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cbirt · 1 year
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MACHINE LEARNING FOR BIOMARKER DISCOVERY USING NGS DATA
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In this article, we will be exploring how machine learning (ML) techniques can be used to identify and analyze biomarkers from next generation sequencing (NGS) data. Biomarkers are specific biological molecules or characteristics that can be used to identify the presence or severity of a particular disease or condition. They play a crucial role in medical diagnosis, treatment, and prognosis, and their discovery and validation is an important area of research in the field of biomedical science. Next Generation Sequencing is a powerful tool that allows researchers to analyze large amounts of genetic data quickly and accurately. By combining the capabilities of machine learning with next-generation sequencing data, we can unlock the potential to identify and validate new biomarkers that can improve our understanding of diseases and lead to more effective treatments.
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longhaulerbear · 4 months
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bpod-bpod · 8 months
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More the Better
Images of immunofluorescence highlighting signature molecules and traditional histology methods from the same tumour section generate biomarkers highly predictive of cancer progression rate
Read the published research paper here
Image from work by Jia-Ren Lin, Yu-An Chen and Daniel Campton, and colleagues
Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)
Published in Nature Cancer, June 2023
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jcmarchi · 5 months
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Scientists 3D Print Self-Heating Microfluidic Devices - Technology Org
New Post has been published on https://thedigitalinsider.com/scientists-3d-print-self-heating-microfluidic-devices-technology-org/
Scientists 3D Print Self-Heating Microfluidic Devices - Technology Org
The one-step fabrication process rapidly produces miniature chemical reactors that could be used to detect diseases or analyze substances.
MIT researchers have used 3D printing to produce self-heating microfluidic devices, demonstrating a technique which could someday be used to rapidly create cheap, yet accurate, tools to detect a host of diseases.
MIT researchers developed a fabrication process to produce self-heating microfluidic devices in one step using a multi-material 3D printer. Pictured is an example of one of the devices. Illustration by the researchers / MIT
Microfluidics, miniaturized machines that manipulate fluids and facilitate chemical reactions, can be used to detect disease in tiny samples of blood or fluids. At-home test kits for Covid-19, for example, incorporate a simple type of microfluidic.
But many microfluidic applications require chemical reactions that must be performed at specific temperatures.
These more complex microfluidic devices, which are typically manufactured in a clean room, are outfitted with heating elements made from gold or platinum using a complicated and expensive fabrication process that is difficult to scale up.
Instead, the MIT team used multimaterial 3D printing to create self-heating microfluidic devices with built-in heating elements, through a single, inexpensive manufacturing process. They generated devices that can heat fluid to a specific temperature as it flows through microscopic channels inside the tiny machine.
The self-heating microfluidic devices, such as the one shown, can be made rapidly and cheaply in large numbers, and could someday help clinicians in remote parts of the world detect diseases without the need for expensive lab equipment. Credits: Courtesy of the researchers / MIT
Their technique is customizable, so an engineer could create a microfluidic that heats fluid to a certain temperature or given heating profile within a specific area of the device. The low-cost fabrication process requires about $2 of materials to generate a ready-to-use microfluidic.
The process could be especially useful in creating self-heating microfluidics for remote regions of developing countries where clinicians may not have access to the expensive lab equipment required for many diagnostic procedures.
“Clean rooms in particular, where you would usually make these devices, are incredibly expensive to build and to run. But we can make very capable self-heating microfluidic devices using additive manufacturing, and they can be made a lot faster and cheaper than with these traditional methods. This is really a way to democratize this technology,” says Luis Fernando Velásquez-García, a principal scientist in MIT’s Microsystems Technology Laboratories (MTL) and senior author of a paper describing the fabrication technique.
He is joined on the paper by lead author Jorge Cañada Pérez-Sala, an electrical engineering and computer science graduate student. The research will be presented at the PowerMEMS Conference this month.
An insulator becomes conductive
This new fabrication process utilizes a technique called multimaterial extrusion 3D printing, in which several materials can be squirted through the printer’s many nozzles to build a device layer by layer. The process is monolithic, which means the entire device can be produced in one step on the 3D printer, without the need for any post-assembly.
