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INSTITUTIONAL COMMITMENT

The institution has committed the following in direct support of the IDDRC (Please see letter of support from Bryan Wolfe, Chief Scientific Officer, Children’s Hospital of Philadelphia Research Institute which has been added as an attachment to the Research Plan Overall):

During the next five years:

The Children’s Research Institute has agreed to provide $85,000/yr as a cost-share. This funding will beplaced in a separate account under the supervision of the Center Directorate.

The Children’s Research Institute has agreed to purchase (FY 2016) the following equipment: (a) FlowView Olympus Confocal Microscope/software ($387,000); (b) Gas-Bench II Thermo Electron isotope ratio-mass spectrometer ($209,000); (c) Tandem mass spectrometer ($750,000).

The Children’s Research Institute has agreed to allow 3 cost-shares ($11,236 directs each) to partiallysupport the efforts of Drs. Yudkoff, Schultz and Roberts. The costs for these cost shares will come fromtheir endowed Chairs

Dr. Yudkoff’s endowed chair provides deficit support (~ $20,000/yr) for the Monthly IDDRC Seminar series. CHOP provides $100,000/yr to supplement salaries of clinicians seeking training in IDD-related research The Neuroscience Affinity group (Directed by Michael B. Robinson, Center Co Director) receives $25,000

to help support the costs of service contracts, seminar speakers, and outside reviewers/consultants. The Children’s Research Institute has agreed to support for salary (20% effort) for the Administrative

Assistant who helps to manage the “Training Program in Neurodevelopmental Disabilities”. Support for 10% effort for Dr. Robinson for his role as program director of the T32

In addition, the institution provided us (2014) with $100,000 to support preliminary research for our research project (MEG Studies of Auditory Processing in Minimally/Non-Verbal Children with ASD and Intellectual Disability”; Timothy Roberts, PhD, PI).

GENERAL INFORMATION The Children’s Hospital of Philadelphia (CHOP) is the oldest institution in the country dedicated to the care of children, and the University of Pennsylvania is the first University in the United States. CHOP provides tertiary care for a catchment area that includes 12,000,000 people. Annually, CHOP receives approximately 28,200 inpatient admissions, 86,100 emergency room visits, and over 1 million outpatient visits. A search of the electronic health records at CHOP yields 181,446 unique patients with intellectual or developmental disabilities (IDDS) (Identified using ICD-9 codes for autism spectrum disorder, attention-deficit hyperactivity disorder, intellectual disability, language delay, etc).

The Division of Neurology has about 17,000 outpatient visits per year in 7 locations, about 2000 inpatient admission and an equal number of inpatient consultations. The Division of Metabolism hosts about 3,000 outpatient visits annually. The Regional Autism Center follows over 3,000 children with autism spectrum disorders. Approximately 7,800 children with attention deficit disorder annually visit CHOP outpatient facilities. The CHOP Care Network currently has 60 locations, including 31 Primary Care sites, 15 Specialty Care & Surgery Centers, 3 Urgent Care Centers and 11 Newborn & Pediatric Inpatient Care sites (pediatric inpatient units at affiliated community hospitals). Patient care activities have experienced rapid growth over the past 5 years. The hospital currently has 527 beds to provide a range of inpatient, emergency and outpatient care. CHOP admitted more than 31,000 children in 2014. Its emergency department treatment recorded almost 90,000 visits. Also, the Buerger Center for Advanced Pediatric Care, opening in July 2015, will be the nation’s most state-of-the-art facility for outpatient medicine.

CHOP is consistently recognized as a national leader for advancement of healthcare for children and proudly shares the No. 1 ranking on U.S. News & World Report’s 2014-15 Honor Roll of the nation’s Best Children’s Hospitals. Recent surveys by U.S. News & World Report rated several subspecialty areas and CHOP has ranked in the top four in all ten specialties. For example, in the last survey reported in 2014, two programs were rated #1 (Neonatology and Pulmonology) and three were rated #2 (Cancer, Diabetes & Endocrinology and Neurology & Neurosurgery). Thus, by both fact-based and reputation-based surveys conducted in the past ~5 years, both CHOP and its individual subspecialty programs have consistently been rated the best in the nation. Also, Parents magazine named CHOP No. 1 on its 2013 list of Top 10 Best Children’s Hospitals. CHOP was also awarded Magnet status by the American Nurses Credentialing Center (ANCC)—an achievement met by only 6 percent of hospitals in the United States.

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The University of Pennsylvania Perelman School of Medicine, established in 1765, was the first medical school in the 13 American colonies. Several of the Clinical Practices at the University of Pennsylvania Health System consistently makes the National Honor Roll (U.S. News and World Report), currently ranked #7 overall. The Medical School employs over 2,000 full-time faculty, has twenty-eight departments with numerous divisions and more than 24 Institutes and Research Centers. At this time, the Medical Center campus includes approximately 900,000 sq. ft. of research space. These two institutions provide the home for this Intellectual and developmental Disabilities Research Center. Unlike most other University/Children’s Hospitals, these two institutions reside on contiguous city blocks just west of downtown Philadelphia.

This is a map of the University of Pennsylvania with the Children’s Hospital of Philadelphia’s buildings colored in pale blue. Part of the space in CHOP (1st red arrow), the Abramson Research Center (2nd red arrow), and the Colket Translational Research Building (3rd red arrow) house most of the cores for this IDDRC.

Currently, the Children’s Hospital of Philadelphia has nearly 800,000 gross square feet of research space (84,500 square feet of animal facilities). It manages over 200 million dollars in total research support with 121 million coming from the NIH.

The newly named Raymond G. Perelman Campus includes CHOP’s most state-of-the-art research and clinical facilities: the Ruth and Tristram Colket Jr. Translational Research Building and the Buerger Center for Advanced Pediatric Care. The Colket Translational Research Building opened in 2009 and includes 773,000

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square feet of space—289,000 of which is devoted to research—and currently stands at 11 stories. This building is designed to expand vertically to 23 stories to account for future growth. This facility is home to 45 NIH-funded faculty members and 500 CHOP employees who will occupy wet-bench space on 4 floors. In 2008 a vivarium of ~ 250,000 square feet opened on 4 below-grade floors. The vivarium includes CHOP’s new barrier facility for pathogen-free rodent breeding colonies and immunocompromised rodent strains. The vivarium also includes 17,500 square feet to house non-human primates primary being used with the goal of developing an vaccine directed to HIV. The building is designed to expand to 23 stories in order to accommodate future needs for research growth. Currently, the University of Pennsylvania has over 2 million square feet of research space. Built on its strong tradition in academic medicine and its recent emphasis on fundamental investigation and translational research, the University of Pennsylvania is currently an extremely exciting research environment. Penn Medicine is consistently among the top recipients of funding from the National Institutes of Health. In 2010, the 10-story Smilow Center for Translational Research was completed and includes 531,000 gross square feet of space to support biomedical and translational research. These resources and the commitment to further growth would seemingly make this an ideal location for one of the 15 nationally supported IDDRCs. Research: CHOP has a long and distinguished tradition of basic, translational and clinical research. CHOP has the third largest pediatric research program in the country and was the first children's hospital to initiate a pediatric research department, now known as the Children’s Hospital of Philadelphia Research Institute (formerly the Joseph Stokes Jr. Research Institute). In 1995, CHOP centralized laboratory research from across all CHOP divisions and departments in the Leonard and Madlyn Abramson Pediatric Research Center (ARC). The ARC is a state-of-the-art research facility with over 500,000 gsf, the largest freestanding pediatric research center in the country. The next phase of CHOP'S growth in laboratory research was the construction of a new, freestanding research building across the street from the ARC that has an expanded laboratory animal facility that accommodate non-human primates, principally for AIDS vaccine research, as well as an additional 200,000 gsf of additional laboratory research modules, offices, cores and support services. This building named the Ruth and Tristram Colket Jr. Translational Research Building has the capability of expanding upward to expand our research space by an additional 23 stories. To support the "bench to bedside" philosophy, CHOP has an active and growing research program with many funded programs and clinical centers for children with specialty health needs. More than 300 investigators conduct research through more than 1,200 human (IRB approved) and animal (IACUC approved) research protocols. The research is broadly based and includes studies to understand the basic mechanisms of biological functions and human diseases, as well as testing new drugs, devices, vaccines and other biological agents for safety and efficacy. Larger programmatic areas of investigation include AIDS, cardiac diseases, childhood cancer, cystic fibrosis, diabetes, hemophilia, hypercholesterolemia, hyperinsulinism, mental retardation, neonatal seizures, nutritional disorders, sickle cell diseases, and a number of other major disorders and diseases that affect children. All research activities at CHOP are organized administratively under the JSRI. Dr. Bryan A. Wolf is the Chief Scientific Officer, Dr. Tom Curran is Deputy Scientific Director, Dr. Dennis Durban is Director of Clinical and Translational Research, and Mary Tomlinson is Senior Vice President of Research Administration. An Executive Committee is made up of the Six Department Chairs and Five Research Directors or at-large members. This committee together with the Board of Trustees provides a structure of governance and accountability. CHOP Research Institute Research Core Facilities High-throughput Sequencing Core: The High-Throughput Sequencing (HTS) Core at CHOP and the Beijing Genomics Institute have formed a collaborative genome center called BGI@CHOP. Together, these elements for the HTS Core offer increased capacity, expertise and analytical resources for conducting next-generation sequencing studies. The HTS Core provides automated library construction and high-quality, high-throughput sequencing services for whole genome, whole exome, RNA-SEQ, and ChIP-SEQ. BGI@CHOP Exome workflow passed CAP inspection in April 2014. Biorepository Core: The Biorepository Core collects and organizes biospecimens from investigators across the Research Institute. With a capacity for approximately 7 million samples, the facility is designed to house all of the biospecimens available at CHOP, avoiding specimen duplication, preserving precious biomaterials, and

