111 results on '"Jeremy Freeman"'
Search Results
2. <scp>Postoperative</scp> opioid use following head and neck endocrine surgery: A <scp>multi‐center</scp> prospective study
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Amr F. Hamour, Mirko Manojlovic‐Kolarski, Antoine Eskander, Mathew Biskup, S. Mark Taylor, Frederick Laliberte, Allan Vescan, Ian J. Witterick, Jeremy Freeman, and Eric Monteiro
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General Medicine - Published
- 2023
3. PIGN encephalopathy: Characterizing the epileptology
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Allan Bayat, Guillem de Valles‐Ibáñez, Manuela Pendziwiat, Alexej Knaus, Kerstin Alt, Elisa Biamino, Annette Bley, Sophie Calvert, Patrick Carney, Alfonso Caro‐Llopis, Berten Ceulemans, Janice Cousin, Suzanne Davis, Vincent des Portes, Patrick Edery, Eleina England, Carlos Ferreira, Jeremy Freeman, Blanca Gener, Magali Gorce, Delphine Heron, Michael S. Hildebrand, Aleksandra Jezela‐Stanek, Pierre‐Simon Jouk, Boris Keren, Katja Kloth, Gerhard Kluger, Marius Kuhn, Johannes R. Lemke, Hong Li, Francisco Martinez, Caroline Maxton, Heather C. Mefford, Giuseppe Merla, Hanna Mierzewska, Alison Muir, Sandra Monfort, Joost Nicolai, Jennifer Norman, Gina O'Grady, Barbara Oleksy, Carmen Orellana, Laura Elena Orec, Charlotte Peinhardt, Ewa Pronicka, Monica Rosello, Fernando Santos‐Simarro, Eva Maria Christina Schwaibold, Alexander P. A. Stegmann, Constance T. Stumpel, Elzbieta Szczepanik, Iwona Terczyńska, Julien Thevenon, Andreas Tzschach, Patrick Van Bogaert, Roberta Vittorini, Sonja Walsh, Sarah Weckhuysen, Barbara Weissman, Lynne Wolfe, Alexandre Reymond, Pasquelena De Nittis, Annapurna Poduri, Heather Olson, Pasquale Striano, Gaetan Lesca, Ingrid E. Scheffer, Rikke S. Møller, Lynette G. Sadleir, RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, Klinische Neurowetenschappen, MUMC+: MA Med Staf Spec Neurologie (9), and MUMC+: DA KG Lab Specialisten (9)
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Epilepsy/diagnostic imaging ,Drug Resistant Epilepsy ,PROTEINS ,Electroencephalography ,Intellectual Disability/diagnostic imaging ,HYPOTONIA-SEIZURES SYNDROME ,PHENOTYPE ,congenital disorder of glycosylation ,CONGENITAL-ANOMALIES ,Phenotype ,Neurology ,Seizures ,intellectual disability ,Humans ,epilepsy ,Female ,Human medicine ,Neurology (clinical) ,developmental and epileptic encephalopathy ,PRENATAL-DIAGNOSIS ,Seizures/genetics ,GPI-anchoring disorder ,MUTATION - Abstract
OBJECTIVE: Epilepsy is common in patients with PIGN diseases due to biallelic variants; however, limited epilepsy phenotyping data have been reported. We describe the epileptology of PIGN encephalopathy. METHODS: We recruited patients with epilepsy due to biallelic PIGN variants and obtained clinical data regarding age at seizure onset/offset and semiology, development, medical history, examination, electroencephalogram, neuroimaging, and treatment. Seizure and epilepsy types were classified. RESULTS: Twenty six patients (13 female) from 26 families were identified, with mean age 7 years (range = 1 month to 21 years; three deceased). Abnormal development at seizure onset was present in 25 of 26. Developmental outcome was most frequently profound (14/26) or severe (11/26). Patients presented with focal motor (12/26), unknown onset motor (5/26), focal impaired awareness (1/26), absence (2/26), myoclonic (2/26), myoclonic-atonic (1/26), and generalized tonic-clonic (2/26) seizures. Twenty of 26 were classified as developmental and epileptic encephalopathy (DEE): 55% (11/20) focal DEE, 30% (6/20) generalized DEE, and 15% (3/20) combined DEE. Six had intellectual disability and epilepsy (ID+E): two generalized and four focal epilepsy. Mean age at seizure onset was 13 months (birth to 10 years), with a lower mean onset in DEE (7 months) compared with ID+E (33 months). Patients with DEE had drug-resistant epilepsy, compared to 4/6 ID+E patients, who were seizure-free. Hyperkinetic movement disorder occurred in 13 of 26 patients. Twenty-seven of 34 variants were novel. Variants were truncating (n = 7), intronic and predicted to affect splicing (n = 7), and missense or inframe indels (n = 20, of which 11 were predicted to affect splicing). Seven variants were recurrent, including p.Leu311Trp in 10 unrelated patients, nine with generalized seizures, accounting for nine of the 11 patients in this cohort with generalized seizures. SIGNIFICANCE: PIGN encephalopathy is a complex autosomal recessive disorder associated with a wide spectrum of epilepsy phenotypes, typically with substantial profound to severe developmental impairment.
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- 2022
4. NFTs: License to Own?
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Jeremy Freeman
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General Medicine ,General Chemistry - Abstract
In recent years, NFTs have burst onto the global scene, quickly going from an internet meme to a multi-billion dollar digital industry. These digital assets have everyone talking, but nobody seems to know what they are or whether you actually own anything when you buy one. This article uses extensive philosophical, legal, copyright, and empirical research to explore what is actually being purchased with an NFT. With everything from the morale words of John Locke to warnings from the district office of Manhattan, this article quantifies what NFT ownership entails, which is, essentially, nothing. Although governments acknowledge the possibility of legitimate ownership for NFTs, the lack of regulations and protections, as well as the unclear copyright laws and shady ownership claims make NFTs, for our current legal system at least, essentially worthless.
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- 2022
5. California’s forest carbon offsets buffer pool is severely undercapitalized
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Grayson Badgley, Freya Chay, Oriana S. Chegwidden, Joseph J. Hamman, Jeremy Freeman, and Danny Cullenward
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Global and Planetary Change ,Ecology ,Forestry ,Environmental Science (miscellaneous) ,Nature and Landscape Conservation - Abstract
California operates a large forest carbon offsets program that credits carbon stored in forests across the continental United States and parts of coastal Alaska. These credits can be sold to buyers who wish to justify ongoing emissions, including in California’s cap-and-trade program. Although fossil CO2 emissions have effectively permanent atmospheric consequences, carbon stored in forests is inherently less durable because forests are subject to significant socioeconomic and physical risks that can cause temporarily stored carbon to be re-released into the atmosphere. To address these risks, California’s program is nominally designed to provide a 100-year guarantee on forest carbon claims based on a self-insurance program known as a buffer pool. Projects contribute credits to the buffer pool based on a suite of project-specific risk factors, with buffer pool credits retired as needed to cover carbon losses from events such as wildfire or drought. So long as the buffer pool remains solvent, the program’s permanence claim remains intact. Here, we perform an actuarial analysis of the performance of California’s buffer pool. We document how wildfires have depleted nearly one-fifth of the total buffer pool in less than a decade, equivalent to at least 95 percent of the program-wide contribution intended to manage all fire risks for 100 years. We also show that potential carbon losses from a single forest disease, sudden oak death, could fully encumber all credits set aside for disease and insect risks. These findings indicate that California’s buffer pool is severely undercapitalized and therefore unlikely to be able to guarantee the environmental integrity of California’s forest offsets program for 100 years.
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- 2022
6. Future climate risks from stress, insects and fire across US forests
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William R. L. Anderegg, Oriana S. Chegwidden, Grayson Badgley, Anna T. Trugman, Danny Cullenward, John T. Abatzoglou, Jeffrey A. Hicke, Jeremy Freeman, Joseph J. Hamman, and Lawler, Joshua
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disturbance ,Evolutionary Biology ,Insecta ,Ecology ,Climate Change ,drought ,Forests ,Carbon ,Fires ,United States ,Trees ,Climate Action ,Ecological Applications ,carbon cycle ,Animals ,nature-based climate solutions ,biotic agents ,Ecology, Evolution, Behavior and Systematics - Abstract
Forests are currently a substantial carbon sink globally. Many climate change mitigation strategies leverage forest preservation and expansion, but rely on forests storing carbon for decades to centuries. Yet climate-driven disturbances pose critical risks to the long-term stability of forest carbon. We quantify the climate drivers that influence wildfire and climate stress-driven tree mortality, including a separate insect-driven tree mortality, for the contiguous United States for current (1984-2018) and project these future disturbance risks over the 21st century. We find that current risks are widespread and projected to increase across different emissions scenarios by a factor of >4 for fire and >1.3 for climate-stress mortality. These forest disturbance risks highlight pervasive climate-sensitive disturbance impacts on US forests and raise questions about the risk management approach taken by forest carbon offset policies. Our results provide US-wide risk maps of key climate-sensitive disturbances for improving carbon cycle modeling, conservation and climate policy.
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- 2022
7. Author response for 'Future climate risks from stress, insects and fire across US forests'
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null William R. L. Anderegg, null Oriana S. Chegwidden, null Grayson Badgley, null Anna T. Trugman, null Danny Cullenward, null John T. Abatzoglou, null Jeffrey A. Hicke, null Jeremy Freeman, and null Joseph J. Hamman
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- 2022
8. An unexpected disease course for a patient with diffuse midline glioma
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Vajiranee Malalasekera, Colleen D'Arcy, Cristina Mignone, Alison Wray, Jeremy Freeman, and Jordan Hansford
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Diffuse intrinsic pontine glioma (DIPG), now reclassified as diffuse midline glioma (DMG), is the most common cause of mortality from paediatric central nervous system (CNS) tumours. Diagnosis is made based on characteristic clinical presentation and neuro-imaging findings. Prognosis is poor, with minimal therapeutic options, reflected in a median survival of under 12 months. We present a patient with Pendred syndrome, diagnosed with DMG at 2-years of age with characteristic presentation and neuro-imaging findings, who remains asymptomatic and well at nearly 4-years post diagnosis despite progression of the primary lesion on serial imaging.