To create self-heating microfluidics, the researchers used two materials — a biodegradable polymer known as polylactic acid (PLA) that is commonly used in 3D printing, and a modified version of PLA.
The modified PLA has mixed copper nanoparticles into the polymer, which converts this insulating material into an electrical conductor, Velásquez-García explains. When electrical current is fed into a resistor composed of this copper-doped PLA, energy is dissipated as heat.
“It is amazing when you think about it because the PLA material is a dielectric, but when you put in these nanoparticle impurities, it completely changes the physical properties. This is something we don’t fully understand yet, but it happens and it is repeatable,” he says.
Using a multimaterial 3D printer, the researchers fabricate a heating resistor from the copper-doped PLA and then print the microfluidic device, with microscopic channels through which fluid can flow, directly on top in one printing step. Because the components are made from the same base material, they have similar printing temperatures and are compatible.
Heat dissipated from the resistor will warm fluid flowing through the channels in the microfluidic.
In addition to the resistor and microfluidic, they use the printer to add a thin, continuous layer of PLA that is sandwiched between them. It is especially challenging to manufacture this layer because it must be thin enough so heat can transfer from the resistor to the microfluidic, but not so thin that fluid could leak into the resistor.
The resulting machine is about the size of a U.S. quarter and can be produced in a matter of minutes. Channels about 500 micrometers wide and 400 micrometers tall are threaded through the microfluidic to carry fluid and facilitate chemical reactions.
Importantly, the PLA material is translucent, so fluid in the device remains visible. Many processes rely on visualization or the use of light to infer what is happening during chemical reactions, Velásquez-García explains.
Customizable chemical reactors
The researchers used this one-step manufacturing process to generate a prototype that could heat fluid by 4 degrees Celsius as it flowed between the input and the output. This customizable technique could enable them to make devices which would heat fluids in certain patterns or along specific gradients.
“You can use these two materials to create chemical reactors that do exactly what you want. We can set up a particular heating profile while still having all the capabilities of the microfluidic,” he says.
However, one limitation comes from the fact that PLA can only be heated to about 50 degrees Celsius before it starts to degrade. Many chemical reactions, such as those used for polymerase chain reaction (PCR) tests, require temperatures of 90 degrees or higher. And to precisely control the temperature of the device, researchers would need to integrate a third material that enables temperature sensing.
In addition to tackling these limitations in future work, Velásquez-García wants to print magnets directly into the microfluidic device. These magnets could enable chemical reactions that require particles to be sorted or aligned.
At the same time, he and his colleagues are exploring the use of other materials that could reach higher temperatures. They are also studying PLA to better understand why it becomes conductive when certain impurities are added to the polymer.
“If we can understand the mechanism that is related to the electrical conductivity of PLA, that would greatly enhance the capability of these devices, but it is going to be a lot harder to solve than some other engineering problems,” he adds.
“In Japanese culture, it’s often said that beauty lies in simplicity. This sentiment is echoed by the work of Cañada and Velasquez-Garcia. Their proposed monolithically 3D-printed microfluidic systems embody simplicity and beauty, offering a wide array of potential derivations and applications that we foresee in the future,” says Norihisa Miki, a professor of mechanical engineering at Keio University in Tokyo, who was not involved with this work.
“Being able to directly print microfluidic chips with fluidic channels and electrical features at the same time opens up very exiting applications when processing biological samples, such as to amplify biomarkers or to actuate and mix liquids. Also, due to the fact that PLA degrades over time, one can even think of implantable applications where the chips dissolve and resorb over time,” adds Niclas Roxhed, an associate professor at Sweden’s KTH Royal Institute of Technology, who was not involved with this study.