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providing broad access to data and materials. Initial sample collection focuses on DNA samples, but the facility can also safely store fluids, RNA, tissue samples, and a number of other biospecimens. Biostatistics and Data Management Core (BDMC): The BDMC supports the biostatistical and data management needs from virtually all subspecialties of pediatric medicine and supports studies ranging from narrowly defined basic science projects to large, multi-site clinical trials. The BDMC supports more than 25 funded studies and collaborates with investigators on numerous grant applications each year. It is staffed by a full-time Scientific Director, a Deputy Director, biostatistics and data management/information technology managers, and 15 additional staff members representing the disciplines of biostatistics, data management, and information technology. The BDMC’s Biostatistics subcore provides consultative and analytic support services to investigators interested in basic, pre-clinical, clinical, and epidemiological pediatric studies. The Data Management/Information Technology (DM/IT) subcore provides a selection of services ranging from consultation through full-service data management. Clinical Research Support Office (CRSO): The CRSO assists in the start-up, execution, and completion of clinical research projects, in compliance with local and federal requirements. The office maintains a staff of well-trained study coordinators and project managers who can be assigned to support any type of clinical research study at CHOP. The CRSO Navigator is available to assist/guide investigators with any questions that arise during the design, start up, and execution of their clinical studies. The CRSO is also available to assist investigators with budget preparation, IRB submissions, and IND and IDE applications to the Food and Drug Administration. The CRSO maintains a highly trained staff with expertise on good clinical practices of clinical research, which ensures that study teams comply with all relevant regulatory requirements. Flow Cytometry Core: This core provides access to flow cytometry equipment and analysis software for trained personnel from individual research labs on a fee-for-service basis. The core assists users in the design of experimental protocols that require various flow cytometric methods. The laboratory is capable of both sample preparation and analyses in support of individual research efforts and offers specialized services such as training and mutiparametric cell sorting. Nucleic Acid PCR Core (NAPCore): The NAPCore provides a centralized source for specialized services, technical expertise, and reagents to support the needs of molecular biology investigators. These services include Sanger DNA sequencing, small-scale next-generation sequencing and library assistance, fluorescent fragment analysis (MLPA and microsatellite analysis), microarrays, real-time PCR, oligonucleotide ordering, and sample quality control assessment. While production-level NGS is performed by BGI@CHOP, the NAPCore has additional resources for smaller-scale projects and Sanger sequence validation. The facility has MiSeq and Ion Torrent PGM sequencers, and two electrophoresis units along with support equipment for library preparation, emulsion PCR and bead enrichment. Pathology Core: The Pathology Core provides basic histopathology, immunohistochemistry, tissue microarray, and laser capture microdissection services to researchers at CHOP and within the surrounding academic community. The core offers a full range of histopathology services, including tissue processing, embedding, and cutting for both paraffin and frozen tissue. The core also performs most standard stains as well as immunohistochemistry, antibody workup, fluorescence in situ hybridization, and TUNEL. Tissue microarrays can be constructed, and sophisticated imaging instrumentation is available for virtual microscopy and image analysis. Specialized software is available for image analysis, and to manage and store array data. Protein and Proteomics Core: The Protein and Proteomics Core Facility addresses the growing need for the technological resources to identify, produce, and characterize new proteins. It provides a variety of services for investigators at CHOP, Penn, and outside institutions. These services include producing and characterizing proteins, investigating protein-protein interactions, and characterizing whole proteomes. Some services are provided on a user-operated, sign-up basis, whereas others are performed as full-service by the dedicated facility personnel. The core has a full range of equipment needed for protein production and biochemical and cell biological experiments, specialized instrumentation and computational capabilities necessary for state-of-the-art proteomics experiments, its own computing infrastructure and a variety of software. Laboratory Animal Facility (LAF): The CHOP Research Institute has two laboratory animal facilities (LAFs), one located in the ARC and the other in the CTRB. The LAFs provide care, housing, husbandry, and veterinary care for CHOP’s animal colonies. Accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC), the LAFs ensure humane care and use of animals, including training,

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compliance oversight, administration and operations, clinical veterinary services, and animal husbandry. The LAFs work closely with the Institutional Animal Care and Use Committee (IACUC) to ensure that CHOP’s animal care and use program supports research, while simultaneously adhering to the regulations that govern the use of animals and the principles that underlie the ethical use of animals in research. Small Animal Imaging Facility: The Small Animal Imaging Facility is a state-of-the-art lab that satisfies investigators' imaging needs in a "clean" environment necessary for longitudinal studies. The facility is open to all CHOP and Penn investigators whose animals are housed in the facility. Services include MRI, PET-CT, SPECT-CT, Optical Imaging, Ultrasound, and NMR/Microimaging. NMR/Microimaging Services at CHOP feature a 400 MHz (9.4Tesla) high-resolution wide-bore spectrometer equipped with a HP computer. The system can perform most of the traditional high-resolution NMR experiments as well as microimaging of specimens and small models. The services are available not only to CHOP investigators but also to investigators affiliated with large center program or private research institutions. Transgenic Mouse Core: The Transgenic Mouse Core enables investigators to generate transgenic and chimeric mouse lines in-house without quarantine delays. An in vitro fertilization service is available to overcome any breeding problems that can impact valuable mouse lines. Providing a single male mouse enables the core to fertilize embryos in vitro, and the resulting fertilized embryos can then be transferred into surrogate mother mice or cryopreserved. Other services include production of transgenic mice by microinjection of DNA directly into embryonic stem cell nuclei; generation of knockout mice by microinjection of modified ES cells into blastocysts; mouse line rederivation; and embryo and sperm cryopreservation. Bioanalytical Core: The Bioanalytical Core specializes in developing and validating robust liquid chromatography/tandem mass spectrometry methods for the analysis of natural products, drugs, and metabolites in various biological samples (blood, dried blood spots, plasma, urine, and tissue). With extensive experience in method development and validation, the core performs method validations, partial validations, cross-matrix validations, or combinations required to meet project needs. Validation studies are performed in accordance with the US Food and Drug Administration Guidance for Industry, Bioanalytical Method Validation. The core has developed assays for investigational and marketed drugs used for pain, oncology, cardiology, and infectious diseases. These assays are typically used to support pediatric drug discovery and development. Metabolomics Core: The Metabolomic Core provides investigators with a resource that facilitates the analysis of major metabolic pathways in humans, animals, and in vitro systems. The analytical repertoire includes the measurement – both in vivo and in vitro – of flux through major pathways of intermediary metabolism, including glycolysis, the tricarboxylic acid cycle, the oxidation of fatty acids and amino acids, the urea cycle and protein synthesis and degradation; determination of in vivo metabolic rate in freely moving organisms; and determination of selected drugs and/or drug metabolites with triple-stage quadruple mass spectrometry. Stem Cell Core: The Stem Cell Core provides expertise and quality-control reagents for the culture and differentiation of human embryonic stem cells (ESCs) and human induced pluripotent stem cells (iPSCs) for the CHOP and Penn communities. The facility maintains five of the new NIH-approved human ESC lines and several human iPSC lines. Healthcare Analytics Unit (HAU) Core: A service unit of two centers at CHOP (CPCE and PolicyLab), the HAU serves as a resource for investigators who want to use administrative or other existing data to answer research questions; offers programmer/analysts services to pull, clean, manage, model, and analyze data; and provides the expertise of the center's faculty members with their advanced training in clinical epidemiology and public health. The unit supports and provides access to several databases. Research IS Web Services Core: The Research IS Web Services Core designs and supports web sites for investigators, labs, studies, core facilities, outreach programs, Research Affinity Groups, and Centers of Emphasis, as well as providing web development for Research Administration. The team develops a variety of client-side and database-driven web applications, including search and data gathering functionality, custom login and access restriction, and more. Web Services posts new content and site updates daily as part of their service to internal clients. In addition, the team provides development support to, and day-to-day administration of, Institute-wide web presences, including the Research Institute public website, the Research Institute intranet, and the Share (Wiki) collaborative environment. Viral Vector Cores: As part of the Center for Cellular and Molecular Therapeutics, the Research Vector Core

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has expanded its capacity to provide infrastructure support for investigators interested in using viral vectors in their research model systems. The Clinical Vector Core uses a patented vector production technology and a highly efficient purification process that utilizes combined column and gradient centrifugation-based process steps. This system has manufactured clinical grade AAV vectors that have demonstrated excellent safety in several clinical studies. CHOP-Research Institute Centers of Emphasis The following centers are directly related to the activities of the IDDRC. Several of these centers have been developed during the past five years and dramatically expand the research opportunities available to our scientific community. Center for Applied Genomics (CAG): The CAG develops new and better ways to diagnose and treat children affected by complex medical disorders by translating basic research findings into medical innovations. CAG aims to discover the genetic causes of both common and rare childhood diseases, including autism, epilepsy, schizophrenia, diabetes, and pediatric cancer. Ultimately, CAG’s objective is to discover genetic markers to accurately diagnose patient subsets with genetic abnormalities that guide physicians to the most appropriate therapies. CAG is one of the world's largest genetics research programs, and the only center at a pediatric hospital to have large-scale access to state-of-the-art high-throughput genotyping and sequencing technology. It operates one of the world’s largest whole exome and whole genome sequencing laboratories, which has led to numerous discoveries to elucidate the causes of pediatric disease. Center for Autism Research (CAR): The CAR coordinates and supports research into the causes of the autism spectrum disorders (ASDs). The CAR research programs are predicated on the theory that effective treatments will follow from a better understanding of causal mechanisms. CAR establishes a broad-based research program aimed at fundamental discoveries into causes of ASDs. CAR establishes programs of research focused on developmental, neurobiological, and genetic mechanisms of the ASDs, with a particular emphasis on understanding the individual differences across the spectrum. CAR faculty also engage in research to evaluate the current standard of care for patients with an ASD and to test the effectiveness of promising new treatments. Department of Biomedical and Health Informatics (DBHi): The Department of Biomedical and Health Informatics (DBHi) is the home for the development of innovative solutions to healthcare's immediate and long-term informatics needs. DBHi provides the expertise and infrastructure needed to maximize the value of information relevant to all biomedical research activities occurring at CHOP. This endeavor blends the disciplines of bioinformatics and clinical informatics, which themselves require excellence in and integration of various knowledge domains, including biology, medicine, statistics, mathematics, linguistics, and computer science. The aim of CMBI is to empower investigators, clinical staff, patients, and families to most effectively use the ever-expanding totality of pediatric health information. In turn, these processes are expected to result in more effective pediatric healthcare interventions. Particular foci of interest include genomic and functional genomic discovery, genome-enabled medicine, biomedical data integration and dissemination, eHealth, and clinical decision support. Center for Cellular and Molecular Therapeutics (CCMT): The CCMT facilitates rapid translation of pre-clinical discoveries into clinical application. One of few such programs based at a pediatric institution, CCMT collaborates with other major programs to pursue new therapies for inherited and acquired disorders. CCMT also serves as an educational resource for investigators, clinicians, students, patient families, and the general public. CCMT has dedicated resources and personnel to help facilitate rapid translation. In addition, given the complicated nature and the government's stringent regulations of cell and gene therapy, the center guides and assists investigators through the regulatory approval process. Center for Childhood Cancer Research (CCCR): The CCCR represents a highly integrated basic, translational, and clinical research environment dedicated to more targeted, more effective, and less toxic therapy for cancer in children. This goal is realized by uniting the diverse talents of investigators in CHOP's renowned multidisciplinary program in pediatric cancer research, patient care, and molecular profiling. Recruitment of leading talent in areas that can facilitate this progress, spanning the laboratory and clinical research spectrum, enable CCCR’s mission. CCCR's organization supports an environment where the latest scientific findings from cutting-edge basic research can be translated into innovative clinical trials, designed to dramatically improve the cure rates for pediatric cancers while simultaneously reducing long-term side effects.