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- 2022
9. ANZAED eating disorder treatment principles and general clinical practice and training standards
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Marion Roberts, Jeremy Freeman, Kate Fleming, Fiona Sutherland, Michelle Roberton, Shane Jeffrey, Anjanette Casey, Susan Hart, Beth Shelton, Kim Hurst, Tracey D. Wade, Gabriella Heruc, Andrew Wallis, Christopher Thornton, Rachel Knight, Garalynne Stiles, and Anthea Fursland
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050103 clinical psychology ,Standards ,Mental health professional ,Dietetics ,lcsh:RC435-571 ,medicine.medical_treatment ,Best practice ,Psychological intervention ,Guideline ,Clinical practice ,Dietitian ,03 medical and health sciences ,Behavioral Neuroscience ,0302 clinical medicine ,Quality of life (healthcare) ,Nursing ,Intervention (counseling) ,lcsh:Psychiatry ,medicine ,Psychoeducation ,Training ,0501 psychology and cognitive sciences ,Nutrition and Dietetics ,05 social sciences ,Professional development ,Eating disorder ,medicine.disease ,Mental health ,030227 psychiatry ,Treatment ,Psychiatry and Mental health ,Eating disorders ,Psychological ,Psychology - Abstract
Introduction Eating disorders are complex to manage, and there is limited guidance around the depth and breadth of knowledge, skills and experience required by treatment providers. The Australia & New Zealand Academy for Eating Disorders (ANZAED) convened an expert group of eating disorder researchers and clinicians to define the clinical practice and training standards recommended for mental health professionals and dietitians providing treatment for individuals with an eating disorder. General principles and clinical practice standards were first developed, after which separate mental health professional and dietitian standards were drafted and collated by the appropriate members of the expert group. The subsequent review process included four stages of consultation and document revision: (1) expert reviewers; (2) a face-to-face consultation workshop attended by approximately 100 health professionals working within the sector; (3) an extensive open access online consultation process; and (4) consultation with key professional and consumer/carer stakeholder organisations. Recommendations The resulting paper outlines and describes the following eight eating disorder treatment principles: (1) early intervention is essential; (2) co-ordination of services is fundamental to all service models; (3) services must be evidence-based; (4) involvement of significant others in service provision is highly desirable; (5) a personalised treatment approach is required for all patients; (6) education and/or psychoeducation is included in all interventions; (7) multidisciplinary care is required and (8) a skilled workforce is necessary. Seven general clinical practice standards are also discussed, including: (1) diagnosis and assessment; (2) the multidisciplinary care team; (3) a positive therapeutic alliance; (4) knowledge of evidence-based treatment; (5) knowledge of levels of care; (6) relapse prevention; and (7) professional responsibility. Conclusions These principles and standards provide guidance to professional training programs and service providers on the development of knowledge required as a foundation on which to build competent practice in the eating disorder field. Implementing these standards aims to bring treatment closer to best practice, and consequently improve treatment outcomes, reduce financial cost to patients and services and improve patient quality of life.
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- 2020
10. Recurrent interactions in local cortical circuits
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Ravi Pancholi, Jason D. Wittenbach, H. Freyja Ólafsdóttir, Jeremy Freeman, Simon Peron, Bettina Voelcker, and Karel Svoboda
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0301 basic medicine ,Computer science ,Models, Neurological ,Population ,Neurophysiology ,Sensory system ,Biology ,Stimulus (physiology) ,Somatosensory system ,Article ,Synapse ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Encoding (memory) ,Animals ,Computer Simulation ,education ,030304 developmental biology ,Neurons ,education.field_of_study ,0303 health sciences ,Multidisciplinary ,Tactile discrimination ,Somatosensory Cortex ,Pattern completion ,Cortical neurons ,030104 developmental biology ,Touch ,Receptive field ,Excitatory postsynaptic potential ,Neuroscience ,030217 neurology & neurosurgery - Abstract
The majority of cortical synapses are local and excitatory. Local recurrent circuits could implement amplification, allowing for pattern completion and other computations1. Cortical circuits contain subnetworks, consisting of neurons with similar receptive fields and elevated connectivity relative to the network average2,3. Understanding the computations performed by these subnetworks during behavior has been hampered by the fact that cortical neurons encoding different types of information are spatially intermingled and distributed over large brain volumes 4,5. We used computational modeling, optical recordings and manipulations to probe the function of recurrent coupling in layer (L) 2/3 of the somatosensory cortex during tactile discrimination. A model of L2/3 dynamics revealed that recurrent excitation enhances sensory signals via amplification, but only for subnetwork with elevated connectivity. Networks with high amplification were sensitive to damage: loss of a few subnetwork members degraded stimulus encoding. We tested this prediction experimentally by mapping neuronal selectivity5 and photoablating6,7 neurons with specific selectivity. In L2/3 of the somatosensory cortex, ablating a small proportion (10-20, < 5 % of the total) of neurons representing touch dramatically reduced responses in the spared touch representation, but not other representations. Network models further predicted that degradation following ablation should be greatest among spared neurons with stimulus responses that were most similar to the ablated population. Consistent with this prediction, ablations most strongly impacted neurons with selectivity similar to the ablated population. Our data shows that recurrence among cortical neurons with similar selectivity can drive input-specific amplification during behavior.
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- 2020
11. Expert advice for prescribing cannabis medicines for patients with epilepsy-drawn from the Australian clinical experience
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John Lawson, Terry O'Brien, Myfanwy Graham, Elianne Renaud, Dean Jones, Jeremy Freeman, Nicholas Lawn, and Jennifer H. Martin
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Pharmacology ,Adult ,Analgesics ,Epilepsy ,Cannabinoids ,Seizures ,Australia ,Hallucinogens ,Humans ,Pharmacology (medical) ,Child ,Cannabis - Abstract
There is international interest for consensus advice for prescribers working in the field of drug resistant epilepsy intending to trial potential therapies that are nonregistered or off-label. Cannabinoids are one such therapy. In 2017, the New South Wales State Government (Australia) set up a cannabinoid prescribing guidance service for a wide variety of indications, based on known pharmacology together with the relevant new literature as it became available. Increasing interest in cannabis medicines use outside this State over the following 5 years together with a paucity of registration-standard clinical trials, lack of information around dosing issues, drug interactions and biological plausibility meant there remained a large unmet need for such advice. To address the unmet need in epilepsy, and until medicines were registered or regulator quality data were available, it was agreed to bring together a working group comprising paediatric and adult epilepsy specialists, clinical pharmacists., clinical pharmacologists and cannabis researchers from across Australia to develop interim consensus advice for prescribers. Although interim, this consensus advice addresses much of the current practice gap by providing an informed overview of the different cannabis medicines currently available for use in the treatment of epilepsy in paediatric and adult settings, with information on dose, drug interactions, toxicity, type of seizure and frequency of symptom relief. As such it supplements the limited evidence currently available from clinical trials with experience from front-line practice. It is expected that this consensus advice will be updated as new evidence emerges and will provide guidance for a subsequent Guideline.
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- 2022
12. EPILEPSY INTERIM EXPERT ADVICE FOR PRESCRIBING CANNABIS MEDICINES
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John Lawson, Terry OBrien, Myf Graham, Elianne Renaud, Dean Jones, Jeremy Freeman, Nicholas Lawn, and Jennifer Martin
- Abstract
There is international interest for consensus advice for prescribers working in the field of drug resistant epilepsy intending to trial potential therapies which are non-registered or off-label. Cannabinoids are one such therapy. In Australia in 2017, the New South Wales State Government set up a cannabinoid prescribing guidance service for a wide variety of indications, based on known pharmacology together with the relevant new literature as it became available. Increasing interest in cannabis medicines outside NSW over the following last five years together with a paucity of registration-standard clinical trials and lack of information around dosing issues, drug interactions and biological plausibility means there remains a large unmet need for such advice. To address the unmet need, and until medicines were registered or regulator quality data was available, it was agreed to bring together a working group comprising paediatric and adult epilepsy specialists, clinical pharmacists. pharmacologists and cannabis researchers from across Australia, to develop interim ‘Consensus Advice’ for prescribers. Although interim, this consensus advice addresses much of the current practice gap by providing an informed overview of the different cannabis medicines currently available for use in the treatment of epilepsy in paediatric and adult settings, with information on dose, drug interactions, toxicity and type and frequency of symptom and seizure relief. As such it supplements the limited evidence currently available from clinical trials with experience from front-line practice. It is expected that this consensus advice will be updated as new evidence emerges and will provide guidance for a subsequent Guideline.
- Published
- 2021
13. Systematic over-crediting in California's forest carbon offsets program
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Joseph Hamman, Barbara Haya, Grayson Badgley, Anna T. Trugman, William R. L. Anderegg, Danny Cullenward, and Jeremy Freeman
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Global and Planetary Change ,Conservation of Natural Resources ,Offset (computer science) ,Forest inventory ,Ecology ,Natural resource economics ,Forest management ,Carbon offset ,Adverse selection ,Forests ,California ,Carbon ,Greenhouse Gases ,Incentive ,Greenhouse gas ,Market price ,Environmental Chemistry ,Environmental science ,Humans ,General Environmental Science - Abstract
Carbon offsets are widely used by individuals, corporations, and governments to mitigate their greenhouse gas emissions on the assumption that offsets reflect equivalent climate benefits achieved elsewhere. These climate-equivalence claims depend on offsets providing real and additional climate benefits beyond what would have happened, counterfactually, without the offsets project. Here, we evaluate the design of California's prominent forest carbon offsets program and demonstrate that its climate-equivalence claims fall far short on the basis of directly observable evidence. By design, California's program awards large volumes of offset credits to forest projects with carbon stocks that exceed regional averages. This paradigm allows for adverse selection, which could occur if project developers preferentially select forests that are ecologically distinct from unrepresentative regional averages. By digitizing and analyzing comprehensive offset project records alongside detailed forest inventory data, we provide direct evidence that comparing projects against coarse regional carbon averages has led to systematic over-crediting of 30.0 million tCO2 e (90% CI: 20.5-38.6 million tCO2 e) or 29.4% of the credits we analyzed (90% CI: 20.1%-37.8%). These excess credits are worth an estimated $410 million (90% CI: $280-$528 million) at recent market prices. Rather than improve forest management to store additional carbon, California's forest offsets program creates incentives to generate offset credits that do not reflect real climate benefits.
