MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with the Allen Mouse Brain Reference Atlas

An experimental coronal mouse brain section automatically aligned to the Allen Mouse Brain Reference Atlas

Analyzing cellular populations within specific anatomies in brain images requires expertise in both neuroanatomy and cellular identification. This typically involves a scientist comparing experimental images with a reference atlas and manually delineating anatomical regions and marking cell populations within. NeuroInfo®, a revolutionary new technology from MBF Bioscience, enables researchers to automatically identify and delineate mouse brain regions based on the publicly available Allen Mouse Brain Reference Atlas.

“NeuroInfo has the potential to greatly improve our understanding of how mental disorders influence neuronal cell populations,” says Nathan O’Connor Ph.D., product manager at MBF Bioscience. “Because it makes identifying brain regions substantially faster and more accurate, researchers will be able to explore many more brain regions.”

“The Allen Mouse Brain Reference Atlas is a valuable tool to assist scientists in their research. We’re thrilled that MBF has chosen to integrate this resource into NeuroInfo,” stated Amy Bernard, Ph.D., Product Architect at the Allen Institute for Brain Science.

“Using this remarkable technology, neuroscientists will obtain more repeatable, objective analyses that have been possible to date. Thanks to the integration with the Allen Mouse Brain Reference Atlas, these analyses will be more standardized so that they can be compared across experiments and laboratories,” says Jack Glaser, President.

NeuroInfo can be used with MBF Bioscience’s slide scanning software and virtually all commercial whole slide scanners. The data from NeuroInfo seamlessly integrates with MBF Bioscience’s products including Neurolucida, Stereo Investigator, Biolucida, and BrainMaker.

The tools in NeuroInfo allow researchers to automatically delineate anatomies in the experimental specimens, and detect cells within these anatomies. NeuroInfo yields data that can be invaluable to better understand the organization and composition of the nervous system, and to further knowledge in neurogenomics, transcriptomics, proteomics, and connectomics.

The National Institute of Mental Health provides funding to support the development of NeuroInfo.

Researchers cited MBF Bioscience systems in 27 papers between 08/18/2017 and 09/01/2017

Stereo Investigator:journal images sm

Balu, D. T., Presti, K. T., Huang, C. C. Y., Muszynski, K., Radzishevsky, I., Wolosker, H., . . . Coyle, J. T. (2017). Serine Racemase and D-serine in the Amygdala are Dynamically Involved in Fear Learning. Biological Psychiatry. doi: 10.1016/j.biopsych.2017.08.012.

Boulanger, J. J., & Messier, C. (2017). Oligodendrocyte progenitor cells are paired with GABA neurons in the mouse dorsal cortex: Unbiased stereological analysis. Neuroscience. doi: http://dx.doi.org/10.1016/j.neuroscience.2017.08.018.

Farrand, A. Q., Helke, K. L., Gregory, R. A., Gooz, M., Hinson, V. K., & Boger, H. A. (2017). Vagus nerve stimulation improves locomotion and neuronal populations in a model of Parkinson’s disease. Brain Stimulation. doi: https://doi.org/10.1016/j.brs.2017.08.008.

Figueiredo, T. H., Harbert, C. L., Pidoplichko, V., Almeida-Suhett, C. P., Pan, H., Rossetti, K., . . . Marini, A. M. (2017). Alpha-Linolenic Acid Treatment Reduces the Contusion and Prevents the Development of Anxiety-Like Behavior Induced by a Mild Traumatic Brain Injury in Rats.  Molecular Neurobiology. doi: 10.1007/s12035-017-0732-y.

Guan, J., Yang, B., Fan, Y., & Zhang, J. (2017). GPER Agonist G1 Attenuates Neuroinflammation and Dopaminergic Neurodegeneration in Parkinson Disease. Neuroimmunomodulation, 0(0), 60-66.

Loris, Z. B., Hynton, J. R., Pieper, A. A., & Dietrich, W. D. (2017). Beneficial Effects of Delayed P7C3-A20 Treatment After Transient MCAO in Rats. Translational Stroke Research. doi: 10.1007/s12975-017-0565-z.

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Researchers cited MBF Bioscience systems in 32 papers between 08/11/2017 and 08/18/2017

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Bazzigaluppi, P., Beckett, T. L., Koletar, M. M., Lai, A. Y., Joo, I. L., Brown, M. E., . . . Stefanovic, B. (2017). Early stage attenuation of phase amplitude coupling in the hippocampus and medial prefrontal cortex in a transgenic rat model of AD. Journal of Neurochemistry, n/a-n/a. doi: 10.1111/jnc.14136.