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The Center for Injury Research and Prevention (CIRP): CIRP advances the safety and health of children, adolescents, and young adults through comprehensive research resulting in practical tools to reduce injury and promote recovery. The CIRP turns research into action, advancing the science and creating a tangible impact on injury research and prevention. The center addresses injuries comprehensively from prevention to after-the-injury healing; translates rigorous scientific research to usable, age-appropriate tools and practical steps for families, professionals, and policymakers; asks and answers important questions from an interdisciplinary perspective; and engages with a broad range of organizations including, universities, government entities, nonprofits, foundations, and corporations, to ensure research results extend to the real world. Center of Mitochondrial and Epigenomic Medicine (CMEM): The CMEM is poised to advance the understanding of, and potential treatments for, a multitude of disorders and diseases that involve mitochondria. Scientists and physicians need to understand normal energy flow, the disturbance of energy flow during disease, and communication between the mitochondria and nuclear DNA. This crosstalk is mediated by the epigenomic, inherited modifications in gene expression. CMEM is investigating mitochondrial and epigenomic dysfunction and treatment for a wide range of clinical problems such as autism, epilepsy, heart disease, diabetes and obesity, forms of blindness, Alzheimer and Parkinson disease, cancer, and aging. In addition to examining the essential roles of mitochondria, the CMEM team is exploring how mitochondrial genes influence adaptation to extremes in our environment such as arctic cold, tropical heat or high altitude. Center for Pediatric Clinical Effectiveness (CPCE): The mission of the CPCE is to discover and disseminate knowledge about best practices in the management of pediatric disease. CPCE provides infrastructure for training in and performance of clinical effectiveness research aimed at understanding the best ways to prevent, diagnose, and treat diseases in children. It builds on the existing research expertise and infrastructure at CHOP to create an environment and opportunities for the exchange of ideas among clinical effectiveness researchers, facilitate the performance of clinical effectiveness research through a pilot grant program and assistance with projects that use existing national and local databases, and educate the next generation of clinical effectiveness investigators in the methods of clinical epidemiology. PolicyLab: PolicyLab aims to achieve optimal child health and well being by informing program and policy changes through interdisciplinary research. It develops evidence-based solutions for the most challenging health-related issues affecting children. PolicyLab’s experience caring for children and families drives its “evidence to action” approach to improving children’s health. This approach requires that PolicyLab projects involve practitioners, policymakers, and families throughout the research process, from design to dissemination. By partnering with stakeholders, PolicyLab engages in research that is both responsive to community needs and relevant to policy priorities and work to identify the programs, practices, and policies that support the best outcomes for children and their families. UNIVERSITY OF PENNSYLVANIA SCHOOL OF MEDICINE The David Mahoney Institute of Neurological Sciences has the distinction of being the first research organization to receive NIH funding for training in the neurosciences. Established in 1953 as an interdisciplinary institute designed to continue the outstanding early work at Penn on the biophysics of the nervous system, the Institute has approximately 150 faculty from six schools within the university, and 32 different departments. The collective research interests encompass almost every aspect of the nervous system and include computational, developmental, systems, behavioral/cognitive and cellular/molecular neuroscience, as well as the neurobiology of disease. The Department of Neuroscience at the U of P was founded in 1992 to recognize the growing importance of neuroscience as a scientific discipline. Department laboratories pursue a wide variety of research interests reflecting the entire range of modern neuroscience. The Department lies at the heart of the campus-wide Institute of Neurological Sciences, the first research organization in the country to receive NIH funding for training in the neurosciences. The mission of the Department is to study the function and dysfunction of the nervous system, and to train medical, graduate and undergraduate students so they can become leaders of a new generation of neuroscientists. The Department of Neurology at the U of P currently stands first among all US Neurology Departments in NIH extramural grant support. It accepts 7 new residents/year, selected from the very top candidates entering the field. The majority of these residents elect to pursue a career in academic neuroscience.

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Penn Centers and Institutes: The University of Pennsylvania School of Medicine has a number of freestanding, interdisciplinary centers and institutes, which are listed below. Penn Medicine Neuroscience Center: The Penn Medicine Neuroscience Center (PMNC) at the University of Pennsylvania Perelman School of Medicine and Health System was created in 2006 to integrate and strengthen Penn’s interdisciplinary, world-class neuroscience programs in patient care, education, and research. The PMNC promotes collaborations among clinical specialists, basic science and clinical researchers, and the educators who train the future generations of neuroscience physicians and scientists. The PMNC supports the practice of translational medicine in which groundbreaking research is moved from the laboratory into clinical trials and, ultimately, into clinical practice to benefit patients. In short, the PMNC represents a model for integrated clinical care, research, and education. It encourages interdisciplinary thinking and unites a diverse group of clinicians, researchers, and educators through a unifying vision, strategic thinking, program development, and shared resources. The Center of Neurobiology and Behavior (CNB) is an interdisciplinary research program with core faculty, space and administration within the Department of Psychiatry. The primary scientific objective of the CNB is to foster interdisciplinary research and training in the basic neural and molecular mechanisms underlying complex behavior, including but not limited to psychopathologic behavior. The placement of the CNB within the Department of Psychiatry fosters a bi-directional translation of research between clinical and basic research programs. The CNB was established in 1996 in order to consolidate and to give a specific identity to existing basic science programs within Psychiatry. The Leonard Davis Institute of Health Economics (LDI) was established at the University of Pennsylvania in 1967, two years after Congress enacted Medicare. It was created in response to growing national concern over the lack of good research and education to inform policies critical to the financing and management of the nation's increasingly costly and complex health care system. Today, LDI is considered one of the world's leading university-based programs in health services and health economics research. LDI and its Senior Fellows are among the pioneers in interdisciplinary health services research that has helped guide health policies at all levels of government and the private sector. Over 200 LDI Senior Fellows work to improve the health of the public through studies on the medical, economic, and social issues that influence how health care is organized, financed, managed, and delivered in the United States and worldwide. The Centers for Sleep and Respiratory Neurobiology are interacting, complementary clinical and research programs. Together, these programs operate the clinical and research sleep laboratories of the Hospital of the University of Pennsylvania, and together, they are developing clinical methods and guidelines for the evaluation and treatment of sleep disorders within the Penn Health System. Studies are evaluating the neural/ventilatory mechanisms that underlie sleep apnea syndromes, and the mutifactorial causes of both hypersomnia and insomnia in the elderly. Ongoing studies are also examining the neurophysiology of arousal and fatigue in humans, and performance deficits associated with fatigue/sleep deprivation. Cell and Developmental Biology Cell biology and developmental biology are highly interdependent fields of biomedical research, with advances in one field pushing the boundaries of the other in the pursuit to understand of the complex biological processes that underlie cellular function and embryonic development. The genome revolution, in combination with equally revolutionary developments in cellular imaging and microscopy, now provide cell and developmental biologists with extraordinary experimental tools to investigate the complexity of gene regulatory pathways that propel embryonic development and the functional activities of cellular structures and organelles that mediate cellular functions, as well as a unique opportunity to apply this knowledge to understand of the cellular basis of specific human diseases and birth defects and to develop genetic and cell therapies to treat these disease conditions. Cell and developmental biology clearly have an exciting future for discovery in the biological and medical sciences. The Department has 21 faculty with cutting edge research programs in cellular and developmental biology. Our developmental biologists pursue questions of how developmental signals and transcription regulatory networks transform apparently uniform, newly fertilized eggs into organisms with a complexity of specialized cells, tissues and organs, organized within a functional body plan. These studies utilize a diversity of model organisms, Drosophila, Zebrafish, Xenopus, Chick and Mouse, utilizing current genetic, molecular, biochemical and microscopy approaches. Our cell biologists utilize similar approaches to pursue questions of how individual cells control and execute complex cellular functions, including cell division, intracellular trafficking of ions and molecules, cell motility and muscle contraction.

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The Center for Excellence for Diversity in Health Education and Research, now in its 20th year of operation, is a unit in the Perelman School of Medicine whose purpose is to establish, facilitate, conduct and evaluate programs and projects that will enhance the health of underrepresented minorities, particularly African American and Hispanic Americans. The Center operates as an integral part of UPENN and the UPHS. In this capacity, it collaborates extensively with all units of the University that share its mission and goals. One of the Center's principal efforts is preparing minority physicians for positions of leadership in medicine with an emphasis on faculty development. The Center's activities and programs will ultimately improve the health of minorities through promoting the growth of leaders in the biomedical sciences who are concerned and focused on these issues. The Center emphasized diversity, multiculturalism and interdisciplinary collaboration in education and research. Programs within the center include recruitment, mentoring and career development, tutoring and related activities at all levels of preparation in medicine. The Department of Medical Ethics and Health Policy is based in the Perelman School of Medicine at the University of Pennsylvania. Under the direction of the department chair, Ezekiel Emanuel, MD, PhD, the Department stands as one of the premier institutions of research and education in medical ethics in the world. The Department's distinguished faculty produce and disseminate scholarship and conduct one of the leading bioethics master’s programs in the world. In addition to their own projects, faculty members supervise research being carried out by undergraduates, graduate students, medical students, doctoral students and post-doctoral fellows. The Department serves as the hub for interdisciplinary research and collaboration on topics across four research areas in biomedical ethics: neuro- and mental healthcare ethics, health policy, behavioral economics, research ethics, global bioethics, and the ethics of healthcare allocation. Our health policy research follows three tracks: reducing low-value services; economic and health impacts of policies, such as smoking cessation and workplace wellness; and implementation sciences, with specific effort towards replicating effective programs in the healthcare delivery system. The Orphan Disease Center was formed in 2011, and was led by H. Lee Sweeney, PhD, William Maul Measey Professor of the Department of Physiology, from 2012-2014. Since January 2015, James M. Wilson, MD, PhD, Professor of Pathology and Laboratory Medicine, serves as the current Director of the Center. The mission is to improve the quality of life for those afflicted with rare diseases with a transformative approach to the development of highly effective, innovative therapies. It emphasizes platform technologies that can be deployed with a high probability of success across a range of diseases for which there is substantial unmet need without consideration of disease prevalence. The Center will strive to assure access of these novel therapies to all affected populations. March of Dimes Prematurity Research Center at The University of Pennsylvania In November of 2014, the March of Dimes joined with the University of Pennsylvania and other leading hospitals to launch the fourth transdisciplinary research center aimed exclusively at finding what causes preterm birth. The University of Pennsylvania research team includes over 40 faculty-level investigators, trainees, and staff and is led by its principal investigator Deborah Driscoll, M.D., and project leaders Rebecca Simmons, M.D., Michal Elovitz, M.D., and Dr. Samuel Parry, M.D. Three key research themes are being pursued via transdisciplinary interactions that will generate new research hypotheses and strategies to prevent preterm birth. The basic premise of the March of Dimes Prematurity Research Center at the University of Pennsylvania is that the causes of preterm birth involve highly interactive biologic and environmental factors that will not be uncovered by singular studies from isolated disciplines. Rather, the guiding premise is based on a commitment to craft investigational collaborations, integrated datasets, and innovative analytic tools that will generate new insights into the complex causes of preterm birth. Our virtual transdisciplinary and transinstitutional center assembles scientists from diverse fields to share knowledge and integrate data systems to transform one another’s perspectives and craft a rich analytic framework to understand what has until now remained a mystery. Administrative Core (Core A) The administrative core is housed in housed in 500 square feet of space on the 5th of the Abramson Research Building. Equipment includes two small portable projectors, a MacPro portable computer, and institutionally provided copy machine that is capable of scanning, copying, and faxing. Clinical Translational Core (Core B)