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- 2021
14. Credentialing for eating disorder clinicians: a pathway for implementation of clinical practice standards
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Kim Hurst, Mandy Goldstein, Shane Jeffrey, Hilary Smith, Gabriella Heruc, Jeremy Freeman, Siân A. McLean, and Beth Shelton
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050103 clinical psychology ,lcsh:RC435-571 ,media_common.quotation_subject ,Credentialing ,Practice standards ,03 medical and health sciences ,Behavioral Neuroscience ,0302 clinical medicine ,Quality of life (healthcare) ,Promotion (rank) ,lcsh:Psychiatry ,medicine ,0501 psychology and cognitive sciences ,media_common ,Medical education ,Nutrition and Dietetics ,05 social sciences ,Professional development ,Workforce development ,medicine.disease ,Mental health ,030227 psychiatry ,Treatment ,Psychiatry and Mental health ,Eating disorders ,restrict ,Commentary ,Psychology - Abstract
Advances are needed to ensure safe and effective treatment is available for people with eating disorders. Recently developed clinical practice and training standards for mental health professionals and dietitians represent a significant step in this direction by providing a consensus statement on eating disorder treatment as a foundation on which to build competent practice. This commentary argues that a credentialing system could promote implementation of these practice standards through formal recognition of qualifications, knowledge, training and professional activities to meet minimum standards for delivery of safe and effective eating disorder treatment. Drivers for credentialing include the imperative to provide safe and effective care, promotion of workforce development in eating disorder practice and, importantly, readily available and transparent information for referrers, consumers, and carers to identify health professionals credentialed to provide eating disorder treatment. However, a number of factors must be considered to ensure that credentialing does not restrict access to care, such as prohibitively narrow criteria to become credentialed, absence of pathways for education, training, or professional development opportunities, and lack of consultation with or endorsement by stakeholders of the credentialing criteria, application and approval processes, and ways of identifying credentialed practitioners. Further work, including development of credentialing criteria and aligned training opportunities, currently being undertaken by the Australia & New Zealand Academy for Eating Disorders and the National Eating Disorders Collaboration in consultation with stakeholders in the eating disorders sector and health professions will advance understanding of the feasibility of a system of credentialing for eating disorders within Australia and New Zealand. The availability of clinical practice and training standards, supported by implementation pathways, including credentialing of eating disorders practitioners, aim to improve quality of life, reduce financial burden, and close the treatment gap.
- Published
- 2020
15. Climate risks to carbon sequestration in US forests
- Author
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William R. L. Anderegg, O. Chegwidden, Danny Cullenward, Grayson Badgley, John T. Abatzoglou, Anna T. Trugman, Jeremy Freeman, Jeffrey A. Hicke, and Joseph Hamman
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Climate change mitigation ,Disturbance (ecology) ,Natural resource economics ,Global warming ,Environmental science ,Carbon sink ,Climate change ,Carbon sequestration ,Climate policy ,Carbon cycle - Abstract
Forests are currently a substantial carbon sink globally. Many climate change mitigation strategies rely on forest preservation and expansion, but the effectiveness of these approaches hinges on forests sequestering carbon for centuries despite anthropogenic climate change. Yet climate-driven disturbances pose critical risks to the long-term stability of forest carbon. We quantify the key climate drivers that fuel wildfire, drought, and insects, for the United States over 1984-2018 and project future disturbance risks over the 21st century. We find that current risks are widespread and projected to increase across different emission scenarios by a factor of 4-14 for fire and 1.3-1.8 for drought and insects. Our results provide insights for carbon cycle modeling, conservation, and climate policy, underscoring the escalating climate risks facing forests and the need for emissions reductions to mitigate climate change.
- Published
- 2021
16. Systematic over-crediting in California’s forest carbon offsets program
- Author
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William R. L. Anderegg, Danny Cullenward, Barbara Haya, Grayson Badgley, Jeremy Freeman, Joseph Hamman, and Anna T. Trugman
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Incentive ,Offset (computer science) ,Forest inventory ,Natural resource economics ,Greenhouse gas ,Forest management ,Carbon offset ,Adverse selection ,Market price ,Business - Abstract
Carbon offsets are widely used by individuals, corporations, and governments to mitigate their greenhouse gas emissions on the assumption that offsets reflect equivalent climate benefits achieved elsewhere. These climate-equivalence claims depend on offsets providing “additional” climate benefits beyond what would have happened, counterfactually, without the offsets project. Here, we evaluate the design of California’s prominent forest carbon offsets program and demonstrate that its climate-equivalence claims fall far short on the basis of directly observable evidence. By design, California’s program awards large volumes of offset credits to forest projects with carbon stocks that exceed regional averages. This paradigm allows for adverse selection, which could occur if project developers preferentially select forests that are ecologically distinct from unrepresentative regional averages. By digitizing and analyzing comprehensive offset project records alongside detailed forest inventory data, we provide direct evidence that comparing projects against coarse regional carbon averages has led to systematic over-crediting of 30.0 million tCO2e (90% CI: 20.5 to 38.6 million tCO2e) or 29.4% of the credits we analyzed (90% CI: 20.1 to 37.8%). These excess credits are worth an estimated $410 million (90% CI: $280 to $528 million) at recent market prices. Rather than improve forest management to store additional carbon, California’s offsets program creates incentives to generate offset credits that do not reflect real climate benefits.Significance StatementForest carbon offsets are increasingly prominent in corporate and government “net zero” emission strategies, but face growing criticism about their efficacy. California’s forest offsets program is frequently promoted as a high-quality approach that improves on the failures of earlier efforts. Our analysis demonstrates, however, that substantial ecological and statistical shortcomings in the design of California’s forest offset protocol generate offset credits that do not reflect real climate benefits. Looking globally, our results illustrate how protocol designs with easily exploitable rules can undermine policy objectives and highlight the need for stronger governance in carbon offset markets.
- Published
- 2021
17. cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices
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Martin B, Colin Megill, Angela Oliveira Pisco, Kinsella M, Smith T, Cool J, Haliburton G, Lombardo M, Mani A, Badajoz S, Prins L, Griffin F, Justin T. Kiggins, Dunitz M, McCandless B, Weiden M, Weaver C, Jeremy Freeman, Huang T, Antony M. Carr, Sidney M Bell, and Chambers S
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Annotation ,Information retrieval ,Computer science ,Interface (Java) ,Scalability ,Feature (machine learning) ,Reuse ,Categorical variable ,Codebase ,Reusability - Abstract
Quickly and flexibly exploring high-dimensional datasets, such as scRNAseq data, is underserved but critical for hypothesis generation, dataset annotation, publication, sharing, and community reuse. cellxgene is a highly generalizable, web-based interface for exploring high dimensional datasets along categorical, continuous and spatial dimensions, as well as feature annotation. cellxgene is differentiated by its ability to performantly handle millions of observations, and bridges a critical gap by enabling computational and experimental biologists to iteratively ask questions of private and public datasets. In doing so, cellxgene increases the utility and reusability of datasets across the single-cell ecosystem.The codebase can be accessed at https://github.com/chanzuckerberg/cellxgene. For questions and inquiries, please contact cellxgene@chanzuckerberg.com.
- Published
- 2021
18. ANZAED practice and training standards for mental health professionals providing eating disorder treatment
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Jeremy Freeman, Andrew Wallis, Marion Roberts, Christopher Thornton, Beth Shelton, Kim Hurst, Tracey D. Wade, Gabriella Heruc, Anthea Fursland, and Rachel Knight
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050103 clinical psychology ,lcsh:RC435-571 ,Guideline ,Practice standards ,General practitioner ,03 medical and health sciences ,Behavioral Neuroscience ,0302 clinical medicine ,Nursing ,Intervention (counseling) ,lcsh:Psychiatry ,medicine ,Mental health clinician ,Training ,0501 psychology and cognitive sciences ,Nutrition and Dietetics ,Social work ,05 social sciences ,Professional development ,Psychologist ,Mental health nurse ,Occupational therapist ,Service provider ,Professional responsibility ,medicine.disease ,Mental health ,030227 psychiatry ,Social worker ,Treatment ,Psychiatry and Mental health ,Eating disorders ,Workforce ,Psychology - Abstract
Introduction The Australia & New Zealand Academy for Eating Disorders (ANZAED) recently developed general principles and clinical practice standards recommended for mental health clinicians and dietitians providing treatment for people with eating disorders. Separate mental health practice and training standards were then devised as a foundation for strengthening the workforce and providing guidance to professional training programs and service providers on the minimal standards required for practice in the eating disorder field. Recommendations The present recommendations for mental health professionals providing eating disorder treatment describe the following practice and training standards: eating disorder treatment foundations (including co-ordination of services, establishing a positive therapeutic alliance, professional responsibility and knowledge of levels of care), assessment, diagnosis, intervention (including evidence-based intervention, managing psychiatric risk and managing co-morbid mental health problems), and monitoring and evaluation. Conclusions Further work is required to disseminate these standards to clinicians providing services across Australia to people with eating disorders, and to support adherence in the clinic room where they can translate to improved outcomes for clients. Pathways to supporting adherence include expert supervision of practice, incorporation in training and supervised practice in university settings, and support with checklists that can be used by consumers and referring professionals.