Bull, C., Cooper, C., Lindahl, V., Fitting, S., Persson, A. I., Grandér, R., . . . Blomgren, K. (2017). Exercise in Adulthood after Irradiation of the Juvenile Brain Ameliorates Long-Term Depletion of Oligodendroglial Cells. Radiation Research, 0(0), null. doi: 10.1667/rr14737.1.

Edler, M. K., Sherwood, C. C., Meindl, R. S., Hopkins, W. D., Ely, J. J., Erwin, J. M., . . . Raghanti, M. A. (2017). Aged chimpanzees exhibit pathologic hallmarks of Alzheimer’s disease. Neurobiology of Aging. doi: http://dx.doi.org/10.1016/j.neurobiolaging.2017.07.006.

Fernandez, G. M., & Savage, L. M. (2017). Adolescent binge ethanol exposure alters specific forebrain cholinergic cell populations and leads to selective functional deficits in the prefrontal cortex. Neuroscience. doi: https://doi.org/10.1016/j.neuroscience.2017.08.013.

Hong, J., Wang, L., Zhang, T., Zhang, B., & Chen, L. (2017). Sigma-1 receptor knockout increases α-synuclein aggregation and phosphorylation with loss of dopaminergic neurons in substantia nigra. Neurobiology of Aging. doi: https://doi.org/10.1016/j.neurobiolaging.2017.08.007.

Li, W.-Y., Wang, Y., Zhai, F.-G., Sun, P., Cheng, Y.-X., Deng, L.-X., & Wang, Z.-Y. (2017). AAV-KLF7 Promotes Descending Propriospinal Neuron Axonal Plasticity after Spinal Cord Injury. Neural Plasticity, 2017.

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Researchers cited MBF Bioscience systems in 12 papers during the week of 07/10/2017

Stereo Investigator:

Abdurakhmanova, S., Chary, K., Kettunen, M., Sierra, A., & Panula, P. (2017). Behavioral and stereological characterization of Hdc KO mice: relation to Tourette syndrome. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24279. http://dx.doi.org/10.1002/cne.24279

Filice, F., Celio, M. R., Babalian, A., Blum, W., & Szabolcsi, V. (2017). Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24276. http://dx.doi.org/10.1002/cne.24276

Han, S.-W., Kim, Y.-C., & Narayanan, N. S. (2017). Projection targets of medial frontal D1DR-expressing neurons. Neuroscience Letters. doi: http://dx.doi.org/10.1016/j.neulet.2017.06.057http://www.sciencedirect.com/science/article/pii/S0304394017305487

Lee, J. Q., Sutherland, R. J., & McDonald, R. J. (2017). Hippocampal damage causes retrograde but not anterograde memory loss for context fear discrimination in rats. Hippocampus, n/a-n/a. doi: 10.1002/hipo.22759. http://dx.doi.org/10.1002/hipo.22759

Ma, E. L., Smith, A. D., Desai, N., Cheung, L., Hanscom, M., Stoica, B. A., . . . Faden, A. I. (2017). Bidirectional brain-gut interactions and chronic pathological changes after traumatic brain injury in mice. Brain, Behavior, and Immunity. doi: http://dx.doi.org/10.1016/j.bbi.2017.06.018http://www.sciencedirect.com/science/article/pii/S0889159117302076

Mahar, I., Labonte, B., Yogendran, S., Isingrini, E., Perret, L., Davoli, M. A., . . . Mechawar, N. (2017). Disrupted hippocampal neuregulin-1/ErbB3 signaling and dentate gyrus granule cell alterations in suicide. [Original Article]. Transl Psychiatry, 7, e1161. doi: 10.1038/tp.2017.132. http://dx.doi.org/10.1038/tp.2017.132

Shyng, C., Nelvagal, H. R., Dearborn, J. T., Tyynelä, J., Schmidt, R. E., Sands, M. S., & Cooper, J. D. (2017). Synergistic effects of treating the spinal cord and brain in CLN1 disease. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1701832114. http://www.pnas.org/content/early/2017/06/27/1701832114.abstract

Venezia, S., Refolo, V., Polissidis, A., Stefanis, L., Wenning, G. K., & Stefanova, N. (2017). Toll-like receptor 4 stimulation with monophosphoryl lipid A ameliorates motor deficits and nigral neurodegeneration triggered by extraneuronal α-synucleinopathy. [journal article]. Molecular Neurodegeneration, 12(1), 52. doi: 10.1186/s13024-017-0195-7. http://dx.doi.org/10.1186/s13024-017-0195-7

Neurolucida:

Morecraft, R. J., Binneboese, A., Stilwell-Morecraft, K. S., & Ge, J. (2017). Localization of Orofacial Representation in the Corona Radiata, Internal Capsule and Cerebral Peduncle in Macaca mulatta. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24275. http://dx.doi.org/10.1002/cne.24275

Santello, M., Bisco, A., Nevian, N. E., Lacivita, E., Leopoldo, M., & Nevian, T. (2017). The brain-penetrant 5-HT7 receptor agonist LP-211 reduces the sensory and affective components of neuropathic pain. Neurobiology of Disease. doi: http://dx.doi.org/10.1016/j.nbd.2017.07.005http://www.sciencedirect.com/science/article/pii/S0969996117301584

Scott, B. H., Saleem, K. S., Kikuchi, Y., Fukushima, M., Mishkin, M., & Saunders, R. C. (2017). Thalamic connections of the core auditory cortex and rostral supratemporal plane in the macaque monkey. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24283. http://dx.doi.org/10.1002/cne.24283

Biolucida:

Sakano, H., Zorio, D. A. R., Wang, X., Ting, Y. S., Noble, W. S., MacCoss, M. J., . . . Wang, Y. (2017). Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24281. http://dx.doi.org/10.1002/cne.24281

Researchers cited MBF systems in 29 papers between 6/30/2017 to 7/14/2017

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Abdurakhmanova, S., Chary, K., Kettunen, M., Sierra, A., & Panula, P. (2017). Behavioral and stereological characterization of Hdc KO mice: relation to Tourette syndrome. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24279.

Arathoon, L. R., Gleave, J. A., Trinh, D., Lizal, K. E., Giguère, N., Barber, J. H. M., . . . Nash, J. E. (2017). Sirtuin 3 rescues neurons through the stabilisation of mitochondrial biogenetics in the virally-expressing mutant α-synuclein rat model of parkinsonism. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.06.009.

Chen, L., Wang, X., Lin, Z.-X., Dai, J.-G., Huang, Y.-F., & Zhao, Y.-N. (2017). Preventive Effects of Ginseng Total Saponins on Chronic Corticosterone-Induced Impairment in Astrocyte Structural Plasticity and Hippocampal Atrophy. Phytotherapy Research, n/a-n/a. doi: 10.1002/ptr.5859.

Collette, J. C., Choubey, L., & Smith, K. M. (2017). ­Glial and stem cell expression of murine Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system. PeerJ, 5, e3519. doi: 10.7717/peerj.3519.

Filice, F., Celio, M. R., Babalian, A., Blum, W., & Szabolcsi, V. (2017). Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24276.

Finkelstein, D. I., Billings, J. L., Adlard, P. A., Ayton, S., Sedjahtera, A., Masters, C. L., . . . Cherny, R. A. (2017). The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson’s disease. Acta Neuropathologica Communications, 5(1), 53. doi: 10.1186/s40478-017-0456-2.

Han, S.-W., Kim, Y.-C., & Narayanan, N. S. (2017). Projection targets of medial frontal D1DR-expressing neurons. Neuroscience Letters. doi: http://dx.doi.org/10.1016/j.neulet.2017.06.057.

Lee, J. Q., Sutherland, R. J., & McDonald, R. J. (2017). Hippocampal damage causes retrograde but not anterograde memory loss for context fear discrimination in rats. Hippocampus, n/a-n/a. doi: 10.1002/hipo.22759.

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Researchers cited MBF systems in 8 papers during the week of 06/19/2017

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Kaur, C., Pal, I., Saini, S., Jacob, T. G., Nag, T. C., Thakar, A., . . . Roy, T. S. (2017). Comparison of unbiased stereological estimation of total number of cresyl violet stained neurons and parvalbumin positive neurons in the adult human spiral ganglion. Journal of Chemical Neuroanatomy. doi: https://doi.org/10.1016/j.jchemneu.2017.06.004.

Mani, B. K., Osborne-Lawrence, S., Mequinion, M., Lawrence, S., Gautron, L., Andrews, Z. B., & Zigman, J. M. (2017). The role of ghrelin-responsive mediobasal hypothalamic neurons in mediating feeding responses to fasting. Molecular Metabolism. doi: 10.1016/j.molmet.2017.06.011. http://dx.doi.org/10.1016/j.molmet.2017.06.011

Martinez, E. M., Young, A. L., Patankar, Y. R., Berwin, B. L., Wang, L., von Herrmann, K. M., . . . Havrda, M. C. (2017). Nlrp3 is required for inflammatory changes and nigral cell loss resulting from chronic intragastric rotenone exposure in mice. Toxicological Sciences. https://academic.oup.com/toxsci/article-abstract/doi/10.1093/toxsci/kfx1…