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Clinical: The Clinical Translational Core (CTC) is built from and will share resources with the Center for Autism Research (CAR). CAR was founded in 2007, and more than 1500 families have participated in studies at CAR since that date. CAR is not part of the Children’s Hospital fee-for-service operations. However, CAR maintains a very active research clinic for evaluating patients and controls for research studies. With 3 full-time PhD-level Clinical Assistant Professors of Psychology (not counting research faculty with clinical training and licensure), 3 postdocs in clinical psychology receiving advanced mentored training in clinical aspects of autism research, and 5 MA level clinicians, CAR’s Research Clinic completes an average of 15 diagnostic and phenotypic characterizations per week. The Research Clinic has 7 assessment rooms to monitor clinician reliability and for research protocols that require video coding of participant behaviors. Office: The primary office and dry lab space for the CTC is located on the 8th floor of the Clinical Research Building. Within the 13,500 square feet of contiguous clinical and computer lab space on this floor are a conference room for staff meetings that can seat about 18, three small conference rooms, two waiting rooms (one for infants and children, the other for older children and adults) with a common reception space, one open lab space with 12 desks, 10 cubicle offices, and 49 enclosed offices spaces. Of the 49 enclosed offices, there are seven assessment rooms (four of which have three wall mounted motorized cameras), one video control room, one EEG-dedicated room (with an eye tracker), a separate infrared eye tracking dedicated lab with 2 additional eye trackers, one mock MRI dedicated room, and a room dedicated to other computer based experiments. The space allows CAR to see up to seven families simultaneously. The dedicated video control room receives direct feeds from each assessment room for permanent archiving of research evaluations onto a 2 TB hard drive, as well as to removable media. The remaining 36 offices are used as shared or unshared office space for faculty and staff. Physical Resources and Relevant Equipment: Computer: CAR /CTC has 13 high-end workstations running either Linux or Windows, and multiple laptop and desktop computers for other research assistants, students and postdocs, with a variety of software such as Analyze, Adobe Creative, E-Prime and similar software for experiment programming (e.g., PsychoPy). The CTC has access to three Linux servers running in a cluster environment utilizing the Oracle Grid Engine to manage and distribute execution of parallel user jobs. These servers are physically located in a secured data

room with key card security entry and are accessed remotely by users using Virtual Network Computing and XWindows emulation software. The internal hard drives on each server are setup in a RAID configuration for data protection. The data are further protected by nightly backups to the six terabyte Storage Area Network (SAN) provided by CHOP. The SAN data storage is maintained by an off-site

commercial data center with high standards of data security. Lastly, the CTC has access to a CHOP-maintained >2000 core Linux cluster for massively parallel computation. Markerless Motion Capture Laboratory: The CTC has access to a large (20 foot, 11 inch by 13 foot, 2 inch, state of the art motion capture lab), configured with 16 integrated 640x480 high throughput 60 Hz 2-dimensional RGB cameras, and four integrated Kinect V2 3-dimensional motion capture cameras. A single KinectV2 unit is positioned separately from the more robust multi-camera setups, allowing us to compare the very robust signal in the high dimensional capture space to same data collected by a single Kinect – set up this way so that we can emulate home home-based data collection based on a single Kinect. The lab is comparing home and lab based motion capture with the goal being collecting as much behavior in natural environments as possible. Motion capture is completely markerless, which is important when working individuals with sensory sensitivities, which is true of many individuals with an intellectual or developmental disability. Sixteen directional microphones (each containing an array of 4 individual microphones) acquire high fidelity audio recordings. This configuration of microphones allows for precise assignment of noise direction due to the differences in the size and onset latency of acquired waveforms. Audio data can then be synchronized to video data.

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Markerless motion capture lab: Data collection space (without toys and playground like apparatus that are deployed for studies of younger children). Currently data processing include skeletal assignment with machine learning algorithms developed and validated at CAR for labeling of 29 bones and 27 joints, creating 4D datasets for analyses. Language Recording and Processing. The CTC is equipped to record and analyze large quantities of natural language data collected in the lab (e.g. the motion capture lab) and the real world. Our language team works closely with UPenn's Linguistic Data Consortium (https://www.ldc.upenn.edu/) to stay on the cutting edge of language acquisition and analysis techniques. The CTC currently has access to 13 Language Environment Analysis (LENA) recording devices and 40+ specially designed shirts/overalls to fit individuals from 3 months old through adult. These small, wearable devices can be mailed to families, allowing researchers to collect 10 continuous hours of audio data per day. LENA software quickly produces reports on child and adult utterance rates, turn-taking, and patterns of language production over time. Raw audio files can be analyzed for acoustic variables (e.g., prosody). For granular research questions, the CTC has access to 4 computers devoted to transcription; a team of transcriptionists approved by the LDC use XTrans software to produce highly reliable word-level data. (Current projects at CAR include analyzing the home language environments of infants at high risk of developing ASD, comparing language produced by children with ASD in different types of preschools, and assessing the language produced by school-aged children during diagnostic evaluations.) Arousal. The CTC has dedicated lab space at CAR for the measuring physiologic correlates of Emotion and Anxiety, including heart rate, skin conductance (synced with eyetracking and EEG). The lab space has two Biopac systems for electrocardiography, electromyography, skin conductance, and respiration measurement. specializes in the development of experimental paradigms involving live, gaze-contingent eyetracking with concurrent peripheral nervous system measurement. The lab has an Eyelink 1000 eyetracker dedicated to gaze-contingent eyetracking paradigms. CTC collaborators are actively developing procedures that use cutting-edge technology to measure psychophysiology outside of the laboratory setting, in real-world contexts. Eyetracking: The CTC has access to three desk-mounted eyetrackers that allow for the unobtrusive measurement of eyegaze. The Tobii™ X120 eye tracker (accuracy of 0.5 degrees, sample rate of 120Hz) has dedicated lab space within our office suite and comes equipped with the Tobii Studio™ software, a comprehensive platform for recording and analyzing eye gaze and other data. Our SR Research Eyelink 1000 (accuracy of 0.5 degrees, sample rate of 500Hz) also comes with a comprehensive software platform and is optimized for gaze-contingent eyetracking paradigms (though it is well-suited to a wide variety of eyetracking tasks). Database Resources: CAR uses the Research Electronic Data Capture (REDCap) data management system as well as the Qualtrics survey engine to store both a comprehensive library of psychometric and demographic data entry forms as well as screening and study related data. REDCap is a secure, web-based application designed exclusively to support data capture for research studies; Qualtrics uses a Research Suite to enhance

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its base functionality. Both services have routine security, failover, and nightly backup services (http://www.qualtrics.com/security-statement/; https://redcap.research.chop.edu/artifacts/doc/GrantIRBLanguage.docx) . In every case, identifying data (PHI) is stored separately from study-related assessment and questionnaire results, with discrete permissioning allowing for limited access to PHI, which is only stored on CHOP servers. Data is consolidated from REDCap and Qualtrics into a secure SQL database located behind CHOP’s firewall to provide for advanced data integration and analysis. CAR’s data management system is overseen by a full-time database manager, Joy Payton, who has nearly 2 decades of information technology experience. Other: Recruitment: Philadelphia is the 5th largest metropolitan area in the country, and CHOP aims to assist families in the area through an extensive network of primary care pediatric practices encompassing about 200 primary care CHOP pediatricians, serving a catchment area of more than 12 million people. Research recruitment is also facilitated by CHOP’s Pediatric Research Consortium (PeRC), the primary care practice-based research network (PBRN) at CHOP. PeRC relies on the ambulatory electronic health record (EHR) system, a technological tool that affords immediate electronic access to clinical information and communication at the point of care. PeRC gathers and aggregates data across the pediatric network using the EHR. PeRC enables researchers to place “prompts” (study ads) in front of clinicians at the time that they are seeing a child with ASD, for any medical issue, so that they can directly describe research opportunities to the family during that visit. Through this mechanism, PeRC provides (on a weekly basis) the research team with a list of patients who have expressed interest in being contacted for a research study. Community liaison: To organize recruitment efforts for all of CAR’s studies and to spearhead our community relations, CAR has a full time community liaison, Lauren DePolo, MEd. CAR staff attends around 50 regional events each year, including our own Distinguished Lecture Series (attendance of 75-150 parents and community professionals) and our annual Huddle Up for Autism (in partnership with the Philadelphia Eagles), which attracts 5,000 individuals with a connection to ASD. autismMatch: Several years ago, CAR received a 1 year NIH R01 grant to establish a large autism research registry called “autismMatch”, which matches families who are interested in taking part in autism research and who live in Pennsylvania and nearby states with researchers at CAR and other academic research institutions. CAR launched autismMatch in April 2010 and, as of January 2015, we had 2,527 people who consented and completed the Background Information form; and 2,287 people who completed ALL steps of enrollment (consent, BI form, and appropriate behavior form: M-CHAT or SCQ). Our newsletter reaches nearly 10,000 families and service providers in the metro region. ASD research at CHOP and Penn also benefits from the activities of the Regional Autism Center (RAC) at CHOP, which has evaluated more than 5,000 children for a diagnosis of ASD in the last ten years, most seen before the age of five years. These families are frequently invited into research studies at CAR. In addition, CAR can recruit from an additional pool of approximately 10,000 persons with ASD seen through other clinical services at CHOP.

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Biostatistics and Bioinformatics (Core C) The Department of Biostatistics & Epidemiology and the Center for Clinical Epidemiology & Biostatistics (CCEB): The Department of Biostatistics and Epidemiology (DBE) is comprised of two distinct divisions (Biostatistics and Epidemiology) and serves as the primary academic home for faculty in the field biostatistics. Notably the DBE now includes a Division of Biostatistics at CHOP; the five faculty members who comprise this division have secondary appointments in the UPenn Department of Pediatrics. Research interests include causal modeling, clinical trials, repeated measures and longitudinal data analysis, measurement error, survival models, functional data including imaging and statistical genetics. The DBE is also the primary home for the Graduate Group in Epidemiology and Biostatistics, one of seven graduate groups that comprise Biomedical Graduate Studies at the University of Pennsylvania Perelman School of Medicine. Since its inception in 2000, over 50 students have completed their doctorate in Biostatistics. The current program has 22 enrolled students, and is projected to grow to a size of 35 students by 2020. More globally, the Center for Clinical Epidemiology and Biostatistics (CCEB) provides the primary collaboratory for Epidemiology and Biostatistics research at Penn and CHOP. Members of the CCEB are individuals from schools across the University with a demonstrated research interest in Clinical Epidemiology and/or Biostatistics. Members include research from a range of disciplines, including applied and pure mathematics, behavioral medicine, biostatistics and statistics, clinical pharmacy, decision science, economics, epidemiology, genetic counseling, genetics, health service and administration, health policy, history and sociology of science, information science, pharmacology and toxicology, psychiatry, public health, sociology, and social work. CCEB serves as an umbrella organization for faculty who are engaged in hundreds of different active clinical research projects, both hospital- and community-based. The culture within the CCEB supports collaboration on research projects with multiple other divisions within the Perelman School of Medicine, UPenn and CHOP. Notably, the CCEB has substantial resources that are particularly germane to the success of the IDDRC at CHOP/Penn. These include multiple floors of office space in a single building, Blockley Hall, service centers that include the Biostatistical Analysis Center (a group of programmers and MS level statisticians) and the Clinical Research Computing Unit (CRCU). Animal Studies: Not applicable. Computing: See Clinical Research Computing Unit (CRCU) description in Service Center section below. Office: The CCEB occupies approximately 150 offices plus 20 workstation/computing pods, located on seven floors in Blockley Hall, totaling approximately 50,000 net sq. ft. Within this space, the CCEB maintains one seminar room with capacity for 60 people and four 16-person conference rooms, all with state-of the art presentation facilities. Blockley Hall is adjacent to the main Medical School buildings and a short walk from Wistar, the Hospital of the University of Pennsylvania, the Children's Hospital of Philadelphia, the Clinical Research Building, the John Morgan Building, and the main campus of the University. The CCEB has additional offices within the University City Science Center complex located on the “Avenue of Technology,” at the edge of the Penn campus. The CCEB occupies approximately 4,600 sq. ft. of space at one location, including a large conference room and offices for approximately 15 staff. An additional 6,600 sq. ft. is provided at the other location, with office space for approximately 50 staff. This space includes two conference rooms and a machine room configured with controlled HVAC and electrical uninterrupted power supplies providing controlled air and power. Service Centers: The CCEB oversees three service centers: the Biostatistics Analysis Center (BAC), the Biostatistics and Epidemiology Consultation Center (BECC), and the Clinical Research Computing Unit (CRCU). Of importance to this proposal is the CRCU, which supports computing facilities and is described below. Clinical Research Computing Unit: The Clinical Research Computing Unit (CRCU) was established in 1997 to develop and implement a technology base and hire professional staff within the Biostatistics Unit of the CCEB to conduct clinical and patient-oriented research at Penn Medicine. These resources allowed CCEB faculty to compete successfully for Data Coordinating Centers (DCCs) of federally-funded, large-scale, multicenter clinical trials, and epidemiological studies. These technology resources also permitted CCEB faculty and staff to provide essential collaborative clinical research support for University investigators throughout the wide

