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Brain Biobank

Posted in Human neural progenitor sells, Neurohumoral Transmission, Neurological Diseases, Neuroscience, Organ-on-a-Chip & 3D Printing in Life Sciences, Proteins, Proteomics, Regenerative Biology and Medicine, Signaling, Signaling & Cell Circuits, Stem Cells for Regenerative Medicine, Translational Science, tagged biobank, BioP3 device, cell function correlation, EPR spectroscopy, genetics & genomics, α-synuclein, magnetic resonance, monomeric, Neurological treatments, neuropsychiatry, Neuroscience, NMR spectroscopy, protein structure, regenerative medicine, Spinal Cord Injury, spinal cord repair, stem cells, Translational Research on March 29, 2016| 1 Comment »

Brain Biobank and studies of disease structure correlates

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Unveiling Psychiatric Diseases

Researchers create neuropsychiatric cellular biobank

By DAVID CAMERON   November 12, 2015   http://hms.harvard.edu/news/unveiling-psychiatric-diseases

Image: iStock/mstroz

Researchers from Harvard Medical School and Massachusetts General Hospital have completed the first stage of an important collaboration aimed at understanding the intricate variables of neuropsychiatric disease—something that currently eludes clinicians and scientists.

The research team, led by Isaac Kohane at HMS and Roy Perlis at Mass General, has created a neuropsychiatric cellular biobank—one of the largest in the world.

It contains induced pluripotent stem cells, or iPSCs, derived from skin cells taken from 100 people with neuropsychiatric diseases such as schizophrenia, bipolar disorder and major depression, and from 50 people without neuropsychiatric illness.

In addition, a detailed profile of each patient, obtained from hours of in-person assessment as well as from electronic medical records, is matched to each cell sample.

As a result, the scientific community can now for the first time access cells representing a broad swath of neuropsychiatric illness. This enables researchers to correlate molecular data with clinical information in areas such as variability of drug reactions between patients. The ultimate goal is to help treat, with greater precision, conditions that often elude effective management.

The cell collection and generation was led by investigators at Mass General, who in collaboration with Kohane and his team are working to characterize the cell lines at a molecular level. The cell repository, funded by the National Institutes of Health, is housed at Rutgers University.

“This biobank, in its current form, is only the beginning,” said Perlis, director of the MGH Psychiatry Center for Experimental Drugs and Diagnostics and HMS associate professor of psychiatry. “By next year we’ll have cells from a total of four hundred patients, with additional clinical detail and additional cell types that we will share with investigators.”

A current major limitation to understanding brain diseases is the inability to access brain biopsies on living patients. As a result, researchers typically study blood cells from patients or examine post-mortem tissue. This is in stark contrast with diseases such as cancer, for which there are many existing repositories of highly characterized cells from patients.

The new biobank offers a way to push beyond this limitation.

 

A Big Step Forward

While the biobank is already a boon to the scientific community, researchers at MGH and the HMS Department of Biomedical Informatics will be adding additional layers of molecular data to all of the cell samples. This information will include whole genome sequencing and transcriptomic and epigenetic profiling of brain cells made from the stem cell lines.

Collaborators in the HMS Department of Neurobiology, led by Michael Greenberg, department chair and Nathan Marsh Pusey Professor of Neurobiology,  will also work to examine characteristics of other types of neurons derived from these stem cells.

“This can potentially alter the entire way we look at and diagnose many neuropsychiatric conditions,” said Perlis.

One example may be to understand how the cellular responses to medication correspond to the patient’s documented responses, comparing in vitro with in vivo. “This would be a big step forward in bringing precision medicine to psychiatry,” Perlis said.

“It’s important to recall that in the field of genomics, we didn’t find interesting connections to disease until we had large enough samples to really investigate these complex conditions,” said Kohane, chair of the HMS Department of Biomedical Informatics.

“Our hypothesis is that here we will require far fewer patients,” he said. “By measuring the molecular functioning of the cells of each patient rather than only their genetic risk, and combining that all that’s known of these people in terms of treatment response and cognitive function, we will discover a great deal of valuable information about these conditions.”

Added Perlis, “In the early days of genetics, there were frequent false positives because we were studying so few people. We’re hoping to avoid the same problem in making cellular models, by ensuring that we have a sufficient number of cell lines to be confident in reporting differences between patient groups.”

