (MPUH) Portiuncula University Hospital (PUH) Roscommon University Hospital (RUH) Sligo University Hospital (SUH) University Hospital Galway (UHG)

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MEDICAL

AXIM Biotech Develops Rapid Quantitative Tear Test for MMP-9, An Inflammatory Biomarker of Dry Eye Disease

AXIM Biotech | March 10, 2022

AXIM Biotechnologies, Inc (OTCQB: AXIM) (“AXIM Biotech,” “AXIM” or “the Company”), an international healthcare solutions company targeting dry eye disease (DED), today announced that it has successfully developed a rapid quantitative tear test for MMP-9, an inflammatory biomarker for Dry Eye Disease. Dry Eye Disease, though widespread, is under-diagnosed, in part because symptoms do not always correlate with objective signs. It has a highly variable symptom profile at different stages of the disease, and there is often a discordance between signs and symptoms. A patient can have severe symptoms yet show no sign of ocular surface damage, while others have advanced ocular surface damage, yet report no symptoms. This lack of correlation between clinical signs and symptoms of Dry Eye Disease makes diagnosing and treating patients a challenge. Often times, inflammation is present before the clinical signs of Dry Eye Disease. The challenge has been in early detection of inflammation. Matrix metalloproteinase-9 (MMP-9), an inflammatory biomarker consistently elevated in the tears of dry eye patients, may accelerate early diagnosis when detected. The central role of inflammation in ocular surface disease is widely recognized, but our ability to measure this in the clinic has been limited to the InflammaDry test that measures tear matrix metalloproteinase (MMP) levels and provides a positive/negative result around a threshold of 40ng/ml of MMP-9. This 'yes or no' report has clinical value, but it is limited. Currently available MMP-9 testing does not detect a reduction in tear MMP-9 levels until the concentration drops below 40ng/ml and thus may miss clinically significant improvement that did not reach that threshold.” Dr. Joseph Tauber, AXIM’s Chief Medical Officer. The clinical benefits of the quantitative test for MMP-9 as a tool for accurate diagnosis of Dry Eye Disease and subsequent treatment include more accurate pre-surgical and post-surgical outcomes. Post-surgical complications, such as corneal wound healing, is facilitated by identifying dry eye prior to surgery. The availability of quantitative tear MMP-9 testing would be a significant advance in our ability to measure the degree of inflammation affecting our dry eye patients, allowing for more objective classification of their disease, Equally important would be the ability to measure improvement in control of inflammation that is the goal of many of our therapies for ocular surface disease, including pharmaceuticals, thermal pulsation treatments and even light based therapies.” Dr. Joseph Tauber. Some reports indicate that nearly half of all U.S. adults experience dry eye symptoms and 33% of patients in eye care clinics present with complaints about dry eye. Given the size of the market, AXIM made the strategic decision to develop a test for MMP-9 to assist in early detection of Dry Eye Disease. Together with our Lactoferrin and IgE Tests and now with the addition of our MMP-9 Test, AXIM will be positioned to corner the market for Dry Eye Disease diagnostic testing.” John Huemoeller, AXIM’s CEO. About AXIM® Biotechnologies Founded in 2014, AXIM® Biotechnologies, Inc. (AXIM) is a vertically integrated research and development company focused on improving the landscape for diagnosis of ophthalmological conditions such as Dry Eye Disease (DED) through rapid diagnostic tests. Additionally, it owns IP and has conducted research on SARS-CoV-2 (COVID-19) rapid neutralizing antibody tests to detect levels of functional neutralizing antibodies that are believed to prevent SARS-CoV-2 from entering the host cells, as well as for oncological indications.