- Published
- 2020
19. Climate-driven risks to the climate mitigation potential of forests
- Author
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Stephen W. Pacala, James T. Randerson, Philippe Ciais, William R. L. Anderegg, Grayson Badgley, Christopher B. Field, John Nickerson, Jeffrey A. Hicke, Robert B. Jackson, Deborah N. Huntzinger, Jeremy Freeman, Anna T. Trugman, Scott J. Goetz, Danny Cullenward, Christa M. Anderson, Ann M. Bartuska, SCHOOL OF BIOLOGICAL SCIENCES UNIVERSITY OF UTAH SALT LAKE CITY USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), University of California [Santa Barbara] (UCSB), University of California, World Wildlife Fund, Washington, RESOURCES FOR THE FUTURE WASHINGTON DC USA, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ICOS-ATC (ICOS-ATC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Stanford University, School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], DEPARTMENT OF GEOGRAPHY UNIVERSITY OF IDAHO MOSCOW IDAHO USA, PRINCETON UNIVERSITY DEPARTMENT OF ECOLOGY AND EVOLUTIONARY BIOLOGY PRINCETON USA, DEPARTMENT OF EARTH SYSTEM SCIENCES UNIVERSITY OF CALIFORNIA IRVINE CA USA, University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
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Sociology of scientific knowledge ,Carbon Sequestration ,010504 meteorology & atmospheric sciences ,Policy making ,Climate Change ,Climate change ,Carbon sequestration ,Forests ,01 natural sciences ,Natural (archaeology) ,Fires ,03 medical and health sciences ,Policy Making ,030304 developmental biology ,0105 earth and related environmental sciences ,0303 health sciences ,Multidisciplinary ,business.industry ,Environmental resource management ,Carbon sink ,Vegetation ,15. Life on land ,[SHS.ECO]Humanities and Social Sciences/Economics and Finance ,Droughts ,13. Climate action ,Environmental science ,business - Abstract
Risks to mitigation potential of forests Much recent attention has focused on the potential of trees and forests to mitigate ongoing climate change by acting as sinks for carbon. Anderegg et al. review the growing evidence that forests' climate mitigation potential is increasingly at risk from a range of adversities that limit forest growth and health. These include physical factors such as drought and fire and biotic factors, including the depredations of insect herbivores and fungal pathogens. Full assessment and quantification of these risks, which themselves are influenced by climate, is key to achieving science-based policy outcomes for effective land and forest management. Science , this issue p. eaaz7005
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- 2020
20. Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function
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Burkhard Höckendorf, Yu Mu, Masashi Tanimoto, Philipp J. Keller, Misha B. Ahrens, Jeremy Freeman, Minoru Koyama, Stephan Preibisch, Nikita Vladimirov, Avinash Pujala, Chen Wang, Chao-Tsung Yang, and Jason D. Wittenbach
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0301 basic medicine ,Computer science ,Cellular level ,Online Systems ,Biochemistry ,Online analysis ,03 medical and health sciences ,Functional brain ,0302 clinical medicine ,Neural Pathways ,Zebrafish larvae ,Animals ,Molecular Biology ,Swimming ,Zebrafish ,Neurons ,Brain Mapping ,Behavior, Animal ,Brain ,Cell Biology ,Functional mapping ,030104 developmental biology ,Larva ,Optomotor response ,Neuroscience ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Whole-brain imaging allows for comprehensive functional mapping of distributed neural pathways, but neuronal perturbation experiments are usually limited to targeting predefined regions or genetically identifiable cell types. To complement whole-brain measures of activity with brain-wide manipulations for testing causal interactions, we introduce a system that uses measured activity patterns to guide optical perturbations of any subset of neurons in the same fictively behaving larval zebrafish. First, a light-sheet microscope collects whole-brain data that are rapidly analyzed by a distributed computing system to generate functional brain maps. On the basis of these maps, the experimenter can then optically ablate neurons and image activity changes across the brain. We applied this method to characterize contributions of behaviorally tuned populations to the optomotor response. We extended the system to optogenetically stimulate arbitrary subsets of neurons during whole-brain imaging. These open-source methods enable delineating the contributions of neurons to brain-wide circuit dynamics and behavior in individual animals.
- Published
- 2018
21. Contextual modulation of sensitivity to naturalistic image structure in macaque V2
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Jeremy Freeman, Eero P. Simoncelli, Corey M. Ziemba, and J. Anthony Movshon
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0301 basic medicine ,Physiology ,Computer science ,Surround suppression ,Action Potentials ,Stimulus (physiology) ,Macaque ,03 medical and health sciences ,Spatial Processing ,0302 clinical medicine ,biology.animal ,Modulation (music) ,medicine ,Animals ,Visual Pathways ,Visual Cortex ,Neurons ,Image structure ,biology ,General Neuroscience ,Visual field ,Macaca fascicularis ,030104 developmental biology ,Visual cortex ,medicine.anatomical_structure ,Pattern Recognition, Visual ,Receptive field ,Visual Fields ,Neuroscience ,Photic Stimulation ,030217 neurology & neurosurgery - Abstract
The stimulus selectivity of neurons in V1 is well known, as is the finding that their responses can be affected by visual input to areas outside of the classical receptive field. Less well understood are the ways selectivity is modified as signals propagate to visual areas beyond V1, such as V2. We recently proposed a role for V2 neurons in representing the higher order statistical dependencies found in images of naturally occurring visual texture. V2 neurons, but not V1 neurons, respond more vigorously to “naturalistic” images that contain these dependencies than to “noise” images that lack them. In this work, we examine the dependency of these effects on stimulus size. For most V2 neurons, the preference for naturalistic over noise stimuli was modest when presented in small patches and gradually strengthened with increasing size, suggesting that the mechanisms responsible for this enhanced sensitivity operate over regions of the visual field that are larger than the classical receptive field. Indeed, we found that surround suppression was stronger for noise than for naturalistic stimuli and that the preference for large naturalistic stimuli developed over a delayed time course consistent with lateral or feedback connections. These findings are compatible with a spatially broad facilitatory mechanism that is absent in V1 and suggest that a distinct role for the receptive field surround emerges in V2 along with sensitivity for more complex image structure. NEW & NOTEWORTHY The responses of neurons in visual cortex are often affected by visual input delivered to regions of the visual field outside of the conventionally defined receptive field, but the significance of such contextual modulations are not well understood outside of area V1. We studied the importance of regions beyond the receptive field in establishing a novel form of selectivity for the statistical dependencies contained in natural visual textures that first emerges in area V2.
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- 2018
22. Development of Pharmacodynamic Assays to Assess Ex Vivo Masp-2 Inhibition and Their Use to Characterize the Pharmacodynamics of Narsoplimab (OMS721) in Humans and Monkeys
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Jeremy Freeman, Marither Chuidian, Jason Cummings, and Thomas Dudler
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business.industry ,Pharmacodynamics ,Immunology ,Medicine ,Cell Biology ,Hematology ,Pharmacology ,business ,Biochemistry ,Ex vivo - Abstract
Introduction Narsoplimab (OMS721) is a fully human monoclonal antibody that binds to and inhibits mannan-binding lectin-associated serine protease 2 (MASP-2). MASP-2 is the key enzyme responsible for activation of the lectin pathway of the complement system. The lectin pathway is activated when plasma is exposed to molecular patterns present on microbes and injured host cell surfaces, initiating a proteolytic cascade that results in the activation of complement components C4, C2, C3 and C5 to yield multiple biologically active products. Inhibiting MASP-2 activity prevents lectin-mediated generation of complement activation products, thereby reducing inflammation and tissue injury. Narsoplimab is the first lectin pathway-specific complement inhibitor in clinical development. In published clinical studies and case reports, improvement has been observed in narsoplimab-treated patients with hematopoietic stem cell transplant-associated thrombotic microangiopathy, immunoglobulin A (IgA) nephropathy and atypical hemolytic uremic syndrome. Here we describe the development of pharmacodynamic (PD) assays to quantify MASP-2 inhibition ex vivo and their use to study duration of action and to establish the pharmacokinetic (PK)/PD relationship of narsoplimab in monkeys and humans. Methods PD assays to measure lectin pathway activity, a measure of MASP-2 activity, in minimally diluted (90%) serum from human and monkey were developed using immobilized mannan as a lectin pathway-specific complement activator with C4b as the activation endpoint. ELISA and flow cytometry assay platforms were employed to assess the PD response of monkeys or normal healthy human volunteers administered narsoplimab, respectively. The PD response was used to characterize the time-course and dose-response of lectin pathway inhibition by narsoplimab. Drug concentration data obtained from matched serum samples were used to estimate the ex vivo EC50 of lectin pathway inhibition in monkeys and humans. Lectin pathway-specific complement activation assays applicable to minimally diluted serum samples were developed by evaluating the time-course of lectin-induced complement activation response under varying reaction temperatures and selecting optimized test conditions within the dynamic range of the assay platform. The test methods were used to characterize monkey and human lectin pathway inhibition profiles of narsoplimab in vitro, and the flow cytometric method was validated for analysis of human serum samples. Results The PD assays were used to characterize the PD response of monkeys administered a single intravenous (IV) bolus injection of narsoplimab at 0.05, 0.15, 0.5, 1.5 or 5 mg/kg, and of normal human healthy volunteers administered a single IV infusion of the drug at 0.25, 0.625 or 2 mg/kg, or 6 weekly IV infusions at 2 or 4 mg/kg. A clear, dose-dependent initial PD response was observed in monkeys in the dose range of 0.5 mg/kg to 5 mg/kg, which subsequently declined over time. In humans, a minimal PD response was observed at 0.025 mg/kg. A near maximal initial PD response was seen at 0.675 mg/kg or higher, followed by a decline over time. In the 6-week repeat-dose study, once-weekly dosing of narsoplimab at 2 mg/kg resulted in a mean trough PD response of ~55% lectin pathway inhibition, which increased to an ~80% mean trough response with once-weekly dosing of 4 mg/kg. PK sample analysis revealed a clear PK/PD relationship in monkeys and humans. Modeling of the PK/PD relationship in monkeys indicated an EC50 value of ~7 µg/mL (~ 46 nM), which is comparable to the IC50 value of lectin pathway inhibition in vitro (33 nM). In humans, modeling of the PK/PD relationship data indicated an EC50 value of ~500 ng/mL (3.3 nM), again very similar to the IC50 value of lectin pathway inhibition in vitro (3.4 nM). Conclusion We successfully developed PD assays to monitor blockade of lectin pathway activation in monkeys and humans administered narsoplimab. Using a validated PD assay, we demonstrate that a high level of lectin pathway blockade can be maintained in normal human healthy volunteers by once-weekly administration of narsoplimab at 4 mg/kg IV. We also demonstrate a consistent PK/PD relationship across the study population, indicating that narsoplimab concentration ranges can be used to target the desired level of lectin pathway inhibition. Figure 1 Disclosures Freeman: Omeros Corporation: Current Employment. Cummings:Omeros Corporation: Current Employment. Chuidian:Omeros Corporation: Current Employment. Dudler:Omeros Corporation: Current Employment.