Written by Adam Zewe
Source: Massachusetts Institute of Technology
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innonurse · 2 years
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htfmireport · 8 days
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medicomunicare · 11 days
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Il ruolo degli ormoni sessuali nel controllo e nella responsività biologica dei diversi tipi di tumore mammario
Gli ormoni sessuali sono una parte importante sia della patogenesi che nella progressione del carcinoma mammario. Ognuni di essi ha le sue azioni molecolari sulle cellule tumorali, mediate dalla loro interazione con i recettori nucleari che ahnno funzione di fattori di trascrizione. Regolarmente il carcinoma mammario è molto responsivo agli estrogeni, eccetto la forma triplo-negativa che non…
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gqresearch24 · 1 month
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Cancer Diagnostics Market Outlook Report 2024-2030: Trends, Strategic Insights and Growth Opportunities | GQ Research
The Cancer Diagnostics market is set to witness remarkable growth, as indicated by recent market analysis conducted by GQ Research. In 2023, the global Cancer Diagnostics market showcased a significant presence, boasting a valuation of USD  18.2 Billion. This underscores the substantial demand for Cancer Diagnostics technology and its widespread adoption across various industries.
Get Sample of this Report at: https://gqresearch.com/request-sample/global-cancer-diagnostics-market/
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Projected Growth: Projections suggest that the Cancer Diagnostics market will continue its upward trajectory, with a projected value of USD 45.2 Billion by 2030. This growth is expected to be driven by technological advancements, increasing consumer demand, and expanding application areas.
Compound Annual Growth Rate (CAGR): The forecast period anticipates a Compound Annual Growth Rate (CAGR) of 12 %, reflecting a steady and robust growth rate for the Cancer Diagnostics market over the coming years.
Technology Adoption:
In the Cancer Diagnostics market, technology adoption is crucial for enhancing the accuracy, sensitivity, and speed of cancer detection and monitoring. Laboratories, clinics, and healthcare facilities continually adopt advanced diagnostic technologies, including imaging modalities such as MRI, CT scans, and PET scans, as well as molecular diagnostic techniques like PCR, next-generation sequencing (NGS), and immunoassays. The integration of artificial intelligence (AI) and machine learning algorithms further enhances diagnostic precision and aids in the interpretation of complex data, driving the adoption of innovative technologies for early detection, prognosis, and treatment optimization.
Application Diversity:
Cancer diagnostics encompass a wide range of applications across screening, diagnosis, staging, treatment selection, and monitoring of cancer patients. From screening tests such as mammography and Pap smears for breast and cervical cancer, to biopsy analysis and genetic testing for personalized treatment strategies, the diversity of diagnostic approaches enables tailored management of different cancer types and stages. Additionally, advancements in liquid biopsy techniques facilitate non-invasive detection of circulating tumor cells and cell-free DNA, offering new opportunities for early detection and monitoring of cancer progression and treatment response.
Consumer Preferences:
Consumer preferences in the Cancer Diagnostics market are driven by factors such as accuracy, reliability, convenience, and affordability. Patients and healthcare providers prioritize diagnostic tests that offer high sensitivity and specificity, allowing for early detection and accurate staging of cancer. Preferences also extend to non-invasive or minimally invasive testing methods that minimize patient discomfort and procedural risks. Furthermore, accessibility to diagnostic services, insurance coverage, and reimbursement policies influence consumer decisions, shaping the adoption of specific diagnostic technologies and testing modalities.
Technological Advancements:
Technological advancements drive innovation in cancer diagnostics, enabling the development of novel biomarkers, imaging agents, and diagnostic platforms with improved performance and clinical utility. Breakthroughs in genomics, proteomics, and metabolomics facilitate the identification of cancer-specific biomarkers for early detection and personalized treatment selection. Advanced imaging technologies, such as functional MRI and molecular imaging probes, enhance spatial resolution and sensitivity for tumor localization and characterization. Moreover, the integration of digital pathology, telemedicine, and point-of-care testing solutions expands access to cancer diagnostics in diverse healthcare settings, driving technological advancements towards precision medicine approaches.
Market Competition:
The Cancer Diagnostics market is highly competitive, with numerous players competing to offer innovative diagnostic solutions and services. Established companies, including diagnostic laboratories, medical device manufacturers, and biotechnology firms, leverage their expertise, brand recognition, and global distribution networks to maintain market leadership. Meanwhile, startups and research institutions contribute to market dynamism by developing disruptive technologies and diagnostic assays targeting specific cancer types or molecular pathways. Pricing strategies, regulatory compliance, and strategic partnerships are key determinants of competitive positioning in the market, influencing market share and customer acquisition.