The generation of stem cell lines and characterization of patients and brain cell lines is funded jointly by the the National Institute of Mental Health, the National Human Genome Research Institute and a grant from the Centers of Excellence in Genomic Science program.

 

On C.T.E. and Athletes, Science Remains in Its Infancy

by BENEDICT CAREY  MARCH 27, 2016   http://www.nytimes.com/2016/03/28/health/cte-brain-disease-nfl-football-research.html

$16 Million for Brain Research, but $0 from N.F.L.

By KEN BELSON   DEC. 22, 2015    http://www.nytimes.com/2015/12/23/sports/football/grant-of-nearly-16-million-for-cte-researchers.html

http://www.nytimes.com/2014/10/13/science/researchers-replicate-alzheimers-brain-cells-in-a-petri-dish.html

https://static01.nyt.com/images/2014/10/13/us/ALZHEIMERS/ALZHEIMERS-master675.jpg

A three-dimensional human neural cell culture model of Alzheimer’s disease

Se Hoon Choi, Young Hye Kim, Matthias Hebisch, et al.

http://www.nature.com/articles/nature13800.epdf

Alzheimer’s disease is the most common form of dementia, characterized by two pathological hallmarks: amyloid-β plaques and neurofibrillary tangles¹. The amyloid hypothesis of Alzheimer’s disease posits that the excessive accumulation of amyloid-β peptide leads to neurofibrillary tangles composed of aggregated hyperphosphorylated tau^{2, 3}. However, to date, no single disease model has serially linked these two pathological events using human neuronal cells. Mouse models with familial Alzheimer’s disease (FAD) mutations exhibit amyloid-β-induced synaptic and memory deficits but they do not fully recapitulate other key pathological events of Alzheimer’s disease, including distinct neurofibrillary tangle pathology^{4, 5}. Human neurons derived from Alzheimer’s disease patients have shown elevated levels of toxic amyloid-β species and phosphorylated tau but did not demonstrate amyloid-β plaques or neurofibrillary tangles^{6, 7, 8, 9, 10, 11}. Here we report that FAD mutations in β-amyloid precursor protein and presenilin 1 are able to induce robust extracellular deposition of amyloid-β, including amyloid-β plaques, in a human neural stem-cell-derived three-dimensional (3D) culture system. More importantly, the 3D-differentiated neuronal cells expressing FAD mutations exhibited high levels of detergent-resistant, silver-positive aggregates of phosphorylated tau in the soma and neurites, as well as filamentous tau, as detected by immunoelectron microscopy. Inhibition of amyloid-β generation with β- or γ-secretase inhibitors not only decreased amyloid-β pathology, but also attenuated tauopathy. We also found that glycogen synthase kinase 3 (GSK3) regulated amyloid-β-mediated tau phosphorylation. We have successfully recapitulated amyloid-β and tau pathology in a single 3D human neural cell culture system. Our unique strategy for recapitulating Alzheimer’s disease pathology in a 3D neural cell culture model should also serve to facilitate the development of more precise human neural cell models of other neurodegenerative disorders.

 

 

Figure 2: Robust increases of extracellular amyloid-β deposits in 3D-differentiated hNPCs with FAD mutations.close

a, Thin-layer 3D culture protocol. HC, histochemistry; IF, immunofluorescence; IHC, immunohistochemistry. b, Amyloid-β deposits in 6-week differentiated control and FAD ReN cells in 3D Matrigel (green, GFP; blue, 3D6; scale bar, …

 

Stem Cell-Based Spinal Cord Repair Enables Robust Corticospinal Regeneration

March 29, 2016 by mburatov  

In the March 28th, 2016 issue of the journal Nature Medicine, Mark Tuszynski and his colleagues from the University of California, San Diego, in collaboration with colleagues from Japan and Wisconsin, report that they were able to successfully coax stem cell-derived neurons to regenerate damaged corticospinal tracts in rats. Furthermore, this regeneration produced observable, functional benefits.

What is the “corticospinal tract” you ask? The corticospinal tracts are part of the “pyramidal tracts” that include the corticospinal and corticobulbar tracts. The pyramidal tracts are the main controllers of voluntary movement and connect their nerve fibers eventually to cells that serve voluntary muscles and allow them to contract. We call such nerves “motor nerves,” and the corticospinal nerve tracts are among the most important of the motor nerve tracts.