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- 2020
23. starfish: scalable pipelines for image-based transcriptomics
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Deep Ganguli, Brian Long, Kevin A. Yamauchi, Tony Tung, Jeremy Freeman, Matthew Cai, Justin T. Kiggins, Ambrose J. Carr, and Shannon Axelrod
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Pipeline transport ,biology ,Computer science ,Computer graphics (images) ,Starfish ,Scalability ,Python (programming language) ,biology.organism_classification ,computer ,Image based ,computer.programming_language - Published
- 2021
24. Improving data quality in neuronal population recordings
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Jeremy Freeman, Kenneth D. Harris, Rodrigo Quian Quiroga, and Spencer L. Smith
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0301 basic medicine ,Computer science ,media_common.quotation_subject ,Action Potentials ,Article ,Field (computer science) ,03 medical and health sciences ,0302 clinical medicine ,Optical imaging ,Data accuracy ,Animals ,Humans ,Quality (business) ,Function (engineering) ,Neuronal population ,media_common ,Neurons ,Extramural ,General Neuroscience ,Optical Imaging ,Brain ,Data Accuracy ,Electrophysiological Phenomena ,030104 developmental biology ,Data quality ,Nerve Net ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Understanding how the brain operates requires understanding how large sets of neurons function together. Modern recording technology makes it possible to simultaneously record the activity of hundreds of neurons, and technological developments will soon allow recording of thousands or tens of thousands. As with all experimental techniques, these methods are subject to confounds that complicate the interpretation of such recordings, and could lead to erroneous scientific conclusions. Here, we discuss methods for assessing and improving the quality of data from these techniques, and outline likely future directions in this field.
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- 2016
25. Technologies for imaging neural activity in large volumes
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Spencer L. Smith, Jeremy Freeman, and Na Ji
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0301 basic medicine ,Fluorescence-lifetime imaging microscopy ,Computer science ,media_common.quotation_subject ,Real-time computing ,Image processing ,Article ,03 medical and health sciences ,Sampling (signal processing) ,Image Processing, Computer-Assisted ,Biological neural network ,Animals ,Humans ,Function (engineering) ,media_common ,Neurons ,General Neuroscience ,Optical Imaging ,Volume (computing) ,Brain ,Microscopy, Fluorescence, Multiphoton ,030104 developmental biology ,Temporal resolution ,Nerve Net ,Focus (optics) ,Neuroscience - Abstract
Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Collecting data from individual planes, conventional microscopy cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here, we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for the processing and analysis of volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics, and help elucidate how brain regions work in concert to support behavior.
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- 2016
26. Two Myofilament-Based Approaches to Prevent Genetic Dilated Cardiomyopathy
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Claire E. Branley, Joelle Tudor, Kristina B. Kooiker, Jil C. Tardiff, Jeremy Freeman, Michael Regnier, and Farid Moussavi-Harami
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Myofilament ,medicine.medical_specialty ,business.industry ,Internal medicine ,Biophysics ,Cardiology ,Medicine ,Dilated cardiomyopathy ,business ,medicine.disease - Published
- 2020
27. Ribonucleotide Reductase is Essential in Adult Cardiomyocytes
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Farid Moussavi-Harami, Amy Martinson, Joelle Tudor, Djelli Berisha, Claire E. Branley, Jeremy Freeman, and Kristina B. Kooiker
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Ribonucleotide reductase ,Biochemistry ,Chemistry ,Biophysics - Published
- 2020
28. Vigabatrin with hormonal treatment versus hormonal treatment alone (ICISS) for infantile spasms: 18-month outcomes of an open-label, randomised controlled trial
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Finbar J K O'Callaghan, Stuart W Edwards, Fabienne Dietrich Alber, Mario Cortina Borja, Eleanor Hancock, Anthony L Johnson, Colin R Kennedy, Marcus Likeman, Andrew L Lux, Mark T Mackay, Andrew A Mallick, Richard W Newton, Melinda Nolan, Ronit Pressler, Dietz Rating, Bernhard Schmitt, Christopher M Verity, John P Osborne, Maysara Abdel Aziz, Triloknath Acharya, Carolyn Adcock, Robert Jones, Rachel Howells, Ben Marsh, Kemi Adejare, Rashmi Adiga, Mary Wheater, Mansoor Ahmed, Mohammad Sawal, Chhavi Goel, MAS Ahmed, Michael Alber, Markus Wolff, Susanne Ruf, Asya Al-Kharusi, Hassan Al-Moasseb, Ruchi Arora, Richard Beach, Patricia Atkinson, Kunle Ayonrinde, Pronab Bala, Nicola Bamford, Nagi Barakat, Nigel Basheer, Peter Baxter, Santosh Mordekar, Chris Rittey, Ingo Borggraefe, Peter Borusiak, Sabine Cagnoli, Richard Brown, Sophie Calvert, Duncan Cameron, Ramesh Chaniyil, Ravi Chinthapalli, Gabriel Chow, William Whitehouse, Vinodhini Clarke, Chris Cooper, Alexane Datta, Selwyn D'Costa, Christian de Goede, Helen Basu, David Deekollu, Adela Della Marina, Penelope Dison, Colin Dunkley, Megan Eaton, Julie Ellison, Robert Pugh, Penny Fallon, Hani Faza, Imti Choonara, Richard Morton, Mal Ratnayaka, Colin Ferrie, Amanda Freeman, Stephen Warriner, Maria Garcia, Malihe Ghazavi, Frances Gibbon, John Gibbs, Des Ginbey, Iolanda Guarino, Rajesh Gupta, Mary Hanlon, Siân Harris, Paul Munyard, Cheryl Hemingway, Christin Eltze, Marios Kaliakatsos, Velayutham Murugan, Robert Robinson, Jeen Tan, Daniel Hindley, Adrian Hughes, Akmal Hussain, Greg Boden, Munir Hussain, Nahin Hussain, Lyvia Dabydeen, Kate Irwin, Julia Jacobs, Praveen Jauhari, Philip Minchom, Simon Jones, Michael Karenfort, Reinhard Keimer, Colin Kennedy, Fenella Kirkham, Andrea Whitney, Martin Kirkpatrick, Alice Jollands, Rachel Kneen, Anand Iyer, Amy McTague, Stefan Spinty, Ramesh Kumar, Gerhard Kurlemann, Matthew Lee, Eman Jurges, Robert Levy, Helen Lewis, Hilary Lewis, Andrew Lloyd Evans, Ne-Ron Loh, John Osborne, Finbar O'Callaghan, Hilary Maddicks, Thomas Luecke, Andrew Lux, Anirban Majumdar, Kayal Vijayakumar, Mark MacKay, Jeremy Freeman, Michael Hayman, Andrew Kornberg, Rick Leventer, Monique Ryan, Tyson Ware, Penny Mancais, Katina Marinaki, Albert Massarano, Satheesh Mathew, Ailsa McLellan, Colin Melville, Leena Mewasingh, Hiltrud Muhle, Eisawi Nagmeldin, Jeyashree Natarajan, Suresh Nelapatla, Jailosi Gondwe, Richard Newton, Imelda Hughes, Tim Martland, Gary McCullagh, Grace Vassallo, Stephen Nirmal, Suzanne Davis, Rakesh Patel, Cynthia Sharpe, Anas Olabi, Kevin O'Neill, Jim Gould, Axel Panzer, Manuela Theophil, Srinivas Parepalli, Frank Hinde, Martin Smith, Alasdair Parker, Manali Chitre, Sunny Philip, Rajat Gupta, Evangeline Wassmer, Mike Pike, Tony McShane, Nandhini Prakash, Beena Padmakumar, Clair Pridmore, Viola Prietsch, Peter Krieg, Ros Quinlivan, Michael Quinn, Andrew Collinson, Usha Rajalingam, Karl Rakshi, Tekki Rao, Asha Ravi, Rob Rifkin, Helen Roper, Piers Rowlandson, Lynette Sadleir, Sanjay Sahi, Arun Saraswatula, Siobhan O'Sullivan, Kethar Saravanan, Alastair Scammell, Sudhakar Rao, Susanne Schubert-Bast, David J Scott, Fraser Scott, Matthew Pye, Ayaz Shah, Elma Stephen, Shambhu Shah, Andrew Butterfill, Pauline Shute, Rajeeva Singh, Brigid Allogoa, Ravinder Singh, Gyanranjan Sinha, Puthuval Sivakumar, Robert Smith, Sivaranjini Sriskandan, Martin Steinert, Michael Strassburg, Susi Strozzi, Geeta Subramanian, Andrew Tandy, University of Zurich, and O'Callaghan, Finbar J K
- Subjects
Pediatrics ,medicine.medical_specialty ,Combination therapy ,610 Medicine & health ,Vigabatrin ,law.invention ,03 medical and health sciences ,Epilepsy ,0302 clinical medicine ,Pharmacotherapy ,Randomized controlled trial ,law ,030225 pediatrics ,medicine ,Developmental and Educational Psychology ,Pediatrics, Perinatology, and Child Health ,2735 Pediatrics, Perinatology and Child Health ,3204 Developmental and Educational Psychology ,Intention-to-treat analysis ,business.industry ,medicine.disease ,10036 Medical Clinic ,Pediatrics, Perinatology and Child Health ,Prednisolone ,Hormonal therapy ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