Environmental Considerations:
Environmental considerations in the Cancer Diagnostics market primarily revolve around minimizing the environmental impact of diagnostic procedures and technologies. Efforts to reduce the use of hazardous chemicals and radioactive materials in diagnostic tests contribute to environmental sustainability and occupational safety in healthcare settings. Furthermore, the adoption of digital imaging technologies and electronic health records (EHRs) reduces paper waste and energy consumption associated with traditional film-based imaging and record-keeping practices. As the demand for cancer diagnostics continues to grow, industry stakeholders are increasingly mindful of implementing eco-friendly practices and optimizing resource utilization throughout the diagnostic process..
Regional Dynamics: Different regions may exhibit varying growth rates and adoption patterns influenced by factors such as consumer preferences, technological infrastructure and regulatory frameworks.
Key players in the industry include:
F. Hoffmann-La Roche Ltd.
GE Healthcare
Abbott
Illumina Inc
Qiagen N.V.
Siemens Healthcare GmbH
Thermo Fisher Scientific Inc
Hologic Inc
Koninklijke Philips N.V.
Bio-Rad Laboratories Inc.
The research report provides a comprehensive analysis of the Cancer Diagnostics market, offering insights into current trends, market dynamics and future prospects. It explores key factors driving growth, challenges faced by the industry, and potential opportunities for market players.
For more information and to access a complimentary sample report, visit Link to Sample Report: https://gqresearch.com/request-sample/global-cancer-diagnostics-market/
About GQ Research:
GQ Research is a company that is creating cutting edge, futuristic and informative reports in many different areas. Some of the most common areas where we generate reports are industry reports, country reports, company reports and everything in between.
Contact:
Jessica Joyal
+1 (614) 602 2897 | +919284395731 Website - https://gqresearch.com/
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drforambhuta · 1 month
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The Significance of Biopsies in Preventative Healthcare:
Historically, biopsies have primarily been used to diagnose suspected illnesses or track known ailments. Nevertheless, their utilization in preventive healthcare has been constrained. By integrating biopsies into routine health screenings, healthcare providers gain access to extensive insights into an individual's cellular health, facilitating the early detection of abnormalities prior to clinical manifestation. Biopsies offer valuable information on genetic predispositions, tissue microenvironment, biomarker discovery, and monitoring treatment response, thereby facilitating tailored preventive measures and enhancing patient outcomes.
1. Genetic Susceptibility: Biopsies uncover genetic mutations or variances that predispose individuals to specific diseases, such as cancer or autoimmune disorders. Early identification of these genetic indicators enables targeted interventions and personalized preventive measures. With advancements in genomic sequencing technologies, biopsies now play a crucial role in understanding an individual's genetic makeup, facilitating proactive steps to mitigate disease risks.
2. Cellular Environment: The cellular microenvironment captured through biopsies provides crucial insights into inflammation, oxidative stress, and tissue restructuring. Changes in the tissue microenvironment often precede clinical signs of disease, making them valuable indicators for early detection and intervention. Through analysis of biopsy samples, healthcare providers can identify subtle alterations indicative of disease onset or progression, enabling timely interventions to halt or mitigate disease advancement.
3. Biomarker Discovery: Examination of biopsy samples aids in identifying specific biomarkers associated with disease risk or progression. These biomarkers serve as early warning signs of disease and inform proactive management strategies. From circulating tumor cells in cancer patients to cardiac biomarkers in individuals at risk of cardiovascular disease, biopsies offer a glimpse into the molecular landscape of health and disease, empowering healthcare providers to intervene preemptively.
4. Monitoring Treatment Response: For individuals undergoing treatment for chronic conditions like cancer, biopsies serve as invaluable tools for monitoring treatment response at the cellular level. Real-time assessment of treatment effectiveness and disease progression permits adjustments in treatment protocols to optimize outcomes and minimize adverse effects. Additionally, biopsies enable the identification of treatment-resistant cell subpopulations, guiding the selection of alternative therapeutic approaches for improved patient outcomes.