These neural tracts are collectively called “pyramidal tracts” because they pass through a small area of the brain stem known as the pyramids, which lie on the ventral side of the medulla oblongata. Both pyramidal tracts originate in the forebrain; specifically from the so-called “motor cortex” of the forebrain. The motor cortex lies just in front of the central sulcus of the forebrain. In the motor cortex, lies thousands of “upper motor neurons” that extend their axons down to the brain stem and spinal cord.

In the brain stem, the majority of these corticospinal tracts crossover (or decussate) to the other side of the brain stem and travel down the opposite side of the spinal cord. The corticospinal axons extend all the way down the spinal cord, until they make a connection (synapse) with a “lower motor neuron” that extends its axon to the skeletal muscles that it will direct to contract. The corticobulbar tract contains nerves that conduct nerve impulses from cranial nerves and these help the muscles of the face and neck contract, and are involved in facial expressions, swallowing, chewing, and so on.

Damage to the upper motor neurons as a result of a stroke can rob a person of the ability to move, since the muscles that are attached to the upper motor neurons cannot receive any signals to contract. Likewise, damage to the axonal tracts (also known as nerve fibers) can paralyze a patient and rob them of their ability to move.

The director of this research project, Mark Tuszynski, MD, PhD, professor in the UC San Diego School of Medicine Department of Neurosciences and director of the UC San Diego Translational Neuroscience Institute, said: “The corticospinal projection is the most important motor system in humans. It has not been successfully regenerated before. Many have tried, many have failed – including us, in previous efforts.”

“We humans use corticospinal axons for voluntary movement,” said Tuszynski. “In the absence of regeneration of this system in previous studies, I was doubtful that most therapies taken to humans would improve function. Now that we can regenerate the most important motor system for humans, I think that the potential for translation is more promising.”

 

Novel use of EPR spectroscopy to study in vivo protein structure

http://www.news-medical.net/whitepaper/20160315/Novel-use-of-EPR-spectroscopy-to-study-in-vivo-protein-structure.aspx

α-synuclein

α-synuclein is a protein found abundantly throughout the brain. It is present mainly at the neuron ends where it is thought to play a role in ensuring the supply of synaptic vesicles in presynaptic terminals, which are required for the release of neurotransmitters to relay signals between neurons. It is critical for normal brain function.

However, α-synuclein is also the primary protein component of the cerebral amyloid deposits characteristic of Parkinson’s disease and its precursor is found in the amyloid plaques of Alzheimer’s disease. Although α-synuclein is present in all areas of the brain, these disease-state amyloid plaques only arise in distinct areas.

Alpha-synuclein protein. May play role in Parkinson’s and Alzheimer’s disease.  © molekuul.be / Shutterstock.com

Imaging of isolated samples of α-synuclein in vitro indicate that it does not have the precise 3D folded structure usually associated with proteins. It is therefore classed as an intrinsically disordered protein. However, it was not known whether the protein also lacked a precise structure in vivo.

There have been reports that it can form helical tetramers. Since the 3D structure of a biological protein is usually precisely matched to the specific function it performs, knowing the structure of α-synuclein within a living cell will help elucidate its role and may also improve understanding of the disease states with which it is associated.

If α-synuclein remains disordered in vivo, it may be possible for the protein to achieve different structures, and have different properties, depending on its surroundings.

Techniques for determining protein structure

It has long been known that elucidating the structure of a protein at an atomic level is fundamental for understanding its normal function and behavior. Furthermore, such knowledge can also facilitate the development of targeted drug treatments. Unfortunately, observing the atomic structure of a protein in vivo is not straightforward.

X-ray diffraction is the technique usually adopted for visualizing structures at atomic resolution, but this requires crystals of the molecule to be produced and this cannot be done without separating the molecules of interest from their natural environment. Such processes can modify the protein from its usual state and, particularly with complex structures, such effects are difficult to predict.

The development of nuclear magnetic resonance (NMR) spectroscopy improved the situation by making it possible for molecules to be analyzed under in vivo conditions, i.e. same pH, temperature and ionic concentration.