BACKGROUND: Infantile spasms constitute a severe form of epileptic encephalopathy. In the International Collaborative Infantile Spasms Study (ICISS), we showed that combining vigabatrin with hormonal therapy was more effective than hormonal therapy alone at stopping spasms between days 14 and 42 of treatment. In this planned follow-up, we aimed to assess whether combination therapy was associated with improved developmental and epilepsy outcomes at 18 months of age.METHODS: In ICISS, a multicentre, open-label, randomised controlled trial, infants were enrolled from 102 hospitals (three in Australia, 11 in Germany, two in New Zealand, three in Switzerland, and 83 in the UK). Eligible infants had a clinical diagnosis of infantile spasms and a hypsarrhythmic (or similar) electroencephalogram (EEG) no more than 7 days before enrolment. Participants were randomly assigned (1:1) by a secure website to receive hormonal therapy with vigabatrin or hormonal therapy alone. If parents consented, there was an additional randomisation (1:1) of type of hormonal therapy used (prednisolone or tetracosactide depot). Block randomisation was stratified for hormonal treatment and risk of developmental impairment. Parents and clinicians were not masked to therapy, but investigators assessing epilepsy and developmental outcomes at 18 months were masked to treatment allocation. Minimum doses were oral prednisolone 10 mg four times a day or intramuscular tetracosactide depot 0·5 mg (40 IU) on alternate days with or without oral vigabatrin 100 mg/kg per day. The primary outcome at 18 months was development as assessed by the Vineland Adaptive Behaviour Scales (VABS) composite score. Secondary outcomes were the presence or absence of epileptic seizures or infantile spasms in the previous 28 days, as recorded by parents and carers, and the use of any anti-epileptic treatment (including ketogenic diet) in the previous 28 days. Analysis was by intention to treat. The trial is registered with the ISRCTN registry, number 54363174, and EudraCT, number 2006-000788-27.FINDINGS: Between March 7, 2007, and May 22, 2014, 766 infants were screened and, of those, 377 were randomly assigned to hormonal therapy with vigabatrin (n=186) or hormonal therapy alone (n=191). 362 infants were assessed for developmental and epilepsy outcomes at 18 months, 181 in each treatment group. Mean VABS scores did not differ significantly between the combination therapy group and the hormonal therapy alone group (73·9 [SE 1·3] vs 72·7 [1·4], difference -1·2 [95% CI -4·9 to 2·6], p=0·55). Presence of epilepsy at the assessment at age 18 months was similar in both treatment groups (54 [30·0%] of 180 infants who received combination therapy vs 52 [29·2%] of 178 who received hormonal therapy alone; difference 0·8% [95% CI -8·8 to 10·4], p=0·90). Presence of spasms was also similar in both treatment groups (27 [15·0%] of 180 infants on combination therapy vs 28 [15·7%] of 178 on hormonal therapy alone; difference 0·7% [95% CI -6·9 to 8·3], p=0·85). At the 18-month assessment, 158 (44·1%) of 358 infants were on some form of anti-epileptic treatment. Initial control of spasms between days 14 and 42 of treatment was associated with higher mean VABS scores at 18 months (79·1 [SE 1·2] vs 63·2 [1·1], difference 15·9 [95% CI 12·4 to 19·5], pINTERPRETATION: Combination therapy did not result in improved developmental or epilepsy outcomes at 18 months. However, early clinical response to treatment was associated with improved developmental and epilepsy outcomes at 18 months. Longer lead-time to treatment was associated with poorer outcomes. Rapid diagnosis and effective treatment of infantile spasms could therefore improve outcomes.FUNDING: The Castang Foundation, Bath Unit for Research in Paediatrics, National Institute of Health Research, the Royal United Hospitals Bath NHS Foundation Trust, BRONNER-BENDER Stiftung/Gernsbach, University Children's Hospital Zurich.
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- 2018
29. Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
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Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D. Harris, Ben Bolte, Timothy A. Machado, Dario Ringach, Jasmine Stone, Luke E. Rogerson, Nicolas J Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Roman-Roson, Lucas Theis, Andreas S. Tolias, and Matthias Bethge
- Subjects
Databases, Factual ,Computer science ,Models, Neurological ,Action Potentials ,Inference ,Calcium Measurement ,Machine learning ,computer.software_genre ,Retina ,Computational biology ,Mice ,03 medical and health sciences ,Neural activity ,0302 clinical medicine ,Calcium imaging ,Biological neural network ,Animals ,lcsh:QH301-705.5 ,030304 developmental biology ,0303 health sciences ,business.industry ,FOS: Clinical medicine ,Optical Imaging ,SIGNAL (programming language) ,Neurosciences ,Molecular Imaging ,Range (mathematics) ,lcsh:Biology (General) ,Benchmark (computing) ,Calcium ,Spike (software development) ,Artificial intelligence ,business ,computer ,030217 neurology & neurosurgery ,Algorithms ,Retinal Neurons - Abstract
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike trains from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.
- Published
- 2018
30. Medical cannabis for paediatric developmental-behavioural and psychiatric disorders
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Daryl, Efron and Jeremy, Freeman
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Clinical Trials as Topic ,Evidence-Based Medicine ,Attention Deficit Disorder with Hyperactivity ,Autism Spectrum Disorder ,Intellectual Disability ,Humans ,Medical Marijuana ,Anxiety ,Child ,Pediatrics ,Central Nervous System Agents ,Phytotherapy - Published
- 2018
31. Binder 2.0 - Reproducible, interactive, sharable environments for science at scale
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Kyle Kelley, T. Head, Gladys Nalvarte, Chris Holdgraf, Brian E. Granger, Jupyter, Andrew Osheroff, Yuvi Panda, Benjamin Ragan-Kelley, Matthias Bussonnier, Jessica Zosa Forde, Carol Willing, Jeremy Freeman, Michael Pacer, and Fernando Perez
- Subjects
Scale (ratio) ,Computer science ,business.industry ,Process engineering ,business - Published
- 2018
32. Engineering elastic properties into an anti-TNFα monoclonal antibody
- Author
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Anhdao T Darcy, Leslie Alessandri, Lucia Eaton, Sahana Bose, David Banach, Silvino Sousa, Gregory M. Preston, Jeremy Freeman, David Winarta, Dana I. Filoti, Reema Raghavendra, Nathan Brown, David Ouellette, Ivan Correia, Alexander V. Ivanov, and Ramkrishna Sadhukhan
- Subjects
musculoskeletal diseases ,mab ,Necrosis ,medicine.drug_class ,polymer ,tnfα ,elastin ,Inflammation ,Monoclonal antibody ,tem ,medicine ,fusion protein ,elastomeric ,lcsh:QH301-705.5 ,biology ,Chemistry ,General Engineering ,Fusion protein ,lcsh:Biology (General) ,anti-tnfα ,biology.protein ,Cancer research ,Tumor necrosis factor alpha ,Antibody ,medicine.symptom ,Elastin - Abstract
Injecting anti-tumor necrosis factor (TNF)α antibodies into patient joints at the site of inflammation, inter-articular (IA) delivery, has demonstrated modest success for treatment of Spondyloarthritis (SpA), Rheumatoid Arthritis (RA), and osteoarthritis. However, IA delivery is not the treatment route of choice due to rapid clearance from the site of administration. Elastin-like polypeptides (ELPs) are reported to undergo phase transition; forming reversible aggregates above their transition temperature, which when injected into IA space have a 25-fold longer half-life compared to the soluble form. Here, we fused an ELP repeat to the C-terminus of each heavy chain of an anti-TNFα monoclonal antibody (mAb) and provide detailed characterization of the fusion IgG molecule. Expression and purification yielded homogenous protein confirmed by gels, hydrophobic-interaction chromatography, Capilary Electrophoresis (CE), Mass Spectrometry (MS), and analytical ultracentrifugation. The ELPs altered hydrophobicity and pI of the parent mAb and new elastic properties were imparted to the molecule; forming large stable complexes with a hydrodynamic radius of 40 nm above 39°C that dissociated into soluble, active monomer below 37°C. The fusion mAb retained its affinity and ability to neutralize TNFα as determined by surface plasmon resonance and cell-based assay, respectively, with equal potency to unmodified anti-TNFα mAb. Differential-scanning calorimetry studies show stabilization of adjacent CH2 and CH3 domains in the fusion molecule and the aggregated molecule was found to be fully functional after 7 days at 37°C. For the first time, we reveal architecture of an ELP-fusion mAb and binding to antigen using single-particle-transmission-electron microscopy. Unstructured ELP was visualized at the C-terminus and binding to antigen was shown at the N-terminus. Collectively, these studies indicate that it is possible to impart elastic properties to a monoclonal antibody while retaining purity, stability, and ability to effectively bind and neutralize antigen.