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array of basic science and clinical departments, Centers and Institutes, thus enhancing their likelihood of funding success. In 2002, the CRCU expanded its focus in response to overall research project growth within the CCEB and the University, evolving from within the Biostatistics Unit of the CCEB to a CCEB-wide organizational service center for both the Biostatistics and Epidemiology divisions. The CRCU now has two faculty Co-Directors representing each of these divisions, ensuring that the overall strategy and goals of the service center are aligned with the goals of the CCEB and the University research mission. CRCU personnel are directly responsible for the clinical data management systems (DMS) and research computing associated with multiple NIH-sponsored multicenter multi-study registry and clinical trial networks. The CRCU conducts studies in accordance with FDA Bioresearch Monitoring Program and International Conference on Harmonization (ICH) guidelines, when applicable. The necessity for compliance with these guidelines is determined in collaboration with PIs according to the scientific goals, sponsorship, and content of the study. The CRCU occupies a suite of offices with a total area of 6,600 square feet, located in Suite 560, on the 5th floor of 3535 Market Street. The building has a guarded lobby and limited access, requiring an electronic passkey. This space has been allocated to the CRCU for staff offices, machine room space and operational areas in support of large-scale, multicenter clinical trials, clinical and patient-oriented research projects, and multi-institutional health services research projects. The CCEB operates a research computing facility in support of biostatistical, epidemiologic, basic, clinical and translational health research. The CCEB’s computing environment is the responsibility of the Clinical Research Computing Unit (CRCU), a designated “Core Research Facility” situated within the CCEB. The CRCU offers two distinct types of services: research computing, data and project management for clinical trials, epidemiologic studies, and cooperative basic science studies; and research computing and information technology Tier III support to faculty, and staff within the CCEB. The CCEB computing environment is maintained within a Penn Medicine Data Center facility at 3440 Market Street. The overall environment is equipped with major HVAC, UPS power conditioning (with diesel generator backup for extended outages), and discrete computer network capabilities, all designed to ensure availability and protection of the computer technologies used by the CCEB, thereby allowing the CCEB’s computer systems to be managed and protected. The CCEB maintains its research computing environment by using current leading-edge technologies available and suitable for its research mission. These technologies are acquired through commercial vendor sources and open-source venues, and are maintained in “production quality” configurations. Computing technologies and resources are identified below within major functional information technology (IT) environments.

1. IT Staffing – the CRCU maintains a highly experienced and skilled complement of in-house, Penn employee IT personnel in the Biomedical Research Computing Unit. Personnel focus exclusively on maintaining and providing the fundamental security essentials of Confidentiality, Integrity and Availability for the environments 2 – 4 below.

2. Network Environments - The firewalled data communication networks support the secure transfer and movement of all the data, application logic, and computer programs and project information developed. This category of activity encompasses: Physical Networks, Logical Networks, and security within these networks.

3. Computing Hardware Environments - The hardware configurations on which all applications and software are built, run, and supported. This category of activity encompasses: Infrastructure Services Platforms, Data Storage Platforms, High Performance Computing Platforms, Database Services Platforms, and Business Continuity/Recovery Platforms.

4. Software/Application Environments - The applications and research software used to develop, maintain, process, and analyze data are supported. This category of activity encompasses: Operating Systems, Statistical Applications, Database Applications, and Printing/Scanning.

These categories of IT activity receive full-time, dedicated attention. Standard Operating Procedure documents prescribe controls and activities specifically formulated to meet the specific regulatory compliance

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frameworks of multiple sponsoring agencies. These include a Memo of Understanding with the Veterans Administration, FISMA for the National Institutes of Health and 21 CFR Part 11 for the Food and Drug Administration.

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Analytical Neurochemistry (Core D) Stable Isotopes/Mass Spectrometry: The GC-MS core is located on fifth floor of the Abramson Research Center Building. This facility includes 2200 square foot laboratory space where equipments are located and the work is to be performed. All necessary fume hoods and biosafety cabinets are part of the core. Six PC Computers, three Power-Macs (G5) and MAC-Books are available for the staff in the core. These units are connected to the institute data base and used for data medium, data analyses and storage. The research focus of the Mass Spectrometry Core is the use of stable isotopes to measure metabolite turnover and fluxes in both in vivo and in vitro studies. Examples include the turnover of small molecules such as glucose, amino acids, urea and ammonia as well as the measurement of total body protein synthesis. Isotopic enrichment (mole % excess, MPE) in a given 15N or 13C labeled metabolites will be calculated from GC-MS chromatogram. The production of 15N or 13C labeled metabolite (nmoles/g tissue or mg protein) will be calculated by the product of MPE/100 time concentration (nmoles/g or nmoles/mg protein). In in vitro experiments, the rate of utilization of 15N or 13C labeled precursor will be fitted to a single or double exponential function (y= Ae-kt + Be-kt), depending upon the results obtained. The rate of 13C or 15N labeled products production during the course of incubation will be fitted either to a linear regression or to an exponential function B=A (1-ekt). Numerous kinetic models have been developed to calculate the flux of carbons through the TCA cycle. We will monitor the flux of 13C using the 13C labeling pattern of glutamate as described. Formation of 13C glutamate isotopomer (from 13C-labeled palmitate or pyruvate) reflects the incorporation of 13C-labeled acetyl-CoA and its flux through the TCA-cycle. The release of 13CO2 (nmol. mg protein-1.min-1) will be monitored. Flux through pyruvate dehydrogenase will be calculated by the formation of 13CO2 (nmoles. mg protein-1. min-1) from [1-13C]pyruvate. In vivo experiments with 15N-labeled glutamine, ammonia, [2H5]phenylalanine or [13C]urea as a precursor, the average systemic rates of the precursor appearance (Ra) will be determined from plasma isotopic enrichment (MPE) using steady-state equations, i.e., Ra = I x [(Ei/Ep) - 1]. I is the infusion rate of the tracer (nmoles/min/kg), Ei and Ep are the isotopic enrichment (MPE) of the infused tracer and plasma enrichment at the plateau, respectively. If the precursor appearance is not at steady state, a non-steady-state equation will be employed. From the Ra value one can calculate the endogenous production and protein turnover. The Ra value for urea will be used to calculate the rate of conversion of any given 15N precursor to total urea nitrogen. The Ra of glutamine in plasma will represent the sum of the de novo synthesis of glutamine and the glutamine released from protein breakdown. The rate of release of glutamine from protein breakdown will be calculated as follows: B Glutamine = Ra of phenylalanine x 1.07, where the fraction 1.07 represents the relation between glutamine and phenylalanine in mixed muscle protein. The rate of de novo synthesis of glutamine is the difference between the Ra of glutamine and B glutamine. In addition, we will determine the incorporation of [2H5]phenylalanine into muscle, liver and kidney protein and calculate the % of [2H5]phenylalanine (nmol/mg protein) relative to total phenylalanine in tissue protein as a marker of protein synthesis or breakdown. Major Equipment: Our mass spectrometers now number 7. They include 3 Hewlett-Packard/Agilent gas chromatography-mass spectrometry systems, each with an automated sampling system that permits the analysis of up to 99 unattended samples. Each system is controlled by an individual computer/work station with Windows-based propietary software from HP/Agilent. These instruments are used primarily for the analysis of 15N, 2H and 13C in glucose, amino acids, fatty acids, primary amines and organic acids (particularly tricarboxylic acid cycle intermediates such as citrate, ketoglutarate, succinate, malate). Our isotope ratio-mass spectrometry instruments are utilized primarily for the analysis of 13CO2 in metabolic studies as well as the analysis of 2H2O and 13CO2 in doubly-labelled water studies to measure the in vivo metabolic rate in a freely moving organisms. Instruments utilized to this end include our SIRA-12 IR-MS with a Europa GC inlet as well as our Thermo Finnigan DeltaPLUS continuous flow isotope ratio-mass spectrometer. The latter is equipped with an autosampler that permits unattended analysis of 50 samples. Sensitivity of the latter instrument (atom % excess) characteristically exceeds 10-5. We also maintain 2 LC-MS triple stage quadrupole systems. One is a VG Quattro II LC-MS unit and the other is an Agilent 6400 LC-triple stage quadurpole system. The latter is used primarily to perform metabolomic

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research, or the profiling in a single sample of > 100 individual metabolites in order to create a metabolic “fingerprint”. We anticipate that this instrument will prove useful for the analysis of biogenic amines during the coming funding cycle. It also will be used to create a diagnostic profile in the blood of children with inborn errors of metabolism. The core also offers the doubly labeled water method for determination of the metabolic rate in a freely moving individual and is able to quantitate the oxidation of specific metabolites by measuring the rate of 13C-carbon dioxide production following the administration of a precursor such as 13C-labeled glucose. We recently (2009) have added a Metabolomics facility that will make use of a newly acquired (2009) Agilent 6400 liquid chromatography-triple stage quadrupole mass spectrometry system. High Performance Liquid Chromatography: From Waters, a millennium Chromatography Workstation, 6 HPLC pumps (5-510s, 1-515), 3 gradient controllers, a 2487 UV/VIS detector, and 3 automated injectors (717 WISPs). An ESA Coulochem III, electrochemical detector, and 3 McPherson FL-750 fluorimeters. In addition, three Varian HPLC systems equipped with UV and Fluorescent detectors are used to measure amino acid levels as an integral part of stable isotope analysis and determination of flux rates. Neurochemistry: From Beckman, two Avanti J-E high speed centrifuges, a J2-21 centrifuge with rotors, an ultracentrifuge, a TLS6500 scintillation counter with DPM capabilities, a Beckman g counter, a Spectramax 190 microtiter plate reader, and a DU640C spectrophotometer. A McIllwain tissue chopper, 1 cell harvester, gel rigs with power supplies for DNA/RNA analyses, and a Perkin Elmer 9700 GeneAmp PCR machine. For protein analyses we have 2 Biorad Protein II gel apparati, 2 Hoeffer SE60 Gel apparati, 10 minigel apparati, a Hoeffer TE transfer apparatus, 3 table top Eppendorf centrifuges (two are refrigerated), an Alpha Innotech Chemimager, and a LiCor Odyssey Gel documentation system. We have 3 -20o C freezers, a -70° freezer, and associated balances, homogenizes, and a pH meter. Protein and Proteomics Core is located in a 2,000 sq. ft. laboratory on the 8th floor of the Abramson Pediatric Research Center. Physical space comprises benches, 2 chemical hoods, a refrigerated Gem box, tissue culture room and three equipment rooms. The usual range of equipment needed for protein production and biochemical and cell biological experiments is available. The lab is also very well equipped with the more specialized instrumentation and computational capabilities necessary for state of the art proteomics experiments. Major equipment:

Mass Spectrometers: (1) Thermo LTQ-Orbitrap-Elite hybrid linear-Orbitrap-D20 with Electron-Transfer Dissociation (ETD) (2) Thermo LTQ-Orbitrap XL hybrid linear-orbitrap (3) Waters Xevo TQS triple quadrupole with Trizaic ion source Ion Sources: 2 New Objective PicoView dual column nano-ESI sources, ADVION NanoMate 96 well ESI source, Thermo micro-ion sources, HESI probe for Orbitrap Elite

HPLC equipment: 2 Eksigent nano LC2D Ultra HPLC systems with autosampler and CHIP-LC Nanoflex (dedicated to the two Orbitrap mass spectrometers); 2 Waters nanoAcquity 2D UPLC systems (one dedicated to triple quad MS, the other reserved for method development and offline first dimension separations); Shimadzu HPLC system (5 to 400 uL/min); Waters H-class UPLC system (primarily used for offline multidimensional proteome fractionation); GE Amersham Biosciences AKTA FPLC system with wide range of chromatographic media.

Heraus HERAsafe laminar flow hood, 2 New Brunswick InnOva4230 refrigerated incubator/shakers, New Brunswick C24KC refrigerated incubator/shaker

BiaCore 3000 Surface Plasmon Resonance Beckman Optima XE-100 ultracentrifuge Beckman-Coulter Optima XL-100 ultracentrifuge, 3 fixed angle rotors, SW-55Ti and SW-41Ti rotors Jasco J-810 spectropolarimeter (with fluorescence, variable temperature, and automatic titration);

Agilent 8453 UV-Vis spectrophotometer, Nanodrop spectrophotometer Pressure BioSciences, Inc. Barocycler NEP2320 (for proteome sample preparation) Retsch MM400 ball mill grinder (for cryogenic tissue homogenization)

Computing Infrastructure & Software: In addition to the computers dedicated to instrument control and data acquisition the core is equipped with an additional 9 Windows XP workstations and servers. Four of these have fully licensed Thermo Xcalibur with Bioworks and SEQUEST database search software installed and two

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with Proteome Discoverer. Another 64 bit dual hex-core CPU Windows XP server is dedicated to database searching with Matrix Science MASCOT software. APEX Quantitative Proteomics Tool (J. Craig Venter Institute) is implemented for label-free quantification experiments. The SageN Sorcerer2 5 CPU LINUX cluster is dedicated to SEQUEST database searches and calculation of probability of phosphorylation site localization using the ASCORE algorithm. Another 24 core cpu Windows XP 64 bit workstation with 48 GB RAM is used primarily for MaxQuant processing of stable isotope labeling by amino acids in cell culture (SILAC) or in mammals (SILAM) protein and phosphoproteome quantification experiments. This computer is also used for our recently purchased Bionic software. The Institute for Systems Biology Trans-Proteomic Pipeline software is fully implemented on most of our workstations. All laboratory computers are Ethernet connected and we have virtually unlimited space on our institutional Storage Area Network for data archiving and secure redundant backup. Bioenergetics: Within the main laboratory space and equipment hall there is one -80°C freezer, one -140°C freezer, liquid nitrogen storage tank, two -20°C freezers, and dedicated use of a walk-in 4°C cold room adjacent to the main laboratory. Dr. Falk’s laboratory has 2 Fisher I26/R refrigerated platform shakers with 1L platforms, two 4°C refrigerators, 15°C and 20°C incubators, 2 vented chemical hoods, 2 chemical storage cabinets, exclusive access to two 4’ cell culture hoods, four 37°C CO2 incubators, 2 ovens, 3 Nikon light microscopes, 1 Zeiss Axioscope 2 fluorescence microscope fitted for DIC, 1 Leica MZFLIII fluorescence light microscope, 1 Jenco inverted microscope for cell culture, Nikon 12-bit digital monochrome camera with NIS-elements BR imaging software, 5 Applied Biosystems thermocyclers for PCR, 1 gradient thermocycler, light box, Western blotting minigel apparatus, gel electrophoresis equipment, Biomate 3 spectrophotometer, Qubit analyzer, MilliQ Biocel RNAse/DNAse-free water filtration system, Hansatech oxytherm oxygen electrode, 2 Oroboros Oxygraph-2K high-resolution oxygen electrode for polarography of which one is adapted with fluorescence module and dedicated computer, two IKA homogenizers, sonicator, 2 rotary shakers, Eppendorf 5810R benchtop centrifuge, 3 microfuges, 2 minifuges, 2 water baths, 4 dry blocks, 5 stirring hotplates, 2 balances, electronic Accumet pH meter with standard and microelectrodes, and multiple complete Pipet sets including dedicated sets both for cell culture and molecular applications. Six Lenovo desktop computers, one Apple desktop computer, two Dell and 1 MacBook Air laptop computers, two scanners, one fax machine, and one inkjet printer are available in the laboratory for use by researchers and students.

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Neuroimaging and Neurocircuitry (Core E) Magnetoencephalography: Magnetoencephalography (MEG) recordings will be performed at the Lurie Family Foundations MEG Imaging Center (Director Timothy P.L. Roberts), a 1,330 sq. ft. laboratory within The Children's Hospital of Philadelphia Radiology Department. It houses two state-of-the-art biomagnetometer systems (275-channel biomagnetometer VSM Medtech Inc. and 306-channel Elekta Vectorview). Both are equipped with capability for simultaneous 64-channel EEG. In addition to these adult MEG systems, in the Spring of 2013 a 123-channel small-scale infant MEG was installed (Artemis 123™), a MEG system Drs. Roberts (and Edgar) designed in collaboration with Tristan Technologies. Established in 2005, the laboratory is fully-staffed with trained technologists and nursing staff for patient comfort and safety. Dr. Roberts supervises day-to-day activities in the lab. Led by Dr. Bloy, two staff computing specialists, three post-doctoral students, 7 research assistants and coordinators and 4 experienced technologists assist with and help support laboratory research. MEG data are primarily analyzed in the MEG analysis lab located within the Lurie Family Foundations MEG Imaging Center. In addition to the MEG analysis lab, office space is available in the Radiology Department for cognitive testing. A waiting room is adjacent to the MEG laboratory and available for parental/guardian use during the child’s evaluations. The Lurie Family Foundations MEG Imaging Center has also become a training center for graduate and postdoctoral students (currently 3 postdocs), as well as Radiology residents. The main research thrust of the Lurie Family Foundations MEG Imaging Center is to investigate structural and functional abnormalities in Autism Spectrum Disorders (ASD) and related intellectual disabilities, with a specific focus on auditory processes, using combined sMRI and MEG. The superior temporal resolution of whole-cortex MEG and the excellent spatial resolution of magnetic source imaging (MSI; combining MEG and sMRI data) are ideal to elucidate the pathophysiological mechanisms characteristic of intellectual disabilities. Magnetic Resonance Imaging (3T human, 7T small animal): Human MRI: IDDRC Neuroimaging and Neurocircuitry Core MRI is performed at The Children's Hospital of Philadelphia in a dedicated research MRI laboratory designed for pediatric patients. In particular, a Siemens 3T wide-bore 32-channel Magnetom Verio™ TIM system is available at the CHOP Radiology Department. This system is strictly dedicated to research. The Verio system is the first 3 Tesla with 70 cm open bore design, and thus offers greater patient access and comfort. The Verio system is equipped with a 32-channel head coil, designed with an open view and a detachable mirror for visual stimulation experiments and to reduce claustrophobia. This research MRI system has 32 independent RF receiver channels and allows up to 102 integrated coil elements to be simultaneously connected. The gradient performance in each axis has a maximum amplitude of 45 mT/m, minimum rise time of 225 μs, and maximum slew rate of 200 T/m/s. Since a large amount of activity on this scanner centers on functional brain mapping, multiple stimulus delivery systems are available including auditory and visual stimulus presentation systems (Avotec, Resonance Technologies Inc., Siemens, In-vivo). Furthermore, a fiber-optic MRI-compatible 4-button behavioral response system is installed for simultaneous assessment of behavioral task performance (Current Designs). An MRI-compatible eye-tracking continuous pupil monitoring system (SMI) is available for both Avotec and Resonance Technologies systems. The research magnet undergoes daily quality assurance to ensure the acquisition of the highest quality images required for research. An identically-equipped 3T Verio™ MRI scanner is available at a CHOP community satellite outpatient center (King of Prussia, PA) and is available for research use. Some families find this location more convenient for access. A second research-dedicated MRI is pending installation. This is a state of the art Siemens 3T Prisma system with “connectome-quality” 80mT/m gradient coils enabling high resolution diffusion weighted imaging (DTI, HARDI etc.). All above fMRI capabilities and ancillary hardware will be integrated. Furthermore, in addition to 7 other clinical MRI systems, CHOP has already installed a clinical 3T Prisma system, from which preliminary structural and multi-band accelerated echo-planar diffusion data has been obtained. This system is in close proximity to our research space and is available for research utilization pending installation of the dedicated research Prisma system, anticipated in 2016. Subjects are registered and escorted by the research nurse coordinator between MEG and MRI facilities. The MRI scanners are operated by 4 experienced and research-dedicated technologists, who have been trained in research imaging methods by Dr Roberts since 2005; patients may be accompanied by their parents/ guardians. A “child-friendly” mock scanner (Nordic Neurolabs) is in close proximity and is used to acclimatize children to the MRI environment. Due to close collaboration between Dr Roberts and Dr Elliott (U. Penn) and equivalent research agreements with Siemens, the Prisma systems at the two sites will be kept in close