More recently, increases in the sensitivity of NMR and the use of isotope labelling have enabled determinations of the atomic level structure and dynamics of proteins to be determined within living cells¹. NMR has been used to determine the structure of a bacterial protein within living cells² but it is difficult to achieve sufficient quantities of the required protein within mammalian cells and to keep the cells alive for NMR imaging to be conducted.

Electron paramagnetic resonance (EPR) spectroscopy for determining protein structure

Recently, researchers have managed to overcome these obstacles by using in-cell NMR and electron paramagnetic resonance (EPR) spectroscopy. EPR spectroscopy is a technique that is similar to NMR spectroscopy in that it is based on the measurement and interpretation of the energy differences between excited and relaxed molecular states.

In EPR spectroscopy it is electrons that are excited, whereas in NMR signals are created through the spinning of atomic nuclei. EPR was developed to measure radicals and metal complexes, but has also been utilized to study the dynamic organization of lipids in biological membranes³.

EPR has now been used for the first time in protein structure investigations and has provided atomic-resolution information on the structure of α-synuclein in living mammalians^4,5.

Bacterial forms of the α-synuclein protein labelled with 15N isotopes were introduced into five types of mammalian cell using electroporation. Concentrations of α-synuclein close to those found in vivo were achieved and the 15N isotopes allowed the protein to be clearly defined from other cellular components by NMR. The conformation of the protein was then determined using electron paramagnetic resonance (EPR).

The results showed that within living mammalian cells α-synuclein remains as a disordered and highly dynamic monomer. Different intracellular environments did not induce major conformational changes.

Summary

The novel use of EPR spectroscopy has resolved the mystery surrounding the in vivo conformation of α-synuclein. It showed that α-synuclein maintains its disordered monomeric form under physiological cell conditions. It has been demonstrated for the first time that even in crowded intracellular environments α-synuclein does not form oligomers, showing that intrinsic structural disorder can be sustained within mammalian cells.

References

1. Freedberg DI and Selenko P. Live cell NMR Annu. Rev. Biophys. 2014;43:171–192.
2. Sakakibara D, et al. Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 2009;458:102–105.
3. Yashroy RC. Magnetic resonance studies of dynamic organisation of lipids in chloroplast membranes. Journal of Biosciences 1990;15(4):281.
4. Alderson TA and Bax AD. Parkinson’s Disease. Disorder in the court. Nature 2016; doi:10.1038/nature16871.
5. Theillet FX, et al. Structural disorder of monomeric α-synuclein persists in mammalian cells. Nature 2016; doi:10.1038/nature16531.

 

Spinal cord reconstitution with homologous neural grafts enables robust corticospinal regeneration

Ken Kadoya, Paul Lu, Kenny Nguyen, Corinne Lee-Kubli, Hiromi Kumamaru, Lin Yao, et al.

Nature Medicine(2016)          http://dx.doi.org:/10.1038/nm.4066

The corticospinal tract (CST) is the most important motor system in humans, yet robust regeneration of this projection after spinal cord injury (SCI) has not been accomplished. In murine models of SCI, we report robust corticospinal axon regeneration, functional synapse formation and improved skilled forelimb function after grafting multipotent neural progenitor cells into sites of SCI. Corticospinal regeneration requires grafts to be driven toward caudalized (spinal cord), rather than rostralized, fates. Fully mature caudalized neural grafts also support corticospinal regeneration. Moreover, corticospinal axons can emerge from neural grafts and regenerate beyond the lesion, a process that is potentially related to the attenuation of the glial scar. Rat corticospinal axons also regenerate into human donor grafts of caudal spinal cord identity. Collectively, these findings indicate that spinal cord ‘replacement’ with homologous neural stem cells enables robust regeneration of the corticospinal projection within and beyond spinal cord lesion sites, achieving a major unmet goal of SCI research and offering new possibilities for clinical translation.