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CELL AND GENE THERAPY

Childhood Trauma and Genetics Linked to Increased Obesity Risk

DRI | March 10, 2022

New research from the Healthy Nevada Project® found associations between genetics, obesity, and childhood trauma, linking social health determinants, genetics, and disease. The study, which was published this week in Frontiers in Genetics, found that participants with specific genetic traits and who experience childhood traumas are more likely to suffer from adult obesity. In 2016, DRI and Renown Health launched the Healthy Nevada Project®, the nation’s first community-based, population health study, which now has more than 60,000 participants. The project is a collaboration with personal genomics company, Helix, and combines genetic, environmental, social, and clinical data to address individual and community health needs with the goal of improving health across the state and the nation. The new study focuses on Adverse Childhood Experiences (ACEs), which are traumatic and unsafe events that children endure by the age of 18. Over 16,000 participants in the Healthy Nevada Project® answered a mental health survey, and more than 65 percent of these individuals self-reported at least one ACE occurrence. These 16,000 participants were cross-referenced with their genetic makeup, and clinical Body Mass Index (BMI) measures. According to the research team’s findings, study participants who had experienced one or more types of ACE were 1.5 times more likely to become obese adults. Participants who experienced four or more ACEs were more than twice as likely to become severely obese. Our analysis showed a steady increase in BMI for each ACE a person experienced, which indicates a very strong and significant association between the number of adverse childhood experiences and adult obesity, More importantly, participants’ BMI reacted even more strongly to the occurrence of ACEs when paired with certain mutations in several genes, one of which is strongly associated with schizophrenia.” lead author Karen Schlauch, Ph.D., of DRI. We know that genetics affect disease in the Healthy Nevada Project®, and now we are recognizing that ACEs also affect disease, Our new study shows that the combination of genes and environmental factors like ACEs, as well as many social determinants of health, can lead to more serious health outcomes than either variable alone. More broadly, this new work emphasizes how important it is for population genetic studies to consider the impact of social determinants on health outcomes.” Healthy Nevada Project® Principal Investigator Joseph Grzymski, Ph.D., of DRI and Renown Health. The study team believes that it is important for clinical caregivers to understand the strong impact that negative childhood experiences such as ACEs can have on both child and adult health. The researchers hope the information from this study will encourage doctors and nurses to conduct simple screenings for ACEs and consider a patient’s social environment and history in combination with genetics when developing treatment plans for better patient health. According to the 2019 Youth Behavior Risk Survey (YRBS), 25.6 percent of Washoe County teenagers are overweight or obese. Obesity is a serious health concern for children and adolescents. According to the Centers for Disease Control and Prevention, obese children and adolescents are more likely to become obese as adults. Obese and overweight children and adolescents are at risk for multiple health problems during their youth, which are likely to be more severe as adults, Obese and overweight youth are more likely to have risk factors associated with cardiovascular diseases, such as high blood pressure, high cholesterol, and type 2 diabetes. Losing weight, in addition to a healthy diet, helps to prevent and control multiple chronic diseases and improves quality of life for a lifetime.” Max J. Coppes, MD, PhD, MBA, FAAP, Nell J Redfield Chair of Pediatrics at the University of Nevada Reno School of Medicine, Physician in Chief of Renown Children's Hospital. We’d like to thank all of the Healthy Nevada Project® participants who provided information to make our work possible, Our research illustrates that it’s not just genetics that cause disease, but that our environment and life experiences interact with our genes to impact our health in ways that we are only beginning to understand.” Robert Read, M.S., of DRI. About DRI The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education.

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MEDICAL

HealthPartners, Helix partner to create DNA testing program that helps families better understand their genetic health

Helix | March 09, 2022

HealthPartners and leading genomics company, Helix, are launching myGenetics, a population genomics program that will provide important health information to families across Minnesota and surrounding states. The myGenetics program hopes to enroll more than 100,000 participants over four years. Genomic data generated will be integrated with patient health records and shared during their personal clinical care. Through the partnership, HealthPartners will be able to identify risk earlier and potentially mitigate serious disease. In similar programs, as many as 1 in 75 participants were found to be at risk for a serious health issue, of which 90 percent would not have been discovered through traditional practice. We see population genomics as a critical step in our efforts to improve the health of the communities we serve across Minnesota and surrounding states, By understanding the role genetics play in an individual's health, we can deliver more personalized care and improve the lives of our patients." Steve Connelly, MD, co-executive medical director at HealthPartners. The program aligns with HealthPartners ongoing drive to deliver simple, personalized, affordable care. The program will be strictly voluntary and will come at no cost to the patient. It's a partnership both HealthPartners and Helix say will help advance precision medicine and greater health equity. We are thrilled to partner deeply with one of the leading integrated delivery networks in the nation. We are excited to enable population access to preventable and actionable genetic insights and to empower providers and patients to make more informed medical decisions, The partnership will also generate cutting edge insights on the best ways to improve quality outcomes, close care gaps and lower the cost of care." James Lu, MD, PhD, CEO and co-founder of Helix. HealthPartners will leverage Helix's end-to-end genomic platform and unique Sequence Once, Query OftenTM model. It allows patient access to genetic data in a cost-efficient manner while also advancing ongoing genomics research. Helix has helped to launch similar programs at the Mayo Clinic, Renown Health and most recently, the Medical University of South Carolina. About Helix Helix is the leading population genomics and viral surveillance company operating at the intersection of clinical care, research, and data analytics. Through its CLIA / CAP laboratory, its end-to-end workflow, and data analytics platforms, Helix enables health systems, life sciences companies, payers, and government partners to accelerate the integration of genomic data into patient care and public health decision making. About HealthPartners HealthPartners is dedicated to improving health and well-being in partnership with members, patients and the community. As an integrated health system, it provides care to more than one million patients and coverage to more than 1.8 million medical and dental health plan members nationwide. HealthPartners also provides medical education and conducts research through HealthPartners Institute.