- Published
- 2018
33. Direct Detection of Multiple Acidic Proton Sites in Zeolite HZSM-5
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Kuizhi Chen, Jeffery L. White, Eric Sheets, Maryam Abdolrhamani, Garrett Ward, and Jeremy Freeman
- Subjects
chemistry.chemical_classification ,Alkane ,education.field_of_study ,Chemistry ,Inorganic chemistry ,Population ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Biochemistry ,Catalysis ,0104 chemical sciences ,Ion ,Colloid and Surface Chemistry ,Hydrocarbon ,Reagent ,Moiety ,0210 nano-technology ,Zeolite ,Brønsted–Lowry acid–base theory ,education - Abstract
Direct observation of multiple reactive sites in the zeolite HZSM-5, a member of the MFI family of zeolite structures, contradicts the traditional view of only one type of active protonic species in industrially important zeolites. In addition to the well-known Bronsted acid site proton, two other protonic species undergo room-temperature hydrogen–deuterium exchange with an alkane hydrocarbon reagent, including one zeolite moiety characterized by a broad 1H chemical shift at ca. 12–15 ppm that is reported here for the first time. Although the ca. 13 ppm chemical shift value is consistent with computational predictions from the literature for a surface-stabilized hydroxonium ion in a zeolite, data suggest that the signal does not arise from hydroxonium species but rather from hydroxyls on extra-lattice aluminol species proximate to Bronsted lattice sites, i.e., a small population of highly deshielded acid sites. Double-resonance experiments show that this species is proximate to Al atoms, similar to the Br...
- Published
- 2017
34. Fire-Driven Decline of Endemic Allosyncarpia Monsoon Rainforests in Northern Australia
- Author
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Jeremy Russell-Smith, Jeremy Freeman, and Andrew Edwards
- Subjects
0106 biological sciences ,Canopy ,010504 meteorology & atmospheric sciences ,Landsat Fire History ,Biodiversity ,Rainforest ,Monsoon ,010603 evolutionary biology ,01 natural sciences ,Kakadu National Park ,0105 earth and related environmental sciences ,Fire regime ,biology ,Allosyncarpia ,National park ,woody thickening ,Myrtaceae ,Forestry ,lcsh:QK900-989 ,canopy change ,biology.organism_classification ,Geography ,Arnhem Land ,lcsh:Plant ecology - Abstract
Although contemporary fire regimes in fire-prone Australian savannas are recognised as having major impacts on an array of biodiversity and environmental values, a number of studies have observed significant monsoon rainforest expansion in recent decades. Here we assess the status of a locally extensive endemic monsoon rainforest type, dominated by Allosyncarpia ternata (Myrtaceae), restricted to sandstone terrain including in the World Heritage property, Kakadu National Park. We undertook assessments of: (1) geographic correlates of Allosyncarpia forest distribution; (2) change in canopy cover at 40 representative forest patches at topographically exposed sites with reference to a 60-year aerial photo and fine-scale image archive, and fire mapping data; and (3) structural characteristics associated with sites exhibiting stable, contracting, and increasing canopy cover. Mean canopy cover at sampled forest patches declined by 9.5% over the study period. Most canopy loss occurred at the most fire-susceptible patches. Assessment of structural characteristics at sampled sites illustrated that canopy expansion represented vegetative recovery rather than expansion de novo. The study (1) confirms the vulnerability of exposed margins of this forest type to fire incursions; (2) illustrates the magnitude of, and describes solutions for addressing, the regional conservation management challenge; and (3) serves as a reminder that, in savanna environments, severe fire regimes can substantially outweigh the woody growth-enhancing effects of other regional (e.g., increased rainfall) and global-scale (e.g., atmospheric CO2 fertilisation) drivers.
- Published
- 2017
- Full Text
- View/download PDF
35. A Cellular Resolution Map of Barrel Cortex Activity during Tactile Behavior
- Author
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Karel Svoboda, Jeremy Freeman, Vijay Iyer, Caiying Guo, and Simon Peron
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RNA, Untranslated ,Neuroscience(all) ,Models, Neurological ,Action Potentials ,Mice, Transgenic ,Sensory system ,Mice ,Neural activity ,Orientation ,Animals ,Learning ,Neurons ,Afferent Pathways ,Brain Mapping ,integumentary system ,Glutamate Decarboxylase ,Active touch ,General Neuroscience ,Somatosensory Cortex ,Barrel cortex ,Optogenetics ,Luminescent Proteins ,Nonlinear Dynamics ,Cellular resolution ,Touch ,Vibrissae ,Exploratory Behavior ,Calcium ,Psychology ,Neuroscience - Abstract
Summary Comprehensive measurement of neural activity remains challenging due to the large numbers of neurons in each brain area. We used volumetric two-photon imaging in mice expressing GCaMP6s and nuclear red fluorescent proteins to sample activity in 75% of superficial barrel cortex neurons across the relevant cortical columns, approximately 12,000 neurons per animal, during performance of a single whisker object localization task. Task-related activity peaked during object palpation. An encoding model related activity to behavioral variables. In the column corresponding to the spared whisker, 300 layer (L) 2/3 pyramidal neurons (17%) each encoded touch and whisker movements. Touch representation declined by half in surrounding columns; whisker movement representation was unchanged. Following the emergence of stereotyped task-related movement, sensory representations showed no measurable plasticity. Touch direction was topographically organized, with distinct organization for passive and active touch. Our work reveals sparse and spatially intermingled representations of multiple tactile features. Video Abstract
- Published
- 2015
- Full Text
- View/download PDF
36. The Anorexia Nervosa Genetics Initiative: Study description and sample characteristics of the Australian and New Zealand arm
- Author
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Gu Zhu, Cynthia M. Bulik, Laura M. Thornton, Nicholas G. Martin, Warren Ward, Janice Russell, Martin A. Kennedy, Sarah Maguire, Elizabeth K. Hughes, A. Kate Fairweather-Schmidt, Anthea Fursland, Jeremy Freeman, Tracey D. Wade, Sloane Madden, Katherine M. Kirk, Fiona Wagg, Julie McCormack, Susan M Sawyer, Amy Mao, Felicity C Martin, Richard Parker, Christine Morgan, Kerrie McAloney, Jennifer Jordan, and Phillipa Hay
- Subjects
Adult ,Male ,medicine.medical_specialty ,Anorexia Nervosa ,Adolescent ,International Cooperation ,Sample (statistics) ,Computer-assisted web interviewing ,Body Mass Index ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,mental disorders ,medicine ,Humans ,Psychiatry ,Genetics ,Clinical interview ,Patient Selection ,High mortality ,Australia ,General Medicine ,medicine.disease ,030227 psychiatry ,Psychiatry and Mental health ,Eating disorders ,Anorexia nervosa (differential diagnoses) ,Etiology ,Female ,Psychology ,Body mass index ,030217 neurology & neurosurgery ,Clinical psychology ,Genome-Wide Association Study ,New Zealand - Abstract
Objectives:Anorexia nervosa is a severe psychiatric disorder with high mortality rates. While its aetiology is poorly understood, there is evidence of a significant genetic component. The Anorexia Nervosa Genetics Initiative is an international collaboration which aims to understand the genetic basis of the disorder. This paper describes the recruitment and characteristics of the Australasian Anorexia Nervosa Genetics Initiative sample, the largest sample of individuals with anorexia nervosa ever assembled across Australia and New Zealand.Methods:Participants completed an online questionnaire based on the Structured Clinical Interview Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) eating disorders section. Participants who met specified case criteria for lifetime anorexia nervosa were requested to provide a DNA sample for genetic analysis.Results:Overall, the study recruited 3414 Australians and 543 New Zealanders meeting the lifetime anorexia nervosa case criteria by using a variety of conventional and social media recruitment methods. At the time of questionnaire completion, 28% had a body mass index ⩽ 18.5 kg/m2. Fasting and exercise were the most commonly employed methods of weight control, and were associated with the youngest reported ages of onset. At the time of the study, 32% of participants meeting lifetime anorexia nervosa case criteria were under the care of a medical practitioner; those with current body mass index < 18.5 kg/m2were more likely to be currently receiving medical care (56%) than those with current body mass index ⩾ 18.5 kg/m2(23%). Professional treatment for eating disorders was most likely to have been received from general practitioners (45% of study participants), dietitians (42%) and outpatient programmes (42%).Conclusions:This study was effective in assembling the largest community sample of people with lifetime anorexia nervosa in Australia and New Zealand to date. The proportion of people with anorexia nervosa currently receiving medical care, and the most common sources of treatment accessed, indicates the importance of training for general practitioners and dietitians in treating anorexia nervosa.
- Published
- 2017
- Full Text
- View/download PDF
37. Motion Direction Biases and Decoding in Human Visual Cortex
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Helena X. Wang, David J. Heeger, Jeremy Freeman, and Elisha P. Merriam
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Adult ,Male ,Nerve net ,Motion Perception ,Stimulus (physiology) ,computer.software_genre ,Young Adult ,Voxel ,medicine ,Humans ,Motion perception ,Visual Cortex ,Communication ,Quantitative Biology::Neurons and Cognition ,medicine.diagnostic_test ,business.industry ,General Neuroscience ,Pattern recognition ,Articles ,Response bias ,Visual cortex ,medicine.anatomical_structure ,Female ,Artificial intelligence ,Cues ,Nerve Net ,Functional magnetic resonance imaging ,Psychology ,business ,computer ,Photic Stimulation ,Psychomotor Performance ,Decoding methods - Abstract
Functional magnetic resonance imaging (fMRI) studies have relied on multivariate analysis methods to decode visual motion direction from measurements of cortical activity. Above-chance decoding has been commonly used to infer the motion-selective response properties of the underlying neural populations. Moreover, patterns of reliable response biases across voxels that underlie decoding have been interpreted to reflect maps of functional architecture. Using fMRI, we identified a direction-selective response bias in human visual cortex that: (1) predicted motion-decoding accuracy; (2) depended on the shape of the stimulus aperture rather than the absolute direction of motion, such that response amplitudes gradually decreased with distance from the stimulus aperture edge corresponding to motion origin; and 3) was present in V1, V2, V3, but not evident in MT+, explaining the higher motion-decoding accuracies reported previously in early visual cortex. These results demonstrate that fMRI-based motion decoding has little or no dependence on the underlying functional organization of motion selectivity.