There are many good hospitals in India that offer health checkup packages to undergo regular health checkups. You can choose a full body health checkup that may or may not include biopsy depending on your individual health needs and doctor's recommendations.
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jessicapinedaw · 1 month
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Biomarkers Market Share, Trends, Size, Segmentation And Forecast To 2031
The Insight Partners offers investors a comprehensive study of the Biomarkers market from the perspective of entrepreneurs in their most recent research report, ” Biomarkers Market Share, Size and Trends Analysis | 2031″ Examining current market conditions yields insightful information for businesses. This report provides insights into market possibilities, obstacles, and incentives that…
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eurofinsadvinus · 3 months
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Elevate your clinical outcomes with our cutting-edge Molecular Biomarker Panels! 🧬Eurofins Advinus leads the way in Discovery Biology Services, offering tailored solutions for precise clinical predictions. Harness the power of molecular biomarkers to revolutionize your research. Connect with our experts - [email protected]
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cbirt · 3 months
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When analyzing omics data, regression analysis is an essential tool for identifying biomarkers. For the analysis of graph-structured data, graph neural networks (GNNs) are the most popular deep learning model. Their ability to consistently identify biomarkers across several datasets and their prediction accuracy is, nevertheless, limited. These difficulties arise from the distinct graph structure of biological signaling networks, which have many targets and intricate relationships.
Researchers from Washington University developed a novel GNN model architecture called PathFormer in this study to address these issues. PathFormer ranks biomarkers and predicts disease diagnosis by methodically integrating signaling networks, prior knowledge, and omics data. In comparison results, PathFormer performed better than GNN models, showing a 30% increase in illness diagnostic accuracy and strong repeatability of biomarker ranking across several datasets. With two separate transcriptome datasets for cancer and Alzheimer’s disease, this improvement was verified, indicating that PathFormer is a useful tool for other omics data processing investigations.
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gitzette · 3 months
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Discover the groundbreaking role of SMOC1 in Alzheimer's research! Uncover how this protein could revolutionize early detection and offer new hope in the battle against Alzheimer's. Dive into the latest insights with our article. #AlzheimersResearch #SMOC1 #Proteomics
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jcmarchi · 3 days
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From steel engineering to ovarian tumor research
New Post has been published on https://thedigitalinsider.com/from-steel-engineering-to-ovarian-tumor-research/
From steel engineering to ovarian tumor research
Ashutosh Kumar is a classically trained materials engineer. Having grown up with a passion for making things, he has explored steel design and studied stress fractures in alloys.
Throughout Kumar’s education, however, he was also drawn to biology and medicine. When he was accepted into an undergraduate metallurgical engineering and materials science program at Indian Institute of Technology (IIT) Bombay, the native of Jamshedpur was very excited — and “a little dissatisfied, since I couldn’t do biology anymore.”
Now a PhD candidate and a MathWorks Fellow in MIT’s Department of Materials Science and Engineering, Kumar can merge his wide-ranging interests. He studies the effect of certain bacteria that have been observed encouraging the spread of ovarian cancer and possibly reducing the effectiveness of chemotherapy and immunotherapy.
“Some microbes have an affinity toward infecting ovarian cancer cells, which can lead to changes in the cellular structure and reprogramming cells to survive in stressful conditions,” Kumar says. “This means that cells can migrate to different sites and may have a mechanism to develop chemoresistance. This opens an avenue to develop therapies to see if we can start to undo some of these changes.”
Kumar’s research combines microbiology, bioengineering, artificial intelligence, big data, and materials science. Using microbiome sequencing and AI, he aims to define microbiome changes that may correlate with poor patient outcomes. Ultimately, his goal is to engineer bacteriophage viruses to reprogram bacteria to work therapeutically.
Kumar started inching toward work in the health sciences just months into earning his bachelor’s degree at IIT Bombay.