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MEDICAL

AXIM Biotech Develops Rapid Quantitative Tear Test for MMP-9, An Inflammatory Biomarker of Dry Eye Disease

AXIM Biotech | March 10, 2022

AXIM Biotechnologies, Inc (OTCQB: AXIM) (“AXIM Biotech,” “AXIM” or “the Company”), an international healthcare solutions company targeting dry eye disease (DED), today announced that it has successfully developed a rapid quantitative tear test for MMP-9, an inflammatory biomarker for Dry Eye Disease. Dry Eye Disease, though widespread, is under-diagnosed, in part because symptoms do not always correlate with objective signs. It has a highly variable symptom profile at different stages of the disease, and there is often a discordance between signs and symptoms. A patient can have severe symptoms yet show no sign of ocular surface damage, while others have advanced ocular surface damage, yet report no symptoms. This lack of correlation between clinical signs and symptoms of Dry Eye Disease makes diagnosing and treating patients a challenge. Often times, inflammation is present before the clinical signs of Dry Eye Disease. The challenge has been in early detection of inflammation. Matrix metalloproteinase-9 (MMP-9), an inflammatory biomarker consistently elevated in the tears of dry eye patients, may accelerate early diagnosis when detected. The central role of inflammation in ocular surface disease is widely recognized, but our ability to measure this in the clinic has been limited to the InflammaDry test that measures tear matrix metalloproteinase (MMP) levels and provides a positive/negative result around a threshold of 40ng/ml of MMP-9. This 'yes or no' report has clinical value, but it is limited. Currently available MMP-9 testing does not detect a reduction in tear MMP-9 levels until the concentration drops below 40ng/ml and thus may miss clinically significant improvement that did not reach that threshold.” Dr. Joseph Tauber, AXIM’s Chief Medical Officer. The clinical benefits of the quantitative test for MMP-9 as a tool for accurate diagnosis of Dry Eye Disease and subsequent treatment include more accurate pre-surgical and post-surgical outcomes. Post-surgical complications, such as corneal wound healing, is facilitated by identifying dry eye prior to surgery. The availability of quantitative tear MMP-9 testing would be a significant advance in our ability to measure the degree of inflammation affecting our dry eye patients, allowing for more objective classification of their disease, Equally important would be the ability to measure improvement in control of inflammation that is the goal of many of our therapies for ocular surface disease, including pharmaceuticals, thermal pulsation treatments and even light based therapies.” Dr. Joseph Tauber. Some reports indicate that nearly half of all U.S. adults experience dry eye symptoms and 33% of patients in eye care clinics present with complaints about dry eye. Given the size of the market, AXIM made the strategic decision to develop a test for MMP-9 to assist in early detection of Dry Eye Disease. Together with our Lactoferrin and IgE Tests and now with the addition of our MMP-9 Test, AXIM will be positioned to corner the market for Dry Eye Disease diagnostic testing.” John Huemoeller, AXIM’s CEO. About AXIM® Biotechnologies Founded in 2014, AXIM® Biotechnologies, Inc. (AXIM) is a vertically integrated research and development company focused on improving the landscape for diagnosis of ophthalmological conditions such as Dry Eye Disease (DED) through rapid diagnostic tests. Additionally, it owns IP and has conducted research on SARS-CoV-2 (COVID-19) rapid neutralizing antibody tests to detect levels of functional neutralizing antibodies that are believed to prevent SARS-CoV-2 from entering the host cells, as well as for oncological indications.