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Tang Prize for 2014: Immunity and Cancer

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Discovery process, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Drug Toxicity, Evolutionary cognition, Experimental validation, Human Immune System in Health and in Disease, International Global Work in Pharmaceutical, Monoclonal Immunotherapy, Pharmaceutical Analytics, Pharmacologic toxicities, Proteomics, Technology Transfer: Biotech and Pharmaceutical, Translational Effectiveness, Translational Research, Translational Science, tagged Cancer - General, Cancer immunology, chemical structure, chemo regimens, chemoresistance, immunosupression, research, T-cell biology, therapeutic toxicity reduction, Translational Research on June 20, 2014| 1 Comment »

Larry Bernstein, MD, FCAP

http://pharmaceuticalinnovation.com/6-19-2014/larryhbern/Tang Prize for 2014: Immunity and Cancer

 

2014 Tang Prize in Biopharmaceutical Sciences awards to James P. Allison and Tasuku Honjo For the discoveries of CTLA-4 and PD-1 as immune inhibitory molecules that led to their applications in cancer immunotherapy 2014/06/19.

Founded by Dr. Samuel Yin in December 2012, the Tang Prize recognizes scholars conducting revolutionary research in the four major fields of Sustainable Development, Biopharmaceutical Science, Sinology, and the Rule of Law. The Prize is awarded with each category a cash reward of over US$1 million (NT$50 million). The Tang Prize Foundation hopes that recipients of the Prize will continue to innovate while cultivating and nurturing new talent in their respective fields.
Academia Sinica was commissioned by the Tang-Prize Foundation to administer the selection of Tang-Prize Laureates for the category of Biopharmaceutical Science, recognizing original biopharmaceutical or biomedical research that has led to significant advances towards preventing, diagnosing and/or treating major human diseases to improve human health.
James P. Allison and Tasuku Honjo were chosen among nearly a hundred nominees for their discoveries of CTLA-4 and PD-1 as immune inhibitory molecules, revealing ways to harness our incredibly powerful immune system to fight cancer and marking the beginning of the immunotherapy revolution.
A critical process in the immune response involves presentation of antigens to T cells by antigen-presenting cells, two key cell types in our immune system. This process is highly regulated by molecules that stimulate the response to ensure our mounting a sufficient immune response, especially in the event of invasion by pathogens, but also by molecules that inhibit the process to ensure the response is not excessive. Indeed, there is now a family of proteins on T cells involved in this regulatory process, which is designated the “CD28 receptor family” co-receptors, as CD28 is the first protein identified to have such function. They are divided into co-receptors transmitting stimulatory signals and co-receptors transmitting inhibitory signals. Each of these has its counterpart (ligand) on antigen-presenting cells belonging to the “B7 family”. Two most prominent inhibitory receptors on T cells are called CTLA-4 (cytotoxic T lymphocyte antigen-4, as it is first identified on cytotoxic T lymphocytes) and PD-1 (program death-1, as it is first identified to be associated with a type of cell death process called programmed cell death). Their ligands are designated as B7-1/B7-2 and PD-L1/PD-L2, respectively. These are also referred to as immune checkpoint receptors and ligands.
Our immune system is not perfect and at times, the regulatory mechanisms might be faulty, which in fact may be the basis of a variety of diseases. For example, autoimmune diseases may be related to the suppressive mechanism becoming weak and the individuals can mount excessive immune responses even to their own cells and tissues. Also, our immune system is capable of recognizing cancer cells and attacking them, in a process called immune surveillance. However, cancer cells are also equipped with machineries to evade the host anti-tumor activity, which is described as immune escape. For example, cancer cells can also express B7 family ligands on their surfaces and, by engaging the co-receptors transmitting inhibitory signals on T cells, they can inhibit the host anti-tumor T cell activity. By recognizing how cancer cells escape the immune surveillance, scientists have developed novel approaches to interfere with the ability of cancer cells to suppress the immune response, thus enhancing the ability of the host immune system to inhibit cancer cell growth.
Dr. James Allison, Chairman, Department of Immunology and Executive Director, Immunotherapy Platform at the University of Texas, MD Anderson Cancer Center, is one of two scientist to identify CTLA-4 as an inhibitory receptor on T-cells in 1995 and was the first to recognize it as a potential target for cancer therapy.  His team then developed an antibody that blocks CTLA-4 activity and showed in 1996 that this antibody is able to help reject several different types of tumors in mouse models. This subsequently led to development of a monoclonal antibody drug, which has undergone clinical trials against stage 4 melanoma and been approved for treatment of melanoma by the U.S. FDA in 2011.
Dr. Tasuku Honjo, Professor, Department of Immunology and Genomic Medicine, Kyoto University, discovered PD-1 in 1992. His group subsequently established that PD-1 is an inhibitor regulator of the T cell response. Additional studies from his and other laboratories established that this protein plays a critical role in the regulation of tumor immunity and stimulated many groups to generate its blocker for the treatment of cancer. Antibodies against PD-1 have been approved by the U.S. FDA as an investigational new drug and developed for the treatment of cancer. One such antibody produced complete or partial responses in non-small-cell lung cancer, melanoma, and renal-cell cancer in clinical trials, and is predicted to be launched in 2015 for treatment of non-small cell lung cancer; this has been stated by some as having the potential to “change the landscape” of the treatment for lung cancer. Another antibody, shown to achieve a substantial response rate also in patients with non-small cell lung cancer, is currently in clinical trial for many types of cancers. In addition, combination therapy (anti-CTLA-4 plus anti-PD-1) has been shown to dramatically improve the long-term survival rates in cancer patients.
This is an exciting time in our fight against cancer. The discoveries by Dr. Allison and Dr. Honjo have spurred additional development of therapeutic approaches along the line of immunotherapy and brought new hope that many types of cancers can be cured.
In addition, dysregulation in immune checkpoint pathways may be intimately involved in other illnesses, such as allergy, infectious diseases, and autoimmune diseases. Thus, the approach of targeting immune stimulatory and inhibitory molecules also promises to lead to the development of new therapies for these diseases.
Dr. Allison’s and Dr. Honjo’s discoveries have opened a new therapeutic era in medicine.