“I realized engineering is so flexible that its applications extend to any field,” he says, adding that he started working with biomaterials “to respect both my degree program and my interests.”
“I loved it so much that I decided to go to graduate school,” he adds.
Starting his PhD program at MIT, he says, “was a fantastic opportunity to switch gears and work on more interdisciplinary or ‘MIT-type’ work.”
Kumar says he and Angela Belcher, the James Mason Crafts Professor of biological engineering and materials science, began discussing the impact of the microbiome on ovarian cancer when he first arrived at MIT.
“I shared my enthusiasm about human health and biology, and we started brainstorming,” he says. “We realized that there’s an unmet need to understand a lot of gynecological cancers. Ovarian cancer is an aggressive cancer, which is usually diagnosed when it’s too late and has already spread.”
In 2022, Kumar was awarded a MathWorks Fellowship. The fellowships are awarded to School of Engineering graduate students, preferably those who use MATLAB or Simulink — which were developed by the mathematical computer software company MathWorks — in their research. The philanthropic support fueled Kumar’s full transition into health science research.
“The work we are doing now was initially not funded by traditional sources, and the MathWorks Fellowship gave us the flexibility to pursue this field,” Kumar says. “It provided me with opportunities to learn new skills and ask questions about this topic. MathWorks gave me a chance to explore my interests and helped me navigate from being a steel engineer to a cancer scientist.”
Kumar’s work on the relationship between bacteria and ovarian cancer started with studying which bacteria are incorporated into tumors in mouse models.
“We started looking closely at changes in cell structure and how those changes impact cancer progression,” he says, adding that MATLAB image processing helps him and his collaborators track tumor metastasis.
The research team also uses RNA sequencing and MATLAB algorithms to construct a taxonomy of the bacteria.
“Once we have identified the microbiome composition,” Kumar says, “we want to see how the microbiome changes as cancer progresses and identify changes in, let’s say, patients who develop chemoresistance.”
He says recent findings that ovarian cancer may originate in the fallopian tubes are promising because detecting cancer-related biomarkers or lesions before cancer spreads to the ovaries could lead to better prognoses.
As he pursues his research, Kumar says he is extremely thankful to Belcher “for believing in me to work on this project.
“She trusted me and my passion for making an impact on human health — even though I come from a materials engineering background — and supported me throughout. It was her passion to take on new challenges that made it possible for me to work on this idea. She has been an amazing mentor and motivated me to continue moving forward.”
For her part, Belcher is equally enthralled.
“It has been amazing to work with Ashutosh on this ovarian cancer microbiome project,” she says. “He has been so passionate and dedicated to looking for less-conventional approaches to solve this debilitating disease. His innovations around looking for very early changes in the microenvironment of this disease could be critical in interception and prevention of ovarian cancer. We started this project with very little preliminary data, so his MathWorks fellowship was critical in the initiation of the project.”
Kumar, who has been very active in student government and community-building activities, believes it is very important for students to feel included and at home at their institutions so they can develop in ways outside of academics. He says that his own involvement helps him take time off from work.
“Science can never stop, and there will always be something to do,” he says, explaining that he deliberately schedules time off and that social engagement helps him to experience downtime. “Engaging with community members through events on campus or at the dorm helps set a mental boundary with work.”
Regarding his unusual route through materials science to cancer research, Kumar regards it as something that occurred organically.
“I have observed that life is very dynamic,” he says. “What we think we might do versus what we end up doing is never consistent. Five years back, I had no idea I would be at MIT working with such excellent scientific mentors around me.”
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lupusnews · 4 months
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medicomunicare · 3 months
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Medicina rigenerativa per il rene: la possibilità che si apre capendo tutti gli stadi molecolari del danno
Come si forma il rene nell’embriogenesi? Il rene dei mammiferi, il metanefro, è il terzo paio di organi escretori a formarsi durante l’embriogenesi e l’unico a persistere nell’animale postnatale. La sua formazione comporta una complessa interazione tra la gemma ureterale ramificata, che formerà i dotti collettori, e il mesenchima circostante, che dà origine a tutti i tipi di cellule epiteliali…
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