Read More

CELL AND GENE THERAPY

Childhood Trauma and Genetics Linked to Increased Obesity Risk

DRI | March 10, 2022

New research from the Healthy Nevada Project® found associations between genetics, obesity, and childhood trauma, linking social health determinants, genetics, and disease. The study, which was published this week in Frontiers in Genetics, found that participants with specific genetic traits and who experience childhood traumas are more likely to suffer from adult obesity. In 2016, DRI and Renown Health launched the Healthy Nevada Project®, the nation’s first community-based, population health study, which now has more than 60,000 participants. The project is a collaboration with personal genomics company, Helix, and combines genetic, environmental, social, and clinical data to address individual and community health needs with the goal of improving health across the state and the nation. The new study focuses on Adverse Childhood Experiences (ACEs), which are traumatic and unsafe events that children endure by the age of 18. Over 16,000 participants in the Healthy Nevada Project® answered a mental health survey, and more than 65 percent of these individuals self-reported at least one ACE occurrence. These 16,000 participants were cross-referenced with their genetic makeup, and clinical Body Mass Index (BMI) measures. According to the research team’s findings, study participants who had experienced one or more types of ACE were 1.5 times more likely to become obese adults. Participants who experienced four or more ACEs were more than twice as likely to become severely obese. Our analysis showed a steady increase in BMI for each ACE a person experienced, which indicates a very strong and significant association between the number of adverse childhood experiences and adult obesity, More importantly, participants’ BMI reacted even more strongly to the occurrence of ACEs when paired with certain mutations in several genes, one of which is strongly associated with schizophrenia.” lead author Karen Schlauch, Ph.D., of DRI. We know that genetics affect disease in the Healthy Nevada Project®, and now we are recognizing that ACEs also affect disease, Our new study shows that the combination of genes and environmental factors like ACEs, as well as many social determinants of health, can lead to more serious health outcomes than either variable alone. More broadly, this new work emphasizes how important it is for population genetic studies to consider the impact of social determinants on health outcomes.” Healthy Nevada Project® Principal Investigator Joseph Grzymski, Ph.D., of DRI and Renown Health. The study team believes that it is important for clinical caregivers to understand the strong impact that negative childhood experiences such as ACEs can have on both child and adult health. The researchers hope the information from this study will encourage doctors and nurses to conduct simple screenings for ACEs and consider a patient’s social environment and history in combination with genetics when developing treatment plans for better patient health. According to the 2019 Youth Behavior Risk Survey (YRBS), 25.6 percent of Washoe County teenagers are overweight or obese. Obesity is a serious health concern for children and adolescents. According to the Centers for Disease Control and Prevention, obese children and adolescents are more likely to become obese as adults. Obese and overweight children and adolescents are at risk for multiple health problems during their youth, which are likely to be more severe as adults, Obese and overweight youth are more likely to have risk factors associated with cardiovascular diseases, such as high blood pressure, high cholesterol, and type 2 diabetes. Losing weight, in addition to a healthy diet, helps to prevent and control multiple chronic diseases and improves quality of life for a lifetime.” Max J. Coppes, MD, PhD, MBA, FAAP, Nell J Redfield Chair of Pediatrics at the University of Nevada Reno School of Medicine, Physician in Chief of Renown Children's Hospital. We’d like to thank all of the Healthy Nevada Project® participants who provided information to make our work possible, Our research illustrates that it’s not just genetics that cause disease, but that our environment and life experiences interact with our genes to impact our health in ways that we are only beginning to understand.” Robert Read, M.S., of DRI. About DRI The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education.

Read More

MEDICAL

HealthPartners, Helix partner to create DNA testing program that helps families better understand their genetic health

Helix | March 09, 2022

HealthPartners and leading genomics company, Helix, are launching myGenetics, a population genomics program that will provide important health information to families across Minnesota and surrounding states. The myGenetics program hopes to enroll more than 100,000 participants over four years. Genomic data generated will be integrated with patient health records and shared during their personal clinical care. Through the partnership, HealthPartners will be able to identify risk earlier and potentially mitigate serious disease. In similar programs, as many as 1 in 75 participants were found to be at risk for a serious health issue, of which 90 percent would not have been discovered through traditional practice. We see population genomics as a critical step in our efforts to improve the health of the communities we serve across Minnesota and surrounding states, By understanding the role genetics play in an individual's health, we can deliver more personalized care and improve the lives of our patients." Steve Connelly, MD, co-executive medical director at HealthPartners. The program aligns with HealthPartners ongoing drive to deliver simple, personalized, affordable care. The program will be strictly voluntary and will come at no cost to the patient. It's a partnership both HealthPartners and Helix say will help advance precision medicine and greater health equity. We are thrilled to partner deeply with one of the leading integrated delivery networks in the nation. We are excited to enable population access to preventable and actionable genetic insights and to empower providers and patients to make more informed medical decisions, The partnership will also generate cutting edge insights on the best ways to improve quality outcomes, close care gaps and lower the cost of care." James Lu, MD, PhD, CEO and co-founder of Helix. HealthPartners will leverage Helix's end-to-end genomic platform and unique Sequence Once, Query OftenTM model. It allows patient access to genetic data in a cost-efficient manner while also advancing ongoing genomics research. Helix has helped to launch similar programs at the Mayo Clinic, Renown Health and most recently, the Medical University of South Carolina. About Helix Helix is the leading population genomics and viral surveillance company operating at the intersection of clinical care, research, and data analytics. Through its CLIA / CAP laboratory, its end-to-end workflow, and data analytics platforms, Helix enables health systems, life sciences companies, payers, and government partners to accelerate the integration of genomic data into patient care and public health decision making. About HealthPartners HealthPartners is dedicated to improving health and well-being in partnership with members, patients and the community. As an integrated health system, it provides care to more than one million patients and coverage to more than 1.8 million medical and dental health plan members nationwide. HealthPartners also provides medical education and conducts research through HealthPartners Institute.

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