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hardware and software alignment, with ADNI and BIRN phantoms routinely scanned on both devices, monthly “human phantom” calibrations (using the exact protocol proposed) and residual variance quantified for covariate analysis. Finally, as a result of our research agreement with Siemens, we have access to all product sequences as well as many pre-release “Works in Progress” pulse sequences (e.g. multi-band echo planar, advanced diffusion 511 and edited spectroscopy 529). Additionally we are able to program our own sequences on any of the scanners. An on-site engineer is available at all times to maintain scanners. Small Animal Imaging: The IDDRC Neuroimaging and Neurocircuitry Core capitalizes on the CHOP multimodality small animal imaging facility, housed in a 1600 sq. ft. facility located centrally within the recently established laboratory animal facility. IDDRC small animal imaging services are directed by Dr. Hao Huang, recently recruited to augment CHOP research imaging faculty. In addition to the main preparation, operation and analysis areas, it comprises a radioisotope hot lab with fume hood, a lead-shielded PET/CT, SPECT/CT room and RF-shielded MRI suite, as well as a computing and MRI engineering room. Several newly-installed imaging systems are available to investigators with primary IDDRC services centering on the MRI: 7T Bruker/Siemens ClinScan™ operating Siemens Syngo MRI acquisition software, version VB15B, with 12.9cm diameter high performance gradient coils. This system is equipped with all standard and advanced imaging packages, identical to those encountered on clinical Siemens MRI scanners. A Caliper Life Sciences (Xenogen) IVIS Spectrum 3D biofluorescence, bioluminescence optical tomography system is the state-of-the-art hardware for optical imaging, which represents the first step in adopting imaging-based approaches into biological investigations. Nuclear Magnetic Resonance and Ex-vivo MRI: The NMR facility is a research and analytical facility available to the Hospital's research community and to investigators affiliated with large center programs or private research institutions. The facility features a 400 MHz (9.4Tesla) high-resolution wide-bore spectrometer equipped with a HP computer. The system can perform most of the traditional high-resolution NMR experiments as well as microimaging of specimens and small models. Computer: The MEG analysis room is equipped with a dual-monitor Linux workstation, 3 high performance Dell desktop computers (Intel D Processor 940 with Dual Core Technology (3.2 GHz, 800FSB, 4GB Dual Channel DDR SDRAM at 533Mhz), 24” monitor, and a 500GB Performance RAID), and two standard Dell desktop computers for Microsoft Office functions (Word, PowerPoint, etc). Data archiving is implemented using a 2TB local RAID drive, with longer-term storage on the department MAS (Medical Archive Solution). Analysis software is built around proprietary CTF/Neuromag solutions, but is supplemented by 3rd party (e.g., BESA, BrainVoyager), and in-house software (MatLab). The Image Analysis Laboratory in the Dept, of Radiology at CHOP houses linux-based 3.8GHz Intel-Xeon image server and analysis workstations. The short-term server is directly connected to the MRI scanners, allowing DICOM image transfer; it is equipped with RAID-configured expandable 1TB serial ATA harddisks and 4GB RAM. Server and workstation software includes MatLab and IDL environments, the VoxBo™ image software, MRIcro™, ImageJ™, FreeSurfer, SPM, FSL for functional imaging and a variety of in-house code developments for physiologically-specific parameter mapping. Windows-based PCs additionally support irfanview™, MRIcro™, ImageJ™ and (in collaboration with Dr Mori at Johns Hopkins University) DTIstudio™ for white matter tractography. Workstations can be accessed locally, or from physician/researcher offices using X-emulators, including XWin-32™. Furthermore, the IDDRC Neuroimaging and Neurocircuitry Core provides access for imaging data storage analysis to the CHOP storage area network (SAN). The SAN utilized in the study is an Isilon system, a global large filesystem and NAS share, currently with 389TB capacity and expandable to 14PB (petabytes). Data on the Isilon is secure and is automatically backed up twice daily. In addition to the SAN, for computationally intensive analyses, IDDRC NNC users have access to the CHOP cluster, operating the majority of routinely used software packages described above. The processing facility presently comprises a 38-node Dell cluster (2304 total processing cores), with the following features: 2 x head nodes, 36 x compute nodes (4 x 16 core AMD x86_64 processors, 128GB RAM). The cluster uses the Bright computing cluster management suite, with SGE for job scheduling and fourteen data rate (FDR) InifiBand interconnects. Institutional commitment ensures the maintenance and upgrade of this resource to meet the Core user needs.

Robinson U54 Renewal of Center 2015

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The small animal imaging facility additionally incorporates a dedicated visualization and quantitative analysis suite, built upon a Vital Images Vitrea Web server with thin client applications as well as 3 powerstations housed in a central review area. The selection of a clinical visualization suite enhances the ease of bench-bedside translation via an imaging conduit. Office: MEG and MRI data are primarily analyzed in the MEG analysis lab located within the Dept. of Radiology. The analysis room comfortably seats 4 individuals (typically research assistants). In addition to the MEG/MRI analysis lab, office space is available in the Radiology Department for postdoctoral students. Dr Roberts’ office is located in the Neuroradiology section of the Dept. of Radiology, geographically close to both MEG and MRI facilities. Diagnostic and cognitive testing is performed in a room adjacent to the Lurie Family Foundations MEG Imaging Center. Neurocircuitry and Patch Recording Facilities: Located in Abramson 409, the Cellular Electrophysiology and Functional Imaging Core combines 3 approaches: Patch clamp recording, voltage-sensitive dye imaging, and multiphoton imaging of calcium indicator loaded neurons, on three separate rigs. The patch clamp recording setup is equipped with an inverted, epifluorescence microscope, manipulators, patch amplifiers, and stimulators. The voltage-sensitive dye imaging rig is equipped with a fixed stage, upright epifluorescence microscope, temperature-controlled brain slice chamber, manipulators, patch and field potential amplifiers, stimulators, and a Redshirtimaging NeuroCCD camera capable of imaging at up to 5 kHz framerates. The multiphoton imaging rig is equipped with a Prairie Imaging Technologies multiphoton scanhead mounted on an upright microscope, a MaiTai laser, temperature-controlled brain slice chamber, patch amplifier, manipulators, and stimulators. The Cellular Electrophysiology and Functional Cellular Imaging Core is located in 2200 square feet on the 4th floor within Coulter Lab in Abramson Research Center. There are a total of 8 multifunction electrophysiological setups contained within this space, together with animal dissection facilities, tissue preparation and maintenance facilities, electrode fabrication equipment. The core combines 4 approaches: Patch clamp recording, voltage-sensitive dye imaging, calcium imaging (multiphoton imaging of calcium indicator loaded cells), and confocal microscopy of live/fixed cells/tissues. In addition, 200 sq. ft. of space on the 2nd floor within the animal facility contains a multi-photon microscopy system equipped with a treadmill/trackball system in a virtual reality environment. This allows functional imaging in awake, behaving animals. The slice patch clamp recording setup is equipped with an Olympus BX61 upright epifluorescence microscope, Scientifica micromanipulators, Axon MultiClamp 700B patch clamp amplifiers, Axon pClamp/Clampex9 Digidata1322A recording system, AMPI Master-8 electrical stimulus generator, and Warner Instrument temperature-controlled brain slice chamber. The cell culture patch clamp recording setup is equipped with a Leica inverted epifluorescence microscope, micromanipulators, Axon Axopatch1D patch clamp amplifier, Axon pClamp/Clampex8 Digidata1200 recording system, Warner Instrument fluid controller and temperature-controller. The voltage-sensitive dye imaging rig is equipped with an Olympus BX51 fixed stage upright epifluorescence microscope, a high power LED with a Uniblitz electrical shutter, an interfacial brain slice chamber, temperature controller, Syskiyou manual micromanipulators, an Axon Axopatch200B patch clamp amplifier, and Axon CyberAmp 320 field potential amplifiers, an Axon pClamp/Clampex9 Digidata1322A recording system, an Accupulser signal generator and stimulus isolator, and a Redshirt Imaging NeuroCCD camera. The NeuroCCD is capable of imaging at up to 5 kHz framerates. With a 4x Objective lens, one can image a 2 mm x 2 mm area with a pixel resolution of 25 microns, or with a 20x Objective lens one can image a 400 micron x 400 micron area with a pixel resolution of 5 microns. The fast confocal microscopy system is equipped with a Nikon FN1 upright epifluorescence microscope, a Nikon Sweptfield Fast Confocal Scanner, a Photometrics Cascade 512B EM-CCD camera, a Photometrics Cascade 128 EM-CCD camera, an Axopatch200B patch clamp amplifier, a pClamp/Clampex8 Digidata1322A recording system, Sutter Instrument micromanipulator systems, an AMPI Master-8 electrical stimulus generator, a Warner Instrument temperature-controlled imaging chamber, a Coherent OBIS 488nm solid state laser, a Coherent Sapphire 561nm solid state laser, and a NEOS Acousto Optical Modulator. The equipment is best suited for conducting calcium imaging on brain slices. The fast confocal microscopy is capable of imaging at up to 400 Hz framerates with pixel resolution of about a half micron.

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One multiphoton imaging rig is equipped with an Olympus BX61 upright microscope, a Prairie Technologies Ultima multiphoton scanhead, a Spectra Physics MaiTai DeepSee laser, temperature-controlled brain slice chamber, an Axon MultiClamp700B patch amplifier, a pClamp/Clampex9 Digidata1322A recording system, Sutter Instrument micro manipulators, and stimulators. The equipment is best suited for imaging live slice tissues. The Prairie multiphoton microscopy is capable of imaging at up to 1 Hz full frame and at higher frame rates with constrained pixel number, with a pixel resolution of about a micron. The confocal microscopy rig is equipped with an Olympus IX81 inverted microscope, Olympus FV1000 laser confocal scanner, temperature-controlled imaging chamber. FV1000 equipped with a solid state laser, multi-line argon ion laser, and two HeNe lasers. Available laser lines: 405nm, 456nm, 488nm, 515nm, 543nm, 633nm. The equipment is best suited for imaging live cell culture as well as immuno-stained fixed tissue slices. The FV1000 confocal microscopy is capable of imaging at up to 2 Hz full frame, around 15Hz with limited number of pixels, with spatial resolution of about a few hundreds nanometers. A second Multiphoton microscopy slice physiology rig is equipped with a Thorlab B-scope with resonance scanning, a SpectraPhysics MaiTai DeepSee femtosecond laser, a temperature controlled brain slice chamber, an Axon MultiClamp700B patch amplifier, a pClamp/Clampex10 Digidata1550A recording system, Sutter Instrument micro manipulators, and stimulators. The equipment is best suited for imaging live slice tissues. The Thorlab multiphoton microscopy is capable of imaging at up to 30 Hz full frame and up to 400 Hz with a constrained region of interest (ROI). A third Multiphoton microscopy in vivo physiology rig is equipped with a Thorlab B-scope with resonance scanning, a SpectraPhysics MaiTaiDeepSee femtosecond pulsed laser, an Axon MultiClamp700B patch amplifier, a pClamp/Clampex10 Digidata1440 recording system, Sutter Instrument micro manipulators, and stimulators. The equipment is best suited for calcium imaging of live animals in acute preparations. A fourth Multiphoton microscopy in vivo rig in the 2nd floor in the animal facility is equipped with a Thorlab B-scope with resonance scanning, a SpectraPhysics MaiTaiDeepSee femtosecond pulsed laser, and Phenosys trackball and TFT display. The equipment is best suited for chronic calcium imaging of awake behaving animals. EEG and In Vivo Recording Facilities: Located both in room 204 Abramson research building animal facility and in room C604 Colket Research building animal facility at CHOP is the EEG and in vivo recording facilities sub core. The two research building containing the animal facilities are connected to the by a pedestrian bridge. The recording facilities are in dedicated 100 and 200 square feet procedure rooms. All the mice for these experiments are in a single housing room with ventilated cages and a built in water system. Surgeries/Electrode implantations are performed in separate procedure room with a dedicated stereotaxic frame (David Kopf Instruments), anesthesia machine, autoclave, bead sterilizer, and surgical drill. The facilities are AAALAC certified. The recording rooms each contain three Stellate Harmonie EEG machines with 2Khz bandwidth amplifiers and the ability to record 4 mice simultaneously. There are 12 x Triangle biosystems preamplifiers with fine wire cables and 12 x Plastics1 commutators for interfacing the EEG machine with the recording pedestals. We have 12 cages with water bottles and individual video cameras at each facility. At the Colket recording room, there is an AM systems model 1600 16 channel (20kHz/channel) extracellular amplifier with SciWorks digital acquisition system for higher bandwidth recordings to perform single unit and LFP recordings and analysis. There are 4 Dell Optiplex computers for physiological recordings, EEG review and analysis located in Abramson 509H for review and analysis of the data recorded in the animal facilities.