Po, K. K.-t., Leung, J. W.-h., Chan, J. N.-m., Fung, T. K.-h., Sánchez-Vidaña, D. I., Sin, E. L.-l., . . . Siu, A. M.-h. (2017). Protective effect of Lycium Barbarum polysaccharides on dextromethorphan-induced mood impairment and neurogenesis suppression. Brain Research Bulletin, 134, 10-17. doi: https://doi.org/10.1016/j.brainresbull.2017.06.014.  Continue reading “Researchers cited MBF systems in 8 papers during the week of 06/19/2017” »

Researchers cited MBF systems in 25 papers between 6/10/2017 and 6/16/2017

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Arawaka, S., Sato, H., Sasaki, A., Koyama, S., & Kato, T. (2017). Mechanisms underlying extensive Ser129-phosphorylation in α-synuclein aggregates. Acta Neuropathologica Communications, 5(1), 48.

Birkl, C., Carassiti, D., Hussain, F., Langkammer, C., Enzinger, C., Fazekas, F., . . . Ropele, S. (2017). Assessment of ferritin content in multiple sclerosis brains using temperature-induced R*2 changes. Magnetic Resonance in Medicine, n/a-n/a. doi: 10.1002/mrm.26780.

Boudewyn, L. C., Sikora, J., Kuchar, L., Ledvinova, J., Grishchuk, Y., Wang, S. L., . . . Walkley, S. U. (2017). N-butyl-deoxynojirimycin delays motor deficits, cerebellar microgliosis, and Purkinje cell loss in a mouse model of mucolipidosis type IV. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.06.003.

Chaves, P. P., Valdoria, C. M., Amorim, M. C. P., & Vasconcelos, R. O. (2017). Ontogenetic development of the inner ear saccule and utricle in the Lusitanian toadfish: Potential implications for auditory sensitivity. Hearing Research. doi: https://doi.org/10.1016/j.heares.2017.06.008.

Ebenezer, G. J., Liu, Y., Judge, D. P., Cunningham, K., Truelove, S., Carter, N. D., . . . Polydefkis, M. (2017). Cutaneous nerve biomarkers in transthyretin familial amyloid polyneuropathy. Annals of Neurology, n/a-n/a. doi: 10.1002/ana.24972.

Fischer, D. L., Kemp, C. J., Cole-Strauss, A., Polinski, N. K., Paumier, K. L., Lipton, J. W., . . . Sortwell, C. E. (2017). Subthalamic Nucleus Deep Brain Stimulation Employs TrkB Signaling for Neuroprotection and Functional Restoration. The Journal of Neuroscience.

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Researchers cited MBF systems in 25 papers between 5/27/2017 and 6/9/2017

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Bastidas, J., Athauda, G., De La Cruz, G., Chan, W.-M., Golshani, R., Berrocal, Y., . . . Pearse, D. D. (2017). Human schwann cells exhibit long-term cell survival, are not tumorigenic and promote repair when transplanted into the contused spinal cord. Glia, n/a-n/a. doi: 10.1002/glia.23161.

Claflin, D. I., Schmidt, K. D., Vallandingham, Z. D., Kraszpulski, M., & Hennessy, M. B. (2017). Influence of postnatal glucocorticoids on hippocampal-dependent learning varies with elevation patterns and administration methods. Neurobiology of Learning and Memory. doi: https://doi.org/10.1016/j.nlm.2017.05.010.

Dioli, C., Patricio, P., Trindade, R., Pinto, L. G., Silva, J. M., Morais, M., . . . Sotiropoulos, I. (2017). Tau-dependent suppression of adult neurogenesis in the stressed hippocampus.  Molecular Psychiatry. doi: 10.1038/mp.2017.103.

Giesert, F., Glasl, L., Zimprich, A., Ernst, L., Piccoli, G., Stautner, C., . . . Wurst, W. (2017). The pathogenic LRRK2 R1441C mutation induces specific deficits modeling the prodromal phase of Parkinson’s disease in the mouse. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.05.013.

Gumusoglu, S. B., Fine, R. S., Murray, S. J., Bittle, J. L., & Stevens, H. E. (2017). The role of IL-6 in neurodevelopment after prenatal stress. Brain, Behavior, and Immunity. doi: https://doi.org/10.1016/j.bbi.2017.05.015.

Issa, J. P. M., Trawitzki, B. F., Ervolino, E., Macedo, A. P., & Lilge, L. (2017). Low-intensity laser therapy efficacy evaluation in FVB mice subjected to acute and chronic arthritis. [journal article]. Lasers in Medical Science, 1-9. doi: 10.1007/s10103-017-2235-5.