 

Supplementary figure:

unleashes immune system to attack cancer cells

 

 

 

 

 

 

 

 

 

 

 

 

 

Dr. Samuel Yin, founder of the Tang Prize, is currently chairman of the Ruentex Group and chief development officer, chief technology officer, and chief engineer of Ruentex Construction & Development. He is also an adjunct professor in the department of civil engineering at National Taiwan University and a professor at Peking University, where he advises PhD students.

Dr. Yin read history at Chinese Culture University. He received a master’s degree in business administration at National Taiwan University and a doctorate in business administration at National Chengchi University.

In addition to his academic background in the humanities and business administration, Dr. Yin’s great interest in and devotion to interdisciplinary studies have made him an award-winning civil engineer and educator.

In 2004, Dr. Yin was named fellow of the Chinese Institute of Civil and Hydraulic Engineering. In 2008, he was invited to join Russia’s International Academy of Engineering and also awarded the Engineering Prowess Medal, the academy’s highest honour. In 2010, Dr. Yin received the Henry L. Michel Award for Industry Advancement of Research by the prestigious American Society of Civil Engineers (ASCE) for his contribution in the area of construction technology research. He was the first person without an academic background in engineering to receive the award.

Driven by a firm belief that he should give back to the society that has enabled him to achieve so much, Dr. Yin has been investing in philanthropy and education for a long time, in the hope of creating a positive force in society and making a better world.

Dr. Yin’s biggest dream was to set up an international award. He has long had great respect and admiration for the Nobel Prize, so he established an award modeled on the Nobel. The Tang Prize rewards excellent research in the areas of Sustainable Development, Biopharmaceutical Science, Sinology (excluding literary works), and Rule of Law. Dr. Yin hopes to encourage experts to dedicate themselves to innovative research in these fields and to spur human development with first-class research.

Dr. Yin’s relentless enthusiasm for philanthropy was instilled through his upbringing, particularly the example set by his late father Yin Shu-Tien. Dr. Yin established a foundation in memory of his grandfather, Yin Xun-Ruo, to provide scholarships to students of families originating in Shandong Province to study Chinese literature and history. When Yin senior passed away, Dr. Yin also set up the Kwang-Hua Education Foundation to help with China’s higher education programs.

In the past few years, Dr. Yin has set up a number of foundations to serve people on both sides of the Taiwan Strait and to foster more talented people for the nation (the Yin Xun-Ruo Educational Foundation, the Yin Shu-Tien Medical Foundation, the Kwang-Hua Education Foundation, and the Guanghua School of Management of Peking University). In 2012, Dr. Yin set up a global award, the Tang Prize, to spread his philanthropy across the world.

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