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Preclinical Models (Core F) Rodent Behavioral Testing Service: The administrative office and wet lab bench space of the core are located on the 10th floor near the Abel lab. The core behavioral testing suites are located in the CHOP Colket Translational Research Building, C level and the Penn Smilow Center for Translational Research sixth floor animal facility. There are and 12 rooms in the Colket Building and 19 rooms in the Smilow Center dedicated to behavior testing. These rooms provide for mouse housing, surgical procedures as well as behavioral testing rooms for investigators on this proposal. The core works closely with faculty and researchers in these facilities and faculty members from these facilities are on the Core Steering Committee. Human Stem Cell Service: The iPSC Core Facility has 1500 sq ft of space on the 5th floor of the Colket Translational Research Building (CTRB); across the street from ARC at CHOP and Penn Smilow Center for Translational Research. This area includes ~500 sq feet of space for tissue culture in dedicated rooms with space for the proposed research as part of the ongoing efforts in this application. The laboratory is equipped with all of the necessary supplies as well as large and small equipment for tissue culture and molecular biology studies. Tissue Culture Service: The cell culture facility on the 5th flloor of the Abramson Research building occupies three contiguous rooms. One room is used for the establishment of cultures from animals and contains a large 2-3 person laminar flow, C02 euthanizing facility, several Leica dissecting microscopes, and necessary water baths for incubations. The second room, used for the maintenance and treatment of cultures, contains two laminar flow hoods, a Nikon inverted microscope with fluorescence, and a dual chamber Heureus tissue culture incubator. The third room is reserved for microscopy and has several Leica epifluorescent microscopes with camera systems. The laboratory contains low and high speed refrigerated centrifuges dedicated for tissue culture use only, one -80 freezer, one liquid nitrogen freezer, plus a Miltenyi Macs system for cell separation. Computers: The Rodent Behavioral Testing Service uses 7 Dell Optiplex (model 9000 series) computers with 17 (20-, 21-, and 24-inch) displays for data analysis, word processing and literature searches and two printers (HP Laserjet 3600, 4600). Software includes Microsoft Office, Prism Graphpad and SPSS for statistical analysis, Sleepsign 2.0 for EEG trace analysis and Avisoft-SASlabPro for USV analysis. Matlab, Freezescan, Topscan and HVS Image video tracking systems are used for analysis of observational based behaviors. Five Dell Precision T3400 PCs, equipped with webcams (Microsoft Lifecam and iSpy64) are used for data acquisition for object recognition, Morris water maze/Barnes mazes novelty suppressed feeding, marble burying and open field activity monitoring systems. Two Dell Optiplex 755 PCs are used for electrophysiological data acquisition. A Dell Optiplex computer is used for Classical Conditioning data acquisition and analysis. A Dell Optiplex runs SD Instruments Most computers are connected to PennNet, and/or AIRSAS, the computer network at the University of Pennsylvania. A Dell computer runs Columbis Instruments mutlidevice activity software for homecage activity monitoring. For acquisition of image for analysis 3 Sony high definition cameras, 2 Infrared capable cameras and webcams with adjustable tripods and mounting brackets are used to record footage of observation based behavior. The core also has a recently acquired two 2TB My Passport WD portable hard drives and Synology 2413 External Storage Array with 5 4TB 7.2K RPM Universal SATA 3Gbps hard drives plus 5 Single Blank Hard Drive Filler Panels (allowing for expansion of storage). Behavior Testing Equipment: The Colket building contains the following equipment: Rotarod, Open Field chamber, Light-dark box, home cage activity trackers, Morris Water maze, Barnes maze, Elevated plus maze, Elevated zero maze, grip strength meter, 4 fear conditioning chambers and acoustic startle/ppi boxes. The Smilow Center has the following equipment in its mouse facility: Avisoft Ultrasonic Vocalization microphone in a sound attenuating chamber, EEG/EMG acquisition equipment for 18 mice, 16 activity monitoring light and sound proof chambers with individual lights, 8 classical conditioning chambers, 2 open field arenas and 8 object recognition setup, 4 marble burying chambers, 4 novelty suppressed feeding boxes, 4 three chamber social interaction arenas, 2 olfactory habituation/dishabituation cages, 2 Morris water mazes, 1 cross maze, 1 radial arm maze, a passive avoidance chamber, 3 forced swim cylinders, 2 elevated zero mazes, 2 Rotarods (40rpm and 80 rpm), VonFrey fibers/testing platform, incremental hot and cold plate, grip strength meters, Randall–Selitto pressure meter, Plantar Test (Hargreaves Apparatus), dry Y-maze, swimming Y maze, 4 righting reponse brackets, 6 conditioned place preference chambers and a cliff avoidance platform. In addition, the core has a fully operational small animal surgery suite with 2 stereotaxic frames, dissection microscope, isoflurane vaporizer and gas scavenger and micro infusion pumps. This equipment is readily

Robinson U54 Renewal of Center 2015

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available and could be applied to assess physical and neurological health, arousal, anxiety, social interaction, communication, behavioral inflexibility and cognition in models of intelectellectual and developemental disabilities. Research Project: “MEG Studies of Auditory Processing in Minimally/Non-Verbal Children with ASD and Intellectual Disability” Laboratory: Magnetoencephalography (MEG) recordings will be performed at the Lurie Family Foundations MEG Imaging Center (Director Timothy P.L. Roberts), a 1,330 sq. ft. laboratory within The Children's Hospital of Philadelphia Radiology Department. It houses two state-of-the-art biomagnetometer systems (275-channel biomagnetometer VSM Medtech Inc. and 306-channel Elekta Vectorview). Both are equipped with capability for simultaneous 64-channel EEG. In addition to these adult MEG systems, in the Spring of 2013 a 123-channel small-scale infant MEG was installed (Artemis 123™), a MEG system Drs. Roberts (and Edgar) designed in collaboration with Tristan Technologies. The primary equipment for this study will be the 275-channel VSM MedTech device, used to acquire the reference data on HFA and TD in prior studies. Established in 2005, the laboratory is fully-staffed with trained technologists and nursing staff for patient comfort and safety. Dr. Roberts supervises day-to-day activities in the lab. Led by Dr. Bloy, two staff computing specialists, three post-doctoral students, 7 research assistants and coordinators and 4 experienced technologists assist with and help support laboratory research. MEG data are primarily analyzed in the MEG analysis lab located within the Lurie Family Foundations MEG Imaging Center. In addition to the MEG analysis lab, office space is available in the Radiology Department for cognitive testing. A waiting room is adjacent to the MEG laboratory and available for parental/guardian use during the child’s evaluations. The Lurie Family Foundations MEG Imaging Center has also become a training center for graduate and postdoctoral students (currently 3 postdocs), as well as Radiology residents. The main research thrust of the Lurie Family Foundations MEG Imaging Center is to investigate structural and functional abnormalities in Autism Spectrum Disorders (ASD) and related intellectual disabilities, with a specific focus on auditory processes and language. Computer: The MEG analysis room is equipped with a dual-monitor Linux workstation, 3 high performance Dell desktop computers (Intel D Processor 940 with Dual Core Technology (3.2 GHz, 800FSB, 4GB Dual Channel DDR SDRAM at 533Mhz), 24” monitor, and a 500GB Performance RAID), and two standard Dell desktop computers for Microsoft Office functions (Word, PowerPoint, etc). Data archiving is implemented using a 2TB local RAID drive, with longer-term storage on the department MAS (Medical Archive Solution). Analysis software is built around proprietary CTF/Neuromag solutions, but is supplemented by 3rd party (e.g., BESA, BrainVoyager), and in-house software (MatLab). The Image Analysis Laboratory in the Dept, of Radiology at CHOP houses linux-based 3.8GHz Intel-Xeon image server and analysis workstations. The short-term server is directly connected to the MRI scanners, allowing DICOM image transfer; it is equipped with RAID-configured expandable 1TB serial ATA harddisks and 4GB RAM. Server and workstation software includes MatLab and IDL environments, the VoxBo™ image software, MRIcro™, ImageJ™, FreeSurfer, SPM, FSL for functional imaging and a variety of in-house code developments for physiologically-specific parameter mapping. Windows-based PCs additionally support irfanview™, MRIcro™, ImageJ™ and (in collaboration with Dr Mori at Johns Hopkins University) DTIstudio™ for white matter tractography. Workstations can be accessed locally, or from physician/researcher offices using X-emulators, including XWin-32™. Furthermore, the IDDRC Neuroimaging and Neurocircuitry Core provides access for imaging data storage analysis to the CHOP storage area network (SAN). The SAN utilized in the study is an Isilon system, a global large filesystem and NAS share, currently with 389TB capacity and expandable to 14PB (petabytes). Data on the Isilon is secure and is automatically backed up twice daily. In addition to the SAN, for computationally intensive analyses, IDDRC NNC users have access to the CHOP cluster, operating the majority of routinely used software packages described above. The processing facility presently comprises a 38-node Dell cluster (2304 total processing cores), with the following features: 2 x head nodes, 36 x compute nodes (4 x 16 core AMD x86_64 processors, 128GB RAM). The cluster uses the Bright computing cluster management suite, with SGE for job scheduling and fourteen data rate (FDR) InifiBand interconnects. Institutional commitment ensures the maintenance and upgrade of this resource to meet the Core user needs.

Robinson U54 Renewal of Center 2015

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Clinical: Dr Kuschner has behavioral evaluation space adjacent to the MEG lab in Children’s Seashore House, as well as office and clinical space in the Center for Autism Research (directed by Dr Schultz). This close proximity to Dr Schultz will facilitate subject flow through the IDDRC Clinical and Translational Core, which he also directs. A dedicated clinical effort has resulted in MEG-PLAN, a strategic approach to improve the imaging yield for low-functioning populations and subjects who might otherwise have difficulty completing assessments. Dr Kuschner has spearheaded these approaches. Office: MEG and MRI data are primarily analyzed in the MEG analysis lab located within the Dept. of Radiology. The analysis room comfortably seats 4 individuals (typically research assistants). In addition to the MEG/MRI analysis lab, office space is available in the Radiology Department for postdoctoral students. Dr Roberts’ office is located in the Neuroradiology section of the Dept. of Radiology, geographically close to both MEG and MRI facilities. Diagnostic and cognitive testing is performed in a room adjacent to the Lurie Family Foundations MEG Imaging Center.

Robinson U54 Renewal of Center 2015