Liu, H., Rose, M. E., Ma, X., Culver, S., Dixon, C. E., & Graham, S. H. (2017). In vivo transduction of neurons with TAT-UCH-L1 protects brain against controlled cortical impact injury. Plos one, 12(5), e0178049. doi: 10.1371/journal.pone.0178049.

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Researchers cited MBF systems in 25 papers between 5/16/2017 and 5/26/2017

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Baxter, V. K., Glowinski, R., Braxton, A. M., Potter, M. C., Slusher, B. S., & Griffin, D. E. (2017). Glutamine antagonist-mediated immune suppression decreases pathology but delays virus clearance in mice during nonfatal alphavirus encephalomyelitis. Virology, 508, 134-149. doi: https://doi.org/10.1016/j.virol.2017.05.013.

Brzozowska, N. I., Smith, K. L., Zhou, C., Waters, P. M., Cavalcante, L. M., Abelev, S. V., . . . Arnold, J. C. (2017). Genetic deletion of P-glycoprotein alters stress responsivity and increases depression-like behavior, social withdrawal and microglial activation in the hippocampus of female mice. Brain, Behavior, and Immunity. doi: https://doi.org/10.1016/j.bbi.2017.05.008.

Chareyron, L. J., Banta Lavenex, P., Amaral, D. G., & Lavenex, P. (2017). Functional organization of the medial temporal lobe memory system following neonatal hippocampal lesion in rhesus monkeys. Brain Structure and Function, 1-16. doi: 10.1007/s00429-017-1441-z.

Kwan, T., Floyd, C. L., Patel, J., Mohaimany-Aponte, A., & King, P. H. (2017). Astrocytic expression of the RNA regulator HuR accentuates spinal cord injury in the acute phase. Neuroscience Letters, 651, 140-145. doi: https://doi.org/10.1016/j.neulet.2017.05.003.

Newville, J., Valenzuela, C. F., Li, L., Jantzie, L. L., & Cunningham, L. A. (2017). Acute oligodendrocyte loss with persistent white matter injury in a third trimester equivalent mouse model of fetal alcohol spectrum disorder. Glia, n/a-n/a. doi: 10.1002/glia.23164.

Onger, M. E., Kaplan, S., Geuna, S., Türkmen, A. P., Muratori, L., Altun, G., & Altunkaynak, B. Z. (2017). Possible effects of some agents on the injured nerve in obese rats: A stereological and electron microscopic study. Journal of Cranio-Maxillofacial Surgery. doi: https://doi.org/10.1016/j.jcms.2017.05.004.

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Researchers cited MBF systems in 17 papers during the week of 05/08/2017

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Day, N. L., Carle, M. S., & Floyd, C. L. (2017). Post-injury administration of a combination of memantine and 17β-estradiol is protective in a rat model of traumatic brain injury. Neurochemistry International. doi: https://doi.org/10.1016/j.neuint.2017.04.018.

El-Agnaf, O., Overk, C., Rockenstein, E., Mante, M., Florio, J., Adame, A., . . . Rissman, R. A. (2017). Differential effects of immunotherapy with antibodies targeting α-synuclein oligomers and fibrils in a transgenic model of synucleinopathy. Neurobiology of Disease, 104, 85-96. doi: https://doi.org/10.1016/j.nbd.2017.05.002.

Matsuda, W., Ehara, A., Nakadate, K., Yoshimoto, K., & Ueda, S. (2017). Effects of environmental enrichment on the activity of the amygdala in micrencephalic rats exposed to a novel open field. Congenital Anomalies, n/a-n/a. doi: 10.1111/cga.12228.

Musacchio, T., Rebenstorff, M., Fluri, F., Brotchie, J. M., Volkmann, J., Koprich, J. B., & Ip, C. W. (2017). STN-DBS is neuroprotective in the A53T α-synuclein Parkinson’s disease rat model. Annals of Neurology, n/a-n/a. doi: 10.1002/ana.24947.

Soares, J. I., Valente, M. C., Andrade, P. A., Maia, G. H., & Lukoyanov, N. V. (2017). Reorganization of the septohippocampal cholinergic fiber system in experimental epilepsy. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24235.

Yoshii, Y., Inoue, T., Uemura, Y., Iwasaki, Y., Yada, T., Nakabeppu, Y., & Noda, M. (2017). Complexity of Stomach–Brain Interaction Induced by Molecular Hydrogen in Parkinson’s Disease Model Mice. Neurochemical Research, 1-8. doi: 10.1007/s11064-017-2281-1.  Continue reading “Researchers cited MBF systems in 17 papers during the week of 05/08/2017” »