- Published
- 2014
38. Derivation of Phase 3 dosing for peginterferon lambda-1a in chronic hepatitis C, Part 2: Exposure-response analyses for efficacy and safety variables
- Author
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Matthew Hruska, Phyllis Chan, Jeremy Freeman, Maria Arantxa Horga, Juan-Carlos Lopez-Talavera, Alaa Ahmad, Xiaodong Wang, J. Hillson, and Vikram Kansra
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Pharmacology ,medicine.medical_specialty ,Anemia ,Bilirubin ,business.industry ,Hepatitis C virus ,Ribavirin ,Cmax ,virus diseases ,Neutropenia ,medicine.disease_cause ,medicine.disease ,Gastroenterology ,chemistry.chemical_compound ,chemistry ,Pharmacodynamics ,Internal medicine ,medicine ,Pharmacology (medical) ,Dosing ,business - Abstract
This is the second of two manuscripts detailing the pharmacodynamic derivation of peginterferon lambda-1a (Lambda) dosing and treatment durations for Phase 3 studies in hepatitis C virus (HCV) infection, based on Phase 2 data. Herein, we describe the derivation of regression models for 12-week on-treatment virologic response and safety outcomes at 120, 180, and 240 μg Lambda with ribavirin. In patients with HCV genotypes 1 or 4, there was a significant (P = 0.024) relationship between undetectable HCV-RNA at Week 4 and Lambda exposure (AUC or Cmax), with the largest difference between adjacent dose levels between the 180 and 120 μg exposure ranges. Risk of Grade 3–4 aminotransferase or bilirubin elevations relative to a peginterferon alfa-2a/ribavirin control were related to Lambda exposure for all patients, and the largest increase between adjacent dose levels was seen for 240 versus 180 μg. Anemia and neutropenia events were lower than control across all doses and exposures. Based on these data and those in our previous manuscript, Phase 3 studies will evaluate fixed 180 µg doses of Lambda in combination with ribavirin and a direct-acting antiviral for 24–48 weeks in HCV genotypes 1 or 4 or 12–24 weeks in genotypes 2 or 3.
- Published
- 2014
39. Parathyroid Carcinoma
- Author
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Lukasz Czerwonka, Nidal Muhanna, and Jeremy Freeman
- Published
- 2016
40. Coarse-Scale Biases for Spirals and Orientation in Human Visual Cortex
- Author
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David J. Heeger, Jeremy Freeman, and Elisha P. Merriam
- Subjects
Adult ,Male ,Visual perception ,Stimulus (physiology) ,computer.software_genre ,Brain mapping ,Foveal ,Voxel ,Orientation ,Image Processing, Computer-Assisted ,medicine ,Humans ,Clockwise ,Visual Cortex ,Brain Mapping ,Communication ,medicine.diagnostic_test ,business.industry ,General Neuroscience ,Pattern recognition ,Magnetic Resonance Imaging ,Visual cortex ,medicine.anatomical_structure ,Visual Perception ,Female ,Artificial intelligence ,business ,Psychology ,Functional magnetic resonance imaging ,computer ,Photic Stimulation - Abstract
Multivariate decoding analyses are widely applied to functional magnetic resonance imaging (fMRI) data, but there is controversy over their interpretation. Orientation decoding in primary visual cortex (V1) reflects coarse-scale biases, including an over-representation of radial orientations. But fMRI responses to clockwise and counter-clockwise spirals can also be decoded. Because these stimuli are matched for radial orientation, while differing in local orientation, it has been argued that fine-scale columnar selectivity for orientation contributes to orientation decoding. We measured fMRI responses in human V1 to both oriented gratings and spirals. Responses to oriented gratings exhibited a complex topography, including a radial bias that was most pronounced in the peripheral representation, and a near-vertical bias that was most pronounced near the foveal representation. Responses to clockwise and counter-clockwise spirals also exhibited coarse-scale organization, at the scale of entire visual quadrants. The preference of each voxel for clockwise or counter-clockwise spirals was predicted from the preferences of that voxel for orientation and spatial position (i.e., within the retinotopic map). Our results demonstrate a bias for local stimulus orientation that has a coarse spatial scale, is robust across stimulus classes (spirals and gratings), and suffices to explain decoding from fMRI responses in V1.
- Published
- 2013
41. A functional and perceptual signature of the second visual area in primates
- Author
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J. Anthony Movshon, Eero P. Simoncelli, Corey M. Ziemba, David J. Heeger, and Jeremy Freeman
- Subjects
Visual perception ,Models, Neurological ,Observation ,Electroencephalography ,Visual system ,Macaque ,Choice Behavior ,Article ,Extrastriate cortex ,biology.animal ,Orientation ,medicine ,Psychophysics ,Image Processing, Computer-Assisted ,Animals ,Humans ,Computer Simulation ,Visual Pathways ,Visual Cortex ,Neurons ,biology ,medicine.diagnostic_test ,Orientation (computer vision) ,General Neuroscience ,Magnetic Resonance Imaging ,Oxygen ,Visual cortex ,medicine.anatomical_structure ,Visual Perception ,Macaca ,Psychology ,Neuroscience ,Photic Stimulation - Abstract
There is no generally accepted account of the function of the second visual cortical area (V2), partly because no simple response properties robustly distinguish V2 neurons from those in primary visual cortex (V1). We constructed synthetic stimuli replicating the higher-order statistical dependencies found in natural texture images and used them to stimulate macaque V1 and V2 neurons. Most V2 cells responded more vigorously to these textures than to control stimuli lacking naturalistic structure; V1 cells did not. Functional magnetic resonance imaging (fMRI) measurements in humans revealed differences between V1 and V2 that paralleled the neuronal measurements. The ability of human observers to detect naturalistic structure in different types of texture was well predicted by the strength of neuronal and fMRI responses in V2 but not in V1. Together, these results reveal a particular functional role for V2 in the representation of natural image structure.
- Published
- 2013
42. Selectivity and tolerance for visual texture in macaque V2
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Jeremy Freeman, J. Anthony Movshon, Eero P. Simoncelli, and Corey M. Ziemba
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0301 basic medicine ,Visual perception ,genetic structures ,Texture (music) ,Visual system ,Macaque ,03 medical and health sciences ,0302 clinical medicine ,Form perception ,biology.animal ,Orientation ,medicine ,Animals ,Computer vision ,Visual Pathways ,Visual hierarchy ,Visual Cortex ,Neurons ,Multidisciplinary ,biology ,Orientation (computer vision) ,business.industry ,eye diseases ,Electrophysiology ,Form Perception ,Macaca fascicularis ,030104 developmental biology ,Visual cortex ,medicine.anatomical_structure ,PNAS Plus ,Visual Perception ,Artificial intelligence ,Psychology ,business ,030217 neurology & neurosurgery ,Photic Stimulation - Abstract
As information propagates along the ventral visual hierarchy, neuronal responses become both more specific for particular image features and more tolerant of image transformations that preserve those features. Here, we present evidence that neurons in area V2 are selective for local statistics that occur in natural visual textures, and tolerant of manipulations that preserve these statistics. Texture stimuli were generated by sampling from a statistical model, with parameters chosen to match the parameters of a set of visually distinct natural texture images. Stimuli generated with the same statistics are perceptually similar to each other despite differences, arising from the sampling process, in the precise spatial location of features. We assessed the accuracy with which these textures could be classified based on the responses of V1 and V2 neurons recorded individually in anesthetized macaque monkeys. We also assessed the accuracy with which particular samples could be identified, relative to other statistically matched samples. For populations of up to 100 cells, V1 neurons supported better performance in the sample identification task, whereas V2 neurons exhibited better performance in texture classification. Relative to V1, the responses of V2 show greater selectivity and tolerance for the representation of texture statistics.
- Published
- 2016
43. Author response: Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion
- Author
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Chao-Tsung Yang, Owen Randlett, Misha B. Ahrens, Florian Engert, Timothy W. Dunn, Alexander F. Schier, Eva A. Naumann, Yu Mu, Jeremy Freeman, and Sujatha Narayan
- Subjects
Neural activity ,biology ,biology.organism_classification ,Zebrafish ,Neuroscience - Published
- 2016
44. Large-Scale Neuroscience: From Analytics to Insight
- Author
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Gary Marcus and Jeremy Freeman
- Subjects
Scale (ratio) ,Computer science ,Analytics ,business.industry ,business ,Data science - Published
- 2015
45. Lessons from Evolution
- Author
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Gary Marcus, Jeremy Freeman, and Leah Krubitzer
- Subjects
Computer science - Published
- 2015
46. Whole Brain Simulation
- Author
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Jeremy Freeman, Gary Marcus, and Sean Hill
- Subjects
Computer science ,Neuroscience ,Brain simulation - Published
- 2015
47. The Miswired Brain, Genes, and Mental Illness
- Author
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Kevin J. Mitchell, Gary Marcus, and Jeremy Freeman
- Subjects
medicine.medical_specialty ,business.industry ,Medicine ,business ,Psychiatry ,Mental illness ,medicine.disease ,Gene - Published
- 2015
48. Whole Brain Neuroimaging and Virtual Reality
- Author
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Misha B. Ahrens, Jeremy Freeman, and Gary Marcus
- Subjects
Cognitive science ,Neuroimaging ,Functional neuroimaging ,Virtual reality ,Psychology - Published
- 2015
49. Neuroscience in 2064: A Look at the Last Century
- Author
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Jeremy Freeman, Gary Marcus, and Christof Koch
- Subjects
Cognitive science ,Psychology - Published
- 2015
50. The Computational Brain
- Author
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Gary Marcus and Jeremy Freeman
- Subjects
Computer science - Published
- 2015
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